Publications

use of biomarkers in irritable bowel syndrome: to predict the future, look at the past.		2015	26448457
nonmedical uses of antibiotics: time to restrict their use?	the global crisis of antibiotic resistance has reached a point where, if action is not taken, human medicine will enter a postantibiotic world and simple injuries could once again be life threatening. new antibiotics are needed urgently, but better use of existing agents is just as important. more appropriate use of antibiotics in medicine is vital, but the extensive use of antibiotics outside medical settings is often overlooked. antibiotics are commonly used in animal husbandry, bee-keeping, f ...	2015	26444324
a rare case of guillain-barré syndrome presenting with abdominal pain.	guillain-barré syndrome (gbs) is a heterogeneous condition that encompasses acute immune-mediated polyneuropathies. gbs is the most frequent cause of acute neuromuscular paralysis worldwide and constitutes one of the most serious emergencies in neurology. description of case: as it presents extremely rarely with the first symptom being abdominal pain, herein we report the case of a 48-year-old man who presented with acute abdominal pain and diagnosed with gbs. the patient required mechanical ven ...	2015	27703314
the intestinal microbiome in bariatric surgery patients.	with nearly 39% of the worldwide adult population classified as obese, much of the globe is facing a serious public health challenge. increasing rates of obesity, coupled with the failure of many behavioural and pharmacological interventions, have contributed to a rise in popularity of bariatric surgery as a treatment for obesity. surgery-mediated weight loss was initially thought to be a direct result of mechanical alterations causing restriction and calorie malabsorption. however, the mounting ...	2015	26426680
irritable bowel syndrome: is it "irritable brain" or "irritable bowel"?	irritable bowel syndrome (ibs) has been recognized as one of the most common and best studied disorders among the group of functional gastrointestinal disorders. it is a functional bowel disorder in which abdominal pain or discomfort is associated with defecation or a change in bowel habit. in the western world, ibs appears to affect up to 20% of the population at any given time but in asian countries, the median value of ibs prevalence defined by various criteria ranges between 6.5% and 10.1%, ...	2015	26752904
blurred lines: pathogens, commensals, and the healthy gut.		2015	26664968
from laboratory research to a clinical trial: copper alloy surfaces kill bacteria and reduce hospital-acquired infections.	this is a translational science article that discusses copper alloys as antimicrobial environmental surfaces. bacteria die when they come in contact with copper alloys in laboratory tests. components made of copper alloys were also found to be efficacious in a clinical trial.	2015	26163568
the zinc transport systems and their regulation in pathogenic fungi.	zinc is an essential micronutrient required for many enzymes that play essential roles in a cell. it was estimated that approximately 3% of the total cellular proteins are required for zinc for their functions. zinc has long been considered as one of the key players in host-pathogen interactions. the host sequesters intracellular zinc by utilizing multiple cellular zinc importers and exporters as a means of nutritional immunity. to overcome extreme zinc limitation within the host environment, pa ...	2015	26539032
neuroimmune pharmacological approaches.	intestinal inflammation is a major health problem which impairs the quality of life, impacts mental health and is exacerbated by stress and psychiatric disturbances which, in turn, can affect disease prognosis and response to treatment. accumulating evidence indicates that the immune system is an important interface between intestinal inflammation and the enteric, sensory, central and autonomic nervous systems. in addition, the neuroimmune interactions originating from the gastrointestinal tract ...	2015	26426677
high-frequency variation of purine biosynthesis genes is a mechanism of success in campylobacter jejuni.	phenotypic variation is prevalent in the zoonotic pathogen campylobacter jejuni, the leading agent of enterocolitis in the developed world. heterogeneity enhances the survival and adaptive malleability of bacterial populations because variable phenotypes may allow some cells to be protected against future stress. exposure to hyperosmotic stress previously revealed prevalent differences in growth between c. jejuni strain 81-176 colonies due to resistant or sensitive phenotypes, and these isolated ...	2015	26419875
postharvest intervention technologies for safety enhancement of meat and meat based products; a critical review.	globally, the demand for safe, healthy and nutritious meat and allied products possesses improved taste with extended shelf life is mounting. microbial safety is among the imperative challenges that prevails in meat products because they provide an ideal medium for the growth of microorganisms particularly pathogenic bacteria. the incidence of these microbes can result quality deterioration of products leading towards food borne diseases when consumed by peoples. several preservation technologie ...	2015	26787929
postharvest intervention technologies for safety enhancement of meat and meat based products; a critical review.	globally, the demand for safe, healthy and nutritious meat and allied products possesses improved taste with extended shelf life is mounting. microbial safety is among the imperative challenges that prevails in meat products because they provide an ideal medium for the growth of microorganisms particularly pathogenic bacteria. the incidence of these microbes can result quality deterioration of products leading towards food borne diseases when consumed by peoples. several preservation technologie ...	2015	26787929
thermodynamics of abc transporters.	abc transporters form the largest of all transporter families, and their structural study has made tremendous progress over recent years. however, despite such advances, the precise mechanisms that determine the energy-coupling between atp hydrolysis and the conformational changes following substrate binding remain to be elucidated. here, we present our thermodynamic analysis for both abc importers and exporters, and introduce the two new concepts of differential-binding energy and elastic confo ...	2015	26408021
thermodynamics of abc transporters.	abc transporters form the largest of all transporter families, and their structural study has made tremendous progress over recent years. however, despite such advances, the precise mechanisms that determine the energy-coupling between atp hydrolysis and the conformational changes following substrate binding remain to be elucidated. here, we present our thermodynamic analysis for both abc importers and exporters, and introduce the two new concepts of differential-binding energy and elastic confo ...	2015	26408021
