bluuebunny/crossref_metadata_2025 huggingface dataset:
SPARC modulates expression of extracellular matrix genes in human trabecular meshwork cells
Authors: Wei Hai‐Ying , Liu Jing‐Lei , Lv Bing‐Jie , Xing Lin , Fu Shao‐Ying
Published: December 2011

Purpose:  To investigate the effects of secreted protein acidic and rich in cysteine (SPARC) on the expression of components of the extracellular matrix (ECM) in cultured human trabecular meshwork (TM) cells.

Methods:  Cultured human trabecular cells were transfected with small interfering RNAs (siRNAs) specific for the human SPARC gene. Protein and mRNA expressions of fibronectin (FN) and the α1chains of collagen I and collagen III were quantified.

Results:  After silencing of the SPARC gene by transfection of cells with SPARC siRNA, the expression of COL1A1 and COL3A1 mRNAs and proteins was significantly enhanced, as compared to that in the control group (all, p < 0.001). In contrast, SPARC siRNA significantly reduced the expression of FN and SPARC mRNAs and FN protein, as compared to that in the control group (all, p < 0.001.).

Conclusions:  SPARC modulates the expression of several ECM genes in cultured human TM cells.
THE MORAL SIGNIFICANCE OF GRATITUDE IN KANT'S ETHICS
Authors: SMIT HOUSTON , TIMMONS MARK
Published: December 2011

abstract

In this essay, we examine the grounds, nature and content, status, acquisition and role, and justification of gratitude in Kant's ethical system, making use of student notes from Kant's lectures on ethics. We are especially interested in questions about the significance of gratitude in Kant's ethics. We examine Kant's claim that gratitude is a sacred duty, because it cannot be discharged, and explain how this claim is consistent with his insistence that “ought” implies “can.” We argue that for Kant a proper understanding of self‐esteem is importantly related to, if not necessary for, possession of the virtue of gratitude.
INTELLECTUAL VIRTUE AND THE JUSTIFICATION OF PERSONS
Authors: LEONARD DAVID H.
Published: December 2011

abstract

In this paper, I develop a model of personal justification that is rooted in the intellectual virtues and the concept of epistemic praise. In particular, I show how a character‐based understanding of the virtues gives rise to an important emphasis on agents and how this provides the resources for dealing with several problems in epistemology.
Atypical Listeria monocytogenes Serotype 4b Strains Harboring a Lineage II-Specific Gene Cassette
Authors: Lee Sangmi , Ward Todd J. , Graves Lewis M. , Wolf Leslie A. , Sperry Kate , Siletzky Robin M. , Kathariou Sophia
Published: December 2011

Listeria monocytogenes
is the etiological agent of listeriosis, a severe food-borne illness. The population of
L. monocytogenes
is divided into four lineages (I to IV), and serotype 4b in lineage I has been involved in numerous outbreaks. Several serotype 4b epidemic-associated clonal groups (ECI, -II, and -Ia) have been identified. In this study, we characterized a panel of strains of serotype 4b that produced atypical results with a serotype-specific multiplex PCR and possessed the
lmo0734
to
lmo0739
gene cassette that had been thought to be specific to lineage II. The cassette was harbored in a genomically syntenic locus in these isolates and in lineage II strains. Three distinct clonal groups (groups 1 to 3) were identified among these isolates based on single-nucleotide polymorphism-based multilocus genotyping (MLGT) and DNA hybridization data. Groups 1 and 2 had MLGT haplotypes previously encountered among clinical isolates and were composed of clinical isolates from multiple states in the United States. In contrast, group 3 consisted of clinical and environmental isolates solely from North Carolina and exhibited a novel haplotype. In addition, all group 3 isolates had DNA that was resistant to MboI, suggesting methylation of adenines at GATC sites. Sequence analysis of the
lmo0734
to
lmo0739
gene cassette from two strains (group 1 and group 3) revealed that the genes were highly conserved (>99% identity). The data suggest relatively recent horizontal gene transfer from lineage II
L. monocytogenes
into
L. monocytogenes
serotype 4b and subsequent dissemination among at least three distinct clonal groups of
L. monocytogenes
serotype 4b, one of which exhibits restrictions in regional distribution.
Porticoccus hydrocarbonoclasticus sp. nov., an Aromatic Hydrocarbon-Degrading Bacterium Identified in Laboratory Cultures of Marine Phytoplankton
Authors: Gutierrez Tony , Nichols Peter D. , Whitman William B. , Aitken Michael D.
Published: December 2011

