Since time immemorial, in search for rescue for their disease, people looked for drugs in nature. The traditional use of medicinal plants can lead to the discovery of new potent botanical agents in the treatment of several diseases. Some 7000 natural compounds are currently used in modern medicine; most of these had been used for centuries by traditional healers and the global market value of medicinal plant products exceeds $100 billion per annum. In spite of the development of pharmacological agents for the treatment of chronic diseases, the use of medicinal plants continues to flourish. Over the last century, the drastic changes of human life style and eating habits lead to the emergence of various chronic diseases. The decreasing efficacy of some synthetic drugs and the increasing contraindications of their usage make the usage of natural drugs topical again. Thus, the study of phytotherapy for chronic diseases treatment might yield an excellent return in potential sources of medicinal plants which play vital roles in disease prevention and their promotion and use fit into all existing prevention strategies. In this issue, we aim to present some recent advances in the use of medicinal plants for treating the chronic diseases such as diabetes, cancer, cardiovascular diseases, inflammation, and neurologic disorders. Hydrangea paniculata, slows down the progression of membranous glomerulonephritis by anti-inflammatory effects and inhibiting immune complex deposition,” investigated the renoprotective activity of skimmin, one of the major pharmacologically active molecules present in Hydrangea paniculata. They studied also the underlying mechanisms of the observed renoprotective effects of skimmin in a rat model of membranous glomerulonephritis induced by cationic bovine serum albumin which may be the inhibition of IL1β and IL-6 expression. In another study “Traditional Chinese medicine Tang-Luo-Ning ameliorates sciatic nerve injuries in streptozotocin-induced diabetic rats,” D.-W. Zou et al. describe the beneficial effect of Tang-Luo-Ning (TLN), an effective traditional Chinese medicine for the treatment of diabetic peripheral neuropathy (DPN). To illustrate the underlying neural protection mechanisms of TLN, the effect of TLN on electrophysiology and sciatic nerve morphology was investigated in a model of streptozotocin-induced DPN. G. Belcaro et al., “Grape seed procyanidins in pre- and mild hypertension: a registry study,” studied the efficacy of a standardized grape seed procyanidins extract in decreasing blood pressure when associated with nondrug intervention (diet and lifestyle modification) in a controlled registry study involving healthy prehypertensive and mildly hypertensive subjects. The authors supported that the effect on blood pressure adds to the beneficial effects of grape seed procyanidins on the cardiovascular disease phenotype associated with the oxidation of membrane lipids . A study titled  by C. C. Velusami et al. demonstrates that both methanol and successive water extracts of Nelumbo nucifera petals had an effect on inhibition of lipid storage in adipocytes and increasing lipolysis. In addition, methanol extract exhibited the concentration dependent inhibitory effect on lipase activity. Furthermore, Nelumbo nucifera petal extracts showed evident agonist and antagonist activity towards serotonin and cannabinoid receptors, respectively, while it showed no effects towards melanocyte concentrating hormone and melanocortin receptors. Another clinical study performed by G. Belcaro et al. “Greenselect Phytosome for borderline metabolic syndrome” demonstrates that Greenselect Phytosome, a proprietary lecithin formulation of a caffeine-free green tea catechin extract, was especially effective for weight/waist changes in a controlled registry study on asymptomatic subjects borderline for metabolic syndrome factors and with increased plasma oxidative stress. A. Hunyadi et al., “Metabolic effects of mulberry leaves: exploring potential benefits in type 2 diabetes and hyperuricemia,” report a series of relevant in vitro and in vivo studies on the bioactivity of an extract of mulberry leaves and its fractions. In vivo antihyperglycemic and antihyperuricemic activity, plasma antioxidant status, in vitro glucose consumption by adipocytes in the presence or absence of insulin, xanthine oxidase inhibition, free radical scavenging activity, and inhibition of lipid peroxidation were analyzed.In a clinical study, “Effect of eucalyptus oil inhalation on pain and inflammatory responses after total knee replacement: a randomized clinical trial,” Y. S. Jun et al. demonstrate the beneficial effects of eucalyptus oil inhalation on pain and inflammatory responses after total knee replacement surgery. S. Zhang et al., “Skimmin, a coumarin from Andrographis paniculata nees for treating lung adenocarcinomas,” Y.-T. Tung et al. have studied the antipulmonary cancer effects of andrographolide in a lung tumor mouse model induced by human vascular endothelial growth factor A165 (hVEGF-A165). The antiangiogenesis and chemotherapeutic potential of andrographolide may provide a cure for pulmonary tumors in the future. Z.-Z. Meng et al., “Effect of Xiaoyaosan decoction on learning and memory deficit in rats induced by chronic immobilization stress,” observed the effect of Xiaoyaosan (XYS) decoction on chronic immobilization stress- (CIS-) induced learning and memory deficit in rats from behaviors and changes of proteins in hippocampus. The findings suggested that XYS decoction may be helpful in reversing CIS-induced learning and memory deficit by increasing the levels of postsynaptic density protein 95 and synaptophysin on the hippocampal nerve synapses and improving synaptic plasticity.In addition, known bioactive constituents of mulberry were identified and quantified. A study performed by H.-M. Zhao et al., “Si Shen Wan inhibits mRNA expression of apoptosis-related molecules in p38 MAPK signal pathway in mice with colitis,” demonstrated that Si Shen Wan, a formula of traditional Chinese medicine used to treat ulcerative colitis, allergic colitis, and chronic colitis, effectively inhibited mRNA expression of apoptosis-related molecules in p38 MAPK signal pathway to downregulate colonic epithelial cells apoptosis in colonic mucosa from mice with colitis. In another study “Therapeutic potential of andrographolide isolated from the leaves of Garcinia origin (–)-HCA,” summarizes the update of chemical constituents, significance of in vivo/clinical antiobesity effects, and the importance of the current market potential of Garcinia/hydroxycitric acid especially as a potential supplement for weight management and as antiobesity agent. A study realized by Y. Liang et al., “Effects of the Chinese traditional prescription Xiaoyaosan decoction on chronic immobilization stress-induced changes in behavior and ultrastructure in rat hippocampus,” demonstrated the potential mechanism of Xiaoyaosan (XYS) decoction's antidepressant-like effect in α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors related to synaptic plasticity in the hippocampus rats induced by chronic immobilization stress. The study demonstrates that XYS decoction may produce an antidepressant-like effect, which appears to be involved with AMPA receptors related synaptic plasticity of hippocampus. In another study “Citrus Bergamia Risso elevates intracellular Ca2+ intracellular stores in human umbilical vein endothelial cells,” G. H. Seol et al. demonstrate that Citrus Bergamia Risso mobilizes Ca2+ from primary intracellular stores via Ca2+-induced and IP3-mediated Ca2+ release and affect promotion of Ca2+ influx, likely via an store-operated Ca2+ mechanism. This finding supports the potential roles of bergamottin in cardiovascular function. J. Hoscheid et al., “Inhibitory effect of the hexane fraction of the ethanolic extract of the fruits of Pterodon pubescens Benth in acute and chronic inflammation,” confirm the anti-inflammatory activity of the hexane fraction of an ethanolic extract of Pterodon pubescens Benth. The anti-inflammatory activity was measured with increasing doses of the hexane fraction by using a carrageenan-induced rat model of pleurisy and a rat model of complete Freund's adjuvant-induced arthritis. The results of biochemical, hematological, and histological analyses indicated a significant decrease in glucose, cholesterol, and triglycerides levels and reduction in the number of total leukocytes and mononuclear cells. The study demonstrates also the absence of toxicity for the doses used. H. Park et al., “Ampelopsis Radix protects dopaminergic neurons against 1-methyl-4-phenylpyridinium/1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced toxicity in Parkinson's disease models in vitro and in vivo,” have demonstrated that Ampelopsis Radix has neuroprotective effects with antioxidant mechanisms in Parkinson's disease models. The standardized extract of Ampelopsis Radix protected dopaminergic neurons by inhibiting reactive oxygen species generation in vitro, showed potent radical scavenging activities in vitro, and protected the dopaminergic neurons in the brain in the mouse Parkinson's disease model leading to motor improvements. Another paper by H. Ha et al., “Antiatopic dermatitis effect of Artemisia iwayomogi in dust mice extract-sensitized Nc/Nga mice,” demonstrates the anti-inflammatory and antiatopic dermatitis effects of Artemisia iwayomogi both in vitro and in vivo. Artemisia iwayomogi inhibited the nitric oxide and histamine productions in RAW264.7 and MC/9 cells. Furthermore, isochlorogenic acid A, chlorogenic acid, and scopoletin were demonstrated to be the major components of this plant. Additionally, in the mice, the topical application of Artemisia iwayomogi reduced the dermatitis scores in the dorsal skin and ears and reduced the plasma levels of IgE. E. Panzarini et al., “Administration dependent antioxidant effect of Carica papaya seeds water extract,” demonstrate that Carica papaya seeds water extract is potentially useful for protection against oxidative stress. The authors have assessed the antioxidant activities of the Carica papaya seeds water extract against hydrogen peroxide oxidative stress in human skin Detroit 550 fibroblasts. An in vivo study by M.-H. Chen et al., “Antidiabetic and antihyperlipidemic effects of Clitocybe nuda on glucose transporter 4 and AMP-activated protein kinase phosphorylation in high-fat-fed mice,” demonstrates that amelioration of diabetic and dyslipidemic state by Clitocybe nuda extract in high-fat-fed mice occurred by regulation of GLUT4, glucose-6-phosphatase, and AMP-activated protein kinase phosphorylation. The plant extract decreased hepatic glucose production in the liver and enhanced glucose uptake in skeletal muscle. This study presents a deep analysis of mechanisms of action involved in the antidiabetic and antihyperlipidemic activities of Clitocybe nuda.A review conducted by L. O. Chuah et al., “Updates on antiobesity effect ofAfter the first volume of this special issue published in 2012, we hope that this issue will present valuable information for scientists and clinicians.


