bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and analysis of immunoreactive proteins of Shigella flexneri in human sera and stool specimens
Authors: Singh Kirnpal Kaur Banga , Salleh Mohd Zaki , Ahmed Naveed , Yean Yean Chan , Ismail Asma 
Published: May 2024

Background
The method currently available to diagnose shigellosis is insensitive and has many limitations. Thus, this study was designed to identify specific antigenic protein(s) among the cell surface associated proteins (SAPs) of Shigella that would be valuable in the development of an alternative diagnostic assay for shigellosis, particularly one that could be run using a stool sample rather than serum.

Methods
The SAPs of clinical isolates of S. dysenteriae, S. boydii, Shigella flexneri, and S. sonnei were extracted from an overnight culture grown at 37 °C using acidified-glycine extraction methods. Protein profiles were observed by SDS-PAGE. To determine if antibodies specific to certain Shigella SAPs were present in both sera and stool suspensions, Western blot analysis was used to detect the presence of IgA, IgG, and IgM.

Results
Immunoblot analysis revealed that sera from patients infected with S. flexneri recognized 31 proteins. These SAP antigens are recognized by the host humoral response during Shigella infection. Specific antibodies against these antigens were also observed in intestinal secretions of shigellosis patients. Of these 31 S. flexneri proteins, the 35 kDa protein specifically reacted against IgA present in patients’ stool suspensions. Further study illustrated the immunoreactivity of this protein in S. dysenteriae, S. boydii, and S. sonnei. This is the first report that demonstrates the presence of immunoreactive Shigella SAPs in stool suspensions. The SAPSs could be very useful in developing a simple and rapid serodiagnostic assay for shigellosis directly from stool specimens.
146
Sm–
142
Nd systematics measured in enstatite chondrites reveals a heterogeneous distribution of
142
Nd in the solar nebula
Authors: Gannoun Abdelmouhcine , Boyet Maud , Rizo Hanika , El Goresy Ahmed 
Published: April 2011

The short-lived
146
Sm–
142
Nd chronometer (
T
1/2
= 103 Ma) is used to constrain the early silicate evolution of planetary bodies. The composition of bulk terrestrial planets is then considered to be similar to that of primitive chondrites that represent the building blocks of rocky planets. However for many elements chondrites preserve small isotope differences. In this case it is not always clear to what extent these variations reflect the isotope heterogeneity of the protosolar nebula rather than being produced by the decay of parent isotopes. Here we present Sm–Nd isotopes data measured in a comprehensive suite of enstatite chondrites (EC). The EC preserve
142
Nd/
144
Nd ratios that range from those of ordinary chondrites to values similar to terrestrial samples. The EC having terrestrial
142
Nd/
144
Nd ratios are also characterized by small
144
Sm excesses, which is a pure p-process nuclide. The correlation between
144
Sm and
142
Nd for chondrites may indicate a heterogeneous distribution in the solar nebula of p-process matter synthesized in supernovae. However to explain the difference in
142
Nd/
144
Nd ratios, 20% of the p-process contribution to
142
Nd is required, at odds with the value of 4% currently proposed in stellar models. This study highlights the necessity of obtaining high-precision
144
Sm measurements to interpret properly measured
142
Nd signatures. Another explanation could be that the chondrites sample material formed in different pulses of the lifetime of asymptotic giant branch stars. Then the isotope signature measured in SiC presolar would not represent the unique s-process signature of the material present in the solar nebula during accretion.
Antimicrobial peptide killing of African trypanosomes
Authors: HARRINGTON J. M. 
Published: April 2011

SummaryThe diseases caused by trypanosomes are medically and economically devastating to the population of Sub‐Saharan Africa. Parasites of the genus Trypanosoma infect both humans, causing African sleeping sickness, and livestock, causing Nagana. The development of effective treatment strategies has suffered from severe side effects of approved drugs, resistance and major difficulties in delivering drugs. Antimicrobial peptides (AMPs) are ubiquitous components of immune defence and are being rigorously pursued as novel sources of new therapeutics for a variety of pathogens. Here, we review the role of AMPs in the innate immune response of the tsetse fly to African trypanosomes, catalogue trypanocidal AMPs from diverse organisms and highlight the susceptibility of bloodstream form African trypanosomes to killing by unconventional toxic peptides.
Non‐esterified polyunsaturated fatty acids distinctly modulate the mitochondrial and cellular ROS production in normoxia and hypoxia
Authors: Schönfeld Peter , Schlüter Thomas , Fischer Klaus‐Dieter , Reiser Georg 
Published: April 2011

