bluuebunny/crossref_metadata_2025_split huggingface dataset:
Involvement of Agrobacterium tumefaciens Galacturonate Tripartite ATP-Independent Periplasmic (TRAP) Transporter GaaPQM in Virulence Gene Expression
Authors: Zhao Jinlei , Binns Andrew N. 
Published: December 2015

ABSTRACT

Monosaccharides capable of serving as nutrients for the soil bacterium
Agrobacterium tumefaciens
are also inducers of the
vir
regulon present in the tumor-inducing (Ti) plasmid of this plant pathogen. One such monosaccharide is galacturonate, the predominant monomer of pectin found in plant cell walls. This ligand is recognized by the periplasmic sugar binding protein ChvE, which interacts with the VirA histidine kinase that controls
vir
gene expression. Although ChvE is also a member of the ChvE-MmsAB ABC transporter involved in the utilization of many neutral sugars, it is not involved in galacturonate utilization. In this study, a putative tripartite ATP-independent periplasmic (TRAP) transporter, GaaPQM, is shown to be essential for the utilization of galacturonic acid; we show that residue R169 in the predicted sugar binding site of the GaaP is required for activity. The gene upstream of
gaaPQM
(
gaaR
) encodes a member of the GntR family of regulators. GaaR is shown to repress the expression of
gaaPQM
, and the repression is relieved in the presence of the substrate for GaaPQM. Moreover, GaaR is shown to bind putative promoter regions in the sequences required for galacturonic acid utilization. Finally,
A. tumefaciens
strains carrying a deletion of
gaaPQM
are more sensitive to galacturonate as an inducer of
vir
gene expression, while the overexpression of
gaaPQM
results in strains being less sensitive to this
vir
inducer. This supports a model in which transporter activity is crucial in ensuring that
vir
gene expression occurs only at sites of high ligand concentration, such as those at a plant wound site.
Optical Sensing of Microbial Life on Surfaces
Authors: Fischer M. , Triggs G. J. , Krauss T. F. 
Published: December 2015

ABSTRACT
The label-free detection of microbial cells attached to a surface is an active field of research. The field is driven by the need to understand and control the growth of biofilms in a number of applications, including basic research in natural environments, industrial facilities, and clinical devices, to name a few. Despite significant progress in the ability to monitor the growth of biofilms and related living cells, the sensitivity and selectivity of such sensors are still a challenge. We believe that among the many different technologies available for monitoring biofilm growth, optical techniques are the most promising, as they afford direct imaging and offer high sensitivity and specificity. Furthermore, as each technique offers different insights into the biofilm growth mechanism, our analysis allows us to provide an overview of the biological processes at play. In addition, we use a set of key parameters to compare state-of-the-art techniques in the field, including a critical assessment of each method, to identify the most promising types of sensors. We highlight the challenges that need to be overcome to improve the characteristics of current biofilm sensor technologies and indicate where further developments are required. In addition, we provide guidelines for selecting a suitable sensor for detecting microbial cells on a surface.
Oxygen Affects Gut Bacterial Colonization and Metabolic Activities in a Gnotobiotic Cockroach Model
Authors: Tegtmeier Dorothee , Thompson Claire L. , Schauer Christine , Brune Andreas 
Published: December 2015

ABSTRACT

The gut microbiota of termites and cockroaches represents complex metabolic networks of many diverse microbial populations. The distinct microenvironmental conditions within the gut and possible interactions among the microorganisms make it essential to investigate how far the metabolic properties of pure cultures reflect their activities in their natural environment. We established the cockroach
Shelfordella lateralis
as a gnotobiotic model and inoculated germfree nymphs with two bacterial strains isolated from the guts of conventional cockroaches. Fluorescence microscopy revealed that both strains specifically colonized the germfree hindgut. In diassociated cockroaches, the facultatively anaerobic strain EbSL (a new species of
Enterobacteriaceae
) always outnumbered the obligately anaerobic strain FuSL (a close relative of
Fusobacterium varium
), irrespective of the sequence of inoculation, which showed that precolonization by facultatively anaerobic bacteria does not necessarily favor colonization by obligate anaerobes. Comparison of the fermentation products of the cultures formed
in vitro
with those accumulated
in situ
indicated that the gut environment strongly affected the metabolic activities of both strains. The pure cultures formed the typical products of mixed-acid or butyrate fermentation, whereas the guts of gnotobiotic cockroaches accumulated mostly lactate and acetate. Similar shifts toward more-oxidized products were observed when the pure cultures were exposed to oxygen, which corroborated the strong effects of oxygen on the metabolic fluxes previously observed in termite guts. Oxygen microsensor profiles of the guts of germfree, gnotobiotic, and conventional cockroaches indicated that both gut tissue and microbiota contribute to oxygen consumption and suggest that the oxygen status influences the colonization success.
Mapping the Distribution of Cysts from the Toxic Dinoflagellate Cochlodinium polykrikoides in Bloom-Prone Estuaries by a Novel Fluorescence
In Situ
Hybridization Assay
Authors: Hattenrath-Lehmann Theresa K. , Zhen Yu , Wallace Ryan B. , Tang Ying-Zhong , Gobler Christopher J. 
Published: December 2015

