bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity of the helminth community of the Pampean grassland mouse (Akodon azarae) on poultry farms in central Argentina
Authors: Miño M.H. , Rojas Herrera E.J. , Notarnicola J. , Robles M. del R. , Navone G.T. 
Published: January 2012

AbstractThis paper describes the helminth community of the Pampean grassland mouse (Akodon azarae) inhabiting poultry farms in central Argentina. Winter diversity (season of high rodent abundance) has been compared to spring diversity (season of low rodent abundance). Species richness was seven in both seasons: five nematodes (Syphacia carlitosi,Stilestrongylusspp.,Trichuris laevitestis,Pterygodermatites (Paucipectines) azaraiandProtospirura numidica criceticola) and two cestodes (adults of Cyclophyllidea andTaenia taeniaeformishepatic cysts). No difference in richness was detected between host sexes in each season or among host age classes. However, the helminth community showed 67% similarity between winter and spring, with diversity being significantly higher in spring (H = 0.873) than in winter (H = 0.546;P < 0.0005). This could be attributed to different factors, such as host abundance, host diet or environmental factors, that affect the transmission of each species differently. On the other hand,Stilestrongylusspp. andS. carlitosishowed higher dominance and intensity in both seasons compared to their cohabiting species,P. (P.) azaraiandT. laevitestis, respectively. The lower values of the latter two species may be related to a crowding effect due to their large body sizes. This is the first report of cestodes inA. azarae. The finding ofT. taeniaeformisstrobilocerci could be important in the epidemiology of parasitosis in domestic animals of the farms.
Socioeconomic status and child health: what is the role of health care, health conditions, injuries and maternal health?
Authors: Allin Sara , Stabile Mark 
Published: January 2012

AbstractThere is a persistent relationship between socioeconomic status and health that appears to have its roots in childhood. Not only do children in families with lower income and with mothers with lower levels of education have worse health on average than those with greater socioeconomic advantage, but also the gradient appears to steepen with age. This study contributes to the literature on the relationship between socioeconomic status and child health by testing the hypothesis that the increasing effect of family income on children's health with age relates to the children's use of health care services. It also investigates the role of specific health conditions, injuries or maternal health in explaining the steepening gradient. Drawing on a nationally representative survey from Canada, the National Longitudinal Survey of Children and Youth from the period 1994/95–2008/09, this study provides further evidence of a steepening socioeconomic gradient in child health with age. It finds that accounting for health care use does not explain the steepening gradient and that the protective effect of income appears to be greater for those who had contact with the health system, in particular with regard to physician care and prescription drug use.
Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic
Authors: Allen Lisa Zeigler , Allen Eric E , Badger Jonathan H , McCrow John P , Paulsen Ian T , Elbourne Liam D H , Thiagarajan Mathangi , Rusch Doug B , Nealson Kenneth H , Williamson Shannon J , Venter J Craig , Allen Andrew E 
Published: January 2012

Abstract
Metagenomic data sets were generated from samples collected along a coastal to open ocean transect between Southern California Bight and California Current waters during a seasonal upwelling event, providing an opportunity to examine the impact of episodic pulses of cold nutrient-rich water into surface ocean microbial communities. The data set consists of ∼5.8 million predicted proteins across seven sites, from three different size classes: 0.1–0.8, 0.8–3.0 and 3.0–200.0 μm. Taxonomic and metabolic analyses suggest that sequences from the 0.1–0.8 μm size class correlated with their position along the upwelling mosaic. However, taxonomic profiles of bacteria from the larger size classes (0.8–200 μm) were less constrained by habitat and characterized by an increase in Cyanobacteria, Bacteroidetes, Flavobacteria and double-stranded DNA viral sequences. Functional annotation of transmembrane proteins indicate that sites comprised of organisms with small genomes have an enrichment of transporters with substrate specificities for amino acids, iron and cadmium, whereas organisms with larger genomes have a higher percentage of transporters for ammonium and potassium. Eukaryotic-type glutamine synthetase (GS) II proteins were identified and taxonomically classified as viral, most closely related to the GSII in Mimivirus, suggesting that marine Mimivirus-like particles may have played a role in the transfer of GSII gene functions. Additionally, a Planctomycete bloom was sampled from one upwelling site providing a rare opportunity to assess the genomic composition of a marine Planctomycete population. The significant correlations observed between genomic properties, community structure and nutrient availability provide insights into habitat-driven dynamics among oligotrophic versus upwelled marine waters adjoining each other spatially.
Expression of the blood-group-related glycosyltransferase B4galnt2 influences the intestinal microbiota in mice
Authors: Staubach Fabian , Künzel Sven , Baines Andrea C , Yee Andrew , McGee Beth M , Bäckhed Fredrik , Baines John F , Johnsen Jill M 
Published: January 2012

