Low let-7 levels resulted in up-regulation of oncogenes including MYCN, AURKB and LIN28 itself, the latter through a direct feedback mechanism. Targeting LIN28, or restoring let-7 levels, both led to effective inhibition of this pathway. In summary, paediatric malignant GCTs show biological differences from their adult counterparts at a genomic and protein-coding transcriptome level, whereas they both display very similar microRNA expression profiles. These similarities and differences may be exploited for diagnostic and/or therapeutic purposes.Genomic and protein-coding transcriptomic data have suggested that germ cell tumours (GCTs) of childhood are biologically distinct from those of adulthood. Global messenger RNA profiles segregate malignant GCTs primarily by histology, but then also by age, with numerous transcripts showing age-related differential expression. Such differences are likely to account for the heterogeneous clinico-pathological behaviour of paediatric and adult malignant GCTs. In contrast, as global microRNA signatures of human tumours reflect their developmental lineage, we hypothesized that microRNA profiles would identify common biological abnormalities in all malignant GCTs owing to their presumed shared origin from primordial germ cells. MicroRNAs are short, non-protein-coding RNAs that regulate gene expression via translational repression and/or mRNA degradation. We showed that all malignant GCTs over-express the miR-371–373 and miR-302/367 clusters, regardless of patient age, histological subtype or anatomical tumour site. Furthermore, bioinformatic approaches and subsequent Gene Ontology analysis revealed that these two over-expressed microRNAs clusters co-ordinately down-regulated genes involved in biologically significant pathways in malignant GCTs. The translational potential of this finding has been demonstrated with the detection of elevated serum levels of miR-371–373 and miR-302/367 microRNAs at the time of malignant GCT diagnosis, with levels falling after treatment. The tumour-suppressor  In addition to considering genomic and protein-coding transcriptomic changes, we will emphasize findings from expression profiling studies of short non-protein-coding RNAs, termed microRNAs, in GCTs. Our improving knowledge of the molecular mechanisms underlying the pathogenesis of GCTs is contributing to the identification of new biomarkers and therapeutic targets, and the development of clinico-biological algorithms for disease segmentation and risk stratification. Combined with the developing collaborations between international clinical trial groups, we can be cautiously optimistic that these approaches will, in the foreseeable future, improve the clinical management of the children, adolescents and young adults affected by this disease , regardless of patient age, tumour site and histological subtype Teilum, . Despiteet al., et al., et al., et al., et al., et al., et al., et al., et al., et al., 1996bet al., et al., Malignant GCTs rapidly became a highly curable disease, even when diagnosed at advanced clinical stages, with the advent of cisplatin-based chemotherapy in the 1970s  located at the common region of 12p gain (12p13.31), suggesting that they are likely to be important in tumorigenesis. However, other non-seminomatous tumours, for example YSTs, which also have 12p gain, do not over-express these genes, suggesting other mechanisms must be important.As the only consistent structural chromosomal abnormality in malignant GCTs of adult patients, 12p gain is implicated in invasive malignant GCT development. The observation that the pre-invasive testicular lesion intratubular germ cell neoplasia unclassified demonstrates a similar pattern of overall genomic changes to those seen in invasive TGCTs, except for 12p gain, supports this theory  and novel  cancer genes in TGCT pathogenesis. Gene expression patterns in malignant GCTs characteristic of embryonic stem cells (ESCs) were confirmed and a distinctive transcriptomic programme was identified for individual histological subtypes , TFAP2C and UTF] and paediatric YSTs were associated with genes such as AFP, those involved in differentiation , lipid metabolism  and proliferation pathways  are not only involved in normal PGC development, resulting in oogenesis and spermatogenesis, but are also implicated in GCT development  are associated with the development of bilateral GCTs  in seminomas, resulting in phosphorylation of KIT and PI3K and therefore constitutive activation of the PI3K pathway, even in the absence of KITLG . Although MAPK1 is globally expressed in adult GCTs, mutations of KRAS and BRAF are rare events, pointing to the involvement of KIT as an upstream protein in activation of RAS/RAF signalling  of target mRNAs, and whose expression profiles are dysregulated in cancer  reported data from 48 paediatric samples, including gonadal and extragonadal  malignant GCTs . Consistent with these observations, the miR-29 family is under-expressed in YSTs, when compared with seminomas  and human choriogonadotrophin (HCG) assist malignant GCT diagnosis, they have limitations in sensitivity and specificity  family of microRNAs, which regulate cell proliferation  is not a feature of malignant GCTs (Palmer et al., LIN28 over-expression (Murray et al., LIN28/let-7 axis represent promising targets for novel therapies in malignant GCTs. As well as depleting LIN28, an alternative strategy is direct replacement of let-7 family members (Murray et al., et al., In addition, low LIN28/let-7 axis in all malignant GCTs also suggests a pathway that may be a target for the development of novel therapeutic agents.Our increasing knowledge of the biology of malignant GCTs needs to be harnessed to improve outcomes for both adult and paediatric patients. In particular, genomic and protein-coding transcriptomic data confirm that malignant GCTs of childhood are biologically distinct from those of adulthood and provide evidence supporting the different management approaches employed in patients of different ages. In contrast, all malignant GCTs over-express the miR-371–373 and miR-302/367 clusters regardless of patient age, histological subtype or anatomical tumour site. The detection of elevated serum levels of these microRNAs at the time of malignant GCT diagnosis, with levels falling after treatment, highlights the universal diagnostic potential of this finding. In addition, the dysregulation of the Further studies are now required, integrating genomic changes using high-resolution methods with combined analysis of mRNA and microRNA expression profiles in malignant GCTs from both adult and paediatric patients with good and adverse clinical outcomes. These approaches are likely to identify regulatory pathways and networks associated with treatment sensitivity and resistance. In particular, such studies should aim to define further the clinical relevance of age-specific biological characteristics of malignant GCTs. These insights may assist the optimal management of affected patients and identify biological targets suitable for the development of novel therapeutic agents. The ultimate aim of this approach will be to improve clinical outcomes for this under-investigated patient group, both through improved survival of patients with poor-risk disease and reduced late-effects of treatment for those with low-risk disease.


