bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft Genome Sequence of Multitrait Plant Growth-Promoting
Bacillus
sp. Strain RZ2MS9
Authors: Batista Bruna Durante , Taniguti Lucas Mitsuo , Almeida Jaqueline Raquel , Azevedo João Lúcio , Quecine Maria Carolina 
Published: December 2016

ABSTRACT

Bacillus
sp. strain RZ2MS9 is a multitrait soybean and maize growth-promoting bacterium isolated in Brazil from guarana's rhizosphere. Here, we present the draft genome sequence of RZ2MS9 and its genes involved in many features related to plant growth promotion.
Draft Genome Sequence of the Commensal Escherichia coli Strain F-18
Authors: Ormsby Michael J. , Johnson Síle A. , Wall Daniel M. 
Published: December 2016

ABSTRACT

Here, we report the draft genome sequence of
Escherichia coli
strain F-18, originally isolated from the feces of a healthy individual in 1977. The draft genome is 5,246,829 bp, with a G+C content of 50.50%, and it encodes 4,933 predicted coding sequences (CDSs), 10 rRNAs, and 84 tRNAs.
Draft Genome Sequence of the Phosphate-Solubilizing Bacterium Pseudomonas argentinensis Strain SA190 Isolated from the Desert Plant
Indigofera argentea
Authors: Lafi Feras F. , Alam Intikhab , Geurts Rene , Bisseling Ton , Bajic Vladimir B. , Hirt Heribert , Saad Maged M. 
Published: December 2016

ABSTRACT

Pseudomonas argentinensis
strain SA190 is a plant endophytic-inhabiting bacterium that was isolated from root nodules of the desert plant
Indigofera argentea
collected from the Jizan region of Saudi Arabia. Here, we report the genome sequence of SA190, highlighting several functional genes related to plant growth–promoting activity, environment adaption, and antifungal activity.
The Transcriptional Regulator CpsY Is Important for Innate Immune Evasion in Streptococcus pyogenes
Authors: Vega Luis A. , Valdes Kayla M. , Sundar Ganesh S. , Belew Ashton T. , Islam Emrul , Berge Jacob , Curry Patrick , Chen Steven , El-Sayed Najib M. , Le Breton Yoann , McIver Kevin S. 
Published: December 2016

ABSTRACT

As an exclusively human pathogen,
Streptococcus pyogenes
(the group A streptococcus [GAS]) has specifically adapted to evade host innate immunity and survive in multiple tissue niches, including blood. GAS can overcome the metabolic constraints of the blood environment and expresses various immunomodulatory factors necessary for survival and immune cell resistance. Here we present our investigation of one such factor, the predicted LysR family transcriptional regulator CpsY. The encoding gene,
cpsY
, was initially identified as being required for GAS survival in a transposon-site hybridization (TraSH) screen in whole human blood. CpsY is homologous with transcriptional regulators of
Streptococcus mutans
(MetR),
Streptococcus iniae
(CpsY), and
Streptococcus agalactiae
(MtaR) that regulate methionine transport, amino acid metabolism, resistance to neutrophil-mediated killing, and survival
in vivo
. Our investigation indicated that CpsY is involved in GAS resistance to innate immune cells of its human host. However, GAS CpsY does not manifest the
in vitro
phenotypes of its homologs in other streptococcal species. GAS CpsY appears to regulate a small set of genes that is markedly different from the regulons of its homologs. The differential expression of these genes depends on the growth medium, and CpsY modestly influences their expression. The GAS CpsY regulon includes known virulence factors (
mntE
,
speB
,
spd
,
nga
[
spn
],
prtS
[
SpyCEP
], and
sse
) and cell surface-associated factors of GAS (
emm1
,
mur1.2
,
sibA
[
cdhA
], and
M5005_Spy0500
). Intriguingly, the loss of CpsY in GAS does not result in virulence defects in murine models of infection, suggesting that CpsY function in immune evasion is specific to the human host.
Differential Macrophage Polarization from Pneumocystis in Immunocompetent and Immunosuppressed Hosts: Potential Adjunctive Therapy during Pneumonia
Authors: Nandakumar Vijayalakshmi , Hebrink Deanne , Jenson Paige , Kottom Theodore , Limper Andrew H. 
Published: December 2016