These genes are thought to be functionally important for optimal viral replication and persistence in infected individuals. Primate lentiviruses can be classified by the composition of these accessory genes. While viruses of the HIV type1 (HIV-1) group have vpx gene derived from HIV-2 GL-AN clone (Kawamura et al., Although PPM consisting of seven consecutive prolines has been demonstrated to be required for efficient HIV-2 Vpx translation, thereby acquiring viral infectivity in macrophages, the effects of PPM mutations on the degradation of Vpx in cells was not formally analyzed as yet (Fujita et al., Various expression plasmids were transfected into human 293T cells (Lebkowski et al., Proteasomal degradation is generally triggered by the polyubiquitin modification of lysine residues in a protein. There are three lysines in the Vpx of HIV-2 GL-AN clone (Khamsri et al., In total, proteasomal or lysosomal degradation does not account for the extremely low expression level of Vpx exhibited by the PPM mutants. This is consistent with our previous conclusion that PPM is critical for efficient translation of Vpx (Miyake et al.,


Assessment of lymph node status is a critical issue in the surgical management of gallbladder cancer. The aim of this study was to compare the anatomical location of positive nodes, number of positive nodes, and lymph node ratio (LNR) as prognostic predictors in gallbladder cancer.χ2 scores calculated with the Cox proportional hazards regression model.We conducted a retrospective analysis of 135 patients with gallbladder cancer who underwent a radical resection with regional lymphadenectomy. A total of 2,245 regional lymph nodes were retrieved . The location of positive nodes was classified according to the AJCC staging manual (7th edition). ‘Optimal’ cutoff values were determined for the number of positive nodes and LNR based on maximal P < 0.001), number of positive nodes , and LNR  as significant prognostic factors. Multivariate analysis identified number of positive nodes as an independent prognostic factor ( P = 0.004); however, location of positive nodes and LNR failed to remain as an independent variable.Lymph node metastasis was found histologically in 59 (44%) patients. The ‘optimal’ cutoff values for the number of positive nodes and LNR were determined to be three nodes and 10%, respectively. Univariate analysis identified location of positive nodes  is valid for stratifying patients based on the prognosis after resection. Lymph node status  is an established prognostic factor in various gastrointestinal malignancies-7. Thereet al.[et al.[In the cases of gallbladder cancer, both the American Joint Committee on Cancer  and the et al. first reet al.) in patiet al.. Howeverl.[et al. were theχ2 scores calculated by the Cox proportional hazards regression model.The current study compared the prognostic power of positive node location , numberFrom May 1982 to January 2009, 148 consecutive patients underwent a radical resection for gallbladder cancer in the study department, defined as a resection of both the primary tumor and regional lymph nodes. Thirteen patients with an invasive primary malignant tumor in other organs were excluded, leaving 135 patients for this retrospective study. They included 94 women and 41 men with ages ranging from 37 to 85  years.en bloc regional lymph node dissection. Late-stage diseases often required more extensive resections such as major hepatectomy , pancreaticoduodenectomy (the Whipple procedure or pylorus-preserving procedure), or major hepatectomy combined with pancreaticoduodenectomy , duodenum (n = 4), portal vein (n = 3), stomach (n = 1), and inferior vena cava (n = 1). Among the total of 135 patients, 111 underwent an initial radical resection and 24 underwent a radical second resection after a prior simple cholecystectomy for presumed benign disease.en bloc. In the patients who underwent a pancreaticoduodenectomy, the right portion of the superior mesenteric node group was also dissected together with the above node groups. In some patients with early-stage disease, advanced age, or comorbid diseases, a less aggressive regional lymphadenectomy was performed at the discretion of the individual surgeons. In this series, 48 patients with suspected (or confirmed) regional nodal disease also underwent a dissection of the paraaortic lymph nodes [The regional lymph nodes of the gallbladder included the cystic duct, pericholedochal, posterior superior (posterosuperior) pancreaticoduodenal, retroportal, right celiac, and hepatic artery node groups,14,17. I artery),14,17.All pathological findings were documented by using the AJCC cancer staging manual (7th edition). The priImmediately after resection, the surgeon(s) retrieved lymph nodes from the node-bearing adipose tissues of the fresh surgical specimen, and grouped them according to location. A total of 2,829 lymph nodes  were retrieved from the 135 patients. A representative section, 3-μm thick, was cut from each lymph node retrieved, and the nodes examined for metastases on routine histological examination using hematoxylin and eosin.The number of positive lymph nodes as well as the total lymph node count (TLNC) was recorded for each patient. Paraaortic lymph nodes (if any) were not included in the TLNC, and any metastases detected in these lymph nodes were categorized as distant metastases and designated as pM1. Thus, iThree parameters were used to assess the nodal status in individual patients: the location of positive lymph nodes, the number of positive lymph nodes, and LNR. The location of positive nodes was classified into three categories: pN0, pN1, pN2, according to the AJCC cancer staging manual (7th edition). LNR wasThree patients died post-resection during a hospital stay, giving an in-hospital mortality rate of 2%. Adjuvant treatment after resection was administered at the discretion of the individual surgeons. Thirty-six patients received oral administration of 5-fluorouracil or its derivatives. Eight patients received intravenous administration of 5-fluorouracil alone or in combination with other agents. Six patients received intravenous administration of gemcitabine. No patients received adjuvant radiotherapy.Patients discharged home were followed regularly in outpatient clinics every one to six months for at least five years, with a median follow-up period of 146  months. At the time of disease status assessment, 53 patients had died of tumor recurrence and 19 patients had died of other causes with no evidence of tumor recurrence. One patient was alive with recurrent disease, and the remaining 62 patients were alive without the disease.Medical records and survival data were obtained for all patients. The survival time in each patient was defined as the interval between the date of the definitive resection and the date of the last follow-up or death. Only deaths from tumor recurrence were treated as failure cases in the analysis of disease-specific survival (DSS). The Kaplan-Meier method was used to estimate cumulative DSS rates, and the log rank test was used to evaluate differences between groups.χ2 scores, which were calculated using the Cox proportional hazards regression model. Eleven conventional variables  were found to be significant by univariate analysis  was used for all statistical evaluations. All tests were two-tailed, and A total of 2,245 regional lymph nodes were retrieved from the 135 patients, with TLNC per patient ranging from 3 to 55 . Of the study patients, 59 (44%) had a total of 252 positive lymph nodes; the number of positive nodes ranged from 1 to 26  per patient, and LNR ranged from 2.6% to 93% .χ2 score, the ‘optimal’ cutoff value was three nodes for the number of positive nodes , number of positive lymph nodes , LNR , pM classification, histological type, histological grade, lymphatic vessel invasion, venous invasion, perineural invasion, and residual tumor status as significant prognostic factors  and the 59 patients with TLNC > 16  P = 0.10; Table2P = 0.707).We then focused on a subgroup of 76 patients without nodal disease (pN0) for further survival analysis. Even in this subgroup of patients, no significant difference in DSS was noted between 51 with TLNC ≤ 16  and 25 with TLNC > 16   recommended ‘analysis of a minimum of three lymph nodes’ for accurate staging of gallbladder cancer. Howeveret al. and Mayo[et al. disclose[et al.. The abo[et al.-5,12,18.et al.[et al.[et al.[et al.[In contrast, Japanese hepatobiliary surgeons, including us, maintain an aggressive attitude toward regional lymphadenectomy for gallbladder cancer,13,14,23et al. and Mayo[et al. independ[et al. and Negi[et al. independ[et al.,18) is wet al.[et al.[et al.[et al.[In various gastrointestinal malignancies, evaluating a limited number of lymph nodes may result in an underestimated number of positive nodes, leading to ‘stage migration’ -5,12,18.et al., Lee et [et al., Sakata [et al., and Sie[et al. for pancet al.[χ2 scores calculated by the Cox proportional hazards regression model  and the et al. suggesteet al.), of poset al.). In addThe current study has several limitations: the retrospective nature of the analysis, the relatively small number of patients spanning a long period of time, some variability in the degree of nodal dissection, and the short follow-up time for some patients. We believe, however, that these limitations did not greatly affect the results of the study as the differences between groups were too marked to have resulted from bias. In addition, the role of the number of positive nodes in assessing the nodal status for gallbladder cancer is now more clearly defined than previously based on the current study. Our results thus provide useful information for accurately staging nodal disease, predicting prognosis after resection, and selecting candidates for adjuvant chemotherapy after resection. The current study also emphasizes the need to retrieve a larger number of lymph nodes than ever  in rThe number of positive lymph nodes better predicts the outcome after resection than either location of positive lymph nodes or LNR in gallbladder cancer, provided that lymph node evaluation is sufficient. Dividing the number of positive lymph nodes into three categories  is valid for stratifying patients based on the prognosis after resection.Written informed consent was obtained from the patients for publication of this report.AJCC, American Joint Committee on Cancer; DSS, Disease-specific survival; LNR, Lymph node ratio; TLNC, Total lymph node count.The authors declare that they have no competing interests.YS conceived the study and drafted the manuscript. JS helped to draft the manuscript and performed statistical analyses. TW performed chart review and follow-up of the study cohort. TO helped with chart review and patient follow-up. YA provided histological data. KH was responsible for the whole study and participated in its coordination. All authors read and approved the final manuscript.