the increased severity in patients presenting to hospital with diarrhea in dhaka, bangladesh since the emergence of the hybrid strain of vibrio cholerae o1 is not unique to cholera patients.	a hybrid strain of vibrio cholerae o1 el tor that expresses a classical cholera toxin (ct) emerged in 2001. this hybrid variant rapidly replaced the previous el tor strain around the world. the global emergence of this variant coincided with anecdotal reports that cholera patients were presenting with more severe dehydration and disease in many locations.	2015	26409202
evidence for the sialylation of pila, the pi-2a pilus-associated adhesin of streptococcus agalactiae strain nem316.	streptococcus agalactiae (or group b streptococcus, gbs) is a commensal bacterium present in the intestinal and urinary tracts of approximately 30% of humans. we and others previously showed that the pi-2a pilus polymers, made of the backbone pilin pilb, the tip adhesin pila and the cell wall anchor protein pilc, promote adhesion to host epithelia and biofilm formation. affinity-purified pi-2a pili from gbs strain nem316 were recognized by n-acetylneuraminic acid (neunac, also known as sialic ac ...	2015	26407005
novel gm1 ganglioside-like peptide mimics prevent the association of cholera toxin to human intestinal epithelial cells in vitro.	cholera is an acute diarrheal disease caused by infection in the gastrointestinal tract by the gram-negative bacterium, vibrio cholerae, and is a serious public health threat worldwide. there has not been any effective treatment for this infectious disease. cholera toxin (ct), which is secreted by v. cholerae, can enter host cells by binding to gm1, a monosialoganglioside widely distributed on the plasma membrane surface of various animal epithelial cells. the present study was undertaken to gen ...	2015	26405107
novel gm1 ganglioside-like peptide mimics prevent the association of cholera toxin to human intestinal epithelial cells in vitro.	cholera is an acute diarrheal disease caused by infection in the gastrointestinal tract by the gram-negative bacterium, vibrio cholerae, and is a serious public health threat worldwide. there has not been any effective treatment for this infectious disease. cholera toxin (ct), which is secreted by v. cholerae, can enter host cells by binding to gm1, a monosialoganglioside widely distributed on the plasma membrane surface of various animal epithelial cells. the present study was undertaken to gen ...	2015	26405107
site-specific ser/thr/tyr phosphoproteome of sinorhizobium meliloti at stationary phase.	sinorhizobium meliloti, a facultative microsymbiont of alfalfa, should fine-tune its cellular processes to live saprophytically in soils characterized with limited nutrients and diverse stresses. in this study, tio2 enrichment and lc-ms/ms were used to uncover the site-specific ser/thr/tyr phosphoproteome of s. meliloti in minimum medium at stationary phase. there are a total of 96 unique phosphorylated sites, with a ser/thr/tyr distribution of 63:28:5, in 77 proteins. phosphoproteins identified ...	2015	26401955
mosaic composition of riba and wspb genes flanking the virb8-d4 operon in the wolbachia supergroup b-strain, wstr.	the obligate intracellular bacterium, wolbachia pipientis (rickettsiales), is a widespread, vertically transmitted endosymbiont of filarial nematodes and arthropods. in insects, wolbachia modifies reproduction, and in mosquitoes, infection interferes with replication of arboviruses, bacteria and plasmodia. development of wolbachia as a tool to control pest insects will be facilitated by an understanding of molecular events that underlie genetic exchange between wolbachia strains. here, we used n ...	2015	26400107
mosaic composition of riba and wspb genes flanking the virb8-d4 operon in the wolbachia supergroup b-strain, wstr.	the obligate intracellular bacterium, wolbachia pipientis (rickettsiales), is a widespread, vertically transmitted endosymbiont of filarial nematodes and arthropods. in insects, wolbachia modifies reproduction, and in mosquitoes, infection interferes with replication of arboviruses, bacteria and plasmodia. development of wolbachia as a tool to control pest insects will be facilitated by an understanding of molecular events that underlie genetic exchange between wolbachia strains. here, we used n ...	2015	26400107
high-resolution structures of lactobacillus salivarius transketolase in the presence and absence of thiamine pyrophosphate.	probiotic bacterial strains have been shown to enhance the health of the host through a range of mechanisms including colonization, resistance against pathogens, secretion of antimicrobial compounds and modulation of the activity of the innate immune system. lactobacillus salivarius ucc118 is a well characterized probiotic strain which survives intestinal transit and has many desirable host-interaction properties. probiotic bacteria display a wide range of catabolic activities, which determine t ...	2015	26457526
mechanisms of resistance to aminoglycoside antibiotics: overview and perspectives.	aminoglycoside (ag) antibiotics are used to treat many gram-negative and some gram-positive infections and, importantly, multidrug-resistant tuberculosis. among various bacterial species, resistance to ags arises through a variety of intrinsic and acquired mechanisms. the bacterial cell wall serves as a natural barrier for small molecules such as ags and may be further fortified via acquired mutations. efflux pumps work to expel ags from bacterial cells, and modifications here too may cause furt ...	2015	26877861
mechanisms of resistance to aminoglycoside antibiotics: overview and perspectives.	aminoglycoside (ag) antibiotics are used to treat many gram-negative and some gram-positive infections and, importantly, multidrug-resistant tuberculosis. among various bacterial species, resistance to ags arises through a variety of intrinsic and acquired mechanisms. the bacterial cell wall serves as a natural barrier for small molecules such as ags and may be further fortified via acquired mutations. efflux pumps work to expel ags from bacterial cells, and modifications here too may cause furt ...	2015	26877861
identification and biochemical characterization of the novel α2,3-sialyltransferase wbwa from pathogenic escherichia coli serotype o104.	the sialyl-t antigen sialylα2-3galβ1-3galnac is a common o-glycan structure in human glycoproteins and is synthesized by sialyltransferase st3gal1. the enterohemorrhagic escherichia coli serotype o104 has the rare ability to synthesize a sialyl-t antigen mimic. we showed here that the wbwa gene of the e. coli o104 antigen synthesis gene cluster encodes an α2,3-sialyltransferase wbwa that transfers sialic acid from cmp-sialic acid to galβ1-3galnacα-diphosphate-lipid acceptor. nuclear magnetic res ...	2015	26391208
proteomics of the organohalide-respiring epsilonproteobacterium sulfurospirillum multivorans adapted to tetrachloroethene and other energy substrates.	organohalide respiration is an environmentally important but poorly characterized type of anaerobic respiration. we compared the global proteome of the versatile organohalide-respiring epsilonproteobacterium sulfurospirillum multivorans grown with different electron acceptors (fumarate, nitrate, or tetrachloroethene [pce]). the most significant differences in protein abundance were found for gene products of the organohalide respiration region. this genomic region encodes the corrinoid and fes c ...	2015	26387727