ABSTRACT

Cochlodinium polykrikoides
is a cosmopolitan dinoflagellate that is notorious for causing fish-killing harmful algal blooms (HABs) across North America and Asia. While recent laboratory and ecosystem studies have definitively demonstrated that
Cochlodinium
forms resting cysts that may play a key role in the dynamics of its HABs, uncertainties regarding cyst morphology and detection have prohibited even a rudimentary understanding of the distribution of
C. polykrikoides
cysts in coastal ecosystems. Here, we report on the development of a fluorescence
in situ
hybridization (FISH) assay using oligonucleotide probes specific for the large subunit (LSU) ribosomal DNA (rDNA) of
C. polykrikoides
. The LSU rDNA-targeted FISH assay was used with epifluorescence microscopy and was iteratively refined to maximize the fluorescent reaction with
C. polykrikoides
and minimize cross-reactivity. The final LSU rDNA-targeted FISH assay was found to quantitatively recover cysts made by North American isolates of
C. polykrikoides
but not cysts formed by other common cyst-forming dinoflagellates. The method was then applied to identify and map
C. polykrikoides
cysts across bloom-prone estuaries. Annual cyst and vegetative cell surveys revealed that elevated densities of
C. polykrikoides
cysts (>100 cm
−3
) during the spring of a given year were spatially consistent with regions of dense blooms the prior summer. The identity of cysts in sediments was confirmed via independent amplification of
C. polykrikoides
rDNA. This study mapped
C. polykrikoides
cysts in a natural marine setting and indicates that the excystment of cysts formed by this harmful alga may play a key role in the development of HABs of this species.
Gastric Metaplasia Induced by Helicobacter pylori Is Associated with Enhanced SOX9 Expression via Interleukin-1 Signaling
Authors: Serizawa Takako , Hirata Yoshihiro , Hayakawa Yoku , Suzuki Nobumi , Sakitani Kosuke , Hikiba Yohko , Ihara Sozaburo , Kinoshita Hiroto , Nakagawa Hayato , Tateishi Keisuke , Koike Kazuhiko 
Published: December 2015

ABSTRACT

Histopathological changes of the gastric mucosa after
Helicobacter pylori
infection, such as atrophy, metaplasia, and dysplasia, are considered to be precursors of gastric cancer, yet the mechanisms of histological progression are unknown. The aim of this study was to analyze the histopathological features of the gastric mucosa in mice infected with
H. pylori
strain PMSS1 in relation to gastric stem cell marker expression. C57BL/6J mice infected with PMSS1 were examined for histopathological changes, levels of proinflammatory cytokines, and expression of stem cell markers. Histopathological gastritis scores, such as atrophy and metaplasia, and levels of proinflammatory cytokines, such as tumor necrosis factor alpha (TNF-α) and interleukin-1β (IL-1β), were increased after PMSS1 infection. Expression levels of the cell proliferation and stem cell markers CD44 and SOX9 were also significantly increased in PMSS1-infected mice. Importantly, almost all metaplastic cells induced by PMSS1 infection expressed SOX9. When IL-1 receptor (IL-1R) knockout mice were infected with PMSS1, metaplastic changes and expression levels of stem cell markers were significantly decreased compared with those in wild-type (WT) mice. In conclusion,
H. pylori
infection induced the expression of cytokines and stem cell markers and histopathological metaplasia in the mouse gastric mucosa. SOX9 expression, in particular, was strongly associated with metaplastic changes, and these changes were dependent on IL-1 signaling. The results suggested the importance of SOX9 in gastric carcinogenesis.
Evaluation of Matrix-Assisted Laser Desorption Ionization−Time of Flight Mass Spectrometry for Identification of Mycobacterium species, Nocardia species, and Other Aerobic Actinomycetes
Authors: Buckwalter S. P. , Olson S. L. , Connelly B. J. , Lucas B. C. , Rodning A. A. , Walchak R. C. , Deml S. M. , Wohlfiel S. L. , Wengenack N. L. 
Published: December 2015