A marine bacterium, designated strain MCTG13d, was isolated from a laboratory culture of the dinoflagellate
Lingulodinium polyedrum
CCAP1121/2 by enrichment with polycyclic aromatic hydrocarbons (PAHs) as the sole carbon source. Based on 16S rRNA gene sequence comparisons, the strain was most closely related to
Porticoccus litoralis
IMCC2115
T
(96.5%) and to members of the genera
Microbulbifer
(91.4 to 93.7%) and
Marinimicrobium
(90.4 to 92.0%). Phylogenetic trees showed that the strain clustered in a distinct phyletic line in the class
Gammaproteobacteria
for which
P. litoralis
is presently the sole cultured representative. The strain was strictly aerobic, rod shaped, Gram negative, and halophilic. Notably, it was able to utilize hydrocarbons as sole sources of carbon and energy, whereas sugars did not serve as growth substrates. The predominant isoprenoid quinone of strain MCTG13d was Q-8, and the dominant fatty acids were C
16:1ω7c
, C
18:1ω7c
, and C
16:0
. DNA G+C content for the isolate was 54.9 ± 0.42 mol%. Quantitative PCR primers targeting the 16S rRNA gene of this strain showed that this organism was common in other laboratory cultures of marine phytoplankton. On the basis of phenotypic and genotypic characteristics, strain MCTG13d represents a novel species of
Porticoccus
, for which the name
Porticoccus hydrocarbonoclasticus
sp. nov. is proposed. The discovery of this highly specialized hydrocarbon-degrading bacterium living in association with marine phytoplankton suggests that phytoplankton represent a previously unrecognized biotope of novel bacterial taxa that degrade hydrocarbons in the ocean.
Isolation and Characterization of Enterocin W, a Novel Two-Peptide Lantibiotic Produced by Enterococcus faecalis NKR-4-1
Authors: Sawa Naruhiko , Wilaipun Pongtep , Kinoshita Seisuke , Zendo Takeshi , Leelawatcharamas Vichien , Nakayama Jiro , Sonomoto Kenji
Published: December 2011

Enterococcus faecalis
NKR-4-1 isolated from pla-ra produces a novel two-peptide lantibiotic, termed enterocin W, comprising Wα and Wβ. The structure of enterocin W exhibited similarity with that of plantaricin W. The two peptides acted synergistically, and their order of binding to the cell membrane was important for their inhibitory activity.
Microbial Community Composition and Dynamics of Moving Bed Biofilm Reactor Systems Treating Municipal Sewage
Authors: Biswas Kristi , Turner Susan J.
Published: December 2011

Moving bed biofilm reactor (MBBR) systems are increasingly used for municipal and industrial wastewater treatment, yet in contrast to activated sludge (AS) systems, little is known about their constituent microbial communities. This study investigated the community composition of two municipal MBBR wastewater treatment plants (WWTPs) in Wellington, New Zealand. Monthly samples comprising biofilm and suspended biomass were collected over a 12-month period. Bacterial and archaeal community composition was determined using a full-cycle community approach, including analysis of 16S rRNA gene libraries, fluorescencein situhybridization (FISH) and automated ribosomal intergenic spacer analysis (ARISA). Differences in microbial community structure and abundance were observed between the two WWTPs and between biofilm and suspended biomass. Biofilms from both plants were dominated byClostridiaand sulfate-reducing members of theDeltaproteobacteria(SRBs). FISH analyses indicated morphological differences in theDeltaproteobacteriadetected at the two plants and also revealed distinctive clustering between SRBs and members of theMethanosarcinales, which were the onlyArchaeadetected and were present in low abundance (<5%). Biovolume estimates of the SRBs were higher in biofilm samples from one of the WWTPs which receives both domestic and industrial waste and is influenced by seawater infiltration. The suspended communities from both plants were diverse and dominated by aerobic members of theGammaproteobacteriaandBetaproteobacteria.This study represents the first detailed analysis of microbial communities in full-scale MBBR systems and indicates that this process selects for distinctive biofilm and planktonic communities, both of which differ from those found in conventional AS systems.
Development of a Rapid and Sensitive Method Combining a Cellulose Ester Microfilter and a Real-Time Quantitative PCR Assay To Detect Campylobacter jejuni and Campylobacter coli in 20 Liters of Drinking Water or Low-Turbidity Waters
Authors: Tissier Adeline , Denis Martine , Hartemann Philippe , Gassilloud Benoît
Published: December 2011

Investigations of
Campylobacter jejuni
and
Campylobacter coli
in samples of drinking water suspected of being at the origin of an outbreak very often lead to negative results. One of the reasons for this failure is the small volume of water typically used for detecting these pathogens (10 to 1,000 ml). The efficiencies of three microfilters and different elution procedures were determined using real-time quantitative PCR to propose a procedure allowing detection of
Campylobacter
in 20 liters of drinking water or low-turbidity water samples. The results showed that more than 80% of the bacteria inoculated in 1 liter of drinking water were retained on each microfilter. An elution with a solution containing 3% beef extract, 0.05 M glycine at pH 9, combined with direct extraction of the bacterial genomes retained on the cellulose ester microfilter, allowed recovery of 87.3% (±22% [standard deviation]) of
Campylobacter
per 1 liter of tap water. Recoveries obtained from 20-liter volumes of tap water spiked with a
C. coli
strain were 69.5% (±10.3%) and 78.5% (±15.1%) for 91 CFU and 36 CFU, respectively. Finally, tests performed on eight samples of 20 liters of groundwater collected from an alluvial well used for the production of drinking water revealed the presence of
C. jejuni
and
C. coli
genomes, whereas no bacteria were detected with the normative culture method in volumes ranging from 10 to 1,000 ml. In the absence of available epidemiological data and information on bacterial viability, these last results indicate only that the water resource is not protected from contamination by
Campylobacter
.
S-Layer Homology Domain Proteins Csac_0678 and Csac_2722 Are Implicated in Plant Polysaccharide Deconstruction by the Extremely Thermophilic Bacterium Caldicellulosiruptor saccharolyticus
Authors: Ozdemir Inci , Blumer-Schuette Sara E. , Kelly Robert M.
Published: December 2011