Abstract
Glycans on mucosal surfaces have an important role in host–microbe interactions. The locus encoding the blood-group-related glycosyltransferase β-1,4-N-acetylgalactosaminyltransferase 2 (B4galnt2) is subject to strong selective forces in natural house-mouse populations that contain a common allelic variant that confers loss of B4galnt2 gene expression in the gastrointestinal (GI) tract. We reasoned that altered glycan-dependent intestinal host–microbe interactions may underlie these signatures of selection. To determine whether B4galnt2 influences the intestinal microbial ecology, we profiled the microbiota of wild-type and B4galnt2-deficient siblings throughout the GI tract using 16S rRNA gene pyrosequencing. This revealed both distinct communities at different anatomic sites and significant changes in composition with respect to genotype, indicating a previously unappreciated role of B4galnt2 in host–microbial homeostasis. Among the numerous B4galnt2-dependent differences identified in the abundance of specific bacterial taxa, we unexpectedly detected a difference in the pathogenic genus, Helicobacter, suggesting Helicobacter spp. also interact with B4galnt2 glycans. In contrast to other glycosyltransferases, we found that the host intestinal B4galnt2 expression is not dependent on presence of the microbiota. Given the long-term maintenance of alleles influencing B4galnt2 expression by natural selection and the GI phenotypes presented here, we suggest that variation in B4galnt2 GI expression may alter susceptibility to GI diseases such as infectious gastroenteritis.
Establishment of ultra long‐lived cell lines by transfection of TERT into normal human fibroblast TIG‐1 and their characterization
Authors: Kamada Mizuna , Kumazaki Tsutomu , Matsuo Taira , Mitsui Youji , Takahashi Tomoko 
Published: January 2012

AbstractTo establish useful human normal cell lines, TERT (telomerase reverse transcriptase) cDNA was transfected into normal female lung fibroblast, TIG‐1. After long‐term‐sub‐cultivation of 74 individual clones selected for resistance to G418, we obtained 55 cultures with normal range of life span [75 PDL (population doubling level)], 16 cultures with extended life span (75–140 PDL). In addition, 3 immortal cell strains and unexpectedly, one ultra long‐lived cell line (ULT‐1) with life span of 166 PDL were established. IMT‐1, one of the immortal cell strains was confirmed to maintain long telomere length, high telomerase activity and an extremely low level of p16INK4A. They also showed moderate p53 and p21CIP1 expression, keeping vigorous growth rate even at 450 PDL. High level of fibronectin and collagen 1α expression confirmed IMT‐1 as normal fibroblasts, although one X chromosome had been lost. ULT‐1, however, kept a near normal karyotypes and had shortening of telomere length, high expression of p16INK4A, moderate levels of senescence associated‐β‐galactosidase positive cells and decreased growth rate only after 150 PDs (population doublings), and finally reached senescence at 166 PDL with morphology of normal senescent fibroblasts. As resources of standard normal human cell, abundant vials of early and middle passages of ULT‐1 have been stocked. The use of the cell line is discussed, focusing on isograft of artificial skin and screening of anti‐aging or safe chemical agents.
Supraorbital Keyhole Approach to Upper Basilar Artery Aneurysms via the Optico-Carotid Window: A Cadaveric Anatomic Study and Preliminary Application
Authors: Ma Y. , Lan Q. 
Published: January 2012

AbstractNo anatomic data are available addressing the surgical indication for upper BA aneurysms via the supraorbital keyhole approach (SOKA).An anatomic study of the SOKA to the upper BA via the optico-carotid window (OCW) was designed. Our clinical experience is reported.After completing the SOKA craniotomy on 8 cadaveric heads, the width and length of OCW and the length of the supraclinoid internal carotid artery (SCICA) were measured. Measurement of the following was carried out through the OCW: (i) linear distance (a) of the BA from the most proximal point of visualization of the BA to the posterior clinoid process level, (ii) perpendicular distance (b) from the most distal point of visualization along the elongation of the BA to the anterior fossa level. After posterior clinoidectomy and orbitectomy, the measurement of (a) and (b) was repeated.The width and length of OCW and the SCICA length were 7.6±2.1 mm, 11.6±2.3 mm, and 12.7±2.4 mm. The distance (a) was 5.0±1.2 mm, increased by 3.4±1.0 mm after posterior clinoidectomy. The distance (b) was 12.8±2.6 mm, increased by 3.3±1.2 mm after orbitectomy. 9 aneurysms were completely clipped.When the width and length of the OCW are > 5 mm and > 7 mm, respectively, the SOKA can meet the requirement of exposure and manipulation of the upper BA. The upper BA aneurysms located < 10 mm higher than the anterior fossa and not more than 5 mm lower than the PCP can be treated via the SOKA. Posterior clinoidectomy and orbitectomy can increase the proximal and the distal exposure of the BA, respectively.
The ultraviolet photodissociation of CS2: The S(1D2) channel
Authors: Brouard M. , Campbell E. K. , Cireasa R. , Johnsen A. J. , Yuen W.-H. 
Published: January 2012

