bluuebunny/crossref_metadata_2025 huggingface dataset:
Xenorhabdus ishibashii sp. nov., isolated from the entomopathogenic nematode Steinernema aciari
Authors: Kuwata Ryusei , Qiu Li-hong , Wang Wen , Harada Yuki , Yoshida Mutsuhiro , Kondo Eizo , Yoshiga Toyoshi
Published: August 2012

Gram-negative bacteria of the genus

Xenorhabdus

exhibit a mutualistic association with steinernematid entomopathogenic nematodes and a pathogenic relationship with insects. Here we describe two isolates of the entomopathogenic nematode Steinernema aciari collected from China and Japan. 16S rRNA gene sequence similarity and phylogenetic analysis indicated that the isolates obtained from S. aciari belonged to the genus

Xenorhabdus

. Multilocus sequence analysis based on five universal protein-coding gene sequences revealed that the isolates were closely related to

Xenorhabdus ehlersii

DSM 16337T and

Xenorhabdus griffiniae

ID10T but that they exhibited <97 % sequence similarity with these reference strains, which indicated that the isolates were distinct from previously described species. Based on these genetic differences and several differential phenotypic traits, we propose that the isolates represent a novel species of the genus

Xenorhabdus

, for which we propose the name Xenorhabdus ishibashii sp. nov. The type strain is GDh7T ( = DSM 22670T  = CGMCC 1.9166T).
Species composition, relative abundance and habitat association of small mammals along the altitudinal gradient of Jiren Mountain, Jimma, Ethiopia
Authors: Habtamu Tadesse , Bekele Afework
Published: August 2012

To document the species composition, relative abundance and habitat association of small mammals, wet and dry season surveys were conducted along the altitudinal gradient of Jiren Mountain, Jimma area, Ethiopia. Sherman traps were used to capture small mammals from the six habitats: wetland, mixed plantation, open shrub, eucalyptus plantation, montane grassland and coffee plantation. The 393 trap nights, from the six habitat types, yielded 106 individual small mammals of tweleve species. The trapped rodents were Lophuromys flavopunctatus, Stenocephalemys albipes, Desmomys harringtoni, Mus mahomet, Lemniscomys barbarous, L. striatus, Tachyoryctes splendens, Mastomys natalensis and the insectivores Crocidura fumosa and C. turba. Two species of rodents Hystrix cristata and Helioscuirus gambianus were observed. Lophuromys flavopunctatus and S. albipes contributed 83.8% of the total capture. L. flavopunctatus, S. albipes and D. harringtoni were distributed in all habitats and gradients. T. splendens was captured from montane habitat, while the zebra mice were associated with the lower altitude habitats. Lophuromys flavopunctatus and M. natalensis extended their range deep into the coffee plantation habitats. Uncontrolled vegetation exploitation of the mountains for timber production and fire wood collection are the major threats. Conservation of the area to reduce the anthropogenic pressure is essential.
Evolution of innate and adaptive immune systems in jawless vertebrates
Authors: Kasamatsu Jun
Published: August 2012

Because jawless vertebrates are the most primitive vertebrates, they have been studied to gain understanding of the evolutionary processes that gave rise to the innate and adaptive immune systems in vertebrates. Jawless vertebrates have developed lymphocyte‐like cells that morphologically resemble the T and B cells of jawed vertebrates, but they express variable lymphocyte receptors (VLRs) instead of the T and B cell receptors that specifically recognize antigens in jawed vertebrates. These VLRs act as antigen receptors, diversity being generated in their antigen‐binding sites by assembly of highly diverse leucine‐rich repeat modules. Therefore, jawless vertebrates have developed adaptive immune systems based on the VLRs. Although pattern recognition receptors, including Toll‐like receptors (TLRs) and Rig‐like receptors (RLRs), and their adaptor genes are conserved in jawless vertebrates, some transcription factor and inflammatory cytokine genes in the TLR and RLR pathways are not present. However, like jawed vertebrates, the initiation of adaptive immune responses in jawless vertebrates appears to require prior activation of the innate immune system. These observations imply that the innate immune systems of jawless vertebrates have a unique molecular basis that is distinct from that of jawed vertebrates. Altogether, although the molecular details of the innate and adaptive immune systems differ between jawless and jawed vertebrates, jawless vertebrates have developed versions of these immune systems that are similar to those of jawed vertebrates.
Genetic characterization of swine influenza viruses isolated in Japan between 2009 and 2012
Authors: Matsuu Aya , Uchida Yuko , Takemae Nobuhiro , Mawatari Takahiro , Kasai Yoneyama Shuji , Kasai Tomoe , Nakamura Ryoko , Eto Mariko , Saito Takehiko
Published: August 2012

Eleven swine influenza viruses (SIVs) isolated from pigs in Japanese institutions between 2009 and 2012 were genetically characterized. Seven H1N1 were shown to have originated from A(H1N1)pdm09 viruses. Two H1N2 viruses contained H1 and N2 genes of Japanese H1N2 SIV origin together with internal genes of A(H1N1)pdm09 viruses. Two H3N2 viruses isolated during animal quarantine were identified as triple reassortant H3N2 viruses maintained among pigs in North America. This study shows that A(H1N1)pdm09 viruses and their reassortant strains are already present in domestic pigs in Japan and that novel SIVs are possibly being imported from abroad.
Nitrogen uptake and leaching loss of thirteen temperate grass species under high N loading
Authors: Moir J. L. , Edwards G. R. , Berry L. N.
Published: August 2012

