Publications

commentary.		2015	25552856
mechanisms of bacterial morphogenesis: evolutionary cell biology approaches provide new insights.	how darwin's "endless forms most beautiful" have evolved remains one of the most exciting questions in biology. the significant variety of bacterial shapes is most likely due to the specific advantages they confer with respect to the diverse environments they occupy. while our understanding of the mechanisms generating relatively simple shapes has improved tremendously in the last few years, the molecular mechanisms underlying the generation of complex shapes and the evolution of shape diversity ...	2015	25664446
genome-wide gene order distances support clustering the gram-positive bacteria.	initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ...	2015	25653643
genome-wide gene order distances support clustering the gram-positive bacteria.	initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ...	2015	25653643
lengths of orthologous prokaryotic proteins are affected by evolutionary factors.	proteins of the same functional family (for example, kinases) may have significantly different lengths. it is an open question whether such variation in length is random or it appears as a response to some unknown evolutionary driving factors. the main purpose of this paper is to demonstrate existence of factors affecting prokaryotic gene lengths. we believe that the ranking of genomes according to lengths of their genes, followed by the calculation of coefficients of association between genome ...	2015	26114113
differential distribution of type ii crispr-cas systems in agricultural and nonagricultural campylobacter coli and campylobacter jejuni isolates correlates with lack of shared environments.	crispr (clustered regularly interspaced palindromic repeats)-cas (crispr-associated) systems are sequence-specific adaptive defenses against phages and plasmids which are widespread in prokaryotes. here we have studied whether phylogenetic relatedness or sharing of environmental niches affects the distribution and dissemination of type ii crispr-cas systems, first in 132 bacterial genomes from 15 phylogenetic classes, ranging from proteobacteria to actinobacteria. there was clustering of distinc ...	2015	26338188
effects of hangeshashinto on growth of oral microorganisms.	oral mucositis (om) in cancer patients induced by chemotherapy or radiotherapy has a significant impact on quality of life, and causes considerable morbidity. oral microorganisms are likely to intensify the inflammatory process and aggravate the formation of ulcers. hangeshashinto (hst), a japanese kampo medicine, has been reported to be effective when used as a gargle for the treatment of om. to clarify the effects of hst on oral microorganisms, we assessed its antimicrobial activity against 27 ...	2015	26170876
traditional uses, phytochemistry, and pharmacology of olea europaea (olive).	aim of the review. to grasp the fragmented information available on the botany, traditional uses, phytochemistry, pharmacology, and toxicology of olea europaea to explore its therapeutic potential and future research opportunities. material and methods. all the available information on o. europaea was collected via electronic search (using pubmed, scirus, google scholar, and web of science) and a library search. results. ethnomedical uses of o. europaea are recorded throughout the world where it ...	2015	25802541
mouse genome engineering via crispr-cas9 for study of immune function.	clustered regularly interspaced palindromic repeats (crispr)-associated (cas9) technology has proven a formidable addition to our armory of approaches for genomic editing. derived from pathways in archaea and bacteria that mediate the resistance to exogenous genomic material, the crispr-cas9 system utilizes a short single guide rna (sgrna) to direct the endonuclease cas9 to virtually anywhere in the genome. upon targeting, cas9 generates dna double-strand breaks (dsbs) and facilitates the repair ...	2015	25607456
reducing the risk of pet-associated zoonotic infections.		2015	25897046
structures of bacteroides fragilis uridine 5'-diphosphate-n-acetylglucosamine (udp-glcnac) acyltransferase (bflpxa).	uridine 5'-diphosphate-n-acetylglucosamine (udp-glcnac) acyltransferase (lpxa) catalyzes a reversible reaction for adding an o-acyl group to the glcnac in udp-glcnac in the first step of lipid a biosynthesis. lipid a constitutes a major component of lipopolysaccharides, also referred to as endotoxins, which form the outer monolayer of the outer membrane of gram-negative bacteria. ligand-free and udp-glcnac-bound crystal structures of lpxa from bacteroides fragilis nctc 9343, the most common path ...	2015	25945572
detection of mycobacteria, mycobacterium avium subspecies, and mycobacterium tuberculosis complex by a novel tetraplex real-time pcr assay.	mycobacterium tuberculosis complex, mycobacterium avium, and many other nontuberculous mycobacteria are worldwide distributed microorganisms of major medical and veterinary importance. considering the growing epidemiologic significance of wildlife-livestock-human interrelation, developing rapid detection tools of high specificity and sensitivity is vital to assess their presence and accelerate the process of diagnosing mycobacteriosis. here we describe the development and evaluation of a novel t ...	2015	25588660
development of a new real-time pcr system for simultaneous detection of bacteria and fungi in pathological samples.	a novel system for simultaneous detection of pathogenic bacteria and fungi in pathological samples was developed using a real-time polymerase chain reaction (pcr) system. this system, designated the "multi-microbial real-time pcr", has the potential to simultaneously detect 68 bacterial and 9 fungal species in a 96-well plate format. all probe-primer sets were designed to produce amplicons smaller than 210 bp using formalin-fixed paraffin-embedded samples as input. the specificity and sensitivit ...	2015	26823918
hypothetical protein ct398 (cdsz) interacts with σ(54) (rpon)-holoenzyme and the type iii secretion export apparatus in chlamydia trachomatis.	a significant challenge to bacteriology is the relatively large proportion of proteins that lack sufficient sequence similarity to support functional annotation (i.e. hypothetical proteins). the aim of this study was to apply protein structural homology to gain insights into a candidate protein of unknown function (ct398) within the medically important, obligate intracellular bacterium chlamydia trachomatis. c. trachomatis is a major human pathogen responsible for numerous infections throughout ...	2015	26173998
mechanisms of drug resistance: quinolone resistance.	quinolone antimicrobials are synthetic and widely used in clinical medicine. resistance emerged with clinical use and became common in some bacterial pathogens. mechanisms of resistance include two categories of mutation and acquisition of resistance-conferring genes. resistance mutations in one or both of the two drug target enzymes, dna gyrase and dna topoisomerase iv, are commonly in a localized domain of the gyra and pare subunits of the respective enzymes and reduce drug binding to the enzy ...	2015	26190223