The photodissociation of CS2 has been investigated using velocity-map ion imaging of the S(1D2) atomic photofragments following excitation at 193 nm and at longer wavelengths close to the S(1D2) channel threshold. The experiments probe regions both above and below the energetic barrier to linearity on the \documentclass[12pt]{minimal}\begin{document}$^{1}\Sigma _{u}^{+}(^{1}B_{2})$\end{document}Σu+1(B21) potential energy surface. The imaging data in both regions indicate that the electronic angular momentum of the S(1D2) atom products is unpolarized, but also reveal different dissociation dynamics in the two regions. Excitation above the barrier to linearity yields an inverted CS(1Σ+) vibrational population distribution, whereas the long-wavelength state-to-state results following excitation below the barrier reveal CS(1Σ+)(v, J) coproduct state distributions which are consistent with a statistical partitioning of the energy. Below the barrier, photofragment excitation spectra point to an enhancement of the singlet channel for K = 1, relative to K = 0, where K is the projection of the angular momentum along the principal axis, in agreement with previous work. However, the CS cofragment product state distributions are found to be insensitive to K. It is proposed that dissociation below the barrier to linearity occurs primarily on a surface with a significant potential energy well and without an exit channel barrier, such as that for the ground electronic state. However, oscillatory structure is also observed in the kinetic energy release distributions, which is shown to be consistent with a mapping of parent molecule bending motion. This could indicate the operation of competing direct and indirect dissociation mechanisms below the barrier to linearity.
Delayed Environmental Enrichment Reverses Sevoflurane-induced Memory Impairment in Rats
Authors: Shih Jennifer , May Laura D. V. , Gonzalez Heidi E. , Lee Elaine W. , Alvi Rehan S. , Sall Jeffrey W. , Rau Vinuta , Bickler Philip E. , Lalchandani Gopal R. , Yusupova Marianna , Woodward Elliott , Kang Heejae , Wilk Alan J. , Carlston Colleen M. , Mendoza Mortay V. , Guggenheim Jeremy N. , Schaefer Maximilian , Rowe Allison M. , Stratmann Greg 
Published: January 2012

Background
Anesthesia given to immature rodents causes cognitive decline, raising the possibility that the same might be true for millions of children undergoing surgical procedures under general anesthesia each year. We tested the hypothesis that anesthesia-induced cognitive decline in rats is treatable. We also tested if anesthesia-induced cognitive decline is aggravated by tissue injury.

Methods
Seven-day old rats underwent sevoflurane anesthesia (1 minimum alveolar concentration, 4 h) with or without tail clamping. At 4 weeks, rats were randomized to environmental enrichment or normal housing. At 8 weeks rats underwent neurocognitive testing, which consisted of fear conditioning, spatial reference memory, and water maze-based memory consolidation tests, and interrogated working memory, short-term memory, and early long-term memory.

Results
Sevoflurane-treated rats had a greater escape latency when the delay between memory acquisition and memory retrieval was increased from 1 min to 1 h, indicating that short-term memory was impaired. Delayed environmental enrichment reversed the effects of sevoflurane on short-term memory and generally improved many tested aspects of cognitive function, both in sevoflurane-treated and control animals. The performance of tail-clamped rats did not differ from those rats receiving anesthesia alone.

