Question:
You will be presented with the full text of a biomedical research paper. Please write an abstract for this paper. Your response should include the abstract and no additional text.

Paper text:
there is a subgroup of patients with temporomandibular disorder who nomadically pass from one dentist to another seeking  bite correction  .
their occlusal discomfort is characterized by an uncomfortable sensation mainly affecting corrected dentition , crowns , or dentures in which no abnormality is clinically detectable .
this phenomenon is known as the phantom bite syndrome ( marbach 1976 , 1978 ; marbach et al 1983 ; jagger and korszun 2004 ) . despite repeated failures of dental surgery , these individuals persist in seeking bite correction from a succession of dentists .
the condition is refractory to most treatments including psychotherapy ( marbach 1976 , 1996 ) .
we have reported previously that tricyclic antidepressants can be effective in treating phantom bite syndrome ( toyofuku 2000 ) .
however , the patients non - acceptance of the anticholinergic side - effects of these drugs usually prevents high enough doses being achieved .
milnacipran is an antidepressant which , similarly to the tricyclics , inhibits the reuptake of serotonin and norepinephrine but without the side - effects of the older antidepressants .
recently it has been reported that milnacipran has been used to treat various oral psychosomatic disorders such as glossodynia and temporomandibular disorder ( toyofuku 2003 ; toyofuku et al 2003 ; toyofuku and miyako 2004 ) .
we present here a preliminary study of the efficacy and safety of milnacipran in a series of patients complaining of occlusal discomfort and diagnosed as suffering from phantom bite syndrome .
we report here the results with 7 patients who came to the department of dentistry and oral surgery at the fukuoka university hospital in japan in 20032004 complaining of occlusal discomfort and diagnosed as suffering from phantom bite syndrome .
six patients were outpatients and one was hospitalized for severe fatigue and because of difficulty of attending the hospital since she lives on a remote island .
all patients met the following criteria ; preoccupation with their dental occlusion and a false belief that their dental occlusion was abnormal , a long history of repeated dental surgery treatment failures with persistent requests for the occlusal treatment that they are convinced they need , no history of significant psychiatric illness , absence of obvious psychosocial problems .
they all had a relatively high intelligence and socioeconomic status which enabled then to undergo endless costly and time - consuming dental treatments .
milnacipran was initially administered at 30 mg / day on a twice daily schedule and adjusted weekly according to clinical symptoms and tolerance . the effect on occlusal discomfort
was measured using a 100 mm visual analogue scale ( vas ) where baseline severity was arbitrarily set to 100 .
severity of depression was assessed using the zung self - rating scale for depression ( sds ) .
( marked improvement with only occasional mild symptoms ) ,  mild  ( some improvement but with considerable residual symptoms ) , or  poor  ( little or no improvement ) .
one patient was lost to follow - up after 2 weeks because he refused to continue , stating that he was  feeling well  .
five of the remaining 6 patients were improved at the end of the 4-week treatment period , 3 markedly , and 2 mildly improved .
patient 6 was unco - operative and refused to complete the vas and sds self - rating evaluations at the end of the study .
she insisted , however , that she had had no improvement at all over the 4 weeks of the study . during the study she refused any increase of the dose of milnacipran , insisting on dental surgery bite correction instead of medication .
scores of 0 improvement were therefore used for this patient for the sds and vas analyses ( table 2 ) .
overall , the occlusal discomfort felt by the patients was considerably decreased between baseline and week 4 ( table 2 ) .
the level of depressive symptoms was also decreased as indicated by a 47.8% decrease in sds .
there was , however , no correlation between individual reductions in sds and vas values .
three patients reported adverse effects ( headache , dizziness , and nausea , table 2 ) .
all effects , however , were slight and transient , disappearing within a few days .
patients exhibiting the phantom bite syndrome are considered to be refractory to most dental treatment .
they become increasingly difficult to manage after repeated failures of dental surgery resulting in frustration for both the dentist and the patient who is usually convinced of the incompetence of their dentist and moves on to another dentist .
the present study suggests that milnacipran may be a beneficial treatment for such oral psychosomatic disorder patients with occlusal discomfort known as phantom bite syndrome .
this is a small number , it is the largest study on phantom bite to have been reported to date .
the department of dentistry and oral surgery at fukuoka university has an excellent reputation in the treatment of dental psychosomatic disorders and for this reason patients are referred to this department by psychosomatic doctors from all over southern japan .
in addition 40% of patients in the present study came spontaneously to the department because of its reputation among patients .
in addition to the small number of patients , the obvious weakness of the study resides in its open - label design .
however , the refractory nature of the disorder ( the average duration at the beginning of the study was over 3 years ) gives some credence to the observed results .
this technique probably lacked precision , however , since some of the patients said they had difficulty in expressing quantitatively their symptom on a visual analogue scale .
the development of other patient - rated measures such as a modified  faces scale  as used to quantify pain in children ( bieri et al 1990 ) would clearly be helpful for studying this and similar oral psychosomatic conditions .
none of the patients had any history of significant psychiatric illness , indeed they were all strongly resistant to the idea of psychiatric referral or treatment .
six of the 7 patients were , however , mildly depressed as rated by the zung sds scale and one more moderately depressed . in 5 out of 6 patients completing the study , the depression scores improved considerably to a level considered to be asymptomatic . in general , however , there was no correlation in this study between the decrease in sds score and decrease in occlusal discomfort as indicated by the vas .
this result and clinical observations suggests that the efficacy of milnacipran in reducing occlusal discomfort is more likely to be a direct effect on the somatosensory system rather than on any associated depression .
milnacipran and other serotonin - norepinephrine reuptake inhibitors have been shown to be effective on a variety of pain disorders both associated with , and independent of , depression ( briley 2003 , 2004 ) .
milnacipran is not , however , an analgesic as such and these effects have been suggested to involve an action on serotonin and norepinephrine neurotransmission ( stahl and briley 2004 ) .
the action of milnacipran appears to be to correct the erroneous integration of peripheral signals by the central nervous system .
a further example of milnacipran correcting erroneous integration of peripheral signals is in fibromyalgia where normally non - painful stimuli are perceived as pain signals ( allodynia ) ( vitton et al 2004 ) .
it would seem likely that the effect of milnacipran on phantom bite seen in the present study is another manifestation of this activity on the two monoamines systems where the occlusal discomfort experienced by the patient is the result of an erroneous integration of peripheral signals . in conclusion , after 4 weeks treatment , 5 of the 6 patients completing the study responded to milnacipran with clinically significant improvements in their occlusal discomfort .
this suggests that milnacipran may be an effective and well tolerated treatment for phantom bite in oral psychosomatic disorder patients .
phantom bite is , however , a chronic syndrome and the promising effects seen here after 4 weeks need to be followed up over a much longer time period .

Answer:
phantom bite syndrome is characterized by an uncomfortable sensation mainly affecting corrected dentition in which no abnormality is clinically detectable . despite repeated failures of dental surgery , sufferers persist in seeking bite correction from a succession of dentists .
 the etiology  pathogenesis of phantom bite is unknown but some consider the syndrome to be a psychosomatic disorder .
 seven patients with this syndrome were treated with the serotonin and norepinephrine reuptake inhibitor milnacipran for 4 weeks .
 one patient withdrew after 2 weeks because he was feeling
 well  .
 at the end of the study , 5 of the 6 patients completing the study reported significant improvements , with a mean decrease in occlusal discomfort of 55.3% , as indicated by a visual analogue scale .
 this result appeared to be independent of any antidepressant effect .
 only minor and transient side - effects were observed . it is suggested that milnacipran may be a helpful treatment for phantom bite but this needs to be confirmed by further and longer term studies .


Question:
You will be presented with the full text of a biomedical research paper. Please write an abstract for this paper. Your response should include the abstract and no additional text.