Diabetes is a progressive metabolic disorder that can ultimately lead to serious chronic vascular complications including renal failure, vision loss, and cardiac dysfunction , a novel class of non-coding RNAs of 22~24 nucleotides in length, act as post-transcriptional regulators of gene expression by binding to the 3′-untranslated region (3′-UTR) of target mRNA that induces mRNA degradation and/or translational repression (Lim et al., Cardiomyocyte hypertrophy, myocardial fibrosis, and cardiomyocyte apoptosis are important features of diabetic cardiomyopathy (Ruiz and Chakrabarti, in vitro, indicating that overexpression of miR-223 might be a compensatory response to restore glucose metabolism in diabetic heart (Lu et al., Hyperglycemia, oxidative stress and mitochondrial damage are involved in the etiology of diabetes-induced cardiac dysfunction and diabetic cardiomyopathy (Shantikumar et al., Accumulating evidence has indicated that circulating miRNAs can be used as sensitive biomarkers for certain diseases such as cardiovascular diseases and cancers Fabbri, . DespiteTaken together, desregulated miRNAs are potentially involved in the etiology and pathogenetic processes of diabetic cardiomyopathy. An in-depth understanding of their functional roles and molecular mechanisms in the development of diabetic cardiomyopathy will provide better prospects to identify sensitive clinical biomarkers and novel therapeutic targets for diabetic cardiomyopathy.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Production of fuels and chemicals through a fermentation-based manufacturing process that uses renewable feedstock such as lignocellulosic biomass is a desirable alternative to petrochemicals. Although it is still in its infancy, synthetic biology offers great potential to overcome the challenges associated with lignocellulose conversion. In this review, we will summarize the identification and optimization of synthetic biological parts used to enhance the utilization of lignocellulose-derived sugars and to increase the biocatalyst tolerance for lignocellulose-derived fermentation inhibitors. We will also discuss the ongoing efforts and future applications of synthetic integrated biological systems used to improve lignocellulose conversion. One of the daunting challenges faced by the modern world is our unsustainable dependence on petroleum as the primary source for transportation fuels and many chemical products including solvents, fertilizers, pesticides, and plastics Service, . To fulfd-glucose linked by β-1,4 glycosidic bonds while a mixture of pentoses, especially d-xylose, and hexoses comprises the main component of hemicellulose (20–40% of biomass dry weight)  represents arguably the most important renewable feedstock on the planet. Lignocellulose is a complex matrix of various polysaccharides, phenolic polymers, and proteins that are present in the cell walls of woody plants Saha, . Converst) Saha, . Lignin t) Saha, . Chemicat) Saha, . After pt) Saha,  and therse Saha, . Althougse Saha, . Third, se Saha, . For exase Saha, , 2011. Ise Saha, . The conse Saha, . OverlimDespite government incentives and mandates, these grand challenges have prohibited the commercialization of lignocellulose conversion into fuels and chemicals at low cost  , yield , and productivity (4 g/L/h) in a complex medium  and then converts pyruvate into ethanol and CO2  after extensive metabolic engineering and adaptive laboratory evolution  and yield (0.48 g/g xylose) using mineral salts medium  in 16 h  to release catabolite repression; (2) overexpression of a glucose transporter from Z. mobilis to restore glucose transport and metabolism; (3) overexpression of genes rpiA, tktA, rpe, and talB to increase pentose phosphate pathway. Recently, a completely different approach to decrease glucose repression has been developed , organic acids, and phenolic compounds Saha, . FurfuraE. coli and S. cerevisiae  conferred the tolerance to furan aldehydes including furfural and 5-HMF in E. coli (Miller et al., E. coli biocatalysts (Wang et al., A significant amount of effort has been contributed to the identification and optimization of biological components to increase the resistance to furan aldehydes, especially furfural Table . The toxS. cerevisiae gene disruption library was screened for mutants with growth deficiencies in the presence of furfural and ZWF1 was found to relate to furfural tolerance (Gorsich et al., ZWF1 increased furfural tolerance (Gorsich et al., ZWF1 encodes glucose-6-phosphate dehydrogenase, which catalyzes the first step of the pentose phosphate pathway, the major pathway providing NADPH when utilizing glucose as the carbon source. A similar approach using genome-wide RNAi screen showed that inactivation of the SIZ1 gene increased furfural tolerance (Xiao and Zhao, SIZ1 encodes E3 SUMO-protein ligase and inactivation of SIZ1 increases the tolerance to oxidative stress besides furfural (Xiao and Zhao, S. cerevisiae cells and to cause damage to mitochondria, vacuole membranes, and cytoskeletons (Allen et al., YAP1 or its target genes CTA1 and CTT1encoding catalases increased tolerance to furan aldehydes (Kim and Hahn, E. coli. The expression of the genes in major oxidative regulons such as OxyR and SoxRS regulons is not activated by the presence of furfural (Miller et al., E. coli, an oxidoreductase UcpA with an undefined function was found to be associated with furfural tolerance by a transcriptomic analysis and its overexpression increased furan aldehyde tolerance (Wang et al., E. coli on plates. Beneficial plasmids containing the thyA gene were recovered from all three genomic libraries. The thyA gene encodes thymidylate synthase, important for dTMP biosynthesis, suggesting furfural toxicity is possibly related to DNA damage (Zheng et al., E. coli mutants led to the discovery of some polyamine transporters including PotE, PuuP, PlaP, and PotABCD with a beneficial role for furfural tolerance (Geddes et al., E. coli (Glebes et al., lpcA, groESL, ahpC, yhiH, rna, and dicA genes are associated with furfural tolerance although the overexpression of these genes individually only showed limited positive effect (Glebes et al., E. coli the tolerance to furan aldehydes (Wang et al., A variety of genomic and transcriptomic approaches have yielded many beneficial genetic traits related to furan aldehydes tolerance Table . S. cerepntAB and the deletion of the yqhD gene together, made cells less tolerance to furfural than the cells with either one of these two beneficial genetic traits alone (Wang et al., There are at least two major challenges for designing such an integrated detoxification system. First, most epistatic interactions between beneficial genetic traits are not predictable and the experimental search for the optimal combination of multiple effector genes is time-consuming and labor-intensive (Sandoval et al., Efficient xylose metabolism and tolerance to furan aldehydes are desired features of microbial catalysts used in lignocellulose conversion. Past efforts of synthetic biology focused on identification and optimization of individual biological parts needed for a successful lignocellulose conversion. We have gradually accumulated much knowledge about xylose metabolism and transport, glucose repression, and furan aldehyde toxicity. Limited success of lignocellulose conversion has been achieved using these individual optimized parts (Sandoval et al., The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Diabetes is a risk factor for Alzheimer disease (AD). Apolipoprotein E (ApoE) and several genes related to AD have recently been identified by genome-wide association studies (GWAS) as being closely linked to lipid metabolism. Lipid metabolism and glucose-energy metabolism are closely related. Here, we review the emerging evidence regarding the roles of lipid and glucose metabolism in the modulation of β-amyloid, tau, and neurodegeneration during the pathogenesis of AD. Disruption of homeostasis of lipid and glucose metabolism affects production and clearance of β-amyloid and tau phosphorylation, and induces neurodegeneration. A more integrated understanding of the interactions among lipid, glucose, and protein metabolism is required to elucidate the pathogenesis of AD and to develop next-generation therapeutic options. Familial AD is caused by mutations in the amyloid precursor protein (Goate et al., ApoE is an essential regulator of cholesterol metabolism and is the strongest genetic risk factor for AD Ashford, . The Apoin vitro experiment in which transient membrane cholesterol loading increased Aβ42 secretion (Marquer et al., Moreover, independently of ApoEε4, high levels of low-density lipoprotein cholesterol and low levels of high-density lipoprotein cholesterol are associated with higher amyloid-PET indices (Reed et al., In addition to the ApoE gene, recent GWAS studies have identified novel risk genes for AD (Hollingworth et al., in vivo and in vitro, statins reduced the Aβ level in the brain (Fassbender et al., Although clinical studies have indicated that statins have no beneficial effect on cognitive function (McGuinness et al., Normal tau promotes the assembly and stabilization of microtubules. However, hyperphosphorylated tau sequesters normal tau and disrupts microtubules, forming NFT (Iqbal et al., As the largest pool of cholesterol resides in neuronal myelin membranes, disorders that impair sterol synthesis or intracellular trafficking of lipids in neurons cause hypomyelination and neurodegeneration (Saher and Stumpf, +-ob/ob mice, generated by crossing diabetic ob/ob mice, display increased Aβ deposition in the cerebral vasculature (Takeda et al., Diabetes in midlife is associated with mild cognitive impairment (MCI; Roberts et al., db/db mice (Kim et al., in vitro and in animal models (Kickstein et al., Several neuropathological studies suggest that the magnitude of NFTs in the brain at autopsy is not different between AD patients with and without diabetes Kalaria, . HoweverDiabetes causes structural deficits in the brain (Sato and Morishita, Recent large, long-term, randomized controlled trials suggest that a multidisciplinary intervention, including exercise and diet, could improve or maintain cognitive function in at-risk elderly people (Ngandu et al., The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Stem cell (SC) research holds the promise of controlling and/or curing a variety of diseases. SC applications include cell therapy, disease modeling, and developmental biology. This commentary focuses on an important study that examined Notch signaling in murine satellite muscle SCs  in which Notch signaling is specifically blocked in the satellite SC using the dominant negative pan-Notch inhibitor, dnMaml1. The Pax7-Cre+/dnMaml1+ mutant mice showed myopathy manifested as muscle damage and weakness as early as 6 months of age and a shortened life span of about 8 months. The satellite SC pool was totally depleted in the mutant mice due to skewing of the balance between self-renewal and differentiation to differentiation rather than self-renewal. Further, the progeny of myoblasts showed reduced proliferation compared to controls. These experiments and others post cardiotoxin (CTX)-induced injury provided evidence that Notch pathway blockade leads to loss of quiescence and depletion of the satellite SC pool. These results are concordant with reports of other studies that blocked murine Notch pathway signaling by selectively inhibiting the recombining binding protein-Jj (RBP-Jj), a nuclear factor involved in the canonical Notch signaling pathway (Bjornson et al., To add further complexity, NOTCH family members have been shown to carry out different and sometimes opposing functions in the same tissue and/or cell type (Yin et al., NOTCH gene mutations have been found in approximately 15% of HNSCC (Gaykalova et al., NOTCH1 may act as a tumor suppressor gene in HNSCC (Pickering et al., In addition to its important role in muscle development, regeneration and repair, the NOTCH pathway is dysfunctional commonly in several developmental, vascular and cardiac diseases, including leukoencephalopathy and pulmonary arterial hypertension (Fouillade et al., Notch1 knockout mice (Nicolas et al., The Lin et al.  paper isTargeted therapies against stemness regulatory pathways like NOTCH are promising in a variety of disorders. Owing to the high possibility of muscle side effects after long-term administration, we recommend following patients by physical exam for muscle wasting and avoiding concomitant use of steroids, which can lead to myopathies. The study by Lin and colleagues  highlighThe authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Selective motor neuron degeneration is a hallmark of amyotrophic lateral sclerosis (ALS). Around 10% of all cases present as familial ALS (FALS), while sporadic ALS (SALS) accounts for the remaining 90%. Diverse genetic mutations leading to FALS have been identified, but the underlying causes of SALS remain largely unknown. Despite the heterogeneous and incompletely understood etiology, different types of ALS exhibit overlapping pathology and common phenotypes, including protein aggregation and mitochondrial deficiencies. Here, we review the current understanding of mechanisms leading to motor neuron degeneration in ALS as they pertain to disrupted cellular clearance pathways, ATP biogenesis, calcium buffering and mitochondrial dynamics. Through focusing on impaired autophagic and mitochondrial functions, we highlight how the convergence of diverse cellular processes and pathways contributes to common pathology in motor neuron degeneration. SOD1; Rosen, Amyotrophic lateral sclerosis (ALS) is an adult-onset neurodegenerative disease characterized by loss of large motor neurons in the brain and spinal cord, resulting in progressive voluntary muscle wasting and respiratory failure. Patient death typically ensues 3–5 years following symptom onset . AMPK, activated by a drop in cellular energy, phosphorylates ULK1 on Serine 317 and Serine 777 , a well-established autophagosomal marker  have emerged as the most common cause of both sporadic and familial ALS  and Parkin. Mutations in The downstream events that link the targeting of depolarized mitochondria by PINK1-Parkin to the canonical autophagy core machinery are not yet entirely clear. Direct interaction of Parkin with Beclin1 represents one possible explanation  to glycolysis and induction of mitophagy without compromising membrane polarization. Importantly, PINK1 stabilization is not required for this process; iron chelation-induced mitophagy is efficiently activated in fibroblasts deficient in Parkin  mutations have been linked with ALS and other degenerative diseases, including dementia . In this process, electrons pass along a sequence of protein complexes (I-IV) located in the inner mitochondrial membrane  Polymerase 1 (PARP1), thereby increasing its activity and potentiating PARP1-induced cell death (Joshi et al., Further evidence concerning additional roles for constituents of the autophagy machinery in traditional caspase-dependent pathways implicates even broader contributions to cell death. For example, cleavage of the autophagy-related gene Motor neuron cell death in both familial and sporadic forms of ALS is attributable to necroptosis (Re et al., SOD1 or VCP-associated inclusion body myopathy mutant models did not suggest a similar beneficial effect (Zhang et al., SOD1 mutant mice lacking mature lymphocytes, a modest survival increase was noted following rapamycin treatment (Staats et al., SOD1 mutant model (Castillo et al., ATG genes through an mTOR-independent pathway.That protein aggregates are characteristic of ALS and other neurodegenerative diseases suggests that the autophagy pathway may be an attractive therapeutic target for the prevention and treatment of neurodegeneration (Vidal et al., G2019SLRRK2 mutation implicates autophagic induction as an early event. Accordingly, RNAi-mediated knockdown of autophagy factors LC3 or ATG7 is sufficient to rescue neurite length (Plowey et al., Atg7-deficient mice that negatively regulating autophagy is sufficient to promote cell survival of hippocampal pyramidal neurons following ischemic insult (Koike et al., Although direct defects in autophagy genes may not be the causal link in all cases of ALS, dysfunction of autophagy exacerbates disease phenotypes (Bruijn et al., As increasing evidence suggests a prominent role for mitochondrial dysfunction and oxidative stress in motor neuron degeneration, enhancing mitochondrial health represents a promising strategy for treating ALS and related diseases. In line with this, long-term users of the antioxidant vitamin E show a decreased risk for ALS (Wang et al., Atg genes is sufficient to cause neurodegeneration in mice, suggesting a prominent role for autophagic clearance pathways in neurodegenerative disease (Hara et al., Protein aggregates are chief characteristics of many neurodegenerative diseases, including ALS (Blokhuis et al., BME, NM, and YCM conceived of, drafted, edited, and approved the corresponding review.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