rho gtpases as pathogen targets: focus on curable sexually transmitted infections.	pathogens have evolved highly specialized mechanisms to infect hosts. several microorganisms modulate the eukaryotic cell surface to facilitate their engulfment. once internalized, they hijack the molecular machinery of the infected cell for their own benefit. at different stages of phagocytosis, particularly during invasion, certain pathogens manipulate pathways governed by small gtpases. in this review, we focus on the role of rho proteins on curable, sexually transmitted infections caused by ...	2015	26023809
bridging topological and functional information in protein interaction networks by short loops profiling.	protein-protein interaction networks (ppins) have been employed to identify potential novel interconnections between proteins as well as crucial cellular functions. in this study we identify fundamental principles of ppin topologies by analysing network motifs of short loops, which are small cyclic interactions of between 3 and 6 proteins. we compared 30 ppins with corresponding randomised null models and examined the occurrence of common biological functions in loops extracted from a cross-vali ...	2015	25703051
network representations of immune system complexity.	the mammalian immune system is a dynamic multiscale system composed of a hierarchically organized set of molecular, cellular, and organismal networks that act in concert to promote effective host defense. these networks range from those involving gene regulatory and protein-protein interactions underlying intracellular signaling pathways and single-cell responses to increasingly complex networks of in vivo cellular interaction, positioning, and migration that determine the overall immune respons ...	2015	25625853
outer membrane vesicles as platform vaccine technology.	outer membrane vesicles (omvs) are released spontaneously during growth by many gram-negative bacteria. they present a range of surface antigens in a native conformation and have natural properties like immunogenicity, self-adjuvation and uptake by immune cells which make them attractive for application as vaccines against pathogenic bacteria. in particular with neisseria meningitidis, they have been investigated extensively and an omv-containing meningococcal vaccine has recently been approved ...	2015	26912077
membrane topology and biochemical characterization of the escherichia coli baca undecaprenyl-pyrophosphate phosphatase.	several integral membrane proteins exhibiting undecaprenyl-pyrophosphate (c55-pp) phosphatase activity were previously identified in escherichia coli that belonged to two distinct protein families: the baca protein, which accounts for 75% of the c55-pp phosphatase activity detected in e. coli cell membranes, and three members of the pap2 phosphatidic acid phosphatase family, namely pgpb, ybjg and lpxt. this dephosphorylation step is required to provide the c55-p carrier lipid which plays a centr ...	2015	26560897
pathogenesis of myeloproliferative neoplasms: role and mechanisms of chronic inflammation.	myeloproliferative neoplasms (mpns) are a heterogeneous group of clonal diseases characterized by the excessive and chronic production of mature cells from one or several of the myeloid lineages. recent advances in the biology of mpns have greatly facilitated their molecular diagnosis since most patients present with mutation(s) in the jak2, mpl, or calr genes. yet the roles played by these mutations in the pathogenesis and main complications of the different subtypes of mpns are not fully eluci ...	2015	26538820
development of real-time pcr assays for the detection of moraxella macacae associated with bloody nose syndrome in rhesus (macaca mulatta) and cynomolgus (macaca fascicularis) macaques.	moraxella macacae is a recently described bacterial pathogen that causes epistaxis or so-called bloody nose syndrome in captive macaques. the aim of this study was to develop specific molecular diagnostic assays for m. macacae and to determine their performance characteristics.	2015	26365904
opposite and coordinated rotation of amphitrichous flagella governs oriented swimming and reversals in a magnetotactic spirillum.	current knowledge regarding the mechanism that governs flagellar motor rotation in response to environmental stimuli stems mainly from the study of monotrichous and peritrichous bacteria. little is known about how two polar flagella, one at each cell pole of the so-called amphitrichous bacterium, are coordinated to steer the swimming. here we fluorescently labeled the flagella of magnetospirillum magneticum amb-1 cells and took advantage of the magnetically controllable swimming of this bacteriu ...	2015	26240070
lessons in fundamental mechanisms and diverse adaptations from the 2015 bacterial locomotion and signal transduction meeting.	in response to rapid changes in their environment, bacteria control a number of processes, including motility, cell division, biofilm formation, and virulence. research presented in january 2015 at the biennial bacterial locomotion and signal transduction (blast) meeting in tucson, az, illustrates the elegant complexity of the nanoarrays, nanomachines, and networks of interacting proteins that mediate such processes. studies employing an array of biophysical, genetic, cell biology, and mathemati ...	2015	26195592
ileal mucosa-associated lymphoid tissue lymphoma presenting with small bowel obstruction: a case report.	extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue (malt lymphoma) of the gastrointestinal tract commonly involves the stomach in the setting of concurrent helicobacter pylori (h. pylori) infection. primary ileal malt lymphoma is rare, and has not been associated with a specific infectious disease. we report a case of a 58-year-old man who presented to the emergency department with constipation and abdominal distension, and signs of an obstructing mass on computed tomography ...	2015	26178711
acylation of biomolecules in prokaryotes: a widespread strategy for the control of biological function and metabolic stress.	acylation of biomolecules (e.g., proteins and small molecules) is a process that occurs in cells of all domains of life and has emerged as a critical mechanism for the control of many aspects of cellular physiology, including chromatin maintenance, transcriptional regulation, primary metabolism, cell structure, and likely other cellular processes. although this review focuses on the use of acetyl moieties to modify a protein or small molecule, it is clear that cells can use many weak organic aci ...	2015	26179745
investigating reports of complex regional pain syndrome: an analysis of hpv-16/18-adjuvanted vaccine post-licensure data.	complex regional pain syndrome (crps) is a chronic pain disorder that typically follows trauma or surgery. suspected crps reported after vaccination with human papillomavirus (hpv) vaccines led to temporary suspension of proactive recommendation of hpv vaccination in japan. we investigated the potential crps signal in relation to hpv-16/18-adjuvanted vaccine (cervarix®) by database review of crps cases with independent expert confirmation; a disproportionality analysis and analyses of temporalit ...	2015	26501109
mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator.	ferric uptake regulator (fur) plays a key role in the iron homeostasis of prokaryotes, such as bacterial pathogens, but the molecular mechanisms and structural basis of fur-dna binding remain incompletely understood. here, we report high-resolution structures of magnetospirillum gryphiswaldense msr-1 fur in four different states: apo-fur, holo-fur, the fur-feoab1 operator complex and the fur-pseudomonas aeruginosa fur box complex. apo-fur is a transition metal ion-independent dimer whose binding ...	2015	26134419
architecture and roles of periplasmic adaptor proteins in tripartite eﬄux assemblies.	recent years have seen major advances in the structural understanding of the different components of tripartite eﬄux assemblies, which encompass the multidrug eﬄux (mdr) pumps and type i secretion systems. the majority of these investigations have focused on the role played by the inner membrane transporters and the outer membrane factor (omf), leaving the third component of the system - the periplasmic adaptor proteins (paps) - relatively understudied. here we review the current state of knowle ...	2015	26074901
extensive infectious myelitis post bariatric surgery.	inflammatory myelopathy is an inflammatory neurological disorder of the spinal cord (myelopathy). it occurs in 1 (severe) to 8 (mild) cases/million per year. it is often referred to in the literature as "transverse myelitis" or "acute transverse myelitis". myelopathy and by extension myelitis, can present as pyramidal (motor), sensory, and/or autonomic dysfunction to varying degrees. symptoms typically develop over hours to days and worsen over days to weeks. sensory symptoms usually present as ...	2015	25879204
presence of zoonotic agents in engorged ticks and hedgehog faeces from erinaceus europaeus in (sub) urban areas.	european hedgehogs (erinaceus europaeus) are hosts for ixodes hexagonus and i. ricinus ticks, which are vectors for zoonotic microorganisms. in addition, hedgehogs may carry several enteric zoonoses as well. it is unclear to what extent a presence of pathogens in hedgehogs poses a risk to public health, as information on the presence of zoonotic agents in hedgehogs in urban areas is relatively scarce.	2015	25885888
genome-wide dna methylation analysis of haloferax volcanii h26 and identification of dna methyltransferase related pd-(d/e)xk nuclease family protein hvo_a0006.	restriction-modification (rm) systems have evolved to protect the cell from invading dnas and are composed of two enzymes: a dna methyltransferase and a restriction endonuclease. although rm systems are present in both archaeal and bacterial genomes, dna methylation in archaea has not been well defined. in order to characterize the function of rm systems in archaeal species, we have made use of the model haloarchaeon haloferax volcanii. a genomic dna methylation analysis of h. volcanii strain h2 ...	2015	25904898
molecular pathogenesis of malt lymphoma.	approximately 8% of all non-hodgkin lymphomas are extranodal marginal zone b cell lymphoma of mucosa associated lymphoid tissue (malt), also known as malt lymphoma, which was first described in 1983 by isaacson and wright. malt lymphomas arise at a wide range of different extranodal sites, with the highest frequency in the stomach, followed by lung, ocular adnexa, and thyroid, and with a low percentage in the small intestine. interestingly, at least 3 different, apparently site-specific, chromos ...	2015	25922601
regulation of bacterial virulence by csr (rsm) systems.	most bacterial pathogens have the remarkable ability to flourish in the external environment and in specialized host niches. this ability requires their metabolism, physiology, and virulence factors to be responsive to changes in their surroundings. it is no surprise that the underlying genetic circuitry that supports this adaptability is multilayered and exceedingly complex. studies over the past 2 decades have established that the csra/rsma proteins, global regulators of posttranscriptional ge ...	2015	25833324
the challenge of efflux-mediated antibiotic resistance in gram-negative bacteria.	the global emergence of multidrug-resistant gram-negative bacteria is a growing threat to antibiotic therapy. the chromosomally encoded drug efflux mechanisms that are ubiquitous in these bacteria greatly contribute to antibiotic resistance and present a major challenge for antibiotic development. multidrug pumps, particularly those represented by the clinically relevant acrab-tolc and mex pumps of the resistance-nodulation-division (rnd) superfamily, not only mediate intrinsic and acquired mult ...	2015	25788514
a new player at the flagellar motor: flil controls both motor output and bias.	the bacterial flagellum is driven by a bidirectional rotary motor, which propels bacteria to swim through liquids or swarm over surfaces. while the functions of the major structural and regulatory components of the flagellum are known, the function of the well-conserved flil protein is not. in salmonella and escherichia coli, the absence of flil leads to a small defect in swimming but complete elimination of swarming. here, we tracked single motors of these bacteria and found that absence of fli ...	2015	25714720
proteomic profiling of the outer membrane fraction of the obligate intracellular bacterial pathogen ehrlichia ruminantium.	the outer membrane proteins (omps) of gram-negative bacteria play a crucial role in virulence and pathogenesis. identification of these proteins represents an important goal for bacterial proteomics, because it aids in vaccine development. here, we have developed such an approach for ehrlichia ruminantium, the obligate intracellular bacterium that causes heartwater. a preliminary whole proteome analysis of elementary bodies, the extracellular infectious form of the bacterium, had been performed ...	2015	25710494
exploring the existence of lipid rafts in bacteria.	an interesting concept in the organization of cellular membranes is the proposed existence of lipid rafts. membranes of eukaryotic cells organize signal transduction proteins into membrane rafts or lipid rafts that are enriched in particular lipids such as cholesterol and are important for the correct functionality of diverse cellular processes. the assembly of lipid rafts in eukaryotes has been considered a fundamental step during the evolution of cellular complexity, suggesting that bacteria a ...	2015	25652542
extranodal marginal zone lymphoma of the lung: evolution from an underlying reactive lymphoproliferative disorder.	extranodal marginal zone lymphoma (enmzl) of mucosa-associated lymphoid tissue (malt) is a problematic and sometimes controversial diagnosis. while commonly seen in the stomach in the setting of chronic helicobacter pylori infection, other extranodal sites, such as the lung, may also present with disease. enmzl is clinically and morphologically heterogeneous; however, regardless of presentation, the etiology lies in the accumulation of lymphoid tissue in non-traditional sites. this phenomenon is ...	2015	26457231
