bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sporadic Isolation of Sabin-Like Polioviruses and High-Level Detection of Non-Polio Enteroviruses during Sewage Surveillance in Seven Italian Cities, after Several Years of Inactivated Poliovirus Vaccination
Authors: Battistone A. , Buttinelli G. , Fiore S. , Amato C. , Bonomo P. , Patti A. M. , Vulcano A. , Barbi M. , Binda S. , Pellegrinelli L. , Tanzi M. L. , Affanni P. , Castiglia P. , Germinario C. , Mercurio P. , Cicala A. , Triassi M. , Pennino F. , Fiore L. 
Published: May 2014

ABSTRACT
Sewage surveillance in seven Italian cities between 2005 and 2008, after the introduction of inactivated poliovirus vaccination (IPV) in 2002, showed rare polioviruses, none that were wild-type or circulating vaccine-derived poliovirus (cVDPV), and many other enteroviruses among 1,392 samples analyzed. Two of five polioviruses (PV) detected were Sabin-like PV2 and three PV3, based on enzyme-linked immunosorbent assay (ELISA) and PCR results. Neurovirulence-related mutations were found in the 5′ noncoding region (5′NCR) of all strains and, for a PV2, also in VP1 region 143 (Ile > Thr). Intertypic recombination in the 3D region was detected in a second PV2 (Sabin 2/Sabin 1) and a PV3 (Sabin 3/Sabin 2). The low mutation rate in VP1 for all PVs suggests limited interhuman virus passages, consistent with efficient polio immunization in Italy. Nonetheless, these findings highlight the risk of wild or Sabin poliovirus reintroduction from abroad. Non-polio enteroviruses (NPEVs) were detected, 448 of which were coxsackievirus B (CVB) and 294 of which were echoviruses (Echo). Fifty-six NPEVs failing serological typing were characterized by sequencing the VP1 region (nucleotides [nt] 2628 to 2976). A total of 448 CVB and 294 Echo strains were identified; among those strains, CVB2, CVB5, and Echo 11 predominated. Environmental CVB5 and CVB2 strains from this study showed high sequence identity with GenBank global strains. The high similarity between environmental NPEVs and clinical strains from the same areas of Italy and the same periods indicates that environmental strains reflect the viruses circulating in the population and highlights the potential risk of inefficient wastewater treatments. This study confirmed that sewage surveillance can be more sensitive than acute flaccid paralysis (AFP) surveillance in monitoring silent poliovirus circulation in the population as well as the suitability of molecular approaches to enterovirus typing.
Modulation of Endogenous Indole-3-Acetic Acid Biosynthesis in Bacteroids within Medicago sativa Nodules
Authors: Bianco C. , Senatore B. , Arbucci S. , Pieraccini G. , Defez R. 
Published: May 2014

ABSTRACT

To evaluate the dose-response effects of endogenous indole-3-acetic acid (IAA) on
Medicago
plant growth and dry weight production, we increased the synthesis of IAA in both free-living and symbiosis-stage rhizobial bacteroids during
Rhizobium
-legume symbiosis. For this purpose, site-directed mutagenesis was applied to modify an 85-bp promoter sequence, driving the expression of
iaaM
and
tms2
genes for IAA biosynthesis. A positive correlation was found between the higher expression of IAA biosynthetic genes in free-living bacteria and the increased production of IAA under both free-living and symbiotic conditions. Plants nodulated by RD65 and RD66 strains, synthetizing the highest IAA concentration, showed a significant (up to 73%) increase in the shoot fresh weight and upregulation of nitrogenase gene,
nifH
, compared to plants nodulated by the wild-type strain. When these plants were analyzed by confocal microscopy, using an anti-IAA antibody, the strongest signal was observed in bacteroids of
Medicago sativa
RD66 (
Ms
-RD66) plants, even when they were located in the senescent nodule zone. We show here a simple system to modulate endogenous IAA biosynthesis in bacteria nodulating legumes suitable to investigate which is the maximum level of IAA biosynthesis, resulting in the maximal increase of plant growth.
Purine Biosynthesis, Biofilm Formation, and Persistence of an Insect-Microbe Gut Symbiosis
Authors: Kim Jiyeun Kate , Kwon Jeong Yun , Kim Soo Kyoung , Han Sang Heum , Won Yeo Jin , Lee Joon Hee , Kim Chan-Hee , Fukatsu Takema , Lee Bok Luel 
Published: May 2014

