bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clostridiaceae and Enterobacteriaceae as active fermenters in earthworm gut content
Authors: Wüst Pia K , Horn Marcus A , Drake Harold L 
Published: July 2010

Abstract
The earthworm gut provides ideal in situ conditions for ingested heterotrophic soil bacteria capable of anaerobiosis. High amounts of mucus- and plant-derived saccharides such as glucose are abundant in the earthworm alimentary canal, and high concentrations of molecular hydrogen (H2) and organic acids in the alimentary canal are indicative of ongoing fermentations. Thus, the central objective of this study was to resolve potential links between fermentations and active fermenters in gut content of the anecic earthworm Lumbricus terrestris by 16S ribosomal RNA (rRNA)-based stable isotope probing, with [13C]glucose as a model substrate. Glucose consumption in anoxic gut content microcosms was rapid and yielded soluble organic compounds (acetate, butyrate, formate, lactate, propionate, succinate and ethanol) and gases (carbon dioxide and H2), products indicative of diverse fermentations in the alimentary canal. Clostridiaceae and Enterobacteriaceae were users of glucose-derived carbon. On the basis of the detection of 16S rRNA, active phyla in gut contents included Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Proteobacteria, Tenericutes and Verrucomicrobia, taxa common to soils. On the basis of a 16S rRNA gene similarity cutoff of 87.5%, 82 families were detected, 17 of which were novel family-level groups. These findings (a) show the large diversity of soil taxa that might be active during gut passage, (b) show that Clostridiaceae and Enterobacteriaceae (fermentative subsets of these taxa) are selectively stimulated by glucose and might therefore be capable of consuming mucus- and plant-derived saccharides during gut passage and (c) indicate that ingested obligate anaerobes and facultative aerobes from soil can concomitantly metabolize the same source of carbon.
Mass Spectrometry, Nutrition and Protein Turnover
Authors: Affolter Michael 
Published: July 2010

Protein turnover is the result of synthesis of new and breakdown of old proteins in the body thereby providing a mechanism for the maintenance of optimally functioning proteins. Quantification of protein turnover rates is essential to understand these fundamental biological processes in all living organisms. Over the last decades, mass spectrometry has greatly contributed to the progress in the analysis of protein synthesis and breakdown and stable-isotope labelled tracers play a key role for the detailed quantitative measurement of protein metabolism. Isotope ratio and atmospheric pressure mass spectrometry enable the precise, accurate, and sensitive determination of isotope enrichments. More recently, methods have been developed to study total protein metabolism and multiplexed protein analysis for a comprehensive profiling at proteome level. Addressing protein turnover dynamics represent some technical challenges for proteome-wide analysis, i.e. the high isotope enrichment needed for proteome-wide studies is still difficult to achieve in animals and humans.Nutrition plays a key role in the anabolic signalling for the stimulation of skeletal muscle protein synthesis. The combination of physical training and adequate protein intake acts synergistically to enhance muscle mass and performance. Studies in the elderly population confirmed the potential to address sarcopenia, the gradual loss of muscle mass and function with ageing, by adapted nutrition with adequate daily protein intake and resistance-type exercise training, allowing a substantial gain in skeletal muscle mass, strength, and functional performance.
A system-level investigation into the cellular toxic response mechanism mediated by AhR signal transduction pathway
Authors: Gim Jungsoo , Kim Ho-Shik , Kim Junil , Choi Minsoo , Kim Jeong-Rae , Chung Yeun Jun , Cho Kwang-Hyun 
Published: July 2010