ABSTRACT

The value of matrix-assisted laser desorption ionization−time of flight mass spectrometry (MALDI-TOF MS) for the identification of bacteria and yeasts is well documented in the literature. Its utility for the identification of mycobacteria and
Nocardia
spp. has also been reported in a limited scope. In this work, we report the specificity of MALDI-TOF MS for the identification of 162
Mycobacterium
species and subspecies, 53
Nocardia
species, and 13 genera (totaling 43 species) of other aerobic actinomycetes using both the MALDI-TOF MS manufacturer's supplied database(s) and a custom database generated in our laboratory. The performance of a simplified processing and extraction procedure was also evaluated, and, similar to the results in an earlier literature report, our viability studies confirmed the ability of this process to inactivate
Mycobacterium tuberculosis
prior to analysis. Following library construction and the specificity study, the performance of MALDI-TOF MS was directly compared with that of 16S rRNA gene sequencing for the evaluation of 297 mycobacteria isolates, 148
Nocardia
species isolates, and 61 other aerobic actinomycetes isolates under routine clinical laboratory working conditions over a 6-month period. MALDI-TOF MS is a valuable tool for the identification of these groups of organisms. Limitations in the databases and in the ability of MALDI-TOF MS to rapidly identify slowly growing mycobacteria are discussed.
Dimerization of the SP1 Region of HIV-1 Gag Induces a Helical Conformation and Association into Helical Bundles: Implications for Particle Assembly
Authors: Datta Siddhartha A. K. , Clark Patrick K. , Fan Lixin , Ma Buyong , Harvin Demetria P. , Sowder Raymond C. , Nussinov Ruth , Wang Yun-Xing , Rein Alan 
Published: December 2015

ABSTRACT
HIV-1 immature particle (virus-like particle [VLP]) assembly is mediated largely by interactions between the capsid (CA) domains of Gag molecules but is facilitated by binding of the nucleocapsid (NC) domain to nucleic acid. We previously investigated the role of SP1, a “spacer” between CA and NC, in VLP assembly. We found that small changes in SP1 drastically disrupt assembly and that a peptide representing the sequence around the CA-SP1 junction is helical at high but not low concentrations. We suggested that by virtue of such a concentration-dependent change, this region could act as a molecular switch to activate HIV-1 Gag for VLP assembly. A leucine zipper domain can replace NC in Gag and still lead to the efficient assembly of VLPs. We find that SP1 mutants also disrupt assembly by these Gag-Zip proteins and have now studied a small fragment of this Gag-Zip protein, i.e., the CA-SP1 junction region fused to a leucine zipper. Dimerization of the zipper places SP1 at a high local concentration, even at low total concentrations. In this context, the CA-SP1 junction region spontaneously adopts a helical conformation, and the proteins associate into tetramers. Tetramerization requires residues from both CA and SP1. The data suggest that once this region becomes helical, its propensity to self-associate could contribute to Gag-Gag interactions and thus to particle assembly. There is complete congruence between CA/SP1 sequences that promote tetramerization when fused to zippers and those that permit the proper assembly of full-length Gag; thus, equivalent interactions apparently participate in VLP assembly and in SP1-Zip tetramerization.

IMPORTANCE
Assembly of HIV-1 Gag into virus-like particles (VLPs) appears to require an interaction with nucleic acid, but replacement of its principal nucleic acid-binding domain with a dimerizing leucine zipper domain leads to the assembly of RNA-free VLPs. It has not been clear how dimerization triggers assembly. Results here show that the SP1 region spontaneously switches to a helical state when fused to a leucine zipper and that these helical molecules further associate into tetramers, mediated by interactions between hydrophobic faces of the helices. Thus, the correct juxtaposition of the SP1 region makes it “association competent.” Residues from both capsid and SP1 contribute to tetramerization, while mutations disrupting proper assembly in Gag also prevent tetramerization. Thus, this region is part of an associating interface within Gag, and its intermolecular interactions evidently help stabilize the immature Gag lattice. These interactions are disrupted by proteolysis of the CA-SP1 junction during virus maturation.
NP1 Protein of the Bocaparvovirus Minute Virus of Canines Controls Access to the Viral Capsid Genes via Its Role in RNA Processing
Authors: Fasina Olufemi O. , Dong Yanming , Pintel David J. 
Published: December 2015