ABSTRACT

The
Riptortus-Burkholderia
symbiotic system is an experimental model system for studying the molecular mechanisms of an insect-microbe gut symbiosis. When the symbiotic midgut of
Riptortus pedestris
was investigated by light and transmission electron microscopy, the lumens of the midgut crypts that harbor colonizing
Burkholderia
symbionts were occupied by an extracellular matrix consisting of polysaccharides. This observation prompted us to search for symbiont genes involved in the induction of biofilm formation and to examine whether the biofilms are necessary for the symbiont to establish a successful symbiotic association with the host. To answer these questions, we focused on
purN
and
purT
, which independently catalyze the same step of bacterial purine biosynthesis. When we disrupted
purN
and
purT
in the
Burkholderia
symbiont, the Δ
purN
and Δ
purT
mutants grew normally, and only the Δ
purT
mutant failed to form biofilms. Notably, the Δ
purT
mutant exhibited a significantly lower level of cyclic-di-GMP (c-di-GMP) than the wild type and the Δ
purN
mutant, suggesting involvement of the secondary messenger c-di-GMP in the defect of biofilm formation in the Δ
purT
mutant, which might operate via impaired purine biosynthesis. The host insects infected with the Δ
purT
mutant exhibited a lower infection density, slower growth, and lighter body weight than the host insects infected with the wild type and the Δ
purN
mutant. These results show that the function of
purT
of the gut symbiont is important for the persistence of the insect gut symbiont, suggesting the intricate biological relevance of purine biosynthesis, biofilm formation, and symbiosis.
Murein Lytic Enzyme TgaA of Bifidobacterium bifidum MIMBb75 Modulates Dendritic Cell Maturation through Its Cysteine- and Histidine-Dependent Amidohydrolase/Peptidase (CHAP) Amidase Domain
Authors: Guglielmetti Simone , Zanoni Ivan , Balzaretti Silvia , Miriani Matteo , Taverniti Valentina , De Noni Ivano , Presti Ilaria , Stuknyte Milda , Scarafoni Alessio , Arioli Stefania , Iametti Stefania , Bonomi Francesco , Mora Diego , Karp Matti , Granucci Francesca 
Published: May 2014

ABSTRACT

Bifidobacteria are Gram-positive inhabitants of the human gastrointestinal tract that have evolved close interaction with their host and especially with the host's immune system. The molecular mechanisms underlying such interactions, however, are largely unidentified. In this study, we investigated the immunomodulatory potential of
Bifidobacterium bifidum
MIMBb75, a bacterium of human intestinal origin commercially used as a probiotic. Particularly, we focused our attention on TgaA, a protein expressed on the outer surface of MIMBb75's cells and homologous to other known bacterial immunoactive proteins. TgaA is a peptidoglycan lytic enzyme containing two active domains: lytic murein transglycosylase (LT) and cysteine- and histidine-dependent amidohydrolase/peptidase (CHAP). We ran immunological experiments stimulating dendritic cells (DCs) with the
B. bifidum
MIMBb75 and TgaA, with the result that both the bacterium and the protein activated DCs and triggered interleukin-2 (IL-2) production. In addition, we observed that the heterologous expression of TgaA in
Bifidobacterium longum
transferred to the bacterium the ability to induce IL-2. Subsequently, immunological experiments performed using two purified recombinant proteins corresponding to the single domains LT and CHAP demonstrated that the CHAP domain is the immune-reactive region of TgaA. Finally, we also showed that TgaA-dependent activation of DCs requires the protein CD14, marginally involves TRIF, and is independent of Toll-like receptor 4 (TLR4) and MyD88. In conclusion, our study suggests that the bacterial CHAP domain is a novel microbe-associated molecular pattern actively participating in the cross talk mechanisms between bifidobacteria and the host's immune system.
Going Wireless: Fe(III) Oxide Reduction without Pili by Geobacter sulfurreducens Strain JS-1
Authors: Smith Jessica A. , Tremblay Pier-Luc , Shrestha Pravin Malla , Snoeyenbos-West Oona L. , Franks Ashley E. , Nevin Kelly P. , Lovley Derek R. 
Published: May 2014

