bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacteriological, Biochemical, and Immunological Modifications in Human Colostrum After Holder Pasteurisation
Authors: Espinosa‐Martos I. , Montilla A. , de Segura A. Gómez , Escuder D. , Bustos G. , Pallás C. , Rodríguez J.M. , Corzo N. , Fernández L. 
Published: December 2012

ABSTRACTObjective:The objective of this work was to evaluate the effect of Holder pasteurisation of human colostrum on a variety of microbiological, biochemical, and immunological parameters.Methods:Colostrum samples from 10 donors, and 8 samples of mature milk used as controls, were heated at 62.5°C for 30 minutes. Bacterial counts and the concentration of furosine, lactose, myoinositol, glucose, lactulose, cytokines, and immunoglobulins were determined before and after the heat treatment.Results:Mean bacterial counts in nonpasteurised colostrum samples oscillated between 2.72 and 4.13 log10 colony‐forming units per millilitre in the agar media tested. Holder pasteurisation led to the destruction of the bacteria originally present in the samples. Furosine was detected in all samples before pasteurisation and increased significantly after the heat treatment (from 6.60 to 20.59 mg/100 g protein). Lactulose content was below the detection limit in nonpasteurised colostrum, but it was detected in all samples and quantified in 7 of them (from 10.68 to 38.02 mg/L) after Holder pasteurisation. Lactose, glucose, and myoinositol concentrations did not change after Holder pasteurisation. The concentrations of most cytokines and immunoglobulins were significantly higher in colostrum than in mature milk samples. Immunoglobulin content, both in colostrum and in milk samples, was reduced during pasteurisation, whereas, among cytokines, only macrophage inflammatory protein‐1β, interleukin‐7, and granulocyte‐macrophage‐colony‐stimulating factor concentrations were affected by this heat treatment.Conclusions:Lactulose and furosine content could be used as heat treatment indicators in colostrum samples. Holder pasteurisation modified the immunological profile of both colostrum and mature milk.
Transformation of Thylakoid Membranes during Differentiation from Vegetative Cell into Heterocyst Visualized by Microscopic Spectral Imaging
Authors: Kumazaki Shigeichi , Akari Masashi , Hasegawa Makoto 
Published: December 2012

Abstract
Some filamentous cyanobacteria carry out oxygenic photosynthesis in vegetative cells and nitrogen fixation in specialized cells known as heterocysts. Thylakoid membranes in vegetative cells contain photosystem I (PSI) and PSII, while those in heterocysts contain predominantly PSI. Therefore, the thylakoid membranes change drastically when differentiating from a vegetative cell into a heterocyst. The dynamics of these changes have not been sufficiently characterized in situ. Here, we used time-lapse fluorescence microspectroscopy to analyze cells of Anabaena variabilis under nitrogen deprivation at approximately 295 K. PSII degraded simultaneously with allophycocyanin, which forms the core of the light-harvesting phycobilisome. The other phycobilisome subunits that absorbed shorter wavelengths persisted for a few tens of hours in the heterocysts. The whole-thylakoid average concentration of PSI was similar in heterocysts and nearby vegetative cells. PSI was best quantified by selective excitation at a physiological temperature (approximately 295 K) under 785-nm continuous-wave laser irradiation, and detection of higher energy shifted fluorescence around 730 nm. Polar distribution of thylakoid membranes in the heterocyst was confirmed by PSI-rich fluorescence imaging. The findings and methodology used in this work increased our understanding of how photosynthetic molecular machinery is transformed to adapt to different nutrient environments and provided details of the energetic requirements for diazotrophic growth.
Variations in the Rhythms of Respiration and Nitrogen Fixation in Members of the Unicellular Diazotrophic Cyanobacterial Genus Cyanothece
Authors: Bandyopadhyay Anindita , Elvitigala Thanura , Liberton Michelle , Pakrasi Himadri B. 
Published: December 2012

