bluuebunny/crossref_metadata_2025 huggingface dataset:
Reduced glutathione and procaine hydrochloride protect the nucleoprotein structure of boar spermatozoa during freeze–thawing by stabilising disulfide bonds
Authors: Yeste Marc , Flores Eva , Estrada Efrén , Bonet Sergi , Rigau Teresa , Rodríguez-Gil Joan E.
Published: October 2012

One important change the head of boar spermatozoa during freeze–thawing is the destabilisation of its nucleoprotein structure due to a disruption of disulfide bonds. With the aim of better understanding these changes in frozen–thawed spermatozoa, two agents, namely reduced glutathione (GSH) and procaine hydrochloride (ProHCl), were added at different concentrations to the freezing media at different concentrations and combinations over the range 1–2 mM. Then, 30 and 240 min after thawing, cysteine-free residue levels of boar sperm nucleoproteins, DNA fragmentation and other sperm functional parameters were evaluated. Both GSH and ProHCl, at final concentrations of 2 mM, induced a significant (P < 0.05) increase in the number of non-disrupted sperm head disulfide bonds 30 and 240 min after thawing compared with the frozen–thawed control. This effect was accompanied by a significant (P < 0.05) decrease in DNA fragmentation 240 min after thawing. Concomitantly, 1 and 2 mM GSH, but not ProHCl at any of the concentrations tested, partially counteracted the detrimental effects caused by freeze–thawing on sperm peroxide levels, motility patterns and plasma membrane integrity. In conclusion, the results show that both GSH and ProHCl have a stabilising effect on the nucleoprotein structure of frozen–thawed spermatozoa, although only GSH exerts an appreciable effect on sperm viability.
Persistent loss of IL-27 responsiveness in CD8+ memory T cells abrogates IL-10 expression in a recall response
Authors: Perona-Wright Georgia , Kohlmeier Jacob E. , Bassity Elizabeth , Freitas Tori C. , Mohrs Katja , Cookenham Tres , Situ Haozhong , Pearce Edward J. , Woodland David L. , Mohrs Markus
Published: October 2012

CD8+ T cells are central to the eradication of intracellular pathogens, but they can also act to limit inflammation and immunopathology. During primary respiratory viral infection CD8+ effector T cells release the immunosuppressive cytokine IL-10, which is essential for host survival. Here we report that CD8+ T-cell–derived IL-10 is absent in a recall response. We show in mice that the lack of IL-10 is due to a persistent loss of IL-27 responsiveness in CD8+ memory T cells, caused by down-regulation of the common cytokine receptor, glycoprotein 130. CD8+ memory T cells secreted less IL-10 when activated in the presence of IL-27 than did naïve controls, and retroviral expression of glycoprotein 130 restored IL-10 and reduced IFN-γ production upon restimulation. We demonstrate that human CD8+ memory cells are also characterized by impaired IL-27 responsiveness. Our data suggest that CD8+ T-cell activation involves a persistent loss of specific cytokine receptors that determines the functional potential of these cells during rechallenge infection.
MED12 mutations link intellectual disability syndromes with dysregulated GLI3-dependent Sonic Hedgehog signaling
Authors: Zhou Haiying , Spaeth Jason M. , Kim Nam Hee , Xu Xuan , Friez Michael J. , Schwartz Charles E. , Boyer Thomas G.
Published: October 2012

Recurrent missense mutations in the RNA polymerase II Mediator subunit MED12 are associated with X-linked intellectual disability (XLID) and multiple congenital anomalies, including craniofacial, musculoskeletal, and behavioral defects in humans with FG (or Opitz-Kaveggia) and Lujan syndromes. However, the molecular mechanism(s) underlying these phenotypes is poorly understood. Here we report that MED12 mutations R961W and N1007S causing FG and Lujan syndromes, respectively, disrupt a Mediator-imposed constraint on GLI3-dependent Sonic Hedgehog (SHH) signaling. We show that the FG/R961W and Lujan/N1007S mutations disrupt the gene-specific association of MED12 with a second Mediator subunit, CDK8, identified herein to be a suppressor of GLI3 transactivation activity. In FG/R961W and Lujan/N1007S patient-derived cells, we document enhanced SHH pathway activation and GLI3-target gene induction coincident with impaired recruitment of CDK8 onto promoters of GLI3-target genes, but not non–GLI3-target genes. Together, these findings suggest that dysregulated GLI3-dependent SHH signaling contributes to phenotypes of individuals with FG and Lujan syndromes and further reveal a basis for the gene-specific manifestation of pathogenic mutations in a global transcriptional coregulator.
A resurrected mammalian
hAT
transposable element and a closely related insect element are highly active in human cell culture
Authors: Li Xianghong , Ewis Hosam , Hice Robert H. , Malani Nirav , Parker Nicole , Zhou Liqin , Feschotte Cédric , Bushman Frederic D. , Atkinson Peter W. , Craig Nancy L.
Published: October 2012

Chromosome structure and function are influenced by transposable elements, which are mobile DNA segments that can move from place to place.
hAT
elements are a superfamily of DNA cut and paste elements that move by excision and integration. We have characterized two
hAT
elements,
TcBuster
and
Space Invaders
(
SPIN
), that are members of a recently described subfamily of
hAT
elements called
Buster
elements. We show that
TcBuster
, from the red flour beetle
Tribolium castaneum
, is highly active in human cells.
SPIN
elements are currently inactive elements that were recently highly active in multiple vertebrate genomes, and the high level of sequence similarity across widely diverged species and patchy phylogenetic distribution suggest that they may have moved between genomes by horizontal transfer. We have generated an intact version of this element,

