bluuebunny/crossref_metadata_2025_split huggingface dataset:
Porcine zona pellucida glycoprotein ZP4 is responsible for the sperm-binding activity of the ZP3/ZP4 complex
Authors: Yonezawa Naoto , Kanai-Kitayama Saeko , Kitayama Tetsushi , Hamano Ayumi , Nakano Minoru 
Published: October 2011

SummaryThe zona pellucida (ZP) is a transparent envelope that surrounds the mammalian oocyte and mediates species-selective sperm–egg interactions. Porcine and bovine ZPs consist of glycoproteins ZP2, ZP3, and ZP4. In both pig and bovine a heterocomplex consisting of ZP3 and ZP4 binds to sperm, however it is not clarified whether ZP3 or ZP4 in the complex is responsible for the sperm binding. Previously, we have established a baculovirus-Sf9 cell expression system for porcine ZP glycoproteins. A mixture of recombinant ZP3 (rZP3) and rZP4 displayed sperm-binding activity toward bovine sperm but not porcine sperm, probably due to differences in carbohydrate structure between the native and recombinant ZP glycoproteins. In this study, a mixture of porcine rZP3 and native ZP4 (nZP4) inhibited the binding of porcine sperm to the ZP. In contrast, a mixture of porcine nZP3 and rZP4 did not inhibit the binding of porcine sperm, although the mixture inhibited the binding of bovine sperm. The porcine rZP3/nZP4 mixture bound to the acrosomal region of porcine sperm, in a manner similar to that of the nZP3/nZP4 mixture. nZP3 was precipitated with rZP4, and nZP4 was precipitated with rZP3 by utilising theN-terminal tags on the recombinant proteins. These results indicated that nZP4, but not rZP4, is necessary for binding activity of porcine ZP3/ZP4 complex towards porcine sperm and further suggested that the carbohydrate structures of ZP4 in the porcine ZP3/ZP4 complex are responsible for porcine sperm-binding activity of the complex.
Massive multiplication of genome and ribosomes in dormant cells (akinetes) of Aphanizomenon ovalisporum (Cyanobacteria)
Authors: Sukenik Assaf , Kaplan-Levy Ruth N , Welch Jessica Mark , Post Anton F 
Published: October 2011

Abstract
Akinetes are dormancy cells commonly found among filamentous cyanobacteria, many of which are toxic and/or nuisance, bloom-forming species. Development of akinetes from vegetative cells is a process that involves morphological and biochemical modifications. Here, we applied a single-cell approach to quantify genome and ribosome content of akinetes and vegetative cells in Aphanizomenon ovalisporum (Cyanobacteria). Vegetative cells of A. ovalisporum were naturally polyploid and contained, on average, eight genome copies per cell. However, the chromosomal content of akinetes increased up to 450 copies, with an average value of 119 genome copies per akinete, 15-fold higher than that in vegetative cells. On the basis of fluorescence in situ hybridization, with a probe targeting 16S rRNA, and detection with confocal laser scanning microscopy, we conclude that ribosomes accumulated in akinetes to a higher level than that found in vegetative cells. We further present evidence that this massive accumulation of nucleic acids in akinetes is likely supported by phosphate supplied from inorganic polyphosphate bodies that were abundantly present in vegetative cells, but notably absent from akinetes. These results are interpreted in the context of cellular investments for proliferation following a long-term dormancy, as the high nucleic acid content would provide the basis for extended survival, rapid resumption of metabolic activity and cell division upon germination.
Introduction to the Baltimore Ecosystem Study, Long-Term Ecological Research Project, Phase III
Authors: Pickett Steward 
Published: October 2011

AbstractThe Baltimore Ecosystem Study (BES) is one of two urban Long-Term Ecological Research (LTER) projects in the United States. It began its third funding cycle in 2011. Although the project continues key measurements that were started in 1997 at the inception of the research, the third phase is characterized by a new conceptual framework. Phase III of BES focuses on metropolitan Baltimore, Maryland, as a system poised for transition from a "sanitary city" -- characterized by engineered environmental solutions, management via discrete disciplines, and government control to a "sustainable city" -- which would be characterized by additional biological solutions, collaborative management, and polycentric and multi-level governance. In such a situation, the guiding research question becomes, "What are the effects of adaptive processes aimed at sustainability in the Baltimore socio-ecological system?" Adaptive processes are those social and biophysical features and actions which allow a complex system to adjust to changing internal and external drivers. The full proposal and other details of BES can be discovered on the project website: www.beslter.org
A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome
Authors: Pantano Lorena , Estivill Xavier , Martí Eulalia 
Published: October 2011