Paper text:
in their companion article , tononi and cirelli argue that i have missed the big picture by conflating questions of sleep function with the underlying mechanisms . as i have discussed elsewhere
[ 2 , 3 ] , understanding sleep function is of central importance to biology .
any theory of sleep function must also grapple with universal traits of sleep , some of which were enumerated in their response .
there are other theories of sleep function and many of the theoretical arguments made in support of shy ( e.g. , a need for offline states , sleep homeostasis , and brain metabolism ) apply to them .
my position is that this evaluation must always include a discussion of mechanisms , because they can not be disentangled from functional questions .
the underlying message from tononi and cirelli is that what really matters is the
the end result  [ 1 , page 4 ] rather than how you get there .
i find this an odd position to take and a backward step in our pursuit of sleep function .
the goal of science is to understand how nature works . that includes an empirical pursuit of physical mechanisms .
scientists should therefore be skeptical of any theory of sleep function that fails to elucidate the underlying mechanisms that govern the proposed function . in this regard ,
the proponents of shy are in an indefensible position when they argue that the mechanisms have   no bearing on whether the core claim of shy is true or false  [ 1 , page 3 ] .
they have bearing because if the underlying mechanisms are not sleep dependent then the theory is wrong .
incidentally , the theory is also wrong if the proposed mechanisms do not exist . while it may be true that these mechanisms are complex and perhaps different in different species , that is not a reason to ignore them . on the contrary , that is a reason to explore them .
. indeed , i do find shy confusing because the proposed mechanisms ( to date ) seem inconsistent with what is actually known about synaptic plasticity .
moreover , their imprecise terminology fogs the issue . they claim that they never meant that the potentiation in wakefulness is hebbian ( i.e. , some form of ltp ) , yet it is difficult to draw any other conclusion based on their own words . their liberal and interchangeable use of the words  long - term potentiation  ,  ltp ,  or
this is because  ltp  is not short - hand for  stronger synapse ;  it has a precise meaning and commonly refers to hebbian processes . in their rebuttal
, they back peddle from their past specific language regarding the significance of neuromodulator release and the expression of plasticity molecules in shy .
there is , however , little ambiguity in their original description of how these events purportedly promote ltp ( or ltp - like events ) during wake versus sleep [ 4 , 5 ] .
the concepts and terminology of synaptic homeostasis and scaling predate shy   and there is simply no mistaking the broad similarities between synaptic scaling and what is described in shy .
for example , here is a more complete excerpt from tononi and cirelli .     like activity - dependent synaptic scaling ( emphasis added ) , however , sleep - dependent downscaling would affect most or all of a neuron 's synapses . in this respect , downscaling is conceptually different from long - term depression , which affects select groups of synapses , or depotentiation , which affects only recently potentiated ones
therefore , their use of these terms , if in fact they mean something else , is perplexing . the distinctions they make between their version of downscaling and scaling proper are welcome , but quite subtle when compared to the overall similarities .
for example , synaptic homeostasis is not only manifested at the level of firing rates as implied by tononi and cirelli .
that is one outcome of a homeostatic adjustment of synaptic weights in a network , as measured , for example , by mepscs [ 7 , 8 ] .
this point seems moot , since tononi and cirelli cite changes in firing rates and mepscs as evidence of shy [ 9 , 10 ] .    in the end , it really does not matter what new name they give to their process ( or set of processes ) that weakens synapses .
the point i was making , and which they missed , is that any form of plasticity ( especially if possibly novel ) should be examined through the prism of known facts about hebbian and non - hebbian plasticity .
case in point : i never stated that the  downscaling  of shy is identical to synaptic scaling as currently understood in the field .
i instead argued that since the concepts of scaling figure prominently in shy , and because scaling is an accepted means of globally adjusting synaptic weight , it is logical to examine the claims of shy based on what is known about synaptic scaling .
 synaptic renormalization  from synaptic scaling , but this name change does not inoculate shy against scrutiny .
  the veracity and validity of a scientific theory is not solely determined by the amount of data piled on one side of a scale .
it is also determined by a careful examination of each piece of evidence , pro and con . upon close examination
, threads of supportive findings may unravel , and when contrary evidence is properly considered , an otherwise impressive mass of findings may collapse . a large part of their response is a long catalog of supportive data  some of which i included in my review .
however , as i pointed out , careful examination reveals alternative explanations for some of their results .
they also largely ignore evidence consistent with net increases in synaptic strength after sleep , or findings that question their hypothesized relationship between synaptic potentiation and slow - wave electroencephalographic activity ( swa ) [ 11 , 12 ] .
these findings are consistent with my original discussion   and completely in opposition to predictions of shy .
when these are also considered the universality of shy , and its utility as an explanation for why we sleep , becomes questionable .
  in my original review , i considered biological processes other than sleep that might explain some findings ascribed to shy .
these included the cumulative effects of natural patterns in brain temperature ( and in mammals , glucocorticoid release ) across the 24-hour day or after sleep deprivation .
tononi and cirelli present a number of arguments against these ideas , but i have a better idea
for example , why not examine the effects of cooling or warming on drosophila synaptic proteins ( which are altered by changes in temperature as small as 8c ; not as they state 20c ) ?
tononi and cirelli argue strenuously that shy is a theory of function , yet they support their argument with cellular and molecular findings that have no demonstrable function . rather than elaborate upon already dense theoretical arguments about the functional importance of shy , why not demonstrate it empirically ? in science , no argument , no matter how beautifully crafted , trumps a good experiment .
  in his discussion of sleep theories 50 years ago , nathaniel kleitman reminded his readers of the cautionary tale of ptolemy of alexandria .
ptolemy was a revered scholar in the 2nd century ad who codified hundreds of years of prior greek astronomy and mathematics into what came to be known as the ptolemaic universe .
the ptolemaic universe held that the stars , planets and sun revolved around the earth , embedded in overlapping crystalline spheres .
this theory of the natural world was elegant , mathematical , and even highly predictive of astronomical events .
the lesson from ptolemy is that scientific theories are ultimately judged not only by their power to explain , but by the validity of their physical mechanisms .
tononi and cirelli argue that for shy to be valid , it does not matter how synapses are weaker after a sleep period , just that they are .
but ptolemy reminds us that this is not enough ; scientific truth comes from asking hard questions about how things actually work .
i do not question their results , showing for example , changes in evoked responses or mrnas consistent with shy .
first , they have not identified how sleep actually alters synaptic strength in any species .
second , they have not experimentally excluded the role of other biological processes that coincide with sleep .
a final consideration is that if shy is a scientific hypothesis , then tononi and cirelli should propose an experimental outcome that would force a rejection of shy .

Answer:
in a recent article i reviewed an influential theory of sleep function , the  synaptic homeostasis hypothesis ( shy . )  according to shy , sleep renormalizes synapses that are potentiated during prior wakefulness .
 i concluded that while shy is a seminal theory with important implications about sleep function and the brain , its underlying mechanisms are poorly defined . in an accompanying article , the authors of shy responded at length .
 their reply is thoughtful and provocative , but unfortunately many of the points i raised were not accurately represented or addressed . in this brief commentary , i attempt to clarify some points of confusion .
 i also explain why any theory of sleep function is incomplete without an understanding of the underlying cellular mechanisms .


Question:
You will be presented with the full text of a biomedical research paper. Please write an abstract for this paper. Your response should include the abstract and no additional text.