guillain-barré syndrome: clinical profile and management.	guillain-barré syndrome (gbs) is a fulminant polyradiculoneuropathy that is acute, frequently severe and autoimmune in nature. etiology of gbs is incompletely understood, prognosis is usually good with early detection and prompt treatment. this retrospective study was done to evaluate clinical profile, epidemiological, laboratory, and electrodiagnostic features of patients with gbs and mode of management, complications and prognostic factors.	2015	26421004
matrix metalloproteinase-2 mediates intestinal immunopathogenesis in campylobacter jejuni-infected infant mice.	increased levels of the matrix metalloproteinases (mmps)-2 and -9 (also referred to gelatinase-a and -b, respectively) can be detected in the inflamed gut. we have recently shown that synthetic gelatinase blockage reduces colonic apoptosis and pro-inflammatory immune responses following murine campylobacter (c.) jejuni infection. in order to dissect whether mmp-2 and/or mmp-9 is involved in mediating c. jejuni-induced immune responses, infant mmp-2(-/-), mmp-9(-/-), and wildtype (wt) mice were p ...	2015	26495129
the abundant free-living amoeba, acanthamoeba polyphaga, increases the survival of campylobacter jejuni in milk and orange juice.	campylobacter jejuni is a common cause of human bacterial diarrhea in most parts of the world. most c. jejuni infections are acquired from contaminated poultry, milk, and water. due to health care costs and human suffering, it is important to identify all possible sources of infection. unpasteurized milk has been associated with several outbreaks of c. jejuni infection. campylobacter has been identified on fresh fruit, and other gastrointestinal pathogens such as salmonella, e. coli o157:h7 and ...	2015	26387556
first report and molecular characterization of a campylobacter jejuni isolate with extensive drug resistance from a travel-associated human case.		2015	26239988
rapid, semiquantitative assay to discriminate among compounds with activity against replicating or nonreplicating mycobacterium tuberculosis.	the search for drugs that can kill replicating and nonreplicating mycobacterium tuberculosis faces practical bottlenecks. measurement of cfu and discrimination of bacteriostatic from bactericidal activity are costly in compounds, supplies, labor, and time. testing compounds against m. tuberculosis under conditions that prevent the replication of m. tuberculosis often involves a second phase of the test in which conditions are altered to permit the replication of bacteria that survived the first ...	2015	26239979
proteomics of aggregatibacter actinomycetemcomitans outer membrane vesicles.	aggregatibacter actinomycetemcomitans is an oral and systemic pathogen associated with aggressive forms of periodontitis and with endocarditis. outer membrane vesicles (omvs) released by this species have been demonstrated to deliver effector proteins such as cytolethal distending toxin (cdt) and leukotoxin (ltxa) into human host cells and to act as triggers of innate immunity upon carriage of nod1- and nod2-active pathogen-associated molecular patterns (pamps). to improve our understanding of t ...	2015	26381655
visual detection of human antibodies using sugar chain-immobilized fluorescent nanoparticles: application as a point of care diagnostic tool for guillain-barré syndrome.	sugar chain binding antibodies have gained substantial attention as biomarkers due to their crucial roles in various disorders. in this study, we developed simple and quick detection method of anti-sugar chain antibodies in sera using our previously developed sugar chain-immobilized fluorescent nanoparticles (sfnps) for the point-of-care diagnostics. sugar chain structure on sfnps was modified with the sugar moieties of the gm1 ganglioside via our original linker molecule to detect anti-gm1 anti ...	2015	26378448
biomarkers of guillain-barré syndrome: some recent progress, more still to be explored.	guillain-barré syndrome (gbs), the axonal subtype of which is mainly triggered by c. jejuni with ganglioside-mimicking lipooligosaccharides (los), is an immune-mediated disorder in the peripheral nervous system (pns) accompanied by the disruption of the blood-nerve barrier (bnb) and the blood-cerebrospinal fluid barrier (b-csf-b). biomarkers of gbs have been extensively explored and some of them are proved to assist in the clinical diagnosis and in monitoring disease progression as well as in as ...	2015	26451079
mouse siglec-1 mediates trans-infection of surface-bound murine leukemia virus in a sialic acid n-acyl side chain-dependent manner.	siglec-1 (sialoadhesin, cd169) is a surface receptor on human cells that mediates trans-enhancement of hiv-1 infection through recognition of sialic acid moieties in virus membrane gangliosides. here, we demonstrate that mouse siglec-1, expressed on the surface of primary macrophages in an interferon-α-responsive manner, captures murine leukemia virus (mlv) particles and mediates their transfer to proliferating lymphocytes. the mlv infection of primary b-cells was markedly more efficient than th ...	2015	26370074
campylobacter jejuni increases flagellar expression and adhesion of noninvasive escherichia coli: effects on enterocytic toll-like receptor 4 and cxcl-8 expression.	campylobacter jejuni is the most common cause of bacterium-induced gastroenteritis, and while typically self-limiting, c. jejuni infections are associated with postinfectious intestinal disorders, including flares in patients with inflammatory bowel disease and postinfectious irritable bowel syndrome (pi-ibs), via mechanisms that remain obscure. based on the hypothesis that acute campylobacteriosis may cause pathogenic microbiota dysbiosis, we investigated whether c. jejuni may activate dormant ...	2015	26371123
the abcedcba-encoded abc transporter and the virb operon-encoded type iv secretion system of brucella ovis are critical for intracellular trafficking and survival in ovine monocyte-derived macrophages.	brucella ovis infection is associated with epididymitis, orchitis and infertility in rams. most of the information available on b. ovis and host cell interaction has been generated using murine macrophages or epithelial cell lines, but the interaction between b. ovis and primary ovine macrophages has not been studied. the aim of this study was to evaluate the role of the b. ovis abcedcba-encoded abc transporter and the virb operon-encoded type iv secretion system (t4ss) during intracellular surv ...	2015	26366863
correcting inconsistencies and errors in bacterial genome metadata using an automated curation tool in excel (autocure).	whole-genome data are invaluable for large-scale comparative genomic studies. current sequencing technologies have made it feasible to sequence entire bacterial genomes with relative ease and time with a substantially reduced cost per nucleotide, hence cost per genome. more than 3,000 bacterial genomes have been sequenced and are available at the finished status. publically available genomes can be readily downloaded; however, there are challenges to verify the specific supporting data contained ...	2015	26442252