The intensification of grazed pasture systems in New Zealand has resulted in increased nitrate () leaching and associated significant reductions in water quality, resulting from high N loading in the cow urine patch. A glasshouse soil column experiment was conducted at Lincoln University examining the N uptake capacities and leaching losses of sixteen commercial and ‘weed’ pasture grasses, comprising thirteen species. Three dairy cow urine N treatments (N loading rates) were applied in May 2010: 0 (N0), 300 (N300) and 700 (N700) kg N ha−1. Grass was harvested at 21‐d intervals, leachates collected to quantify N leaching losses and root mass measured. Shoot yield, root mass, N uptake and N leaching loss varied significantly between species (P < 0·001) and were strongly driven by N loading rate. The highest yielding species at N700 were Lolium multiflorum ‘Feast 2’ and ‘Tama’ (782 and 743 g DM m−2), while Festuca arundinacea ‘Flecha’ and Lolium perenne ‘Alto' were lowest yielding (375 and 419 g DM m−2). Plant N uptake and root mass followed a similar trend, and only moderate increases in total plant N uptake were observed for most species when urine N application rate was increased from N300 to N700. N leaching loss was highest at N700 for F. arundinacea ‘Flecha’ (378 kg N ha−1) and lowest for L. multiflorum ‘Feast 2’ and ‘Tama’ (134 and 130 kg N ha−1). Strong negative linear relationships were observed between N leaching loss, plant N uptake and root mass. The results indicate that species such as L. multiflorum may play a critical role in reducing pasture N leaching losses, while traditionally sown L. perenne, and also F. arundinacea, may be less suitable.
Identification of a new HLA‐G allele, HLA‐G*01:18, in a Canadian Caucasian individual
Authors: Roger J. , Faucher M.‐C. , Roger M.
Published: August 2012

We identified a novel HLA‐G allele with a protein‐modifying mutation in a Canadian Caucasian Individual.
Gene expression profiling demonstrates differential expression of osteopontin in follicular thyroid carcinomas compared to normal thyroid tissue in dogs
Authors: Metivier K. S. , Deitz K. , Xu W. W. , Conzemius M. , Wilke V. L.
Published: August 2012

Follicular thyroid carcinoma (FTC) is an aggressive tumour in dogs with little known about its molecular pathogenesis. The overall goal of this study was to examine FTC and normal thyroid tissue gene expression. Microarray analysis was performed on a pilot group of five FTC‐affected dogs and four healthy dogs, and then osteopontin validated with quantitative polymerase chain reaction (PCR) and immunohistochemistry (IHC) of thyroid tissue from non‐invasive FTC, invasive FTC and healthy dogs. On microarray analysis, 489 transcripts were differentially expressed between FTC and normal thyroid: 242 transcripts were down‐regulated and 247 were up‐regulated. Osteopontin expression was markedly increased in tumour tissue compared to normal thyroid tissue. Quantitative PCR and IHC confirmed differential expression of osteopontin in both tumour types (invasive and non‐invasive) compared to normal thyroid tissue. There is justification for further investigation of osteopontin as a potential molecular marker for screening and monitoring of canine FTC.
Discovery of HLA‐DRB1*03:20 allele in a Taiwanese volunteer hematopoietic stem cell donor and the probable HLA‐A, ‐B, ‐C and ‐DRB1 haplotype in association with DRB1*03:20
Authors: Yang K. L. , Lee S. K. , Yang S. Y. , Kao R. H. , Lin C. L. , Lin P. Y.
Published: August 2012

The allele HLA‐DRB1*03:20, a variant of DRB1*03, was first reported to the IMGT HLA database in April 2001 without indication on the ethnicity of the blood donor (Cell ID: HC 125775). We found a Taiwanese volunteer hematopoietic stem cell donor carries DRB1*03:20 by a sequence‐based typing (SBT) method. The DNA sequence of DRB1*03:20 is identical to the sequence of DRB1*03:01:01 in exon 2, except a nucleotide substitution at position 341(T→C) (GTT→GCT at codon 85). The nucleotide replacement produced an amino acid variation at residue 85 (V→A). We hypothesize that DRB1*03:20 was probably derived from DRB1*03:01:01 via a nucleotide point mutation event. The probable HLA haplotype in association with DRB1*03:20 was deduced as A*11:02‐B*58:01‐C*07:02‐DRB1*03:20. We here report the Taiwanese/Chinese ethnicity of DRB1*03:20.
Importance of Riboflavin Kinase in the Pathogenesis of Stroke
Authors: Zou Ying‐Xin , Zhang Xiu‐Hua , Su Feng‐Yun , Liu Xia
Published: August 2012

Aims

To explore risk factors for stroke independent of hypertension and the relationship between riboflavin kinase (RFK) and stroke.

Methods

Gene expression profiling in the brains of spontaneously hypertensive rats (SHR) and stroke‐prone spontaneously hypertensive rats (SHRSP) was comparatively analyzed by gene chips. The differentially expressed gene RFK was further verified by q‐PCR and Western blot. The protective role of RFK‐regulated flavins (including riboflavin, flavin mononucleotide, and flavin adenine dinucleotide) in stroke was observed in middle cerebral artery occlusion (MCAO) mice. Influence of flavins on apoptosis and death in oxygen and glucose deprivation (OGD)‐treated neurons was examined by flow cytometry. Bax and Bcl‐2 proteins were detected by Western blot.

Results

Of the 76 differentially expressed genes, 41 genes were upregulated, and 35 genes were downregulated in SHRSP as compared with SHR. RFK was significantly downregulated in SHRSP. Flavins markedly decreased infarct area in MCAO mice, inhibited apoptosis and death in OGD‐treated neurons, and decreased Bax protein expression.