Paper text:
nontuberculous mycobacteria ( ntm ) have emerged as an increasingly important pathogen in the last two decades . unlike other environmental pathogens that are largely opportunistic in patients with malignancy and immunodeficiency , as well as transplant recipients , ntm can cause significant disease in otherwise healthy individuals .
the ntm most commonly associated with pulmonary infection is the mycobacterium avium complex ( mac ) , which is a microbial complex of mycobacterium avium and mycobacterium intracellulare .
there have been many reports concerning its radiologic findings.123 ) although uncommon , several cases of solitary pulmonary nodules ( spn ) caused by mac pulmonary infections have been reported,456 ) which is different from the typical presentation of mac .
however , a case of a multiple cavitating nodular infection with neither a fibrotic change nor nodular bronchiectasis associated with m. intracellulare has not been reported .
we present the case of a 67-year - old asian woman who had a m. intracellulare infection presenting with multiple cavitating pulmonary nodules , which was differentiated from metastatic lung disease by percutaneous transthoracic needle aspiration ( pcna ) .
she presented to a local clinic after a single occurrence of hemoptysis 10 days prior .
the color of the hemoptysis was scarlet and the amount was 1/2 cup of soju , korean distilled spirits .
she had been diagnosed with type 2 diabetes mellitus ( dm ) 2 years prior at a local clinic , and had since been taking metformin 500 mg after breakfast and dinner .
glycosylated hemoglobin was 6.7% , and she had good control of her blood sugar levels during hospitalization .
after a chest ct was obtained at the local clinic , she was transferred to our hospital to investigate the multiple cavitary pulmonary nodules that were found on the ct scan .
when the patient visited our hospital , her initial vital signs showed a blood pressure of 110/70 mm hg , heart rate of 80 beats / min , respiratory rate of 16 breaths / min , and body temperature of 36.8. both pupil responses to light were normal and there was no abnormality in the conjunctivae and sclerae .
on auscultation , neither crackles nor wheezing was heard in both lung fields , and the heart sound was regular without murmur .
at the first visit to our hospital , the patient did not have any symptoms .
there were several round nodules in both the upper lung zone and right middle lung zone , and patch consolidation in the left lower lung zone on the chest radiography , which is suggestive of mycobacterium tuberculosis ( mtb ) or metastatic lung disease ( figure 1 ) .
similarly , the chest ct showed centrilobular nodules with a tree - in - bud appearance and three round cavitary nodules in the left apex , the right upper lobe posterior segment , and the right lower lobe superior segment , suggestive of mtb or metastatic lung disease ( figure 2 ) .
we isolated the patient because we could not exclude the possibility of mtb along with metastatic lung disease .
the initial laboratory parameters were as follows : total leukocyte count 7,500/mm ( neutrophil 64.6% , lymphocyte 21.1% , monocyte 0.44% ) ; hemoglobin level 12.8 g / dl ; and platelet count 217,000/mm .
the level of c - reactive protein was 0.03 mg / dl and other parameters were within the normal limit on the blood chemistry tests .
additionally , the coagulation profile was checked , and the prothrombin time was 11.1 seconds ( international normalized ratio 1.35 ) .
for further evaluation , we planned to perform a bronchoscopy and pcna , and the additional imaging examinations were not performed because chest imaging was obtained on the day of the initial hospital visit .
the results of three smears for acid - fast bacilli , and a nucleic acid amplification test for mtb and ntm in sputum were all negative . for further evaluation ,
a bronchoscopy was performed on the left upper lobe apical segmental bronchus , the right upper lobe posterior segmental bronchus , and the right lower lobe superior segmental bronchus .
the smear test of the bronchoscopic washing fluid was positive for acid - fast bacilli .
the result of nucleic acid amplification was negative for mtb , but positive for ntm .
therefore , the patient was diagnosed with ntm , so the patient 's quarantine was lifted .
after 7 days , heavy colonies with confluent growth in ogawa 's egg medium were detected in the bronchial washing fluid culture .
after 2 weeks , several colonies with confluent growth in the mycobacterium growth indicator tube 's egg medium were detected in the bronchial washing fluid culture .
the precise species was identified using a polymerase chain reaction - restriction fragment length polymorphism - based method that identified differences in the rpob gene.7 ) the colonies were subsequently identified as m. intracellulare . to rule out metastatic lung disease ,
the lung tissue from the biospy showed chronic granulomatous inflammation with caseating necrosis ( figure 3a , b ) .
for further evaluation , a nucleic acid amplification for mtb and ntm with a stain for acid - fast bacilli was conducted using tissue from the pcna .
the additional report showed that both the nucleic acid amplication for ntm and the stain for acid - fast bacilli were positive ( figure 3c ) , and there were no malignant cells .
this finding was consistent with ntm infection , and we could exclude metastatic lung disease . in conclusion ,
the lung tissue from the biospy confirmed the diagnosis obtained from the bronchial washing fluid culture . with the diagnosis of ntm infection
the patient was prescribed a medication regimen that included rifampin ( 450 mg ) , ethambutol ( 800 mg ) , and clarithromycin ( 1,000 mg ) . a drug susceptibility test for clarithromycin
was performed , and the result showed that the m. intracellulare was sensitive to clarithromycin .
the patient started to complain of nausea and vomiting , and had poor oral intake 7 days after taking the medication for ntm .
we changed the time for taking the medication from before meals to before bed , after which her symptoms improved .
there were no other complications such as an abnormal liver function test or optic neuritis .
we have performed blood tests and chest radiography to monitor the side effects and the disease progression .
m. avium is the more important pathogen in a disseminated disease , whereas m. intracellulare is the more common respiratory pathogen .
the chest radiography and ct scans showed abnormalities typical of the two forms of mac lung disease .
the traditionally recognized presentation of mac lung disease is as an apical fibrocavitary lung disease with large cavities , located in the upper lobe .
this form of the disease usually occurs in men with a history of cigarette smoking , excessive alcohol use , and underlying lung disease in their late 40s and early 50s . if not treated , this form of mac is rapidly progressive within a relatively short time period , 1 to 2 years
mac lung disease also presents with bronchiectatic nodular infiltrates , usually involving the right middle lobe or the lingula segment , predominantly in postmenopausal and non - smoking women .
this form of the disease has a tendency to progress much slower than the fibrocavitary disease , therefore long - term follow - ups lasting from months to years may be necessary to determine clinical or radiographic changes . in this indolent form of the disease
spn is identified as focal , round , or oval areas of increased opacity in the lung that measure 3 cm in diameter .
these nodules are frequently discovered incidently on chest radiography or chest ct.8 ) spn is often assumed to be attributable to mtb infection.9 ) however , it has been shown in case reports that spn can be attributable to mac lung infection.456 ) in 2009 , sekine et al.10 ) reported a case of a mac pulmonary infection presenting with multiple nodules , which was an unusual presentation of a mac pulmonary infection . unlike mtb
therefore , the isolation of mac species from a respiratory sample is not sufficient evidence of ntm lung disease . in 1997 , the american thoracic society issued a revised set of diagnostic criteria for ntm pulmonary disease . according to these criteria ,
a patient with ntm lung disease must have compatible symptoms and signs , and a compatible chest radiography or chest ct abnormalities .
the current case did not strictly satisfy the diagnostic criteria proposed by the american thoracic society in terms of radiographic findings .
the diagnostic criteria of ntm lung disease must be expanded to such cases of spn , multiple nodules , and multiple cavitary nodules , as in our case . in our case , we could not initially rule out mtb lung infection due to the chest ct findings , which showed multiple cavitating nodules with centrinodular nodules .
we did not suspect mac lung infection because there was neither bronchiectasis in the right upper lobe or the left lingular segment nor a fibrotic change in the upper lobe .
while the bronchoscopy findings were sufficient to diagnose the patient with mac lung infection , we also conducted a pcna to rule out metastatic lung disease .
, we differentiated the atypical presentation of mac lung infection from mtb lung disease or metastatic lung disease .
ntm have emerged as an increasingly important pathogen in the last two decades . in korea ,
there has been an increasing prevalence of mac infections , and an increasing number of cases presenting with atypical findings .
our case report highlights the importance of differentiating among mtb , mac infection , and metastatic lung disease in cases of multiple cavitary nodules .
clinicians should consider the possibility of mac lung infection with various findings on chest radiography and chest ct .
we believe that pcna can be a valuable diagnostic tool for differentiating mtb and mac , and differentiating between malignant diseases and infectious diseases when a pulmonary nodule is revealed on chest radiography or chest ct scans . in conclusion , to the best of our knowledge , this is a very rare report of a mac pulmonary infection presenting with multiple cavitary nodules . as the prevalence of mac infections increases , more cases start to show atypical radiographic findings , compared to the typical apical fibrocavitary or bronchiectatic nodular forms . other forms of mac have been reported , such as spn and multiple nodules . in this report , we present another form of mac pulmonary infection .
therefore , clinicians should consider the possibility of mac lung disease with various findings on chest radiography or chest ct scans .
in addition , pcna can be a useful diagnostic tool for evaluating multiple nodules to differentiate metastatic lung diseases from infectious diseases such as mtb or mac lung infections .

Answer:
nontuberculous mycobacteria ( ntm ) have been increasingly recognized as an important cause of chronic pulmonary infections .
 the mycobacterium avium complex ( mac ) , which is composed of two species , mycobacterium avium and mycobacterium intracelluare , is the most commonly encountered pathogen associated with ntm lung disease . mac pulmonary infection typically presents in a fibrocavitary form or a nodular bronchiectatic form .
 however , there have been atypical presentations of mac pulmonary infections , including solitary pulmonary nodules ( spn ) .
 there have been several previous reports of spn due to mac infection in the united states , japan , and korea . in 2009 ,
 sekine and colleagues reported a case of mac pulmonary infection presenting with multiple nodules . to date , however , there have been no cases of ntm lung infection with multiple cavitary pulmonary nodules , and neither a fibrotic change nor nodular bronchiectasis .
 the present case showed a multiple cavitating nodular lung infection due to mac , which is very rare and different from the typical presentation of mac pulmonary infections .
 we also showed that percutaneous transthoracic needle aspiration can be a useful diagnostic tool to evaluate a case of multiple cavitary nodules .


Question:
You will be presented with the full text of a biomedical research paper. Please write an abstract for this paper. Your response should include the abstract and no additional text.