proteomic contributions to our understanding of vaccine and immune responses.	vaccines are one of the greatest public health successes; yet, due to the empirical nature of vaccine design, we have an incomplete understanding of how the genes and proteins induced by vaccines contribute to the development of both protective innate and adaptive immune responses. while the advent of genomics has enabled new vaccine development and facilitated understanding of the immune response, proteomics identifies potentially new vaccine antigens with increasing speed and sensitivity. in a ...	2015	26172619
new insights into the biological role of the osmoregulated periplasmic glucans in pathogenic and symbiotic bacteria.	this review emphasizes the biological roles of the osmoregulated periplasmic glucans (opgs). osmoregulated periplasmic glucans occur in almost all α-, β- and γ-proteobacteria. this polymer of glucose is required for full virulence. the roles of the opgs are complex and vary depending on the species. here, we outline the four major roles of the opgs through four different pathogenic and one symbiotic bacterial models (dickeya dadantii, salmonella enterica, pseudomonas aeruginosa, brucella abortus ...	2015	26265506
reactive oxygen species and mitochondria: a nexus of cellular homeostasis.	reactive oxygen species (ros) are integral components of multiple cellular pathways even though excessive or inappropriately localized ros damage cells. ros function as anti-microbial effector molecules and as signaling molecules that regulate such processes as nf-kb transcriptional activity, the production of dna-based neutrophil extracellular traps (nets), and autophagy. the main sources of cellular ros are mitochondria and nadph oxidases (noxs). in contrast to nox-generated ros, ros produced ...	2015	26432659
chemoenzymatic assembly of bacterial glycoconjugates for site-specific orthogonal labeling.	the cell surfaces of bacteria are replete with diverse glycoconjugates that play pivotal roles in determining how bacteria interact with the environment and the hosts that they colonize. studies to advance our understanding of these interactions rely on the availability of chemically defined glycoconjugates that can be selectively modified under orthogonal reaction conditions to serve as discrete ligands to probe biological interactions, in displayed arrays and as imaging agents. herein, enzymes ...	2015	26352466
ecology of anti-biofilm agents ii: bacteriophage exploitation and biocontrol of biofilm bacteria.	bacteriophages are the viruses of bacteria. in the guise of phage therapy they have been used for decades to successfully treat what are probable biofilm-containing chronic bacterial infections. more recently, phage treatment or biocontrol of biofilm bacteria has been brought back to the laboratory for more rigorous assessment as well as towards the use of phages to combat environmental biofilms, ones other than those directly associated with bacterial infections. considered in a companion artic ...	2015	26371011
geranylgeranylacetone selectively binds to the hsp70 of helicobacter pylori and alters its coccoid morphology.	geranylgeranylacetone (gga) is used to treat patients suffering from peptic ulcers and gastritis. we examined the effect of gga on helicobacter pylori, which is a causative factor of gastrointestinal diseases. previously, we have reported that gga binds specifically to the molecular chaperone hsp70. in this paper, we report that gga bounds to h. pylori hsp70 (product of the dnak gene) with 26-times higher affinity than to human hsp70, and induced large conformational changes as observed from sur ...	2015	26345206
isph-rps1 and isph-ubia: "rosetta stone" proteins.	the protein isph, (e)-1-hydroxy-2-methyl-but-2-enyl 4-diphosphate (hmppp) reductase, is an essential 4fe-4s cluster-containing protein in the methylerythritol phosphate pathway for isoprenoid biosynthesis. using a sequence similarity network we found that there are >400 isph proteins that are about twice as large as most of the isphs studied to date since their isph domains are fused to either the ribosomal protein s1 (rps1), or to a ubia (4-hydroxybenzoate octaprenyltransferase)-like protein. m ...	2015	26865948
trachoma and ocular chlamydial infection in the era of genomics.	trachoma is a blinding disease usually caused by infection with chlamydia trachomatis (ct) serovars a, b, and c in the upper tarsal conjunctiva. individuals in endemic regions are repeatedly infected with ct throughout childhood. a proportion of individuals experience prolonged or severe inflammatory episodes that are known to be significant risk factors for ocular scarring in later life. continued scarring often leads to trichiasis and in-turning of the eyelashes, which causes pain and can even ...	2015	26424969
multifaceted roles of extracellular dna in bacterial physiology.	in textbooks, dna is generally defined as the universal storage material for genetic information in all branches of life. beyond this important intracellular role, dna can also be present outside of living cells and is an abundant biopolymer in aquatic and terrestrial ecosystems. the origin of extracellular dna in such ecological niches is diverse: it can be actively secreted or released by prokaryotic and eukaryotic cells by means of autolysis, apoptosis, necrosis, bacterial secretion systems o ...	2015	26328805
multifaceted roles of extracellular dna in bacterial physiology.	in textbooks, dna is generally defined as the universal storage material for genetic information in all branches of life. beyond this important intracellular role, dna can also be present outside of living cells and is an abundant biopolymer in aquatic and terrestrial ecosystems. the origin of extracellular dna in such ecological niches is diverse: it can be actively secreted or released by prokaryotic and eukaryotic cells by means of autolysis, apoptosis, necrosis, bacterial secretion systems o ...	2015	26328805
extraintestinal pathogenic escherichia coli, a common human pathogen: challenges for vaccine development and progress in the field.	extraintestinal pathogenic escherichia coli (expec) is the most common gram-negative bacterial pathogen in humans. expec causes the vast majority of urinary tract infections (utis), is a leading cause of adult bacteremia, and is the second most common cause of neonatal meningitis. increasing multidrug resistance among expec strains constitutes a major obstacle to treatment and is implicated in increasing numbers of hospitalizations and deaths and increasing healthcare costs associated with expec ...	2015	26333944