Conclusions

Physiological downregulation of RFK may be a new potential risk factor for stroke, which probably affects the absorbance and utility of riboflavin and further destroys the protective effect of flavins on stroke. RFK might act as a therapeutic target for stroke.
Emerging Hazelnut Cultivation and the Severe Threat of Bacterial Blight in Chile
Authors: Lamichhane Jay Ram , Grau Pablo , Varvaro Leonardo
Published: August 2012

Severe attacks of bacterial blight were observed on young plants throughout the hazelnut growing areas in Chile. The incidence of the disease in nurseries and fields ranged from 60–90%. The causal agent was identified as Xanthomonas arboricola pv. corylina, based on phenotypic and genetic tests.
Acute Gastrointestinal Infection Induces Long-Lived Microbiota-Specific T Cell Responses
Authors: Hand Timothy W. , Dos Santos Liliane M. , Bouladoux Nicolas , Molloy Michael J. , Pagán Antonio J. , Pepper Marion , Maynard Craig L. , Elson Charles O. , Belkaid Yasmine
Published: August 2012

Recognizing Escaped Commensals

In order to coexist peacefully, the billions of bacteria in our gut and our immune system have reached a détente. An intestinal mucosal firewall exists, so bacteria remain localized to the gut, where the immune system is tightly regulated so that these bacteria are tolerated. Enteric infections, however, lead to a breach in this mucosal firewall, resulting in exposure of the peripheral immune system to the intestinal bacterial contents. What is the result? Using oral
Toxoplasma gondii
infection in mice,

Hand
et al.

(p.
1553
, published online 23 August) show that, besides the
T. gondii
–specific T cell response, a commensal bacteria–specific T cell response is elicited. The CD4
+
T cell–specific response was tracked to a commensal-derived flagellin, and these T cells expanded after
T. gondii
infection and formed long-lived memory cells able to respond to subsequent challenges. Thus, enteric infections can lead to the formation of commensal bacteria–specific, long-lived memory T cells that reside throughout the body—which may play a role in intestinal pathologies such as inflammatory bowel disease.
Molecular Mechanics of Cardiac Myosin-Binding Protein C in Native Thick Filaments
Authors: Previs M. J. , Previs S. Beck , Gulick J. , Robbins J. , Warshaw D. M.
Published: August 2012

Understanding a Broken Heart

Cardiac myosin-binding protein C (cMyBP-C) is a thick filament–associated sarcomeric protein that modulates cardiac contractility in a phosphorylation-dependent manner; mutations in the
MYBC3
gene are the leading cause of hypertrophic cardiomyopathy.

Previs
et al.

(p.
1215
, published online 23 August; see the Perspective by

Burghardt and Ajtai

) have isolated native myosin thick filaments from transgenic mouse hearts, which retained the spatial distribution of cMyBP-C in the thick filament. Imaging of a single actin filament being propelled along the thick filament showed that the N-terminal 29-kD domain of cMyBP-C slows actomyosin motion in parts of the thick filament corresponding to the C-zones in which the thick filaments are cross-bridged. This effect on actomyosin contractility was tuned by graded phosphorylation of four serines adjacent to the 29-kD domain. The findings may explain the appearance of a cMyBP-C fragment in the serum of patients with cardiac ischemia and why cMyBP-C haploinsufficiency associated with cardiomyopathy patients might trigger a hypertrophic response.
Genome Sequencing Identifies a Basis for Everolimus Sensitivity
Authors: Iyer Gopa , Hanrahan Aphrothiti J. , Milowsky Matthew I. , Al-Ahmadie Hikmat , Scott Sasinya N. , Janakiraman Manickam , Pirun Mono , Sander Chris , Socci Nicholas D. , Ostrovnaya Irina , Viale Agnes , Heguy Adriana , Peng Luke , Chan Timothy A. , Bochner Bernard , Bajorin Dean F. , Berger Michael F. , Taylor Barry S. , Solit David B.
Published: August 2012

Tumor genome sequencing reveals the molecular basis of a patient’s unexpected and dramatic response to a cancer drug.
Escherichia coli Nissle 1917 Targets and Restrains Mouse B16 Melanoma and 4T1 Breast Tumors through Expression of Azurin Protein
Authors: Zhang Yunlei , Zhang Youming , Xia Liqiu , Zhang Xiangli , Ding Xuezhi , Yan Fu , Wu Feng
Published: August 2012

Many studies have demonstrated that intravenously administered bacteria can target and proliferate in solid tumors and then quickly be released from other organs. Here, we employed the tumor-targeting property of
Escherichia coli
Nissle 1917 to inhibit mouse B16 melanoma and 4T1 breast tumors through the expression of azurin protein. For this purpose, recombinant azurin-expressing
E. coli
Nissle 1917 was developed. The levels of
in vitro
and
in vivo
azurin secretion in the engineered bacterium were determined by immunochemistry. Our results demonstrated that B16 melanoma and orthotopic 4T1 breast tumor growth were remarkably restrained and pulmonary metastasis was prevented in immunocompetent mice. It is worth noting that this therapeutic effect partially resulted from the antitumor activity of neutrophils and lymphocytes due to inflammatory responses caused by bacterial infections. No toxicity was observed in the animal during the experiments. This study indicates that
E. coli
Nissle 1917 could be a potential carrier to deliver antitumor drugs effectively for cancer therapy.
Changes in the Gut Microbiome of the Sea Lamprey during Metamorphosis
Authors: Tetlock Amanda , Yost Christopher K. , Stavrinides John , Manzon Richard G.
Published: August 2012