The genus
Caldicellulosiruptor
contains extremely thermophilic bacteria that grow on plant polysaccharides. The genomes of
Caldicellulosiruptor
species reveal certain surface layer homology (SLH) domain proteins that have distinguishing features, pointing to a role in lignocellulose deconstruction. Two of these proteins in
Caldicellulosiruptor saccharolyticus
(Csac_0678 and Csac_2722) were examined from this perspective. In addition to three contiguous SLH domains, the Csac_0678 gene encodes a glycoside hydrolase family 5 (GH5) catalytic domain and a family 28 carbohydrate-binding module (CBM); orthologs to Csac_0678 could be identified in all genome-sequenced
Caldicellulosiruptor
species. Recombinant Csac_0678 was optimally active at 75°C and pH 5.0, exhibiting both endoglucanase and xylanase activities. SLH domain removal did not impact Csac_0678 GH activity, but deletion of the CBM28 domain eliminated binding to crystalline cellulose and rendered the enzyme inactive on this substrate. Csac_2722 is the largest open reading frame (ORF) in the
C. saccharolyticus
genome (predicted molecular mass of 286,516 kDa) and contains two putative sugar-binding domains, two Big4 domains (bacterial domains with an immunoglobulin [Ig]-like fold), and a cadherin-like (Cd) domain. Recombinant Csac_2722, lacking the SLH and Cd domains, bound to cellulose and had detectable carboxymethylcellulose (CMC) hydrolytic activity. Antibodies directed against Csac_0678 and Csac_2722 confirmed that these proteins bound to the
C. saccharolyticus
S-layer. Their cellular localization and functional biochemical properties indicate roles for Csac_0678 and Csac_2722 in recruitment and hydrolysis of complex polysaccharides and the deconstruction of lignocellulosic biomass. Furthermore, these results suggest that related SLH domain proteins in other
Caldicellulosiruptor
genomes may also be important contributors to plant biomass utilization.
Binding of Human GII.4 Norovirus Virus-Like Particles to Carbohydrates of Romaine Lettuce Leaf Cell Wall Materials
Authors: Esseili Malak A. , Wang Qiuhong , Saif Linda J.
Published: December 2011

Norovirus (NoV) genogroup II genotype 4 (GII.4) strains are the dominant cause of the majority of food-borne outbreaks, including those that involve leafy greens, such as lettuce. Since human NoVs use carbohydrates of histo-blood group antigens as receptors/coreceptors, we examined the role of carbohydrates in the attachment of NoV to lettuce leaves by using virus-like particles (VLPs) of a human NoV/GII.4 strain. Immunofluorescence analysis showed that the VLPs attached to the leaf surface, especially to cut edges, stomata, and along minor veins. Binding was quantified using enzyme-linked immunosorbent assay (ELISA) performed on cell wall materials (CWM) from innermost younger leaves and outermost lamina of older leaves. The binding to CWM of older leaves was significantly (
P
< 0.05) higher (1.5- to 2-fold) than that to CWM of younger leaves. Disrupting the carbohydrates of CWM or porcine gastric mucin (PGM) (a carbohydrate control) using 100 mM sodium periodate (NaIO
4
) significantly decreased the binding an average of 17% in younger leaves, 43% in older leaves, and 92% for PGM. In addition, lectins recognizing GalNAc, GlcNAc, and sialic acid at 100 μg/ml significantly decreased the binding an average of 41%, 33%, and 20% on CWM of older leaves but had no effect on younger leaves. Lectins recognizing α-
d
-Gal, α-
d
-Man/α-
d
-Glc, and α-
l
-Fuc showed significant inhibition on CWM of older leaves as well as that of younger leaves. All lectins, except for the lectin recognizing α-
d
-Gal, significantly inhibited NoV VLP binding to PGM. Collectively, our results indicate that NoV VLPs bind to lettuce CWM by utilizing multiple carbohydrate moieties. This binding may enhance virus persistence on the leaf surface and prevent effective decontamination.
Transcription Factor Efg1 Shows a Haploinsufficiency Phenotype in Modulating the Cell Wall Architecture and Immunogenicity of Candida albicans
Authors: Zavrel Martin , Majer Olivia , Kuchler Karl , Rupp Steffen
Published: December 2011

TheCandida albicanstranscription factor Efg1 is known to be involved in many different cellular processes, including morphogenesis, general metabolism, and virulence. Here we show that besides its manifold roles, Efg1 also has a prominent effect on cell wall structure and composition, strongly affecting the structural glucan part. Deletion of only one allele ofEFG1already results in severe phenotypes for cell wall biogenesis, comparable to those with deletion of both alleles, indicative of a severe haploinsufficiency forEFG1. The observed defects in structural setup of the cell wall, together with previously reported alterations in expression of cell surface proteins, result in altered immunogenic properties of strains with compromised Efg1 function. This is shown by interaction studies with macrophages and primary dendritic cells. The structural changes in the cell wall carbohydrate meshwork presented here, together with the manifold changes in cell wall protein composition and metabolism reported in other studies, contribute to the altered immune response mounted by innate immune cells and to the altered virulence phenotypes observed for strains lackingEFG1.
Heterogeneous Expression of the Virulence-Related Adhesin Epa1 between Individual Cells and Strains of the Pathogen Candida glabrata
Authors: Halliwell Samantha C. , Smith Matthew C. A. , Muston Philippa , Holland Sara L. , Avery Simon V.
Published: December 2011