extraintestinal pathogenic escherichia coli, a common human pathogen: challenges for vaccine development and progress in the field.	extraintestinal pathogenic escherichia coli (expec) is the most common gram-negative bacterial pathogen in humans. expec causes the vast majority of urinary tract infections (utis), is a leading cause of adult bacteremia, and is the second most common cause of neonatal meningitis. increasing multidrug resistance among expec strains constitutes a major obstacle to treatment and is implicated in increasing numbers of hospitalizations and deaths and increasing healthcare costs associated with expec ...	2015	26333944
nanoparticles as potential new generation broad spectrum antimicrobial agents.	the rapid emergence of antimicrobial resistant strains to conventional antimicrobial agents has complicated and prolonged infection treatment and increased mortality risk globally. furthermore, some of the conventional antimicrobial agents are unable to cross certain cell membranes thus, restricting treatment of intracellular pathogens. therefore, the disease-causing-organisms tend to persist in these cells. however, the emergence of nanoparticle (np) technology has come with the promising broad ...	2015	26329777
recombinant antibody production evolves into multiple options aimed at yielding reagents suitable for application-specific needs.	antibodies have been a pillar of basic research, while their relevance in clinical diagnostics and therapy is constantly growing. consequently, the production of both conventional and fragment antibodies constantly faces more demanding challenges for the improvement of their quantity and quality. the answer to such an increasing need has been the development of a wide array of formats and alternative production platforms. this review offers a critical comparison and evaluation of the different o ...	2015	26330219
polymorphism of crispr shows separated natural groupings of shigella subtypes and evidence of horizontal transfer of crispr.	clustered, regularly interspaced, short palindromic repeats (crispr) act as an adaptive rna-mediated immune mechanism in bacteria. they can also be used for identification and evolutionary studies based on polymorphisms within the crispr locus. we amplified and analyzed 6 crispr loci from 237 shigella strains belonging to the 4 species groups, as well as 13 escherichia coli strains. the crispr-associated (cas) gene sequence arrays of these strains were screened and compared. the crispr sequences ...	2015	26327282
isolation and characterization of a novel helicobacter species, helicobacter jaachi sp. nov., from common marmosets (callithrix jaachus).	purpose-bred common marmosets from domestic sources housed in a us research facility, and used in multiple drug discovery programmes, were noted to have a high incidence of spontaneous inflammatory bowel disease and sporadic cholecystitis and cholangiohepatitis. inflammatory infiltrates increased in incidence and severity with age. because helicobacter spp. have been linked to gastrointestinal diseases, samples from the gastrointestinal tracts of 39 marmosets were screened for helicobacter spp. ...	2015	26297446
high-throughput bacterial functional genomics in the sequencing era.	high-throughput functional genomic technologies are accelerating progress in understanding the diversity of bacterial life and in developing a systems-level understanding of model bacterial organisms. here we highlight progress in deep-sequencing-based functional genomics, show how whole genome sequencing is enabling phenotyping in organisms recalcitrant to genetic approaches, recount the rapid proliferation of functional genomic approaches to non-growth phenotypes, and discuss how advances are ...	2015	26336012
applying complement therapeutics to rare diseases.	around 350 million people worldwide suffer from rare diseases. these may have a genetic, infectious, or autoimmune basis, and several include an inflammatory component. launching of effective treatments can be very challenging when there is a low disease prevalence and limited scientific insights into the disease mechanisms. as a key trigger of inflammatory processes, complement has been associated with a variety of diseases and has become an attractive therapeutic target for conditions involvin ...	2015	26341313
comprehensive reports on the latest advances in gastroenterology and hepatology from:: the 50th annual meeting of the european association for the study of the liverapril 22-26, 2015vienna, austriadigestive disease week 2015may 16-19, 2015washington, dc.		2015	26523126
non-coeliac gluten sensitivity and reproductive disorders.	an association between coeliac disease and fertility disorders is well recognised in the current literature, but the information related to non-coeliac gluten sensitivity (ncgs) and infertility is lacking. this case highlights a possible role of treating ncgs in the reversal of infertility.	2015	26468350
defects in nadph oxidase genes nox1 and duox2 in very early onset inflammatory bowel disease.	defects in intestinal innate defense systems predispose patients to inflammatory bowel disease (ibd). reactive oxygen species (ros) generated by nicotinamide-adenine dinucleotide phosphate (nadph) oxidases in the mucosal barrier maintain gut homeostasis and defend against pathogenic attack. we hypothesized that molecular genetic defects in intestinal nadph oxidases might be present in children with ibd.	2015	26301257
xenobiotics: interaction with the intestinal microflora.	the human body is host to 100 trillion gut microbes, approximately 10-times more than all human cells. it is estimated that the approximately 500-1000 species residing in the human gut encode 150-fold more unique genes than the human genome. the gut microbiota has important functions in metabolic processing, such as energy production, immune cell development, food digestion, and epithelial homeostasis. it has been increasingly recognized that a dysregulated gut microbiome contributes in a signif ...	2015	26323631
role of the tet38 efflux pump in staphylococcus aureus internalization and survival in epithelial cells.	we previously identified the protein tet38 as a chromosomally encoded efflux pump of staphylococcus aureus that confers resistance to tetracycline and certain unsaturated fatty acids. tet38 also contributes to mouse skin colonization. in this study, we discovered a novel regulator of tet38, named tetracycline regulator 21 (tetr21), that bound specifically to the tet38 promoter and repressed pump expression. a δtetr21 mutant showed a 5-fold increase in tet38 transcripts and an 8-fold increase in ...	2015	26324534
lectin-based analysis of fucosylated glycoproteins of human skim milk during 47 days of lactation.	glycoproteins of human milk are multifunctional molecules, and their fucosylated variants are potentially active molecules in immunological events ensuring breastfed infants optimal development and protection against infection diseases. the expression of fucosylated glycotopes may correspond to milk maturation stages. the relative amounts of fucosylated glycotopes of human skim milk glycoproteins over the course of lactation from the 2(nd) day to the 47(th) day were analyzed in colostrums, trans ...	2015	26318738