J. Neurochem. (2011) 10.1111/j.1471‐4159.2011.07286.xAbstractThere is an intense discussion about the subcellular origin of the generation of reactive oxygen species (ROS) under hypoxia. Since this fundamental question can be addressed only in a cellular system, the O2‐sensing rat pheochromocytoma (PC12) cells were used. Severe hypoxia is known to elevate non‐esterified fatty acids. Therefore, the site(s) of ROS generation were studied in cells which we simultaneously exposed to hypoxia (1% oxygen) and free fatty acids (FFA). We obtained the following results: (i) at hypoxia, ROS generation increases in PC12 cells but not in mitochondria isolated therefrom. (ii) Non‐esterified polyunsaturated fatty acids (PUFA) enhance the ROS release from PC12 cells as well as from mitochondria, both in normoxia and in hypoxia. (iii) PUFA‐induced ROS generation by PC12 cells is not decreased either by inhibitors of the cell membrane NAD(P)H oxidase or inhibitors impairing the PUFA metabolism. (iv) PUFA‐induced ROS generation of mitochondria is paralleled by a decline of the NADH‐cytochrome c reductase activity (reflecting combined enzymatic activity of complex I plus III). (v) Mitochondrial superoxide indicator (MitoSOXred)‐loaded cells exposed to PUFA exhibit increased fluorescence indicating mitochondrial ROS generation. In conclusion, elevated PUFA levels enhance cellular ROS level in hypoxia, most likely by impairing the electron flux within the respiratory chain. Thus, we propose that PUFAs are likely to act as important extrinsic factor to enhance the mitochondria‐associated intracellular ROS signaling in hypoxia.
Regulation of P‐glycoprotein by orphan nuclear receptors in human brain microvessel endothelial cells
Authors: Chan Gary N. Y. , Hoque Md. Tozammel , Cummins Carolyn L. , Bendayan Reina 
Published: April 2011

J. Neurochem. (2011) 118, 163–175.AbstractIn mammalian systems, pregnane X receptor (PXR) and constitutive androstane receptor (CAR) have been recognized as xenobiotic‐sensors which can up‐regulate the functional expression of drug transporters, such as P‐glycoprotein (P‐gp). In the brain, an increase in P‐gp expression can further limit drug permeability across the blood–brain barrier (BBB) and potentially reduce CNS pharmacotherapy efficacy. At present, the involvement of human PXR (hPXR) and CAR (hCAR) in the regulation of P‐gp expression at the human BBB is unknown. In this study, we investigate the role of hPXR and hCAR in the regulation of P‐gp expression using a human cerebral microvessel endothelial cell culture system. We demonstrate that activation of hPXR and hCAR by their respective ligands leads to P‐gp induction at both mRNA and protein levels, while pharmacological inhibitors of hPXR and hCAR prevent ligand‐mediated P‐gp induction. Ligand‐induced nuclear translocation of hPXR is observed, although such effect could not be demonstrated for hCAR. Furthermore, down‐regulation of hPXR and hCAR proteins using small‐interfering RNA decreased P‐gp expression. Our findings provide first evidence for P‐gp regulation by hPXR and hCAR at the human BBB and suggest insights on how to achieve selective P‐gp regulation at this site.
Sustained TRPA1 activation in vivo
Authors: Koivisto A. 
Published: April 2011

AbstractTransient receptor potential A1 (TRPA1) is a calcium permeable non‐selective cation channel that is selectively localized to peptidergic C‐fibres in the pain pathway. TRPA1 is highly conserved across the animal kingdom and it is able to detect a wide range of potentially toxic environmental chemicals. An unusual mechanism of TRPA1 activation was recently elucidated in which reactive agonists bind covalently to cysteines and lysine in the intracellular N‐terminus. Despite a covalent activation mechanism, only transient TRPA1 activation is seen in the maintained presence of reactive agonists in whole‐cell patch clamp experiments. I suggest that previous patch clamp studies are performed under conditions that do not fully mimic all aspects of TRPA1 activation. Here, I argue that compelling evidence exists for sustained TRPA1 activation in several chronic (neuropathic) pain‐related pathophysiological conditions in vivo. I discuss briefly putative mechanisms that are likely to contribute to and maintain sustained TRPA1 agonist levels through increased production and/or decreased metabolism and inactivation. Chronic pain can be understood as a false alarm evoked by sustained and increased levels of endogenous TRPA1 agonists in various pathophysiological conditions.
Rapid Screening of Epidemiologically Important Salmonella enterica subsp. enterica Serovars by Whole-Cell Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Authors: Dieckmann Ralf , Malorny Burkhard 
Published: April 2011