SPIN
ON

, which is highly active in human cells. In vitro analysis of
TcBuster
and

SPIN
ON

shows that no proteins other than transposase are essential for recombination, a property that may contribute to the ability of
SPIN
to successfully invade multiple organisms. We also analyze the target site preferences of de novo insertions in the human genome of
TcBuster
and

SPIN
ON

and compare them with the preferences of
Sleeping Beauty
and
piggyBac
, showing that each superfamily has a distinctive pattern of insertion. The high-frequency transposition of both
TcBuster
and

SPIN
ON

suggests that these transposon systems offer powerful tools for genome engineering. Finally, we describe a
Saccharomyces cerevisiae
assay for
TcBuster
that will provide a means for isolation of hyperactive and other interesting classes of transposase mutants.
Histone H3K4 demethylation is negatively regulated by histone H3 acetylation in
Saccharomyces cerevisiae
Authors: Maltby Vicki E. , Martin Benjamin J. E. , Brind’Amour Julie , Chruscicki Adam T. , McBurney Kristina L. , Schulze Julia M. , Johnson Ian J. , Hills Mark , Hentrich Thomas , Kobor Michael S. , Lorincz Matthew C. , Howe LeAnn J.
Published: October 2012

Histone H3 lysine 4 trimethylation (H3K4me3) is a hallmark of transcription initiation, but how H3K4me3 is demethylated during gene repression is poorly understood. Jhd2, a JmjC domain protein, was recently identified as the major H3K4me3 histone demethylase (HDM) in
Saccharomyces cerevisiae
. Although
JHD2
is required for removal of methylation upon gene repression, deletion of
JHD2
does not result in increased levels of H3K4me3 in bulk histones, indicating that this HDM is unable to demethylate histones during steady-state conditions. In this study, we showed that this was due to the negative regulation of Jhd2 activity by histone H3 lysine 14 acetylation (H3K14ac), which colocalizes with H3K4me3 across the yeast genome. We demonstrated that loss of the histone H3-specific acetyltransferases (HATs) resulted in genome-wide depletion of H3K4me3, and this was not due to a transcription defect. Moreover, H3K4me3 levels were reestablished in HAT mutants following loss of
JHD2
, which suggested that H3-specific HATs and Jhd2 serve opposing functions in regulating H3K4me3 levels. We revealed the molecular basis for this suppression by demonstrating that H3K14ac negatively regulated Jhd2 demethylase activity on an acetylated peptide in vitro. These results revealed the existence of a general mechanism for removal of H3K4me3 following gene repression.
Evidence for the role of endosymbionts in regional-scale habitat partitioning by hydrothermal vent symbioses
Authors: Beinart Roxanne A. , Sanders Jon G. , Faure Baptiste , Sylva Sean P. , Lee Raymond W. , Becker Erin L. , Gartman Amy , Luther George W. , Seewald Jeffrey S. , Fisher Charles R. , Girguis Peter R.
Published: October 2012

Deep-sea hydrothermal vents are populated by dense communities of animals that form symbiotic associations with chemolithoautotrophic bacteria. To date, our understanding of which factors govern the distribution of host/symbiont associations (or holobionts) in nature is limited, although host physiology often is invoked. In general, the role that symbionts play in habitat utilization by vent holobionts has not been thoroughly addressed. Here we present evidence for symbiont-influenced, regional-scale niche partitioning among symbiotic gastropods (genus
Alviniconcha
) in the Lau Basin. We extensively surveyed
Alviniconcha
holobionts from four vent fields using quantitative molecular approaches, coupled to characterization of high-temperature and diffuse vent-fluid composition using gastight samplers and in situ electrochemical analyses, respectively. Phylogenetic analyses exposed cryptic host and symbiont diversity, revealing three distinct host types and three different symbiont phylotypes (one
ε-
proteobacteria and two
γ-
proteobacteria) that formed specific associations with one another. Strikingly, we observed that holobionts with ε-proteobacterial symbionts were dominant at the northern fields, whereas holobionts with
γ-
proteobacterial symbionts were dominant in the southern fields. This pattern of distribution corresponds to differences in the vent geochemistry that result from deep subsurface geological and geothermal processes. We posit that the symbionts, likely through differences in chemolithoautotrophic metabolism, influence niche utilization among these holobionts. The data presented here represent evidence linking symbiont type to habitat partitioning among the chemosynthetic symbioses at hydrothermal vents and illustrate the coupling between subsurface geothermal processes and niche availability.
T cell receptor/CARMA1/NF-κB signaling controls T-helper (Th) 17 differentiation
Authors: Molinero Luciana L. , Cubre Alan , Mora-Solano Carolina , Wang Ying , Alegre Maria-Luisa
Published: October 2012