microbiological food safety surveillance in china.	microbiological food safety surveillance is a system that collects data regarding food contamination by foodborne pathogens, parasites, viruses, and other harmful microbiological factors. it helps to understand the spectrum of food safety, timely detect food safety hazards, and provide relevant data for food safety supervision, risk assessment, and standards-setting. the study discusses the microbiological surveillance of food safety in china, and introduces the policies and history of the natio ...	2015	26343705
bile salts modulate the mucin-activated type vi secretion system of pandemic vibrio cholerae.	the causative agent of cholera, vibrio cholerae, regulates its diverse virulence factors to thrive in the human small intestine and environmental reservoirs. among this pathogen's arsenal of virulence factors is the tightly regulated type vi secretion system (t6ss). this system acts as an inverted bacteriophage to inject toxins into competing bacteria and eukaryotic phagocytes. v. cholerae strains responsible for the current 7th pandemic activate their t6ss within the host. we established that t ...	2015	26317760
haemophilus influenzae: using comparative genomics to accurately identify a highly recombinogenic human pathogen.	haemophilus influenzae is an opportunistic bacterial pathogen that exclusively colonises humans and is associated with both acute and chronic disease. despite its clinical significance, accurate identification of h. influenzae is a non-trivial endeavour. h. haemolyticus can be misidentified as h. influenzae from clinical specimens using selective culturing methods, reflecting both the shared environmental niche and phenotypic similarities of these species. on the molecular level, frequent geneti ...	2015	26311542
the cell shape-determining csd6 protein from helicobacter pylori constitutes a new family of l,d-carboxypeptidase.	helicobacter pylori causes gastrointestinal diseases, including gastric cancer. its high motility in the viscous gastric mucosa facilitates colonization of the human stomach and depends on the helical cell shape and the flagella. in h. pylori, csd6 is one of the cell shape-determining proteins that play key roles in alteration of cross-linking or by trimming of peptidoglycan muropeptides. csd6 is also involved in deglycosylation of the flagellar protein flaa. to better understand its function, b ...	2015	26306031
unconventional n-linked glycosylation promotes trimeric autotransporter function in kingella kingae and aggregatibacter aphrophilus.	glycosylation is a widespread mechanism employed by both eukaryotes and bacteria to increase the functional diversity of their proteomes. the nontypeable haemophilus influenzae glycosyltransferase hmw1c mediates unconventional n-linked glycosylation of the adhesive protein hmw1, which is encoded in a two-partner secretion system gene cluster that also encodes hmw1c. in this system, hmw1 is modified in the cytoplasm by sequential transfer of hexose residues. in the present study, we examined king ...	2015	26307167
non-enteric infections, antibiotic use, and risk of development of functional gastrointestinal disorders.	gastrointestinal infections are risk factors for irritable bowel syndrome (ibs) and functional dyspepsia (fd). we investigated whether non-enteric infections and antibiotic exposure are also associated with the development of functional gastrointestinal disorders (fgids).	2015	26303310
differential editosome protein function between life cycle stages of trypanosoma brucei.	uridine insertion and deletion rna editing generates functional mitochondrial mrnas in trypanosoma brucei. the mrnas are differentially edited in bloodstream form (bf) and procyclic form (pf) life cycle stages, and this correlates with the differential utilization of glycolysis and oxidative phosphorylation between the stages. the mechanism that controls this differential editing is unknown. editing is catalyzed by multiprotein ∼20s editosomes that contain endonuclease, 3'-terminal uridylyltrans ...	2015	26304125
arsp: a methylarsenite efflux permease.	trivalent organoarsenic compounds are far more toxic than either pentavalent organoarsenicals or inorganic arsenite. many microbes methylate inorganic arsenite (as(iii)) to more toxic and carcinogenic methylarsenite (mas(iii)). additionally, monosodium methylarsenate (msma or mas(v)) has been used widely as an herbicide and is reduced by microbial communities to mas(iii). roxarsone (3-nitro-4-hydroxybenzenearsonic acid) is a pentavalent aromatic arsenical that is used as antimicrobial growth pro ...	2015	26234817
fleq coordinates flagellum-dependent and -independent motilities in pseudomonas syringae pv. tomato dc3000.	motility plays an essential role in bacterial fitness and colonization in the plant environment, since it favors nutrient acquisition and avoidance of toxic substances, successful competition with other microorganisms, the ability to locate the preferred hosts, access to optimal sites within them, and dispersal in the environment during the course of transmission. in this work, we have observed that the mutation of the flagellar master regulatory gene, fleq, alters bacterial surface motility and ...	2015	26296726
experimental evolution of enhanced growth by bacillus subtilis at low atmospheric pressure: genomic changes revealed by whole-genome sequencing.	knowledge of how microorganisms respond and adapt to low-pressure (lp) environments is limited. previously, bacillus subtilis strain wn624 was grown at the near-inhibitory lp of 5 kpa for 1,000 generations and strain wn1106, which exhibited increased relative fitness at 5 kpa, was isolated. genomic sequence differences between ancestral strain wn624 and lp-evolved strain wn1106 were identified using whole-genome sequencing. lp-evolved strain wn1106 carried amino acid-altering mutations in the co ...	2015	26296725
oral campylobacter species: initiators of a subgroup of inflammatory bowel disease?	in recent years, a number of studies detected a significantly higher prevalence of campylobacter species such as campylobacter concisus (c. concisus) in intestinal biopsies and fecal samples collected from patients with inflammatory bowel disease (ibd) compared to controls. most of these campylobacter species are not of zoonotic origin but are human oral campylobacter species. bacterial species usually cause diseases in the location where they colonize. however, c. concisus and other oral campyl ...	2015	26309350
commensal microbiome promotes resistance to local and systemic infections.	in this review, to illustrate the resistance mechanism for pathogen insult, we discussed the role of the intestinal microbiome in promoting resistance to local gastrointestinal tract infections and to respiratory tract infections.	2015	26265621
two-step ligand binding in a (βα)8 barrel enzyme: substrate-bound structures shed new light on the catalytic cycle of hisa.	hisa is a (βα)8 barrel enzyme that catalyzes the amadori rearrangement of n'-[(5'-phosphoribosyl)formimino]-5-aminoimidazole-4-carboxamide ribonucleotide (profar) to n'-((5'-phosphoribulosyl) formimino)-5-aminoimidazole-4-carboxamide-ribonucleotide (prfar) in the histidine biosynthesis pathway, and it is a paradigm for the study of enzyme evolution. still, its exact catalytic mechanism has remained unclear. here, we present crystal structures of wild type salmonella enterica hisa (sehisa) in its ...	2015	26294764