Synovial fluid is a viscous solution found in the cavities of synovial joints. The principal role of synovial fluid is to reduce friction between the articular cartilages of synovial joints during movement. The presence of high molar mass hyaluronan (HA) in this fluid gives it the required viscosity for its function as lubricant solution. Inflammation oxidation stress enhances normal degradation of hyaluronan causing several diseases related to joints.This review describes hyaluronan properties and distribution, applications and its function in synovial joints, with short review for using thiol compounds as antioxidants preventing HA degradations under inflammation conditions. The human skeleton consists of both fused and individual bones supported and supplemented by ligaments, tendons, and skeletal muscles. Articular ligaments and tendons are the main parts holding together the joint(s). In respect of movement, there are freely moveable, partially moveable, and immovable joints. Synovial joints , the free.g. those covering the bone ends in the knee joint – belong to mechanically highly stressed tissues in the human body. At walking, running, or sprinting the strokes frequency attain approximately 0.5, 2.5 or up to 10 Hz.In a healthy synovial joint, heads of the bones are encased in a smooth  cartilage layer. These tough slippery layers – et al.,in vivo.Cartilage functions also as a shock absorber. This property is derived from its high water entrapping capacity as well as from the structure and intermolecular interactions among polymeric components that constitute the cartilage tissue  are localized/embedded. Their primary function is to continuously extrude high-molar-mass hyaluronans (HAs) into synovial fluid.The synovial fluid (SF) of natural joints normally functions as a biological lubricant as well as a biochemical pool through which nutrients and regulatory cytokines traverse. SF contains molecules that provide low-friction and low-wear properties to articulating cartilage surfaces.et al.,et al., 2001), hyaluronan (HA)   comprised of tissue macrophage A cells, fibroblast-like B cells ,  it has b2•–, H2O2, •OH) are generated in abundance by synovial neutrophils from RA patients, as compared with synovial neutrophils of osteoarthritis (OA) patients and peripheral neutrophils of both RA and OA patients   and/or catalase, which suggests the possibility that there is pathologic oxidative damage to synovial fluid components in RA patients. Dahl et al.  to be in sterically favorable equatorial positions while all of the small hydrogen atoms occupy the less sterically favorable axial positions. Thus, the structure of the disaccharide is energetically very stable. HA is also unique in its size, reaching up to several million Daltons and is synthesized at the plasma membrane rather than in the Golgi, where sulfated glycosaminoglycans are added to protein cores   in cosmetic surgery. It is reported that injection of such products into the dermis, can reduce facial lines and wrinkles in the long term with fewer side-effects and better tolerability compared with the use of collagen  initiated by the HO2.Propagation phase: formation of a peroxy-type C-macroradical of hyaluronan in a process of oxygenation after entrapping a molecule of OFormation of a hyaluronan-derived hydroperoxide via the reaction with another hyaluronan macromolecule.Formation of highly unstable alkoxy-type C-macroradical of hyaluronan on undergoing a redox reaction with a transition metal ion in a reduced state.et al.,et al.,et al.,et al.,et al.,Termination phase: quick formation of alkoxy-type C-fragments and the fragments with a terminal C=O group due to the glycosidic bond scission of hyaluronan. Alkoxy-type C fragments may continue the propagation phase of the free-radical hyaluronan degradation reaction. Both fragments are represented by reduced molar masses  preserving the redox status of cells and protecting tissues against damage caused by the elevated reactive oxygen/nitrogen species (ROS/RNS) levels, by which oxidative stress might be indicated.In vitro. High molecular weight hyaluronan samples were exposed to free-radical chain degradation reactions induced by ascorbate in the presence of Cu(II) ions, the so called Weissberger's oxidative system. The concentrations of both reactants  were comparable to those that may occur during an early stage of the acute phase of joint inflammation  balance and regulates signaling pathways during oxidative stress/conditions. GSH is mainly cytosolic in the concentration range of ca. 1–10 mM; however, in the plasma as well as in SF, the range is only 1–3 µM , another significant precursor of the GSH biosynthesis, has broadly been used as effective antioxidant in a form of nutritional supplement  ions to Cu(I), forming N-acetyl-l-cysteinyl radical that may subsequently react with molecular O2 to give O2•– , when added at the beginning of the reaction, exhibited a clear antioxidative effect within ca. 60 and 80 min, respectively  is a cystine-depleting compound with antioxidative and anti-inflammatory properties; it is used for treatment of cystinosis – a metabolic disorder caused by deficiency of the lysosomal cystine carrier. CAM is widely distributed in organisms and considered to be a key regulator of essential metabolic pathways , when added before the onset of the reaction, exhibited an antioxidative effect very similar to that of GSH . Moreove


Recently, the Notch system has been shown to be an important bridge between APCs and T cell communication circuits. In the present review, we discuss recent findings that explore the mechanisms in the linkage of innate and adaptive immunity, including granulomatous formation though TLRs and Notch activation.Granulomas represent a spectrum of inflammatory sequestration responses that may be initiated by a variety of agents, including non-infectious environmental factors and infectious microbial pathogens. Although this reaction is designed to be protective, the associated tissue injury is often responsible for a profound degree of pathology. While many of the mechanisms that sustain the development of the granuloma are enigmatic, it is accepted that the maintenance of this inflammatory process is dependent upon dynamic interactions between an inciting agent, inflammatory mediators, various immune and inflammatory cells, and structural cells of the involved tissue. The best studied of the host-dependent processes during granuloma development is the innate and adaptive immune response. The innate immune response by antigen-presenting cells  is initiated quickly to protect from overwhelming pathogens, but with time, can also activate the adaptive immune response. APCs, essential regulators of the innate immune response, can respond to microbial ligands through Toll-like receptors (TLRs), which function in the recognition of microbial components and play an important role to link the innate and adaptive immune responses. CD4 The granulomatous response is a complex host defense mechanism that has evolved to provide containment of infectious and/or environmental agents Warren, . The maiThe initial response to infection is the engagement of the host's innate immune system that triggers a rapid, multifaceted anti-infectious response involving the release of proinflammatory cytokines and eventually leads to the activation of the adaptive immune response -γ, Interleukin (IL)-12, and tumor necrosis factor (TNF) were necessary for lung lesion progression , were shown to be maintained by IL-4, IL-5, and IL-13, hallmarks of a type 2 response  or Schistosoma mansoni antigen followed by a pulmonary challenge with sized Sepharose beads coated with a known amount of tuberculin purified protein derivative (PPD) , that promote a dominant Th2 response  (Herbert et al., +, 15–30% are CD8+ T cells, and there are also about 2%γδ T cells (Tsai et al., + T cells in the control of mycobacterial infection has been highlighted by many studies in knockout mice, and also in HIV patients (Ladel et al., The typical granuloma contains mostly macrophages and DCs, surrounded by T lymphocytes, while myeloid DCs also have been found in the granulomas of tuberculosis patients and mouse tuberculin models (Ulrichs and Kaufmann, Innate immunity is the first line of host defense directed against invading pathogens and is designed to maintain host integrity (Si-Tahar et al., M. tuberculosis infection in vivo (Bafica et al., Mycobacterium tuberculosis (Bafica et al., Microbial products, including mycobacterium antigen, activate specific TLRs, which in turn induce specific gene transcription resulting in the up-regulation and secretion of select chemokines and cytokines (Krutzik and Modlin, + Th cells (Kumar et al., Pathogens such as bacteria, helminths, fungi, and viruses are recognized by and activate APCs, which in turn activate CD4in vitro data will require a number of in vivo studies using diverse granulomatous models, including bacterial, parasitic, and fungal, as well as autoimmune models.In addition, it has been shown that Notch proteins are also important in the induction of Th responses (Amsen et al., −/− mice when compared to wild-type mice, Th2 cytokine levels of IL-4, IL-5, and IL-13 were increased in these knockout mice (Ito et al., −/− mice and defined a role for TLR9 in the induction of both Notch ligand Dll4 and Th17 expression using both in vivo and in vitro approaches (Ito et al., −/− mice exhibited significantly larger granuloma formation, following an impaired Th17-like response with decreased expression of Dll4 on DCs from TLR9−/− mice compared with WT mice. Dll4 was the primary Notch ligand upregulated by mycobacterial infection of DCs in WT mice. When Dll4 was specifically blocked in vivo using anti-Dll4 Ab during mycobacteria-induced pulmonary granuloma formation, Th17 cellular responses were significantly inhibited and larger granulomas were observed. Moreover, in in vitro experiments, anti-dll4 antibody specifically blocked IL-17 production by CD4+ T cells, while overexpression of Dll4 augmented IL-17 production by CD4+ T cells, suggesting that Dll4 plays an important role in promoting Th17 activity during a mycobacterial challenge. In contrast, the observed histologic alterations in lung granuloma development in TLR9−/− mice also coincided with a significant decrease in lung myeloid DCs, which are crucial to the differentiation of Th17 cells, as well as decreased levels of dll4 on DCs when compared with wild-type mice. This impaired migration of lung myeloid DCs in granuloma was attributed to decreased production of chemokine CCL20. Chemokines constitute a family of structurally related chemotactic cytokines that direct the migration of leukocytes throughout the body under both physiological and inflammatory conditions (Matsushima, in vivo in normal mice via homeostatic proliferation express CCR6 as well as CCL20 (Hirota et al., −/− mice and in lungs with anti-dll4 Ab is correlated with not only impaired DC migration but also reduced numbers of Th17 cells in lungs during mycobacteria induced pulmonary granuloma formation (Ito et al., While the mechanism of granuloma formation is unclear, this distinct cellular response is considered a histologic hallmark for a protective immune response, involving both innate and adaptive immunity. TLR9 is known to play a role in the regulation of Th1 responses (Bafica et al., Schistosoma mansoni eggs to the lungs (Schaller et al., Our data suggest that an understanding of Dll4 regulation of Th17 responses through Notch may provide mechanistic approaches for modifying and controlling the immune response induced by the Th17 phenotype. Moreover, a number of studies have demonstrated that Notch proteins are important in the induction of Th1 responses. In the presence of functional MyD88, PAMP binding to TLR up-regulates Dll4, which causes the differentiation of naïve Th cells to a Th1 phenotype. In addition, when Dll ligands are overexpressed on APCs or are cross-linked as fusion proteins, they also promote Th1 cell differentiation (Maekawa 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.