IL-17–producing CD4 T cells play a key role in immune responses against extracellular bacteria and autoimmunity. Nuclear factor κB (NF-κB) is required for T-cell activation and selected effector functions, but its role in Th17 differentiation is controversial. Using genetic mouse models that impede T-cell–NF-κB signaling either downstream of the T-cell receptor (TCR) or of IκB kinase β (IKKβ), we demonstrate that NF-κB signaling controls not only survival and proliferation of activated T cells, but, if cell survival and cell-cycle progression are enabled, has an additional role in promoting completion of Th17 differentiation. CARD-containing MAGUK protein 1 (CARMA1), an adapter required for TCR/NF-κB signaling, was necessary for acquisition of IL-17A, IL-17F, IL-21, IL-22, IL-23R, and CCR6 expression in T cells cultured under Th17 conditions. In proliferating cells, lack of CARMA1 selectively prevented Th17, but not Th1 or Th2 differentiation, in a cell-intrinsic manner. Consistent with these data, CARMA1-KO mice were resistant to experimental autoimmune encephalomyelitis. Surprisingly, transcription factors essential for Th17 differentiation such as RORγt, AHR, and IRF4 were normally induced in CARMA1-KO T cells activated under Th17 conditions, suggesting that the Th17 differentiation program was initiated normally. Instead, chromatin loci of Th17 effector molecules failed to acquire an open conformation in CARMA1-KO T cells. Our results demonstrate that TCR/CARMA1/NF-κB controls completion of Th17 differentiation by enabling chromatin accessibility of Th17 effector molecule loci.
Hepatitis B virus X protein targets the Bcl-2 protein CED-9 to induce intracellular Ca
2+
increase and cell death in
Caenorhabditis elegans
Authors: Geng Xin , Harry Brian L. , Zhou Qinghua , Skeen-Gaar Riley Robert , Ge Xiao , Lee Eui Seung , Mitani Shohei , Xue Ding
Published: October 2012

HBx is a multifunctional hepatitis B virus (HBV) protein that is crucial for HBV infection and pathogenesis and a contributing cause of hepatocyte carcinogenesis. However, the host targets and mechanisms of action of HBx are poorly characterized. We show here that expression of HBx in
Caenorhabditis elegans
induces both necrotic and apoptotic cell death, mimicking an early event of liver infection by HBV. Genetic and biochemical analyses indicate that HBx interacts directly with the B-cell lymphoma 2 (Bcl-2) homolog CED-9 (cell death abnormal) through a Bcl-2 homology 3 (BH3)-like motif to trigger both cytosolic Ca
2+
increase and cell death. Importantly, Bcl-2 can substitute for CED-9 in mediating HBx-induced cell killing in
C. elegans
, suggesting that CED-9 and Bcl-2 are conserved cellular targets of HBx. A genetic suppressor screen of HBx-induced cell death has produced many mutations, including mutations in key regulators from both apoptosis and necrosis pathways, indicating that this screen can identify new apoptosis and necrosis genes. Our results suggest that
C. elegans
could serve as an animal model for identifying crucial host factors and signaling pathways of HBx and aid in development of strategies to treat HBV-induced liver disorders.
Climate variability and conflict risk in East Africa, 1990–2009
Authors: O’Loughlin John , Witmer Frank D. W. , Linke Andrew M. , Laing Arlene , Gettelman Andrew , Dudhia Jimy
Published: October 2012

Recent studies concerning the possible relationship between climate trends and the risks of violent conflict have yielded contradictory results, partly because of choices of conflict measures and modeling design. In this study, we examine climate–conflict relationships using a geographically disaggregated approach. We consider the effects of climate change to be both local and national in character, and we use a conflict database that contains 16,359 individual geolocated violent events for East Africa from 1990 to 2009. Unlike previous studies that relied exclusively on political and economic controls, we analyze the many geographical factors that have been shown to be important in understanding the distribution and causes of violence while also considering yearly and country fixed effects. For our main climate indicators at gridded 1° resolution (∼100 km), wetter deviations from the precipitation norms decrease the risk of violence, whereas drier and normal periods show no effects. The relationship between temperature and conflict shows that much warmer than normal temperatures raise the risk of violence, whereas average and cooler temperatures have no effect. These precipitation and temperature effects are statistically significant but have modest influence in terms of predictive power in a model with political, economic, and physical geographic predictors. Large variations in the climate–conflict relationships are evident between the nine countries of the study region and across time periods.
Glucagon-like peptide-1 receptor dimerization differentially regulates agonist signaling but does not affect small molecule allostery
Authors: Harikumar Kaleeckal G. , Wootten Denise , Pinon Delia I. , Koole Cassandra , Ball Alicja M. , Furness Sebastian G. B. , Graham Bim , Dong Maoqing , Christopoulos Arthur , Miller Laurence J. , Sexton Patrick M.
Published: October 2012

The glucagon-like peptide-1 receptor (GLP-1R) is a family B G protein-coupled receptor and an important drug target for the treatment of type II diabetes, with activation of pancreatic GLP-1Rs eliciting glucose-dependent insulin secretion. Currently, approved therapeutics acting at this receptor are peptide based, and there is substantial interest in small molecule modulators for the GLP-1R. Using a variety of resonance energy transfer techniques, we demonstrate that the GLP-1R forms homodimers and that transmembrane helix 4 (TM4) provides the primary dimerization interface. We show that disruption of dimerization using a TM4 peptide, a minigene construct encoding TM4, or by mutation of TM4, eliminates G protein-dependent high-affinity binding to GLP-1(7-36)NH
2
but has selective effects on receptor signaling. There was <10-fold decrease in potency in cAMP accumulation or ERK1/2 phosphorylation assays but marked loss of intracellular calcium mobilization by peptide agonists. In contrast, there was near-complete abrogation of the cAMP response to an allosteric agonist, compound 2, but preservation of ERK phosphorylation. Collectively, this indicates that GLP-1R dimerization is important for control of signal bias. Furthermore, we reveal that two small molecule ligands are unaltered in their ability to allosterically modulate signaling from peptide ligands, demonstrating that these modulators act
in cis
within a single receptor protomer, and this has important implications for small molecule drug design.
Nonsymbolic number and cumulative area representations contribute shared and unique variance to symbolic math competence
Authors: Lourenco Stella F. , Bonny Justin W. , Fernandez Edmund P. , Rao Sonia
Published: October 2012