Vertebrate metamorphosis is often marked by dramatic morphological and physiological changes of the alimentary tract, along with major shifts in diet following development from larva to adult. Little is known about how these developmental changes impact the gut microbiome of the host organism. The metamorphosis of the sea lamprey (
Petromyzon marinus
) from a sedentary filter-feeding larva to a free-swimming sanguivorous parasite is characterized by major physiological and morphological changes to all organ systems. The transformation of the alimentary canal includes closure of the larval esophagus and the physical isolation of the pharynx from the remainder of the gut, which results in a nonfeeding period that can last up to 8 months. To determine how the gut microbiome is affected by metamorphosis, the microbial communities of feeding and nonfeeding larval and parasitic sea lamprey were surveyed using both culture-dependent and -independent methods. Our results show that the gut of the filter-feeding larva contains a greater diversity of bacteria than that of the blood-feeding parasite, with the parasite gut being dominated by
Aeromonas
and, to a lesser extent,
Citrobacter
and
Shewanella
. Phylogenetic analysis of the culturable
Aeromonas
from both the larval and parasitic gut revealed that at least five distinct species were represented. Phenotypic characterization of these isolates revealed that over half were capable of sheep red blood cell hemolysis, but all were capable of trout red blood cell hemolysis. This suggests that the enrichment of
Aeromonas
that accompanies metamorphosis is likely related to the sanguivorous lifestyle of the parasitic sea lamprey.
Prevalence and Population Structure of Vibrio vulnificus on Fishes from the Northern Gulf of Mexico
Authors: Tao Zhen , Larsen Andrea M. , Bullard Stephen A. , Wright Anita C. , Arias Covadonga R.
Published: August 2012

The prevalence of
Vibrio vulnificus
on the external surfaces of fish from the northern Gulf of Mexico was determined in this study. A collection of 242 fish comprising 28 species was analyzed during the course of 12 sampling trips over a 16-month period. The prevalence of
V. vulnificus
was 37% but increased up to 69% in summer. A positive correlation was found between the percentages of
V. vulnificus
-positive fish and water temperatures, while salinity and
V. vulnificus
-positive fish prevalence were inversely correlated. A general lineal model (percent
V. vulnificus
-positive fish = 0.5930 − 0.02818 × salinity + 0.01406 × water temperature) was applied to best fit the data. Analysis of the population structure was carried out using 244 isolates recovered from fish. Ascription to 16S rRNA gene types indicated that 157 isolates were type A (62%), 72 (29%) were type B, and 22 (9%) were type AB. The percentage of type B isolates, considered to have greater virulence potential, was higher than that previously reported in oyster samples from the northern Gulf of Mexico. Amplified fragment length polymorphism (AFLP) was used to resolve the genetic diversity within the species. One hundred twenty-one unique AFLP profiles were found among all analyzed isolates, resulting in a calculated Simpson's index of diversity of 0.991. AFLP profiles were not grouped on the basis of collection date, fish species, temperature, or salinity, but isolates were clustered into two main groups that correlated precisely with 16S rRNA gene type. The population of
V. vulnificus
associated with fishes from the northern Gulf of Mexico is heterogeneous and includes strains of great virulence potential.
Identification of Cj1051c as a Major Determinant for the Restriction Barrier of Campylobacter jejuni Strain NCTC11168
Authors: Holt Jeffrey P. , Grant Andrew J. , Coward Christopher , Maskell Duncan J. , Quinlan Jennifer J.
Published: August 2012

Campylobacter jejuniis a leading cause of human diarrheal illness in the world, and research on it has benefitted greatly by the completion of several genome sequences and the development of molecular biology tools. However, many hurdles remain for a full understanding of this unique bacterial pathogen. One of the most commonly used strains for genetic work withC. jejuniis NCTC11168. While this strain is readily transformable with DNA for genomic recombination, transformation with plasmids is problematic. In this study, we have identified a determinant of this to becj1051c, predicted to encode a restriction-modification type IIG enzyme. Knockout mutagenesis of this gene resulted in a strain with a 1,000-fold-enhanced transformation efficiency with a plasmid purified from aC. jejunihost. Additionally, this mutation conferred the ability to be transformed by plasmids isolated from anEscherichia colihost. Sequence analysis suggested a high level of variability of the specificity domain between strains and that this gene may be subject to phase variation. We provide evidence thatcj1051cis active in NCTC11168 and behaves as expected for a type IIG enzyme. The identification of this determinant provides a greater understanding of the molecular biology ofC. jejunias well as a tool for plasmid work with strain NCTC11168.
Contribution of Spores to the Ability of Clostridium difficile To Adhere to Surfaces
Authors: Joshi Lovleen Tina , Phillips Daniel S. , Williams Catrin F. , Alyousef Abdullah , Baillie Les
Published: August 2012

Clostridium difficile
is the commonest cause of hospital-acquired infection in the United Kingdom. We characterized the abilities of 21 clinical isolates to form spores; to adhere to inorganic and organic surfaces, including stainless steel and human adenocarcinoma cells; and to germinate. The composition of culture media had a significant effect on spore formation, as significantly more spores were produced in brain heart infusion broth (Student's
t
test;
P
= 0.018). The spore surface relative hydrophobicity (RH) varied markedly (14 to 77%) and was correlated with the ability to adhere to stainless steel. We observed no correlation between the ribotype and the ability to adhere to steel. When the binding of hydrophobic (DS1813; ribotype 027; RH, 77%) and hydrophilic (DS1748; ribotype 002; RH, 14%) spores to human gut epithelial cells at different stages of cell development was examined, DS1813 spores adhered more strongly, suggesting the presence of surface properties that aid attachment to human cells. Electron microscopy studies revealed the presence of an exosporium surrounding DS1813 spores that was absent from spores of DS1748. Finally, the ability of spores to germinate was found to be strain and medium dependent. While the significance of these findings to the disease process has yet to be determined, this study has highlighted the importance of analyzing multiple isolates when attempting to characterize the behavior of a bacterial species.
Diversity, Physiology, and Niche Differentiation of Ammonia-Oxidizing Archaea
Authors: Hatzenpichler Roland
Published: August 2012

Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, has been suggested to have been a central part of the global biogeochemical nitrogen cycle since the oxygenation of Earth. The cultivation of several ammonia-oxidizing archaea (AOA) as well as the discovery that archaeal ammonia monooxygenase (
amo
)-like gene sequences are nearly ubiquitously distributed in the environment and outnumber their bacterial counterparts in many habitats fundamentally revised our understanding of nitrification. Surprising insights into the physiological distinctiveness of AOA are mirrored by the recognition of the phylogenetic uniqueness of these microbes, which fall within a novel archaeal phylum now known as
Thaumarchaeota
. The relative importance of AOA in nitrification, compared to ammonia-oxidizing bacteria (AOB), is still under debate. This minireview provides a synopsis of our current knowledge of the diversity and physiology of AOA, the factors controlling their ecology, and their role in carbon cycling as well as their potential involvement in the production of the greenhouse gas nitrous oxide. It emphasizes the importance of activity-based analyses in AOA studies and formulates priorities for future research.
Peptide-Guided Surface-Enhanced Raman Scattering Probes for Localized Cell Composition Analysis
Authors: Athamneh Ahmad I. M. , Senger Ryan S.
Published: August 2012

The ability to control the localization of surface-enhanced Raman scattering (SERS) nanoparticle probes in bacterial cells is critical to the development of analytical techniques that can nondestructively determine cell composition and phenotype. Here, selective localization of SERS probes was achieved at the outer bacterial membrane by using silver nanoparticles functionalized with synthetic hydrophobic peptides.
Enzymatic Glycosylation of Nonbenzoquinone Geldanamycin Analogs via Bacillus UDP-Glycosyltransferase
Authors: Wu Cheng-Zhu , Jang Jae-Hyuk , Woo Mihee , Ahn Jong Seog , Kim Joong Su , Hong Young-Soo
Published: August 2012

Geldanamycin (GM) is a naturally occurring anticancer agent isolated from several strains of
Streptomyces hygroscopicus
. However, its potential clinical utility is compromised by its severe toxicity and poor water solubility. For this reason, considerable efforts are under way to make new derivatives that have both good clinical efficacy and high water solubility. On the other hand, glycosylation is often a step that improves the water solubility and/or biological activity in many natural products of biosynthesis. Here, we report the facile production of glucose-conjugated nonbenzoquinone GM analogs using the
Bacillus
UDP-glycosyltransferase BL-C. Five aglycon substrates containing nonbenzoquinone aromatic rings were chosen to validate the
in vitro
glycosylation reaction. Putative glucoside compounds were determined through the presence of a product peak(s) and were also verified using LC/MS analyses. Further, the chemical structures of new glucoside compounds 6 and 7 were elucidated using spectroscopy data. These glucoside compounds showed a dramatic improvement in water solubility compared with that of the original aglycon, nonbenzoquinone GM.
Degradation of the Twin-Arginine Translocation Substrate YwbN by Extracytoplasmic Proteases of Bacillus subtilis
Authors: Krishnappa Laxmi , Monteferrante Carmine G. , van Dijl Jan Maarten
Published: August 2012

Bacterial twin-arginine translocases can export fully folded proteins from the cytoplasm. Such proteins are usually resistant to proteolysis. Here we show that multiple extracellular proteases degrade the
B. subtilis
Tat substrate YwbN. This suggests either that secreted YwbN is not fully folded or that folded YwbN exposes protease cleavage sites.
Next-Generation Sequencing of Microbial Communities in the Athabasca River and Its Tributaries in Relation to Oil Sands Mining Activities
Authors: Yergeau Etienne , Lawrence John R. , Sanschagrin Sylvie , Waiser Marley J. , Korber Darren R. , Greer Charles W.
Published: August 2012

The Athabasca oil sands deposit is the largest reservoir of crude bitumen in the world. Recently, the soaring demand for oil and the availability of modern bitumen extraction technology have heightened exploitation of this reservoir and the potential unintended consequences of pollution in the Athabasca River. The main objective of the present study was to evaluate the potential impacts of oil sands mining on neighboring aquatic microbial community structure. Microbial communities were sampled from sediments in the Athabasca River and its tributaries as well as in oil sands tailings ponds. Bacterial and archaeal 16S rRNA genes were amplified and sequenced using next-generation sequencing technology (454 and Ion Torrent). Sediments were also analyzed for a variety of chemical and physical characteristics. Microbial communities in the fine tailings of the tailings ponds were strikingly distinct from those in the Athabasca River and tributary sediments. Microbial communities in sediments taken close to tailings ponds were more similar to those in the fine tailings of the tailings ponds than to the ones from sediments further away. Additionally, bacterial diversity was significantly lower in tailings pond sediments. Several taxonomic groups of
Bacteria
and
Archaea
showed significant correlations with the concentrations of different contaminants, highlighting their potential as bioindicators. We also extensively validated Ion Torrent sequencing in the context of environmental studies by comparing Ion Torrent and 454 data sets and by analyzing control samples.
Unveiling the Expression Characteristics of IspC, a Cell Wall-Associated Peptidoglycan Hydrolase in Listeria monocytogenes, during Growth under Stress Conditions
Authors: Ronholm Jennifer , Cao Xudong , Lin Min
Published: August 2012