DING proteins constitute a recently discovered protein family that is ubiquitous in eukaryotes. The structural insights and the physiological involvements of these intriguing proteins are hereby deciphered. ab initio the complete and exact sequence of this 38 kDa protein by utilizing mass spectrometry and X-ray data in tandem. Taking advantage of this first complete eukaryotic DING sequence, a immunohistochemistry study was undertaken to check the presence of DING proteins in various mice tissues, revealing that these proteins are widely expressed. Finally, the structure of a bacterial representative from Pseudomonas fluorescens was solved at sub-angstrom resolution, allowing the molecular mechanism of the phosphate binding in these high-affinity proteins to be elucidated.DING proteins constitute an intriguing family of phosphate-binding proteins that was identified in a wide range of organisms, from prokaryotes and archae to eukaryotes. Despite their seemingly ubiquitous occurrence in eukaryotes, their encoding genes are missing from sequenced genomes. Such a lack has considerably hampered functional studies. In humans, these proteins have been related to several diseases, like atherosclerosis, kidney stones, inflammation processes and HIV inhibition. The human phosphate binding protein is a human representative of the DING family that was serendipitously discovered from human plasma. An original approach was developed to determine  MS experiments, including ESI-MS on intact HPBP, were used to correct errors from crystallographic sequencing, including those for the few peptides that could not be sequenced. Finally, this technique allowed, ab initio and without ambiguities, the 38 kDa HPBP to be sequenced  fragmentation in LC-MS/MS and MALDI-MS/MS experiments to be obtained. The primary sequence obtained by X-ray crystallography was used like an ‘Ariane wire’, useful to align peptide sequences subsequently obtained by mass spectrometry, without the need of having overlapping peptides. It can be noted that X-ray crystallography techniques provided important information that can barely be obtained using MS, such as the exact number of amino acids and the presence of the disulfide bridges, and the discrimination of residues that possess the same mass (Leu, Ile, 3.et al., 2008Taking advantage of obtaining the HPBP sequence (Diemer et al., 2010Leishmania major genome and western blot studies on plant tissues (Perera et al., 2008et al., 2010et al., 2007DING proteins were observed in all tested tissues, namely brain, skin, heart, aorta, lung and liver, suggesting that these proteins are widely expressed within the organism (Collombet SJ suppresses expression of HIV-1 genome (Darbinian et al., 2008SJ with human C/EBPβ transcription factor and viral Tat transactivator. Moreover, p27SJ possesses a phosphatase activity inducing a dysregulation at S and G2/M phases in cell cycles related to alteration of the Erk1/2 phosphorylation state (Darbinian et al., 2009et al., 2005The immunohistochemistry study also reveals that the DING protein cellular localization is tissue-dependent, being exclusively nuclear in neurons, and nuclear and cytoplasmic in the heart muscle. The nuclear localization of DING proteins fits well with previous observations concerning biological activities of DING proteins, showing a clear involvement of these proteins in complex processes within the nucleus. For example, p274.et al., 2006Pseudomonas fluorescens called PfluDING (Ahn et al., 2007et al., 2007a            et al., 1999Escherichia coli phosphate-binding protein. Interestingly, the unique feature of DING proteins compared with pstS is the presence of four protruding loops at the protein surface (Fig. 2b            Two structures of DING representatives are available: the structure of HPBP (Morales 5.K            D of approximately 1 µM (Ahn et al., 2007et al., 2009Although their phosphate-binding ability has not been clearly related to their biological functions until now, DING proteins are able to bind phosphate with high affinity. Indeed, it has been shown that HPBP and PfluDING bind phosphate with a a            K            a values of the phosphate moiety, PfluDING binds only dibasic phosphate both at acidic and basic pH. The structures show that the phosphate ion is bound via 11 normal hydrogen bonds plus a highly energetic hydrogen bond, between a phosphate oxygen and the carboxylate side chain of Asp62 (Fig. 3b            K            a of atoms in the binding site. Indeed, the fact that PfluDING binds only dibasic phosphate both at acidic and basic pH can be explained by the finding of a very positively charged binding site, capable of altering dramatically the phosphate pK            a.The quality of the obtained data allows most of the H atoms in the protein structure to be located precisely (Fig. 36.ab initio HPBP using mass spectrometry and X-ray data in tandem. Taking advantage of the very high diffracting power of DING protein crystals, we elucidated the molecular mechanism of phosphate binding in high-affinity proteins. These studies illustrate that DING proteins are widely expressed in eukaryotic tissues, and their cellular localization is tissue-dependent, albeit being mostly nuclear. This nuclear localization partly explains some observed biological activities, such as the role in the cell cycle and the inhibition of the HIV replication by interacting with the viral protein Tat and the human transcription factor CEBP/β. The involvement of DING proteins in several important human diseases, together with their genetic mystery and our findings of unknown HMW-DING in eukaryotes, enhance the emerging scientific interest on this protein family.The DING proteins family is an intriguing protein family that seems ubiquitous in eukaryotes, albeit their coding genes are missing. This unconventional protein family requires, for its investigation, some methodological developments. For example, an original approach was developed in order to sequence


Cytokinins (CKs) are a large group of plant hormones which play a crucial role in many physiological processes in plants. One of the interesting functions of CKs is the control of programmed cell death (PCD). It seems that all CKs-dependent phenomena including PCD are accompanied by special multi-step phosphorelay signaling pathway. This pathway consists of three elements: histidine kinase receptors (HKs), histidine phosphotransfer proteins (HPs) and response regulators (RRs). This review shows the résumé of the latest knowledge about CKs signaling pathways in many physiological processes in plants with special attention paid to PCD process. Programmed cell death (PCD) is a process that normally occurs during seed germination, development and senescence. This process is crucial for proper functioning of all multicellular organisms, both plants and animals —kinetin and benzylaminopurine —at high concentrations are able to induce PCD in plants  of roots which seems to be crucial for this synthesis. In cells, CKs are present in chloroplasts or as complexes bound with tRNA  or aromatic compounds  and their derivates. Derivates of zeatin and iP as well as their sugar conjugates are most popular, but their occurrence depends on plant species, stage of development and tissue , a purine-derived CK, discovered as a degradation product of DNA, plays a crucial role in plant cell division. It was isolated by Professor Scoog in 1955 and now it seems that it is the best-known CK  Fig. . Active A. thaliana  and organismal response to stress, pathogens, senescence  which are responsible for reception of the CK signals  that mediate phosphoryl group transfer between AHKs and ARRs were also characterized  were observed. In rice, only two of HPs (OHP3 and OHP4) are involved in the CK signaling multi-step phosphorelay system. The RRs present in rice are also divided into two groups: OsRRs and ORRs. The former is similar to type-A ARRs  were described as negative regulators of CK signaling, whereas type-B  seems also to play a positive role in transcription factors engaged in CK signaling . They were closely related to AHK4, AHK3, and AHK2 receptors, respectively  and A. thaliana (L.) Heynh. In both carrot and Arabidopsis, PCD was induced by accelerating senescence or senescence-like process both in vitro (in cell cultures) and in vivo  is engaged in CK-stimulated induction of PCD (Vescovi et al. Zea mays and Arabidopsis (Caesar et al. The question arises V. faba ssp. minor after kinetin treatment (Kunikowska et al. Subcellular AHK localization sheds a new light on hormone functioning (Caesar et al.