Humans and nonhuman animals share the capacity to estimate, without counting, the number of objects in a set by relying on an approximate number system (ANS). Only humans, however, learn the concepts and operations of symbolic mathematics. Despite vast differences between these two systems of quantification, neural and behavioral findings suggest functional connections. Another line of research suggests that the ANS is part of a larger, more general system of magnitude representation. Reports of cognitive interactions and common neural coding for number and other magnitudes such as spatial extent led us to ask whether, and how, nonnumerical magnitude interfaces with mathematical competence. On two magnitude comparison tasks, college students estimated (without counting or explicit calculation) which of two arrays was greater in number or cumulative area. They also completed a battery of standardized math tests. Individual differences in both number and cumulative area precision (measured by accuracy on the magnitude comparison tasks) correlated with interindividual variability in math competence, particularly advanced arithmetic and geometry, even after accounting for general aspects of intelligence. Moreover, analyses revealed that whereas number precision contributed unique variance to advanced arithmetic, cumulative area precision contributed unique variance to geometry. Taken together, these results provide evidence for shared and unique contributions of nonsymbolic number and cumulative area representations to formally taught mathematics. More broadly, they suggest that uniquely human branches of mathematics interface with an evolutionarily primitive general magnitude system, which includes partially overlapping representations of numerical and nonnumerical magnitude.
Sleep spindles are locally modulated by training on a brain–computer interface
Authors: Johnson Lise A. , Blakely Tim , Hermes Dora , Hakimian Shahin , Ramsey Nick F. , Ojemann Jeffrey G.
Published: October 2012

The learning of a motor task is known to be improved by sleep, and sleep spindles are thought to facilitate this learning by enabling synaptic plasticity. In this study subjects implanted with electrocorticography (ECoG) arrays for long-term epilepsy monitoring were trained to control a cursor on a computer screen by modulating either the high-gamma or mu/beta power at a single electrode located over the motor or premotor area. In all trained subjects, spindle density in posttraining sleep was increased with respect to pretraining sleep in a remarkably spatially specific manner. The pattern of increased spindle activity reflects the functionally specific regions that were involved in learning of a highly novel and salient task during wakefulness, supporting the idea that sleep spindles are involved in learning to use a motor-based brain–computer interface device.
Complete mitochondrial DNA genome sequences from the first New Zealanders
Authors: Knapp Michael , Horsburgh K. Ann , Prost Stefan , Stanton Jo-Ann , Buckley Hallie R. , Walter Richard K. , Matisoo-Smith Elizabeth A.
Published: October 2012

The dispersal of modern humans across the globe began ∼65,000 y ago when people first left Africa and culminated with the settlement of East Polynesia, which occurred in the last 1,000 y. With the arrival of Polynesian canoes only 750 y ago, Aotearoa/New Zealand became the last major landmass to be permanently settled by humans. We present here complete mitochondrial genome sequences of the likely founding population of Aotearoa/New Zealand recovered from the archaeological site of Wairau Bar. These data represent complete mitochondrial genome sequences from ancient Polynesian voyagers and provide insights into the genetic diversity of human populations in the Pacific at the time of the settlement of East Polynesia.
Cxcr4 regulation of interneuron migration is disrupted in 22q11.2 deletion syndrome
Authors: Meechan Daniel W. , Tucker Eric S. , Maynard Thomas M. , LaMantia Anthony-Samuel
Published: October 2012

Interneurons are thought to be a primary pathogenic target for several behavioral disorders that arise during development, including schizophrenia and autism. It is not known, however, whether genetic lesions associated with these diseases disrupt established molecular mechanisms of interneuron development. We found that diminished 22q11.2 gene dosage—the primary genetic lesion in 22q11.2 deletion syndrome (22q11.2 DS)—specifically compromises the distribution of early-generated parvalbumin-expressing interneurons in the
Large Deletion
(
LgDel
) 22q11.2DS mouse model. This change reflects cell-autonomous disruption of interneuron migration caused by altered expression of the cytokine C-X-C chemokine receptor type 4 (Cxcr4), an established regulator of this process. Cxcr4 is specifically reduced in
LgDel
migrating interneurons, and genetic analysis confirms that diminished
Cxcr4
alters interneuron migration in
LgDel
mice. Thus, diminished 22q11.2 gene dosage disrupts cortical circuit development by modifying a critical molecular signaling pathway via Cxcr4 that regulates cortical interneuron migration and placement.
Structure of Sputnik, a virophage, at 3.5-Å resolution
Authors: Zhang Xinzheng , Sun Siyang , Xiang Ye , Wong Jimson , Klose Thomas , Raoult Didier , Rossmann Michael G.
Published: October 2012

“Sputnik” is a dsDNA virus, referred to as a virophage, that is coassembled with Mimivirus in the host amoeba. We have used cryo-EM to produce an electron density map of the icosahedral Sputnik virus at 3.5-Å resolution, sufficient to verify the identity of most amino acids in the capsid proteins and to establish the identity of the pentameric protein forming the fivefold vertices. It was also shown that the virus lacks an internal membrane. The capsid is organized into a
T
= 27 lattice in which there are 260 trimeric capsomers and 12 pentameric capsomers. The trimeric capsomers consist of three double “jelly-roll” major capsid proteins creating pseudohexameric capsomer symmetry. The pentameric capsomers consist of five single jelly-roll proteins. The release of the genome by displacing one or more of the pentameric capsomers may be the result of a low-pH environment. These results suggest a mechanism of Sputnik DNA ejection that probably also occurs in other big icosahedral double jelly-roll viruses such as Adenovirus. In this study, the near-atomic resolution structure of a virus has been established where crystallization for X-ray crystallography was not feasible.
MDA5 assembles into a polar helical filament on dsRNA
Authors: Berke Ian C. , Yu Xiong , Modis Yorgo , Egelman Edward H.
Published: October 2012