a case of a laryngeal malt lymphoma in a patient with a history of gastric malt.	we are reporting a case of a 62-year-old african american woman with a history of gastric malt lymphoma successfully treated with radiation who presented with a laryngeal malt lymphoma 4 years after her original diagnosis. she received definitive radiation with a complete response. the case presented is unique for the rare presentation of a malt lymphoma in the larynx, especially in light of the patient's previously treated gastric malt lymphoma years ago.	2015	25664189
current and past strategies for bacterial culture in clinical microbiology.	a pure bacterial culture remains essential for the study of its virulence, its antibiotic susceptibility, and its genome sequence in order to facilitate the understanding and treatment of caused diseases. the first culture conditions empirically varied incubation time, nutrients, atmosphere, and temperature; culture was then gradually abandoned in favor of molecular methods. the rebirth of culture in clinical microbiology was prompted by microbiologists specializing in intracellular bacteria. th ...	2015	25567228
inositol 1,4,5-trisphosphate receptor type 1 autoantibodies in paraneoplastic and non-paraneoplastic peripheral neuropathy.	recently, we described a novel autoantibody, anti-sj/itpr1-igg, that targets the inositol 1,4,5-trisphosphate receptor type 1 (itpr1) in patients with cerebellar ataxia. however, itpr1 is expressed not only by purkinje cells but also in the anterior horn of the spinal cord, in the substantia gelatinosa and in the motor, sensory (including the dorsal root ganglia) and autonomic peripheral nervous system, suggesting that the clinical spectrum associated with autoimmunity to itpr1 may be broader th ...	2016	27776522
primary b-cell mucosa-associated lymphoid tissue lymphoma of the hard palate and parotid gland: report of one case and review of the literature.	a 61-year-old woman was admitted to our hospital with an ulcerated palate mass and swelling of the right parotid gland. incisional biopsy from the hard palate revealed an extranodal marginal zone b-cell lymphoma, also called mucosa-associated lymphoid tissue (malt) lymphoma. final diagnosis was malt lymphoma of the parotid gland with concomitant involvement of an extremely seldom site of involvement: the hard palate. to our knowledge, this report illustrates the first case of malt lymphoma of th ...	2016	27738485
transition metals and virulence in bacteria.	transition metals are required trace elements for all forms of life. due to their unique inorganic and redox properties, transition metals serve as cofactors for enzymes and other proteins. in bacterial pathogenesis, the vertebrate host represents a rich source of nutrient metals, and bacteria have evolved diverse metal acquisition strategies. host metal homeostasis changes dramatically in response to bacterial infections, including production of metal sequestering proteins and the bombardment o ...	2016	27617971
how rheumatoid arthritis can result from provocation of the immune system by microorganisms and viruses.	the pathogenesis of rheumatoid arthritis (ra), similar to development of a majority of inflammatory and autoimmune disorders, is largely due to an inappropriate or inadequate immune response to environmental challenges. among these challenges, infectious agents are the undisputed leaders. since the 1870s, an impressive list of microorganisms suspected of provoking ra has formed, and the list is still growing. although a definite causative link between a specific infectious agent and the disease ...	2016	27582741
mucosa-associated lymphoid tissue lymphoma of the sigmoid colon discovered on routine screening colonoscopy in patient with hepatitis c and helicobacter pylori infection.	mucosa-associated lymphoid tissue (malt) lymphoma is predominantly found in the stomach. rarely, it is found in the proximal colon and even less so in the sigmoid colon. we present a rare case of primary sigmoid colon malt lymphoma in a patient with concomitant helicobacter pylori and hepatitis c infection. we also review current imaging, staging, and therapeutic modalities. to our knowledge, this is the first sigmoid colon malt lymphoma reported in the united states.	2016	27807552
evaluation of a protective effect of in ovo delivered campylobacter jejuni omvs.	campylobacter jejuni is the most prevalent cause of a food-borne gastroenteritis in the developed world, with poultry being the main source of infection. campylobacter jejuni, like other gram-negative bacteria, constitutively releases outer membrane vesicles (omvs). omvs are highly immunogenic, can be taken up by mammalian cells, and are easily modifiable by recombinant engineering. we have tested their usefulness for an oral (in ovo) vaccination of chickens. four groups of 18-day-old chicken em ...	2016	27383607
calcium binding protects e-cadherin from cleavage by helicobacter pylori htra.	the cell adhesion and tumor suppressor protein e-cadherin is an important factor in the establishment and maintenance of epithelial integrity. e-cadherin is a single transmembrane protein, which consists of an intracellular domain (ic), a transmembrane domain (td), and five extracellular domains (ec). ec domains form homophilic interactions in cis and trans that require calcium binding to the linker region between the ec domains. in our previous studies, we identified the serine protease high te ...	2016	27274359
challenges with using names to link digital biodiversity information.		2016	27346955
exploring the secretomes of microbes and microbial communities using filamentous phage display.	microbial surface and secreted proteins (the secretome) contain a large number of proteins that interact with other microbes, host and/or environment. these proteins are exported by the coordinated activities of the protein secretion machinery present in the cell. a group of bacteriophage, called filamentous phage, have the ability to hijack bacterial protein secretion machinery in order to amplify and assemble via a secretion-like process. this ability has been harnessed in the use of filamento ...	2016	27092113
the interplay between the microbiome and the adaptive immune response in cancer development.	the data from different studies suggest a bacterial role in cancer genesis/progression, often modulating the local immune response. this is particularly so at the mucosal level where the bacterial presence is strong and the immune system is highly reactive. the epithelial surfaces of the body, such as the skin and mucosa, are colonized by a vast number of microorganisms, which represent the so-called normal microbiome. normally the microbiome does not cause a proinflammatory response because the ...	2016	27366226
measuring escherichia coli gene expression during human urinary tract infections.	extraintestinal escherichia coli (e. coli) evolved by acquisition of pathogenicity islands, phage, plasmids, and dna segments by horizontal gene transfer. strains are heterogeneous but virulent uropathogenic isolates more often have specific fimbriae, toxins, and iron receptors than commensal strains. one may ask whether it is the virulence factors alone that are required to establish infection. while these virulence factors clearly contribute strongly to pathogenesis, bacteria must survive by m ...	2016	26784237