We investigated the relevance of gene expression heterogeneity to virulence properties of a major fungal pathogen,
Candida glabrata
. The organism's key virulence-associated factors include glycosylphosphatidylinositol-anchored adhesins, encoded subtelomerically by the
EPA
gene family. Individual-cell analyses of expression revealed very striking heterogeneity for Epa1, an adhesin that mediates ∼95% of adherence to epithelial cells
in vitro
. The heterogeneity in Epa1 was markedly greater than that known for other yeast genes. Sorted cells expressing high or low levels of Epa1 exhibited high and low adherence to epithelial cells, indicating a link between gene expression noise and potential virulence. The phenotypes of sorted subpopulations reverted to mixed phenotypes within a few generations. Variation in single-cell Epa1 protein and mRNA levels was correlated, consistent with transcriptional regulation of heterogeneity. Sir-dependent transcriptional silencing was the primary mechanism driving heterogeneous Epa1 expression in
C. glabrata
BG2, but not in CBS138 (ATCC 2001). Inefficient silencing in the latter strain was not due to a difference in
EPA1
sequence or (sub)telomere length and was overcome by ectopic
SIR3
expression. Moreover, differences between strains in the silencing dependence of
EPA1
expression were evident across a range of clinical isolates, with heterogeneity being the greatest in strains where
EPA1
was subject to silencing. The study shows how heterogeneity can impact the virulence-related properties of
C. glabrata
cell populations, with potential implications for microbial pathogenesis more broadly.
Synthetic Lethality of the
lytE cwlO
Genotype in Bacillus subtilis Is Caused by Lack of
d
,
l
-Endopeptidase Activity at the Lateral Cell Wall
Authors: Hashimoto Masayuki , Ooiwa Seika , Sekiguchi Junichi
Published: December 2011

Bacterial peptidoglycan acts as an exoskeleton to protect the bacterial cell. Although peptidoglycan biosynthesis by penicillin-binding proteins is well studied, few studies have described peptidoglycan disassembly, which is necessary for a dynamic structure that allows cell growth. In
Bacillus subtilis
, more than 35 genes encoding cell wall lytic enzymes have been identified; however, only two
d
,
l
-endopeptidases (
lytE
and
cwlO
) are involved in cell proliferation. In this study, we demonstrated that the
d
,
l
-endopeptidase activity at the lateral cell wall is essential for cell proliferation. Inactivation of LytE and CwlO by point mutation of the catalytic residues caused cell growth defects. However, the forced expression of LytF or CwlS, which are paralogs of LytE, did not suppress
lytE cwlO
synthetic lethality. Subcellular localization studies of these
d
,
l
-endopeptidases showed LytF and CwlS at the septa and poles, CwlO at the cylindrical part of the cell, and LytE at the septa and poles as well as the cylindrical part. Furthermore, construction of N-terminal and C-terminal domain-swapped enzymes of LytE, LytF, CwlS, and CwlO revealed that localization was dependent on the N-terminal domains. Only the chimeric proteins that were enzymatically active and localized to the sidewall were able to suppress the synthetic lethality, suggesting that the lack of
d
,
l
-endopeptidase activity at the cylindrical part of the cell leads to a growth defect. The functions of LytE and CwlO in cell morphogenesis were discussed.
A Transposon Site Hybridization Screen IdentifiesgalUandwecBCas Important for Survival of Yersinia pestis in Murine Macrophages
Authors: Klein Kathryn A. , Fukuto Hana S. , Pelletier Mark , Romanov Galina , Grabenstein Jens P. , Palmer Lance E. , Ernst Robert , Bliska James B.
Published: December 2011

Yersinia pestisis able to survive and replicate within murine macrophages. However, the mechanism by whichY. pestispromotes its intracellular survival is not well understood. To identify genes that are important forY. pestissurvival in macrophages, a library comprised of ∼31,500Y. pestisKIM6+ transposon insertion mutants (input pool) was subjected to negative selection in primary murine macrophages. Genes underrepresented in the output pool of surviving bacteria were identified by transposon site hybridization to DNA oligonucleotide microarrays. The screen identified several genes known to be important for survival ofY. pestisin macrophages, includingphoPQand members of the PhoPQ regulon (e.g.,pmrF). In addition, genes predicated to encode a glucose-1-phosphate uridylyltransferase (galU), a UDP-N-acetylglucosamine 2-epimerase (wecB) and a UDP-N-acetyl-d-mannosamine dehydrogenase (wecC) were identified in the screen. Viable-count assays demonstrated that a KIM6+galUmutant and a KIM6+wecBCmutant were defective for survival in murine macrophages. ThegalUmutant was studied further because of its strong phenotype. The KIM6+galUmutant exhibited increased susceptibility to the antimicrobial peptides polymyxin B and cathelicidin-related antimicrobial peptide (CRAMP). Polyacrylamide gel electrophoresis demonstrated that the lipooligosaccharide (LOS) of thegalUmutant migrated faster than the LOS of the parent KIM6+, suggesting the core was truncated. In addition, the analysis of LOS isolated from thegalUmutant by mass spectrometry showed that aminoarabinose modification of lipid A is absent. Therefore, addition of aminoarabinose to lipid A and complete LOS core (galU), as well as enterobacterial common antigen (wecBandwecC), is important for survival ofY. pestisin macrophages.
Role of ArlRS in Autolysis in Methicillin-Sensitive and Methicillin-Resistant Staphylococcus aureus Strains
Authors: Memmi Guido , Nair Dhanalakshmi R. , Cheung Ambrose
Published: December 2011