Melanoma differentiation-associated protein 5 (MDA5) detects viral dsRNA in the cytoplasm. On binding of RNA, MDA5 forms polymers, which trigger assembly of the signaling adaptor mitochondrial antiviral-signaling protein (MAVS) into its active fibril form. The molecular mechanism of MDA5 signaling is not well understood, however. Here we show that MDA5 forms helical filaments on dsRNA and report the 3D structure of the filaments using electron microscopy (EM) and image reconstruction. MDA5 assembles into a polar, single-start helix around the RNA. Fitting of an MDA5 homology model into the structure suggests a key role for the MDA5 C-terminal domain in cooperative filament assembly. Our study supports a signal transduction mechanism in which the helical array of MDA5 within filaments nucleates the assembly of MAVS fibrils. We conclude that MDA5 is a polymerization-dependent signaling platform that uses the amyloid-like self-propagating properties of MAVS to amplify signaling.
Elucidating secondary organic aerosol from diesel and gasoline vehicles through detailed characterization of organic carbon emissions
Authors: Gentner Drew R. , Isaacman Gabriel , Worton David R. , Chan Arthur W. H. , Dallmann Timothy R. , Davis Laura , Liu Shang , Day Douglas A. , Russell Lynn M. , Wilson Kevin R. , Weber Robin , Guha Abhinav , Harley Robert A. , Goldstein Allen H.
Published: October 2012

Emissions from gasoline and diesel vehicles are predominant anthropogenic sources of reactive gas-phase organic carbon and key precursors to secondary organic aerosol (SOA) in urban areas. Their relative importance for aerosol formation is a controversial issue with implications for air quality control policy and public health. We characterize the chemical composition, mass distribution, and organic aerosol formation potential of emissions from gasoline and diesel vehicles, and find diesel exhaust is seven times more efficient at forming aerosol than gasoline exhaust. However, both sources are important for air quality; depending on a region’s fuel use, diesel is responsible for 65% to 90% of vehicular-derived SOA, with substantial contributions from aromatic and aliphatic hydrocarbons. Including these insights on source characterization and SOA formation will improve regional pollution control policies, fuel regulations, and methodologies for future measurement, laboratory, and modeling studies.
Cryo-EM structure of gastric H
+
,K
+
-ATPase with a single occupied cation-binding site
Authors: Abe Kazuhiro , Tani Kazutoshi , Friedrich Thomas , Fujiyoshi Yoshinori
Published: October 2012

Gastric H
+
,K
+
-ATPase is responsible for gastric acid secretion. ATP-driven H
+
uptake into the stomach is efficiently accomplished by the exchange of an equal amount of K
+
, resulting in a luminal pH close to 1. Because of the limited free energy available for ATP hydrolysis, the stoichiometry of transported cations is thought to vary from 2H
+
/2K
+
to 1H
+
/1K
+
per hydrolysis of one ATP molecule as the luminal pH decreases, although direct evidence for this hypothesis has remained elusive. Here, we show, using the phosphate analog aluminum fluoride (AlF) and a K
+
congener (Rb
+
), the 8-Å resolution structure of H
+
,K
+
-ATPase in the transition state of dephosphorylation, (Rb
+
)
E2
∼AlF, which is distinct from the preceding Rb
+
-free
E2
P state. A strong density located in the transmembrane cation-binding site of (Rb
+
)
E2
∼AlF highly likely represents a single bound Rb
+
ion, which is clearly different from the Rb
+
-free
E2
AlF or K
+
-bound (K
+
)
E2
∼AlF structures. Measurement of radioactive
86
Rb
+
binding suggests that the binding stoichiometry varies depending on the pH, and approximately half of the amount of Rb
+
is bound under acidic crystallization conditions compared with at a neutral pH. These data represent structural and biochemical evidence for the 1H
+
/1K
+
/1ATP transport mode of H
+
,K
+
-ATPase, which is a prerequisite for generation of the 10
6
-fold proton gradient in terms of thermodynamics. Together with the released
E2
P-stabilizing interaction between the β subunit’s N terminus and the P domain observed in the (Rb
+
)
E2
∼AlF structure, we propose a refined vectorial transport model of H
+
,K
+
-ATPase, which must prevail against the highly acidic state of the gastric lumen.
Cryo-EM structure of the mammalian eukaryotic release factor eRF1–eRF3-associated termination complex
Authors: Taylor Derek , Unbehaun Anett , Li Wen , Das Sanchaita , Lei Jianlin , Liao Hstau Y. , Grassucci Robert A. , Pestova Tatyana V. , Frank Joachim
Published: October 2012

Eukaryotic translation termination results from the complex functional interplay between two eukaryotic release factors, eRF1 and eRF3, and the ribosome, in which GTP hydrolysis by eRF3 couples codon recognition with peptidyl-tRNA hydrolysis by eRF1. Here, using cryo-electron microscopy (cryo-EM) and flexible fitting, we determined the structure of eRF1–eRF3–guanosine 5′-[β,γ-imido]triphosphate (GMPPNP)-bound ribosomal pretermination complex (pre-TC), which corresponds to the initial, pre-GTP hydrolysis stage of factor attachment. Our results show that eukaryotic translation termination involves a network of interactions between the two release factors and the ribosome. Our structure provides mechanistic insight into the coordination between GTP hydrolysis by eRF3 and subsequent peptide release by eRF1.
Meiosis arrest female 1 (MARF1) has nuage-like function in mammalian oocytes
Authors: Su You-Qiang , Sun Fengyun , Handel Mary Ann , Schimenti John C. , Eppig John J.
Published: October 2012