guillain-barré syndrome with hyperreflexia and bilateral papillitis in a child.	guillain-barré syndrome (gbs) is an acute inflammatory polyneuropathy characterized by rapidly progressive symmetric weakness, and areflexia. areflexia is necessary for the diagnosis of gbs. however, recently there have been studies of hyperreflexia with axonal neuropathy form of gbs. we report a 14-year-old boy with gbs, who presented with hyperreflexia and bilateral papillitis. to the best of our knowledge, this is the first pediatric patient presenting with papillitis and hyperreflexia with a ...	2016	27195040
infectious aetiology of marginal zone lymphoma and role of anti-infective therapy.	marginal zone lymphomas have been associated with several infectious agents covering both viral and bacterial pathogens and in some cases a clear aetiological role has been established. pathogenetic mechanisms are currently not completely understood. however, the role of chronic stimulation of the host immune response with persistent lymphocyte activation represents the most convincing explanation for lymphoproliferation. gastric malt lymphoma is strictly associated with helicobacter pylori infe ...	2016	26740867
understanding luminal microorganisms and their potential effectiveness in treating intestinal inflammation.	the human intestine contains 10 bacteria, which outnumber the mammalian cells 10-fold. certain other commensal or infectious agents, like helminthic parasites, become members of this microbial ecosystem, especially in populations living under less hygienic conditions. intestinal microbes, also called the microbiome or microbiota, shape the host immune reactivity to self and nonself throughout life. changes in microbiome composition may impair the maturation of immune regulatory pathways and pred ...	2016	26457381
identification of large disjoint motifs in biological networks.	biological networks provide great potential to understand how cells function. network motifs, frequent topological patterns, are key structures through which biological networks operate. finding motifs in biological networks remains to be computationally challenging task as the size of the motif and the underlying network grow. often, different copies of a given motif topology in a network share nodes or edges. counting such overlapping copies introduces significant problems in motif identificat ...	2016	27716036
characterizing the syphilis-causing treponema pallidum ssp. pallidum proteome using complementary mass spectrometry.	the spirochete bacterium treponema pallidum ssp. pallidum is the etiological agent of syphilis, a chronic multistage disease. little is known about the global t. pallidum proteome, therefore mass spectrometry studies are needed to bring insights into pathogenicity and protein expression profiles during infection.	2016	27606673
contig-layout-authenticator (cla): a combinatorial approach to ordering and scaffolding of bacterial contigs for comparative genomics and molecular epidemiology.	a wide variety of genome sequencing platforms have emerged in the recent past. high-throughput platforms like illumina and 454 are essentially adaptations of the shotgun approach generating millions of fragmented single or paired sequencing reads. to reconstruct whole genomes, the reads have to be assembled into contigs, which often require further downstream processing. the contigs can be directly ordered according to a reference, scaffolded based on paired read information, or assembled using ...	2016	27248146
coevolution theory of the genetic code at age forty: pathway to translation and synthetic life.	the origins of the components of genetic coding are examined in the present study. genetic information arose from replicator induction by metabolite in accordance with the metabolic expansion law. messenger rna and transfer rna stemmed from a template for binding the aminoacyl-rna synthetase ribozymes employed to synthesize peptide prosthetic groups on rnas in the peptidated rna world. coevolution of the genetic code with amino acid biosynthesis generated trna paralogs that identify a last unive ...	2016	26999216
comparative genomic analysis of the flagellin glycosylation island of the gram-positive thermophile geobacillus.	protein glycosylation involves the post-translational attachment of sugar chains to target proteins and has been observed in all three domains of life. post-translational glycosylation of flagellin, the main structural protein of the flagellum, is a common characteristic among many gram-negative bacteria and archaea. several distinct functions have been ascribed to flagellin glycosylation, including stabilisation and maintenance of the flagellar filament, motility, surface recognition, adhesion, ...	2016	27842516
recent developments in detection and enumeration of waterborne bacteria: a retrospective minireview.	waterborne diseases have emerged as global health problems and their rapid and sensitive detection in environmental water samples is of great importance. bacterial identification and enumeration in water samples is significant as it helps to maintain safe drinking water for public consumption. culture-based methods are laborious, time-consuming, and yield false-positive results, whereas viable but nonculturable (vbncs) microorganisms cannot be recovered. hence, numerous methods have been develop ...	2016	27397728
molecular evolution of the oxygen-binding hemerythrin domain.	the evolution of oxygenic photosynthesis during precambrian times entailed the diversification of strategies minimizing reactive oxygen species-associated damage. four families of oxygen-carrier proteins (hemoglobin, hemerythrin and the two non-homologous families of arthropodan and molluscan hemocyanins) are known to have evolved independently the capacity to bind oxygen reversibly, providing cells with strategies to cope with the evolutionary pressure of oxygen accumulation. oxygen-binding hem ...	2016	27336621
histoplasma capsulatum-induced cytokine secretion in lung epithelial cells is dependent on host integrins, src-family kinase activation, and membrane raft recruitment.	histoplasma capsulatum var. capsulatum is a dimorphic fungus that causes histoplasmosis, a human systemic mycosis with worldwide distribution. in the present work, we demonstrate that h. capsulatum yeasts are able to induce cytokine secretion by the human lung epithelial cell line a549 in integrin- and src-family kinase (sfk)-dependent manners. this conclusion is supported by small interfering rna (sirna) directed to α3 and α5 integrins, and pp2, an inhibitor of sfk activation. sirna and pp2 red ...	2016	27148251
characterization and genomic study of the novel bacteriophage hy01 infecting both escherichia coli o157:h7 and shigella flexneri: potential as a biocontrol agent in food.	escherichia coli o157:h7 and shigella flexneri are well-known food-borne pathogens causing severe food poisoning at low infectious doses. bacteriophages have been approved for food applications by the us food and drug administration (fda) and have been suggested as natural food preservatives to control specific food-borne pathogens. to develop a novel natural food preservative against e. coli o157:h7 and s. flexneri, a new bacteriophage needs to be isolated and characterized.	2016	28036349