Bian Zheng) is a traditional diagnostic method to categorize patients' syndromes based on their presented conditions. Currently, combination of Zheng classification and biomedical diagnosis becomes a common model in TCM diagnostics in clinical practice. Clinical treatments of a patient rely on the classification of a specific TCM Zheng. This special issue collects articles describing the clinical trials with TCM Zheng classification, Zheng classification methodology from clinical data, systematic reviews on clinical studies using Zheng classification, and the clinical pharmacological evaluation on TCM interventions using the omics platforms as well as bioinformatics.According to the traditional Chinese medicine (TCM) theory, TCM Zheng  is an analysis on disease presentation by TCM practitioners. Zheng classification  for mild-to-moderate systematic lupus erythematosus: a pilot prospective, single-blinded, randomized controlled study” by Zhong et al. showed that Zi Shen Qing is safe and effective for decreasing severity of systemic lupus erythematosus activity and withdrawal dosage of corticosteroids in the mild-to-moderate patients with “Deficiency of Qi and Yin” Pattern. “Therapeutic efficacy of Fuzheng-Huayu tablet based traditional Chinese medicine syndrome differentiation on hepatitis-B-caused cirrhosis: a multicenter double-blind randomized controlled trail” by Song et al. revealed that Fuzheng-Huayu decreases TCM syndrome scores and improves the quality of life of hepatitis-B-caused cirrhosis patients. The only longitudinal study included in this issue, “Increases in Xu Zheng and Yu Zheng among patients with breast cancer receiving different anticancer drug therapies” by Huang et al. assessed Zheng using the TCM Constitutional Scale. It is significant that more and more clinical trials pay attention to the Zheng classification and put it as a criterion for participants selection and outcome assessment, and such changes not only provide the change to demonstrate the characteristics of TCM therapy, but also provide the more comprehensive assessment of an intervention compared with conventional biomarker-oriented assessment.Among included randomized controlled trials, “Prescription of Chinese herbal medicine and selection of acupoints in pattern-based traditional Chinese medicine treatment for insomnia: a systematic review” by Yeung et al. included 227 studies, 17,916 subjects, and 87 TCM patterns. They highlighted high-quality studies to examine the additional benefits of pattern differentiation and pattern-based TCM treatment. “Modified Dachengqi decoction combined with conventional treatment for treating acute exacerbation of chronic obstructive pulmonary disease: a systematic review based on randomized controlled trials” by Wu et al. analyzed 16 studies involving 1,112 patients and showed that Dachengqi decoction combined with routine treatment enhances the effectiveness. “Tianma Gouteng Yin as adjunctive treatment for essential hypertension: a systematic review of randomized controlled trials” by Wang et al. reveals no confirmed conclusion about the effectiveness and safety of Tianma Gouteng Yin for essential hypertension. “ZHENG-omics application in ZHENG classification and treatment: Chinese personalized medicine” by Dai et al. gives the brief introduction and preliminary validation and discusses strategies and system-oriented technology. “Clinical applications of omics technologies on ZHENG differentiation research in traditional Chinese medicine” by Song summarized the typical omics application in common studied diseases and TCM Zhengs and discussed the main problems and countermeasure of Zheng classification researches. “Syndrome differentiation in Chinese herbal medicine for irritable bowel syndrome: a literature review of randomized trials” by Li et al. involved 735 RCTs and 67,784 patients and indicated that 30.5% studies applied Zheng classification. Reviews and evidences, “Metabonomics-based study of clinical urine samples in suboptimal health with different syndromes” by Cui et al. identified the specific metabolic products of the syndrome of stagnation of liver Qi. “Similar connotation in chronic hepatitis B and nonalcoholic fatty liver patients with dampness-heat syndrome” by Dai et al. discussed the molecular mechanism of similar connotation that exists in chronic hepatitis B and nonalcoholic fatty liver by metabonomics to give the modern understanding of dampness-heat syndrome. “Differences of excess and deficiency Zheng in patients with chronic hepatitis B by urinary metabonomics” by Sun et al. suggested that chronic hepatitis B patients could be categorized into two groups with diverse pathogenesis. “Differences in metabolites of different tongue coatings in patients with chronic hepatitis B” by Zhao demonstrated that tongue coatings have objective material basis. “Metabonomics study of essential hypertension and its Chinese medicine subtypes by using gas chromatography-mass spectrometry and nuclear magnetic resonance spectroscopy” by Li et al. distinctly classified Yin deficiency, Yang-hyperactivity syndrome, and Yin-Yang deficiency syndrome by principal components analysis and partial least squares discriminant analysis. “Visual agreement analyses of traditional Chinese medicine: a multiple-dimensional scaling approach” by Lo et al. developed a novel visual agreement analysis for TCM via multiple-dimensional scaling. “The pattern element scale: a brief tool of traditional medical subtyping for dementia” by Shi et al. evaluated the utility of the new pattern element scale in dementia patients. “Validity of a diagnostic scale for acupuncture: application of the item response theory to the five viscera score” by Tomura first applied the item response theory model to the five viscera score to test its validity by evaluating the ability of the questionnaire items to identify an individual's latent traits. “Interrater reliability of Chinese medicine diagnosis in people with prediabetes” by Grant et al. provides initial evidence of variation in the biomarkers of people with prediabetes according to the different TCM Zhengs. “Validation of the constitution in Chinese medicine questionnaire: does the traditional Chinese medicine concept of body constitution exist?” by Wong et al. adapted and validated the constitution in Chinese medicine questionnaire in Hong Kong Chinese people. “Classification and progression based on CFS-GA and C5.0 boost decision tree of TCM Zheng in chronic hepatitis B” by Chen et al. applied correlation-based feature selection, genetic algorithm, and decision tree for Zheng classification and progression in the TCM treatment of chronic hepatitis B (CHB). “Understanding the molecular mechanism of interventions in treating rheumatoid arthritis patients with corresponding traditional Chinese medicine patterns based on bioinformatics approach” by Jiang et al. indicates that molecular network analysis could provide insight into the full understanding of the underlying mechanism of how TCM pattern impacts the efficacy. “The correlation between high-sensitivity C-reactive protein, matrix metallopeptidase 9, and traditional Chinese medicine syndrome in patients with hypertension” by Wu et al. investigated the relationships between Zheng and the two inflammatory biomarkers in patients with essential hypertension. “Research on Zheng classification fusing pulse parameters in coronary heart disease” by Guo et al. illustrated that the nonlinear dynamic variables of TCM pulse can improve the performances of Zheng classification models. “A two-level model for the analysis of syndrome of acute ischemic stroke: from diagnostic model to molecular mechanism” by Dai et al. analyzed that collateral obstruction syndrome, the integration of diagnostic model and molecular mechanism analysis creates an interesting perspective to better understand Zheng. “Progression from excessive to deficient syndromes in chronic hepatitis B: a dynamical network analysis of miRNA array data” by Chen et al. suggested that miRNAs are important mediators for TCM Zheng classification and could be potential diagnosis and therapeutic molecular markers. “Circulating miR-583 and miR-663 refer to ZHENG differentiation in chronic hepatitis B” by Zhang et al. indicated that 354 putative targets for miR-583 and 68 putative targets for miR-663 were mainly involved in Axon guidance, Neurotrophin, and MAPK signaling pathway; miR-583 and miR-663 may be potential markers for Zheng differentiation in CHB. Besides, “Autophagy inhibition enhances apoptosis induced by dioscin in Huh7 cells” by Hsieh et al. showed that dioscin, a new water-soluble steroidal saponin from Dioscorea nipponica Makino, causes autophagy in Huh7 cells and suggested that dioscin has a cytoprotective effect.Zheng diagnosis for patients is sometimes inconsistent among different practitioners. This is in part due to the paucity of evidence-based diagnostic methods in TCM. To solve this problem, establishment of validated diagnostic tool is inevitable. “Clinical trial on the characteristics of Zheng classification of pulmonary diseases based on infrared thermal imaging technology” by Ni et al. showed that the infrared thermal images characteristics of a different Zheng of pulmonary disease were distinctly different. These studies provide the potential of how to improve the quality of Zheng diagnosis. Further studiese are needed to systematically improve the quality of Zheng diagnosis and the integrate this method with modern medicine.Furthermore, Recently, a great progress has been made in the clinical studies focusing on the exploration of the effect of TCM interventions in the patients with clarified TCM Zheng in some diseases. The randomized controlled trials and systematic reviews provide strong evidence for Zheng classification. This special issue presents, even though partially, the efficacy of TCM practice with integration of TCM Zheng classification, biomedical disease diagnosis, and the biological basis of Zheng. We hope that our readers could share these works and further contribute to this important field.


Although research in mice has elucidated a number of fundamental features of NK cell biology, mouse, and hNK cells significantly differ in their subpopulations, functions, and receptor repertoires. Thus, there is a need for a model that is more closely related to humans and yet allows experimental manipulations. Non-human primate models offer numerous opportunities for the study of NK cells, including the study of the role of NK cells after solid organ and stem cell transplantation, as well as in acute viral infection. Macaque NK cells can be depleted in vivo or adoptively transferred in an autologous system. All of these studies are either difficult or unethical to carry out in humans. Here we highlight recent advances in rhesus NK cell research and their parallels in humans. Using high-throughput transcriptional profiling, we demonstrate that the human CD56bright and CD56dim NK cell subsets have phenotypically and functionally analogous counterparts in rhesus macaques. Thus, the use of non-human primate models offers the potential to substantially advance hNK cell research.Human NK (hNK) cells play a key role in mediating host immune responses against various infectious diseases. For practical reasons, the majority of the data on hNK cells has been generated using peripheral blood lymphocytes. In contrast, our knowledge of NK cells in human tissues is limited, and not much is known about developmental pathways of hNK cell subpopulations  NK cells are lymphocytes that have evolved to provide a first line of immune protection against viruses and malignancies before adaptive immune responses emerge Lanier, . IncreasThe study of murine NK (mNK) cells has clearly elucidated a number of fundamental principles, some of which seem to universally apply to all NK cells, such as the activation of NK cells by absent or altered MHC class I molecule expression, also known as the “missing self hypothesis” , and CD16+ NK cells  on highly purified CD56+, CD16+, and DN rmNK cells. We either utilized rhesus-specific ABI TaqMan assays, when available, (Life Technologies), or custom-designed primers and probes based on rhesus mRNA sequences. A complete list of real-time PCR assays employed in our study is available upon request. All assays were subjected to a rigorous selection process to ensure that targeted rhesus macaque genes were orthologous to human genes.A previous transcriptome analysis study revealed a number of differentially expressed genes in CD56+, CD16+, and DN rmNK cell subsets  revealed a segregation of NK cells into groups corresponding to the CD56s Figure . Similars Figure . Converss Figure  as expecs Figure . In addis Figure . FinallyF Figure .+ and CD16+ NK cells, both in the PCA analysis as well as for most of the gene expression data presented in Figure bright NK cells represent a less mature developmental stage of NK differentiation, whereas CD56dim cells exhibit a more differentiated effector profile  in rhesus macaques with an acquired and transmissible immunodeficiency (Daniel et al., −CD8+CD16+ cells (De Boer et al., + and DN rmNK cell subpopulations, and may have limited the authors' ability to accurately assess the effects of SIV infection on the full repertoire of rmNK cells.Multiple phenotypic and functional changes within the NK cell compartment have been documented in HIV infection (Fauci et al., dim NK cells and an increase of the CD56−CD16+ NK cell subset (Alter et al., + NK cells (Reeves et al., bright and CD56+ cells, respectively, without affecting the frequencies of cells expressing CD62L (Reeves et al., Although NK cells from chronically HIV- or SIV-infected donors display a hyper-activated state, their capacity to respond to PMA and ionomycin is diminished (Azzoni et al., Whereas most hNK studies have focused on NK cell subsets from peripheral blood, much less is known about NK cells in tissues. The complexity and heterogeneity of hNK cells residing in various organs, such as uterus, brain, spleen, liver, pancreas, and skin, as well as various mucosal tissues, including the gut, is an area of research that is garnering increasing interest (Shi et al., + hNK cell subset was recently discovered in human and mouse mucosal-associated lymphoid tissues (Cella et al., + NK cells (Reeves et al., + NK cells displayed an altered functional profile with increasing resemblance to conventional NK cells. These alterations were linked to gut inflammation and the up-regulation of indoleamine 2,3-dioxygenase 1 (Reeves et al., A novel IL-22- and IL-17-producing NKp44+ NK cell subsets in treated HIV-patients with incomplete or suboptimal CD4+ T cell recovery (Sips et al., + NK cells could play a compensatory role in patients with ongoing compromised immunity. However, to our knowledge, the impact of HIV infection on IL-22-producing NKp44+ hNK cells has not yet been addressed.A recent study described an expansion of intraepithelial and lamina propria NKp46in vivo effects of cytokines on lymphocyte homeostasis and disease can be addressed in rhesus macaques (Kuramoto et al., + T cells (Mueller et al., In addition to improved access to tissue samples, a number of experimental procedures that have the potential to significantly advance our understanding of NK cells can be carried out in non-human primates. For instance, the in vivo setting.To evaluate the antiviral contributions of NK cells in control of SIV infection, mouse monoclonal antibodies against CD16 have been administered to rhesus macaques (Choi et al., ex vivo expanded cells. This approach could generate novel insights into NK cell turnover, differentiation, migratory behavior, in vivo killing of target cells, and other areas. Moreover, induced pluripotent stem cells have been used to generate hNK cells with antiviral activity against HIV (Knorr and Kaufman, in vivo NK cell development and differentiation. These and many other experimental manipulations of the immune system in non-human primates open a number of new avenues to address basic immunological questions and highlight the potential of these animal models.Furthermore, non-human primates could also be used in autologous transfer studies using fluorescently labeled cells and Here we present two arguments as to why NK cell research in non-human primate models has the potential to yield significant insights into hNK biology. First, as a consequence of the phylogenetic relatedness of humans and non-human primates, there are many shared properties between hNK and non-human primate NK cells. Second, as an animal model, non-human primates offer access to tissues and allow a variety of manipulations, which the “human model” cannot offer due to ethical constraints. The work in non-human primates is challenging, as animals and their housing are relatively cost-intensive and require dedicated facilities and staff. Nonetheless, we believe that their significance as a disease model and the potential clinical applicability of immunological findings derived from these animals continue to make research in non-human primates highly rewarding.Non-human primate models not only bear relevance for humans as outstanding disease models but also as a valuable resource to address basic immunological questions. The exciting answers to these questions and the lessons non-human primates can teach us certainly deserve a greater consideration by the scientific community.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.