Autolysis plays an essential role in bacterial cell division and lysis with β-lactam antibiotics. Accordingly, the expression of autolysins is tightly regulated by several endogenous regulators, including ArlRS, a two component regulatory system that has been shown to negatively regulate autolysis in methicillin-sensitive
Staphylococcus aureus
(MSSA) strains. In this study, we found that inactivation of
arlRS
does not play a role in autolysis of methicillin-resistant
S. aureus
(MRSA) strains, such as community-acquired (CA)-MRSA strains USA300 and MW2 or the hospital-acquired (HA)-MRSA strain COL. This contrasts with MSSA strains, including Newman, SH1000, RN6390, and 8325-4, where autolysis is affected by ArlRS. We further demonstrated that the striking difference in the roles of
arlRS
between MSSA and MRSA strains is not due to the methicillin resistance determinant
mecA
. Among known autolysins and their regulators, we found that
arlRS
represses
lytN
, while no effect was seen on
atl
,
lytM
, and
lytH
expression in both CA- and HA-MRSA strains. Transcriptional-fusion assays showed that the
agr
transcripts, RNAII and RNAIII, were significantly more downregulated in the
arlRS
mutant of MW2 than the MSSA strain Newman. Importantly, provision of
agr
RNAIII in
trans
to the MW2
arlRS
mutant via a multicopy plasmid induced autolysis in this MRSA strain. Also, the autolytic phenotype in the
arlRS
mutant of MSSA strain Newman could be rescued by a mutation in either
atl
or
lytM
. Together, these data showed that ArlRS impacts autolysis differently in MSSA and MRSA strains.
Association of urinary cadmium excretion with feline hypertension
Authors: Finch N. C. , Syme H. M. , Elliott J.
Published: December 2011

Fifty client‐owned senior cats (32 normotensive and 18 hypertensive) with renal function ranging from normal to moderately reduced were recruited into a prospective cross‐sectional study exploring the association of urinary cadmium excretion and hypertension in cats. Heparinised plasma samples were collected and analysed for routine biochemical parameters. Urine samples were collected via cystocentesis and were analysed for cadmium concentrations using inductively coupled plasma mass spectrometry (ICP‐MS). Blood pressure was measured using the Doppler method. Urinary cadmium concentrations were indexed to urinary creatinineconcentration. Comparison of urinary cadmium excretion was made between hypertensive and normotensive cats.The median (range) urinary cadmium concentration standardised to urinary creatinine concentration (UCdCr) in the normotensive and hypertensive cats was 0.08 (0.02 to 0.37) and 0.12 (0.02 to 1.38) nmol/mmol creatinine. The UCdCr was significantly higher in hypertensive compared with normotensive cats (P=0.016). UCdCr and plasma creatinine concentration remained independent predictors of hypertensive status in a logistic regression model. UCdCr and plasma creatinine concentration were not correlated (r=−0.01, P=0.956). These data suggest cadmium exposure and accumulation in cats may play a role in the development of feline hypertension.
Molecular phylogeny of diploid Hordeum species and incongruence between chloroplast and nuclear datasets
Authors: Wang Huan , Sun Dongfa , Sun Genlou
Published: December 2011

The phylogeny of diploid Hordeum species has been studied using both chloroplast and nuclear gene sequences. However, the studies of different nuclear datasets of Hordeum species often arrived at similar conclusions, whereas the studies of different chloroplast DNA data generally resulted in inconsistent conclusions. Although the monophyly of the genus is well supported by both morphological and molecular data, the intrageneric phylogeny is still a matter of controversy. To better understand the evolutionary history of Hordeum species, two chloroplast gene loci (trnD-trnT intergenic spacer and rps16 gene) and one nuclear marker (thioreoxin-like gene (HTL)) were used to explore the phylogeny of Hordeum species. Two obviously different types of trnD-trnT sequences were observed, with an approximately 210 base pair difference between these two types: one for American species, another for Eurasian species. The trnD-trnT data generally separated the diploid Hordeum species into Eurasian and American clades, with the exception of Hordeum marinum subsp. gussoneanum. The rps16 data also grouped most American species together and suggested that Hordeum flexuosum has a different plastid type from the remaining American species. The nuclear gene HTL data clearly divided Hordeum species into two clades: the Xu + H genome clade and the Xa + I genome clade. Within clades, H genome species were well separated from the Xu species, and the I genome species were well separated from the Xa genome species. The incongruence between chloroplast and nuclear datasets was found and discussed.
Foxgene loci inTakifugu rubripesandTetraodon nigroviridisgenomes and comparison with those of medaka and zebrafish genomes
Authors: Shen Xueyan , Cui Jianzhou , Gong Qingli
Published: December 2011

Members of the Fox gene family of transcriptional regulators are essential for animal development and have been extensively studied in vertebrates. The mouse and human genomes contain at least 40 FOX genes which are divided into 19 subclasses based on the sequence similarity of the highly conserved forkhead domain. Using the genome sequence of the Takifugu rubripes and Tetraodon nigroviridis , we examined the genomic complement of fox genes in these organisms to gain insight into the evolutionary relationship of this gene family. We identified 53 fox genes in Tetraodon nigroviridis and Takifugu rubripes genome by searching the forkhead domain. These genes are divided into 18 subclasses as follows: 8 fox genes in subclass O; 6 in subclass P ; 4 in subclasses D, J, and N; 3 in subclasses A, B, C, E, F, and I; 2 in subclasses K, L, and Q; and 1 in subclasses G, H, M, and R. Together with the forkhead domain sequences of human, chicken, frog, zebrafish, medaka, and Caenorhabditis elegans, the phylogenetic relationship of the fox genes in Takifugu rubripes and Tetraodon nigroviridis were analyzed and compared. The genes structure, general features, and the three-dimensional model of these genes were also discussed.
Isolation of a strawberry gene fragment encoding an actin depolymerizing factor-like protein from genotypes resistant to Colletotrichum acutatum
Authors: Ontivero Marta , Zamora Gustavo Martínez , Salazar Sergio , Ricci Juan Carlos Díaz , Castagnaro Atilio Pedro
Published: December 2011