Orderly regulation of meiosis and protection of germline genomic integrity from transposable elements are essential for male and female gamete development. In the male germline, these processes are ensured by proteins associated with cytoplasmic nuage, but morphologically similar germ granules or nuage have not been identified in mammalian female germ cells. Indeed, many mutations affecting nuage-associated proteins such as PIWI and tudor domain containing proteins 5 and 7 (TDRD5/7) can result in failure of meiosis, up-regulation of retrotransposons, and infertility only in males and not in females. We recently identified MARF1 (meiosis arrest female 1) as a protein essential for controlling meiosis and retrotransposon surveillance in oocytes; and in contrast to PIWI-pathway mutations,
Marf1
mutant females are infertile, whereas mutant males are fertile. Here we put forward the hypothesis that MARF1 in mouse oocytes is a functional counterpart of the nuage-associated components of spermatocytes. We describe the developmental pattern of
Marf1
expression and its roles in retrotransposon silencing and protection from DNA double-strand breaks. Analysis of MARF1 protein domains compared with PIWI and TDRD5/7 revealed that these functional similarities are reflected in remarkable structural analogies. Thus, functions that in the male germline require protein interactions and cooperative scaffolding are combined in MARF1, allowing a single molecule to execute crucial activities of meiotic regulation and protection of germline genomic integrity.
Pragmatic Motivation for Inflectional Middle Voice in Modern Greek
Authors: Manney Linda Joyce
Published: October 2012

The occurrence of inflectional middle voice in Modern Greek texts is motivated by diverse pragmatic pressures which are related to particular components of its semantic structure. The prototypical value of the semantic category instantiated by middle inflection comprises various internally complex components such as HIGH AFFECT and LOW VOLITION of a nonagentive subject, and LOW INDIVIDUATION of an agent-like source. The semantic component of HIGH AFFECT is shown to be analogous to the expressive function of Subject Enhancement, whereas the components of LOW VOLITION and LOW INDIVIDUATION are related to the textual strategy of Agent Defocusing. Both the semantic components and the pragmatic functions of middle voice are encompassed by more general speaker based strategies of foregrounding and/or backgrounding some element of a conceived situation; these strategies are shaped by subsystems of encyclopedic knowledge that are utilized in particular communicative contexts.
Risk Factors for Gastrointestinal Tract Colonization with Extended-Spectrum β-Lactamase (ESBL)–Producing Escherichia coli and Klebsiella Species in Hospitalized Patients
Authors: Han Jennifer H. , Nachamkin Irving , Zaoutis Theoklis E. , Coffin Susan E. , Linkin Darren R. , Fishman Neil O. , Weiner Mark G. , Hu Baofeng , Tolomeo Pam , Lautenbach Ebbing
Published: October 2012

We describe the prevalence of and risk factors for colonization with extended-spectrum β-lactamase (ESBL)–producing Escherichia coli and Klebsiella species (ESBL-EK) in hospitalized patients. The prevalence of colonization with ESBL-EK was 2.6%. Colonization was associated with cirrhosis, longer duration of hospital stay prior to surveillance, and prior exposure to clindamycin or meropenem.
Topological complexity of 𝐻-spaces
Authors: Lupton Gregory , Scherer Jérôme
Published: October 2012

Let

X
X

be a (not-necessarily homotopy-associative)

H
H

-space. We show that

T
C

n
+
1

(
X
)
=

c
a
t

(

X
n

)

\mathrm {TC}_{n+1}(X) = \mathrm {cat}(X^n)

, for

n
≥
1

n \geq 1

, where

T
C

n
+
1

(
−
)

\mathrm {TC}_{n+1}(-)

denotes the so-called higher topological complexity introduced by Rudyak, and

c
a
t

(
−
)

\mathrm {cat}(-)

denotes the Lusternik-Schnirelmann category. We also generalize this equality to an inequality, which gives an upper bound for

T
C

n
+
1

(
X
)

\mathrm {TC}_{n+1}(X)

, in the setting of a space

Y
Y

acting on

X
X

.
Analyzing Farmer Participation Intentions and County Enrollment Rates for the Average Crop Revenue Election Program
Authors: Mitchell Paul D. , Rejesus Roderick M. , Coble Keith H. , Knight Thomas O.
Published: October 2012

The 2008 Farm Bill created the Average Crop Revenue Election (ACRE) program to be a new commodity support program. Using a multinomial logit model to analyze a mail survey administered before the ACRE sign‐up deadline, we identify factors driving farmer intentions regarding ACRE participation. Using a Tobit model to analyze actual county‐level ACRE enrollment rates, we assess the effect of similar factors on actual farmer decisions. Results suggest that primary crops, risk perceptions, risk aversion, and program complexity were important factors affecting participation. Farmer beliefs and attitudes also played key roles, and were changing during the months before the ACRE deadline.
(Z)-5-[(5-Methyl-1H-imidazol-4-yl)methylidene]-2-sulfanylidene-1,3-thiazolidin-4-one monohydrate: a three-dimensional hydrogen-bonded framework structure
Authors: Insuasty Alberto , Insuasty Braulio , Cobo Justo , Glidewell Christopher
Published: October 2012