The consequence is impaired utilisation of glucose in brain cells. Where are published papers denying the results of Edge et al. and Nyenwe et al.?The authors write “Evidence that significant harmful effects are derived from metabolic acidosis by itself has not been provided in human beings and therefore the successful management of metabolic acidosis require the therapy of the underlying causative disorder.” According to Edge et al.  and NyenThe authors write “Both retrospective and prospective studies have consistently documented that sodium bicarbonate therapy does not improve metabolic responses, biochemical parameters, acid-base balance normalisation, or clinical outcomes among patients with DKA, either children or adults.” In diabetic ketoacidosis, life-threatening is only its most severe stage, coma. If the facts presented in paragraph 1 are correct, thus increase of the very low blood-pH in the comatose patient after infusion of alkalising solution (such as sodium bicarbonate) should result in recovery to normal state of consciousness. And this has been reported in reality: lethality of coma in diabetic ketoacidosis is zero with treatment which includes infusions of alkalising solutions, for example, Umpierrez et al. . WithoutIn the paper of Adeva-Andany et al.  there ar


RNA-induced silencing complex (RISC), whose core component is one of the Argonaute family proteins. MiRNAs then direct RISCs to target mRNAs, which are recognized through partial sequence complementarity. Bioinformatic prediction and experimental target gene identification have shown that a miRNA binds mRNAs of hundreds of protein coding genes, which often span a broad spectrum of functional categories  are endogenously encoded single-stranded RNAs of about 22 nucleotides (nts) in length that play essential roles in a large variety of physiological processes in animals and plants Ambros, . Mature  Bartel, . The fun Bartel, . Subsequ5 copies of mature miRNAs in a cell (Calabrese et al., 4 copies per cell (Neilson et al., 4 copies per cell in hepatocytes (Chang et al., 4–1.7 × 105; Janas et al., in vivo mechanism of action of mammalian miRNAs remains to be a central question in the field of miRNA research.However, the model miRNA used in the aforementioned zebrafish study, miR-430, is unique in that its expression is rapidly induced and reaches millions of copies per cell in a few hours after fertilization. This expression level of miR-430 is at least 10 times more than all mature miRNAs combined in a mammalian cell, and serves the single purpose of degrading its target genes, maternal mRNAs, at the maternal-zygotic transition (Giraldez et al., In contrast to these desperate efforts to search for a unified model of miRNA mechanism of action, studies of individual functional targets in primary cells or tissues from miRNA mutant mice are painting a rather different picture. Depending on miRNAs, target genes, and cellular contexts, the outcome of miRNA-target mRNA interactions could be predominantly translation repression or mRNA degradation, or a mixture of both. This heterogeneity in miRNA mechanisms of action has been increasingly recognized as more and more miRNA mutant mice are generated and analyzed (Olive et al., cis-elements in mature miRNAs and target mRNAs determine the mechanism of miRNA action. Future investigation is warranted to identify these cis-elements, if they exist at all.Here we sought to summarize the relative contribution of translation repression and mRNA degradation to miRNA regulation of functional targets in miRNA mutant mice. We focused on miRNA target genes whose protein and mRNA levels were measured concurrently in primary cells or tissues from mutant mice with genetic ablation or transgenic expression of individual miRNA genes. This includes a total of 159 target genes from 77 miRNA mutant mice Table . Our anaFrom a practical standpoint, measuring target gene protein levels is preferred to mRNA levels for the purpose of studying the effect of a miRNA on its target genes. Even for target genes predominantly regulated by mRNA degradation, the miRNA effect can still be captured by measuring their protein abundance. In the same vein, translatome analysis is more appropriate for measuring the global effect of a miRNA on its target genes, while transcriptome analysis often failed to identify any significant effect of miRNA deletion on its target genes, despite the obvious functional consequences in mutant mice (Matkovich et al., The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Citation: Cowie, S. M., P. Knippertz, and J. H. Marsham (2013), Are vegetation-related roughness changes the cause of the recent decrease in dust emission from the Sahel?, Geophys. Res. Lett., 40, 1868–1872, doi:10.1002/grl.50273[1] Since the 1980s, a dramatic downward trend in North African dustiness and transport to the tropical Atlantic Ocean has been observed by different data sets and methods. The precise causes of this trend have previously been difficult to understand, partly due to the sparse observational record. Here we show that a decrease in surface wind speeds associated with increased roughness due to more vegetation in the Sahel is the most likely cause of the observed drop in dust emission. Associated changes in turbulence and evapotranspiration, and changes in large-scale circulation, are secondary contributors. Past work has tried to explain negative correlations between North African dust and precipitation through impacts on emission thresholds due to changes in soil moisture and vegetation cover. The use of novel diagnostic tools applied here to long-term surface observations suggests that this is not the dominating effect. Our results are consistent with a recently observed global decrease in surface wind speed, known as “stilling”, and demonstrate the importance of representing vegetation-related roughness changes in models. They also offer a new mechanism of how land-use change and agriculture can impact the Sahelian climate.  Goudie and Middleton, Engelstaedter and Washington, Zender and Kwon, Moulin and Chiapello, Prospero and Lamb, Evan et al., Olsson et al., Fensholt et al., Mahowald et al., Evan and Mukhopadhyay, Chiapello et al., Mahowald et al., [2] North Africa is the world's largest dust source  A general challenge in investigating the causes of this dust trend is the sparse observational record from source regions. Satellite-based data sets are short and mainly provide aerosol optical thickness but not emission directly [Ackerman and Cox [FDE) as the fraction of all reports containing these ww codes. We purposely omitted the frequently reported ww code 6  to exclude transport events. The seven stations were selected on the basis of a minimum of 1000 dust observations overall during the time period 1984–2010 and at least 500 observations per year for each of the 27 years.[4] We use the seven Sahelian stations of Nouakchott , Nema (61497), Tombouctou (61223), Gao (61226), Niamey (61052), Agadez (61024), and Gouré (61045) see . Wind sp and Cox ). We defu and v wind vectors from the European Centre for Medium-Range Weather Forecasts ERA-Interim reanalysis at a horizontal resolution of 80 km were used for the area inside the blue box shown in DUP) diagnostic parameter  In addition, 6-hourly 10 m Klink [[6] An analysis of the possibility of artificial trends due to instrument changes (as in Klink ) suggestV) decrease from 4.6 ms–1 in the mid-1980s to 3.3 ms–1 in recent years , and FDE and DUP (0.93) reflect the strong control of wind speed on the occurrence of dust emission. Surprisingly, corresponding trends in regionally averaged mean wind and DUP computed from ERA-Interim reanalysis are substantially smaller (dashed lines in –1) and −14%, respectively.[7] e et al. , shows a[8] We have also analyzed the trends for: (a) day/night-time time data, (b) data at each major SYNOP hour , and (c) data in each season. In each case the results are robust , supporting the hypothesis that the observed trends are real and not an artefact of a change in sampling through the period.Helgren and Prospero, Foltz and McPhaden, Fensholt et al., v25 and v75, at which the probability of dust emission is 25% and 75%, respectively  are in boreal winter , while no clear trends are found at higher latitudes (15°N–30°N), which are probably more strongly influenced by the very sparsely vegetated Sahara [Decadal Sahel dust trends analyzed with surface observations and new diagnosticsWind-speed changes dominate over soil changes in recent dust emission decreaseVegetation-induced roughness changes are the main control on wind-speed trends