Actin depolymerizing factors (ADFs) have been recently implicated in plant defense against pathogenic fungi, associated with the cytoskeletal rearrangements that contribute to establish an effective barrier against fungal ingress. In this work, we identified a DNA fragment corresponding to a part of a gene predicted to encode an ADF-like protein in genotypes of Fragaria ananassa resistant to the fungus Colletotrichum acutatum . Bulked segregant analysis combined with AFLP was used to identify polymorphisms linked to resistance in hybrids derived from the cross between the resistant cultivar ‘Sweet Charlie’ and the susceptible cultivar ‘Pájaro’. The sequence of one out of three polymorphic bands detected showed significant BLASTX hits to ADF proteins from other plants. Two possible exons were identified and bioinformatic analysis revealed the presence of the ADF homology domain with two actin-binding sites, an N-terminal phosphorylation site, and a nuclear localization signal. In addition to its possible application in strawberry breeding programs, these finding may contribute to investigate the role of ADFs in plant resistance against fungi.
Identification of conserved microRNAs and their targets in Chinese cabbage (Brassica rapa subsp. pekinensis)
Authors: Wang Jinyan , Hou Xilin , Yang Xuedong
Published: December 2011

The microRNAs (miRNAs) are a new class of small nonprotein-coding RNAs that have been identified to regulate gene expression at the post-transcriptional level by targeting mRNAs for degradation or by inhibiting protein translation. Until now, thousands of miRNAs have been identified in many plants species. However, only 23 miRNAs have been reported from the microRNA database in Chinese cabbage ( Brassica rapa subsp. pekinensis ), one of the most widely cultivated vegetables in China and East Asia. In the present study, 168 potential miRNAs, derived from 22 EST and 119 GSS sequences in Chinese cabbage were identified and classified into 38 miRNA families by well-defined computational analysis, in which most belonged to the miRNA1533, miRNA156, and miRNA2911 families. Totally, there are 129 identified miRNAs potentially targeting 1386 Chinese cabbage EST genes, which play roles in multiple biological and metabolic processes including metabolism, cell growth, signal transduction, stress response, and plant development. Gene ontology analysis, based on these target proteins, showed that 688, 532, and 287 genes were involved in molecular functions, biological processes, and cellular components, respectively. KEGG pathway analysis demonstrated that these miRNAs participated in 214 metabolism pathways, including, amongst others, plant–pathogen interaction, fatty acid metabolism, amino acid metabolism, nitrogen metabolism, plant hormone signal transduction.
Theoretical study of inclusion complexes of dopamine with β-cyclodextrin based on PM6, ONIOM, and natural bonding orbital analysis
Authors: Djemil Rayenne , Khatmi Djameleddine
Published: December 2011

The inclusion process involving β-cyclodextrin (β-CD) with dopamine (DA) was investigated by using PM6, HF, and ONIOM methods. The most stable structure was obtained at the optimum position and angle. The complex orientation in which the catechol ring of dopamine penetrates into the β-CD cavity near primary hydroxyls is preferred in energy. The structures show the presence of several intermolecular hydrogen bond interactions that were studied on the basis of natural bonding orbital analysis, employed to quantify the donor–acceptor interactions between dopamine and β-CD. A study of these complexes in solution was carried out using the CPCM model to examine the influence of solvation on the stability of the dopamine β-CD complex.
Direct benzylation of 1,3-dicarbonyl compounds catalyzed by Cs2.5H0.5PW12O40 in solvent-free conditions
Authors: Rafiee Ezzat , Khodayari Maryam , Joshaghani Mohammad
Published: December 2011

Various 1,3-dicarbonyl compounds reacted readily with benzylic alcohols in the presence of Cs2.5H0.5PW12O40 salt to produce 2-benzylic-1,3-dicarbonyl compounds in high yields. It was found that this catalyst could be completely recovered and reused without loss of its catalytic activities and is thus environmentally conscious especially in solvent-free conditions. The use of this method provides improved modification of the direct benzylation of 1,3-carbonyl compounds in terms of low reaction times, solvent-free conditions, usage of a small amount of the catalyst, and a clean reaction profile. Furthermore, the use of this catalyst is feasible because of its easy preparation, its easy handling, its stability, its easy recovery, its reusability, being environmentally green, its excellent activity, and its selectivity.
Differences in plasma testosterone levels related to social status are more pronounced during mating than nonmating season in the tropical bat Saccopteryx bilineata (greater sac-winged bat)
Authors: Greiner Sabine , Dehnhard Martin , Voigt Christian C.
Published: December 2011