molecular characterization of extended-spectrum beta-lactamases (esbls) produced by clinical isolates of acinetobacter baumannii in saudi arabia.	acinetobacter baumannii is a common opportunistic pathogen that causes major nosocomial infections in hospitals. in this study, we hypothesized a high prevalence of a. baumanni esbl (extended-spectrum beta-lactamase) among all collected isolates.	2015	26290183
advantages and limitations of potential methods for the analysis of bacteria in milk: a review.	contamination concerns in the dairy industry are motivated by outbreaks of disease in humans and the inability of thermal processes to eliminate bacteria completely in processed products. haccp principles are an important tool used in the food industry to identify and control potential food safety hazards in order to meet customer demands and regulatory requirements. milk testing is of importance to the milk industry regarding quality assurance and monitoring of processed products by researchers ...	2015	26787931
advantages and limitations of potential methods for the analysis of bacteria in milk: a review.	contamination concerns in the dairy industry are motivated by outbreaks of disease in humans and the inability of thermal processes to eliminate bacteria completely in processed products. haccp principles are an important tool used in the food industry to identify and control potential food safety hazards in order to meet customer demands and regulatory requirements. milk testing is of importance to the milk industry regarding quality assurance and monitoring of processed products by researchers ...	2015	26787931
the allosteric behavior of fur mediates oxidative stress signal transduction in helicobacter pylori.	the microaerophilic gastric pathogen helicobacter pylori is exposed to oxidative stress originating from the aerobic environment, the oxidative burst of phagocytes and the formation of reactive oxygen species, catalyzed by iron excess. accordingly, the expression of genes involved in oxidative stress defense have been repeatedly linked to the ferric uptake regulator fur. moreover, mutations in the fur protein affect the resistance to metronidazole, likely due to loss-of-function in the regulatio ...	2015	26347726
a case of systemic lupus erythematosus presenting as guillain-barré syndrome.	systemic lupus erythematosus (sle) is an autoimmune systemic disease with multiple organ involvement with high morbidity and mortality rate. among the severe potential fatal complications are those of the central and peripheral nervous system which usually develop during the course of the disease and very rarely from the outset of the disease. we are reporting a rare case of miller-fisher (mfs) variant of guillain-barré syndrome (gbs) as the first manifestation of sle in a 41-year-old female who ...	2015	26366317
defects in polynucleotide phosphorylase impairs virulence in escherichia coli o157:h7.	polynucleotide phosphorylase (pnpase) is reported to regulate virulence in salmonella, yersinia sp. and campylobacter jejuni, yet its role in escherichia coli o157:h7 has not been investigated. to gain insights into its roles in e. coli o157:h7 virulence, pnp deletion mutants were generated and the major virulence factors were compared to their parental wild type strains. deletion of pnp in e. coli o157:h7 dramatically decreased stx2 mrna expression and stx2 protein production, and impaired lamb ...	2015	26347717
a hepatic cancer patient with guillain-barré syndrome during the perioperative period of partial hepatectomy: a case report.	we reported a case of hepatic cancer patient with guillain-barré syndrome during the perioperative period of partial hepatectomy in the present study. we analyzed the clinical data and described the characteristics of this patient.	2015	26550403
gluten introduction, breastfeeding, and celiac disease: back to the drawing board.	this commentary by the leadership of the north american society for the study of celiac disease (nasscd) concerns recent research findings regarding infant feeding practices. celiac disease has increased markedly in recent decades, and seroprevalence studies indicate that this is a true rise, rather than one due to increased awareness and testing. prior studies have suggested that infant feeding practices and timing of initial gluten exposure are central to the development of celiac disease. two ...	2015	26259710
gluten introduction, breastfeeding, and celiac disease: back to the drawing board.	this commentary by the leadership of the north american society for the study of celiac disease (nasscd) concerns recent research findings regarding infant feeding practices. celiac disease has increased markedly in recent decades, and seroprevalence studies indicate that this is a true rise, rather than one due to increased awareness and testing. prior studies have suggested that infant feeding practices and timing of initial gluten exposure are central to the development of celiac disease. two ...	2015	26259710
variant guillain-barré syndrome in a patient with non-hodgkin's lymphoma.	we report a 72-year-old female patient with diffuse large b cell non-hodgkin's lymphoma (nhl) with previous treatment with standard chemotherapy presenting as an acute, ascending, sensorimotor polyneuropathy. nerve conduction studies and lumbar puncture supported a rare, but ominous, axonal variant of guillain-barré syndrome (gbs) known as acute motor and sensory axonal neuropathy (amsan), which is distinguished from the more common, acute demyelinating forms of gbs. previous reports have largel ...	2015	26347834
the cardioprotective power of leaves.	lack of physical activity, smoking and/or inappropriate diet can contribute to the increase of oxidative stress, in turn affecting the pathophysiology of cardiovascular diseases. strong anti-oxidant properties of plant polyphenolic compounds might underlie their cardioprotective activity. this paper reviews recent findings on the anti-oxidant activity of plant leaf extracts and emphasizes their effects on blood platelets, leukocytes and endothelial cells - the targets orchestrating the developme ...	2015	26322095
static self-directed sample dispensing into a series of reaction wells on a microfluidic card for parallel genetic detection of microbial pathogens.	a microfluidic card is described for simultaneous and rapid genetic detection of multiple microbial pathogens. the hydrophobic surface of native acrylic and a novel microfluidic mechanism termed "airlock" were used to dispense sample into a series of 64 reaction wells without the use of valves, external pumping peripherals, multiple layers, or vacuum assistance. this airlock mechanism was tested with dilutions of whole human blood, saliva, and urine, along with mock samples of varying viscositie ...	2015	26260693