transcriptome analysis of the intracellular facultative pathogen piscirickettsia salmonis: expression of putative groups of genes associated with virulence and iron metabolism.	the intracellular facultative bacteria piscirickettsia salmonis is one of the most important pathogens of the chilean aquaculture. however, there is a lack of information regarding the whole genomic transcriptional response according to different extracellular environments. we used next generation sequencing (ngs) of rna (rna-seq) to study the whole transcriptome of an isolate of p. salmonis (favet-inbiogen) using a cell line culture and a modified cell-free liquid medium, with or without iron s ...	2016	28033422
relapsing-remitting severe bickerstaff's brainstem encephalitis - case report and literature review.	bickerstaff's brainstem encephalitis (bbe) is a very rare disease of the central nervous system. aetiology of the disease is auto-immunological. however, it is not entirely understood. clinically bbe manifests in progressive ophthalmoplegia, ataxia and consciousness disturbances. clinical symptoms are usually preceded by an unidentified infection of the upper respiratory tract. usually, the disease has one phase, but individual relapses have also been described. despite quite severe clinical sym ...	2016	28096906
the campylobacter jejuni oxidative stress regulator rrpb is associated with a genomic hypervariable region and altered oxidative stress resistance.	campylobacter jejuni is the leading cause of bacterial foodborne diarrhoeal disease worldwide. despite the microaerophilic nature of the bacterium, c. jejuni can survive the atmospheric oxygen conditions in the environment. bacteria that can survive either within a host or in the environment like c. jejuni require variable responses to survive the stresses associated with exposure to different levels of reactive oxygen species. the marr-type transcriptional regulators rrpa and rrpb have recently ...	2016	28082970
antibodies from multiple sclerosis patients preferentially recognize hyperglucosylated adhesin of non-typeable haemophilus influenzae.	in autoimmune diseases, there have been proposals that exogenous "molecular triggers", i.e., specific this should be 'non-self antigens' accompanying infectious agents, might disrupt control of the adaptive immune system resulting in serious pathologies. the etiology of the multiple sclerosis (ms) remains unclear. however, epidemiologic data suggest that exposure to infectious agents may be associated with increased ms risk and progression may be linked to exogenous, bacterially-derived, antigen ...	2016	28008952
multiple cross displacement amplification combined with gold nanoparticle-based lateral flow biosensor for detection of vibrio parahaemolyticus.	vibrio parahaemolyticus (v. parahaemolyticus) is a marine seafood-borne pathogen causing severe illnesses in humans and aquatic animals. in the present study, multiple cross displacement amplification was combined with a lateral flow biosensor (mcda-lfb) to detect the toxr gene of v. parahaemolyticus in dna extracts from pure cultures and spiked oyster homogenates. amplification was carried out at a constant temperature (62°c) for only 30 min, and amplification products were directly applied to ...	2016	28066368
zika virus infection and guillain-barré syndrome in three patients from suriname.	we present three patients from suriname who were diagnosed with guillain-barré syndrome (gbs) during the zika virus (zikv) outbreak in this country. one patient had a positive zikv urine real-time rt-pcr (qrt-pcr) result. the other two patients had a negative zikv urine qrt-pcr but a positive virus neutralization test and presence of igg antibodies against zikv in the serum. considering the evidence of a past zikv infection and absence of evidence for recent infections with the most common prece ...	2016	28066317
high resolution crystal structure of the catalytic domain of mcr-1.	the newly identified mobile colistin resistant gene (mcr-1) rapidly spread among different bacterial strains and confers colistin resistance to its host, which has become a global concern. based on sequence alignment, mcr-1 should be a phosphoethanolamine transferase, members of the yhjw/yjdb/yijp superfamily and catalyze the addition of phosphoethanolamine to lipid a, which needs to be validated experimentally. here we report the first high-resolution crystal structure of the c-terminal catalyt ...	2016	28000749
antimicrobial properties of plant essential oils against human pathogens and their mode of action: an updated review.	a wide range of medicinal and aromatic plants (maps) have been explored for their essential oils in the past few decades. essential oils are complex volatile compounds, synthesized naturally in different plant parts during the process of secondary metabolism. essential oils have great potential in the field of biomedicine as they effectively destroy several bacterial, fungal, and viral pathogens. the presence of different types of aldehydes, phenolics, terpenes, and other antimicrobial compounds ...	2016	28090211
the cytolethal distending toxin produced by nontyphoidal salmonella serotypes javiana, montevideo, oranienburg, and mississippi induces dna damage in a manner similar to that of serotype typhi.	select nontyphoidal salmonella enterica (nts) serotypes were recently found to encode the salmonella cytolethal distending toxin (s-cdt), an important virulence factor for serotype typhi, the causative agent of typhoid fever. using a pcr-based assay, we determined that among 21 nts serotypes causing the majority of food-borne salmonellosis cases in the united states, genes encoding s-cdt are conserved in isolates representing serotypes javiana, montevideo, and oranienburg but that among serotype ...	2016	27999166
comparative genomics of h. pylori and non-pylori helicobacter species to identify new regions associated with its pathogenicity and adaptability.	the genus helicobacter is a group of gram-negative, helical-shaped pathogens consisting of at least 36 bacterial species. helicobacter pylori (h. pylori), infecting more than 50% of the human population, is considered as the major cause of gastritis, peptic ulcer, and gastric cancer. however, the genetic underpinnings of h. pylori that are responsible for its large scale epidemic and gastrointestinal environment adaption within human beings remain unclear. core-pan genome analysis was performed ...	2016	28078297
use of single molecule sequencing for comparative genomics of an environmental and a clinical isolate of clostridium difficile ribotype 078.	how the pathogen clostridium difficile might survive, evolve and be transferred between reservoirs within the natural environment is poorly understood. some ribotypes are found both in clinical and environmental settings. whether these strains are distinct from each another and evolve in the specific environments is not established. the possession of a highly mobile genome has contributed to the genetic diversity and ongoing evolution of c. difficile. interpretations of genetic diversity have be ...	2016	27964731