ABSTRACTWe explored differential polarization of macrophages during infection using a rat model ofPneumocystispneumonia. We observed enhanced pulmonary M1 macrophage polarization in immunosuppressed (IS) hosts, but an M2 predominant response in immunocompetent (IC) hosts followingPneumocystis cariniichallenge. Increased inflammation and inducible nitric oxide synthase (iNOS) levels characterized the M1 response. However, macrophage ability to produce nitric oxide was defective. In contrast, the lungs of IC animals revealed a prominent M2 gene signature, and these macrophages effectively elicited an oxidative burst associated with clearance ofPneumocystis. In addition, duringP. cariniiinfection the expression of Dectin-1, a critical receptor for recognition and clearance ofP. carinii, was upregulated in macrophages of IC animals but suppressed in IS animals. In the absence of an appropriate cytokine milieu for M2 differentiation,Pneumocystisinduced an M1 response bothin vitroandin vivo. The M1 response induced byP. cariniiwas plastic in nature and reversible with appropriate cytokine stimuli. Finally, we tested whether macrophage polarization can be modulatedin vivoand used to help manage the pathogenesis ofPneumocystispneumonia by adoptive transfer. Treatment with both M1 and M2 cells significantly improved survival ofP. carinii-infected IS hosts. However, M2 treatment provided the best outcomes with efficient clearance ofP. cariniiand reduced inflammation.
Anaplasma marginale Outer Membrane Protein A Is an Adhesin That Recognizes Sialylated and Fucosylated Glycans and Functionally Depends on an Essential Binding Domain
Authors: Hebert Kathryn S. , Seidman David , Oki Aminat T. , Izac Jerilyn , Emani Sarvani , Oliver Lee D. , Miller Daniel P. , Tegels Brittney K. , Kannagi Reiji , Marconi Richard T. , Carlyon Jason A. 
Published: December 2016

ABSTRACTAnaplasma marginalecauses bovine anaplasmosis, a debilitating and potentially fatal tick-borne infection of cattle. BecauseA. marginaleis an obligate intracellular organism, its adhesins that mediate entry into host cells are essential for survival. Here, we demonstrate thatA. marginaleouter membrane protein A (AmOmpA; AM854) contributes to the invasion of mammalian and tick host cells. AmOmpA exhibits predicted structural homology to OmpA ofA. phagocytophilum(ApOmpA), an adhesin that uses key lysine and glycine residues to interact with α2,3-sialylated and α1,3-fucosylated glycan receptors, including 6-sulfo-sialyl Lewis x (6-sulfo-sLex). Antisera against AmOmpA or its predicted binding domain inhibitsA. marginaleinfection of host cells. Residues G55 and K58 are contributory, and K59 is essential for recombinant AmOmpA to bind to host cells. Enzymatic removal of α2,3-sialic acid and α1,3-fucose residues from host cell surfaces makes them less supportive of AmOmpA binding. AmOmpA is both an adhesin and an invasin, as coating inert beads with it confers adhesiveness and invasiveness. Recombinant forms of AmOmpA and ApOmpA competitively antagonizeA. marginaleinfection of host cells, but a monoclonal antibody against 6-sulfo-sLexfails to inhibit AmOmpA adhesion andA. marginaleinfection. Thus, the two OmpA proteins bind related but structurally distinct receptors. This study provides a detailed understanding of AmOmpA function, identifies its essential residues that can be targeted by blocking antibody to reduce infection, and determines that it binds to one or more α2,3-sialylated and α1,3-fucosylated glycan receptors that are unique from those targeted by ApOmpA.
Legionella pneumophila OxyR Is a Redundant Transcriptional Regulator That Contributes to Expression Control of the Two-Component CpxRA System
Authors: Tanner Jennifer R. , Patel Palak G. , Hellinga Jacqueline R. , Donald Lynda J. , Jimenez Celine , LeBlanc Jason J. , Brassinga Ann Karen C. 
Published: December 2016