Abstract
Motivation: Viewing a cellular system as a collection of interacting parts can lead to new insights into the complex cellular behavior. In this study, we have investigated aryl hydrocarbon receptor (AhR) signal transduction pathway from such a system-level perspective. AhR detects various xenobiotics, such as drugs or endocrine disruptors (e.g. dioxin), and mediates transcriptional regulation of target genes such as those in the cytochrome P450 (CYP450) family. On binding with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), however, AhR becomes abnormally activated and conveys toxic effects on cells. Despite many related studies on the TCDD-mediated toxicity, quantitative system-level understanding of how TCDD-mediated toxicity generates various toxic responses is still lacking.
Results: Here, we present a manually curated TCDD-mediated AhR signaling pathway including crosstalks with the hypoxia pathway that copes with oxygen deficiency and the p53 pathway that induces a DNA damage response. Based on the integrated pathway, we have constructed a mathematical model and validated it through quantitative experiments. Using the mathematical model, we have investigated: (i) TCDD dose-dependent effects on AhR target genes; (ii) the crosstalk effect between AhR and hypoxia signals; and (iii) p53 inhibition effect of TCDD-liganded AhR. Our results show that cellular intake of TCDD induces AhR signaling pathway to be abnormally up-regulated and thereby interrupts other signaling pathways. Interruption of hypoxia and p53 pathways, in turn, can incur various hazardous effects on cells. Taken together, our study provides a system-level understanding of how AhR signal mediates various TCDD-induced toxicities under the presence of hypoxia and/or DNA damage in cells.
Contact: ckh@kaist.ac.kr
Supplementary information: Supplementary data are available at Bioinformatics online.
ROAST: rotation gene set tests for complex microarray experiments
Authors: Wu Di , Lim Elgene , Vaillant François , Asselin-Labat Marie-Liesse , Visvader Jane E. , Smyth Gordon K. 
Published: July 2010

Abstract
Motivation: A gene set test is a differential expression analysis in which a P-value is assigned to a set of genes as a unit. Gene set tests are valuable for increasing statistical power, organizing and interpreting results and for relating expression patterns across different experiments. Existing methods are based on permutation. Methods that rely on permutation of probes unrealistically assume independence of genes, while those that rely on permutation of sample are suitable only for two-group comparisons with a good number of replicates in each group.
Results: We present ROAST, a statistically rigorous gene set test that allows for gene-wise correlation while being applicable to almost any experimental design. Instead of permutation, ROAST uses rotation, a Monte Carlo technology for multivariate regression. Since the number of rotations does not depend on sample size, ROAST gives useful results even for experiments with minimal replication. ROAST allows for any experimental design that can be expressed as a linear model, and can also incorporate array weights and correlated samples. ROAST can be tuned for situations in which only a subset of the genes in the set are actively involved in the molecular pathway. ROAST can test for uni- or bi-direction regulation. Probes can also be weighted to allow for prior importance. The power and size of the ROAST procedure is demonstrated in a simulation study, and compared to that of a representative permutation method. Finally, ROAST is used to test the degree of transcriptional conservation between human and mouse mammary stems.
Availability: ROAST is implemented as a function in the Bioconductor package limma available from www.bioconductor.org
Contact: smyth@wehi.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online.
Generalized Heine’s identity for complex Fourier series of binomials
Authors: Cohl Howard S. , Dominici Diego E. 
Published: July 2010

In his treatise, Heine (
Heine 1881
In
Theorie und Anwendungen
) gave an identity for the Fourier series of the function

, with

, and
z
>1, in terms of associated Legendre functions of the second kind

. In this paper, we generalize Heine’s identity for the function

, with

,

and

, in terms of

. We also compute closed-form expressions for some

.
Review article: permissive underfeeding in short‐term nutritional support
Authors: Owais A. E. , Bumby R. F. , MacFie J. 
Published: July 2010

Aliment Pharmacol Ther 2010; 32: 628–636SummaryBackground  The importance of adequate nutritional support in selected patient groups is well established. Traditionally, the amounts of macronutrients provided have been based on a perceived need to achieve, if not exceed, energy and protein balance. In recent years, there has been increasing interest in the concept of ‘permissive underfeeding’.Aim  To determine whether or not there is evidence of benefit for permissive underfeeding in selected groups.Methods  Studies were identified from MEDLINE, Embase and PubMed databases and the Cochrane collaboration. The search was limited from January 1950 to January 2010. Further searches were made from the references of original articles. The literature search revealed 591 abstracts of relevant studies. All abstracts were initially reviewed by the primary author (AO) and those that did not fulfil the inclusion criteria were discarded. The remaining articles were requested and were reviewed independently by two authors (AO, JM).Results  Twelve studies were included in the final analysis. Eight of these were randomized interventional trials. Three were prospective cohort studies and one was a retrospective analysis.Conclusion  This review suggests that permissive underfeeding may be associated with improved outcomes and reduced morbidity in patients requiring short‐term nutritional support.
Enemy of the (immunosuppressed) state: an update on the pathogenesis of Aspergillus fumigatus infection
Authors: Ben‐Ami Ronen , Lewis Russell E. , Kontoyiannis Dimitrios P. 
Published: July 2010