Cryptococcus neoformans, chitin-like molecules associate with capsular glucuronoxylomannan (GXM) to form functionally distinct glycan complexes. Such interactions between glycans that result in the formation of structures with different functions strongly suggest that additional molecular complexes with unknown properties may exist in fungal pathogens. Moreover, the identification of these novel complexes has stimulated the search of new immunogens with potential to protect human and animal hosts against systemic mycoses.The biological properties of fungal immunogens have historically utilized testing of isolated molecules. Recent findings, however, indicate that fungal glycans differing in structure and function can interact to form hybrid complexes with unique properties. In the pathogenic yeast  The surface of fungal cells is rich in polysaccharides and protein- or lipid-bound oligosaccharides  chitooligomers promoted enlargement of GXM fibrils, and (3) exposure of C. neoformans cells to an inhibitor of N-acetylglucosamine synthesis caused a decrease in capsular dimensions (Fonseca et al., C. neoformans to form glycan complexes composed of chitin-derived structures and GXM, their production during infection, impact on the host's immune system, and structural determinants regulating this glycan-glycan interaction were unknown until very recently.The supposition that GXM and chitin-derived structures interact has been confirmed by a number of approaches (Rodrigues et al., N-acetyl amino group of chitin, but not on carboxyl and O-acetyl groups of GXM. Importantly, this study shows that glycan complexes formed by GXM and chitin-derived molecules also arise during macrophage infection. Injection of either isolated molecules or the glycan complexes into mice induced distinctly different cytokine responses. In fact, the glycan complexes were efficient in inducing the production of lung IL-10, IL-17, and TNFα, while the cytokine profiles of mice challenged with either GXM or chitin oligomers alone were similar to cytokine levels in control animals. The fact that glycan complex structures produce enhanced immunosuppressive and pro-inflammatory cytokine responses while chitin oligomers and GXM alone did not suggested that cell-associated C. neoformans glycans form hybrid structures with unique functions.A recent study (Ramos et al., C. neoformans model (Ramos et al., The discovery of the formation of functionally distinct glycan complexes raises a number of puzzling questions. For instance, the surface of fungal pathogens is decorated with many different glycans that coexist in several microenvironments (Nimrichter et al., C. neoformans is in fact increased in the lungs of infected rats (Fonseca et al., in vivo observations demonstrating that chitooligomer detection and capsule enlargement are more evident in host tissues manifesting higher activity of this enzyme (Fonseca et al., Chitooligomers are the products of enzymatic hydrolysis of chitin. Chitinase expression is induced during pulmonary cryptococcosis in rodents (Vicencio et al., C. neoformans. Microscopic examinations of C. neoformans yeast cells, in fact, support this possibility. Co-staining of cryptococci with antibodies raised to GXM and to α1,3 glucan reveal that α1,3 glucan is widely distributed in the capsule (Cordero et al., C. neoformans GXM (Reese and Doering, C. neoformans, the presence of the capsule is well-known to slow down the molecular traffic across the cell surface (Nosanchuk et al., GXM has the potential to associate with a number of hydrophilic components, mainly because of its high efficiency in the formation of hydrogen bonds. Thus, GXM-chitin interactions probably have other counterparts in Surface molecules do not exist in their isolated form in cellular systems and approaches investigating interacting molecules can provide a deeper understanding of complex biological processes than the study of individual purified molecules. The discovery of hybrid glycans with previously unknown functions suggests new venues of investigation on the roles of polysaccharides and glycoconjugates in fungal infections. In addition, the connections between glycan association and functional variation strongly indicate that molecular complexes with still unknown properties may exist in fungal pathogens. This conclusion encourages new perspectives on models aiming at the discovery of protective immunogens.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.


Distal expression quantitative trait loci  are genetic mutations that affect the expression of genes genomically far away. However, the mechanisms that cause a distal eQTL to modulate gene expression are not yet clear. Recent high-resolution chromosome conformation capture experiments along with a growing database of eQTLs provide an opportunity to understand the spatial mechanisms influencing distal eQTL associations on a genome-wide scale. We test the hypothesis that spatial proximity contributes to eQTL-gene regulation in the context of the higher-order domain structure of chromatin as determined from recent Hi-C chromosome conformation experiments. This analysis suggests that the large-scale topology of chromatin is coupled with eQTL associations by providing evidence that eQTLs are in general spatially close to their target genes, occur often around topological domain boundaries and preferentially associate with genes across domains. We also find that within-domain eQTLs that overlap with regulatory elements such as promoters and enhancers are spatially more close than the overall set of within-domain eQTLs, suggesting that spatial proximity derived from the domain structure in chromatin plays an important role in the regulation of gene expression. Expression quantitative trait loci (eQTL) experiments map mutations in a genome to variation in gene expression . They haWe determine whether spatial proximity plays a role in eQTLs regulating their target genes as illustrated in et al. submitted for publication)  spanning 10 publications and six cell types (L. Mangravite ication) . Of theset al.  observed for an edge E with read pairs mapping within the fragments u and v. The total frequency of a fragment v is then defined as et al. afford the use of an error-correction method by Yaffe and Tanay .For each chromosome, Hi-C data in its raw form can be represented as a weighted graph nd Tanay , and we et al. Domain boundaries for the Hi-C assays described earlier in the text were identified using a hidden Markov model  and published in the same location as the Hi-C data. Each domain in this sequence of topological domains n is the number of fragments in et al., yet still enriched for similar chromatin marks. The domain-finding method of Dixon et al. uses a Hidden Markov Model with a local ‘directionality index’ statistic, whereas the method for the alternative definition explicitly encodes the quality score of a domain in a dynamic program. Dixon et al.’s method results in domains at a particular scale of genomic length , whereas the alternative definition identifies domains that persist across multiple length scales.We obtained topological domains for each chromosome from Dixon  domains  that havet al. submitted for publication) (Q of eQTLs.eQTLs were obtained from the eQTL browser (eqtl.uchicago.edu), which compiles genome-wide eQTL data from 10 publications ; National Institutes of Health (NIH) [1R21AI085376 and 1R21HG006913]; Alfred P. Sloan Research Fellow (to C.K.). Funding for open access charge: NIH [IR21HG006913].Conflict of interest statement. None declared.


In this issue Mandl and colleagues replicated the findings of a previous study , observed as an increase in the gray matter (GM) magnetic resonance signal , White matter fraction (wmf = 1 − fgm), TE (78 ms) and b-value (1000 s/mm2) (Mandl et al., To test this hypothesis we simulated the effect which a partial-volume of gray matter would have on parallel and transverse diffusivity using published parameters. Relaxation rates Figure 3 resolution, it is likely that several WM voxels could be contaminated with volumes of GM, even after using standardized white matter templates. Noise in MRI acquisitions is thought to cause an overestimation of FA in both isotropic and anisotropic structures (Pierpaoli and Basser, A more technical consideration is the possible effect of image noise and partial volumes on FA quantification (Basser and Jones, +, K−-ATPase utilization to recover post-activation transmembrane ion gradients, which in turn might translate into changes in vascular oxygenation levels. However, the extant evidence from BOLD fMRI and PET studies does not support a metabolic explanation for the observed effects. In vitro studies in the rat brain—which are free from confounding vascular effects - show that massive depolarization and increases in metabolism have a minimal effect upon WM ADC quantification (Anderson et al., A final possibility is that FA increases may reflect activity-evoked glial swelling associated with increases in extracellular potassium levels (Ransom et al., R2 are excluded, requires 18 separate parameters (Basser and Jones, In order to advance the use of functional DTI, a more detailed exploration of the origin of the observed changes is vital. To describe the basic WM, GM, and CSF model, even when contributions from blood and 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.