The non-H atoms in the organic component of the title compound, C8H7N3OS2·H2O, are almost coplanar, as the dihedral angle between the two ring planes is only 1.8 (2)°; there is a wide C—C—C angle of 127.8 (3)° at the methine C atom linking the two rings. The molecular components are linked into a three-dimensional framework structure by two-centre hydrogen bonds of N—H...O and O—H...N types, together with a three-centre O—H...(N,S) system. Comparisons are made with some (Z)-5-arylmethylidene-2-sulfanylidene-1,3-thiazolidin-4-ones.
Solvatomorphism of 9,9′-[1,3,4-thiadiazole-2,5-diylbis(2,3-thiophendiyl-4,1-phenylene)]bis[9H-carbazole]: isostructurality, modularity and order–disorder theory
Authors: Stöger Berthold , Kautny Paul , Lumpi Daniel , Zobetz Erich , Fröhlich Johannes
Published: October 2012

During a systematic investigation of the crystallization behaviour of 9,9′-[1,3,4-thiadiazole-2,5-diylbis(2,3-thiophendiyl-4,1-phenylene)]bis[9H-carbazole] (I), six single crystalline solvates were obtained and characterized by X-ray diffraction at 100 K. The structure of the hemi-2-butanone (MEK) solvate contains two crystallographically independent molecules of (I) related by pseudo-inversion symmetry. The structure is polytypic and composed of non-polar (I) layers and polar solvent layers. It can be described according to an extended order–disorder (OD) theory with relaxed vicinity condition. The observed polytype is of a maximum degree of order (MDO). Layer triples of the second MDO polytype are shown by twinning by inversion. The mono-benzene and mono-toluene solvates are isostructural. Whereas the (I) layers are isostructural to those of the idealized description of the hemi-MEK solvate, the solvent layers are non-polar, resulting in a fully ordered structure. The toluene molecule is ordered, the benzene molecule features disorder. The (I) layers in the sesqui-dioxane and sesqui-benzene solvates are isostructural and unrelated to those in the hemi-MEK, mono-benzene and mono-toluene solvates. The solvent layers are isopointal in both sesqui-solvates, but the stacking differs significantly. The hemi-dideuterodichloromethane (DCM-d
2) solvate is made up of two kinds of (I) rods, spaced by DCM-d
2 molecules. Rods of one kind are similar to analogous rods in the sesqui-dioxane and the sesqui-benzene solvates, whereas rods of the other kind are only remotely related to rods in the hemi-MEK solvate.
Structural transformation of Sb-based high-speed phase-change material
Authors: Matsunaga Toshiyuki , Kojima Rie , Yamada Noboru , Kubota Yoshiki , Kifune Kouichi
Published: October 2012

The crystal structure of a phase-change recording material (the compound Ag3.4In3.7Sb76.4Te16.5) enclosed in a vacuum capillary tube was investigated at various temperatures in a heating process using a large Debye–Scherrer camera installed in BL02B2 at SPring-8. The amorphous phase of this material turns into a crystalline phase at around 416 K; this crystalline phase has an A7-type structure with atoms of Ag, In, Sb or Te randomly occupying the 6c site in the space group. This structure was maintained up to around 545 K as a single phase, although thermal expansion of the crystal lattice was observed. However, above this temperature, phase separation into AgInTe2 and Sb–Te transpired. The first fragment, AgInTe2, reliably maintained its crystal structure up to the melting temperature. On the other hand, the atomic configuration of the Sb–Te gradually varied with increasing temperature. This gradual structural transformation can be described as a continuous growth of the modulation period γ.
Charge-density distribution in potassium dihydrogen phosphoglycolate – a comparison of phosphate and phosphonate groups
Authors: Mermer Adrian , Starynowicz Przemysław
Published: October 2012

Analysis of the experimental and theoretical charge-density distribution in potassium dihydrogen phosphoglycolate has been performed. The P—O bonds in the phosphate group are more polarized and the P atom is more positively charged than in phosphonate groups. The P—O bonds belong to a transit closed-shell (or polar covalent) class, while the ester C—O bond is a covalent (or shared-shell) bond. The coordination of potassium exerts a small effect on the phosphate group, whereas more pronounced changes,e.g.concerning the ellipticities of the C—O bonds, may be observed. The profiles of Laplacians and ellipticities give more insight in the polarization of the bonds.
EGFR and KRAS mutation analyses from specimens obtained by bronchoscopy and EBUS‐TBNA
Authors: Kang Yeh Rim , Park Hye Yun , Jeon Kyeongman , Koh Won‐Jung , Suh Gee Young , Chung Man Pyo , Kim Hojoong , Kwon O Jung , Choi Yoon‐La , Han Joungho , Um Sang‐Won
Published: October 2012

Backgroud

Procurement of tumor tissue is mandatory for a mutation analysis in patients with non‐small cell lung cancer. The purpose of this study was to evaluate the usefulness of bronchoscopic biopsy and endobronchial ultrasound‐guided transbronchial needle aspiration (EBUS‐TBNA) biopsy for detecting epidermal growth factor receptor (EGFR) and KRAS mutations in routine practice.

Methods

Tumor DNA was extracted from formalin‐fixed paraffin‐embedded tissues, and amplifications of exons 18–21 of EGFR and codons 12, 13 and 61 of KRAS were performed using polymerase chain reaction (PCR). PCR products were subjected to direct sequencing in both directions.

Results

Of 211 consecutive specimens, 201 (95.3%) were available for EGFR mutation analysis, and 196 (92.9%) were adequate for KRAS mutation analysis. EGFR and KRAS mutations were detected in 14.9% and 5.4%, respectively. A median of 16 days was spent from biopsy to the final report for either EGFR or KRAS mutation status. The detection rates for both mutations were similar between bronchoscopic biopsy and EBUS‐TBNA (P > 0.05). Female gender (53.3%), never smoker (63.3%), and adenocarcinoma (96.7%) were predominant in patients with EGFR mutations. Among patients with adenocarcinoma (n = 104), the frequencies of EGFR and KRAS mutations were 27.9% and 10.6%, respectively.