ABSTRACT

Minute virus of canines (MVC) is an autonomous parvovirus in the genus
Bocaparvovirus
. It has a single promoter that generates a single pre-mRNA processed via alternative splicing and alternative polyadenylation to produce at least 8 mRNA transcripts. MVC contains two polyadenylation sites, one at the right-hand end of the genome, (pA)d, and another complex site, (pA)p, within the capsid-coding region. During viral infection, the mRNAs must extend through (pA)p and undergo additional splicing of the immediately upstream 3D∕3A intron to access the capsid gene. MVC NP1 is a 22-kDa nuclear phosphoprotein unique to the genus
Bocaparvovirus
of the
Parvovirinae
which we have shown governs suppression of (pA)p independently of viral genome replication. We show here that in addition to suppression of (pA)p, NP1 is also required for the excision of the MVC 3D∕3A intron, independently of its effect on alternative polyadenylation. Mutations of the arginine∕serine (SR) di-repeats within the intrinsically disordered amino terminus of NP1 are required for splicing of the capsid transcript but not suppression of polyadenylation at (pA)p. 3′-end processing of MVC mRNAs at (pA)p is critical for viral genome replication and the optimal expression of NP1 and NS1. Thus, a finely tuned balance between (pA)p suppression and usage is necessary for efficient virus replication. NP1 is the first parvovirus protein implicated in RNA processing. Its characterization reveals another way that parvoviruses govern access to their capsid protein genes, namely, at the RNA level, by regulating the essential splicing of an intron and the suppression of an internal polyadenylation site.

IMPORTANCE
The
Parvovirinae
are small nonenveloped icosahedral viruses that are important pathogens in many animal species, including humans. Although parvoviruses have only subtle early-to-late expression shifts, they all regulate access to their capsid genes. Minute virus of canines (MVC) is an autonomous parvovirus in the genus
Bocaparvovirus
. It has a single promoter generating a single pre-mRNA which is processed via alternative splicing and alternative polyadenylation to generate at least 8 mRNA transcripts. MVC contains two polyadenylation sites, one at the right-hand end of the genome, (pA)d, and another, (pA)p, within the capsid-coding region. It had not been clear how the potent internal polyadenylation motif is suppressed to allow processing, export, and accumulation of the spliced capsid protein-encoding mRNAs. We show here that MVC NP1, the first parvovirus protein to be implicated in RNA processing, governs access to the MVC capsid gene by facilitating splicing and suppressing internal polyadenylation of MVC pre-mRNAs.
Episodic Diversifying Selection Shaped the Genomes of Gibbon Ape Leukemia Virus and Related Gammaretroviruses
Authors: Alfano Niccolò , Kolokotronis Sergios-Orestis , Tsangaras Kyriakos , Roca Alfred L. , Xu Wenqin , Eiden Maribeth V. , Greenwood Alex D. 
Published: December 2015

ABSTRACTGibbon ape leukemia viruses (GALVs) are part of a larger group of pathogenic gammaretroviruses present across phylogenetically diverse host species of Australasian mammals. Despite the biomedical utility of GALVs as viral vectors and in cancer gene therapy, full genome sequences have not been determined for all of the five identified GALV strains, nor has a comprehensive evolutionary analysis been performed. We therefore generated complete genomic sequences for each GALV strain using hybridization capture and high-throughput sequencing. The four strains of GALV isolated from gibbons formed a monophyletic clade that was closely related to the woolly monkey virus (WMV), which is a GALV strain that likely originated in a gibbon host. The GALV-WMV clade in turn formed a sister group to the koala retroviruses (KoRVs). Genomic signatures of episodic diversifying selection were detected among the gammaretroviruses with concentration in theenvgene across the GALV strains that were particularly oncogenic and KoRV strains that were potentially exogenous, likely reflecting their adaptation to the host immune system.In vitrostudies involving vectors chimeric between GALV and KoRV-B established that variable regions A and B of the surface unit of the envelope determine which receptor is used by a viral strain to enter host cells.IMPORTANCEThe gibbon ape leukemia viruses (GALVs) are among the most medically relevant retroviruses due to their use as viral vectors for gene transfer and in cancer gene therapy. Despite their importance, full genome sequences have not been determined for the majority of primate isolates, nor has comprehensive evolutionary analysis been performed, despite evidence that the viruses are facing complex selective pressures associated with cross-species transmission. Using hybridization capture and high-throughput sequencing, we report here the full genome sequences of all the GALV strains and demonstrate that diversifying selection is acting on them, particularly in the envelope gene in functionally important domains, suggesting that host immune pressure is shaping GALV evolution.
Using palaeomagnetism to determine late Mesoproterozoic palaeogeographic history and tectonic relations of the Sinclair terrane, Namaqua orogen, Namibia
Authors: Panzik J. E. , Evans D. A. D. , Kasbohm J. J. , Hanson R. , Gose W. , Desormeau J. 
Published: December 2015

