bluuebunny/crossref_metadata_2025 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.
Effect of Different Multipurpose Tree Species on Physico-chemical Properties of Loamy Sand Soil Under Rainfed Conditions
Authors: Chaudhary K. H.  , Jat J. R. , Joshi R. V. , Patel, D. J. .
Published: May 2024

A field experiment was conducted at Agroforestry Research Station, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, during 2019-20. The soils of the experimental field was low in organic carbon (0.24 per cent), available nitrogen (143.50 kg N/ha) and DTPA extractable iron (3.18 mg/kg), medium in available phosphorus (Olsen’s P 48.90 kg P2O5/ha), available potash (180.00 kg K2O/ha), manganese (7.8 mg/kg) and zinc (0.79 mg/kg) and high in copper content (0.61 mg/kg). An experiment consisting of six years old Agroforestry tree plantation which consisted of five multipurpose tree species (MPTs) viz., Tectona grandis, Eucalyptus camaldulensis, Gmelina arborea, Casuriana equstifolia and Melia azadiracht were designed in CRD with four replications. The experiment consisting of 96 trees per species with a plot size of 24 m × 16 m under 4 m × 4 m tree spacing. Among the above six tree species significantly the lowest BD (1.56 Mg/m3), higher WHC (27.87 per cent) and soil porosity (38.03 per cent) was recorded under Casuarinas equisetifolia tree species. Similarly the maximum mean organic carbon (0.445 per cent), available N (165.17 kg/ha), available K2O (196.26 kg/ha) and DTPA extractable iron (4.22 mg/kg) and copper (1.05 mg/kg) content were noted under Casuarina equisetifolia tree species. Whereas, the mean maximum available P2O5 (57.92 kg/ha) was noted under Tectona grandis. The mean maximum DTPA extractable manganese (8.34 mg/kg) and zinc (0.925 mg/kg) was noted under Eucalyptus camaldulensis and Melia azadiracht tree species, respectively.
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.
Leucosporidium drummii sp. nov., a member of the Microbotryomycetes isolated from soil
Authors: Yurkov A. M. , Schäfer A. M. , Begerow D.
Published: April 2011

Two strains of a novel teleomorphic basidiomycete were isolated from grassland soil. Standard phenotypic tests and phylogenetic analyses of 26S rRNA gene (D1/D2 domains) and ITS region sequences showed that the species belongs to the core group of the genus Leucosporidium. A novel species, Leucosporidium drummii sp. nov., is proposed to accommodate the two strains, with SEG-3-2-AY220T ( = CBS 11562T = MUCL 52878T) as the type strain. In addition, phylogenetic analysis revealed great genetic variability in the Leucosporidium scottii complex.
Nocardioides ginsengagri sp. nov., isolated from the soil of a ginseng field
Authors: Lee Sang-Hee , Liu Qing-Mei , Lee Sung-Taik , Kim Sun-Chang , Im Wan-Taek
Published: April 2011

A Gram-reaction-positive, rod-shaped, non-motile, non-spore-forming bacterium (strain BX5-10T) was isolated from the soil of a ginseng field on Baekdu Mountain in Jilin district, China. The taxonomic position of this bacterium was determined in an investigation based on a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain BX5-10T was shown to belong to the family Nocardioidaceae and to be most closely related to Nocardioides plantarum NCIMB 12834T (96.5 % sequence similarity), Nocardioides dokdonensis KCTC 19309T (96.2 %) and Nocardioides fonticola NAA-13T (95.1 %). Strain BX5-10T was characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in its cell-wall peptidoglycan, MK-8(H4) as the predominant menaquinone and C18 : 1ω9c, C16 : 0 and C17 : 1ω8c as its major fatty acids. The G+C content of the genomic DNA was 70.3 mol%. The novel strain could be differentiated genotypically and phenotypically from all recognized species of the genus Nocardioides. Based on the results of the phylogenetic analyses and the genotypic and phenotypic data, a novel species, Nocardioides ginsengagri sp. nov., is proposed. The type strain is BX5-10T ( = KCTC 19467T = DSM 21362T).
Patulibacter ginsengiterrae sp. nov., isolated from soil of a ginseng field, and an emended description of the genus Patulibacter
Authors: Kim Kwang Kyu , Lee Keun Chul , Lee Jung-Sook
Published: April 2011