Paper text:
failure of a total knee arthroplasty ( tka ) is often associated with loss of bone from either the proximal aspect of tibia or the distal aspect of the femur .
these defects are usually classified as contained or uncontained.1 the reconstruction of large uncontained defects represents a major challenge to the revision surgeon .
options for reconstruction2 of large defects include metal augments , custom prostheses , massive autogenous bone - grafts and massive allografts .
metal augments are recommended only for small to medium sized defects in elderly low demand patients .
custom prostheses are costly , time consuming to manufacture and may not fit as well as planned or at all at the time of surgery .
autogenous bone - grafting is not suitable for large defects or in situations where structural support is required .
allografts provide a biological solution , have the advantage of easy fashioning to fit irregular defects , restore bone stock and have relatively low cost .
use of femoral head allograft , complete distal femur or proximal femur allograft has been reported in some studies34 ; however , no study has reported use of both distal femur and proximal tibia allograft in a single revision total knee arthroplasty .
we report the first successful use of both complete distal femoral and proximal tibia massive allografts in the reconstruction of large femoral and tibial uncontained defects during revision total knee arthroplasty .
a 70-year - old male patient , farmer by occupation , presented with a swollen , painful and unstable right knee with primary complaint of inability to bear weight .
passive range of motion was painful and limited to 10 degrees of hyperextension to 50 degrees of flexion in april 2005 .
the patient also had a periprosthetic supracondylar fracture of femur following a trivial fall , for which open reduction and internal fixation was done elsewhere eight years back with condylar blade plate .
the skin revealed thick scar tissue on both anterior and lateral aspects of the knee due to secondary wound healing after previous surgeries .
anteroposterior and lateral radiographs [ figure 1 ] revealed severe osteolytic bone defects on femoral and tibial aspects along with primary total knee prosthesis and condylar blade plate in situ .
infection was ruled out preoperatively with bone scan and laboratory markers ( erythrocyte sedimentation rate , c- reactive protein ) .
we decided to reconstruct the knee with structural distal femur and proximal tibia allografts and constrained fixed - bearing revision knee prosthesis ( nexgen , lcck , zimmer , warsaw ) .
anteroposterior and lateral x - rays of right knee showing extensive osteolysis on both femoral and tibial aspects we used the previous midline incision and a medial parapatellar approach .
we removed much necrotic , granulomatous tissue ( biopsy proven ) which usually occurs due to extensive polyethylene wear .
after debridement , the whole proximal tibia [ figure 2 ] presented a massive uncontained defect , classified as type iii according to anderson orthopaedic research institute classification.5 the whole distal femur also presented a large uncontained type iii bone defect involving both medial and lateral femoral condyles [ figure 2 ] .
however , femoral attachment of lateral collateral ligament was deficient , and ligament was identified with a piece of bone .
the intraoperative photograph shows the defect after thorough debridement both proximal tibial and distal femoral cadaveric allografts [ figure 3 ] with a diameter smaller than that of the host bone were selected so that they could be placed within the host cortical shell .
the allografts were taken from our own cadaveric bone bank , where they underwent radiation with 2.5 megarads and were stored at 70c .
two surgical teams were used during the management of the case , for optimal efficiency .
one team prepared the allograft , making appropriate femoral cuts and cementing in a long - stemmed revision femoral component .
cultures were taken from the knee as well as the allograft to rule out any existing infection .
step - cut prepared distal femoral and proximal tibial allografts both the recipient distal femur and proximal tibia were step - cut with minimal bone resection .
on the side table , step - cut was made in both allografts to match that of the host bone and instrumented with trial implants .
the implant allograft composite was put for trial in situ , and the cuts were fine tuned as required .
the revision knee components were cemented [ figure 4 ] on the back - table into the distal femoral and proximal tibial allografts with a long stem .
care was taken during cementing to avoid getting cement on the interface between the graft and the host .
once the cement had set , the construct was implanted with full assembly , matching the two step - cuts .
the residual host femur , with its ligaments and other soft tissues attached , was wrapped around the allograft host junction to serve as a living bone graft [ figure 5 ] .
extensor mechanism alignment and tracking was checked , and the wound was closed in layers . fully prepared composite allograft with lcck implant intraoperative photograph showing invagination of composite allografts into host bone prophylactic antibiotics consisted of an intravenous first - generation cephalosporin for five days , followed by oral antibiotics for seven days .
partial weight bearing was allowed at four weeks , and full weight bearing was started after eight months when there was radiographic evidence of union on both sides .
no wound complication was noted during the entire follow up . at the end of five years of
follow up ( i.e. , in april 2010 ) , the patient was walking full weight bearing and had complete incorporation of allograft and host bone with no signs of osteolysis [ figure 6 ] .
his active range of motion range of motion ( rom ) was 0 - 110 degrees .
anteroposterior and lateral x - rays of the same patient at five - year follow - up showing good allograft incorporation
we removed much necrotic , granulomatous tissue ( biopsy proven ) which usually occurs due to extensive polyethylene wear .
after debridement , the whole proximal tibia [ figure 2 ] presented a massive uncontained defect , classified as type iii according to anderson orthopaedic research institute classification.5 the whole distal femur also presented a large uncontained type iii bone defect involving both medial and lateral femoral condyles [ figure 2 ] .
however , femoral attachment of lateral collateral ligament was deficient , and ligament was identified with a piece of bone .
the intraoperative photograph shows the defect after thorough debridement both proximal tibial and distal femoral cadaveric allografts [ figure 3 ] with a diameter smaller than that of the host bone were selected so that they could be placed within the host cortical shell .
the allografts were taken from our own cadaveric bone bank , where they underwent radiation with 2.5 megarads and were stored at 70c .
two surgical teams were used during the management of the case , for optimal efficiency .
one team prepared the allograft , making appropriate femoral cuts and cementing in a long - stemmed revision femoral component .
cultures were taken from the knee as well as the allograft to rule out any existing infection .
step - cut prepared distal femoral and proximal tibial allografts both the recipient distal femur and proximal tibia were step - cut with minimal bone resection .
on the side table , step - cut was made in both allografts to match that of the host bone and instrumented with trial implants .
the implant allograft composite was put for trial in situ , and the cuts were fine tuned as required .
the revision knee components were cemented [ figure 4 ] on the back - table into the distal femoral and proximal tibial allografts with a long stem .
care was taken during cementing to avoid getting cement on the interface between the graft and the host .
once the cement had set , the construct was implanted with full assembly , matching the two step - cuts .
the residual host femur , with its ligaments and other soft tissues attached , was wrapped around the allograft host junction to serve as a living bone graft [ figure 5 ] .
extensor mechanism alignment and tracking was checked , and the wound was closed in layers . fully prepared composite allograft with lcck implant intraoperative photograph showing invagination of composite allografts into host bone
prophylactic antibiotics consisted of an intravenous first - generation cephalosporin for five days , followed by oral antibiotics for seven days
partial weight bearing was allowed at four weeks , and full weight bearing was started after eight months when there was radiographic evidence of union on both sides .
no wound complication was noted during the entire follow up . at the end of five years of
follow up ( i.e. , in april 2010 ) , the patient was walking full weight bearing and had complete incorporation of allograft and host bone with no signs of osteolysis [ figure 6 ] .
his active range of motion range of motion ( rom ) was 0 - 110 degrees .
anteroposterior and lateral x - rays of the same patient at five - year follow - up showing good allograft incorporation
few options are available to the surgeon for reconstruction of massive bone defects surrounding a failed total knee arthroplasty ( tka ) .
the application of allografts in revision tka is an attractive option . the use of femoral head allografts for the management of large bone defects in revision tka has been reported .
very few studies have also reported using either massive distal femoral or proximal tibial allograft for large defect reconstruction in revision tka.34 our patient presented a unique problem , having severe bone loss on both femoral and tibial aspects . using both massive distal femoral and proximal tibial allografts proved to be a successful mode of treatment with distinct advantages . placing
the allograft within the vascularized host bone will add some structural support to the allograft and provide an environment by which the allograft may eventually incorporate .
one major concern with the use of allografts is the risk of infection . in a large series by lord et al.,6
the risk of infection with the use of small allografts ( femoral heads ) was negligible ; and with the use of larger allografts , acceptable ( 4%-5% ) .
some authors have recommended plate and screw fixation of the allograft in addition to invagination of the graft , to ensure rotational stability . using a stemmed component and avoiding
the use of plate fixation decreases the need for extensive soft tissue dissection , avoids weakening of the graft and may decrease the risk of infection by preserving the soft tissue envelope.7 another concern about the use of massive allografts is their performance in the long term , especially in view of reports showing resorption and failures of allografts used in revision total hip arthroplasty at longer follow ups .
however , use of allografts in anatomically matching sites ( proximal tibia for proximal tibia , distal femur for distal femur ) allows for accurate orientation of trabeculae along the lines of stress .
this technique requires that the allograft is appropriately shaped for intussusception into the host bone with stable struts of host bone maximally contacting step - cuts in the graft.8 the limitation in terms of applicability of this study in practice could be the non - availability of such allografts at many centers .
newer trabecular metal wedges and sleeves may be an option ; however , they are very costly
. these allografts are free for patients at our institute and provide a biological and effective alternative .
there should be a stimulus to establish more and more cadaveric allograft retrieval centers to deal with the complex and often neglected cases of bone loss , which is particularly common in the indian scenario .
the use of dual structural massive allografts provides a stable and durable reconstruction of this uncommon presentation with both femoral and tibial large bone deficiencies encountered during a revision tka . at a five - year follow - up
, we did not find any infection , graft failure or loosening of implant , in spite of using two massive structural allografts in a single revision tka .
further follow up with large number of patients is necessary to determine the long term fate of these allografts .

Answer:
the reconstruction of large uncontained defects represents a major challenge to the revision total knee surgeon , and the outcome of the revision often depends on the management of these bone deficiencies .
 we report the first successful use of both complete distal femoral and proximal tibia massive allografts in the reconstruction of large femoral and tibial uncontained defects during revision total knee arthroplasty . at the five - year follow up ,
 we did not find any infection , graft failure or loosening of implant , in spite of using two massive structural allografts in a single revision total knee arthroplasty .


Question:
You will be presented with the full text of a biomedical research paper. Please write an abstract for this paper. Your response should include the abstract and no additional text.

Paper text:
guillian barre syndrome ( gbs ) is associated in 45 - 75% of cases with cranial nerve involvement .
facial nerve is the commonest to be involved followed by extra ocular muscles and lower cranial nerve involvement .
only two cases has been reported till date with gbs with total paresis of motor cranial nerves . here
a thirteen year old boy presented with acute progressive areflexic flaccid quadriparesis associated with motor cranial nerve involvement with bilateral facial and bulbar weakness .
he had an upper respiratory infection one week preceding the motor weakness which started from the lower limbs . on day seven
after the onset of motor weakness of limbs , the child developed significant bulbar weakness , difficulty in talking and could not move the tongue .
he was totally anarthric . on day nine , he had significant respiratory muscle weakness requiring mechanical ventilatory support . on day fourteen ,
the nerve conduction studies ( ncs ) were suggestive of severe demyelinating motor sensory polyradiculoneuropathy .
his anti - ganglioside antibody panel in the blood showed positive igm gm2 , gt1b , igg gm1,2,3 and gt1b antibodies .
his csf showed albuminocytological dissociation and his antinuclear antibody was negative . his magnetic resonance image ( mri )
he was treated with intravenous immunoglobulin at a daily dose of 0.4 g / kg for five days .
he showed gradual improvement and started swallowing after eight weeks of the onset of illness .
the wasting of the tongue also improved gradually at 3 months after the onset of illness [ figure 2 ] . at 6 months
repeat ncs was suggestive of motor sensory demyelinating radiculoneuropathy with improvement in conduction velocities and compound muscle action potential amplitudes compared to baseline study .
tongue wasting noted at 2 weeks after the onset of motor weakness improvement in tongue weakness and wasting noted at 6 months twelfth nerve involvement , either isolated or as a part of multiple cranial nerve involvement is quite uncommon and only two cases has been reported till date as a part of multiple motor cranial nerve involvement in a case of gbs .
, reported a case of fulminant gbs with quadriplegia and total paresis of motor cranial nerves and polo et al . , reported a case of atypical gbs with multiple cranial neuropathies including xii cranial nerve involvement
twelfth nerve involvement , either isolated or as a part of multiple cranial nerve involvement is quite uncommon and only two cases has been reported till date as a part of multiple motor cranial nerve involvement in a case of gbs .
, reported a case of fulminant gbs with quadriplegia and total paresis of motor cranial nerves and polo et al . , reported a case of atypical gbs with multiple cranial neuropathies including xii cranial nerve involvement
gbs with multiple cranial nerve involvement is a known entity but the involvement of xii cranial nerve is extremely rare .
our patient had multiple cranial neuropathies with involvement of vii , ix , x and xii nerves .
he had a severe form of gbs with areflexic quadriparesis along with respiratory muscle involvement requiring prolonged ventilatory support .
his mri brain was normal supporting that the tongue weakness is due to xii cranial nerve involvement .
twelfth nerve involvement , either isolated or as a part of multiple cranial nerve involvement is quite uncommon and only two cases has been reported till date as a part of multiple motor cranial nerve involvement in a case of gbs .
tan et al . , reported a fulminant case of gbs with quadriparesis with all motor cranial nerve involvement and their ncs showed segmental demyelination which was responsible for such severe involvement and possibly the pathophysiology in this case and our case are similar .
described a 23 years gentleman who developed a progressive illness over ten days with diplopia , facial diplegia and a nasal voice .
subsequently , the patient also developed weakness of the neck and tongue muscles , dysphagia , abolition of reflexes of the left arm and right triceps but without involvement of the respiratory muscles or other limbs .
however , the same patient had involvement of reflexes of left arm and right triceps only without involvement of respiratory muscles and lower limbs .
hence it was thought to an atypical variant of gbs in contrast to our case where he had all the typical features of gbs .
our patient showed anti - gm2 antibody positive which is usually seen in post cmv infection with or without gbs .
usually going on to ventilatory support requirement and the same is found in our patient .
the two previous case reports did not have the autoantibody levels to corroborate the clinical and electrophysiological findings .
the cranial neuropathy in our patient showed gradual recovery and tongue atrophy recovered over next three months . at 6 months
gbs with multiple cranial nerve involvement can rarely involve the xii nerve as well causing significant tongue weakness and such a presentation may be indicative of a severe nature of the disease and it usually recovers over a period of time .