ABSTRACT

Nominally an environmental organism,
Legionella pneumophila
is an intracellular parasite of protozoa but is also the causative agent of the pneumonia termed Legionnaires' disease, which results from inhalation of aerosolized bacteria by susceptible humans. Coordination of gene expression by a number of identified regulatory factors, including OxyR, assists
L. pneumophila
in adapting to the stresses of changing environments.
L. pneumophila
OxyR (OxyR
Lp
) is an ortholog of
Escherichia coli
OxyR; however, OxyR
Lp
was shown elsewhere to be functionally divergent, such that it acts as a transcription regulator independently of the oxidative stress response. In this study, the use of improved gene deletion methods has enabled us to generate an unmarked in-frame deletion of
oxyR
in
L. pneumophila
. Lack of OxyR
Lp
did not affect
in vitro
growth or intracellular growth in
Acanthamoeba castellanii
protozoa and U937-derived macrophages. The expression of OxyR
Lp
does not appear to be regulated by CpxR, even though purified recombinant CpxR bound a DNA sequence similar to that reported for CpxR elsewhere. Surprisingly, a lack of OxyR
Lp
resulted in elevated activity of the promoters located upstream of
icmR
and the
lpg1441-cpxA
operon, and OxyR
Lp
directly bound to these promoter regions, suggesting that OxyR
Lp
is a direct repressor. Interestingly, a strain overexpressing OxyR
Lp
demonstrated reduced intracellular growth in
A. castellanii
but not in U937-derived macrophages, suggesting that balanced expression control of the two-component CpxRA system is necessary for survival in protozoa. Taken together, this study suggests that OxyR
Lp
is a functionally redundant transcriptional regulator in
L. pneumophila
under the conditions evaluated herein.

IMPORTANCE
Legionella pneumophila
is an environmental pathogen, with its transmission to the human host dependent upon its ability to replicate in protozoa and survive within its aquatic niche. Understanding the genetic factors that contribute to
L. pneumophila
survival within each of these unique environments will be key to limiting future point-source outbreaks of Legionnaires' disease. The transcriptional regulator
L. pneumophila
OxyR (OxyR
Lp
) has been previously identified as a potential regulator of virulence traits warranting further investigation. This study demonstrated that
oxyR
is nonessential for
L. pneumophila
survival
in vitro
and
in vivo
via mutational analysis. While the mechanisms of how OxyR
Lp
expression is regulated remain elusive, this study shows that OxyR
Lp
negatively regulates the expression of the
cpxRA
two-component system necessary for intracellular survival in protozoa.
25-Hydroxycholesterol Inhibition of Lassa Virus Infection through Aberrant GP1 Glycosylation
Authors: Shrivastava-Ranjan Punya , Bergeron Éric , Chakrabarti Ayan K. , Albariño César G. , Flint Mike , Nichol Stuart T. , Spiropoulou Christina F. 
Published: December 2016

ABSTRACT

Lassa virus (LASV) infection is a major public health concern due to high fatality rates and limited effective treatment. The interferon-stimulated gene
cholesterol 25-hydroxylase
(
CH25H
) encodes an enzyme that catalyzes the production of 25-hydroxycholesterol (25HC). 25HC is involved in regulating cholesterol biosynthesis and has recently been identified as a potent antiviral targeting enveloped virus entry. Here, we show a previously unrecognized role of CH25H in inhibiting LASV glycoprotein glycosylation and the production of infectious virus. Overexpression of CH25H or treatment with 25HC decreased LASV G1 glycoprotein
N
-glycan maturation and reduced the production of infectious LASV. Depletion of endogenous CH25H using small interfering RNA (siRNA) enhanced the levels of fully glycosylated G1 and increased infectious LASV production. Finally, LASV particles produced from 25HC-treated cells were found to be less infectious, to incorporate aberrantly glycosylated GP1 species, and to be defective in binding alpha-dystroglycan, an attachment and entry receptor. Our findings identify a novel role for CH25H in controlling LASV propagation and indicate that manipulation of the expression of CH25H or the administration of 25HC may be a useful anti-LASV therapy.

IMPORTANCE
Lassa fever is an acute viral hemorrhagic fever in humans caused by Lassa virus (LASV). No vaccine for LASV is currently available. Treatment is limited to the administration of ribavirin, which is only effective when given early in the course of illness.
Cholesterol 25-hydroxylase
(
CH25H
) is a recently identified interferon-stimulated gene (ISG); it encodes an enzyme that catalyzes the production of 25-hydroxycholesterol (25HC), which inhibits several viruses. Here, we identify a novel antiviral mechanism of 25HC that is dependent on inhibiting the glycosylation of Lassa virus (LASV) glycoprotein and reducing the infectivity of LASV as a means of suppressing viral replication. Since N-linked glycosylation is a critical feature of other enveloped-virus glycoproteins, 25HC may be a broad inhibitor of virus infectivity.
Complete Microbiota Engraftment Is Not Essential for Recovery from Recurrent Clostridium difficile Infection following Fecal Microbiota Transplantation
Authors: Staley Christopher , Kelly Colleen R. , Brandt Lawrence J. , Khoruts Alexander , Sadowsky Michael J. 
Published: December 2016