ABSTRACT

Previous studies have suggested that the conductive pili of
Geobacter sulfurreducens
are essential for extracellular electron transfer to Fe(III) oxides and for optimal long-range electron transport through current-producing biofilms. The KN400 strain of
G. sulfurreducens
reduces poorly crystalline Fe(III) oxide more rapidly than the more extensively studied DL-1 strain. Deletion of the gene encoding PilA, the structural pilin protein, in strain KN400 inhibited Fe(III) oxide reduction. However, low rates of Fe(III) reduction were detected after extended incubation (>30 days) in the presence of Fe(III) oxide. After seven consecutive transfers, the PilA-deficient strain adapted to reduce Fe(III) oxide as fast as the wild type. Microarray, whole-genome resequencing, proteomic, and gene deletion studies indicated that this adaptation was associated with the production of larger amounts of the
c
-type cytochrome PgcA, which was released into the culture medium. It is proposed that the extracellular cytochrome acts as an electron shuttle, promoting electron transfer from the outer cell surface to Fe(III) oxides. The adapted PilA-deficient strain competed well with the wild-type strain when both were grown together on Fe(III) oxide. However, when 50% of the culture medium was replaced with fresh medium every 3 days, the wild-type strain outcompeted the adapted strain. A possible explanation for this is that the necessity to produce additional PgcA, to replace the PgcA being continually removed, put the adapted strain at a competitive disadvantage, similar to the apparent selection against electron shuttle-producing Fe(III) reducers in many anaerobic soils and sediments. Despite increased extracellular cytochrome production, the adapted PilA-deficient strain produced low levels of current, consistent with the concept that long-range electron transport through
G. sulfurreducens
biofilms is more effective via pili.
Wipes Coated with a Singlet-Oxygen-Producing Photosensitizer Are Effective against Human Influenza Virus but Not against Norovirus
Authors: Verhaelen Katharina , Bouwknegt Martijn , Rutjes Saskia , de Roda Husman Ana Maria , Duizer Erwin 
Published: May 2014

ABSTRACT

Transmission of enteric and respiratory viruses, including human norovirus (hNoV) and human influenza virus, may involve surfaces. In food preparation and health care settings, surfaces are cleaned with wipes; however, wiping may not efficiently reduce contamination or may even spread viruses, increasing a potential public health risk. The virucidal properties of wipes with a singlet-oxygen-generating immobilized photosensitizer (IPS) coating were compared to those of similar but uncoated wipes (non-IPS) and of commonly used viscose wipes. Wipes were spiked with hNoV GI.4 and GII.4, murine norovirus 1 (MNV-1), human adenovirus type 5 (hAdV-5), and influenza virus H1N1 to study viral persistence. We also determined residual and transferred virus proportions on steel carriers after successively wiping a contaminated and an uncontaminated steel carrier. On IPS wipes only, influenza viruses were promptly inactivated with a 5-log
10
reduction.
D
values of infectious MNV-1 and hAdV-5 were 8.7 and 7.0 h on IPS wipes, 11.6 and 9.3 h on non-IPS wipes, and 10.2 and 8.2 h on viscose wipes, respectively. Independently of the type of wipe, dry cleaning removed, or drastically reduced, initial spot contamination of hNoV on surfaces. All wipes transferred hNoV to an uncontaminated carrier; however, the risk of continued transmission by reuse of wipes after 6 and 24 h was limited for all viruses. We conclude that cleaning wet spots with dry wipes efficiently reduced spot contamination on surfaces but that cross-contamination with noroviruses by wiping may result in an increased public health risk at high initial virus loads. For influenza virus, IPS wipes present an efficient one-step procedure for cleaning and disinfecting contaminated surfaces.
Host Responses to the Pathogen Mycobacterium avium subsp. paratuberculosis and Beneficial Microbes Exhibit Host Sex Specificity
Authors: Karunasena Enusha , McMahon K. Wyatt , Chang David , Brashears Mindy M. 
Published: May 2014