Listeria monocytogenes
serotype 4b is a food-borne pathogen of public health concern, since it accounts for approximately 40% of human listeriosis cases. We have recently identified IspC, a surface-localized peptidoglycan hydrolase, as the antigen recognized by a number of monoclonal antibodies (MAbs) produced against a serotype 4b strain for diagnostic applications. To determine whether IspC, which is well conserved among various serotype 4b strains, is a useful diagnostic marker in antibody-based methods, we assessed the expression of IspC in
L. monocytogenes
cultured under normal and stress conditions. A functional promoter directing the transcription of the
ispC
gene was identified upstream of the
ispC
open reading frame by constructing a promoterless
lacZ
gene fusion with the putative
ispC
promoter region and by 5′ rapid amplification of cDNA ends analysis. Using both the
lacZ
reporter gene system and immunofluorescent staining with an IspC-specific MAb, we provide evidence that IspC is expressed on the cell surface in all growth conditions tested (temperature, osmotic stress, pH, ethanol, oxidative stress, anaerobic conditions, carbon source, and type of growth media) that allow for cellular division, although the level of
ispC
gene expression varies. These results demonstrated the usefulness of IspC as an excellent diagnostic marker for the serotype 4b strains and imply that IspC, in conjunction with specific MAbs, can be targeted for detection and isolation of
L. monocytogenes
serotype 4b strains directly from food, environmental, and clinical samples with minimal or no need for culture enrichment.
Molecular Characterization of Fluoroquinolone-Resistant Aeromonas spp. Isolated from Imported Shrimp
Authors: Shakir Zakiya , Khan Saeed , Sung Kidon , Khare Sangeeta , Khan Ashraf , Steele Roger , Nawaz Mohamed
Published: August 2012

Sixty-three nalidixic acid-resistant
Aeromonas
sp. isolates were obtained from imported shrimp. Phylogenetic analysis of
gyrB
sequences indicated that 18 were
A. enteropelogenes
, 26 were
A. caviae
, and 19 were
A. sobria
. Double missense mutations in the quinolone resistance-determining region (QRDR) of
gyrA
at codon 83 (Ser→Val/Ile) and codon 92 (Leu→Met) coupled with a point mutation of
parC
at codon 80 (Ser→Ile/Phe) conferred high levels of quinolone resistance in the isolates. A majority of
A. enteropelogenes
and
A. caviae
strains harbored toxin genes, whereas only a few
A. sobria
strains harbored these genes. The fluoroquinolone-resistant
Aeromonas
spp. exhibited higher cytotoxicity than fluoroquinolone-sensitive, virulent
Aeromonas
spp. to rat epithelial cells.
Genomic and Transcriptomic Studies of an RDX (Hexahydro-1,3,5-Trinitro-1,3,5-Triazine)-Degrading Actinobacterium
Authors: Chen Hao-Ping , Zhu Song-Hua , Casabon Israël , Hallam Steven J. , Crocker Fiona H. , Mohn William W. , Indest Karl J. , Eltis Lindsay D.
Published: August 2012

Whole-genome sequencing, transcriptomic analyses, and metabolic reconstruction were used to investigate
Gordonia
sp. strain KTR9's ability to catabolize a range of compounds, including explosives and steroids. Aspects of this mycolic acid-containing actinobacterium's catabolic potential were experimentally verified and compared with those of rhodococci and mycobacteria.
Iterative Combinatorial Mutagenesis as an Effective Strategy for Generation of Deacetoxycephalosporin C Synthase with Improved Activity toward Penicillin G
Authors: Ji Junjie , Fan Keqiang , Tian Xiuyun , Zhang Xia , Zhang Yuxiu , Yang Keqian
Published: August 2012

An iterative combinatorial mutagenesis (ICM) strategy was used to engineer deacetoxycephalosporin C synthase of
Streptomyces clavuligerus
(scDAOCS) for improved activity toward penicillin G. Seven mutational sites were repeatedly combined onto a starter mutant (C155Y Y184H V275I C281Y) of scDAOCS. Eleven improved combinatorial mutants were identified from 24 mutants in four rounds of ICM.
Survival and Germination of Bacillus cereus Spores without Outgrowth or Enterotoxin Production during
In Vitro
Simulation of Gastrointestinal Transit
Authors: Ceuppens Siele , Uyttendaele Mieke , Drieskens Katrien , Heyndrickx Marc , Rajkovic Andreja , Boon Nico , Van de Wiele Tom
Published: August 2012

To study the gastrointestinal survival and enterotoxin production of the food-borne pathogen
Bacillus cereus
, an
in vitro
simulation experiment was developed to mimic gastrointestinal passage in 5 phases: (i) the mouth, (ii) the stomach, with gradual pH decrease and fractional emptying, (iii) the duodenum, with high concentrations of bile and digestive enzymes, (iv) dialysis to ensure bile reabsorption, and (v) the ileum, with competing human intestinal bacteria. Four different
B. cereus
strains were cultivated and sporulated in mashed potato medium to obtain an inoculum of 7.0 log spores/ml. The spores showed survival and germination during the
in vitro
simulation of gastrointestinal passage, but vegetative outgrowth of the spores was suppressed by the intestinal bacteria during the final ileum phase. No bacterial proliferation or enterotoxin production was observed, despite the high inoculum levels. Little strain variability was observed: except for the psychrotrophic food isolate, the spores of all strains survived well throughout the gastrointestinal passage. The
in vitro
simulation experiments investigated the survival and enterotoxin production of
B. cereus
in the gastrointestinal lumen. The results obtained support the hypothesis that localized interaction of
B. cereus
with the host's epithelium is required for diarrheal food poisoning.
Versatility in Corrinoid Salvaging and Remodeling Pathways Supports Corrinoid-Dependent Metabolism in Dehalococcoides mccartyi
Authors: Yi Shan , Seth Erica C. , Men Yu-Jie , Stabler Sally P. , Allen Robert H. , Alvarez-Cohen Lisa , Taga Michiko E.
Published: August 2012