ABSTRACT

Bacterial communities from subjects treated for recurrent
Clostridium difficile
infection (rCDI) by fecal microbiota transplantation (FMT), using either heterologous donor stool samples or autologous stool samples, were characterized by Illumina next-generation sequencing. As previously reported, the success of heterologous FMT (90%) was superior to that of autologous FMT (43%) (
P
= 0.019), and post-FMT intestinal bacterial communities differed significantly between treatment arms (
P
< 0.001). Subjects cured by autologous FMT typically had greater abundances of the
Clostridium
XIVa clade and
Holdemania
bacteria prior to treatment, and the relative abundances of these groups increased significantly after FMT compared to heterologous FMT and pre-FMT samples. The typical shift to post-FMT, donor-like assemblages, featuring high relative abundances of genera within the
Bacteroidetes
and
Firmicutes
phyla, was not observed in the autologous FMT subjects. Autologous FMT patient bacterial communities were significantly different in composition than those for heterologous FMT patients and donors (
P
< 0.001). The SourceTracker program, which employs a Bayesian algorithm to determine source contributions to sink communities, showed that patients initially treated by heterologous FMT had significantly higher percentages of engraftment (i.e., similarity to donor communities, mean value of 74%) compared to those who suffered recurrence following autologous FMT (1%) (
P
≤ 0.013). The findings of this study suggest that complete donor engraftment may be not necessary if functionally critical taxa are present in subjects following antibiotic therapy.

IMPORTANCE
This study provides a detailed characterization of fecal bacterial communities in subjects who participated in a previously published randomized clinical trial to treat recurrent
C. difficile
infection (rCDI). Bacterial communities were characterized to determine differences between subjects who received fecal bacteria either from healthy donor stool samples or their own stool samples as “placebo” in order to determine which groups of bacteria were most important in achieving a cure. The results of this study suggested that bacteria associated with secondary bile acid metabolism could potentially provide resistance to infection and that complete transfer of healthy donor microorganisms was not necessary to resolve CDI following unsuccessful antibiotic treatment.
Single-Cell Analysis of the Plasmablast Response to Vibrio cholerae Demonstrates Expansion of Cross-Reactive Memory B Cells
Authors: Kauffman Robert C. , Bhuiyan Taufiqur R. , Nakajima Rie , Mayo-Smith Leslie M. , Rashu Rasheduzzaman , Hoq Mohammad Rubel , Chowdhury Fahima , Khan Ashraful Islam , Rahman Atiqur , Bhaumik Siddhartha K. , Harris Levelle , O'Neal Justin T. , Trost Jessica F. , Alam Nur Haq , Jasinskas Algis , Dotsey Emmanuel , Kelly Meagan , Charles Richelle C. , Xu Peng , Kováč Pavol , Calderwood Stephen B. , Ryan Edward T. , Felgner Phillip L. , Qadri Firdausi , Wrammert Jens , Harris Jason B. 
Published: December 2016

ABSTRACTWe characterized the acute B cell response in adults with cholera by analyzing the repertoire, specificity, and functional characteristics of 138 monoclonal antibodies (MAbs) generated from single-cell-sorted plasmablasts. We found that the cholera-induced responses were characterized by high levels of somatic hypermutation and large clonal expansions. A majority of the expansions targeted cholera toxin (CT) or lipopolysaccharide (LPS). Using a novel proteomics approach, we were able to identify sialidase as another major antigen targeted by the antibody response toVibrio choleraeinfection. Antitoxin MAbs targeted both the A and B subunits, and most were also potent neutralizers of enterotoxigenicEscherichia coliheat-labile toxin. LPS-specific MAbs uniformly targeted the O-specific polysaccharide, with no detectable responses to either the core or the lipid moiety of LPS. Interestingly, the LPS-specific antibodies varied widely in serotype specificity and functional characteristics. One participant infected with the Ogawa serotype produced highly mutated LPS-specific antibodies that preferentially bound the previously circulating Inaba serotype. This demonstrates durable memory against a polysaccharide antigen presented at the mucosal surface and provides a mechanism for the long-term, partial heterotypic immunity seen following cholera.IMPORTANCECholera is a diarrheal disease that results in significant mortality. While oral cholera vaccines are beneficial, they do not achieve equivalent protection compared to infection withVibrio cholerae. Although antibodies likely mediate protection, the mechanisms of immunity following cholera are poorly understood, and a detailed understanding of antibody responses to cholera is of significance for human health. In this study, we characterized the human response to cholera at the single-plasmablast, monoclonal antibody level. Although this approach has not been widely applied to the study of human bacterial infection, we were able to uncover the basis of cross-reactivity between differentV. choleraeserotypes and the likely impact of prior enterotoxigenicEscherichia coliexposure on the response to cholera, as well as identify novel antigenic targets. In addition to improving our understanding of the repertoire and function of the antibody response to cholera in humans, this study has implications for future cholera vaccination efforts.
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
Authors: Miller Rachel A. , Wiedmann Martin 
Published: December 2016