Abstract
In order to accommodate the physiologically incompatible processes of photosynthesis and nitrogen fixation within the same cell, unicellular nitrogen-fixing cyanobacteria have to maintain a dynamic metabolic profile in the light as well as the dark phase of a diel cycle. The transition from the photosynthetic to the nitrogen-fixing phase is marked by the onset of various biochemical and regulatory responses, which prime the intracellular environment for nitrogenase activity. Cellular respiration plays an important role during this transition, quenching the oxygen generated by photosynthesis and by providing energy necessary for the process. Although the underlying principles of nitrogen fixation predict unicellular nitrogen-fixing cyanobacteria to function in a certain way, significant variations are observed in the diazotrophic behavior of these microbes. In an effort to elucidate the underlying differences and similarities that govern the nitrogen-fixing ability of unicellular diazotrophic cyanobacteria, we analyzed six members of the genus Cyanothece. Cyanothece sp. ATCC 51142, a member of this genus, has been shown to perform efficient aerobic nitrogen fixation and hydrogen production. Our study revealed significant differences in the patterns of respiration and nitrogen fixation among the Cyanothece spp. strains that were grown under identical culture conditions, suggesting that these processes are not solely controlled by cues from the diurnal cycle but that strain-specific intracellular metabolic signals play a major role. Despite these inherent differences, the ability to perform high rates of aerobic nitrogen fixation and hydrogen production appears to be a characteristic of this genus.
Evolution from the Prokaryotic to the Higher Plant Chloroplast Signal Recognition Particle: The Signal Recognition Particle RNA Is Conserved in Plastids of a Wide Range of Photosynthetic Organisms
Authors: Träger Chantal , Rosenblad Magnus Alm , Ziehe Dominik , Garcia-Petit Christel , Schrader Lukas , Kock Klaus , Vera Richter Christine , Klinkert Birgit , Narberhaus Franz , Herrmann Christian , Hofmann Eckhard , Aronsson Henrik , Schünemann Danja 
Published: December 2012

Abstract
The protein targeting signal recognition particle (SRP) pathway in chloroplasts of higher plants has undergone dramatic evolutionary changes. It disposed of its RNA, which is an essential SRP component in bacteria, and uses a unique chloroplast-specific protein cpSRP43. Nevertheless, homologs of the conserved SRP54 and the SRP receptor, FtsY, are present in higher plant chloroplasts. In this study, we analyzed the phylogenetic distribution of SRP components in photosynthetic organisms to elucidate the evolution of the SRP system. We identified conserved plastid SRP RNAs within all nonspermatophyte land plant lineages and in all chlorophyte branches. Furthermore, we show the simultaneous presence of cpSRP43 in these organisms. The function of this novel SRP system was biochemically and structurally characterized in the moss Physcomitrella patens. We show that P. patens chloroplast SRP (cpSRP) RNA binds cpSRP54 but has lost the ability to significantly stimulate the GTPase cycle of SRP54 and FtsY. Furthermore, the crystal structure at 1.8-Å resolution and the nucleotide specificity of P. patens cpFtsY was determined and compared with bacterial FtsY and higher plant chloroplast FtsY. Our data lead to the view that the P. patens cpSRP system occupies an intermediate position in the evolution from bacterial-type SRP to higher plant-type cpSRP system.
The R2R3-MYB–Like Regulatory Factor EOBI, Acting Downstream of EOBII, Regulates Scent Production by Activating ODO1 and Structural Scent-Related Genes in Petunia
Authors: Spitzer-Rimon Ben , Farhi Moran , Albo Boaz , Cna’ani Alon , Ben Zvi Michal Moyal , Masci Tania , Edelbaum Orit , Yu Yixun , Shklarman Elena , Ovadis Marianna , Vainstein Alexander 
Published: December 2012

Abstract
Flower scent is a highly dynamic trait, under developmental, spatial, and diurnal regulation. The mechanism governing scent production is only beginning to be unraveled. In petunia (Petunia hybrida), EMISSION OF BENZENOIDS II (EOBII) controls transcription of both the shikimate pathway-regulating MYB factor ODORANT1 (ODO1) and phenylpropanoid scent-related structural genes. A promoter-activation screen identified an R2R3-MYB–like regulatory factor of phenylpropanoid volatile biosynthesis acting downstream of EOBII, designated EOBI. EOBI silencing led to downregulation of ODO1 and numerous structural scent-related genes from both the shikimate and phenylpropanoid pathways. The ability of EOBI to directly activate ODO1, as revealed by electrophoretic mobility shift assay and yeast one-hybrid analysis, place EOBI upstream of ODO1 in regulating substrate availability for volatile biosynthesis. Interestingly, ODO1-silenced transgenic petunia flowers accumulated higher EOBI transcript levels than controls, suggesting a complex feedback loop between these regulatory factors. The accumulation pattern of EOBI transcript relative to EOBII and ODO1, and the effect of up/downregulation of EOBII on transcript levels of EOBI and ODO1, further support these factors' hierarchical relationships. The dependence of scent production on EOBI expression and its direct interaction with both regulatory and structural genes provide evidence for EOBI's wide-ranging involvement in the production of floral volatiles.
The Promiscuous Life of Plant NUCLEAR FACTOR Y Transcription Factors
Authors: Petroni Katia , Kumimoto Roderick W. , Gnesutta Nerina , Calvenzani Valentina , Fornari Monica , Tonelli Chiara , Holt Ben F. , Mantovani Roberto 
Published: December 2012