The disrupted in schizophrenia 1 (DISC1) gene is found at the breakpoint of an inherited chromosomal translocation, and segregates with major mental illnesses. Its potential role in central nervous system (CNS) malfunction has triggered intensive investigation of the biological roles played by DISC1, with the hope that this may shed new light on the pathobiology of psychiatric disease. Such work has ranged from investigations of animal behavior to detailed molecular-level analysis of the assemblies that DISC1 forms with other proteins. Here, we discuss the evidence for a role of DISC1 in synaptic function in the mammalian CNS. Within this family, segregation is observed between the translocation event and a spectrum of psychiatric disorders, including major depression, schizophrenia, and bipolar disease  development in both humans and rodents, and gradually decreases during life  fractions, and has been also shown to be present in dendritic spines by the use of ultrastructural methods  reagents. A recent methodological approach that has been exploited successfully in studies of DISC1 biology is et al., et al., et al., et al., et al., et al., et al., et al., et al., et al., et al., et al., et al., DISC1 knockdown by in utero delivery of short hairpin RNA . The most prevalent observations involve modifications to neurogenesis, neuronal migration, and integration of neurons into the neuronal parenchyma of their final destination. The last of these results in subpopulations of slightly misplaced neurons and alterations in mature neuronal morphology, such as changes in process branching  increases both the number of spines and their size, whereas continuing inhibition of DISC1 expression up to 6 days results in fewer and smaller spines  is injected into the medial prefrontal cortex of young rats , and LTP was also small in both genotypes, probably because the experiments were not performed with GABA receptor antagonists, which is the normal methodology employed for studying perforant pathway LTP in brain slices.Comparatively high levels of DISC1 are expressed both in the dentate gyrus and in its major output region, the hippocampal CA3 subfield. Manipulation of DISC1 is known to produce effects on adult neurogenesis and wiring in this brain area  enhancement of mossy fiber paired-pulse facilitation at all interstimulus intervals examined, but no change in 1-Hz frequency facilitation studied with 20 consecutive stimuli . Kvajo et al. , is probably the most widely studied single pathway in the mammalian brain. Synaptic transmission in this pathway was investigated in mice engineered to express a C-terminal fragment of DISC1 in the forebrain in an inducible and reversible fashion. These animals, which showed a number of behavioral changes when expression of the DISC1 fragment was induced, also had a depressed input–output relationship in the SCCP at the age of 3–4 months. However, no changes in either short-term plasticity or LTP were found . In the DISC1tr cohort, neither pathway showed changes in input–output relationships or short-term synaptic dynamics. Also, the ratio of N-methyl-d-aspartate (NMDA) receptor-mediated and AMPA receptor-mediated components of the synaptic response was not genotype-dependent. Interestingly, however, we found a clear enhancement of theta burst-induced LTP in the SCCP of DISC1tr mice, but a complete loss of LTP in the temporoamonic pathway. The mechanisms underpinning these pathway-specific effects of the truncated form of DISC1 on long-term synaptic plasticity require further investigation. Our article also describes our single-cell recordings used to compare a broad range of intrinsic excitability properties in CA1 pyramidal cells from 4-month-old DISC1tr mice and wild-type littermates. These identified no substantial dependence on genotype.The SCCP has also been studied in DISC1et al., DISC1. These experiments suggested that reducing the level of DISC1 by ˜60% may serve to increase the duration of action potential bursts, although whether this reflects an intrinsic or synaptic change is not apparent from this type of data.One report concerning DISC1 function in hippocampal neurons describes the use of mixed hippocampal cultures prepared from embryonic day 17.5 mouse embryos and grown on multielectrode arrays  by ˜30%, probably reflecting the increased number of spines present under these conditions. Cortical cultures have also been employed to demonstrate that knockdown of DISC1 with siRNA increases NMDA receptor-mediated currents in response to exogenous agonist application .Other neurophysiological studies in the cortex have also employed brain slices. One study examined slices from two different mouse models – the first was the DISC1, et al. . In this et al., , spontanin utero knockdown of DISC1 (Niwa et al., in utero electroporation, have unaltered membrane resistance or membrane potential. However, dopamine D2ergic modulation of electrically evoked excitatory postsynaptic potentials in these deep layer neurons is strongly attenuated when DISC1 is knocked down. This observation is thought to be related to the disturbed dopaminergic innervation of this cortical area produced by the knockdown of DISC1 (Niwa et al., Acutely prepared slices of mouse prefrontal cortex have also been used to study the neurophysiological consequences of et al., et al., et al., et al., et al., et al., et al., et al., DISC1 levels are unquestionably high in postsynaptic elements. Additionally, a number of DISC1 binding partners also show prominent postsynaptic localisation and possess known postsynaptic roles. Consequently, investigations of DISC1 neurophysiology at synapses have tended to concentrate on postsynaptic functionality. However, DISC1 expression appears also to be a feature of some axons and presynaptic terminals (Kirkpatrick in utero electroporation to introduce Cre-dependent inducible expression vectors for full-length DISC1 or a C-terminal truncation of DISC1 or DISC1 RNAi reagents, in addition to channelrhodopsin2. This permitted both expression of both DISC1-related contructs and light-mediated activation to be confined entirely to presynaptic elements. Recording from layer 2/3 cells, the authors found that spontaneous EPSC frequencies were enhanced by a truncated form of DISC1 (Maher & LoTurco, et al. (DISC1 knockdown lowers the probability of release. In future, it will be interesting to determine which proteins DISC1 is interacting with to produce these actions in presynaptic elements. Possibly related to these functional observations of altered presynaptic function is the observation that full-length DISC1 promotes, and C-terminally truncated DISC1 retards, transport along neuronal processes of vesicles containing a synaptic vesicle protein target (Flores et al., A recent elegant study using optogenetic methodologies has provided more direct evidence for presynaptic functions of DISC1 in the neocortex of Wistar rats (Maher & LoTurco, , et al.  in transin vivo studies in appropriate models. Such work is currently ongoing in our group and presumably elsewhere as well, so we should expect to see data on in vivo DISC1-related neurophysiology in the near future.In conclusion, neurophysiological investigation of the neurobiological functions of DISC1 is still in its infancy. We believe that further analyses using neurophysiological measures will provide important insights into the biology of this protein and, consequently, pathways with important roles in psychiatric disease. The data produced to date indicate that alterations to DISC1, such as those that elicit psychiatric disease, can affect multiple processes. As described above, there is evidence for activities on both the presynaptic and postsynaptic sides of the fast chemical synapse, and for interactions with processes controlling long-term synaptic plasticity. The first hints of how these might impact on the behavior of intact complex networks are appearing, although there is a clear need for suitable


Drosophila and vertebrate systems has implicated a family of proteins, the Teneurins, as a new transsynaptic signal in both the peripheral and central nervous systems. The Teneurins have established roles in neuronal wiring, but studies now show their involvement in regulating synaptic connections between neurons and bridging the synaptic membrane and the cytoskeleton. This review will examine the Teneurins as synaptic cell adhesion molecules, explore how they regulate synaptic organization, and consider how some consequences of human Teneurin mutations may have synaptopathic origins.To achieve proper synaptic development and function, coordinated signals must pass between the pre- and postsynaptic membranes. Such transsynaptic signals can be comprised of receptors and secreted ligands, membrane associated receptors, and also pairs of synaptic cell adhesion molecules. A critical open question bridging neuroscience, developmental biology, and cell biology involves identifying those signals and elucidating how they function. Recent work in  The developing neuron has a myriad of tasks to complete along its path to become part of a functioning brain network. The final goal is to form a reliable synaptic connection with its defined partner. While synapse formation has been intensively studied  because of its expression in specific stripes of the fly embryo  has been the most frequently studied synapse in Drosophila, Teneurins have two distinct expression levels. They are highly expressed at connections between select pairs of pre- and postsynaptic partners (Hong et al., all neuromuscular and olfactory connections, a lower, basal level of expression exists, suggesting a more general role. Here, the interaction is heterophilic between presynaptic Ten-a and postsynaptic Ten-m. Perturbation of either component of this basal level at the NMJ causes a myriad of phenotypes including fewer synaptic boutons, failed active zone apposition, disorganization of synaptic proteins, failed pre- and postsynaptic differentiation, and reduced function (Mosca et al., In Drosophila use Teneurins to ensure proper partner matching (Hong et al., Both the olfactory system and the NMJ in These findings revealed a number of facets about Teneurin biology, synaptic regulation, and the logic underlying neuronal development. First, it identified the Teneurins as novel, critical components of the transsynaptic cadre of signals. Ten-a and Ten-m regulate cytoskeletal organization and cooperate with known transsynaptic signals like Neurexin/Neuroligin (Mosca et al., 2+ signaling (Silva et al., Recent evidence further suggests synaptic roles for Teneurins in diverse vertebrate systems. An unbiased proteomics screen (Silva et al., in vivo (O’Sullivan et al., teneurin-3 knockdown impairs the morphology and connectivity of retinal ganglion cells (Antinucci et al., teneurin-3 knockdown, the role of Teneurins at vertebrate synapses remains an exciting question of great importance for future work.Latrophilins regulate excitatory synapse development and strength The Teneurins are one of a critical suite of cell surface molecules for synapse formation, organization, and function. These include cell adhesion molecules, ligand-receptor complexes, and secreted factors (Johnson-Venkatesh and Umemori, The Teneurins are synaptic cell surface molecules with such diverse functions. They are synaptic organizers (Scheiffele et al., Drosophila has compared Teneurin and Neuroligin1 perturbations (Mosca et al., Beyond synaptic induction, the Teneurins also ensure an ordered cytoskeleton, a role which may be more unique to this family. While Nectins can organize actin (Mori et al., Drosophila, only two Teneurins exist, but regulate all of these events (Baumgartner et al., Drosophila NMJ, where Teneurins have been most mechanistically studied, but further consider translation. While the more complex vertebrate nervous systems may have evolved additional mechanisms for controlling synaptic organization absent in the fly, it is important to note the CNS and PNS conservation of Teneurins in the Drosophila (Mosca et al., A critical question is how the Teneurins regulate such diverse processes as neuronal wiring, synapse organization, morphogenesis, and patterning. In At the NMJ, the Teneurins function to organize the cytoskeleton and ensure properly apposed active zones. Muscle Ten-m interacts in a complex with α-spectrin (Mosca et al., While spectrin is also presynaptic, the microtubule cytoskeleton instead is the predominant player in ensuring proper NMJ morphology and function (Hummel et al., neuroligin and ten-a mutants synergize, suggesting an alternative mechanism. Indeed, ultrastructural defects like detached and misshapen active zones following Teneurin perturbation (Mosca et al., Beyond the cytoskeleton, the Teneurins have an independent role in regulating active zone apposition and structure. Teneurin perturbation causes failures (Mosca et al., C. elegans, the Teneurin ten-1 interacts with the Integrin and Dystroglycan homologs ina-1 and dgn-1 and the prolyl 4-hydroxylase phy-1 to regulate collagen IV and maintain basement membranes during embryonic development (Trzebiatowska et al., ten-1 phy-1 double mutants, embryos display gross defects in epidermal development, body wall musculature, and enhanced lethality. These phenotypes also synergize with mutations in collagen IV, leading to a model whereby epidermal TEN-1 binds collagen IV in the basement membrane. In the absence of phy-1, collagen IV is improperly processed and fails to be secreted into the basement membrane to bind TEN-1, weakening the muscle structure. Similar defects and interactions also occur with Integrin and Dystroglycan mutations (Trzebiatowska et al., Teneurins can interact heterophilically with other Teneurins (Oohashi et al., Drosophila, synaptic Integrins and Dystroglycan regulate NMJ development (Hoang and Chiba, pgant3 and pgant35A, two protein alpha-N-acetylgalactosaminyltransferases that regulate integrins. Mutations in these genes control the levels of the synaptic integrin receptor αPS2 and Ten-m (Dani et al., pgant. Further supporting this interplay is evidence that Ten-m and αPS2 directly interact (Graner et al., trans (Graner et al., In Drosophila, Teneurins mediate partner matching and synaptic organization at the same synapses (Hong et al., In in vivo will be able to offer important clarity on these differences are achieved.An intriguing possibility may lie in the Teneurins themselves. If their intrinsic structural properties could distinguish homo- and heterophilic interactions, this would enable both signaling modes with the fewest restrictions Figure . BiophysIn recent years, the synaptic basis of neurological disorders has been more concretely appreciated (Thompson and Luscher, How may the Teneurins be synaptopathic? Teneurin mutations have been implicated in a number of intellectual disabilities. Large regions of the human X and 5th chromosomes containing Teneurins-1 and -2, respectively, are linked to mental retardation (Tucker and Chiquet-Ehrismann, A tantalizing link between Teneurins and synaptopathies rests with bipolar disorder. Genome-wide association studies linked Teneurin-4 mutations to enhanced susceptibility to bipolar disorder (Psychiatric GWAS Consortium Bipolar Disorder Working Group, Drosophila, they order the underlying synaptic cytoskeleton and ensure proper synaptic function, differentiation, and morphology. Understanding their complete synaptic role, however, is in its infancy, and remains an exciting area for future study. Further work is needed to decipher the mechanisms of synaptic Teneurin function, leading to how they affect human brain function. Indeed, while human nervous systems have more complex circuit regulatory requirements than invertebrates, the marked conservation in worm, fly, and mouse models for Teneurin function suggests that their diverse roles may rely on similar core mechanisms. It will be critical to determine how these synaptic roles differ from those of partner matching. Understanding their downstream effectors and how homo- and heterophilic Teneurin signals are distinguished in partner matching vs. synaptic organization will achieve this goal. Linking these mechanistic studies to those of patients with Teneurin mutations will further enhance our understanding of how these proteins function. As future work addresses these questions, the Teneurins may take their place alongside known synaptopathic and ASD genes like Neurexin and Neuroligin as critical synaptic determinants, highlighting their importance in producing a functioning, organized brain.The Teneurins have emerged as transsynaptic, cell surface molecules essential for synaptic organization. In The author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