ABSTRACTDifferences between microbial pathogenesis in male and female hosts are well characterized in disease conditions connected to sexual transmission. However, limited biological insight is available on variances attributed to sex specificity in host-microbe interactions, and it is most often a minimized variable outside these transmission events. In this work, we studied two gut microbes—a pathogen,Mycobacterium aviumsubsp.paratuberculosis, and a probiotic,Lactobacillus animalisNP-51—and the interaction between each agent and the male and female gastrointestinal systems. This trial was conducted in BALB/c mice (n= 5 per experimental group and per sex at a given time point), with analysis at four time points over 180 days. Host responses toM. aviumsubsp.paratuberculosisandL. animaliswere sensitive to sex. Cytokines that were significantly different (P≤ 0.05) between the sexes included interleukin-1α/β (IL-1α/β), IL-17, IL-6, IL-10, IL-12, and gamma interferon (IFN-γ) and were dependent on experimental conditions. However, granulocyte-macrophage colony-stimulating factor (GM-CSF), vascular endothelial growth factor (VEGF), and IL-13/23 showed no sex specificity. A metabolomics study indicated a 0.5- to 2.0-fold (log2scale) increase in short-chain fatty acids (butyrate and acetate) in males and greater increases ino-phosphocholine or histidine from female colon tissues; variances distinct to each sex were observed with age or long-term probiotic consumption. Two genera,StaphylococcusandRoseburia, were consistently overrepresented in females compared to males; other species were specific to one sex but fluctuated depending on experimental conditions. The differences observed suggest that male and female gut tissues and microbiota respond to newly introduced microorganisms differently and that gut-associated microorganisms with host immune system responses and metabolic activity are supported by biology distinct to the host sex.
A Large Nonconserved Region of the Tethering Protein Leashin Is Involved in Regulating the Position, Movement, and Function of Woronin Bodies in Aspergillus oryzae
Authors: Han Pei , Jin Feng Jie , Maruyama Jun-ichi , Kitamoto Katsuhiko 
Published: May 2014

ABSTRACT

The Woronin body is a Pezizomycotina-specific organelle that is typically tethered to the septum, but upon hyphal wounding, it plugs the septal pore to prevent excessive cytoplasmic loss. Leashin (LAH) is a large Woronin body tethering protein that contains highly conserved N- and C-terminal regions and a long (∼2,500-amino-acid) nonconserved middle region. As the involvement of the nonconserved region in Woronin body function has not been investigated, here, we functionally characterized individual regions of the LAH protein of
Aspergillus oryzae
(AoLAH). In an
Aolah
disruptant, no Woronin bodies were tethered to the septum, and hyphae had a reduced ability to prevent excessive cytoplasmic loss upon hyphal wounding. Localization analysis revealed that the N-terminal region of AoLAH associated with Woronin bodies dependently on AoWSC, which is homologous to
Neurospora crassa
WSC (Woronin body sorting complex), and that the C-terminal region was localized to the septum. Elastic movement of Woronin bodies was observed when visualized with an AoLAH N-terminal-region–enhanced green fluorescent protein (EGFP) fusion protein. An N- and C-terminal fusion construct lacking the nonconserved middle region of AoLAH was sufficient for the tethering of Woronin bodies to the septum. However, Woronin bodies were located closer to the septum and exhibited impaired elastic movement. Moreover, expression of middle-region-deleted AoLAH in the
Aolah
disruptant did not restore the ability to prevent excessive cytoplasmic loss. These findings indicate that the nonconserved middle region of AoLAH has functional importance for regulating the position, movement, and function of Woronin bodies.
Identification and Characterization of Glycoproteins on the Spore Surface of Clostridium difficile
Authors: Strong Philippa C. R. , Fulton Kelly M. , Aubry Annie , Foote Simon , Twine Susan M. , Logan Susan M. 
Published: May 2014