Conclusion
Sevoflurane-induced cognitive decline in rats is treatable. Delayed environmental enrichment rescued the sevoflurane-induced impairment in short-term memory. Tissue injury did not worsen the anesthesia-induced memory impairment. These findings may have relevance to neonatal and pediatric anesthesia.
Crystallization and preliminary crystallographic analysis of LipC12, a true lipase isolated through a metagenomics approach
Authors: Martini V. P. , Glogauer A. , Iulek J. , Souza E. M. , Pedrosa F. O. , Krieger N. 
Published: January 2012

LipC12, a true lipase from family I.1 of bacterial lipases which was previously isolated through a metagenomics approach, contains 293 amino acids. Among lipases of known three-dimensional structure, it has a sequence identity of 47% to the lipase fromPseudomonas aeruginosaPAO1. Recombinant N-terminally His6-tagged LipC12 protein was expressed inEscherichia coli, purified in a homogenous form and crystallized in several conditions, with the best crystals being obtained using 2.0 Msodium formate and 0.1 Mbis-tris propane pH 7.0. X-ray diffraction data were collected to 2.70 Å resolution. The crystals belonged to the tetragonal space groupP4122, with unit-cell parametersa=b= 58.62,c = 192.60 Å.
Crystallization and preliminary X-ray diffraction analysis of the metalloregulatory protein DtxR fromThermoplasma acidophilum
Authors: Yeo Hyun Ku , Kang Jina , Park Young Woo , Sung Jung-Suk , Lee Jae Young 
Published: January 2012

The diphtheria toxin repressor (DtxR) is a metal-ion-dependent transcriptional regulator which regulates genes encoding proteins involved in metal-ion uptake to maintain metal-ion homeostasis. DtxR fromThermoplasma acidophilumwas cloned and overexpressed inEscherichia coli. Crystals of N-terminally His-tagged DtxR were obtained by hanging-drop vapour diffusion and diffracted to 1.8 Å resolution. DtxR was crystallized at 296 K using polyethylene glycol 4000 as a precipitant. The crystals belonged to the orthorhombic space groupP21212, with unit-cell parametersa= 61.14,b= 84.61,c= 46.91 Å, α = β = γ = 90°. The asymmetric unit contained approximately one monomer of DtxR, giving a crystal volume per mass (VM) of 2.22 Å3 Da−1and a solvent content of 44.6%.
Crystallization of oligonucleotides containing A-rich repeats suggests a structural contribution to the autoregulation mechanism of PABP translation
Authors: Kikuchi Keita , Shimizu Satoru , Sato Yoshiteru , Morishita Ella Czarina , Takénaka Akio 
Published: January 2012

Eukaryotic poly(A)-binding protein (PABP) commonly binds to the 3′-UTR poly(A) tail of every mRNA, but it also binds to the 5′-UTR of PABP mRNA for autoregulation of its expression. In the sequence of the latter binding site, the contiguous A residues are segmented discretely by the insertion of short pyrimidine oligonucleotides as linkers, so that (A)6–8segments are repeated six times. This differs from the poly(A)-tail sequence, which has a higher binding affinity for PABP. In order to examine whether the A-rich repeats have a functional structure, several RNA/DNA analogues were subjected to crystallization. It was found that some of them could be crystallized. Single crystals thus obtained diffracted to 4.1 Å resolution. The fact that the repeated sequences can be crystallized suggests the possibility that the autoregulatory sequence in PABP mRNA has a specific structure which impedes the binding of PABP. When PABP is excessively produced, it could bind to this sequence by releasing the structure in order to interfere with initiation-complex formation for suppression of PABP translation. Otherwise, PABP at low concentration preferentially binds to the poly(A) tail of PABP mRNA.
Crystallization and preliminary X-ray crystallographic analysis of dioscorin fromDioscorea japonica
Authors: Xue You-Lin , Miyakawa Takuya , Sawano Yoriko , Tanokura Masaru 
Published: January 2012

Dioscorin, the major tuber storage protein in yam, has been reported to possess carbonic anhydrase, trypsin inhibitor, angiotensin-converting enzyme (ACE) inhibitor, free-radical scavenger, dehydroascorbate reductase and monodehydroascorbate reductase activities. Recent research has also found that dioscorin can enhance immune modulationviathe toll-like receptor 4 (TLR-4) signal transduction pathway in RAW 264.7 cells, murine bone-marrow cells and human monocytesex vivo. Resolving the structure of dioscorin would help in better understanding its activities and would provide clues to understanding the mechanism of its multiple functions. The full-length protein (residues 1–246) with an additional His6tag at the N-terminus was expressed inEscherichia coliRosetta (DE3) cells. After His-tag cleavage and purification, the protein was crystallized by the sitting-drop vapour-diffusion method at 278 K. An X-ray diffraction data set was collected to a resolution of 2.11 Å using a synchrotron X-ray source. The crystal belonged to space groupC2221, with unit-cell parametersa= 83.5,b= 156.8,c = 83.6 Å, and was estimated to contain two protein molecules per asymmetric unit.
Crystallization and preliminary X-ray diffraction analysis ofBacillus subtilisYwfE, anL-amino-acid ligase
Authors: Tsuda Takeo , Suzuki Tomomi , Kojima Shuichi 
Published: January 2012