The effective management of cardiac arrhythmias, either of atrial or of ventricular origin, remains a major challenge. Sudden cardiac death due to ventricular tachyarrhythmias remains the leading cause of death in industrialized countries  and a large capacity (mc) per unit area.” This “cable model” considers that the intracellular and extracellular potentials vary along the longitudinal axis only, and that both the cytoplasm and the extracellular spaces can be approximated as ideal ohmic conductors (with ir and er respective resistances per unit length). Hence, propagating cardiac action potentials along a fiber can be described by the following second-order partial differential equation (PDE):ionicI is the nonlinear membrane ionic current density (μA/cm2), defined by the active/stochastic electrical properties of the cell. Alternatively, multiplying by mr, Equation (1) can be re-written asmcmr is the trans-membrane time-constant (e.g., Plonsey, Engelmann  was perhUsing this theoretical framework, Weidmann  demonstrMyocardial infarction and/or acute ischemia provoke profound changes in the passive electrical properties of cardiac muscle (De Groot and Coronel, in vivo. Therefore, del Rio et al. (The role that changes in intrinsic properties of pacemaker cells (Yaniv et al., o et al.  studied The authors hope that this monograph will provide a better appreciation of the crucial role that myocardial passive electrical properties play in not only the maintenance of a normal cardiac rhythm but also how changes in these parameters can trigger atrial and ventricular arrhythmias. The application of this knowledge should facilitate the development of more effective anti-arrhythmic therapies.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Tests al., 2015). This tal., 2015). In thial., 2015). An intin vitro systems for hepatotoxicity, because they may improve the throughput and avoid difficulties due to interspecies extrapolation, because human cells can be used . Howeveeif, 2014; Ghallabeif, 2014, 2014; Cam; Camin val., 2015; Driesseal., 2015; Tolosa al., 2015; Grinberal., 2015). Other


The 13th International Conference on Bioinformatics (InCoB2014) was held for the first time in Australia, at Sydney, July 31-2 August, 2014. InCoB is the annual scientific gathering of the Asia-Pacific Bioinformatics Network (APBioNet), hosted since 2002 in the Asia-Pacific region. Of 106 full papers submitted to the BMC track of InCoB2014, 50 (47.2%) were accepted in BMC Bioinformatics, BMC Genomics and BMC Systems Biology supplements, with three papers in a new BMC Medical Genomics supplement. While the majority of presenters and authors were from Asia and Australia, the increasing number of US and European conference attendees augurs well for the international flavour of InCoB. Next year's InCoB will be held jointly with the Genome Informatics Workshop (GIW), September 9-11, 2015 in Tokyo, Japan, with a view to integrate bioinformatics communities in the region. The 13th InCoB , an official conference of the Asia-Pacific Bioinformatics Network (APBioNet) [We offered authors four tracks to submit manuscripts for potential publication in the supplement issues of BMC Bioinformatics, BMC Systems Biology or BMC Genomics (BMC track) and PeerJ . Of the BMC Medical Genomics [BMC Bioinformatics supplement [BMC Systems Biology supplement [The 20 articles in this supplement cover mainly "genomic" topics, with three medically-oriented papers going into Genomics  for the pplement  comprisepplement . Five mopplement .et al.[de novo assembly software for fungal genome data. Proteogenomics is increasingly used for the accurate annotation of protein coding regions using proteomic data. As currently available proteogenomic tools are tailored specifically for human and eukaryotic data, Uszkoreit et al.[With genome sequencing technologies becoming more and more accessible and affordable, the genetic origin of the Marwari horse was established by whole genome sequencing  while thet al. have assit et al. have devet al.[et al.[et al.[et al.[et al.[Seven papers are devoted to transcriptome analysis addressing a range of challenges from epigenetics ,14 to unet al. have idel.[et al. have pinl.[et al. have idel.[et al. have idel.[et al. have appet al.[Guanine-rich nucleotide sequences form four-stranded G-quadruplex structures. Yano and Kato  have useet al. have devet al. have devet al.[In the era of genomic medicine, it is possible that some approved drug molecules can be used for diseases other than those they were originally approved for. Yang and co-workers  propose et al. have optet al.[et al.[Taguchi and co-workers  have ideet al.. Xu et al.[et al. have devet al.[Papers specifically relating on genome-scale analysis with a disease focus are presented in a new supplement in BMC Medical Genomics and a brief overview of these articles is presented here. With pandemic viral infections spreading rapidly by jet travel, understanding cross-species transmissibility of vectors is addressed by Tan and co-workers  for inflet al. have anaWith the growth in regional bioinformatics meetings, including ISCB-Asia meetings and the 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) in China , there iThe authors declare that they have no competing interests.SR wrote the introduction. CS and SR (Program Committee Co-chairs) managed the review and editorial processes, respectively. TWT supported the post-acceptance manuscript processing.List of Program Committee Members and Additional Reviewers in Alphabetical Order.Click here for file


Picornaviridae and genus Hepatovirus, which is a sole member of this family. HAV has radically different properties from those of other picornaviruses. First, HAV is extremely resistant to degradation caused by environmental conditions, which include thermal denaturation , acid treatment , 20% ether and chloroform, and detergent inactivation . Second, the HAV has a highly de-optimized codon usage and grows slowly in a tissue culture. Third, VP1-2A or PX, which is a 67-residue C-terminal extension of VP1, has been implicated in the particle assembly (Graff et al., Hepatitis A, which is a major global health problem (Nainan et al., Picornavirus family. VP4, which is a small viral protein, was first detected in HAV mature virions. The external surface of HAV exhibits fewer features than those observed in enteroviruses and cardioviruses (Wang et al., Recently, structures of a mature virion and an empty capsid assembly intermediate of HAV were determined by X-ray crystallography (Wang et al., Although the structure of HAV presents significantly different properties compared with other previously characterized viruses, reveals the phylogenic relationship between typical picornaviruses and insect viruses and also indicates a novel uncoating mechanism, several important biological parameters, such as the entry of HAV and release of an RNA genome, still need to be clarified.


International Journal of Molecular Sciences [The author would like to insert the citation after the following sentence, “These RBPs are detected on laser trackswithin one minute after laser irradiation, and are excluded from the laser tracks shortly  [Sciences .et al. [R-loops), they presented several data supporting that the exclusion of these factors is part of a DDR Pi3K-like kinases-dependent mechanism operating at DNA damage sites to prevent R-loops accumulation.The author wants to stress that an important reference has been inadvertently omitted in the appended review. Britton et al.  recently


In a recent review paper on theoretical explanations of affective stimulus-response compatibility (aSRC) effects between positive/negative stimuli and approach/avoidance-related movements, Kozlik et al. ; KNL argKrieglmeyer et al.  report a2. We agree that smiling and frowning are linked to positive and negative affects, respectively, more rigidly than non-facial actions commonly are. We also agree that aSRC effects for facial responses are less affected by instructions of arbitrary action goals  result in greater left frontal activation, while other smiles do not  to AE.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


The use of synthetic non-coding RNAs for post-transcriptional regulation of gene expression has not only become a standard laboratory tool for gene functional studies but it has also opened up new perspectives in the design of new and potentially promising therapeutic strategies. Bioinformatics has provided researchers with a variety of tools for the design, the analysis, and the evaluation of RNAi agents such as small-interfering RNA (siRNA), short-hairpin RNA (shRNA), artificial microRNA (a-miR), and microRNA sponges. More recently, a new system for genome engineering based on the bacterial CRISPR-Cas9 system , was shown to have the potential to also regulate gene expression at both transcriptional and post-transcriptional level in a more specific way. In this mini review, we present RNAi and CRISPRi design principles and discuss the advantages and limitations of the current design approaches. Natural regulatory RNAs are a heterogenous group of endogenous non-coding RNAs that modulate biological processes at many levels through different mechanisms. They have inspired the design of synthetic RNA molecules, such as riboswitches, sensors, and controllers, as key elements for programing cellular behaviors, as well as antisense-based approaches for specific gene expression regulation, which is the focus of this mini-review  was discovered in 1998, when Andrew Fire and Craig C. Mello reported the capability of exogenous double-stranded RNAs (dsRNA) to silence genes in a specific manner in miRNAs are small endogenous non-coding RNAs, typically 18–22 bp long, which derive from longer hairpin-shaped precursors called pre-miRNA Bartel, . A pre-msiRNAs are mostly exogenous dsRNA molecules derived from viral RNAs or artificially introduced into the cell  has been recently proposed . Sequence rules concern the position of the binding site in the target transcript and its nucleotide composition. The target region should be chosen preferably 50-100 nt downstream of the start codon and should avoid the middle of the coding sequence , which possesses the highest affinity toward complementary RNA, Bifunctional oligodeoxynucleotide/antagomiR constructs, which ensure high transfection efficiency and prevention of unintended immune stimulation, and morpholino oligomers, which have been shown to be efficient inhibitors of both pri-miRNA and mature miRNA activity in zebrafish and Xenopus laevis  are efficient sponges with structurally accessible and indigestible miRNA binding sites Figure H Haragu, 2012. TAn exciting and promising advance in the field of artificial gene regulation comes from Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR). CRISPR is a natural adaptive immune system used by archaea and bacteria against phage and plasmids  in order to perform genome editing in eukaryotes  mechanisms, thus this system can be used to either disrupt or edit a gene . Many tools are currently available online for the design of sgRNAs Table .Besides genome-editing applications, the CRISPR/Cas9 system can be employed for gene expression regulation. The system, known as CRISPR interference (CRISPRi), is based on a catalytically dead Cas9 (dCas9) lacking endonuclease activity co-expressed with a sgRNA (Gilbert et al., A “seed” region has been identified as the 12nt region adjacent to the PAM site. Mismatches in the seed region can dramatically reduce the repression, while mismatches in the non-seed area can cause a mild effect. Design guidelines recommend using a length of 20–25 nt as the base-pairing region of the sgRNA (Larson et al., Gilbert et al. also introduced the sunCas9 CRISPRa system, in which expression of a single sgRNA with one binding site is sufficient to turn on genes that are poorly expressed or that increase the expression of well-expressed genes (Gilbert et al., in vivo by site-specific genome engineering (Bassett et al., CRISPRi can also be successfully employed to knock out miRNAs, by using a sgRNA/Cas9 complex targeting the pre-miRNA sequence (Zhao et al., Finally, although current tools for CRISPRi are based on the DNA targeting approach described above, the discovery of other Cas proteins targeting RNA molecules, such as Cmr, suggests an alternative post-transcriptional methodology similar to RNAi (Hale et al., Both RNAi and CRISPRi represent valid approaches for artificial gene regulation and both can suffer from significant side effects which may result from factors beyond sequence match. One clear advantage of CRISPRi over RNAi is that being an exogenous system it does not compete with the endogenous machinery of miRNA processing. Nevertheless, both techniques require more work in terms of enhancing targeting efficiency and reducing side effects.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.http://www.frontiersin.org/Journal/10.3389/fbioe.2014.00065/abstractThe Supplementary Material for this article can be found online at Click here for additional data file.