Abstract

The Sinclair terrane is an important part of the Namaqua orogenic province in southern Namibia containing well-preserved Mesoproterozoic volcano-sedimentary successions suitable for palaeomagnetic and geochronological studies. The Guperas Formation in the upper part of the Sinclair stratigraphic assemblage contains both volcanic and sedimentary rocks cut by a bimodal dyke swarm with felsic members dated herein by U–Pb on zircon at
c.
1105 Ma. Guperas igneous rocks yield a pre-fold direction and palaeomagnetic pole similar to that previously reported. Guperas sedimentary rocks yield positive conglomerate and fold tests, with a maximum concentration of characteristic remanence directions at 100% untilting. The combined Guperas data generate a palaeomagnetic pole of 69.8° N, 004.1° E (
A
95
=7.4°,
N=
9). The 1105 Ma post-Guperas dykes yield stable remanence directions with positive baked-contact tests and a palaeomagnetic pole at 62.3° N, 031.9° E (
A
95
=6.9°,
N=
26), which is coincident with that of the Kalahari-wide Umkondo large igneous province, demonstrating tectonic coherence of the Sinclair terrane with the Kalahari craton at the time of dyke emplacement. These results show that palaeomagnetic and geochronological studies of the Sinclair terrane can provide kinematic constraints on the tectonic evolution of the Namaqua–Natal–Maud orogenic belt and its role in the formation of the Rodinia supercontinent.
Quantifying the Role of Circulating Unconjugated Estradiol in Mediating the Body Mass Index–Breast Cancer Association
Authors: Schairer Catherine , Fuhrman Barbara J. , Boyd-Morin Jennifer , Genkinger Jeanine M. , Gail Mitchell H. , Hoover Robert N. , Ziegler Regina G. 
Published: December 2015

Abstract
Background: Higher body mass index (BMI) and circulating estrogen levels each increase postmenopausal breast cancer risk, particularly estrogen receptor–positive (ER+) tumors. Higher BMI also increases estrogen production.
Methods: We estimated the proportion of the BMI-ER+ breast cancer association mediated through estrogen in a case–control study nested within the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial. Participants included 143 women with invasive ER+ breast cancer and 268 matched controls, all postmenopausal and never having used hormone therapy at baseline. We used liquid chromatography-tandem mass spectrometry to measure 15 estrogens and estrogen metabolites in baseline serum. We calculated BMI from self-reported height and weight at baseline. We estimated the mediating effect of unconjugated estradiol on the BMI-ER+ breast cancer association using Aalen additive hazards and Cox regression models.
Results: All estrogens and estrogen metabolites were statistically significantly correlated with BMI, with unconjugated estradiol most strongly correlated [Pearson correlation (r) = 0.45]. Approximately 7% to 10% of the effect of overweight, 12% to 15% of the effect of obesity, and 19% to 20% of the effect of a 5 kg/m2 BMI increase on ER+ breast cancer risk was mediated through unconjugated estradiol. The BMI–breast cancer association, once adjusted for unconjugated estradiol, was not modified by further adjustment for two metabolic ratios statistically significantly associated with both breast cancer and BMI.
Conclusion: Circulating unconjugated estradiol levels partially mediate the BMI–breast cancer association, but other potentially important estrogen mediators (e.g., bioavailable estradiol) were not evaluated.
Impact: Further research is required to identify mechanisms underlying the BMI–breast cancer association. Cancer Epidemiol Biomarkers Prev; 25(1); 105–13. ©2015 AACR.