aptamers against pathogenic microorganisms.	an important current issue of modern molecular medicine and biotechnology is the search for new approaches to early diagnostic assays and adequate therapy of infectious diseases. one of the promising solutions to this problem might be a development of nucleic acid aptamers capable of interacting specifically with bacteria, protozoa, and viruses. such aptamers can be used for the specific recognition of infectious agents as well as for blocking of their functions. the present review summarizes va ...	2015	26258445
aptamers against pathogenic microorganisms.	an important current issue of modern molecular medicine and biotechnology is the search for new approaches to early diagnostic assays and adequate therapy of infectious diseases. one of the promising solutions to this problem might be a development of nucleic acid aptamers capable of interacting specifically with bacteria, protozoa, and viruses. such aptamers can be used for the specific recognition of infectious agents as well as for blocking of their functions. the present review summarizes va ...	2015	26258445
dps and dpsl mediate survival in vitro and in vivo during the prolonged oxidative stress response in bacteroides fragilis.	bacteroides fragilis is a gram-negative anaerobe and member of the human intestinal tract microbiome, where it plays many beneficial roles. however, translocation of the organism to the peritoneal cavity can lead to peritonitis, intra-abdominal abscess formation, bacteremia, and sepsis. during translocation, b. fragilis is exposed to increased oxidative stress from the oxygenated tissues of the peritoneal cavity and the immune response. in order to survive, b. fragilis mounts a robust oxidative ...	2015	26260459
a new duck circovirus sequence, detected in velvet scoter (melanitta fusca) supports great diversity among this species of virus.	the aim of this study was to investigate the presence of circoviruses in wild bird populations, in poland. circoviruses possess immuno-suppressive properties and might interfere with the health of wild birds.	2015	26253134
increased expression of duox2 is an epithelial response to mucosal dysbiosis required for immune homeostasis in mouse intestine.	dual oxidase 2 (duox2), a hydrogen-peroxide generator at the apical membrane of gastrointestinal epithelia, is up-regulated in patients with inflammatory bowel disease (ibd) before the onset of inflammation, but little is known about its effects. we investigated the role of duox2 in maintaining mucosal immune homeostasis in mice.	2015	26261005
role of the normal gut microbiota.	relation between the gut microbiota and human health is being increasingly recognised. it is now well established that a healthy gut flora is largely responsible for overall health of the host. the normal human gut microbiota comprises of two major phyla, namely bacteroidetes and firmicutes. though the gut microbiota in an infant appears haphazard, it starts resembling the adult flora by the age of 3 years. nevertheless, there exist temporal and spatial variations in the microbial distribution f ...	2015	26269668
inflammatory pouch disease: the spectrum of pouchitis.	restorative proctocolectomy with ileal-pouch anal anastomosis (ipaa) is the operation of choice for medically refractory ulcerative colitis (uc), for uc with dysplasia, and for familial adenomatous polyposis (fap). ipaa can be a treatment option for selected patients with crohn's colitis without perianal and/or small bowel disease. the term "pouchitis" refers to nonspecific inflammation of the pouch and is a common complication in patients with ipaa; it occurs more often in uc patients than in f ...	2015	26269664
neuroinflammation in the peripheral nerve: cause, modulator, or bystander in peripheral neuropathies?	the role of innate and adaptive inflammation as a primary driver or modifier of neuropathy in premorbidly normal nerves, and as a critical player in amplifying neuropathies of other known causes (e.g., genetic, metabolic) is incompletely understood and under-researched, despite unmet clinical need. also, cellular and humoral components of the adaptive and innate immune system are substantial disease modifying agents in the context of neuropathies and, at least in some neuropathies, there is an i ...	2015	26250643
neuroinflammation in the peripheral nerve: cause, modulator, or bystander in peripheral neuropathies?	the role of innate and adaptive inflammation as a primary driver or modifier of neuropathy in premorbidly normal nerves, and as a critical player in amplifying neuropathies of other known causes (e.g., genetic, metabolic) is incompletely understood and under-researched, despite unmet clinical need. also, cellular and humoral components of the adaptive and innate immune system are substantial disease modifying agents in the context of neuropathies and, at least in some neuropathies, there is an i ...	2015	26250643
quercetin influences quorum sensing in food borne bacteria: in-vitro and in-silico evidence.	quorum sensing (qs) plays a vital role in regulating the virulence factor of many food borne pathogens, which causes severe public health risk. therefore, interrupting the qs signaling pathway may be an attractive strategy to combat microbial infections. in the current study qs inhibitory activity of quercetin and its anti-biofilm property was assessed against food-borne pathogens using a bio-sensor strain. in addition in-silico techniques like molecular docking and molecular dynamics simulation ...	2015	26248208
intracellular uropathogenic e. coli exploits host rab35 for iron acquisition and survival within urinary bladder cells.	recurrent urinary tract infections (utis) caused by uropathogenic e. coli (upec) are common and morbid infections with limited therapeutic options. previous studies have demonstrated that persistent intracellular infection of bladder epithelial cells (bec) by upec contributes to recurrent uti in mouse models of infection. however, the mechanisms employed by upec to survive within bec are incompletely understood. in this study we aimed to understand the role of host vesicular trafficking proteins ...	2015	26248231
fecal markers of environmental enteropathy are associated with animal exposure and caregiver hygiene in bangladesh.	undernutrition is estimated to be an underlying cause of over half of all deaths in young children globally. there is a growing body of literature suggesting that increased exposure to enteric pathogens is responsible for environmental enteropathy (ee), a disorder associated with impaired growth in children. to determine if household unsanitary environmental conditions were significantly associated with ee and stunting in children, we conducted a cohort of 216 children (≤ 30 months) in rural ban ...	2015	26055734
functional activation of the flagellar type iii secretion export apparatus.	flagella are assembled sequentially from the inside-out with morphogenetic checkpoints that enforce the temporal order of subunit addition. here we show that flagellar basal bodies fail to proceed to hook assembly at high frequency in the absence of the monotopic protein swrb of bacillus subtilis. genetic suppressor analysis indicates that swrb activates the flagellar type iii secretion export apparatus by the membrane protein flip. furthermore, mutants defective in the flagellar c-ring phenocop ...	2015	26244495