ABSTRACT

In this study, we identify a major spore surface protein, BclA, and provide evidence that this protein is glycosylated. Following extraction of the spore surface, solubilized proteins were separated by one-dimensional PAGE and stained with glycostain to reveal a reactive high-molecular-mass region of approximately 600 kDa. Tandem mass spectrometry analysis of in-gel digests showed this band to contain peptides corresponding to a putative exosporangial glycoprotein (BclA3) and identified a number of glycopeptides modified with multiple N-acetyl hexosamine moieties and, in some cases, capped with novel glycans. In addition, we demonstrate that the glycosyltransferase gene
sgtA
(gene CD3350 in strain 630 and CDR3194 in strain R20291), which is located immediately upstream of the
bclA3
homolog, is involved in the glycosylation of the spore surface, and is cotranscribed with
bclA3
. The presence of anti-β-O-GlcNAc-reactive material was demonstrated on the surface of spores by immunofluorescence and in surface extracts by Western blotting, although each strain produced a distinct pattern of reactivity. Reactivity of the spore surface with the anti-β-O-GlcNAc antibody was abolished in the 630 and R20291 glycosyltransferase mutant strains, while complementation with a wild-type copy of the gene restored the β-O-GlcNAc reactivity. Phenotypic testing of R20291 glycosyltransferase mutant spores revealed no significant change in sensitivity to ethanol or lysozyme. However, a change in the resistance to heat of R20291 glycosyltransferase mutant spores compared to R20291 spores was observed, as was the ability to adhere to and be internalized by macrophages.
HupB, a Nucleoid-Associated Protein of Mycobacterium tuberculosis, Is Modified by Serine/Threonine Protein Kinases
In Vivo
Authors: Gupta Meetu , Sajid Andaleeb , Sharma Kirti , Ghosh Soumitra , Arora Gunjan , Singh Ramandeep , Nagaraja Valakunja , Tandon Vibha , Singh Yogendra 
Published: May 2014

ABSTRACT

HU, a widely conserved bacterial histone-like protein, regulates many genes, including those involved in stress response and virulence. Whereas ample data are available on HU-DNA communication, the knowledge on how HU perceives a signal and transmit it to DNA remains limited. In this study, we identify HupB, the HU homolog of the human pathogen
Mycobacterium tuberculosis
, as a component of serine/threonine protein kinase (STPK) signaling. HupB is extracted in its native state from the exponentially growing cells of
M. tuberculosis
H
37
Ra and is shown to be phosphorylated on both serine and threonine residues. The STPKs capable of modifying HupB are determined
in vitro
and the residues modified by the STPKs are identified for both
in vivo
and the
in vitro
proteins through mass spectrometry. Of the identified phosphosites, Thr
65
and Thr
74
in the DNA-embracing β-strand of the N-terminal domain of HupB (N-HupB) are shown to be crucial for its interaction with DNA. In addition, Arg
55
is also identified as an important residue for N-HupB–DNA interaction. N-HupB is shown to have a diminished interaction with DNA after phosphorylation. Furthermore,
hupB
is shown to be maximally expressed during the stationary phase in
M. tuberculosis
H
37
Ra, while HupB kinases were found to be constitutively expressed (PknE and PknF) or most abundant during the exponential phase (PknB). In conclusion, HupB, a DNA-binding protein, with an ability to modulate chromatin structure is proposed to work in a growth-phase-dependent manner through its phosphorylation carried out by the mycobacterial STPKs.
Acinetobacter baumannii Response to Host-Mediated Zinc Limitation Requires the Transcriptional Regulator Zur
Authors: Mortensen Brittany L. , Rathi Subodh , Chazin Walter J. , Skaar Eric P. 
Published: May 2014