ABSTRACT

Currently, 2,610 different
Salmonella
serovars have been described according to the White-Kauffmann-Le Minor scheme. They are routinely differentiated by serotyping, which is based on the antigenic variability at lipopolysaccharide moieties (O antigens), flagellar proteins (H1 and H2 antigens), and capsular polysaccharides (Vi antigens). The aim of this study was to evaluate the potential of matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry for rapid screening and identification of epidemiologically important
Salmonella enterica
subsp.
enterica
serovars based on specific sets of serovar-identifying biomarker ions. By analyzing 913
Salmonella enterica
subsp.
enterica
strains representing 89 different serovars using MALDI-TOF mass spectrometry, several potentially serovar-identifying biomarker ions were selected. Based on a combination of genus-, species-, subspecies-, and serovar-identifying biomarker ions, a decision tree classification algorithm was derived for the rapid identification of the five most frequently isolated
Salmonella enterica
serovars, Enteritidis, Typhimurium/4,[5],12:i:-, Virchow, Infantis, and Hadar. Additionally, sets of potentially serovar-identifying biomarker ions were detected for other epidemiologically interesting serovars, such as Choleraesuis, Heidelberg, and Gallinarum. Furthermore, by using a bioinformatic approach, sequence variations corresponding to single or multiple amino acid exchanges in several biomarker proteins were tentatively assigned. The inclusivity and exclusivity of the specific sets of serovar-identifying biomarker ions for the top 5 serovars were almost 100%. This study shows that whole-cell MALDI-TOF mass spectrometry can be a rapid method for prescreening
S. enterica
subsp.
enterica
isolates to identify epidemiologically important serovars and to reduce sample numbers that have to be subsequently analyzed using conventional serotyping by slide agglutination techniques.
Sulfate-Reducing Bacterium Desulfovibrio desulfuricans ND132 as a Model for Understanding Bacterial Mercury Methylation
Authors: Gilmour Cynthia C. , Elias Dwayne A. , Kucken Amy M. , Brown Steven D. , Palumbo Anthony V. , Schadt Christopher W. , Wall Judy D. 
Published: April 2011

ABSTRACT

We propose the use of
Desulfovibrio desulfuricans
ND132 as a model species for understanding the mechanism of microbial Hg methylation. Strain ND132 is an anaerobic dissimilatory sulfate-reducing bacterium (DSRB), isolated from estuarine mid-Chesapeake Bay sediments. It was chosen for study because of its exceptionally high rates of Hg methylation in culture and its metabolic similarity to the lost strain
D. desulfuricans
LS, the only organism for which methylation pathways have been partially defined. Strain ND132 is an incomplete oxidizer of short-chain fatty acids. It is capable of respiratory growth using fumarate as an electron acceptor, supporting growth without sulfide production. We used enriched stable Hg isotopes to show that ND132 simultaneously produces and degrades methylmercury (MeHg) during growth but does not produce elemental Hg. MeHg produced by cells is mainly excreted, and no MeHg is produced in spent medium. Mass balances for Hg and MeHg during the growth of cultures, including the distribution between filterable and particulate phases, illustrate how medium chemistry and growth phase dramatically affect Hg solubility and availability for methylation. The available information on Hg methylation among strains in the genus
Desulfovibrio
is summarized, and we present methylation rates for several previously untested species. About 50% of
Desulfovibrio
strains tested to date have the ability to produce MeHg. Importantly, the ability to produce MeHg is constitutive and does not confer Hg resistance. A 16S rRNA-based alignment of the genus
Desulfovibrio
allows the very preliminary assessment that there may be some evolutionary basis for the ability to produce MeHg within this genus.
Bulk Segregant Analysis Followed by High-Throughput Sequencing Reveals the Neurospora Cell Cycle Gene,
ndc-1
, To Be Allelic with the Gene for Ornithine Decarboxylase,
spe-1
Authors: Pomraning Kyle R. , Smith Kristina M. , Freitag Michael 
Published: April 2011