A novel actinobacterial strain, designated P4-5T, was isolated from soil of a ginseng field located in Geumsan County, Republic of Korea. Cells of strain P4-5T were Gram-stain-positive, oxidase- and catalase-positive, motile, short rods and the strain produced creamy white colonies on trypticase soy agar. The isolate contained demethylmenaquinone 7 (DMK-7) as the predominant isoprenoid quinone, C18 : 1ω9c and anteiso-C15 : 0 as major fatty acids, diphosphatidylglycerol, phosphatidylglycerol and several unknown lipids in the polar lipid profile, galactose, glucose, mannose, arabinose, xylose (trace) and rhamnose as cell-wall sugars, and meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The DNA G+C content of strain P4-5T was 74.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing showed that strain P4-5T was related most closely to Patulibacter minatonensis KV-614T and Patulibacter americanus CP177-2T (98.4 and 98.2 % similarity, respectively) and that it formed a separate lineage in the genus Patulibacter. Combined phenotypic and DNA–DNA hybridization data supported the conclusion that strain P4-5T represents a novel species of the genus Patulibacter, for which the name Patulibacter ginsengiterrae sp. nov. is proposed. The type strain is P4-5T ( = KCTC 19427T  = CECT 7603T). An emended description of the genus Patulibacter is also provided.
Antimicrobial peptide killing of African trypanosomes
Authors: HARRINGTON J. M.
Published: April 2011

The 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.x

There 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.

In 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.
Molecular basis of toxicity of Clostridium perfringens epsilon toxin
Authors: Bokori‐Brown Monika , Savva Christos G. , Fernandes da Costa Sérgio P. , Naylor Claire E. , Basak Ajit K. , Titball Richard W.
Published: April 2011

Clostridium perfringensε‐toxin is produced by toxinotypes B and D strains. The toxin is the aetiological agent of dysentery in newborn lambs but is also associated with enteritis and enterotoxaemia in goats, calves and foals. It is considered to be a potential biowarfare or bioterrorism agent by the US Government Centers for Disease Control and Prevention. The relatively inactive 32.9 kDa prototoxin is converted to active mature toxin by proteolytic cleavage, either by digestive proteases of the host, such as trypsin and chymotrypsin, or by C. perfringensλ‐protease. In vivo, the toxin appears to target the brain and kidneys, but relatively few cell lines are susceptible to the toxin, and most work has been carried out using Madin–Darby canine kidney (MDCK) cells. The binding of ε‐toxin to MDCK cells and rat synaptosomal membranes is associated with the formation of a stable, high molecular weight complex. The crystal structure of ε‐toxin reveals similarity to aerolysin from Aeromonas hydrophila, parasporin‐2 from Bacillus thuringiensis and a lectin from Laetiporus sulphureus. Like these toxins, ε‐toxin appears to form heptameric pores in target cell membranes. The exquisite specificity of the toxin for specific cell types suggests that it binds to a receptor found only on these cells.
Seeking the determinants of the elusive functions of Sco proteins
Authors: Banci Lucia , Bertini Ivano , Cavallaro Gabriele , Ciofi‐Baffoni Simone
Published: April 2011

Sco proteins are present in all types of organisms, including the vast majority of eukaryotes and many prokaryotes. It is well established that Sco proteins in eukaryotes are involved in the assembly of the CuA cofactor of mitochondrial cytochrome c oxidase; however their precise role in this process has not yet been elucidated at the molecular level. In particular, some but not all eukaryotes including humans possess two Sco proteins whose individual functions remain unclear. There is evidence that eukaryotic Sco proteins are also implicated in other cellular processes such as redox signalling and regulation of copper homeostasis. The range of physiological functions of Sco proteins appears to be even wider in prokaryotes, where Sco‐encoding genes have been duplicated many times during evolution. While some prokaryotic Sco proteins are required for the biosynthesis of cytochrome c oxidase, others are most likely to take part in different processes such as copper delivery to other enzymes and protection against oxidative stress. The detailed understanding of the multiplicity of roles ascribed to Sco proteins requires the identification of the subtle determinants that modulate the two properties central to their known and potential functions, i.e. copper binding and redox properties. In this review, we provide a comprehensive summary of the current knowledge on Sco proteins gained by genetic, structural and functional studies on both eukaryotic and prokaryotic homologues, and propose some hints to unveil the elusive molecular mechanisms underlying their functions.
Sustained TRPA1 activation in vivo
Authors: Koivisto A.
Published: April 2011

Transient 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

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

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

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

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

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

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

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 aims

The 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.

Methods

30 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.

Results

Lewisyantigen 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).