AbstractThe CCAAT box is one of the most common cis-elements present in eukaryotic promoters and is bound by the transcription factor NUCLEAR FACTOR Y (NF-Y). NF-Y is composed of three subunits, NF-YA, NF-YB, and NF-YC. Unlike animals and fungi, plants have significantly expanded the number of genes encoding NF-Y subunits. We provide a comprehensive classification of NF-Y genes, with a separation of closely related, but distinct, histone fold domain proteins. We additionally review recent experiments that have placed NF-Y at the center of many developmental stress-responsive processes in the plant lineage.
Target of Rapamycin Signaling Regulates Metabolism, Growth, and Life Span in Arabidopsis
Authors: Ren Maozhi , Venglat Prakash , Qiu Shuqing , Feng Li , Cao Yongguo , Wang Edwin , Xiang Daoquan , Wang Jinghe , Alexander Danny , Chalivendra Subbaiah , Logan David , Mattoo Autar , Selvaraj Gopalan , Datla Raju 
Published: December 2012

Abstract
Target of Rapamycin (TOR) is a major nutrition and energy sensor that regulates growth and life span in yeast and animals. In plants, growth and life span are intertwined not only with nutrient acquisition from the soil and nutrition generation via photosynthesis but also with their unique modes of development and differentiation. How TOR functions in these processes has not yet been determined. To gain further insights, rapamycin-sensitive transgenic Arabidopsis thaliana lines (BP12) expressing yeast FK506 Binding Protein12 were developed. Inhibition of TOR in BP12 plants by rapamycin resulted in slower overall root, leaf, and shoot growth and development leading to poor nutrient uptake and light energy utilization. Experimental limitation of nutrient availability and light energy supply in wild-type Arabidopsis produced phenotypes observed with TOR knockdown plants, indicating a link between TOR signaling and nutrition/light energy status. Genetic and physiological studies together with RNA sequencing and metabolite analysis of TOR-suppressed lines revealed that TOR regulates development and life span in Arabidopsis by restructuring cell growth, carbon and nitrogen metabolism, gene expression, and rRNA and protein synthesis. Gain- and loss-of-function Ribosomal Protein S6 (RPS6) mutants additionally show that TOR function involves RPS6-mediated nutrition and light-dependent growth and life span in Arabidopsis.
Natural Variation in Small Molecule–Induced TIR-NB-LRR Signaling Induces Root Growth Arrest via EDS1- and PAD4-Complexed R Protein VICTR inArabidopsis
Authors: Kim Tae-Houn , Kunz Hans-Henning , Bhattacharjee Saikat , Hauser Felix , Park Jiyoung , Engineer Cawas , Liu Amy , Ha Tracy , Parker Jane E. , Gassmann Walter , Schroeder Julian I. 
Published: December 2012

AbstractIn a chemical genetics screen we identified the small-molecule [5-(3,4-dichlorophenyl)furan-2-yl]-piperidine-1-ylmethanethione (DFPM) that triggers rapid inhibition of early abscisic acid signal transduction via PHYTOALEXIN DEFICIENT4 (PAD4)- and ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1)-dependent immune signaling mechanisms. However, mechanisms upstream of EDS1 and PAD4 in DFPM-mediated signaling remain unknown. Here, we report that DFPM generates an Arabidopsis thaliana accession-specific root growth arrest in Columbia-0 (Col-0) plants. The genetic locus responsible for this natural variant, VICTR (VARIATION IN COMPOUND TRIGGERED ROOT growth response), encodes a TIR-NB-LRR (for Toll-Interleukin1 Receptor–nucleotide binding–Leucine-rich repeat) protein. Analyses of T-DNA insertion victr alleles showed that VICTR is necessary for DFPM-induced root growth arrest and inhibition of abscisic acid–induced stomatal closing. Transgenic expression of the Col-0 VICTR allele in DFPM-insensitive Arabidopsis accessions recapitulated the DFPM-induced root growth arrest. EDS1 and PAD4, both central regulators of basal resistance and effector-triggered immunity, as well as HSP90 chaperones and their cochaperones RAR1 and SGT1B, are required for the DFPM-induced root growth arrest. Salicylic acid and jasmonic acid signaling pathway components are dispensable. We further demonstrate that VICTR associates with EDS1 and PAD4 in a nuclear protein complex. These findings show a previously unexplored association between a TIR-NB-LRR protein and PAD4 and identify functions of plant immune signaling components in the regulation of root meristematic zone-targeted growth arrest.
Accounting for missing data in the estimation of contemporary genetic effective population size (Ne)
Authors: Peel D. , Waples R. S. , Macbeth G. M. , Do C. , Ovenden J. R. 
Published: December 2012