Answer:
guillian barre syndrome ( gbs ) is associated with cranial nerve involvement .
 commonest cranial nerves involved were the facial and bulbar ( ixth and xth ) .
 involvement of twelfth cranial nerve is rare in gbs .
 we present a case of gbs in a thirteen years old boy who developed severe tongue weakness and wasting at two weeks after the onset of gbs .
 the wasting and weakness of tongue improved at three months of follow up .
 brief review of the literature about xiith cranial nerve involvement in gbs is discussed .


Question:
You will be shown the title of a chemistry paper, together with sections excerpted from the body of the paper. The paper sections may include HTML tags like `<p>` and `</p>`; please ignore these. Your task is to write an abstract for the paper. Your response should include the abstract and no other text.

Title:
Merochlorins A\xe2\x80\x93D, cyclic meroterpenoid antibiotics biosynthesized in divergent pathways with vanadium-dependent chloroperoxidases

Paper sections:

The molecular logic of biosynthetic halogenation has illuminated four oxidative enzyme families that deliver halogen ions to a diversity of organic scaffolds.1–3 Vanadium-dependent haloperoxidases (VHPOs) are rare bacterial halogenating enzymes that were first characterized from fungi and macroalgae where they catalyze the oxidative halogenation of electron-rich organic substrates.4,5 We recently showed that the napyradiomycin antibiotics6–8 are distinctive streptomycete meroterpenoids, whose linear isoprenoid side chains undergo intramolecular VHPO-mediated cyclization reactions.9,10 Herein, we report the discovery of a new natural product group of chlorinated meroterpenoid antibiotics, merochlorins A–D (1–4, Figure 1), that we demonstrate through in vivo biosynthetic experiments are unique examples of VHPO-derived products.

During our screening campaign to find new anti-cancer and anti-infective agents from marine microorganisms, we isolated Streptomyces sp. strain CNH-189 from a marine sediment sample collected near Oceanside, California.11 We previously reported the discovery of the ansamycin polyketide ansalactam A from this strain,11 and more recently the preliminary characterization of the meroterpenoid antibiotic merochlorin A (1),12 which consists of a highly unusual bicyclo[2.2.1]-heptanone ring system and a propan-2-ylidenecyclopentane moiety. To unambiguously establish its absolute configuration, we solved the crystal structure of a methylated and acetylated derivative of 1 (Figure 1B).

Bioassay-guided fractionation of the crude organic extract of strain CNH-189 facilitated the isolation of two new merochlorin analogues, 2 and 3 (Figure 2). Notably, 1 and 2 are highly active against clinically relevant methicillin-resistant Staphylococcus aureus strains with MICs in the range of 2–4 μg/mL, whereas 3 showed only weak antibiotic properties (Table S4). High-resolution MS (HR-MS) and NMR spectral analysis allowed the complete structural assignment of merochlorins B (2) and C (3), which possess distinctive carbon skeletons unrelated to known natural products [Figure 1; Supporting Information (SI)]. Although 1 and 2 share the same molecular formula, C25H29ClO4, 2 has a unique 6-5-5-fused ring system, composed of dihydroxynaphthalenone and propan-2-ylidenecyclopentane moieties. We established the planar structure of 2 and the fusion of the unusually configured terpenoid residue with the naphthyl unit by extensive two-dimensional NMR spectroscopy. The relative configuration was further determined by interpretation of ROESY correlations as 8S*, 9R*, and 10S*.

The structure of 3, on the other hand, was clearly distinct from 1 and 2 based on its molecular formula of C26H32Cl2O5, containing additional carbon and chlorine atoms. HMBC correlation data not only revealed a different attachment of the terpenoid residue to the naphthyl unit at C-10, but also exposed a second attachment site through an ether linkage between C-19 and C-4 via four-bond correlation from the singlet methyl proton H-21 to C-14. The macrocyclized sesquiterpenoid residue is thus attached on both ends of the tetrahydronaphthoquinone core molecule (Figure 1). Although we established the relative configuration of C-9 and C-10 as 9R* and 10S*, we have not yet assigned the configuration of the isolated C-18 chloro group.

The unique structures of the merochlorins suggested that they are constructed via unusual biotransformations, possibly involving VHPO-dependent catalysis of a chloroetherification reaction similar to napyradiomycin formation.10 To gain access to the biosynthetic gene cluster, we subjected CNH-189 genomic DNA to short-read, paired-end Illumina sequencing. Targeted assembly of portions of the genome with homology to napyradiomycin biosynthesis (nap) genes yielded three contigs with significant sequence similarity to known meroterpenoid gene clusters (Figure S17).9,13–15 A 15.8-kb contig that contained a putative 1,3,6,8-tetrahydroxynaphthalene (THN, 5) synthase16,17 gene (mcl17) was found on fosmid 3D9 in a pCC1FOS-based genomic DNA library of strain CHN-189. We next replaced mcl17 with an apramycin resistance cassette in CNH-189 to link the isolated genes to merochlorin production.18 A comparison of culture extracts from CNH-189Δmcl17 and the wild-type strain by HPLC showed that the mutant was unable to produce merochlorins 1–3 (Figure 2). This confirmed that the THN synthase, encoded by mcl17, is essential for merochlorin production and that the genes identified on fosmid 3D9 likely represent part of the merochlorin biosynthetic gene cluster.

We obtained the complete gene cluster (57.6 kb, Figure 3) from total sequencing of 3D9, isolation of overlapping fosmids, and primer walking. Forty-one open reading frames (ORFs), mcl1–41, were assigned to the cluster and attributed to biosynthetic, resistance, transport, and regulatory functions (Table S6). Several genes have sequence homology to genes from other meroterpenoid clusters, such as mcl2–mcl9 that putatively encode the mevalonate pathway for isoprene biosynthesis;19mcl18, a putative THN monooxygenase gene;20mcl21, a putative methyltransferase gene; and mcl23, a putative aromatic prenyltransferase gene.21 In addition, the mcl cluster includes numerous structural genes that are unprecedented in meroterpenoid clusters, e.g., a putative polyprenyl synthase, mcl22, and a putative iron–sulfur cluster-containing protein, mcl30. Intriguingly, two genes, mcl24 and mcl40, were found to be highly homologous to the nap VHPO genes (Table S6).9

Based on the bioinformatic analysis of the mcl cluster, we concluded that most of the unique biosynthetic capacity for merochlorin production was encoded on fosmid 3D9, except for the putative VHPO Mcl40 (Figure 3). To investigate whether the genes found on 3D9 are sufficient for the formation of the merochlorins and to explore the role of mcl40, we expressed the fosmid heterologously in the genome minimized strain, Streptomyces coelicolor M1154.22 Therefore, 3D9 was redesigned for stable integration into Streptomyces chromosomes via attB/attP-site-specific recombination.23 Culture extracts of the generated S. coelicolor M1154/merLK01 strain were analyzed by HPLC-MS.

Compounds 1 and 2 were accumulated by the mutant, but 3 was not produced (Figures 2, S18). However, we observed a previously unrecognized metabolite, merochlorin D (4). HPLC chromatographic comparison with the CNH-189 wild-type strain also revealed the production of 4 (Figure 2). To obtain sufficient quantities of 4 for structure elucidation, we optimized the culture conditions of CNH-189 to yield approximately 5 mg/L. HR-MS and NMR spectral analysis revealed that 4 was structurally similar to 3, except for the presence of an olefinic proton at C-18 and only one chlorine atom instead of two (Figure 1A). HMBC correlation data confirmed the dimethyl terminal olefin unit, and ROESY data gave the same relative configuration as in 3. Thus, the heterologous pathway expression showed that a 36-kb fragment of the 57.6-kb gene cluster encodes all of the enzymes required for the biosynthesis of 1, 2, and 4. However, the absence of 3 in the mutant extract suggested that one or more essential genes required for its formation are missing on fosmid 3D9. We speculate that 4 is a direct precursor to 3 and that the VHPO Mcl40 may catalyze the unprecedented macromolecular chlorination–cyclization reaction to give the 15-membered ring. In the biosynthesis of the napyradiomycins, NapH1 supports a chloronium-assisted stereoselective cyclization to yield a 6-membered ring, harboring a chlorinated gem-dimethyl ether.10 Similarly, the putative VHPO Mcl40 might use 4 or a less substituted derivative as a substrate to afford the massive 15-membered cyclic ether ring in 3.