PLOS Genetics, Head et al.  with caffeine; e.g., increases in citrate synthase and cytochrome c oxidase mRNA were observed 24 hours after caffeine exposure  during contractions and increased fatigue resistance [2+] and muscle weakness [From an evolutionary perspective, the SR Caweakness , in muscweakness , and in weakness . In thissistance  in non-sweakness .ACTN3 577xx allele promote increased energy expenditure and improved mitochondrial function without requiring an increase in physical activity? Perhaps treatments to induce a controlled SR Ca2+ leak provide such an opportunity, but then the risk of causing impaired muscle function due to excessive Ca2+ leakage has to be overcome.Human evolution and athletic performance are fascinating, but the findings of Head et al. provide additional avenues for future studies with important implications for human health, since the benefits of improved mitochondrial function span far beyond increased exercise capacity. Obesity and the metabolic syndrome are associated with impaired mitochondrial function, and of course, constitute a widespread and rapidly increasing health problem. Could strategies that phenocopy the effects of the


In response: We agree with Berry et al. (Bulinus snails, which can serve as intermediate hosts for Schistosoma haematobium, were found during a malacological survey in 2014 (As stated in our manuscript, we cannot exclude the possibility that our case definition generated false-positives; the potential limitations of our findings have already been discussed (


We discuss Wittmann et al.  “EffectsThe brain integrates partial sensory input with internal representations to construct the elaborate story we know as time Hammond, . Our ord2A receptors in internal clock models (ICMs) in duration discrimination and temporal control of motor performance. The study revealed a decreased ability to accurately produce intervals longer than 3 s and synchronize finger-tapping to auditory beats separated by more than 2 s. This suggests that effects of psilocybin on temporal processing are specific to relatively long durations, attributable to memory, and decision-making components of the ICM (Gibbon et al., Serotonergic hallucinogens generally slow the perceived flow of time Shanon, . PharmacComparable results are observed in Wackermann et al. , assessiTemporal processing of longer durations is impaired in people with schizophrenia Fuchs, . However2A receptor agonists may induce clinical symptoms of schizophrenia such as hallucinations, delusion, psychomotor poverty, and distorted perception (Teixeira et al., 2AR activation have shown to assist NMDAR-dependent memory mechanisms (Zhang and Stackman, 2A R occupancy in the prefrontal cortex of schizophrenic patients (Zhang and Stackman, Psychopharmacological research suggests that drugs such as psilocybin may serve as useful tools for understanding temporal serotonergic signaling mechanisms underlying psychosis, due to their capacity to cause distorted perception in normal subjects (Rammsayer, 2A receptor antagonist ketanserin.Impairments in working memory, selective attention, and executive control, as seen in schizophrenia, lead to distorted sequencing and integration of past, present, and future into a personal narrative. Carter et al.  demonstr2A receptor activity is associated with time distortion in both psychiatric disorders and hallucinogenic experiences. Manipulating antagonists/agonists provides an approach to utilizing psychoactive drugs as tools in research for understanding time perception in the ordinary brain. It would be fruitful to compare healthy subjects under the influence of psilocybin with patients with acute schizophrenia, utilizing a common paradigm as in Wittmann et al. (5-HTn et al. . Howevern et al.  excludesn et al. . An fMRIn et al. . Negativn et al. .Neuroimaging techniques combined with psychophysical tests of time perception (for a review see Grondin, A2 receptor activities. Commonalities across pharmacological treatments and neurological disorders should be explored within a common experimental paradigm to better understand neurochemical processes mediating temporal processing in ordinary states.Slowing of perceived time is induced by psilocybin and schizophrenia; having a common basis in 5-HTKS obtained comprehensive research and drafted original article, with collaboration of JB's efforts. JB provided substantial advisory of research materials and writing processes. Both authors edited and revised the article, insured the integrity of the product, and agreed on the final version for submission.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


The design of biomaterials and the sourcing for appropriate cells are two integrated aspects of tissue engineering to construct a tissue implant for clinical applications. During the past decades, many innovative biomaterials with desirable biological and mechanical properties have emerged, while stem cells have been shown to be a promising cell source to differentiate into many cell types. However, the testing of these bioartificial tissue constructs in the clinical trials is far from satisfactory. How microenvironments in the biomaterials regulate cellular signaling pathways and functions, how stem cell-derived target cells respond to extracellular cues presented by the biomaterials, and how implanted tissue constructs interact with host tissues remain to be investigated. The information of the interplay between cell and biomaterials would be helpful to guide us in improving our current strategy to refine the tissue constructs for effective tissue repair in regenerative medicine. in vivo and in vitro studies. They suggest that well-designed randomized animal trials are needed before moving into clinical trials. Then we introduce three types of innovative biomaterials: (1) bionanocomposites based on bacterial cellulose and magnetic nanoparticles (magnetite) for efficient chronic wounds healing reported by B. Galateanu et al.; (2) the elastomeric poly(ε-caprolatone urethane) (PCLU) scaffolds using a high internal phase emulsion for bone tissue regeneration developed by S. Changotade et al.; and (3) a novel gelatin-alginate-polyacrylamide 3D interpenetrating network with superior performance in promoting chondrogenesis using human adipose-derived stem cells designed by S. Dinescu et al. Most importantly, our special focus will be given to the insight studies on the cell-biomaterial interactions. C.-H. Wang et al. demonstrate that the migration ability of bone marrow stem cells can be regulated by varying the porous structure of the artificial ligaments and this regulation is related to the RhoA/ROCK signaling pathway. M. Deng et al. demonstrate the endothelial differentiation of human adipose-derived stem cells on the polyglycolic acid/polylactic acid (PGA/PLA) mesh and propose the synergistic effect of 3D environments and biochemical signals such as growth factors on the acquisition of mature characteristic endothelial phenotype. S. Fu et al. have investigated the protective effect of neuropeptide Substance P on bone marrow stromal cells against apoptosis induced by serum deprivation through Wnt signaling. J. Michel et al. have reviewed a wide range of hydroxyapatite containing scaffolds and their interactions with mesenchymal stem cells in in vitro and in vivo contexts.In this special issue, we first present a thorough review by M. Ramamoorthi et al. on the efficacy of dental stem cell therapy in bone regeneration in preclinical


Neovascular ocular disorders such as diabetic retinopathy and neovascular age-related macular degeneration (neovascular AMD) are an important cause of blindness in the world . In thesA flow cytometric analysis of vitreous inflammatory cells in patients with proliferative diabetic retinopathy.” Histological and flow cytometric analyses have recently demonstrated the importance of histiocytes/macrophages and T lymphocytes in the development and activation of this disease, but no prediction on the visual prognosis was made. Moreover, higher CD4/CD8 ratio in the vitreous of patients with PDR compared to that in their blood was consistent with local inflammatory response in the disease.Inflammation has an important role in the development of proliferative diabetic retinopathy (PDR) as described in the paper by M. Urbančič et al., 2013, “ ex vivo cultured cells growing out of human fibrovascular epiretinal membranes (fvERMs) from PDR can give insight into their function in immunity, angiogenesis, and retinal detachment, as described in the paper by Z. Veréb et al., 2013, “Functional and molecular characterization of ex vivo cultured epiretinal membrane cells from human proliferative diabetic retinopathy.” Several surface markers such as hematopoietic  and mesenchymal stem cell markers  have recently been reported in fvERMs from patients with PDR. Additionally, secretion of different angiogenesis-related factors  was demonstrated in cells growing out of the fvERMs.Characterization of the cell surface marker phenotype of “Candidate genes for proliferative diabetic retinopathy.” Several pathogenetic mechanisms have been implicated in the development of PDR such as alteration in retinal blood flow, hemostatic abnormalities, metabolic changes, increased oxidative stress, increased polyol and hexosamine pathway flux, activation of protein kinase C isoforms, and increased advanced glycation end-product formation, growth factors, and so forth . The role of epigenetics in diabetic retinopathy is now an emerging area as described in “Epigenetic modifications and diabetic retinopathy” by R. A. Kowluru et al., 2013. It is well known that diabetic environment facilitates epigenetics modifications, which can alter the gene expression without permanent changes in DNA sequence. It has been shown recently that genes encoding mitochondrial superoxide dismutase and matrix metalloproteinase-9 are epigenetically modified, and, by activation of epigenetically modified enzymes, DNA methyltransferases are increased and micro-RNAs responsible for regulating nuclear transcriptional factor and growth factors are upregulated.Epigenetic mechanisms are expected to be involved in the pathogenesis of PDR as well. Gene polymorphisms and epigenetic mechanisms responsible for PDR are reviewed in this paper  in the angiogenic cascades to developing new therapies for retinal vascular diseases. Anti-VEGF agents such as ranibizumab and aflibercept have become increasingly well-established therapies as shown in the paper by M. Hanout et al., 2013,Does the adult human ciliary body epithelium contain “true” retinal stem cells?”). However, until fully accepted as an important treatment modality in different eye disorders, their usefulness must be confirmed in well-designed clinical trials.Stem cell therapy is a promising approach in different diseases, including those causing blindness. Recent reports of retinal stem cells being present in several locations of the adult eye have sparked great hopes that they may be used to treat the millions of people worldwide who suffer from blindness as a result of retinal disease or injury . A populDaniel PetrovičQuan Dong NguyenBorut PeterlinGoran Petrovski