AbstractTheoretical models are often applied to population genetic data sets without fully considering the effect of missing data. Researchers can deal with missing data by removing individuals that have failed to yield genotypes and/or by removing loci that have failed to yield allelic determinations, but despite their best efforts, most data sets still contain some missing data. As a consequence, realized sample size differs among loci, and this poses a problem for unbiased methods that must explicitly account for random sampling error. One commonly used solution for the calculation of contemporary effective population size (Ne) is to calculate the effective sample size as an unweighted mean or harmonic mean across loci. This is not ideal because it fails to account for the fact that loci with different numbers of alleles have different information content. Here we consider this problem for genetic estimators of contemporary effective population size (Ne). To evaluate bias and precision of several statistical approaches for dealing with missing data, we simulated populations with known Ne and various degrees of missing data. Across all scenarios, one method of correcting for missing data (fixed‐inverse variance‐weighted harmonic mean) consistently performed the best for both single‐sample and two‐sample (temporal) methods of estimating Ne and outperformed some methods currently in widespread use. The approach adopted here may be a starting point to adjust other population genetics methods that include per‐locus sample size components.
Presence and Incidence of Izumo Antibodies in Sera of Immunoinfertile Women and Men
Authors: Clark Sydney , Naz Rajesh K. 
Published: December 2012

ProblemSperm antigens that are relevant to fertilization and fertility, and are involved in human immunoinfertility, are being investigated in several laboratories. Izumo is a sperm‐specific protein that has shown to be essential for sperm‐egg fusion. The present study was conducted to examine the expression of Izumo protein in human sperm. Also, the presence and incidence of Izumo antibodies in sera of immunoinfertile women and men were investigated.Method of studyThe expression of Izumo protein in human sperm was examined by the Western blot procedure. Sera from immunoinfertile women (n = 25) and fertile women (n = 23), as well as sera from immunoinfertile men (n = 20) and fertile men (n = 15), were collected and analyzed for immunoreactivity with Izumo peptides in the enzyme‐linked immunosorbent assay (ELISA). Three epitopes of human Izumo, namely one epitope of Izumo1, and two epitopes of Izumo2 [Izumo2 (K‐15), and Izumo2 (T‐17)], respectively, were selected for the present study.ResultsIn the Western blot procedure, the Izumo1 antibody recognized a specific protein band of ~39 kDa in human sperm extract. In ELISA, 56% of the immunoinfertile female sera reacted positively (≧3 S.D. units) with Izumo1, 40% with Izumo2 (K‐15), and 20% with Izumo2 (T‐17) peptide. None of the sera (0%) from fertile women reacted positively (≦3 S.D. units) with any of the three Izumo peptides. None of the sera from immunoinfertile (0%) or fertile men (0%) reacted positively with any of the three Izumo peptides.ConclusionOur findings indicate that human sperm expresses Izumo protein, and the immunoinfertile female sera have circulating isoantibodies against this protein. This is the first study to our knowledge, which examined the presence and incidence of Izumo antibodies in female and male immunoinfertility. These findings may find clinical applications in specific diagnosis and treatment of infertility, and contraceptive vaccine development.
Pregnancy and Antiphospholipid Syndrome
Authors: Lockshin Michael D. 
Published: December 2012

AbstractAPS causes adverse pregnancy outcome, especially in younger patients with SLE or prior thromboses. LAC is the best predictor of adverse outcome. Prior conclusions on the efficacy of heparin for prevention of poor outcome may be suspect. New therapies are under evaluation in animal models but how to introduce them into the clinic is unclear.
Effects of fermented persimmon extract supplements on chemical composition and fermentation characteristics of barley silage
Authors: Kim Sang Bum , Kim Dong Hyeon , Lee Hyuk Jun , Amanullah Sardar M. , Kim Sam Churl 
Published: December 2012