Testosterone (T) concentrations often covary strongly with mating activities in temperate-zone vertebrates. Recent studies suggest that males of tropical species experience lower and year-round constant T levels. Here we studied plasma T concentrations in a tropical mammal with a seasonally invariant social system, the greater sac-winged bat ( Saccopteryx bilineata (Temminck, 1838)). Colony composition remains almost stable throughout the year, although mating is restricted to only a few weeks each year. Males follow one of two mating strategies: they either defend a territory with a female group (harem) or live peripheral without females. First, we compared T within the same individuals between seasons, asking whether T levels are higher during mating season. Second, we tested whether T levels are related to social status, and third, whether T correlates with parasite infection because of an immunosuppressive effect. We found high individual T variations. Testosterone was elevated during the mating season only in harem males and was, on average, higher than in peripheral males. We found no correlation between T and parasite infestation. Although reproduction is seasonal in S. bilineata, T concentrations showed no pronounced seasonal pattern, probably because colony members form long-term relationships and live in a year-round stable social system.
Costs of multiple parasitism for an avian brood parasite, the Brown-headed Cowbird (Molothrus ater)
Authors: Goguen C.B. , Curson D.R. , Mathews N.E.
Published: December 2011

The Brown-headed Cowbird ( Molothrus ater (Boddaert, 1783)) is a generalist brood parasite that often lays into nests that contain conspecific eggs. Although it has often been assumed that this multiple parasitism reduces Cowbird survival, this has rarely been evaluated. We measured Cowbird survival in nests of the Blue-gray Gnatcatcher ( Polioptila caerulea (L., 1766)), Plumbeous Vireo ( Vireo plumbeus Coues, 1866), and Western Tanager ( Piranga ludoviciana (A. Wilson, 1811)) in New Mexico, USA. Our objectives were to measure the costs of intraspecific competition on Cowbird survival in multiply-parasitized nests, evaluate if these costs were related to host size, and to compare the costs of multiple parasitism relative to other mortality sources that occur over the entire nesting cycle. Intraspecific competition reduced Cowbird survival during the nestling period in nests of all three hosts, and was of particular importance in nests of the two smaller hosts. When all sources of egg mortality were considered, however, the costs of multiple parasitism were small compared with the large effects of predation and nest desertion. Given that multiple parasitism reduces Cowbird egg survival, it is unclear why Cowbirds multiply-parasitize. Possible explanations depend on an improved understanding of fecundity and level of host nest selectivity by female Cowbirds.
Controls on fluid flow in transpressive orogens, Taiwan and New Zealand
Authors: Upton P. , Craw D. , Yu B. , Chen Y.-G.
Published: December 2011

Taiwan and the Southern Alps of New Zealand are both young transpressive orogens characterized by rapid uplift and exhumation, high heat flow and vigorous surface processes. However, the distribution of heat flow, hot springs and veins in the two orogens is different. Taiwan has higher heat flow, distributed hot springs and localized veining. The Southern Alps has a narrow heat-flow anomaly, localized warm springs and widespread veining. Both orogens have two fluid-flow systems centred about the drainage divide. Shallow topographically driven meteoric water is restricted to the top 2–4 km. Deep flow is dominated by mineralizing rock-exchanged fluids. Extensional deformation occurs in the divide region of both orogens. At depth, vertical stretching produces subhorizontal veins. At shallower levels, stretching is horizontal and veins are steep. Veins in Taiwan are rare with zones of intense veining where flow has been localized into one site during exhumation from metamorphic to near-surface conditions. Fracturing and veining of the initially weak Slate Belt rocks causes a rheological change, increasing the tensile strength and making it more prone to fracturing, thus focusing fluid flow into the same locale. More uniform rheology in the Southern Alps leads to distributed veining.
First-order splay faults: dip-slip examples
Authors: Scholz Christopher H.
Published: December 2011

First-order splay faults are secondary faults that form at acute angles to the primary fault when the latter becomes critically misaligned with the direction of maximum principal stress. They are first order in the sense that their slip rate is of the same order as their primary fault. First-order splay faults have been previously described for strike-slip faults and examples are here shown of first-order dip-slip splay faults. For dip-slip faults in sedimentary sequences, friction is often anisotropic, being lower parallel to, rather than oblique to, bedding, and the position of the primary fault is often controlled by a décollement guided by a layer of particularly low friction or a structural feature. In this latter situation, the primary fault may become frictionally misaligned with the direction of maximum principal stress and first-order splay faults may then form. Examples shown are megasplays in subduction zones, ramp faults in fold and thrust belts, and synthetic and antithetic splays of low-angle normal faults.
The scope of earthquake geology
Authors: Sibson Richard H.
Published: December 2011

Earthquakes give rise to three principal effects – fault rupture (with subsidiary fracturing), ground shaking from wave propagation, and stress (±fluid-pressure) changes – that influence a wide range of geological processes at varying distances from the source. Many intermittent events are recognizable in the geological record (e.g. an individual turbidite bed in a flysch sequence; renewal of fracture permeability followed by hydrothermal precipitation) and are potentially attributable to seismic events, but positive identification of an earthquake as the cause is often difficult. Earthquake Geology has grown enormously as a discipline since the advent of palaeoseismic techniques for dating prehistoric fault ruptures as an aid to hazard assessment, but has largely focused on surface processes. There is a need to expand our concept of Earthquake Geology to include subsurface as well as surface effects in the full gamut of tectonic settings. The likelihood is that many Earth processes that have hitherto been considered smooth and progressive are, in fact, intermittent and tied to the seismic stress cycle that is integral to deformation in the Earth's crust and lithosphere.
Microstructure and petrology of a Calabrian garnet-bearing pseudotachylyte – a link to lower-crustal seismicity
Authors: Altenberger U. , Prosser G. , Ruggiero M. , Günter C.
Published: December 2011