the capricious nature of bacterial pathogens: phasevarions and vaccine development.	infectious diseases are a leading cause of morbidity and mortality worldwide, and vaccines are one of the most successful and cost-effective tools for disease prevention. one of the key considerations for rational vaccine development is the selection of appropriate antigens. antigens must induce a protective immune response, and this response should be directed to stably expressed antigens so the target microbe can always be recognized by the immune system. antigens with variable expression, due ...	2016	28018352
influence of haem environment on the catalytic properties of the tetrathionate reductase tsda from campylobacter jejuni.	bifunctional dihaem cytochrome c thiosulfate dehydrogenases/tetrathionate reductases (tsda) exhibit different catalytic properties depending on the source organism. in the human food-borne intestinal pathogen campylobacter jejuni, tsda functions as a tetrathionate reductase enabling respiration with tetrathionate as an alternative electron acceptor. in the present study, evidence is provided that cys(138) and met(255) serve as the sixth ligands of haem 1 and haem 2 respectively, in the oxidized ...	2016	27789780
role of recombinant dna technology to improve life.	in the past century, the recombinant dna technology was just an imagination that desirable characteristics can be improved in the living bodies by controlling the expressions of target genes. however, in recent era, this field has demonstrated unique impacts in bringing advancement in human life. by virtue of this technology, crucial proteins required for health problems and dietary purposes can be produced safely, affordably, and sufficiently. this technology has multidisciplinary applications ...	2016	28053975
htra-mediated e-cadherin cleavage is limited to degp and degq homologs expressed by gram-negative pathogens.	the serine proteases htra/degp secreted by the human gastrointestinal pathogens helicobacter pylori (h. pylori) and campylobacter jejuni (c. jejuni) cleave the mammalian cell adhesion protein e-cadherin to open intercellular adhesions. a wide range of bacteria also expresses the htra/degp homologs degq and/or degs, which significantly differ in structure and function.	2016	27931258
complete genome sequence of bacteriophage ma12, which infects both campylobacter jejuni and salmonella enterica serovar enteritidis.	here, we announce the complete genome sequence of salmonella enterica serovar enteritidis (s enteritidis) bacteriophage ma12, a 41-kb chromosome. the strain can infect both campylobacter jejuni (c. jejuni) and s enteritidis and can be used in phage therapy experiments with poultry and poultry meat.	2016	27932636
characterization in helicobacter pylori of a nickel transporter essential for colonization that was acquired during evolution by gastric helicobacter species.	metal acquisition is crucial for all cells and for the virulence of many bacterial pathogens. in particular, nickel is a virulence determinant for the human gastric pathogen helicobacter pylori as it is the cofactor of two enzymes essential for in vivo colonization, urease and a [nife] hydrogenase. to import nickel despite its scarcity in the human body, h. pylori requires efficient uptake mechanisms that are only partially defined. indeed, alternative ways of nickel entry were predicted to exis ...	2016	27923069
genomic insights from whole genome sequencing of four clonal outbreak campylobacter jejuni assessed within the global c. jejuni population.	whole genome sequencing (wgs) is useful for determining clusters of human cases, investigating outbreaks, and defining the population genetics of bacteria. it also provides information about other aspects of bacterial biology, including classical typing results, virulence, and adaptive strategies of the organism. cell culture invasion and protein expression patterns of four related multilocus sequence type 21 (st21) c. jejuni isolates from a significant canadian water-borne outbreak were previou ...	2016	27912729
rapid, sensitive detection of bartonella quintana by loop-mediated isothermal amplification of the groel gene.	trench fever, caused by bartonella quintana, is recognized as a re-emerging and neglected disease. rapid and sensitive detection approaches are urgently required to monitor and help control b. quintana infections. here, loop-mediated isothermal amplification (lamp), which amplifies target dna at a fixed temperature with high sensitivity, specificity and rapidity, was employed to detect b. quintana. thirty-six strains, including 10 b. quintana, 13 other bartonella spp., and 13 other common pathog ...	2016	27916953
heat shock increases conjugation efficiency in clostridium difficile.	clostridium difficile infection has increased in incidence and severity over the past decade, and poses a unique threat to human health. however, genetic manipulation of c. difficile remains in its infancy and the bacterium remains relatively poorly characterised. low-efficiency conjugation is currently the only available method for transfer of plasmid dna into c. difficile. this is practically limiting and has slowed progress in understanding this important pathogen. conjugation efficiency vari ...	2016	27377776
dissecting the interplay between intestinal microbiota and host immunity in health and disease: lessons learned from germfree and gnotobiotic animal models.	this review elaborates the development of germfree and gnotobiotic animal models and their application in the scientific field to unravel mechanisms underlying host-microbe interactions and distinct diseases. strictly germfree animals are raised in isolators and not colonized by any organism at all. the germfree state is continuously maintained by birth, raising, housing and breeding under strict sterile conditions. however, isolator raised germfree mice are exposed to a stressful environment an ...	2016	27980855
draft genome sequences of campylobacter jejuni strains that cause abortion in livestock.	campylobacter jejuni is an intestinal bacterium that can cause abortion in livestock. this publication announces the public release of 15 campylobacter jejuni genome sequences from isolates linked to abortion in livestock. these isolates are part of the 100k pathogen genome project and are from clinical cases at the university of california (uc) davis.	2016	27908990
a dual filtration-based multiplex pcr method for simultaneous detection of viable escherichia coli o157:h7, listeria monocytogenes, and staphylococcus aureus on fresh-cut cantaloupe.	fresh-cut cantaloupe is particularly susceptible to contamination with pathogenic bacteria, such as escherichia coli o157:h7, listeria monocytogenes, and staphylococcus aureus. therefore, development of rapid, yet accurate detection techniques is necessary to ensure food safety. in this study, a multiplex pcr system and propidium monoazide (pma) concentration were optimized to detect all viable pathogens in a single tube. a dual filtration system utilized a filtration membrane with different por ...	2016	27906992
complementation of an aglb mutant of methanococcus maripaludis with heterologous oligosaccharyltransferases.	the oligosaccharyltransferase is the signature enzyme for n-linked glycosylation in all domains of life. in archaea, this enzyme termed aglb, is responsible for transferring lipid carrier-linked glycans to select asparagine residues in a variety of target proteins including archaellins, s-layer proteins and pilins. this study investigated the ability of a variety of aglbs to compensate for the oligosaccharyltransferase activity in methanococcus maripaludis deleted for aglb, using archaellin flab ...	2016	27907170