AbstractThis study was conducted to estimate the effect of fermented persimmon extract (FPE) supplementation levels on chemical composition and fermentation characteristics of barley silage. Barley forage was harvested at 25% dry matter and chopped to 5 cm lengths. The FPE was applied at 0, 0.4, 0.8 and 1.6 g/kg of barley forage (fresh weight basis). After sub‐sampling of barley forages (0 day), a total of 64 laboratory mini silos (5 kg capacity) were ensiled to generate quadruplicate data from each of four treatments for four ensiling durations (2, 6, 40 and 120 days). The chemical compositions and in vitro digestibility of barley forage (0 day) were not affected by FPE supplementation. However, the content (L, P = 0.035) and in vitro digestibility (L, P = 0.041) of neutral detergent fiber on 120‐day barley silage decreased by increasing FPE supplements. Acetate content of barley silage ensiled for 120 days increased (Q, P = 0.004) by increasing FPE supplements, whereas pH (L, P < 0.001), lactate content (Q, P < 0.001) and lactate‐to‐acetate ratio (Q, P < 0.001) decreased. These results indicate that addition of FPE can increase the acetate content which has potential to increase aerobic stability.
Prognostic factors for patients with diffuse large B cell lymphoma and transformed indolent lymphoma undergoing autologous stem cell transplantation in the positron emission tomography era
Authors: Armand Philippe , Welch Sarah , Kim Haesook T. , LaCasce Ann S. , Jacobsen Eric D. , Davids Matthew S. , Jacobson Caron , Fisher David C. , Brown Jennifer R. , Coughlin Erin , Freedman Arnold S. , Chen Yi‐Bin 
Published: December 2012

SummaryIn the positron emission tomography (PET) era, traditional prognostic factors may not apply for patients with relapsed/refractory (R/R) diffuse large B cell lymphoma (DLBCL) undergoing autologous stem cell transplantation (ASCT). Moreover, little is known about prognostic factors in patients transplanted for transformed indolent lymphoma (TIL). We conducted a retrospective study of 143 patients with R/R DLBCL and TIL who were transplanted in the last decade and had a post‐salvage PET scan. We examined prognostic factors in both groups, and constructed a prognostic score for DLBCL patients. For patients with DLBCL, post‐salvage PET response was an important prognostic factor. Advanced age and symptomatic relapse were also significantly associated with outcome. A simple score could stratify patients into three risk groups with 4‐year post‐ASCT overall survival of 84%, 59%, and 10%, and 4‐year progression‐free survival of 67%, 41% and 0% (P < 0·0001 for both). However, none of those factors (including PET response to salvage) appeared relevant for patients with TIL, despite their comparable overall outcome. Our prognostic score for DLBCL patients undergoing ASCT may be useful for prognostication, for stratification in clinical trials, and to motivate the design of new strategies for patients in the high‐risk group, who may not derive benefit from standard ASCT.
Antioxidant vitaminsCandEsupplementation increases markers of haemolysis in sickle cell anaemia patients: a randomized, double‐blind, placebo‐controlled trial
Authors: Arruda Martha M. , Mecabo Grazielle , Rodrigues Celso A. , Matsuda Sandra S. , Rabelo Iara B. , Figueiredo Maria S. 
Published: December 2012

SummaryErythrocytes from sickle cell anaemia (SCA) patients continuously produce larger amounts of pro‐oxidants than normal cells. Oxidative stress seems to primarily affect the membrane and results in haemolysis. The use of antioxidantsin vitroreduces the generation of pro‐oxidants. To evaluate the impact of vitaminsC(VitC) andE(VitE) supplementation inSCApatients, patients over 18 years were randomly assigned to receiveVitC1400 mg + VitE800 mg per day or placebo orally for 180 d. Eighty‐three patients were enrolled (44 vitamins, 39 placebo), median age 27 (18–68) years, 64% female. There were no significant differences between the two groups regarding clinical complications or baseline laboratorial tests. Sixty percent of the patients wereVitCdeficient, 70% wereVitEdeficient. Supplementation significantly increased serumVitCandE. However, no significant changes in haemoglobin levels were observed, and, unexpectedly, there was a significant increase in haemolytic markers with vitamin supplementation. In conclusion,VitC + VitEsupplementation did not improve anaemia and, surprisingly, increased markers of haemolysis in patients withSCAandS‐β0‐thalassaemia. The exact mechanisms to explain this findings and their clinical significance remain to be determined.