ABSTRACT

With the advent of high-throughput DNA sequencing, it is now straightforward and inexpensive to generate high-density small nucleotide polymorphism (SNP) maps. Here we combined high-throughput sequencing with bulk segregant analysis to expedite mutation mapping. The general map location of a mutation can be identified by a single backcross to a strain enriched in SNPs compared to a standard wild-type strain. Bulk segregant analysis simultaneously increases the likelihood of determining the precise nature of the mutation. We present here a high-density SNP map between
Neurospora crassa
Mauriceville-1-c (FGSC2225) and OR74A (FGSC2489), the strains most typically used by
Neurospora
researchers to carry out mapping crosses. We further have demonstrated the utility of the Mauriceville sequence and our approach by mapping the mutation responsible for the only existing temperature-sensitive (ts) cell cycle mutation in
Neurospora
,
nuclear division cycle-1
(
ndc-1
). The single T-to-C point mutation maps to the gene encoding ornithine decarboxylase (ODC),
spe-1
(NCU01271), and changes a Phe to a Ser residue within a highly conserved motif next to the catalytic site of the enzyme. By growth on spermidine and complementation with a wild-type
spe-1
gene, we showed that the defect in
spe-1
is responsible for the ts
ndc-1
mutation. Based on our results, we propose changing
ndc-1
to
spe-1

ndc

, which reflects that this mutation results in an ODC with a specific nuclear division defect.
Cellular Stoichiometry of the Chemotaxis Proteins in Bacillus subtilis
Authors: Cannistraro Vincent J. , Glekas George D. , Rao Christopher V. , Ordal George W. 
Published: April 2011

ABSTRACT

The chemoreceptor-CheA kinase-CheW coupling protein complex, with ancillary associated proteins, is at the heart of chemotactic signal transduction in bacteria. The goal of this work was to determine the cellular stoichiometry of the chemotaxis signaling proteins in
Bacillus subtilis
. Quantitative immunoblotting was used to determine the total number of chemotaxis proteins in a single cell of
B. subtilis
. Significantly higher levels of chemoreceptors and much lower levels of CheA kinase were measured in
B. subtilis
than in
Escherichia coli
. The resulting cellular ratio of chemoreceptor dimers per CheA dimer in
B. subtilis
is roughly 23.0 ± 4.5 compared to 3.4 ± 0.8 receptor dimers per CheA dimer observed in
E. coli
, but the ratios of the coupling protein CheW to the CheA dimer are nearly identical in the two organisms. The ratios of CheB to CheR in
B. subtilis
are also very similar, although the overall levels of modification enzymes are higher. When the potential binding partners of CheD are deleted, the levels of CheD drop significantly. This finding suggests that
B. subtilis
selectively degrades excess chemotaxis proteins to maintain optimum ratios. Finally, the two cytoplasmic receptors were observed to localize among the other receptors at the cell poles and appear to participate in the chemoreceptor complex. These results suggest that there are many novel features of
B. subtilis
chemotaxis compared with the mechanism in
E. coli
, but they are built on a common core.
Cloning of a Novel Collagenase Gene from the Gram-Negative Bacterium Grimontia (Vibrio) hollisae 1706B and Its Efficient Expression in Brevibacillus choshinensis
Authors: Teramura Naoko , Tanaka Keisuke , Iijima Katsumasa , Hayashida Osamu , Suzuki Koki , Hattori Shunji , Irie Shinkichi 
Published: April 2011

ABSTRACT

The collagenase gene was cloned from
Grimontia
(
Vibrio
)
hollisae
1706B, and its complete nucleotide sequence was determined. Nucleotide sequencing showed that the open reading frame was 2,301 bp in length and encoded an 84-kDa protein of 767 amino acid residues. The deduced amino acid sequence contains a putative signal sequence and a zinc metalloprotease consensus sequence, the HEXXH motif.
G. hollisae
collagenase showed 60 and 59% amino acid sequence identities to
Vibrio parahaemolyticus
and
Vibrio alginolyticus
collagenase, respectively. In contrast, this enzyme showed <20% sequence identity with
Clostridium histolyticum
collagenase. When the recombinant mature collagenase, which consisted of 680 amino acids with a calculated molecular mass of 74 kDa, was produced by the
Brevibacillus
expression system, a major gelatinolytic protein band of ∼60 kDa was determined by zymographic analysis. This result suggested that cloned collagenase might undergo processing after secretion. Moreover, the purified recombinant enzyme was shown to possess a specific activity of 5,314 U/mg, an ∼4-fold greater activity than that of
C. histolyticum
collagenase.
Characterization of the Induction and Cellular Role of the BaeSR Two-Component Envelope Stress Response of Escherichia coli
Authors: Leblanc Shannon K. D. , Oates Christopher W. , Raivio Tracy L. 
Published: April 2011