Corrinoids are cobalt-containing molecules that function as enzyme cofactors in a wide variety of organisms but are produced solely by a subset of prokaryotes. Specific corrinoids are identified by the structure of their axial ligands. The lower axial ligand of a corrinoid can be a benzimidazole, purine, or phenolic compound. Though it is known that many organisms obtain corrinoids from the environment, the variety of corrinoids that can serve as cofactors for any one organism is largely unstudied. Here, we examine the range of corrinoids that function as cofactors for corrinoid-dependent metabolism inDehalococcoides mccartyistrain 195.Dehalococcoidesbacteria play an important role in the bioremediation of chlorinated solvents in the environment because of their unique ability to convert the common groundwater contaminants perchloroethene and trichloroethene to the innocuous end product ethene. All isolatedD. mccartyistrains require exogenous corrinoids such as vitamin B12for growth. However, like many other corrinoid-dependent bacteria, none of the well-characterizedD. mccartyistrains has been shown to be capable of synthesizing corrinoidsde novo. In this study, we investigate the ability ofD. mccartyistrain 195 to use specific corrinoids, as well as its ability to modify imported corrinoids to a functional form. We show that strain 195 can use only specific corrinoids containing benzimidazole lower ligands but is capable of remodeling other corrinoids by lower ligand replacement when provided a functional benzimidazole base. This study of corrinoid utilization and modification byD. mccartyiprovides insight into the array of strategies that microorganisms employ in acquiring essential nutrients from the environment.
Heat Resistance and Salt Hypersensitivity in Lactococcus lactis Due to Spontaneous Mutation of
llmg_1816
(
gdpP
) Induced by High-Temperature Growth
Authors: Smith William M. , Pham Thi Huong , Lei Lin , Dou Junchao , Soomro Aijaz H. , Beatson Scott A. , Dykes Gary A. , Turner Mark S.
Published: August 2012

During construction of several gene deletion mutants in
Lactococcus lactis
MG1363 which involved a high-temperature (37.5°C) incubation step, additional spontaneous mutations were observed which resulted in stable heat resistance and in some cases salt-hypersensitive phenotypes. Whole-genome sequencing of one strain which was both heat resistant and salt hypersensitive, followed by PCR and sequencing of four other mutants which shared these phenotypes, revealed independent mutations in
llmg_1816
in all cases. This gene encodes a membrane-bound stress signaling protein of the GdpP family, members of which exhibit cyclic dimeric AMP (c-di-AMP)-specific phosphodiesterase activity. Mutations were predicted to lead to single amino acid substitutions or protein truncations. An independent
llmg_1816
mutant (Δ1816), created using a suicide vector, also displayed heat resistance and salt hypersensitivity phenotypes which could be restored to wild-type levels following plasmid excision.
L. lactis
Δ1816 also displayed improved growth in response to sublethal concentrations of penicillin G. High-temperature incubation of a wild-type industrial
L. lactis
strain also resulted in spontaneous mutation of
llmg_1816
and heat-resistant and salt-hypersensitive phenotypes, suggesting that this is not a strain-specific phenomenon and that it is independent of a plasmid integration event. Acidification of milk by the
llmg_1816
-altered strain was inhibited by lower salt concentrations than the parent strain. This study demonstrates that spontaneous mutations can occur during high-temperature growth of
L. lactis
and that inactivation of
llmg_1816
leads to temperature resistance and salt hypersensitivity.
Functional and Physical Interactions among Saccharomyces cerevisiae α-Factor Receptors
Authors: Gehret Austin U. , Connelly Sara M. , Dumont Mark E.
Published: August 2012

The α-factor receptor Ste2p is a G protein-coupled receptor (GPCR) expressed on the surface of
MAT
a
haploid cells of the yeast
Saccharomyces cerevisiae
. Binding of α-factor to Ste2p results in activation of a heterotrimeric G protein and of the pheromone response pathway. Functional interactions between α-factor receptors, such as dominant-negative effects and recessive behavior of constitutive and hypersensitive mutant receptors, have been reported previously. We show here that dominant-negative effects of mutant receptors persist over a wide range of ratios of the abundances of G protein to receptor and that such effects are not blocked by covalent fusion of G protein α subunits to normal receptors. In addition, we detected dominant effects of mutant C-terminally truncated receptors, which had not been previously reported to act in a dominant manner. Furthermore, coexpression of C-terminally truncated receptors with constitutively active mutant receptors results in enhancement of constitutive signaling. Together with previous evidence for oligomerization of Ste2p receptors, these results are consistent with the idea that functional interactions between coexpressed receptors arise from physical interactions between them rather than from competition for limiting downstream components, such as G proteins.
Gain-of-Function Mutations in
UPC2
Are a Frequent Cause of
ERG11
Upregulation in Azole-Resistant Clinical Isolates of Candida albicans
Authors: Flowers Stephanie A. , Barker Katherine S. , Berkow Elizabeth L. , Toner Geoffrey , Chadwick Sean G. , Gygax Scott E. , Morschhäuser Joachim , Rogers P. David
Published: August 2012

In
Candida albicans
, Upc2 is a zinc-cluster transcription factor that targets genes, including those of the ergosterol biosynthesis pathway. To date, three documented
UPC2
gain-of-function (GOF) mutations have been recovered from fluconazole-resistant clinical isolates that contribute to an increase in
ERG11
expression and decreased fluconazole susceptibility. In a group of 63 isolates with reduced susceptibility to fluconazole, we found that 47 overexpressed
ERG11
by at least 2-fold over the average expression levels in 3 unrelated fluconazole-susceptible strains. Of those 47 isolates, 29 contained a mutation in
UPC2
, whereas the remaining 18 isolates did not. Among the isolates containing mutations in
UPC2
, we recovered eight distinct mutations resulting in putative single amino acid substitutions: G648D, G648S, A643T, A643V, Y642F, G304R, A646V, and W478C. Seven of these resulted in increased
ERG11
expression, increased cellular ergosterol, and decreased susceptibility to fluconazole compared to the results for the wild-type strain. Genome-wide transcriptional analysis was performed for the four strongest Upc2 amino acid substitutions (A643V, G648D, G648S, and Y642F). Genes commonly upregulated by all four mutations included those involved in ergosterol biosynthesis, in oxidoreductase activity, the major facilitator efflux pump encoded by the
MDR1
gene, and the uncharacterized ATP binding cassette transporter
CDR11
. These findings demonstrate that gain-of-function mutations in
UPC2
are more prevalent among clinical isolates than previously thought and make a significant contribution to azole antifungal resistance, but the findings do not account for
ERG11
overexpression in all such isolates of
C. albicans
.
The “Finger,” a Unique Multicellular Morphology of Candida albicans Induced by CO
2
and Dependent upon the Ras1-Cyclic AMP Pathway
Authors: Daniels Karla J. , Pujol Claude , Srikantha Thyagarajan , Soll David R.
Published: August 2012