Conclusions

The 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.
Human papilloma virus detection in neoplastic and non-neoplastic nasopharyngeal tissues in Taiwan
Authors: Huang Cheng-Chih , Hsiao Jenn-Ren , Yang Ming-Wei , Wu Yuan-Hua , Hsu Keng-Fu , Chang Yao , Chen Chaio-Wei , Tsai Sen-Tien , Wei Hsuan-Pei , Jin Ying-Tai
Published: April 2011

Background

Human papilloma virus (HPV) has been implicated in the carcinogenesis and prognosis of certain head and neck cancers. Whether it also has a role in the pathogenesis of nasopharyngeal carcinoma (NPC) in Taiwan is unclear.

Methods

Detection and genotyping of HPVs were performed in 43 primary NPCs (one WHO-I and 42 WHO-II/III) and 40 nasopharyngeal controls using PCR-based HPV genotyping arrays. Localisation of high-risk HPV and Epstein–Barr virus genomes was performed in another 46 primary NPCs (five WHO-I and 41 WHO-II/III) and seven paired metastatic WHO-II/III NPCs using in situ hybridisation.

Results

In the HPV genotyping cohort, oncogenic HPVs were detected equally in WHO-II/III NPCs (31%, 13/42) and nasopharyngeal controls (35%, 14/40). Tumour high-risk HPV status did not correlate with the prognosis of patients with NPC. In the high-risk HPV in situ hybridisation cohort, 14 (88%) of the 16 oncogenic HPV-positive WHO-II/III NPCs showed a unique cytoplasmic/perinuclear staining pattern, which is distinct from the typical dot/punctate nuclear staining pattern indicating HPV genome integration. In addition, oncogenic HPVs were not always retained in NPC cells during the process of metastasis.

Conclusions

This study does not support an association between oncogenic HPV and the carcinogenesis or prognosis of WHO-II/III NPCs in Taiwan.
I'll be a monkey's uncle: a moral challenge to human genetic enhancement research
Authors: Rosoff Philip M
Published: April 2011

The potential for genetic engineering of enhancements to complex human traits has been the subject of vigorous debate for a number of years. Most of the discussion has centered on the possible moral consequences of pursuing enhancements, especially those that might affect complex behaviours and components of personality. Little has been written on the actual process of implementing this technology. This paper presents a ‘thought experiment’ about the likely form of final preclinical testing for a technology to enhance intelligence as a prototypical multiplex trait. The significance and the potential dangers of implementing enhancements in humans, especially to highly valued traits such as intelligence, would mandate a thorough programme of testing in animals, including non-human primates such as chimpanzees. The implications this would have for researchers, society and, most importantly, the animals themselves are discussed, and the paper concludes with a suggestion for a morally justifiable approach to resolve the tragic question of what to do with research animals who have a cognitive capacity that is close to that of humans.
Solar ultraviolet-B radiation and aquatic primary production: damage, protection, and recovery
Authors: Vincent Warwick F. , Roy Suzanne
Published: April 2011

The continuing degradation of the Earth's ozone layer by atmospheric pollutants has generated concern about the impact of increased solar ultraviolet-B radiation (UV-B) on aquatic ecosystems. UV-B is a small (less than 1% of total energy) but highly active component of the solar spectrum that can penetrate to biologically significant depths in lakes and oceans. It has the potential to cause wide-ranging effects, including mutagenesis, chronic depression of key physiological processes, and acute physiological stress that may result in death. There are major uncertainties at present about the appropriate time scales and bioassay protocols for assessing such effects. Algal and cyanobacterial cells have four lines of defence against the toxic effects of UV-B. Some species avoid UV exposure by their choice of habitat or by migration strategies. Many species produce sunscreening pigments that filter out UV wavelengths; mycosporine-like amino acids are an especially important and ubiquitous class of such compounds. Most cells have a variety of defences against the toxic end products of UV radiation, such as radical scavenging by carotenoid pigments and superoxide dismutase. Finally, most cells have at least some ability to identify and repair the UV damage of DNA and other biomolecules. There is a large interspecific variability in the extent of each of these defence strategies. Continuing ozone depletion is not likely to cause an abrupt collapse of photosynthetic production, but may result in subtle, community-level responses that could ultimately impact on higher trophic levels.Key words: Arctic, Antarctic, photosynthesis, UV radiation, UV-B, ozone, atmospheric pollutants.
Declining amphibians in Europe, with particular emphasis on the situation in Britain
Authors: Halliday T. R.
Published: April 2011