Abstract
Motivation: Recent progress in high-throughput sequencing technologies has largely contributed to reveal a highly complex landscape of small non-coding RNAs (sRNAs), including novel non-canonical sRNAs derived from long non-coding RNA, repeated elements, transcription start sites and splicing site regions among others. The published frameworks for sRNA data analysis are focused on miRNA detection and prediction, ignoring further information in the dataset. As a consequence, tools for the identification and classification of the sRNAs not belonging to miRNA family are currently lacking.
Results: Here, we present, SeqCluster, an extension of the currently available SeqBuster tool to identify and analyze at different levels the sRNAs not annotated or predicted as miRNAs. This new module deals with sequences mapping onto multiple locations and permits a highly versatile and user-friendly interaction with the data in order to easily classify sRNA sequences with a putative functional importance. We were able to detect all known classes of sRNAs described to date using SeqCluster with different sRNA datasets.
Availability: tool and video-tutorials are available at http://estivill_lab.crg.es/seqbuster.
Contact: eulalia.marti@crg.es; xavier.estivill@crg.es
Supplementary Information: Supplementary data are available at Bioinformatics online.
Two Ancient Bacterial-like PPP Family Phosphatases from Arabidopsis Are Highly Conserved Plant Proteins That Possess Unique Properties
Authors: Uhrig R. Glen , Moorhead Greg B. 
Published: October 2011

Abstract
Protein phosphorylation, catalyzed by the opposing actions of protein kinases and phosphatases, is a cornerstone of cellular signaling and regulation. Since their discovery, protein phosphatases have emerged as highly regulated enzymes with specificity that rivals their counteracting kinase partners. However, despite years of focused characterization in mammalian and yeast systems, many protein phosphatases in plants remain poorly or incompletely characterized. Here, we describe a bioinformatic, biochemical, and cellular examination of an ancient, Bacterial-like subclass of the phosphoprotein phosphatase (PPP) family designated the Shewanella-like protein phosphatases (SLP phosphatases). The SLP phosphatase subcluster is highly conserved in all plants, mosses, and green algae, with members also found in select fungi, protists, and bacteria. As in other plant species, the nucleus-encoded Arabidopsis (Arabidopsis thaliana) SLP phosphatases (AtSLP1 and AtSLP2) lack genetic redundancy and phylogenetically cluster into two distinct groups that maintain different subcellular localizations, with SLP1 being chloroplastic and SLP2 being cytosolic. Using heterologously expressed and purified protein, the enzymatic properties of both AtSLP1 and AtSLP2 were examined, revealing unique metal cation preferences in addition to a complete insensitivity to the classic serine/threonine PPP protein phosphatase inhibitors okadaic acid and microcystin. The unique properties and high conservation of the plant SLP phosphatases, coupled to their exclusion from animals, red algae, cyanobacteria, archaea, and most bacteria, render understanding the function(s) of this new subclass of PPP family protein phosphatases of particular interest.
Differential resilience of invertebrates to fire
Authors: PRYKE JAMES S. , SAMWAYS MICHAEL J. 
Published: October 2011

AbstractFires are natural to ecosystems in many parts of the world, yet few studies have examined multi‐taxa invertebrate responses to these fires. We sampled a wide range of invertebrate taxa and feeding guilds at sites 3 months, 1 year and 3 years after fire, and in unburned control sites at the same time. A range of invertebrate sampling techniques was used on Table Mountain, in the Cape Floristic Region biodiversity hotspot, an area prone to natural and human‐induced fires. Sampling time differences strongly affected the composition of the whole assemblage, with fire having a major additional influence. Assemblages showed differential resilience to fire, especially in terms of species richness and abundance. One year after fire, the burned sites had the most compositional differences for the surface‐active species compared to control sites, while after 3 years, these sites were similar. Aerial assemblages were very different 3 years after burning, especially the pollination guild. Furthermore, these 3‐year‐old burned sites had the most unique species, suggesting that burning and longer‐term recovery is important for overall diversity. Some components of the invertebrate assemblage were remarkably resilient to fire (particularly ants), while others were far more conservative (pollinators). Nevertheless, fire allows new species to enter the ecosystem and can thus be used to promote local biodiversity if used appropriately. Ants alone should not be used to represent the whole invertebrate assemblage as they do not represent the more fire‐prone groups. A cross‐section of functional guilds is recommended in invertebrate recovery/fire management conservation programmes. These results have general significance in that a variety of feeding guilds need to be sampled when monitoring invertebrate responses to fire.
Prevalence, severity and clinical features of psoriasis in fingernails and toenails in adult patients: Italian experience
Authors: Brazzelli V. , Carugno A. , Alborghetti A. , Grasso V. , Cananzi R. , Fornara L. , De Silvestri A. , Borroni G. 
Published: October 2011