A pseudotachylyte vein enclosed in tilted Hercynian lower crust of the Calabrian Serre Massif provides information on the source of a fossil seismic event. The pseudotachylyte contains euhedral garnet that formed by direct crystallization from a frictional melt and not during a later metamorphic overprint. Pseudotachylyte formation started with grain-size reduction caused by ductile deformation and brittle deformation. Subsequent frictional melting affected almost all phases including quartz but excluding monazite. After rapid cooling, chilled margins composed of glass and iron sulphide droplets formed. The central part of the vein solidified as biotite, and plagioclase crystallized directly from the frictional melt. Garnet occurs in three different grain-size classes; there are significant differences between very small garnets in the chilled margins and larger garnets in the central part of the pseudotachylyte vein. This proves that garnet rapidly crystallized from the pseudotachylyte melt after the seismic event. Garnet composition is used to define the depth of garnet growth, implying that the seismogenic zone was located at a depth of about 21–23 km. The melt temperature was between approximately 1515 and 2040 °C, representing the melting points of β-quartz and monazite, respectively.

This study supports the interpretation from seismic data that lower-crustal seismicity occurs and affirms, by direct observation, that the classical jelly sandwich model of the lithosphere is not always appropriate for crustal sections. In contrast to well-known regions with dry and very strong lower crusts (e.g. the Caledonides), the studied part of the Hercynian lower crust contains significant amounts of biotite, which release aqueous fluids during frictional melting. In addition, fluid inclusions in quartz fragments within the pseudotachylyte indicate that fluids probably played an important role during fault-zone evolution at the time of frictional melting.
Teaching cardiac electrophysiology modeling to undergraduate students: laboratory exercises and GPU programming for the study of arrhythmias and spiral wave dynamics
Authors: Bartocci Ezio , Singh Rupinder , von Stein Frederick B. , Amedome Avessie , Caceres Alan Joseph J. , Castillo Juan , Closser Evan , Deards Gabriel , Goltsev Andriy , Ines Roumwelle Sta. , Isbilir Cem , Marc Joan K. , Moore Diquan , Pardi Dana , Sadhu Sandeep , Sanchez Samuel , Sharma Pooja , Singh Anoopa , Rogers Joshua , Wolinetz Aron , Grosso-Applewhite Terri , Zhao Kai , Filipski Andrew B. , Gilmour Robert F. , Grosu Radu , Glimm James , Smolka Scott A. , Cherry Elizabeth M. , Clarke Edmund M. , Griffeth Nancy , Fenton Flavio H.
Published: December 2011

As part of a 3-wk intersession workshop funded by a National Science Foundation Expeditions in Computing award, 15 undergraduate students from the City University of New York1collaborated on a study aimed at characterizing the voltage dynamics and arrhythmogenic behavior of cardiac cells for a broad range of physiologically relevant conditions using an in silico model. The primary goal of the workshop was to cultivate student interest in computational modeling and analysis of complex systems by introducing them through lectures and laboratory activities to current research in cardiac modeling and by engaging them in a hands-on research experience. The success of the workshop lay in the exposure of the students to active researchers and experts in their fields, the use of hands-on activities to communicate important concepts, active engagement of the students in research, and explanations of the significance of results as the students generated them. The workshop content addressed how spiral waves of electrical activity are initiated in the heart and how different parameter values affect the dynamics of these reentrant waves. Spiral waves are clinically associated with tachycardia, when the waves remain stable, and with fibrillation, when the waves exhibit breakup. All in silico experiments were conducted by simulating a mathematical model of cardiac cells on graphics processing units instead of the standard central processing units of desktop computers. This approach decreased the run time for each simulation to almost real time, thereby allowing the students to quickly analyze and characterize the simulated arrhythmias. Results from these simulations, as well as some of the background and methodology taught during the workshop, is presented in this article along with the programming code and the explanations of simulation results in an effort to allow other teachers and students to perform their own demonstrations, simulations, and studies.
Impact of problem-based learning in a large classroom setting: student perception and problem-solving skills
Authors: Klegeris Andis , Hurren Heather
Published: December 2011

Problem-based learning (PBL) can be described as a learning environment where the problem drives the learning. This technique usually involves learning in small groups, which are supervised by tutors. It is becoming evident that PBL in a small-group setting has a robust positive effect on student learning and skills, including better problem-solving skills and an increase in overall motivation. However, very little research has been done on the educational benefits of PBL in a large classroom setting. Here, we describe a PBL approach (using tutorless groups) that was introduced as a supplement to standard didactic lectures in University of British Columbia Okanagan undergraduate biochemistry classes consisting of 45–85 students. PBL was chosen as an effective method to assist students in learning biochemical and physiological processes. By monitoring student attendance and using informal and formal surveys, we demonstrated that PBL has a significant positive impact on student motivation to attend and participate in the course work. Student responses indicated that PBL is superior to traditional lecture format with regard to the understanding of course content and retention of information. We also demonstrated that student problem-solving skills are significantly improved, but additional controlled studies are needed to determine how much PBL exercises contribute to this improvement. These preliminary data indicated several positive outcomes of using PBL in a large classroom setting, although further studies aimed at assessing student learning are needed to further justify implementation of this technique in courses delivered to large undergraduate classes.