ABSTRACT

Acinetobacter baumannii
is a leading cause of ventilator-associated pneumonia in intensive care units, and the increasing rates of antibiotic resistance make treating these infections challenging. Consequently, there is an urgent need to develop new antimicrobials to treat
A. baumannii
infections. One potential therapeutic option is to target bacterial systems involved in maintaining appropriate metal homeostasis, processes that are critical for the growth of pathogens within the host. The
A. baumannii
inner membrane zinc transporter ZnuABC is required for growth under low-zinc conditions and for
A. baumannii
pathogenesis. The expression of
znuABC
is regulated by the transcriptional repressor Zur. To investigate the role of Zur during the
A. baumannii
response to zinc limitation, a
zur
deletion mutant was generated, and transcriptional changes were analyzed using RNA sequencing. A number of Zur-regulated genes were identified that exhibit increased expression both when
zur
is absent and under low-zinc conditions, and Zur binds to predicted Zur box sequences of several genes affected by zinc levels or the
zur
mutation. Furthermore, the
zur
mutant is impaired for growth in the presence of both high and low zinc levels compared to wild-type
A. baumannii
. Finally, the
zur
mutant exhibits a defect in dissemination in a mouse model of
A. baumannii
pneumonia, establishing zinc sensing as a critical process during
A. baumannii
infection. These results define Zur-regulated genes within
A. baumannii
and demonstrate a requirement for Zur in the
A. baumannii
response to the various zinc levels experienced within the vertebrate host.
Genetic Dissection of the
mamAB
and
mms6
Operons Reveals a Gene Set Essential for Magnetosome Biogenesis in Magnetospirillum gryphiswaldense
Authors: Lohße Anna , Borg Sarah , Raschdorf Oliver , Kolinko Isabel , Tompa Éva , Pósfai Mihály , Faivre Damien , Baumgartner Jens , Schüler Dirk 
Published: May 2014

ABSTRACT

Biosynthesis of bacterial magnetosomes, which are intracellular membrane-enclosed, nanosized magnetic crystals, is controlled by a set of >30 specific genes. In
Magnetospirillum gryphiswaldense
, these are clustered mostly within a large conserved genomic magnetosome island (MAI) comprising the
mms6
,
mamGFDC
,
mamAB
, and
mamXY
operons. Here, we demonstrate that the five previously uncharacterized genes of the
mms6
operon have crucial functions in the regulation of magnetosome biomineralization that partially overlap MamF and other proteins encoded by the adjacent
mamGFDC
operon. While all other deletions resulted in size reduction, elimination of either
mms36
or
mms48
caused the synthesis of magnetite crystals larger than those in the wild type (WT). Whereas the
mms6
operon encodes accessory factors for crystal maturation, the large
mamAB
operon contains several essential and nonessential genes involved in various other steps of magnetosome biosynthesis, as shown by single deletions of all
mamAB
genes. While single deletions of
mamL
, -
P
, -
Q
, -
R
, -
B
, -
S
, -
T
, and -
U
showed phenotypes similar to those of their orthologs in a previous study in the related
M. magneticum
, we found
mamI
and
mamN
to be not required for at least rudimentary iron biomineralization in
M. gryphiswaldense
. Thus, only
mamE
, -
L
, -
M
, -
O
, -
Q
, and -
B
were essential for formation of magnetite, whereas a
mamI
mutant still biomineralized tiny particles which, however, consisted of the nonmagnetic iron oxide hematite, as shown by high-resolution transmission electron microscopy (HRTEM) and the X-ray absorption near-edge structure (XANES). Based on this and previous studies, we propose an extended model for magnetosome biosynthesis in
M. gryphiswaldense
.