To explore whether Mcl40 can indeed support the biosynthesis of 3, we heterologously expressed fosmid clone 6B10, which contains a larger portion of the mcl locus and includes mcl40 (Figure 3). HPLC-MS analysis of the resulting S. coelicolor M1152/merLK30 strain revealed the production of all natural merochlorins, including 3 (Figure 4), suggesting that Mcl40 is involved in the chloronium-assisted macrocyclization of 4 to 3 (Figure 1A). However, the production yields of 3 and 4 were significantly lower compared with the original fosmid clone 3D9, which produced 4 but not 3. We speculate that the loss of the mcl12/13 genes of unknown function in 6B10 may lead to the observed lower merochlorin production levels. With respect to the second homologous VHPO in the mcl cluster, Mcl24, we hypothesize that it may catalyze a chlorination step of an early pathway intermediate to install the polyketide chlorine atom that can be found on all characterized merochlorin molecules.

Although 1–4 have different molecular architectures, they share common structural features, suggesting that they may also share early biosynthetic intermediates (Figure 1A). For example, the aromatic portion of 1–4 is likely derived from THN, similar to other hybrid polyketide–terpenoid metabolites.16 Thus, we propose that THN is the general precursor for two distinct metabolic pathways. The first pathway may proceed through prenylation, chlorination, and two divergent cyclization reactions to produce 1 and 2. The second pathway would generate 3 and 4 and may involve oxidation, methylation, prenylation, and two chlorination reactions. The order of the proposed biotransformations as outlined in Figure 1 is speculative and serves as a model for interrogating the function of merochlorin biosynthetic enzymes that may catalyze new interesting biochemical reactions. This divergent pathway that we propose represents a rare example where a single gene cluster encodes the formation of several architecturally unique metabolites.24

The merochlorins appear to be constructed with the same, rearranged C15-isoprene unit. To the best of our knowledge, the sesquilavandulyl carbon skeleton is unprecedented in bacteria. However, this type of skeleton has been infrequently encountered in plant natural products such as the xanthane roeperanone from Hypericum roeperanu.25 The prenylation substrate may be a preformed sesquilavandulyl diphosphate generated by Mcl22, that shows sequence similarity to undecaprenyl diphosphate synthase. Alternatively, the isoprenoid moiety may simply be formed by the sequential addition of dimethylallyl and geranyl units to a THN-based intermediate.

Only one putative prenyltransferase, Mcl23, is encoded in the mcl cluster. Merochlorins A/B and C/D are likely prenylated at two different positions, suggesting that Mcl23 catalyzes the prenylation at two adjacent carbon atoms at C-8 to give 1 and 2 and at C-10 to furnish 3 and 4 (the carbon atom numbering scheme adopted for the final natural product, Figure 1A). The oxidation state of THN (Figure 1A, 5) supports prenylation at C-4 to give an intermediate that can lead to 1 and 2. However, the same oxidation state does not allow C-3 alkylation to produce 3 and 4. We therefore propose that 5 is first partially oxidized by Mcl18 to the flaviolin hydroquinone, or directly to flaviolin followed by reduction, to produce an intermediate that is activated for alkylation at the C-3 position, which ultimately provides 3.

The genetic basis for the terpene cyclizations involved in the biosynthesis of 1 and 2 remains highly speculative. Notably, homologues to known terpene cyclases are not encoded in the cluster. We hypothesize that the internal olefin on the sesquiterpene attached to 5 undergoes epoxidation or halogenation, activating the molecule for an intramolecular cyclization. Nucleophilic attack by a carbon to form a C–C bond would lead to 1, whereas nucleophilic attack by oxygen to form a C–O bond would lead to 2 (Figure 1A, Paths a and b). In both scenarios, a second cyclization event would follow with concomitant elimination of water or HCl to yield 1 and 2. Because both VHPOs seem to be involved in chlorination reactions, we suspect that an oxidative transformation is more likely to occur in the final steps of 1 and 2 biosynthesis.

In conclusion, we discovered the merochlorins as new streptomycete antibiotics with diverse molecular architectures that derive from a novel pathway involving polyketide and terpenoid biochemistry. Our in vivo biosynthetic results established the genetic basis for merochlorin construction and support the involvement of just the second example of VHPOs in bacterial natural product assembly.

Answer: Meroterpenoids are mixed polyketide-terpenoid natural products with a broad range of biological activities. Herein, we present the structures of four new meroterpenoid antibiotics, merochlorins A\xe2\x80\x93D, produced by the marine bacterium Streptomyces sp. strain CNH-189, which possess novel chemical skeletons unrelated to known bacterial agents. Draft genome sequencing, mutagenesis and heterologous biosynthesis in the genome-minimized model actinomycete Streptomyces coelicolor provided a 57.6 kb gene cluster that contains two genes encoding rare bacterial vanadium-dependent haloperoxidase (VHPO) genes. Pathway expression of two different fosmid clones that differ largely by the presence or absence of the VHPO gene mcl40, resulted in the differential biosynthesis of merochlorin C, suggesting that Mcl40 catalyzes an unprecedented 15-membered chloronium-induced macrocyclization reaction converting merochlorin D to merochlorin C.


Question:
You will be presented with the full text of a biomedical research paper. Please write an abstract for this paper. Your response should include the abstract and no additional text.