AbstractBackground  Psoriasis is a chronic inflammatory skin disease affecting 2.0–6.5% of the European population. Although the most striking clinical features of psoriasis involve the skin, other organs including nails and joints may be affected in a substantial proportion of patients. Literature reports nail involvement in 10–56% of psoriatic patients, with common physical and social impairment. However, the precise prevalence of specific clinical features of nail psoriasis is somewhat under‐reported.Objectives  Our cross‐sectional study aimed at describing the prevalence and the clinical features of nail involvement in adult psoriatic patients in a psoriasis referral centre in northern Italy.Methods  A total of 178 (124 men, 54 women) consecutive adult patients (≥18 years old) with psoriasis were included. Psoriasis Area and Severity Index (PASI) and Nail Psoriasis Severity Index (NAPSI) scores were calculated for each patient. Relevant medical history was recorded.Results  Nail involvement was present in 137 (99 men, 38 women) patients (76.9%). The most common nail abnormality was onycholysis, followed by crumbling, subungual hyperkeratosis, pitting and discoloration. Pitting and onycholysis were the most prevalent patterns observed in fingernails, whereas onycholysis and crumbling were the most frequent changes detected in toenails. The most frequently and severely affected nails were the fourth fingernail and the first toenail. The average PASI score was higher in individuals with nail involvement (12.0 vs. 8.7, P = 0.06). Nail changes were present in 85.7% of patients with psoriatic arthritis.Conclusions  Our study confirms that nail involvement may be overlooked in psoriasis patients. Different psoriatic patterns in the nail affect specific digits more frequently.
Measurement of vascular tone and stroke volume baroreflex gain
Authors: Vaschillo Evgeny G. , Vaschillo Bronya , Buckman Jennifer F. , Pandina Robert J. , Bates Marsha E. 
Published: October 2011

AbstractThe arterial baroreflex system (BRS) consists of at least three closed‐loop control systems: the heart rate (HR), vascular tone (VT), and stroke volume (SV) BRSs. Whereas HR‐BRS gain is well studied, VT‐BRS and SV‐BRS gain are not. This study aimed to develop a method for quantifying VT‐BRS and SV‐BRS gain using an established HR‐BRS gain measurement approach. ECG and beat‐to‐beat blood pressure (BP) were recorded in 31 young healthy participants during three tasks. Sequences of R‐to‐R wave intervals (RRI) of the ECG, pulse transit time (PTT), and SV were measured to assess HR‐, VT‐, and SV‐BRS gain using the cross‐spectral technique of computing the BP‐RRI, BP‐PTT, and BP‐SV transfer functions. Gain in each BRS arch was measured in individuals with intact BRS functioning. Functional overlap and independence was noted in the BRS arches. The implications of the proposed method are discussed.
How Does Investor Sentiment Affect Stock Market Crises? Evidence from Panel Data
Authors: Zouaoui Mohamed , Nouyrigat Geneviève , Beer Francisca 
Published: October 2011

AbstractWe test the impact of investor sentiment on a panel of international stock markets. Specifically, we examine the influence of investor sentiment on the probability of stock market crises. We find that investor sentiment increases the probability of occurrence of stock market crises within a one‐year horizon. The impact of investor sentiment on stock markets is more pronounced in countries that are culturally more prone to herd‐like behavior, overreaction and low institutional involvement.
Tribological Properties of Si3N4/SiC Nano–Nano Composite Ceramics
Authors: Shin Jung‐Hoo , Kumar B. Venkata Manoj , Kim Jae‐Hee , Hong Seong‐Hyeon 
Published: October 2011

Fabrication of Si2N2O phase free, fully densified Si3N4/SiC nano–nano composite ceramics was done by combining a carbothermal reduction treatment (CRT) and a spark plasma sintering (SPS) using commercially available Si3N4 and SiC nano‐powders, and their mechanical and tribological properties were investigated. CRT was conducted at 1450°C for 10 h with a phenolic resin and SPS was carried out at 1550°C for 5 min, which yielded the fully dense (>98% of theoretical density) Si3N4/SiC nano–nano ceramics with ~100 nm grain size. The elastic modulus, hardness, and fracture toughness increased with increasing SiC content up to 20 wt%. The wear rate of Si3N4/SiC nano–nano ceramics decreased from 2.0×10−5 to 6.76×10−6 mm3/Nm with 20 wt% SiC addition, resulting from the increased hardness and fracture toughness.
Topical calcineurin inhibitors in the treatment of atopic dermatitis – an update on safety issues
Authors: Czarnecka‐Operacz Magdalena , Jenerowicz Dorota 
Published: October 2011