ABSTRACT

The bacterial cell envelope is the interface between a bacterium and its environment and is constantly exposed to environmental changes. The BaeSR two-component system regulates one of six envelope stress responses in
Escherichia coli
and is induced by spheroplasting, overexpression of the pilin subunit PapG, and exposure to indole. The known BaeR regulon is small, consisting of eight genes,
mdtABCD-baeSR
,
acrD
, and
spy
, two of which encode the BaeSR two-component system itself. In this study, we investigated the molecular nature of the BaeS-inducing cue and the cellular role of the BaeSR envelope stress response. We demonstrated that at least two flavonoids and sodium tungstate are novel inducers of the BaeSR response. Interestingly, flavonoids and sodium tungstate led to much stronger induction of the BaeSR response in an
mdtA
efflux pump mutant, while indole did not. These findings are consistent with the hypothesis that flavonoids and sodium tungstate are natural substrates of the MdtABC efflux pump. Indole has recently been implicated in cell-cell signaling and biofilm repression through a putative interaction with the LuxR homologue SdiA. Using genetic analyses, we found that induction of the BaeSR response by indole occurs via a pathway separate from the SdiA biofilm pathway. Further, we demonstrated that the BaeSR response does not influence biofilm formation, nor is it involved in indole-mediated inhibition of biofilm formation. We hypothesize that the main function of the Bae response is to upregulate efflux pump expression in response to specific envelope-damaging agents.
Genomes of Two Chronological Isolates (Helicobacter pylori 2017 and 2018) of the West African Helicobacter pylori Strain 908 Obtained from a Single Patient
Authors: Avasthi Tiruvayipati Suma , Devi Singamaneni Haritha , Taylor Todd D. , Kumar Narender , Baddam Ramani , Kondo Shinji , Suzuki Yutaka , Lamouliatte Hervé , Mégraud Francis , Ahmed Niyaz 
Published: April 2011

ABSTRACT

The diverse clinical outcomes of colonization by
Helicobacter pylori
reflect the need to understand the genomic rearrangements enabling the bacterium to adapt to host niches and exhibit varied colonization/virulence potential. We describe the genome sequences of the two serial isolates,
H. pylori
2017 and 2018 (the chronological subclones of
H. pylori
908), cultured in 2003 from the antrum and corpus, respectively, of an African patient who suffered from recrudescent duodenal ulcer disease. When compared with the genome of the parent strain, 908 (isolated from the antrum of the same patient in 1994), the genome sequences revealed genomic alterations relevant to virulence optimization or host-specific adaptation.
Lewisyantigen (blood group 8, BG8) is a useful marker in the histopathological differential diagnosis of flat urothelial lesions of the urinary bladder
Authors: Gunia Sven , Kakies Christoph , May Matthias , Koch Stefan , Erbersdobler Andreas 
Published: April 2011

Background and aimsThe cell-surface carbohydrate Lewisyantigen (blood group 8, BG8) has recently been investigated in bladder cancer, but its role in the differential diagnosis of flat urothelial lesions of the bladder has not yet been systematically evaluated.Methods30 carcinoma in situ (CIS) and 30 non-CIS conditions of the bladder mucosa (four dysplasia and 26 reactive atypia according to consensus diagnoses) were comparatively assessed in terms of their Lewisyantigen staining profiles by two independent clinical pathologists.ResultsLewisyantigen expression differed significantly (p<0.001) between CIS (full thickness expression throughout the entire urothelium including the basal cell layer) and non-CIS conditions (patchy discontinuous expression restricted to individual cells scattered singly throughout the urothelial mucosa). The four dysplastic study cases showed Lewisyantigen expression more closely related to the staining profiles observed in most of the reactive urothelial atypia. κ statistics showed excellent inter-observer agreement between both raters in terms of Lewisyantigen staining evaluation (κ=0.9, p<0.001).ConclusionsThe data hint at the cell-surface carbohydrate Lewisyantigen as a so far neglected diagnostically useful marker to aid in the histological classification of conventionally equivocal flat urothelial lesions of the bladder in contemporary surgical pathology practice.