Paxillin encodes a focal adhesion-associated protein and is involved in the progression and aggressive phenotypes of malignancies through its interactions with the actin cytoskeleton and key signal transduction oncogenes. The present study aimed to investigate the clinicopathological and prognostic significance of paxillin in gastric cancer. The expression of paxillin was evaluated using tissue microarrays of gastric adjacent non-cancerous mucosa, adenoma and carcinoma specimens by immunohistochemistry. Paxillin expression was compared against clinicopathological parameters and the survival time of the patients. Paxillin was highly expressed in gastric adenoma compared with that in non-neoplastic mucosa and carcinoma (P<0.05). Paxillin expression was lower in the younger carcinoma patients compared with that in the elder carcinoma patients (P<0.05). Paxillin expression was negatively correlated with tumor size, depth of invasion and lymph node metastasis, but not with patient gender, lymphatic or venous invasion, or TNM staging (P>0.05). Higher paxillin expression was observed in intestinal-type compared with diffuse-type carcinoma (P<0.05). Kaplan-Meier analysis indicated a positive association between paxillin expression and cumulative survival rate in all, advanced and intestinal-type carcinoma patients (P<0.05). Multivariate analysis using the Cox proportional hazards model indicated that patient age, depth of invasion, lymphatic invasion, lymph node metastasis, TNM staging and Lauren classification were independent prognostic factors for all gastric carcinomas (P<0.05). Aberrant paxillin expression may be involved in the growth, invasion, metastasis and differentiation of gastric carcinoma. Altered paxillin expression may, therefore, be employed as an indicator of pathobiological behaviors and prognosis of gastric carcinomas. Despite a global decline in the incidence and mortality of gastric cancer in the last 60 years, it remains the fourth most common and second most frequent cause of cancer-related mortality. Gastric cancer continues to be a major health concern due to the slow decrease in incidence in Asia and high mortality from diagnosed gastric carcinomas in the West, despite the advanced diagnostic and operative techniques that are commonly used in clinical practice ,2. An inet al and adjacent non-neoplastic mucosa (n=197) collected at Toyama University Hospital  from 1993 to 2006. The adenoma samples were resected from endoscopic biopsy at Toyama University Hospital from 1997 to 2008. The patients with gastric carcinomas were 120 males and 272 females . Archival materials were obtained from the Department of Pathology of Toyama University Hospital. In 151 cases, tumor development was accompanied by lymph node metastasis. None of the patients underwent chemotherapy, radiotherapy and adjuvant treatment prior to surgery. All patients were followed up by consulting their case documents and by telephone.All tissues were fixed in 10% neutralized formalin, embedded in paraffin, cut into 4-μm sections and stained with hematoxylin and eosin (H&E) in order to confirm the histological diagnosis and microscopic characteristics of the specimens. The staging for each gastric carcinoma was evaluated according to the Union for International Cancer Control system, which indicates the extent of tumor spread . HistoloFrom H&E-stained sections of the tumor cases, representative areas of solid tumor were selected for sampling and 2-mm diameter tissue cores per donor block were punched out and transferred to a recipient block with a maximum of 48 cores using a tissue microarrayer . Sections (4-μm) were consecutively cut from the microarrays and transferred to poly-lysine-coated glass slides.Serial sections of TMA were deparaffinized with xylene, rehydrated with alcohol, and subjected to immunohistochemical staining with intermittent microwave radiation, as previously described . Rabbit Immunoreactivity for paxillin showed a cytoplasmic pattern . One hunStatistical evaluation was performed using Spearman’s rank correlation test. Kaplan-Meier survival plots were generated and comparisons between survival curves were made with the log-rank test. Cox proportional hazards model was employed for multivariate analysis. SPSS 17.0 software  was applied to analyze all data, and P<0.05 was considered to indicate a statistically significant difference.As indicated in Follow-up information was available on 392 of the gastric carcinoma patients for periods ranging from 0.2 months to 121 months . de novo carcinogenesis is well understood, particularly in diffuse-type gastric carcinomas (Paxillin is a cytoskeletal protein that was recently identified as a component of focal adhesions and links between F-actin and integrin . In the rcinomas . These fet al(et al(et al(Cai et al found thet al. Li et a al(et al document al(et al found th al(et al. HoweverAlthough all types of gastric cancer are malignant tumors that originate from the same gastric epithelium, the morphological features of the cancers vary substantially in individual patients. According to Lauren classification, gastric intestinal-type carcinoma is characterized by cohesive carcinoma cells that form gland-like tubular structures, such as well- and moderately differentiated carcinoma; while cell cohesion is less apparent or absent in diffuse-type carcinoma, such as poorly differentiated or signet ring cell carcinoma ,17. Our et al(et al(To date, there have been several studies describing the prognostic significance of paxillin expression in malignancies ,12,14,26et al found thIn conclusion, aberrant paxillin expression may be important in the malignant transformation of gastric epithelial cells. Its reduced expression was closely correlated with growth, invasion, metastasis and a worse prognosis of gastric carcinomas. Its expression may be employed to differentiate between the intestinal- and diffuse-type carcinomas. It was considered as a promising marker to indicate the pathobiological behaviors and prognosis of gastric carcinomas.


Historically there has been a distinction between basal ganglia dependent and hippocampus dependent memory systems (e.g., Squire, A newly published study by Foerde et al.  also supThe failure to learn from delayed feedback in patients with hippocampal lesions could be related to the loss of function of area CA1, since CA1 receives afferents from areas known to respond phasically to reinforcing stimulation (Gasbarri et al., Overall, the results described by Foerde et al.  provide


To the Editor: We challenge the conclusions of Feingold et al. that “regional density of livestock is a notable risk factor for nasal carriage of LA-MRSA for persons with and without direct contact with livestock” (Staphylococcus aureus (MRSA), but they retrospectively analyzed 87 culture-confirmed MRSA cases reported to a reference laboratory. These were a mixture of clinical disease isolates and screening  isolates that were unevenly distributed between the groups  was >180 times higher in 352 occupationally exposed persons than in 2,094 rural residents without farm exposure (0.24%) (Finally, the contention of Feingold et al. that pig production in the Netherlands is “greatly overshadowed by the density of pig-farming operations in the United States” is mistaken . Pig den


An elevated resting heart rate is one of the strongest predictors of cardiovascular mortality and is independently associated with sudden cardiac death (SCD). Agents capable of reducing heart rate without significant side effects are therefore of particular interest for the prevention of SCD. Recent human and animal studies have shown that omega-3 fatty acids can reduce heart rate. Our work has shown that omega-3 fatty acids significantly reduce membrane electrical excitability of the cardiac myocyte by lowering its resting membrane potential and the duration of the refractory period through inhibition of ion channels. We propose that these actions may be the underlying mechanisms for the omega-3 fatty acid-induced reduction of heart rate observed in both humans and animals. The heart rate-lowering capability of omega-3 fatty acids may contribute to their preventive effect against SCD. The cardioprotective effects of omega-3 fatty acids have become widely recognized. One of the most significant effects is the prevention of sudden cardiac death (SCD)  is independently associated with SCD. Multiple prospective studies have shown that even after adjusting for common cardiovascular health-related variables, such as age, weight, smoking, alcohol consumption, diabetes, blood pressure, physical activity, blood cholesterol, medications, and socioeconomic status, elevated heart rate remains a risk factor for SCD and a predictor of time to cardiac death (Shaper et al., Given these consistent and robust findings, drugs or supplements that reduce heart rate are of particular interest for preventing SCD. In fact, studies that have examined outcomes for patients with chronic heart failure have revealed that pharmacotherapy to reduce heart rate is associated with better outcomes for at least 5 years (Franke et al., in vitro work provide a likely mechanism by which omega-3 fatty acids act on cardiac myocytes to reduce heart rate.The relationship between omega-3 fatty acids and cardiovascular disease is well studied, and has appeared inconsistent at times (Harris et al., The effect of omega-3 fatty acids on heart rate has been observed in many different populations, both with and without cardiovascular disease. A meta-analysis of 30 randomized, double-blind, placebo-controlled trials concluded that fish oil consumption can significantly reduce heart rate (Mozaffarian et al., In addition, several large-scale, population-based studies showed that increased dietary fish and omega-3 fatty acid intake was associated with a significant reduction in heart rate. Dallongeville et al.  analyzedFish oil also effectively reduces heart rate during times of increased cardiac demand such as exercise. A study of 25 Australian football players revealed that 6g/day of fish oil reduced heart rate during submaximal exercise over a period of 5 weeks (Buckley et al., Another set of interesting findings comes from a population perhaps the least likely to experience cardiovascular illness: infants. Term infants treated with varying amounts of DHA in their formulas for 12 months show that DHA supplementation reduces heart rate compared to infants whose formula does not contain DHA, with no evidence of a dose response (Pivik et al., Finally, Harris and colleagues performed a small prospective study that provides a valuable indication of which mechanisms are likely to underlie the omega-3 fatty acid-driven reduction in heart rate. The group enrolled heart transplant patients, ensuring that their transplants had occurred more than three months prior and there had been no transplant-related hospitalizations (Harris et al., Similar reductions in heart rate due to omega-3 fatty acids have been observed in animals. In a rat model, animals fed a DHA-enriched diet had lower heart rates than animals fed a control diet, a pattern that was achieved by 2 months and maintained until the end of the 32-week study (Ayalew-Pervanchon et al., Overall, it is apparent that a wide range of human and animal subjects, with or without cardiac disease, all respond to omega-3 fatty acid supplementation with reductions in resting and stress-induced heart rates. These findings suggest a highly consistent and robust effect of omega-3 fatty acids on heart rate.Although omega-3 fatty acids may reduce heart rate through several different mechanisms, our early studies demonstrated a direct effect of omega-3 fatty acids on cardiac cell membrane electrical excitability that contributes to reduced heart rate. We used isolated, neonatal rat cardiac myocytes that retain spontaneous beating behavior, allowing us to assess the effect of EPA and DHA on contraction as well as electrophysiological activity without neural or hormonal input. We found that EPA and DHA promptly reduced the contraction rate of the cardiac myocytes by 50–80% without a significant change in the amplitude of the contractions. This effect of omega-3 fatty acids on the excitability of the cells was similar to that produced by the class I antiarrhythmic drug lidocaine Figure , top Ka. In addiThe reduction of electrical excitability of cardiac myocytes by omega-3 fatty acids can be demonstrated directly by their response to electrical pacing (Kang and Leaf, To better elucidate the mechanism of action of omega-3 fatty acids on heart rate, we employed a patch-clamp technique to examine the electrophysiological activity in isolated neonatal rat cardiac myocytes. First, we induced the action potential in the myocytes exposed to EPA or DHA and measured the strength of the current required to elicit an action potential (Kang et al., At this point in our research, the manner by which omega-3 fatty acids reduce membrane excitability was still unclear. Therefore, we tested the effects of omega-3 fatty acids on single ion channel activity in neonatal rat cardiac myocytes. The results demonstrated a prompt inhibitory action of omega-3 fatty acids on the Na+ currents through fast sodium channels responsible for the phase 0 of the action potential in isolated neonatal rat cardiac myocytes. The inhibition of this ion channel was dose, time, and voltage dependent, but not use dependent Figure  Xiao et. SubsequRegulation of heart rate in humans is highly complex. Sympathetic output, vagal tone, and systolic and diastolic left ventricular function are only a few of the factors that contribute to the regulation of heart rate. While omega-3 fatty acids could potentially affect any or all of these factors, our studies strongly suggest a direct impact of omega-3 fatty acids (Leaf et al., 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.