Cryptococcus neoformans (Cn) has become one of the leading causes of mortality in AIDS patients. Understanding the interactions between Cn and phagocytes is fundamental in exploring the pathogenicity of cryptococcal meningoencephalitis. Cn may be extracellular or contained in the monocytes, macrophages, neutrophils, dendritic cells and even endothelial cells. The internalized Cn may proliferate inside the host cells, or cause the lysis of host cells, or leave the host cells via non-lytic exocytosis, or even hijack the host cells (Trojan horse) for the brain dissemination, which are regulated by microbe factors and also immune molecules. Coexistence of protective and deleterious roles of phagocytes in the progression of cryptococcosis warrant further investigation.Meningoencephalitis caused by  Cn has been co-evolved with the phagocyte predators, e.g., amoebas  and proliferates in the brain parenchyma. As Cn is a facultative intracellular pathogen, it is speculated that the transmigrating Cn might be extracellular or within some phagocytes, thereby invading the central nervous system (CNS) via a trans-cellular pathway or Trojan horse pathway  promotes the inflammatory cytokines (Retini et al. The recruited neutrophils in the lung internalize Cn after intratracheal inoculation (Feldmesser et al. Candida albicans infection (Romani et al. Neutrophils are not only phagocytes but also the modulators of immune responses. Depletion of neutrophils results in a Th2 response and renders mice susceptible to high monocytes (Osterholzer et al. Upon Cn airway infection, CCR2 mediates the recruitment of Ly6G+ T cell responses against Cn (Bauman et al. In the lymphnodes, Langerhans cells and myeloid DC induce protective CD4Candida albicans also invades brain endothelial cells via endocytosis (Filler and Sheppard Different from monocytes/macrophages, neutrophils and dendritic cells, endothelial cells are not professional phagocytes. Yet, Cn is observed in the brain endothelial cells of infected mice (Chretien et al. Serological evidences suggest that people may have been infected with environmental Cn in early childhood (Goldman et al.


This special issue on photorespiration focuses on recent advances in this topic. The majority of the papers summarizes and extends contributions given at the 2nd workshop, ‘Photorespiration–key to better crops’, held in Warnemuende, Germany in June 2015. This was organized by the DFG (German Research Foundation)-supported research network, ‘Photorespiration: origins and metabolic integration in interacting compartments’ (FOR 1186–Promics).2 uptake and CO2 release. It is closely associated with photosynthetic CO2 assimilation and represents one of the major highways of carbon metabolism in most plants. By mass flow, surpassed only by photosynthesis, PR actually constitutes the second most important process in the land-based biosphere. Plants using the most widespread C3 type of photosynthesis for CO2 assimilation display particularly massive photorespiratory CO2 production. PR is initiated by competition of O2 with CO2 at the active site of the universal carboxylating enzyme Ribulose 1,5-bisphosphate Carboxylase/Oxygenase (Rubisco) (2-containing atmosphere (The term photorespiration (PR) describes a light-induced biochemical process that converts 2-phosphoglycolate (2PG) into 3-phosphoglycerate (3PGA) and is accompanied by ORubisco) , which pmosphere . To conv2 and NH3. Quantitatively, PR can decrease photosynthesis by up to 30% under current atmospheric concentrations of CO2 and O2 and even more at elevated temperature , chlorophytes, C3 and C4 plants were not viable in ambient air and could only be rescued under artificially enhanced CO2/O2 ratios  highlight the important role of PR in the evolution of C4 photosynthesis via intermediary stages, in which the capacity for PR is lost from leaf mesophyll cells and relocated to the bundle sheath cells. As shown by Döring et al. (this issue), in fully evolved C4 plants such as sorghum, the majority of genes encoding components of PR are also expressed preferentially in bundle sheath cells. Khoshravesh et al. (this issue) highlight the importance of organelle positioning in bundle sheath cells and the relocation of photorespiratory activity to this tissue during the evolution of C4 photosynthesis in grasses. Hagemann et al. (this issue) review the current position on the continuous coevolution of photosynthesis and PR. The evolution of all photorespiratory enzymes was elucidated and it was revealed that the present-day plant photorespiratory enzymes originated from archaeal, bacterial, and cyanobacterial sources, which served as eukaryotic host cell (Archaea), and mitochondrial (proteobacteria) or plastdial (cyanobacteria) endosymbionts, respectively. Moreover, calculating in terms of the geological era, ancient CO2/O2 ratios indicated that photorespiratory metabolism existed from the invention of oxygenic photosynthesis and remained necessary in cells evolving different types of carbon-concentrating mechanisms (CCM).The insight paper and three reviews discuss the current view on PR and its evolution. Sage (this issue) summarized the stepwise development of Cet al. (this issue), by using mutants that lack the activity of mitochondrial NADH dehydrogenase, analysed the role of the mitochondrial electron transport chain in photosynthesis. Using transcriptomic analysis of Lotus japonicus wild type and GS2 mutant plants on a range of different nitrogen concentrations and at ambient and elevated CO2, Pérez-Delgado et al. (this issue) show that primary nitrogen assimilation and PR are transcriptionally co-regulated. They also identify candidate transcription factors mediating this co-ordinated response. Betti et al. (this issue) summarize recent advances obtained in photorespiratory engineering and discuss the potential of realizing gains in crop productivity through manipulation of the photorespiratory pathway. Nunes-Nesi et al. (this issue) explore natural genetic variation in yield and photosynthetic capacity and point to the fact that photorespiratory capacity, in part, is genetically determined. Obata et al. (this issue) review the tight integration of PR with other metabolic pathways which reach beyond the recycling of carbon from the Calvin–Benson cycle, a topic that is further extended by Hodges et al. (this issue). Timm et al. (this issue) focus on the still limited understanding of regulatory interactions between plant PR and photosynthesis and discuss its critical impact for successfully engineering photosynthesis. Montgomery et al. (this issue) also explore the regulatory effect of light reactions on PR in their opinion paper. They employ the framework of modularity in the cyanobacterium Fremyella diplosiphon and suggest a highly controlled interplay among light reactions, PR, and CCM. The opinion paper by Orf et al. (this issue) also centres on cyanobacteria. According to their comparative meta-analysis of cyanobacterial and plant metabolite profiles, the authors propose that cyanobacteria can serve as a much simpler surrogate to study the complex, highly compartmentalized, plant PR metabolism.Another set of contributions deals with the intertwining of the photorespiratory pathway with the central metabolism and its significance for engineering plant productivity. For example, Fromm et al. (this issue). Alonso-Cantabrana and von Caemmerer (this issue) report on using carbon isotope discrimination as a tool to quantify C4-like photosynthesis in C3–C4 intermediate species. Labelling with the stable carbon isotope 13C also revealed a strong effect of reduced mitochondrial malate dehydrogenase activity on PR . Sharwood et al. (this issue) emphasize the importance of standardized and validated protocols for quantifying carbon fixation capacity in plants with differing carbon assimilation strategies, with particular emphasis on quantifying Rubisco activity.A deeper understanding of PR requires technology to determine rates of PR and photosynthesis accurately and this is reviewed by Hanson et al. (this issue). Dellero et al. report on the impact of reduced photorespiratory glycolate oxidase activity on leaf metabolism in Arabidopsis  and review recent advances in the understanding of glyoxylate metabolism in different plant organs . Knocking out glycolate oxidase of Cyanidioschyzon merolae resulted in the first mutant with a photorespiratory phenotype among red algae . This finding revealed that the plant-type photorespiratory cycle using a peroxisomal glycolate oxidase evolved before the split of red and green algae, and it represents a further example that organisms, though carrying a CCM, also depend on functional PR.Four papers deal with the specific role of the central enzyme, glycolate oxidase. The biochemistry of this peroxisomal enzyme converting glycolate into glyoxylate is reviewed by Hodges 4 plants. Not only is it essential to support photosynthetic carbon assimilation, it is also heavily intertwined with other metabolic pathways and is the driving force for the evolution of C4 photosynthesis  would be an important future aim. However, in the long-term, it is also envisaged that synthetic pathways for carbon assimilation (i.e. pathways not existing in nature), that are not affected by oxygen, might become a reality (The past decades of research on the process of PR have revealed that this pathway is an indispensable companion to oxygenic photosynthesis and includes photosynthetic organisms that feature highly efficient CCMs such as cyanobacteria, many algae, and C