ABSTRACT

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 Mississippi isolates, the presence of S-CDT-encoding genes is clade associated. HeLa cells infected with representative strains of these S-CDT-positive serotypes had a significantly higher proportion of cells arrested in the G
2
/M phase than HeLa cells infected with representative strains of S-CDT-negative serotypes Typhimurium, Newport, and Enteritidis. The G
2
/M cell cycle arrest was dependent on CdtB, the active subunit of S-CDT, as infection with isogenic Δ
cdtB
mutants abolished their ability to induce a G
2
/M cell cycle arrest. Infection with S-CDT-encoding serotypes was significantly associated with activation of the host cell’s DNA damage response (DDR), a signaling cascade that is important for detecting and repairing damaged DNA. HeLa cell populations infected with S-CDT-positive serotypes had a significantly higher proportion of cells with DDR protein 53BP1 and γH2AX foci than cells infected with either S-CDT-negative serotypes or isogenic Δ
cdtB
strains. Intoxication with S-CDT occurred via autocrine and paracrine pathways, as uninfected HeLa cells among populations of infected cells also had an activated DDR. Overall, we show that S-CDT plays a significant role in the cellular outcome of infection with NTS serotypes.

IMPORTANCE
The recent discovery that multiple serotypes encode S-CDT, which was previously established as an important virulence factor for serotype Typhi, suggested that this toxin may also contribute to the outcome of infection with nontyphoidal serotypes. In this study, we demonstrate that at a cellular level, S-CDT significantly alters the outcome of infection by inducing DNA damage which is associated with a cell cycle arrest and activation of the host cell’s DDR. Importantly, these results contribute valuable information for assessing the public health implications of S-CDT in infections with NTS serotypes. Our data suggest that infection with
Salmonella
strains that encode S-CDT has the potential to result in DNA damage, which may contribute to long-term sequelae.
Hematologic Complications of Tuberculosis
Authors: Balepur Shyam S. , Schlossberg David 
Published: December 2016

ABSTRACTTuberculosis (TB) affects the production and life span of all hematologic cellular components. In addition, plasma coagulation factors may be affected, resulting in sometimes life-threatening complications. Iron, folate, and vitamin B12metabolism is derailed. The pharmacological agents used for TB therapy may also cause hematologic changes. There are some uncommon manifestations of TB in nontuberculous hematologic patients. There have been some exciting developments in the field of imaging to screen for TB, TB pathophysiology at the cellular level, and our understanding of immune response in TB. Advances have been made in pharmacologic therapeutic options, including discovery of new drugs in the fight against drug-resistant TB, bearing in mind their hematologic effects. This chapter reviews and updates known hematologic effects of TB and its therapy and some lesser known effects of TB in patients with nontuberculous hematologic conditions.
Comparative studies between the influence of single- and multi-walled carbon nanotubes addition on Gd-123 superconducting phase
Authors: Abou-Aly A. I. , Anas M. , Ebrahim Shaker , Awad R. , Eldeen I. G. 
Published: December 2016

The effect of single-walled carbon nanotubes (SWCNTs) and multi-walled carbon nanotubes (MWCNTs) addition on the phase formation and the superconducting properties of GdBa2Cu3O[Formula: see text] phase has been studied. Therefore, composite superconductor samples of type (CNTs)[Formula: see text] GdBa2Cu3O[Formula: see text], 0.0 [Formula: see text] 0.1 wt.% have been synthesized by a standard solid-state reaction technique. The samples have been characterized using X-ray powder diffraction (XRD), scanning electron microscope (SEM) and transmission electron microscope (TEM). The results of XRD show an enhancement in the phase formation up to 0.06 wt.% and 0.08 wt.% for SWCNTs and MWCNTs, respectively. SEM and TEM reveal that CNTs form an electrical network resulting in well-connected superconducting grains. The electrical properties of the prepared samples have been examined by electric resistivity and I–V measurements, and their results reinforce the XRD, SEM and TEM. Consequently, both [Formula: see text] and [Formula: see text] improve as the addition percentage increases up to 0.06 wt.% and 0.08 wt.% for SWCNTs and MWCNTs, respectively.