Paper text:
however , the iron overload in various organs leads to serious problems such as metabolic , endocrine , and growth abnormalities in such patients despite the expanded use of iron - chelator drugs ( 3 - 5 ) . patients with thalassemia intermedia ( ti )
although the rate of iron loading is slower in ti than in tm , patients with ti can eventually develop complications similar to those of the patients with tm , including hepatic , endocrine and cardiac dysfunction ( 6 ) .
moreover , in patients with transfusion independent thalassemia , serum ferritin was a poor predictor of liver iron concentration ; therefore , chelation therapy may be postponed in patients with ti ( 7 ) .
hepcidin is a small peptid hormone secreted by hepatocytes to regulate plasma iron concentration and distribution in different tissues ( 8 , 9 ) .
chronic excess of hepcidin causes iron restricted anemia ( 9 ) , while the hepcidin deficiency leads to iron overload with iron deposition in the liver and parenchyma ( 10 ) .
increased plasma and stored iron stimulate hepcidin production , which in turn blocks dietary iron absorption and consequently iron loading .conversely , hepcidin is suppressed in iron deficiency ( 11 ) .
hepcidin concentration is significantly higher in chronically transfused patients than in non - transfused ones , presumably due to iron overload ( 12 - 16 ) . despite using iron chelatorin patients with thalassemia ,
iron overload is one of the main mortality factors in such patients and hepcidin targeted therapeutics can help with better management of iron overload in patients with thalassemia ( 17 ) .
the current study aimed to determine the correlation between serum ferritin and hepcidin levels in patients with tm and ti , also compare serum hepcidin and ferritin levels between the two groups of patients .
the current cross - sectional study was conducted in hematology research center of shiraz university of medical sciences , shiraz , iran , in 2013 .
the study subjects included 90 patients , 50 tm and 40 ti , selected by systematic random sampling from the 500 tm and 280 ti patients registered at the thalassemia clinic of tertiary state hospital affiliated to shiraz university of medical sciences .
this is a referral center with 45 beds for patients with thalassemia in southern iran .
this study was approved by medical ethics committee of shiraz university of medical sciences ( grant number : 3652 , approval date : 21.03.2011 ) .
the diagnosis of thalassemia was based on complete blood count ( cbc ) , hb electrophoresis and clinical history . in the tm group ,
blood transfusion had been started before two years old and all of them were on regular blood transfusion every - two to four weeks . in the tm group ,
inclusion criteria were age above 10 years old , under regular follow up and regular blood transfusion , and iron chelation therapy . in the ti group ,
inclusion criteria were transfusion independence and taking hydroxyurea ( hu ) 10 - 15 mg / kg / day for a duration of at least ten years .
patients with the history of any recent infection or surgery , congestive heart and liver failures as well as positive viral hepatitis were excluded from the study .
a 2.5 ml sample of venous blood withdrawn from each participant was added to the tubes containing clot activator .
plasma centrifuge was done immediately and 2 ml serum was separated and preserved at -20c , then carried by cold box to the laboratory to check serum hepcidin and ferritin levels .
also , 2 ml sample of venous blood was withdrawn from each patient and added to the tubes of cbc containing ethylenediamine tetraacetic acid edta anti - coagulant .
complete blood count test was performed immediately with peripheral blood smears and then stained with wright stain and the rate of nucleated red blood cells ( nrbc ) per 100 white blood cells ( wbc ) was counted .
fasting serum ferritin was checked by enzyme linked fluorescent assay elfa method , using mini vidas ( biomerievx s.a , france ) machine , and hepcidin was measured by enzyme linked immunosorbent assay elisa method ( competitive assay ) , using elisa reader dynex ( usa ) machine with drg hepcidin kit ( eia 4 705 ) . according to the direction of hepcidin kit manufacturer , the normal range of hepcidin in 5% - 95% of people with the age range of 23 to 67 years
is from 13.3 to 54.4 ng / ml . the normal range of ferritin was considered as 20 - 300 g / lin males 10 - 100
g / l in females before menopause , 20 - 200 g / l in females after menopause and 150 - 500
test of normality was done by shapiro - wilk test . among all the evaluated variables , only age had normal distribution .
descriptive data were summarized as mean and standard deviation , as well as median and interquartile range ( iqr ) , where appropriate .
correlation between serum hepcidin and quantitative variables in each of the two groups of patients with tm and ti was evaluated by spearman correlation test .
quantitative data between the two groups of patients were compared by student t - test and mann - whitney test .
considering the correlation coefficient of 0.68 for urinary hepcidin and serum ferritin levels reported by origa et al .
( 14 ) in 44 patients with thalassemia including 22 tm and 22 ti ,  = 0.05 and  = 0.01 , the sample size was estimated as 29 patients in each group . for higher accuracy , sample size
test of normality was done by shapiro - wilk test . among all the evaluated variables , only age had normal distribution .
descriptive data were summarized as mean and standard deviation , as well as median and interquartile range ( iqr ) , where appropriate .
correlation between serum hepcidin and quantitative variables in each of the two groups of patients with tm and ti was evaluated by spearman correlation test .
quantitative data between the two groups of patients were compared by student t - test and mann - whitney test .
considering the correlation coefficient of 0.68 for urinary hepcidin and serum ferritin levels reported by origa et al .
( 14 ) in 44 patients with thalassemia including 22 tm and 22 ti ,  = 0.05 and  = 0.01 , the sample size was estimated as 29 patients in each group . for higher accuracy ,
the mean age of the patients with tm and ti were 21.4  6.1(from 11 to 33 years ) and 23.7 6.1 years ( from 8 to 38 years old ) respectively , and there was no statistically significant difference between the two groups ( p = 0.076 ) .
considering gender distributions , 21 ( 43.8% ) and 22 ( 55% ) of the subjects in the tm and ti groups were female , respectively ; there was no statistically significant difference ( p = 0.392 ) .
the median iqr for serum hepcidin levels were significantly higher in the tm compared to ti group ( 87.6 , 43.9 vs. 51.8 , 23.4 , p < 0.001 ) .
in addition , the median iqr for serum ferritin levels were 2208 ( 3761 ) , and 465 ( 632 ) in the tm and ti groups respectively ; the difference was statistically significant ( p < 0.001 ) ( table 1 ) .
table 2 indicates the results of correlation between serum hepcidin levels and the evaluated parameters for the subjects with tm and ti .
no statistically significant correlations were found between serum hepcidin with any of the evaluated variables in the two groups . also there were no statistically significant differences in serum hepcidin levels between males and females in patients with tm and ti ( p = 0.107 and p = 0.861 respectively ) .
considering the cut - off point of 54.4 ng / ml for serum hepcidin levels , 44 ( 91.7% ) , and 18 ( 45% ) subjects had hepcidin levels higher than normal range in the tm and ti groups , respectively ( p < 0.001 ) .
abbreviations : iqr , interquartile range ; sd , standard deviation ; nrbc , nucleated red blood cells ; wbc , white blood cell .
data are presented as mean  sd , median ( iqr ) or male / female .
data are presented for n = 40 . statistically significant .   in thalassemia major , it was pre - transfusion hemoglobin   abbreviations : nrbc , nucleated red blood cells ; rs , spearman s rho correlation coefficient ; ti , thalassemia intermedia ; tm , thalassemia major ; wbc , white blood cell .   in thalassemia major , it was pre - transfusion hemoglobin .
determining hepcidin concentrations in subjects with iron - loading anemias may be useful to identify the patients at higher risk of iron toxicity due to severely decreased hepcidin levels ( 17 ) .
based on the current study results , 91.7% of the subjects with tm had serum hepcidin levels above normal compared to the patients with ti , 45% .
also , the median of serum hepcidin levels were significantly higher in the tm compared to ti group that was similar to those of the previous studies ( 14 ) . in iron loading anemias not treated by frequent transfusions , such as beta thalassemia intermedia and congenital dyserythropoietic anemias , urinary and serum hepcidin decrease due to high erythroid signals .
hepcidin deficiency in turn allows excessive iron absorption and development of systemic iron overload ( 12 - 14 , 18 ) .
also , it could be due to more iron overload resulted from regular blood transfusion in the patients with tm compared to ti .
as observed in the current study , ferritin levels were significantly higher in the subjects with tm .
hemoglobin levels were significantly lower in the subjects with tm than in ti , which may be due to the time of blood sampling in the subjects with tm , immediately before transfusion . during transfusion intervals ,
it is known that in patients with ti , there is also increased risk of iron over load due to increased intestinal iron absorption triggered by chronic anemia , ineffective erythropoiesis and decreased serum hepcidin ( 19 , 20 ) .
the current study showed higher erythropoietic activity in the subjects with ti than tm , since the median value for nrbc was significantly higher in ti compared to tm group . in ti group , since all subjects were on hu therapy for a long time , erythropoietic activity was expected to be suppressed and consequently hepcidin level was expected to be higher .
but it did not occur and it seems that hu at a dose of 10 - 15 mg / kg / day was not enough to suppress bone marrow activity and make erythropoiesis ineffective . however , previous reports documented that hu with the same dose was effective in decrease or cessation of the need for regular blood transfusion , as well as increasing hb levels in the patients with thalassemia ( 21 - 24 ) .
the current study showed no significant correlation between serum hepcidin and ferritin levels as a marker of iron overload in any of the tm or ti groups .
this result was in accordance with the previous reports that demonstrated the dominant role of erythropoiesis compared to iron overload in regulation of hepcidin in patients with thalassemia ( 25 - 27 ) .
( 15 ) , the current study found no statistically significant correlation between hepcidin and pre - transfusion hemoglobin levels in tm patients . in a longitudinal study on 31 patients with tm
. the strong point of the current study was large sample size compared to those of the previous reports ; however , there were some limitations in the study , since molecular erythropoietic activity was nit evaluated .   in conclusion , based on the current study results
, there was insignificant correlation between serum hepcidin and ferritin levels as a marker of iron overload in any of the two groups of patients with tm and ti , which supported the results of previous studies that regulation of hepcidin in patients with thalassemia is more affected by erythropoeitic activity than by iron overload .
also serum hepcidin levels were significantly higher in the tm than in ti group , which could mainly result from higher erythropoeitic activity in ti . in the subjects with ti
, it is believed that low dose hu ( 10 - 15 mg / kg / day ) therapy for a long time could increase hb levels and lead to transfusion - independence , but probably not high enough to suppress bone marrow activity and make erythropoiesisin effective .
increased awareness of hepcidin levels in the patients with thalassemia could be helpful to diagnose and manage iron burden in such patients .

Answer:
background : hepcidin is a key regulator of iron absorption in humans
 . it is mainly affected by hypoxia and iron stores.objectives:the current study aimed to determine the correlation between serum hepcidin and ferritin levels in patients with thalassemia major ( tm ) and thalassemia intermedia ( ti).patients and methods : the current cross - sectional study investigated 88 randomly selected patients with thalassemia , 48 tm and 40 ti , registered at the thalassemia clinic of shiraz university of medical sciences , a referral center for thalassemia in southern iran in 2013 .
 all patients with ti were receiving hydroxyurea ( hu ) 10 - 15 mg / kg / day for at least 10 years .
 the serum hepcidin , ferritin levels , hemoglobin ( hb ) and nucleated red blood cell ( rbc ) of the two groups were measured.results:no statistically significant correlation was observed between serum hepcidin and ferritin levels in any of the two groups of patients with tm ( rs = 0.02 , p = 0.892 ) or ti ( rs = 0.055 , p = 0.734 ) .
 the median interquartile range ( iqr ) for serum hepcidin and ferritin levels were significantly higher in tm compared to ti group , ( hepcidin : 87.6 ( 43.9 ) vs. 51.8 ( 23.4 ) , p < 0.001 ; ferritin : 2208 ( 3761 ) vs. 465 ( 632 ) , p
 < 0.001).conclusions : there was insignificant correlation between serum hepcidin and ferritin levels in the two groups of patients with tm and ti .
 it seems that regulation of hepcidin in patients with thalassemia is more affected by erythropoeitic activity than iron stores . also , hepcidin levels were significantly higher in patients with tm than ti , possibly due to higher erythropoeitic activity in ti .
 in ti , it seems that low dose hu increases hb levels and leads to transfusion - independence , but it is not high enough to suppress bone marrow activity and ineffective erythropoiesis .
 consequently , serum hepcidin level decreases .


Question:
You will be shown the title of a chemistry paper, together with sections excerpted from the body of the paper. The paper sections may include HTML tags like `<p>` and `</p>`; please ignore these. Your task is to write an abstract for the paper. Your response should include the abstract and no other text.

Title:
Dynamic Presentation of Immobilized Ligands Regulated through Biomolecular Recognition

Paper sections:

Using engineered materials to recapitulate the essential spatial and temporal characteristics of natural extracellular microenvironments during animal development is the key to successfully guiding cell behavior and fate selection in tissue engineering.1–6 However, it has remained a challenge to mimic the dynamic regulation of signaling ligands immobilized on extracellular matrices or on the surfaces of neighboring cells. Although soluble ligands can be added or removed readily during in vitro studies, the soluble form of a ligand that performs its function in an immobilized state in vivo potentially has opposite and detrimental effects because of competitive binding for cell surface receptors. This has been demonstrated by inhibition of Notch signaling in the presence of non-immobilized Notch ligands and death of anchorage-dependent cells in the presence of soluble RGD peptide.7–9 In recent years, materials capable of dynamically presenting immobilized bioactive ligands to cell surface receptors under physiological conditions have attracted increasing research interest.10–15 However, the methods developed to date have drawbacks including irreversible or imprecise transition between the on/off states and exposure of cells to the soluble counterparts of the ligands during in situ immobilization or cleavage. The limited ability to dynamically regulate immobilized bioactive ligands in engineered systems has hindered the progress of both technological development and fundamental understanding in tissue engineering.