Conclusions

Small tissue samples obtained by bronchoscopic biopsy and EBUS‐TBNA are sufficient for detecting EGFR and KRAS mutations in routine practice. Therefore, concurrent mutational analyses of small tissue samples should be considered at the time of initial diagnosis.
Lung papillary adenocarcinoma complicated with paraneoplastic autoimmune hemolytic anemia: A case report
Authors: Xing Limin , Wang Huaquan , Qu Wen , Fang Fang , Dong Qi‐e , Shao Zonghong
Published: October 2012

A middle‐aged woman presented at our facility and was diagnosed after surgery with lung papillary adenocarcinoma. Seven years earlier, she had suffered from autoimmune hemolytic anemia (AIHA), which was refractory. Following lung surgery, the AIHA was cured.
Additional use of an aldosterone antagonist in patients with mild to moderate chronic heart failure: a systematic review and meta‐analysis
Authors: Hu Li‐jun , Chen Yun‐qing , Deng Song‐bai , Du Jian‐lin , She Qiang
Published: October 2012

Aims

Aldosterone antagonists (AldoAs) have been used to treat severe chronic heart failure (CHF).There is uncertainty regarding the efficacy of using AldoAs in mild to moderate CHF with New York Heart Association (NYHA) classifications of I to II. This study summarizes the evidence for the efficacy of spironolactone (SP), eplerenone (EP) and canrenone in mild to moderate CHF patients.

Methods

PubMed, MEDLINE, EMBASE and OVID databases were searched before June 2012 for randomized and quasi‐randomized controlled trials assessing AldoA treatment in CHF patients with NYHA classes I to II. Data concerning the study's design, patients' characteristics and outcomes were extracted. Risk ratio (RR) and weighted mean differences (WMD) or standardized mean difference were calculated using either fixed or random effects models.

Results

Eight trials involving 3929 CHF patients were included. AldoAs were superior to the control in all cause mortality (RR 0.79, 95% CI 0.66, 0.95) and in re‐hospitalization for cardiac causes (RR 0.62, 95% CI 0.52, 0.74), the left ventricular ejection fraction was improved by AldoA treatment (WMD 2.94%, P = 0.52). Moreover, AldoA therapy decreased the left ventricular end‐diastolic volume (WMD −14.04 ml, P < 0.00001),the left ventricular end‐systolic volume (WMD −14.09 ml, P < 0.00001). A stratified analysis showed a statistical superiority in the benefits of SP over EP in reducing LVEDV and LVESV. AldoAs reduced B‐type natriuretic peptide concentrations (WMD −37.76 pg ml−1, P < 0.00001), increased serum creatinine (WMD 8.69 μmol l−1, P = 0.0003) and occurrence of hyperkalaemia (RR 1.78, 95% CI 1.43, 2.23).

Conclusions

Additional use of AldoAs in CHF patients may decrease mortality and re‐hospitalization for cardiac reasons, improve cardiac function and simultaneously ameliorate LV reverse remodelling.
Tau‐Tubulin Kinase 1 Expression, Phosphorylation and Co‐Localization with Phospho‐Ser422 Tau in the Alzheimer's Disease Brain
Authors: Lund Harald , Cowburn Richard F. , Gustafsson Elin , Strömberg Kia , Svensson Anne , Dahllund Leif , Malinowsky David , Sunnemark Dan
Published: October 2012

Recent reports have implicated tau‐tubulin kinase 1 (TTBK1) in the pathological phosphorylation of tau that occurs in Alzheimer's disease (AD).

The present study was undertaken to provide an extensive characterization of TTBK1 mRNA and protein expression in human brain from AD cases and non‐demented controls so as to better understand the disease relevance of this novel kinase. In situ hybridization and immunohistochemistry revealed abundant expression of TTBK1 in the somatodendritic compartment of cortical and hippocampal neurons of both AD cases and controls. TTBK1 immunoreactivity appeared to vary with the level of phospho‐tau staining, and was strong in the somatodendritic compartment of apparently healthy hippocampal neurons as well as in pre‐tangle neurons where it co‐localized with diffuse phospho‐Ser422 tau staining. Ser422 was confirmed as a TTBK1 substrate in vitro, and an antibody towards the site, in addition to labeling AT8‐positive neurofibrillary tangles (NFTs), neuritic plaques and neuropil threads, also labeled a small population of neurons that were unlabeled with AT8.

These data suggest a role for TTBK1 in pre‐tangle formation prior to the formation of fibrillar tau and strengthen the idea that tau is phosphorylated at Ser422 at an early/intermediate stage in NFT formation.
Evolution of the European guidelines for the clinical development of factor VIII products: little progress towards improved patient management
Authors: Mannucci P. M.
Published: October 2012

In the process of clinical development and licensing of factor VIII (FVIII) products for treatment of haemophilia A, the safety concerns generated in the 1980s by the risk of pathogen transmission were tremendously reduced by the implementation of an array of methods for inactivation/removal of blood borne pathogens. The current focus on the risk of FVIII inhibitors does not stem from a new awareness, because this multifactorial complication has long been recognized. With this background, I believe that the current European regulatory guidelines for the clinical development and licensing of FVIII products fail to reflect the tremendous progress made in terms of clinical efficacy and safety, because they are witnessing a continuous increase in the demands from health agencies to the point that clinical studies have become more and more difficult to carry out. This article reviews the evolution of the European regulations on new FVIII products, lists a number of regulatory requirements whose scientific and/or clinical rationale is perhaps questionable and recommends keeping such requirements in reasonable limits of feasibility, without jeopardizing current high standards of efficacy and safety.