Most experiments exploring the basic biology of pathogenic microbes are performed
in vitro
under conditions that do not usually mimic those of their host niche. Hence, developmental programs initiated by specific host cues may be missed
in vitro
. We have tested the effects of growing low-density agar cultures of the yeast pathogen
Candida albicans
in concentrations of CO
2
found in the gastrointestinal tract. It is demonstrated that in physiological concentrations of CO
2
at 37°C, yeast cells form a heretofore undescribed multicellular “finger” morphology distinct from a previously described stalk-like structure induced by high doses of UV irradiation that kills more than 99.99% of cells. The finger extends aerially, is uniform in diameter, and is visible to the naked eye, attaining lengths of 3 mm. It is composed of a basal yeast cell monolayer adhering to a semispherical crater formed in the agar and connected to a basal bulb of yeast cells at a fragile interface. The bulb extends into the long shaft. We propose that a single, centrally located hypha extending the length of the shaft forms buds at compartment junctions that serve as the source of the yeast cells in the shaft. A mutational analysis reveals finger formation is dependent upon the pathway Ras1→Cdc35→cyclic AMP (cAMP) (PDE2—|)→Tpk2→Tec1. Because of the mechanically fragile interface and the compactness of bulb and shaft, we suggest that the finger may function as a multicellular dispersal mechanism produced in host niches containing high levels of CO
2
.
PAS Domain Residues and Prosthetic Group Involved in BdlA-Dependent Dispersion Response by Pseudomonas aeruginosa Biofilms
Authors: Petrova Olga E. , Sauer Karin
Published: August 2012

Biofilm dispersion by
Pseudomonas aeruginosa
in response to environmental cues is dependent on the cytoplasmic BdlA protein harboring two sensory PAS domains and a chemoreceptor domain, TarH. The closest known and previously characterized BdlA homolog is the flavin adenine dinucleotide (FAD)-binding Aer, the redox potential sensor and aerotaxis transducer in
Escherichia coli
. Here, we made use of alanine replacement mutagenesis of the BdlA PAS domain residues previously demonstrated to be essential for aerotaxis in Aer to determine whether BdlA is a potential sensory protein. Five substitutions (D14A, N23A, W60A, I109A, and W182A) resulted in a null phenotype for dispersion. One protein, the BdlA protein with the G31A mutation (BdlA-G31A), transmitted a constant signal-on bias as it rendered
P. aeruginosa
biofilms hyperdispersive. The hyperdispersive phenotype correlated with increased interaction of BdlA-G31A with the phosphodiesterase DipA under biofilm growth conditions, resulting in increased phosphodiesterase activity and reduced biofilm biomass accumulation. We furthermore demonstrate that BdlA is a heme-binding protein. None of the BdlA protein variants analyzed led to a loss of the heme prosthetic group. The N-terminal PASa domain was identified as the heme-binding domain of BdlA, with BdlA-dependent nutrient-induced dispersion requiring the PASa domain. The findings suggest that BdlA plays a role in intracellular sensing of dispersion-inducing conditions and together with DipA forms a regulatory network that modulates an intracellular cyclic d-GMP (c-di-GMP) pool to enable dispersion.
Characterization of Axial and Proximal Histidine Mutations of the Decaheme Cytochrome MtrA from Shewanella sp. Strain ANA-3 and Implications for the Electron Transport System
Authors: Reyes Carolina , Qian Fang , Zhang Alissa , Bondarev Sergey , Welch Angel , Thelen Michael P. , Saltikov Chad W.
Published: August 2012

Extracellular respiration of solid-phase electron acceptors in some microorganisms requires a complex chain of multihemec-type cytochromes that span the inner and outer membranes. InShewanellaspecies, MtrA, an ∼35-kDa periplasmic decahemec-type cytochrome, is an essential component for extracellular respiration of iron(III). The exact mechanism of electron transport has not yet been resolved, but the arrangement of the polypeptide chain may have a strong influence on the capability of the MtrA cytochrome to transport electrons. The iron hemes of MtrA are bound to its polypeptide chain via proximal (CXXCH) and distal histidine residues. In this study, we show the effects of mutating histidine residues of MtrA to arginine on protein expression and extracellular respiration usingShewanellasp. strain ANA-3 as a model organism. Individual mutations to six out of nine proximal histidines in CXXCH of MtrA led to decreased protein expression. However, distal histidine mutations resulted in various degrees of protein expression. In addition, the effects of histidine mutations on extracellular respiration were tested using ferrihydrite and current production in microbial fuel cells. These results show that proximal histidine mutants were unable to reduce ferrihydrite. Mutations to the distal histidine residues resulted in various degrees of ferrihydrite reduction. These findings indicate that mutations to the proximal histidine residues affect MtrA expression, leading to loss of extracellular respiration ability. In contrast, mutations to the distal histidine residues are less detrimental to protein expression, and extracellular respiration can proceed.