Published information concerning the current status of Europe's amphibians is reviewed. A large proportion of species are categorized as endangered or vulnerable. For those species that have been the subject of intensive study, declines are attributed to a diversity of factors, all arising from human destruction or alteration of the habitat. Current evidence does not support the suggestion that amphibians are universally affected by a single common cause.Key words: amphibian, Europe, decline, habitat loss.
A critical review of mass balance methods for calculating critical loads of nitrogen for forested ecosystems
Authors: Pardo L. H. , Driscoll C. T.
Published: April 2011

Critical loads are used in the assessment of air pollution and regulation of the causative emissions to prevent or mitigate ecological damage. We critically review four mass balance methods for calculating critical loads for nitrogen deposition: the steady-state water chemistry method, the nitrogen mass balance method, the basic cation mass balance method, and the steady-state mass balance method. The critical loads may be calculated with respect to effects of acidification associated with nitrate leaching or effects of elevated nitrogen such as eutrophication, excess nitrate loss, and nutrient imbalances. The most useful method for calculating the critical load for nitrogen with respect to effects of elevated atmospheric deposition of nitrogen is the nitrogen mass balance method. The steady-state water chemistry method can be readily applied for regional-scale calculations because it requires only water chemistry data from synoptic surveys of surface waters and does not explicitly consider biogeochemical processes. Both of the other approaches are severely limited by lack of quantitative information on rates of mineral weathering. If weathering data were available, the steady-state mass balance method could be more effectively used to assess critical loads with respect to acidification. Similarly, the basic cation mass balance method could be used to calculate critical loads for both acidity and elevated nitrogen effects. Because of the complexity of the nitrogen cycle, it is not possible to obtain a single critical load for the whole ecosystem. Rather, one should analyze and synthesize several values of critical loads that reflect different components of the ecosystem and different ecological effects of elevated nitrogen deposition (e.g., acidification and eutrophication effects).Key words: atmospheric deposition of nitrogen, acidification, critical loads, nitrogen cycling.
Land application of sewage sludge: scientific perspectives of heavy metal loading limits in Europe and the United States
Authors: McGrath S. P. , Chang A. C. , Page A. L. , Witter E.
Published: April 2011

Heavy metals in sewage sludges accumulate in soils after successive sludge applications and can be toxic to plants, soil organisms, as well as humans and animals along the food chain. Because of this potential threat, many countries have set limits to the additions of metals in sludges to agricultural land, based on (i) the concentrations of metals in sludge itself, (ii) the loading, or total amount, of metal that can be added and often how quickly this can be applied, and (iii) the maximum concentrations of metals in soil which are allowed to build up after sludge applications. This review, based on regulations in the United States and some west European countries, shows that at present three basic approaches to setting limits can be distinguished: (i) a comprehensive analysis of the pathways of pollutant transfer to selected target organisms and an assessment of the likely harmful effects that metals may have on the target; (ii) setting limits consistent with the lowest observed adverse effect concentrations, which are actual cases of effects due to metals, but not necessarily derived from studies that involved land application of sewage sludge; and (iii) attempting to match the metal inputs to soil to the small losses of metals due to crop removal, soil erosion, and leaching ("metal balance approach"). These approaches are shown to result in widely different numerical limits being set for the same constituent, which is creating unease among the regulatory authorities worldwide. These differences appear to arise from at least two main sources. The first is whether, by a policy decision, zero impact is desired. This leads to very low limits, and is the philosophy behind the metal balance approach. The second is that those approaches that allow some increase in metal concentrations in soils often adopt different target organisms and these models suffer from the limited supply of relevant toxicity data, particularly information obtained from metals applied in sewage sludge. Differences in the philosophy behind environmental protection and in the choices of which organisms to protect explain the different metal limits for sewage sludge which have been adopted in the countries examined.Key words: zinc, cadmium, copper, chromium, nickel, lead, mercury, soil microbes, ecotoxicology, soil protection.
Cadmium in the aquatic environment: a review of ecological, physiological, and toxicological effects on biota
Authors: Wright D. A. , Welbourn P. M.
Published: April 2011