Bacillus subtilisYwfE, an L-amino-acid ligase, catalyzes the formation of an α-dipeptide from L-amino acids in an ATP-dependent manner. In order to elucidate the substrate-recognition mode and the reaction mechanism of this ligase, native and selenomethionine-derivatized (SeMet) crystals of YwfE in the presence of ADP, MgCl2and the dipeptide L-Ala-L-Gln were obtained using the hanging-drop vapour-diffusion method. These crystals diffracted to 1.9 and 2.8 Å resolution, respectively. Preliminary SAD phase calculations using the data set from the SeMet crystal suggested that the crystal belonged to the hexagonal space groupP6522, with unit-cell parametersa=b= 90.85,c = 250.31 Å, and contained one molecule in the asymmetric unit with a solvent content of 57.3%.
Expression, purification and preliminary structural analysis of the coiled-coil domain ofDeinococcus radioduransRecN
Authors: Pellegrino Simone , de Sanctis Daniele , McSweeney Sean , Timmins Joanna 
Published: January 2012

Deinococcus radioduranshas developed an efficient mechanism which allows the integrity of its entire genome to be fully restored after exposure to very high doses of ionizing radiation. Homologous recombination plays a crucial role in this process. RecN is a protein that belongs to the SMC-like protein family and is suggested to be involved in DNA repair. RecN is composed of a globular domain and an antiparallel coiled-coil region which connects the N- and C-termini. It has been suggested that dimerization of RecN occursviathe coiled-coil domain, but to date there is no structural or biochemical evidence for this. Here, SAXS studies and preliminary X-ray diffraction data of crystals of the purified coiled-coil domain of RecN are presented. The structure was solved by single-wavelength anomalous dispersion using SeMet derivatives, and preliminary electron-density maps support the rod-like model derived from the SAXS data. Model building and refinement are still ongoing.
Crystallization and X-ray diffraction analysis of a novel surface-adhesin protein: protein E fromHaemophilus influenzae
Authors: Singh Birendra , Al Jubair Tamim , Förnvik Karolina , Thunnissen Marjolein M. , Riesbeck Kristian 
Published: January 2012

Protein E (PE) is a ubiquitous multifunctional surface protein ofHaemophilusspp. and other bacterial pathogens of thePasteurellaceaefamily.H. influenzaeutilizes PE for attachment to respiratory epithelial cells. In addition, PE interacts directly with plasminogen and the extracellular matrix (ECM) components vitronectin and laminin. Vitronectin is a complement regulator that inhibits the formation of the membrane-attack complex (MAC). PE-mediated vitronectin recruitment at theH. influenzaesurface thus inhibits MAC and protects against serum bactericidal activity. Laminin is an abundant ECM protein and is present in the basement membrane that helps in adherence of H. influenzaeduring colonization. Here, the expression, purification and crystallization of and the collection of high-resolution data for this importantH. influenzaeadhesin are reported. To solve the phase problem for PE, Met residues were introduced and an SeMet variant was expressed and crystallized. Both native and SeMet-containing PE gave plate-like crystals in space groupP21, with unit-cell parametersa= 44,b= 57,c= 61 Å, β = 96°. Diffraction data collected from native and SeMet-derivative crystals extended to resolutions of 1.8 and 2.6 Å, respectively.
Purification, crystallization and preliminary X-ray diffraction analysis of the Hsp40 protein CPIP1 fromNicotiana tabacum
Authors: Griessl Martin H. , Jungkunz Isabel , Sonnewald Uwe , Muller Yves A. 
Published: January 2012

Chaperones promote many different molecular processes, including the folding, targeting and degradation of proteins. The best-studied chaperone system consists of the Hsp70s and their co-chaperones the Hsp40s. Chaperone function can be hijacked by viruses in plants.Potato virus Yinteractsviaits coat protein with an Hsp40 fromNicotiana tabacum, referred to as NtCPIP1, in order to regulate replication. To understand the molecular determinants of this mechanism, different variants of NtCPIP1 were expressed, purified and crystallized. While crystals of wild-type NtCPIP1 diffracted to 8.0 Å resolution, the deletion mutant NtCPIP1-Δ(1:127) crystallized in space groupP21212 and diffracted to 2.4 Å resolution.