SummaryAtopic dermatitis is a common chronic skin disorder whose management is complex. Topical corticosteroids have been the mainstay of atopic dermatitis treatment for more than 50 years but have multiple side effects. Topical calcineurin inhibitors including tacrolimus and pimecrolimus are safe and efficacious in atopic dermatitis. In 2005 the FDA issued “black box” warnings for pimecrolimus cream and tacrolimus ointment because of potential safety risks, including skin cancers and lymphomas. However, these concerns are not supported by current data. Topical calcineurin inhibitors are particularly indicated for treating patients with atopic dermatitis in whom topical corticosteroid therapy cannot be employed or may cause irreversible side effects. They can be used advantageously in problem zones. A novel regimen of proactive treatment has been shown to prevent, delay and reduce exacerbations of atopic dermatitis. Therapy with topical calcineurin inhibitors should be managed by an experienced specialist and each patient should receive proper education on how to use them and what possible unwanted effects may be expected.
Immunogenicity of Mannheimia haemolytica Recombinant Outer Membrane Proteins Serotype 1-Specific Antigen, OmpA, OmpP2, and OmpD15
Authors: Ayalew Sahlu , Shrestha Binu , Montelongo Marie , Wilson Amanda E. , Confer Anthony W. 
Published: October 2011

ABSTRACTWe previously identifiedMannheimia haemolyticaouter membrane proteins (OMPs) that may be important immunogens by using immunoproteomic analyses. Genes for serotype 1-specific antigen (SSA-1), OmpA, OmpP2, and OmpD15 were cloned and expressed, and recombinant proteins were purified. Objective 1 of this study was to demonstrate immunogenicity of the four recombinant OMPs in mice and cattle. Objective 2 was to determine if the addition of individual recombinant OMPs or combinations of them would modify immune responsiveness of mice to the recombinant chimeric protein SAC89, containing the main epitope fromM. haemolyticaouter membrane lipoprotein PlpE and the neutralizing epitope ofM. haemolyticaleukotoxin. Mice vaccinated with recombinant OmpA (rOmpA), rSSA-1, rOmpD15, and rOmpP2 developed significant antibody responses toM. haemolyticaouter membranes and to the homologous recombinant OMP. Cattle vaccinated with rOmpA and rSSA-1 developed significant antibodies toM. haemolyticaouter membranes by day 28, whereas cattle vaccinated with rOmpD15 and rOmpP2 developed only minimal responses. Sera from cattle vaccinated with each of the recombinant proteins stimulated complement-mediated killing of the bacterium. Concurrent vaccination with SAC89 plus any of the four rOMPs singly resulted in increased endpoint anti-SAC89 titers, and for the SAC89/rSSA-1 vaccinees, the response was increased significantly. In contrast, the SAC89/P2/SSA-1 and SAC89/OmpA/P2/D15/SSA-1 combination vaccines resulted in significant decreases in anti-SAC89 antibodies compared to SAC89 vaccination alone. In conclusion, under the conditions of these experiments, vaccination of mice and cattle with rOmpA and rSSA-1 stimulated high antibody responses and may have protective vaccine potential.
Epidemiology of Invasive Streptococcus pyogenes Infections in France in 2007
Authors: Lepoutre A. , Doloy A. , Bidet P. , Leblond A. , Perrocheau A. , Bingen E. , Trieu-Cuot P. , Bouvet A. , Poyart C. , Lévy-Bruhl D. ,   the Microbiologists of the Epibac Network
Published: October 2011