Cadmium is a nonessential element that can be toxic and carcinogenic. On a global scale, the ratio anthropogenic to natural emissions of cadmium is approximately 7:1. Sources of cadmium for freshwater and salt water include atmospheric deposition, direct and via runoff, as well as direct discharges into water or watersheds. Thirty percent of the atmospheric emissions fall onto water. In freshwater, the cadmium ion is the predominant dissolved form, while in seawater, chloride dominates. Much of the cadmium added to aquatic systems accumulates in sediments where it presents a risk to benthic biota and under certain conditions may reenter the water column. The cadmium ion is the most bioavailable to aquatic biota; factors affecting availability include salinity, dissolved organic matter, and hydrogen ion concentration, which affect the chemical forms of cadmium. Hydrogen and other ions, most notably calcium, also affect cadmium uptake and toxicity, through competition and physiological effects. The concentrations of cadmium that result in acute or chronic toxicity vary over several orders of magnitude, with certain freshwater fish and invertebrates being the most sensitive. Long-term field experiments and chronic toxicity tests on invertebrates suggest that the present Canadian guideline of 200 ng Cd∙L−1 for the protection of freshwater biota may be too high. Aquatic animals and plants, like most organisms, produce metal binding proteins, called metallothioneins, in response to cadmium. Some species or varieties within a species of aquatic biota are tolerant to cadmium. The relationship between cadmium tolerance and metallothionein is still incompletely resolved.Key words: cadmium, seawater, freshwater, availability, toxicity, metallothionein, tolerance, food chain.
Chemical and biological aspects of ecotoxicological risk assessment of ionizable and neutral organic compounds in fresh and marine waters: a review
Authors: Wezel Annemarie P
Published: April 2011

The effects of salinity and pH on the partitioning behaviour and toxicity of ionizable and neutral organics and organotin compounds in aquatic ecosystems are reviewed. The pH and pKa are of importance for the distribution over n-octanol and water (Dow) of ionizable compounds. Dow increases with salinity for ionized organics up to 3 times and for organotins up to 1000 times. Neutral acids partition more strongly to the phospholipids than their ions; however, differences are smaller than for Dow. For dissociated phenols, the distribution over the membrane and water (Dmw) depends on counterion concentration. For pentachlorophenol (PCP) and organotins, the uptake rate constant (k1) for the neutral form is up to a factor 10 higher than for the ion. The formation of ion_counterion pairs at higher salinity does not contribute to a higher uptake rate. The adaptation to salinity does not result in different bioconcentration kinetics. There is no general intrinsic susceptibility difference between salt water and freshwater organisms. For ionized organic acids, an increase in toxicity up to 4 times with decreasing salinity is reported frequently. Differences in pH are important for toxicity for compounds with a pKa between 6 and 9. For organophosphates a toxicity increase up to 2.5-fold with salinity was found. Bioconcentration and toxicity of ionizable organics aren't influenced by salinity in the way that Dow is influenced. Quantitative structure activity relationships developed for neutral compounds cannot be used to estimate the bioconcentration or toxicity of partly ionized organics. The deviating partitioning behaviour over water and octanol is no reason to set separate quality criteria for ionizable compounds for marine water and freshwater. However, their toxicity can differ as a result of pH differences. Toxicity data for fresh and marine organisms should always be compared, because unexpected differences in sensitivity can be detected in this way.Key words: salinity, sensitivity, acids, bases, organotin compounds.
Effects of site of origin, time of seed maturation, and seed age on germination behavior of Portulaca oleracea from the Old and New Worlds
Authors: El-Keblawy Ali , Al-Ansari Fatima
Published: April 2011

The effects of site of origin, time of seed maturation, and seed age on germination behavior, in terms of final percentage of germination and time for 50% of final germination were investigated in the widespread weed Portulaca oleracea L. Seeds were collected in August from one population at each of three geographical regions of the Old and New Worlds representing temperate (Southern Ontario, Canada), Mediterranean (Tanta, Egypt), and subtropical (Al-Ain, United Arab Emirates (U.A.E.)) climates. The freshly harvested seeds were incubated in both light and dark at 15, 25, and 40°C. Seeds of the U.A.E. site showed little dormancy and germinated faster under a wider range of incubation conditions than did seeds from the Canadian site. To assess the effect of time of seed maturation on germination behavior, seeds were collected during the different seasons (November, February, May, and August) of the U.A.E. population. The percentage of germination was significantly higher for seeds collected in May and November and germination was significantly faster for those collected in May and August. Response of germination to light and temperature varied according to site of origin and time of seed maturation. Seeds from the Canadian site and those that matured during winter from the U.A.E. site required light and high temperature for optimal germination. The effect of seed age on percentage of germination and rate was significant at the Canadian site but not at the Egyptian and U.A.E. sites. Seed stored for 5 months at room temperature germinated significantly faster and to a higher percentage than freshly harvested seeds. Results are discussed in light of the adaptation of seed dormancy and time of germination to the prevailing environmental conditions.Key words: dormancy, geographical regions, germination, germination rate, Portulaca oleracea, seed age, site of origin, time of seed maturation.