Post-translational modification of lysine residues of specific proteins by ubiquitin modulates the degradation, localization, and activity of these target proteins. Here, we identified gains of ubiquitylation sites in highly conserved regions of human proteins that occurred during human evolution.We analyzed human ubiquitylation site data and multiple alignments of orthologous mammalian proteins including those from humans, primates, other placental mammals, opossum, and platypus. In our analysis, we identified 281 ubiquitylation sites in 252 proteins that first appeared along the human lineage during primate evolution: one protein had four novel sites; four proteins had three sites each; 18 proteins had two sites each; and the remaining 229 proteins had one site each. PML, which is involved in neurodevelopment and neurodegeneration, acquired three sites, two of which have been reported to be involved in the degradation of PML. Thirteen human proteins, including ERCC2  and NBR1, gained human-specific ubiquitylated lysines after the human-chimpanzee divergence. ERCC2 has a Lys/Gln polymorphism, the derived (major) allele of which confers enhanced DNA repair capacity and reduced cancer risk compared with the ancestral (minor) allele. NBR1 and eight other proteins that are involved in the human autophagy protein interaction network gained a novel ubiquitylation site.The gain of novel ubiquitylation sites could be involved in the evolution of protein degradation and other regulatory networks. Although gains of ubiquitylation sites do not necessarily equate to adaptive evolution, they are useful candidates for molecular functional analyses to identify novel advantageous genetic modifications and innovative phenotypes acquired during human evolution. Ubiquitin is a 76-residue polypeptide that is highly conserved among eukaryotes. Ubiquitylation of the lysine residues of substrate proteins targets the ubiquitylated proteins for degradation by the proteasome . The ubiA large number of genetic modifications have occurred in the human lineage during primate evolution that might be responsible for the emergence of human phenotypes ,7. TheseN-acetylglucosamine modification sites [To assess the impact of PTMs on human proteome evolution and to identify candidates for evolutionarily innovative PTM sites, a large amount of PTM data from human cells is needed. Recent progress in high-throughput screening by mass spectrometric analysis has enabled the large-scale characterization of PTM sites in the human proteome, including phosphorylation sites ,18, O-lion sites , lysine on sites , and ubion sites -25.et al.[et al.[et al. and Wagner et al.’s datasets include lysines modified not only by ubiquitin, but also by ubiquitin-like proteins such as SUMO, ISG15, and NEDD8. In this report, we therefore use the term “ubiquitylation” to indicate both ubiquitin and ubiquitin-like protein modifications.We hypothesize that appearance of novel ubiquitylation sites in proteins along the human lineage during primate evolution may have modified protein regulatory networks, potentially resulting in the acquisition of novel phenotypic traits. To address this possibility, we developed a bioinformatics method to systematically identify gains of novel ubiquitylation sites in the human lineage during primate evolution. As a pilot study, we used ubiquitylation data for human proteins reported by Kim et al. and Wagnl.[et al. as inputhttp://www.uniprot.org) and PhosphoSitePlus (http://www.phosphosite.org) [et al.[et al.[We aimed to identify human ubiquitylated lysines located in highly conserved regions of mammalian proteins that first appeared along the human lineage during primate evolution. To do this, a large amount of ubiquitylation site data and multiple sequence alignments of orthologous mammalian proteins are required. To assess ubiquitylation sites, one can use databases containing PTM data, such as UniProt (ite.org) , or largite.org) -23,25. I) [et al. and Wagnl.[et al., as welll.[et al.. The oveThe timing of the gain of a ubiquitylated lysine was determined by finding the branch that enclosed the earliest shared lysine between humans and other primates on the mammalian phylogenetic tree. For example, the human PML residue Lys 394  protein, which is also known as XPD, is involved in transcription-coupled nucleotide excision repair and is implicated in cancer-prone xeroderma pigmentosum, trichothiodystrophy, and Cockayne syndrome . In the The neighbor of BRCA1 gene 1 (NBR1) protein has been identified as one of the principle cargo receptors for selective autophagy of ubiquitylated targets ,32. AbnoPML gene is often fused with the retinoic acid receptor α (RARA) gene, which is associated with acute promyelocytic leukemia [Of the 281 ubiquitylation sites, 269 sites in 243 human proteins were acquired along the human lineage during primate evolution, and are shared with chimpanzees and other primates  has a ubiquitylated Lys 33 that is shared with chimpanzees and gorillas, while other early-diverged primates (including orangutans) and all other mammals examined have a glutamine (Q) residue at this position Figure . NGDN fuThe scavenger receptor class B member 1 (SCARB1) protein is a plasma membrane receptor for high-density lipoprotein cholesterol (HDL). It mediates cholesterol transfer to and from HDL  and is iWe found that 56 novel ubiquitylation sites in 54 proteins first appeared in the common ancestor of catarrhine primates. One representative case is WD repeat-containing protein 35 (WDR35) Lys 684, at which position most other mammals have a glutamic acid (E) Figure . WDR35 hATXN2 gene causes spinocerebellar ataxia type 2 [Of the 281 novel human ubiquitylated lysines, 116 in 107 proteins are shared with simians. One example is ataxin 2 (ATXN2) Lys 349, at which position all the other mammals examined have an arginine (R)  Lys 211 first appeared in primates after their divergence from the common ancestor of Euarchontoglires and is shared in all primates examined  glutamine allele is designated as the mutant, which shows reduced DNA repair capacity; carriers of this minor allele therefore have an increased cancer risk . The gaiInterestingly, among the 252 proteins, nine proteins  have been found in human autophagy protein interaction networks . NBR1 haet al.[Hagai et al. showed tet al.. To explWe developed a bioinformatics method to identify novel ubiquitylation sites that evolved along the human lineage, resulting in the identification of 281 novel ubiquitylation sites. The gain of novel ubiquitylation sites could result in novel ubiquitin-associated protein regulatory interactions. Proteins with a novel ubiquitylation site are useful candidates in the search for genetic modifications implicated in the emergence of novel phenotypes during human evolution.et al.[et al.[To identify ubiquitylation sites in human proteins, we used the large-scale analysis datasets of Kim et al. and Wagnl.[et al.. These rl.[et al.. Peptidehttp://genome.ucsc.edu). The ‘CDS FASTA alignment from multiple alignment’ data, which are derived from the ‘multiz46way’ alignment data [Multiple sequence alignments of the human proteins and orthologous proteins from other mammalian species were obtained from the University of California Santa Cruz (UCSC) Genome Browser Database  was used to collect protein sequences for some species. The multiple sequence alignments were generated using MUSCLE (http://www.drive5.com/muscle).The National Center for Biotechnology Information (NCBI) Protein database  and may differ from those of the UniProt or NCBI Protein databases.Finally, 281 sites in 252 proteins were collected. We examined the multiple alignments to estimate the timing of the gain of the ubiquitylated lysine residue. Possible functional consequences of the gain of the ubiquitylation site were assessed by a literature survey. The positions of the residues noted in this manuscript are derived from the datasets of Kim et al. and Wagnl.[et al., which aThe authors declare that they have no competing interests.YH conceived of this study, conducted the programming work, and prepared the manuscript. DSK participated in the sequence analysis. Both authors read and approved the final manuscript.List of proteins with novel ubiquitylation sites.Click here for fileDetailed alignments of surrounding regions of novel ubiquitylation sites.Click here for filePhylogenetic tree of the 37 mammals used in this study.Click here for file


Our laboratory has been evaluating the potential contribution of environmentally bioavailable neurotoxic metals to the onset, development and progression of AD for about 30 years  is perhaps in vitro and in vivo aluminum promotes inflammatory signaling via the pro-inflammatory transcription factor NF-kB, another prominent feature characteristic of AD brain 2·12H2O, or alum, as a clarification and “finishing” agent  that at physiologically realistic concentrations, aluminum strongly promotes amyloid aggregation and accumulation, a key feature of AD neuropathology Exley, ; (ii) thn Bondy, ; (iii) tn Bondy, ; (v) than Bondy, ; (vi) th Flaten, ], and . A commonly used Tg2576 mouse model overexpresses a mutant form of beta amyloid precursor protein (β APP), APPK670/671L, linked to early-onset familial AD, and develops amyloid plaques and progressive cognitive deficits as the mice age. Tg2576 mice exposed to dietary aluminum have been shown to develop oxidative stress and robust amyloidogenesis, key features of AD neuropathology (Praticò et al., in vitro and in vivo models for AD with AD itself. Indeed, the abundance of specific miRNAs are highly selective, and potential indicators and predictors of human health and disease, including progressive neurological disorders such as AD (Alexandrov et al., We would like here to briefly include some recent genetic data on aluminum and its effects on miRNA abundance in a highly relevant transgenic animal model for AD that shows strong parallels to miRNA profiles which are found in AD brain Figure . There ain vitro studies (Kruck et al., Lastly, more research into the potential contribution of aluminum to the AD process is clearly warranted. There are currently no treatments for AD that effectively prevent or cure AD's insidious onset or propagation. We think it important to emphasize that the most effective clinical treatment yet devised for moderate- to late-stage AD patients was the implementation of the first generation anti-oxidant and trivalent iron/aluminum chelator desferrioxamine to attempt to remove aluminum from the brains of AD patients (Crapper McLachlan 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.