ABSTRACT

Invasive group A streptococcal (GAS) infections cause significant morbidity and mortality. A national survey was initiated to assess the burden of invasive GAS infections in France, describe their clinical characteristics, and assess the molecular characteristics of GAS strains responsible for these infections. The survey was conducted in 194 hospitals, accounting for 51% of acute care hospital admissions in France. Clinical data, predisposing factors, and demographic data were obtained, and all GAS isolates were
emm
sequence typed. We identified 664 cases of invasive GAS infections, with an annual incidence of 3.1 per 100,000 population. The case-fatality ratio was 14% and rose to 43% in the case of streptococcal toxic shock syndrome. Bacteremia without identified focus (22%) and skin/soft tissue infections (30%) were the most frequent clinical presentations. Necrotizing fasciitis was frequent in adults (18%) and uncommon in children (3%). The 3 predominant
emm
types
were emm
1,
emm
89, and
emm
28, accounting for 33%, 16%, and 10% of GAS isolates, respectively. The
emm
1 type was associated with fatal outcomes and was more frequent in children than in adults. Six clusters of cases were identified, with each cluster involving 2 invasive cases due to GAS strains which shared identical GAS
emm
sequence types. Four clusters of cases involved eight postpartum infections, one family cluster involved a mother and child, and one cluster involved two patients in a nursing home. Invasive GAS infection is one of the most severe bacterial diseases in France, particularly in persons aged ≥50 years or when associated with toxic shock syndrome.
Widespread Occurrence of Diverse Human Pathogenic Types of the Fungus Fusarium Detected in Plumbing Drains
Authors: Short Dylan P. G. , O'Donnell Kerry , Zhang Ning , Juba Jean H. , Geiser David M. 
Published: October 2011

ABSTRACTIt has been proposed that plumbing systems might serve as a significant environmental reservoir of human-pathogenic isolates ofFusarium. We tested this hypothesis by performing the first extensive multilocus sequence typing (MLST) survey of plumbing drain-associatedFusariumisolates and comparing the diversity observed to the known diversity of clinicalFusariumisolates. We sampled 471 drains, mostly in bathroom sinks, from 131 buildings in the United States using a swabbing method. We found that 66% of sinks and 80% of buildings surveyed yielded at least oneFusariumculture. A total of 297 isolates ofFusariumcollected were subjected to MLST to identify the phylogenetic species and sequence types (STs) of these isolates. Our survey revealed that the six most common STs in sinks were identical to the six most frequently associated with human infections. We speculate that the most prevalent STs, by virtue of their ability to form and grow in biofilms, are well adapted to plumbing systems. Six majorFusariumSTs were frequently isolated from plumbing drains within a broad geographic area and were identical to STs frequently associated with human infections.
Staphylococcus haemolyticus as an Important Hospital Pathogen and Carrier of Methicillin Resistance Genes
Authors: Barros E. M. , Ceotto H. , Bastos M. C. F. , dos Santos K. R. N. , Giambiagi-deMarval M. 
Published: October 2011

ABSTRACT

Phenotypic and molecular methods were used to characterize the antibiotic resistance of 64 clinical isolates of
Staphylococcus haemolyticus
. By PCR of the
mecA
gene, 87% were found to be methicillin resistant. Approximately 55% harbored staphylococcal cassette chromosome
mec
element (SCC
mec
) type V, and only one SCC
mec
type IV. Many isolates (75%) displayed multiresistance, and pulsotype analysis showed a high diversity.
Cellular Poly(C) Binding Proteins 1 and 2 Interact with Porcine Reproductive and Respiratory Syndrome Virus Nonstructural Protein 1β and Support Viral Replication
Authors: Beura Lalit K. , Dinh Phat X. , Osorio Fernando A. , Pattnaik Asit K. 
Published: October 2011

ABSTRACT

Porcine reproductive and respiratory syndrome virus (PRRSV) infection of swine results in substantial economic losses to the swine industry worldwide. Identification of cellular factors involved in PRRSV life cycle not only will enable a better understanding of virus biology but also has the potential for the development of antiviral therapeutics. The PRRSV nonstructural protein 1 (nsp1) has been shown to be involved in at least two important functions in the infected hosts: (i) mediation of viral subgenomic (sg) mRNA transcription and (ii) suppression of the host's innate immune response mechanisms. To further our understanding of the role of the viral nsp1 in these processes, using nsp1β, a proteolytically processed functional product of nsp1 as bait, we have identified the cellular poly(C)-binding proteins 1 and 2 (PCBP1 and PCBP2) as two of its interaction partners. The interactions of PCBP1 and PCBP2 with nsp1β were confirmed both by coimmunoprecipitation in infected cells and/or in plasmid-transfected cells and also by
in vitro
binding assays. During PRRSV infection of MARC-145 cells, the cytoplasmic PCBP1 and PCBP2 partially colocalize to the viral replication-transcription complexes. Furthermore, recombinant purified PCBP1 and PCBP2 were found to bind the viral 5′ untranslated region (5′UTR). Small interfering RNA (siRNA)-mediated silencing of PCBP1 and PCBP2 in cells resulted in significantly reduced PRRSV genome replication and transcription without adverse effect on initial polyprotein synthesis. Overall, the results presented here point toward an important role for PCBP1 and PCBP2 in regulating PRRSV RNA synthesis.