Here we report a novel method of harnessing the molecular recognition of intelligent biomolecules, in combination with polymer engineering, to create dynamic bioactive surfaces on which the accessibility of immobilized ligands to cell surface receptors is reversibly interconverted with high precision under physiological conditions (Figure 1a). We hypothesized that the accessibility of an immobilized bioactive ligand to cells could be dynamically regulated through reversible co-immobilization and removal of poly(ethylene) glycol (PEG) that, when coimmobilized, shields the surface-bound ligand from access by cells.16 We expected that reversible co-immobilization and removal of PEG could be achieved by exploiting the molecular recognition between a pair of complementary leucine zipper domains A and B, which heterodimerize through non-covalent, reversible interactions.17, 18 In the molecular design illustrated in Figure 1a, a bioactive ligand of interest is fused to one terminus of the leucine zipper A and immobilized on a surface through a residue at the other terminus. The modified surface allows co-immobilization of a B-PEG conjugate, which shields the surface-bound bioactive ligand and converts it to a cell-inaccessible state. To convert the ligand back to a cell-accessible state, non-immobilized polypeptide A is added in excess to compete with the immobilized A for binding to B-PEG so that B-PEG can be removed from the surface. This molecular design allows the immobilized ligand to be reversibly interconverted between cell-accessible and cell-inaccessible states under physiological conditions as many times as needed. The bioactive ligand remains immobilized during the dynamic regulation, so cells will not be exposed to the soluble counterpart of the ligand. An additional advantage of this design is that heterodimerization between A and B allows the bioactive ligand and PEG to be co-immobilized uniformly on the molecular level, preventing the formation of ligand islands free of PEG chains. Such islands would likely form when a conventional co-immobilization method is used, and they would compromise the precise switch of the ligand between cell-accessible and cell-inaccessible states.

The polypeptides and their sequences used in this study are shown in Figure 1b. The complementary leucine zipper domains A and B were chosen because they could heterodimerize with an affinity (in the range between 10−8 M and 10−10 M) higher than that of homo-oligomerization (self-aggregation) of A or B.17, 18 The cell-adhesive RGD peptide was chosen as a model bioactive ligand. A cysteine residue was engineered at the N-terminus of A for surface immobilization. All the polypeptides were genetically engineered and biosynthesized. B-PEG conjugates were prepared by allowing Bcys to react with a large excess of PEG-diacrylate through a Michael-type addition reaction or with a large excess of PEG-maleimide through the thiol-maleimide reaction. After conjugation with PEG, B retained its ability to heterodimerize with A, as revealed from the mobility shift of cysARGD in native gel electrophoresis after cysARGD was incubated with B-PEG (SI, Figure S1).

The ability of the surface-immobilized cysARGD to co-immobilize B-PEG through heterodimerization between A and B and the ability of the co-immobilized PEG to shield the surface-bound RGD from access by cells were examined. First, cysARGD and a control polypeptide cysA were each immobilized on piranha-solution-cleaned gold surfaces through the cysteine residue in the presence of 5 mM tris(2-carboxyethyl)phosphine hydrochloride (TCEP). The surfaces modified with cysARGD supported the adhesion of fibroblasts (NIH 3T3) while those modified with cysA did not (Figure 2a and 2b), suggesting that cell adhesion on cysARGD-functionalized surfaces was regulated through the specific interaction between the RGD peptide and cell surface receptors. Then the cysARGD-functionalized surfaces were incubated with B-PEG conjugates of various PEG lengths (10 kDa, 3.4 kDa, 700 Da, and 258 Da), resulting in further modified surfaces exhibiting different cell adhesion properties depending on the PEG size. When the PEG was 10 kDa, the surfaces did not support cell adhesion (Figure 2c); when the PEG was 3.4 kDa, the surfaces partially supported cell adhesion (Figure 2d); and when the PEG was 700 Da or smaller, the surfaces were as adhesive as the cysARGD-functionalized surfaces without additional modification (Figure 2e, 2f). These results suggested that the immobilized cysARGD allowed co-immobilization of B-PEG through heterodimerization between A and B and the shielding effect provided by the co-immobilized PEG increased with its size.

The reversible switch of the surface-bound RGD between cell-accessible and cell-inaccessible states was performed in the presence of cells under physiological conditions. To demonstrate the accessible-to-inaccessible conversion of the immobilized RGD peptide, fibroblasts were allowed to adhere on a surface as shown in Figure 2a for 3 h. Then B-PEG (PEG: 10 kDa, 300 μM) was added into the culture medium, followed by incubation under shaking (at a speed at which the liquid just started to move to enhance mass transfer) for 2 h. Cell detachment was observed (Figure 3a). A control performed on a cysC10RGD-functionalized surface (C10 is a hydrophilic random coil17) under the same condition did not result in cell detachment (Figure 3b), suggesting that the cell detachment from the cysARGD-functionalized surface was caused by co-immobilization of B-PEG through heterodimerization between A and B. These results not only suggested that the surface-bound cysARGD allowed co-immobilization of B-PEG in the presence of cells under physiological conditions but also showed that even the ligands that had already been engaged in the interactions with cell surface receptors could be converted to the cell-inaccessible state due to the physical, reversible, and dynamic nature of the interactions between ligands and cell surface receptors.

To demonstrate that the cell-inaccessible RGD shielded by PEG could be converted back to the cell-accessible state in the presence of cells, a cysARGD-functionalized surface was further modified with B-PEG (PEG: 10 kDa); cells were seeded on the resulting non-adhesive surface. Non-immobilized polypeptide A (300 μM) was added in the cell culture medium, followed by shaking incubation (to enhance mass transfer) for 2 h and static incubation (to allow cell adhesion) for 3 h sequentially. The surface was converted from non-adhesive (Figure 2c) to cell-adhesive (Figure 3c), suggesting that the non-immobilized A competed with the immobilized cysARGD for binding with B-PEG and most B-PEG molecules could be removed from the surface when the amount of non-immobilized A was sufficiently greater than that of immobilized cysARGD. The RGD peptide in immobilized cysARGD was consequently converted from the cell-inaccessible to cell-accessible state. After the medium was changed, the cell-accessible RGD could be reconverted to be cell-inaccessible by addition of B-PEG.

Because surface immobilization of an A-ligand can be achieved through various chemical approaches, such as those enabled by the unique functional groups introduced through non-natural amino acid analogs,19 the ligands are not limited to cysteine-free peptides and the substrates are not limited to gold surfaces. For example, a thiol-containing A-ligand can be immobilized to the surfaces of hydrogels functionalized with maleimide or ene,20, 21 so that temporal control of immobilized ligands can be coupled with regulation of substrate stiffness to further optimize cell microenvironments for desired outcomes. In addition, this method potentially allows both temporal and spatial control of ligands. For example, a step gradient of a ligand can be created via micro/nano-printing, even though creation of a continuous gradient might be difficult. One limitation of the method is that the interconversion is not instant, so it cannot be used for applications such as guidance of rapid cell migration. However, this method will find use in many other applications such as regulation of stem cell differentiation, which is stepwise and often involved with changes in microenvironmental signals on the order of hours or days. Even though shaking incubation is necessary to overcome the mass transfer limitation and allow the interconversion to occur at 1 or 2 h (the experiment described in Figure 3a was also tested at 1 h and the same result was obtained) and exposure of cells to the shear stress associated with the convective flow may introduce some complexity, it is expected that the fluid velocity required for convective mass transfer to dominate over diffusive mass transfer is small. The scaling analysis based on the length scale of cells and the time scale required for the interconversion to occur under static conditions (ca. 10 h) suggests that a velocity on the order of 10−6 cm/s is enough to result in a Peclet number (the ratio of convective mass transfer to diffusive mass transfer) of 100.22 The shear stress associated with such small velocity is low.

In summary, the molecular engineering approach reported here represents a platform that can be readily adapted to dynamically and reversibly regulate the accessibility of a variety of immobilized bioactive ligands to cell surface receptors under physiological conditions. The materials having such dynamic bioactive surfaces can be used to temporally control the properties of engineered extracellular microenvironments.

Answer: To mimic the dynamic regulation of signaling ligands immobilized on extracellular matrices or on the surfaces of neighboring cells for guidance of cell behavior and fate selection, we have harnessed biomolecular recognition in combination with polymer engineering to create dynamic surfaces on which the accessibility of immobilized ligands to cell surface receptors can be reversibly interconverted under physiological conditions. The cell-adhesive RGD peptide is chosen as a model ligand. RGD is fused to the C-terminus of a leucine zipper domain A and this fusion polypeptide is immobilized on surfaces through a residue at the N-terminus. The immobilized RGD can be converted from a cell-accessible to a cell-inaccessible state by addition of a conjugate of poly(ethylene) glycol (PEG) and another leucine zipper domain B (B-PEG). Heterodimerization between A and B allows co-immobilization of the PEG, which shields RGD from access by cells. The shielded RGD can be converted back to a cell-accessible state by addition of non-immobilized polypeptide A, which competes with the immobilized A for binding to B-PEG and removes B-PEG from the surface. This molecular design offers several advantages: the interconversion is reversible; the ligand remains immobilized during dynamic regulation so that cells are not exposed to the soluble form of the ligand that potentially has detrimental effects; the precision of the on/off states is assured by the molecular-level uniformity of the ligand and PEG co-immobilized through leucine zipper heterodimerization. The method can be readily adapted for dynamic regulation of other immobilized bioactive ligands of interest.