Summary Aspergillus fumigatus is an opportunistic filamentous fungus that is currently the most frequent cause of invasive fungal disease in immunosuppressed individuals. Recent advances in our understanding of the pathogenesis of invasive aspergillosis have highlighted the multifactorial nature of A. fumigatus virulence and the complex interplay between host and microbial factors. In this review, we outline current concepts of immune recognition and evasion, angioinvasion and angiogenesis, secondary metabolism and the fungal stress response, and their respective roles in this often lethal infection.
Optimizing dendritic cell‐based immunotherapy in multiple myeloma: intranodal injections of idiotype‐pulsed CD40 ligand‐matured vaccines led to induction of type‐1 and cytotoxic T‐cell immune responses in patients
Authors: Yi Qing , Szmania Susann , Freeman John , Qian Jianfei , Rosen Nancy A. , Viswamitra Sanjaya , Cottler‐Fox Michele , Barlogie Bart , Tricot Guido , Van Rhee Frits 
Published: July 2010

SummaryVaccination with idiotype (Id) protein‐pulsed dendritic cells (DCs) has been explored in multiple myeloma and the results have been disappointing. To improve the efficacy of DC vaccination in myeloma, we investigated the use of Id‐ and keyhole limpet haemocyanin (KLH)‐pulsed, CD40 ligand‐matured DCs administered intranodally. Nine patients with smouldering or stable myeloma without treatment were enrolled and DC vaccines were administered at weekly intervals for a total of four doses. Following vaccination, all patients mounted Id‐specific γ‐interferon T‐cell response. Interleukin‐4 response was elicited in two, and skin delayed‐type hypersensitivity reaction occurred in seven patients. More importantly, Id‐specific cytotoxic T‐cell responses were also detected in five patients. Most if not all patients mounted a positive T‐cell response to KLH following vaccination. At 1‐year follow‐up, six of the nine patients had stable disease, while three patients had slowly progressive disease even during the vaccination period. At 5‐year follow‐up, four of the six patients continued with stable disease. No major side effects were noted. In summary, intranodal administration of Id‐pulsed CD40 ligand‐matured DCs was able to induce Id‐specific T and B‐cell responses in patients. Current efforts are geared towards breaking tumour‐mediated immune suppression and improving clinical efficacy of this immunotherapy.
Association of Fc receptor‐like 5 (FCRL5) with Graves’ disease is secondary to the effect of FCRL3
Authors: Simmonds Matthew J. , Brand Oliver J. , Barrett Jeffrey C. , Newby Paul R. , Franklyn Jayne A. , Gough Stephen C.L. 
Published: July 2010

SummaryObjective  The Fc receptor‐like 3 (FCRL3) molecule, involved in controlling B‐cell signalling, may contribute to the autoimmune disease process. Recently, a genome‐wide screen detected association of neighbouring gene FCRL5 with Graves’ disease (GD). To determine whether FCRL5 represents a further independent B‐cell signalling GD susceptibility loci, we screened 12 tag SNPs, capturing all known common variation within FCRL5, in 5192 UK Caucasian GD index cases and controls.Design  A case–control association study investigating twelve tag SNPs within FCRL5 which captured the majority of known common variation within this gene region.Patients  A data set comprising 2504 UK Caucasian patients with GD and 2688 geographically matched controls taken from the 1958 British Birth cohort.Measurements  We used the chi‐squared test and haplotype analysis to investigate the association between the tag SNPs and GD before performing logistic regression analysis to determine whether association at FCRL5 was independent of the known FCRL3 association.Results  Three of the FCRL5 tag SNPs, rs6667109, rs3811035 and rs6692977 showed association with GD (P = 0·015–0·001, OR = 1·15–1·16). Logistic regression performed on all FCRL5 and, previously screened, FCRL3 tag SNPs revealed that association with FCRL5 was secondary to linkage disequilibrium with the FCRL3, rs11264798 and rs10489678 SNPs.Conclusions  FCRL5 does not appear to be exerting an independent effect on the development of GD in the UK. Fine mapping of the entire FCRL region is required to determine the exact location of the aetiological variant/s present.
The Reiss Screen for Maladaptive Behaviour: its reliability and internal consistencies
Authors: Sturmey P. , Burcham K. J. , Perkins T. S. 
Published: July 2010