Autism spectrum disorder (ASD) is a set of complex neurodevelopmental disorders. ASD is characterized by early-onset difficulties in social interaction, repetitive behavior, and verbal and non-verbal communication. Worldwide prevalence of ASD is about 1%  .There is both direct and indirect evidence for the role of prenatal testosterone and related androgens in the etiology of autistic traits and ASD. Recently, Baron-Cohen et al.  found dip < 0.05)   in mothers of autistic children compared to control subjects.Autistic-like traits are the first signs of ASD  is a disease that leading to overproduction of adrenal androgens due to an enzyme deficiency [usually of 21 hydroxylase (21-OH)]  and the fourth digit (the “ring” finger) is an indicator of prenatal sex steroid levels Manning, . HoweverSeveral studies have investigated 2D:4D ratios among individuals with ASD, and the majorities of them reported lower 2D:4D ratios in autistic probands [reviewed in Teatero and Netley ]. For exAttention deficit hyperactivity disorder is a group of behavioral symptoms including hyperactivity, inattention, and impulsiveness. ADHD symptoms are often observed in individuals with ASD. Both disorders are more frequent in males than females ; in contrast, the sex ratio was significantly decreased in pregnant women with low levels of anti-Toxoplasma IgG antibodies . Moreover, infected women had significantly more facial hair (p = 0.001) and hair reduction (p = 0.002) than the control group.Ingudomnukul et al.  reportedSeveral complex neurodevelopmental disorders may be associated with higher levels of testosterone, including antisocial and aggressive behavior  that involved in the etiology of various neuropsychiatric disorders (Vyas et al., T. gondii infection (Miller et al., Different mechanisms have been shown to involve in the etiology of neuropsychiatric disorders and behavioral alterations during Several direct and indirect evidences support the role of increased prenatal testosterone in ASD and latent toxoplasmosis. Latent toxoplasmosis may also be involved in the etiology of various testosterone-related medical disorders and plays different roles in the etiology of neuropsychiatric disorders. Taken together with the high prevalence of latent toxoplasmosis in different nations (approximately 25–30% of the world’s human population (Robert-Gangneux and Dardé, The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Journal of the American Academy of Child and Adolescent Psychiatry . On page 169, two of the 95% CIs reported in An error appeared in the article “Cognitive Training for Attention-Deficit/Hyperactivity Disorder: Meta-Analysis of Clinical and Neuropsychological Outcomes From Randomized Controlled Trials” by Samuele Cortese, Maite Ferrin, Daniel Brandeis, et al., published in the March 2015 issue of the


Cell fate conversion is considered as the changing of one type of cells to another type including somatic cell reprogramming (de-differentiation), differentiation, and trans-differentiation. Epithelial and mesenchymal cells are two major types of cells and the transitions between these two cell states as epithelial-mesenchymal transition (EMT) and mesenchymal-epithelial transition (MET) have been observed during multiple cell fate conversions including embryonic development, tumor progression and somatic cell reprogramming. In addition, MET and sequential EMT-MET during the generation of induced pluripotent stem cells (iPSC) from fibroblasts have been reported recently. Such observation is consistent with multiple rounds of sequential EMT-MET during embryonic development which could be considered as a reversed process of reprogramming at least partially. Therefore in current review, we briefly discussed the potential roles played by EMT, MET, or even sequential EMT-MET during different kinds of cell fate conversions. We also provided some preliminary hypotheses on the mechanisms that connect cell state transitions and cell fate conversions based on results collected from cell cycle, epigenetic regulation, and stemness acquisition. As two major types of cells in most animals, epithelial cells are known for their basement membrane, apical-basal axis of polarity, gap junction, immobility, and so on, while the characteristics of mesenchymal cells are almost just opposite, loosely associated, no polarity, and high mobility. Although the two types of cells are so different from each other, the transitions between epithelial and mesenchymal states, epithelial-mesenchymal transition (EMT) and mesenchymal-epithelial transition (MET), have been observed clearly and studied extensively during a variety of biological processes including embryonic development, cancer progression, and somatic cell reprogramming.The first observation of EMT can be dated back to as early as 1890 when some ductal epithelial cells were described to acquire mesenchymal characteristics in breast tumors progression as reviewed previously Nieto, . It is sEMT has been observed in multiple biological processes, especially embryonic development. The generation of adult tissues and organs requires multiple rounds of sequential EMT-MET, which is used to refer an EMT followed with its reversed process, MET  into embryonic stem cells (ESC)-like cells with Oct4, Klf4, c-Myc, and Sox2. The generated cells were named induced pluripotent stem cells (iPSC). iPSC are able to generate tumors containing a variety of tissues from all three germ layers cells after being transplanted into nude mice and viable, fertile live-born progeny by tetraploid complementation (Takahashi and Yamanaka, During the generation of iPSC, multiple changes have been observed with the MEF, including those in gene expression profiles (Brambrink et al., Although MET is necessary for fibroblasts reprogramming, there are still several questions remaining unclear. Firstly, since the process from MEF to iPSC can be considered as a reversed process of embryonic development at least partially, the reversed process of sequential EMT-MET, which is also a sequential EMT-MET, might be observed during iPSC generation. Secondly, the different or even opposite regulatory roles of the four transcriptional factors, like on TGFβ1 and TGFβ receptor 2, make MET induction more complex (Li et al., Briefly, we determined reprogramming efficiencies with totally 74 different infection sequences. One particular infection sequence, Oct4 and Klf4 first, c-Myc next and Sox2 last, generated iPSC with the highest efficiency, about 600% of basal level (Liu et al., The reports on MET during iPSC generation in 2010 suggest this temporary EMT should generate more difficulties for later MET and decrease the reprogramming efficiency at the first glance (Li et al., To explain how short EMT was induced on MEF which are already in mesenchymal state and why sequential EMT-MET promotes iPSC generation, we proposed a new model in previous report (Liu et al., Another available hypothesis is that the optimal mesenchymal state may be more suitable for the cell fate conversions, which is partially supported by the connection between EMT and stem cell characteristics (Hayashida et al., in vitro differentiation of ESC or iPSC is also useful for EMT/MET research because of their similarity to embryonic development and relative simplicity of the system. As a membrane marker for epithelial cells, E-cadherin has also been used as one of the markers for undifferentiated ESC (Li et al., Multiple rounds of sequential EMT-MET make embryonic development an excellent model and hot topic for EMT/MET research Nieto, . HoweverTake the differentiation from iPSC to NSC as an example, immediate up-regulation of N-cadherin, a marker for mesenchymal cells, is essential for the efficient differentiation. However, E-cadherin expression is required to support the self-renewal of NSC (Karpowicz et al., The successful trans-differentiation of somatic cells into functional neurons (Sheng et al., The observations of EMT/MET during different kinds of cell fate conversions do not enable us to answer the question that EMT/EMT is a by-product or a significant cause for cell fate conversions. Take MET during iPSC generation from MEF for example, MEF and iPSC definitely have the characteristics of mesenchymal and epithelial cells respectively. Thus the successful conversion from MEF to iPSC must be accompanied by a MET process. MET is demonstrated to be required for MEF reprogramming, because reprogramming was greatly impaired when EMT was induced or MET was inhibited (Li et al., One way to answer the question above is to study the reprogramming of epithelial cells. Ciliary body epithelial cells have been reported to have higher reprogramming efficiency to iPSC than fibroblasts (Ni et al., Unfortunately, the studies on MET are fewer than those on EMT not only because MET is regarded as a reversed and following process of EMT during embryonic development but also because both MET and EMT employ same regulatory system and most method to inhibit EMT can induce MET (Li et al., 1 phase similar to ESC (Neganova and Lako, Cell cycle regulation is an old topic in cell biology and is observed during almost all kinds of cell fate conversions. iPSC have a high proliferation rate and short G1/S phase, where lies the major difference on cell cycle signatures between MEF and iPSC (Yang et al., On the other hand, EMT and cell cycle regulation are also inter-connected. TGFβ can lead to proliferation arrest and has extensive interaction with p53 (Adorno et al., 0 phase.To explain the positive correlation between proliferation rate and reprogramming efficiency, Dr. Jaenisch’s laboratory has provided a model which suggested the early phase of MEF reprogramming was a stochastic process (Buganim et al., 1 phase, whereas cells are focused to DNA replication in S phase. Thus genes that specify the original cell fate would be silenced in S phase, as partially confirmed by the relative higher DNA methylation in S phase than G1 phase (Brown et al., 1 phase. Since genes specify original cell fate is in a hypo-methylated state in contrast to the hyper-methylated state of genes specify other cell fates, the cells would keep their original fate without outside stimulants. However, when the expression of genes specifying for other cell fates were increased significantly like during iPSC generation and trans-differentiation, the possibility for cells to switch cell fate will increase significantly. In addition, it is also reasonable to propose that decreasing the overall DNA methylation might facilitate cell fate conversion by reducing the methylation levels on the genes specifying for other cell fates. This hypothesis is supported by the study on Tet1 and lysine-specific demethylase 1 (Chen et al., The following question is what kind of events or markers during cell cycle promote reprogramming. One possibility is the DNA methylation regulation during cell cycle progression (Bou Kheir and Lund, As just discussed on DNA methylation, histone modifications are also required to be duplicated and inherited during cell cycle progression (Probst et al., The histone modifications affect cell fate conversions from a variety of aspects (Papp and Plath, +/CD24−/low on cell surface (Al-Hajj et al., +/CD24−/low population with properties associated with mammary epithelial stem cells like abilities to form mammosphere and to differentiate into myoepithelial or luminal epithelial cells (Mani et al., As mentioned above, EMT was first observed in breast cancer and plays critical roles during cancer progression (Thiery et al., However, the studies on ESC and iPSC are not fully consistent with the hypothesis above. ESC as isolated from inner cell mass are considered to be typical epithelial cells. The epithelial marker, E-cadherin, together with proteins like SSEA1, alkaline phosphatase, Oct4, Nanog, and others have been used to determine the undifferentiated state of ESC (Horie et al., We have provided a brief review on the connection between EMT/MET and cell cycle, epigenetic regulation, and stemness to provide possible mechanisms underlying the contributions of EMT/MET to cell fate conversions. Of course, EMT/MET also twists with other biological processes or factors including cell senescence with telomerase reverse transcriptase (Qiao et al., In our opinion, the well established connections between EMT/MET and large amount of biological processes is the major problem faced by researchers who intend to study the contributions of EMT/MET to cell fate conversions. Firstly, the complex interactions among different biological processes make it difficult to study one aspect at one time. For example, cell cycle, DNA methylation, and tumor progresses have been suggested to function together under certain circumstances (Robertson et al., To solve the problem above, one possibility is to put EMT and MET together and study sequential EMT-MET during cell fate conversions. Sequential EMT-MET has been observed during embryonic development and iPSC generation (Liu et al., To explain why temporary EMT before EMT promotes iPSC generation from MEF, we proposed a hypothesized model with optimal mesenchymal and optimal epithelial states as above. Considering the sequential EMT-MET, the preliminary hypothesis that an optimal mesenchymal may function as intermediate for efficient cell fate conversions might be more reasonable. This hypothesis is able to explain the beneficial effects of temporary EMT during iPSC generation and the opposite roles of EMT on stemness regulation. The hypothesis is supported by the chromosomal instability during EMT and in mesenchymal stem cells (Miura et al.,