metagenome phylogenetic profiling of microbial community evolution in a tetrachloroethene-contaminated aquifer responding to enhanced reductive dechlorination protocols.	chlorinated solvent contamination of potable water supplies is a serious problem worldwide. biostimulation protocols can successfully remediate chlorinated solvent contamination through enhanced reductive dechlorination pathways, however the process is poorly understood and sometimes stalls creating a more serious problem. whole metagenome techniques have the potential to reveal details of microbial community changes induced by biostimulation. here we compare the metagenome of a tetrachloroethen ...	2016	27980706
concurrency of guillain-barre syndrome and acute transverse myelitis: a case report and review of literature.	guillain-barré syndrome and acute transverse myelitis manifest as demyelinating diseases of the peripheral and central nervous system. concurrency of these two disorders is rarely documented in literature. a 4-year-old girl presenting with cough, fever, and an impaired walking ability was admitted to hospital. she had no previous complaints in her medical history. a physical examination revealed lack of muscle strength of the lower extremities and deep tendon reflexes. mri could not be carried o ...	2016	28018472
the two-component system arlrs and alterations in metabolism enable staphylococcus aureus to resist calprotectin-induced manganese starvation.	during infection the host imposes manganese and zinc starvation on invading pathogens. despite this, staphylococcus aureus and other successful pathogens remain capable of causing devastating disease. however, how these invaders adapt to host-imposed metal starvation and overcome nutritional immunity remains unknown. we report that arlrs, a global staphylococcal virulence regulator, enhances the ability of s. aureus to grow in the presence of the manganese-and zinc-binding innate immune effector ...	2016	27902777
the 12 gastrointestinal pathogens spectrum of acute infectious diarrhea in a sentinel hospital, shenzhen, china.	acute infectious gastroenteritis is one of the most common diseases among all ages, particularly in developing countries. the pathogen spectrum may differ among different regions and seasons. to investigate the etiology of acute diarrhea in shenzhen, a prospective study was conducted from august 2014 to september 2015. stools from 412 patients with diarrhea (286 of whom were adults) including the general epidemiological information of the patients were collected. the 19 pathogens were detected b ...	2016	27965649
editorial: biofilms from a food microbiology perspective: structures, functions, and control strategies.		2016	27965657
environmental free-living amoebae isolated from soil in khon kaen, thailand, antagonize burkholderia pseudomallei.	presence of burkholderia pseudomallei in soil and water is correlated with endemicity of melioidosis in southeast asia and northern australia. several biological and physico-chemical factors have been shown to influence persistence of b. pseudomallei in the environment of endemic areas. this study was the first to evaluate the interaction of b. pseudomallei with soil amoebae isolated from b. pseudomallei-positive soil site in khon kaen, thailand. four species of amoebae, paravahlkampfia ustiana, ...	2016	27898739
dcite: measuring necessary cladistic information can help you reduce polytomy artefacts in trees.	biologists regularly create phylogenetic trees to better understand the evolutionary origins of their species of interest, and often use genomes as their data source. however, as more and more incomplete genomes are published, in many cases it may not be possible to compute genome-based phylogenetic trees due to large gaps in the assembled sequences. in addition, comparison of complete genomes may not even be desirable due to the presence of horizontally acquired and homologous genes. a decision ...	2016	27898695
the minor flagellin of campylobacter jejuni (flab) confers defensive properties against bacteriophage infection.	a screen of bacteriophages infecting a panel of campylobacter jejuni pt14 gene knock-out mutants identified a role for the minor flagellin encoded by the flab gene, in the defense of the host against cp8unalikevirus bacteriophage cp_f1 infection. inactivation of the flab gene resulted in an increase in the susceptibility of pt14 cultures to infection by cp_f1 and an increase in bacteriophage yields. infection of wild type pt14 with cp_f1 produces turbid plaques in bacterial lawns, from which 78% ...	2016	27965643
azithromycin vs. placebo for the clinical outcome in campylobacter concisus diarrhoea in adults: a randomized, double-blinded, placebo-controlled clinical trial.	campylobacter concisus has been associated with prolonged mild diarrhoea, but investigations regarding the efficacy of antimicrobial treatment have not been reported previously. we initiated a phase 3, single-centre, randomized, double-blinded, placebo-controlled study comparing the efficacy of 500 mg once-daily dose of azithromycin with a 500 mg once-daily dose of placebo for three days, for the treatment of c. concisus diarrhoea in adult patients with a follow-up period of ten days. if symptom ...	2016	27893820
exercise-induced stress behavior, gut-microbiota-brain axis and diet: a systematic review for athletes.	fatigue, mood disturbances, under performance and gastrointestinal distress are common among athletes during training and competition. the psychosocial and physical demands during intense exercise can initiate a stress response activating the sympathetic-adrenomedullary and hypothalamus-pituitary-adrenal (hpa) axes, resulting in the release of stress and catabolic hormones, inflammatory cytokines and microbial molecules. the gut is home to trillions of microorganisms that have fundamental roles ...	2016	27924137
altered intestinal microbiota-host mitochondria crosstalk in new onset crohn's disease.	intestinal microbial dysbiosis is associated with crohn's disease (cd). however, the mechanisms leading to the chronic mucosal inflammation that characterizes this disease remain unclear. in this report, we use systems-level approaches to study the interactions between the gut microbiota and host in new-onset paediatric patients to evaluate causality and mechanisms of disease. we report an altered host proteome in cd patients indicative of impaired mitochondrial functions. in particular, mitocho ...	2016	27876802
beyond antimicrobial resistance: evidence for a distinct role of the acrd efflux pump in salmonella biology.	for over 20 years, bacterial multidrug resistance (mdr) efflux pumps have been studied because of their impact on resistance to antimicrobials. however, critical questions remain, including why produce efflux pumps under non-antimicrobial treatment conditions, and why have multiple pumps if their only purpose is antimicrobial efflux? salmonella spp. possess five efflux pump families, including the resistance-nodulation-division (rnd) efflux pumps. notably, the rnd efflux pump acrd has a unique s ...	2016	27879336