AbstractThe inter‐rater and test‐retest reliabilities, and intemal consistencies of the Reiss Screen for Maladaptive Behavior (Reiss 1987) were evaluated on a random sample of adults with moderate through profound mental retardation living in an institutional setting. Generally, the Reiss Screen showed good inter‐rater reliability, modest to good test‐retest and good intemal consistency. This suggests that the Reiss Screen has moderate to good psychometric robustness.
Adaptive behaviour after schizophrenia in people with Down's syndrome
Authors: Cooper S.‐A. , Duggirala C. , Collacott R. A. 
Published: July 2010

AbstractSeven individuals with Down's syndrome and a past history of schizophrenia were matched for age, sex and residence to adults with Down's syndrome but no past psychiatric history. The AAMD Adaptive Behaviour Scale was completed for all individuals in both groups, at a mean follow‐up period of 6‐4 years after the schizophrenic episode. The skill level of the subject group was found to be the same as for the control group, which rejects the notion of a ‘defect state’ occurring post‐schizophrenia in Down's syndrome. The importance of accurate diagnosis and treatment for this group is stressed.
Bacillus subtilis ilvB operon: an intersection of global regulons
Authors: Shivers Robert P. , Sonenshein Abraham L. 
Published: July 2010

SummaryThe genes of the major Bacillus subtilis operon (ilvB) for biosynthesis of branched‐chain amino acids are subject to multiple mechanisms of regulation. The global regulatory proteins CodY and TnrA bind upstream of the transcription start site and are likely to control transcription initiation, leucine‐specific tRNA regulates transcriptional elongation, and unknown factors differentially cleave the full‐length mRNA. Another global regulator, CcpA, known to be required for ilvB transcription, was shown here to act directly at the ilvB promoter by a novel mechanism. Although CcpA was able to bind to the ilvB promoter region, it stimulated transcription significantly only when CodY was present, suggesting that CcpA acts primarily by interfering with repression by CodY. Additionally, CcpA was shown to control indirectly the expression of other CodY‐regulated target genes, apparently by altering the intracellular level of branched‐chain amino acids.
Double molecular mimicry in Escherichia coli: binding of ribosomal protein L20 to its two sites in mRNA is similar to its binding to 23S rRNA
Authors: Guillier Maude , Allemand Frédéric , Dardel Frédéric , Royer Catherine A. , Springer Mathias , Chiaruttini Claude 
Published: July 2010

SummaryEscherichia coli ribosomal L20 is one of five proteins essential for the first reconstitution step of the 50S ribosomal subunit in vitro. It is purely an assembly protein, because it can be withdrawn from the mature subunit without effect on ribosome activity. In addition, L20 represses the translation of its own gene by binding to two sites in its mRNA. The first site is a pseudoknot formed by a base‐pairing interaction between nucleotide sequences separated by more than 280 nucleotides, whereas the second site is an irregular helix formed by base‐pairing between neighbouring nucleotide sequences. Despite these differences, the mRNA folds in such a way that both L20 binding sites share secondary structure similarity with the L20 binding site located at the junction between helices H40 and H41 in 23S rRNA. Using a set of genetic, biochemical, biophysical, and structural experiments, we show here that all three sites are recognized similarly by L20.
Involvement of a Che‐like signal transduction cascade in regulating cyst cell development in Rhodospirillum centenum
Authors: Berleman James E. , Bauer Carl E. 
Published: July 2010

SummaryHomologues of the E. coli chemotaxis (Che) signal transduction pathway are present in nearly all motile bacteria. Although E. coli contains only one Che cascade, many other bacteria are known to possess multiple sets of che genes. The role of multiple che‐like gene clusters could potentially code for parallel Che‐like signal transduction pathways that have distinctly different input and output functions. In this study, we describe a che‐like gene cluster in Rhodospirillum centenum that controls a developmental cycle. In‐frame deletion mutants of homologues of CheW (ΔcheW3aand ΔcheW3b), CheR (ΔcheR3), CheA (ΔcheA3) and a methyl‐accepting chemotaxis protein (Δmcp3) are defective in starvation‐induced formation of heat and desiccation resistant cyst cells. In contrast, mutants of homologues of CheY (ΔcheY3), CheB (ΔcheB3), and a second input kinase designated as CheS (ΔcheS3) result in cells that are derepressed in the formation of cysts. A model of signal transduction is presented in which there are three distinct Che‐like signal transduction cascades; one that is involved in chemotaxis, one that is involved in flagella biosynthesis and the third that is involved in cyst development.
A directed screen for chlamydial proteins secreted by a type III mechanism identifies a translocated protein and numerous other new candidates
Authors: Subtil Agathe , Delevoye Cédric , Balañá María‐Eugenia , Tastevin Laurence , Perrinet Stéphanie , Dautry‐Varsat Alice 
Published: July 2010

SummaryChlamydiae are strict intracellular parasites that induce their internalization upon contact with the host cell and grow inside an intracellular compartment called an inclusion. They possess a type III secretion (TTS) apparatus, which allows for the translocation of specific proteins in the host cell cytosol. In particular, chlamydial proteins of the Inc family are secreted to the inclusion membrane by a TTS mechanism; other TTS substrates are mostly unknown. Using a secretion assay based on the recognition of TTS signals in Shigella flexneri, we searched for TTS signals in the proteins of unknown function, conserved between three different chlamydial species, Chlamydia pneumoniae, C. trachomatis and C. caviae. We identified 24 new candidate proteins which did not belong to the Inc family. Four of these proteins were also secreted as full‐length proteins by a TTS mechanism in S. flexneri, indicating that their translocation does not require other chlamydial proteins. One of these proteins was detected in the cytosol of infected cells using specific antibodies, directly demonstrating that it is translocated in the host cell during bacterial proliferation. More generally, this work represents the first directed search for TTS effectors not based on genetic information or sequence similarity. It reveals the abundance of proteins secreted in the host cell by chlamydiae.
CsrA post‐transcriptionally represses pgaABCD, responsible for synthesis of a biofilm polysaccharide adhesin of Escherichia coli
Authors: Wang Xin , Dubey Ashok K. , Suzuki Kazushi , Baker Carol S. , Babitzke Paul , Romeo Tony 
Published: July 2010

SummaryThe RNA‐binding protein CsrA represses biofilm formation, while the non‐coding RNAs CsrB and CsrC activate this process by sequestering CsrA. We now provide evidence that the pgaABCD transcript, required for the synthesis of the polysaccharide adhesin PGA (poly‐β‐1,6‐N‐acetyl‐d‐glucosamine) of Escherichia coli, is the key target of biofilm regulation by CsrA. csrA disruption causes an approximately threefold increase in PGA production and an approximately sevenfold increase in expression of a pgaA′–′lacZ translational fusion. A ΔcsrBΔcsrC mutant exhibits a modest decrease in pgaA′–′lacZ expression, while the response regulator UvrY, a transcriptional activator of csrB and csrC, stimulates this expression. Biofilm formation is not regulated by csrA, csrB or uvrY in a ΔpgaC mutant, which cannot synthesize PGA. Gel mobility shift and toeprint analyses demonstrate that CsrA binds cooperatively to pgaA mRNA and competes with 30S ribosome subunit for binding. CsrA destabilizes the pgaA transcript in vivo. RNA footprinting and boundary analyses identify six apparent CsrA binding sites in the pgaA mRNA leader, the most extensive arrangement of such sites in any mRNA examined to date. Substitution mutations in CsrA binding sites overlapping the Shine–Dalgarno sequence and initiation codon partially relieve repression by CsrA. These studies define the crucial mechanisms, though not the only means, by which the Csr system influences biofilm formation.
The role of polar localization in the function of an essential Caulobacter crescentus tyrosine kinase
Authors: Sciochetti Stephen A. , Ohta Noriko , Newton Austin 
Published: July 2010

SummaryDivL is an essential tyrosine kinase in Caulobacter crescentus that controls an early step in the cell division cycle. We show here that DivL dynamically localizes to the stalk‐distal cell pole and less frequently to the stalked cell pole during the S‐phase. The kinase is subsequently released from the cell poles late in division and remains dispersed in the newly divided progeny stalk and swarmer cells. Mutational analysis of DivL in a DivL–GFP fusion protein demonstrated that the extreme C‐terminus and residues in the conserved four‐helix bundle, which is the phosphorylation–dimerization domain, are important for localization. We speculate that the four‐helix bundle of the core catalytic domain may serve as a recognition site for the ‘localization machinery’. Unexpectedly, a DivL protein with mutations in the C‐terminal localization sequence, and an intact catalytic domain, efficiently complemented a divL null mutation. Thus, subcellular localization of DivL is not essential to its function in cell division regulation. Regulation of cell division by DivL does, however, depend on its localization in the cell membrane.