bluuebunny/crossref_metadata_2025 huggingface dataset:
Exploring regulatory mechanisms of CD8
+
T cell contraction
Authors: Prlic Martin , Bevan Michael J.
Published: October 2008

A small fraction of the CD8 T cell effector population that responds to an infection progresses through the contraction phase to the memory stage. The factors regulating the extent of contraction are poorly understood. Competition for limited resources has been widely postulated to be the cause of cell death during the contraction phase, but our data show that competition does not affect contraction kinetics. We go on to demonstrate that all effector cells present at the peak of the response have the potential to become bona fide memory cells, thus excluding selection on the basis of functionality. We propose that the fate of a CD8 effector cell is predetermined before the onset of contraction and discuss possible mechanisms of regulation.
Quality control despite mistranslation caused by an ambiguous genetic code
Authors: Ruan Benfang , Palioura Sotiria , Sabina Jeffrey , Marvin-Guy Laure , Kochhar Sunil , LaRossa Robert A. , Söll Dieter
Published: October 2008

A high level of accuracy during protein synthesis is considered essential for life. Aminoacyl-tRNA synthetases (aaRSs) translate the genetic code by ensuring the correct pairing of amino acids with their cognate tRNAs. Because some aaRSs also produce misacylated aminoacyl-tRNA (aa-tRNA) in vivo, we addressed the question of protein quality within the context of missense suppression by Cys-tRNA
Pro
, Ser-tRNA
Thr
, Glu-tRNA
Gln
, and Asp-tRNA
Asn
. Suppression of an active-site missense mutation leads to a mixture of inactive mutant protein (from translation with correctly acylated aa-tRNA) and active enzyme indistinguishable from the wild-type protein (from translation with misacylated aa-tRNA). Here, we provide genetic and biochemical evidence that under selective pressure,
Escherichia coli
not only tolerates the presence of misacylated aa-tRNA, but can even require it for growth. Furthermore, by using mass spectrometry of a reporter protein not subject to selection, we show that
E. coli
can survive the ambiguous genetic code imposed by misacylated aa-tRNA tolerating up to 10% of mismade protein. The editing function of aaRSs to hydrolyze misacylated aa-tRNA is not essential for survival, and the EF-Tu barrier against misacylated aa-tRNA is not absolute. Rather,
E. coli
copes with mistranslation by triggering the heat shock response that stimulates nonoptimized polypeptides to achieve a native conformation or to be degraded. In this way,
E. coli
ensures the presence of sufficient functional protein albeit at a considerable energetic cost.
Natural history of cervical intraepithelial neoplasia during pregnancy
Authors: SERATI MAURIZIO , UCCELLA STEFANO , LATERZA ROSA M. , SALVATORE STEFANO , BERETTA PAOLO , RIVA CRISTINA , BOLIS PIER FRANCESCO
Published: October 2008

Objective. It is uncertain whether pregnancy influences the natural history of cervical intraepithelial neoplasia (CIN). Our aim was to evaluate the evolution of CIN in pregnant women. Design. Prospective study. Setting. Department of Obstetrics and Gynaecology, University of Insubria, Italy. Population. Women with histological CIN during pregnancy. Methods and main outcome measures. Between 2003 and 2007, women with an abnormal Pap‐smear during pregnancy underwent colposcopy. Patients with histological CIN were followed during pregnancy with colposcopy every 8 weeks and post‐partum evaluation was scheduled 3–6 months after delivery. Women with post‐partum histological diagnosis of CIN 2–3 underwent conization. To understand the impact of pregnancy on the evolution of CIN, women with CIN 1 discovered during pregnancy were compared to a group of non‐pregnant fertile patients with first diagnosis of CIN 1. Results. A total of 78 women were included: 36 (46.2%) with CIN 2–3 and 42 (53.8%) with CIN 1. In women with CIN 2–3, no invasion was suspected during pregnancy and at post‐partum evaluation, no invasive or microinvasive cancer, and 19 (52.7%) persistent CIN 2–3, and 17 (47.3%) regressions were diagnosed. In the group of CIN 1, we recorded six (14.3%) progressions to CIN 2–3, seven (16.6%) persistent CIN 1 and 29 (69%) regressions. The control group of non‐pregnant women had a lower regression rate (37/76: 48.7%) in comparison to pregnant women (p = 0.03). Conclusions. Expectant management for CIN 2–3 diagnosed during gestation is safe. When discovered during pregnancy, CIN 1 has a significantly higher tendency to spontaneous regression in comparison to non‐pregnant condition.
Testing for 22q11 microdeletion in 146 fetuses with nuchal translucency above the 99th percentile and a normal karyotype
Authors: LAUTRUP CHARLOTTE KVIST , KJAERGAARD SUSANNE , BRØNDUM‐NIELSEN KAREN , FAGERBERG CHRISTINA , HERTZ JENS MICHAEL , PETERSEN OLAV BENNIKKE BJØRN , JØRGENSEN METTE WARMING , VOGEL IDA
Published: October 2008

The aim of this study was to examine the value of testing for a 22q11 microdeletion in fetuses with nuchal translucency (NT) above the 99th percentile (>3.5 mm). A 22q11 microdeletion results in the development of 22q11 deletion syndrome, a spectrum of disorders also known as DiGeorge/Velocardiofacial syndrome. A total of 146 pregnancies met the inclusion criteria of NT >3.5 mm between 11+2 and 13+6 weeks’ gestation, no structural malformation and normal karyotype. Chorionic villi samples were tested with either multiplex ligation‐dependent probe amplification (MLPA) or fluorescent in situ hybridization (FISH) analysis for 22q11 microdeletion. None were diagnosed with the microdeletion. The estimated prevalence of 22q11 microdeletion in these otherwise normal fetuses with increased NT is below 2.7%.
History of cesarean before 32 weeks’ gestation and trial of labor: What is the risk of uterine rupture?
Authors: ESTRADE SONIA , SCHMITZ THOMAS , CABROL DOMINIQUE , HUCHON CYRILLE , GOFFINET FRANÇOIS
Published: October 2008

Objectives. To estimate the risk of uterine rupture in women with a previous cesarean delivery before 32 weeks’ gestation and a trial of labor. Design. Retrospective case control study. Setting. Level III maternity center. Methods. Among women with trial of labor, the case and control groups were women with previous cesarean section before and after 32 weeks, respectively. The main outcome was uterine rupture, defined as rupture of the three layers of the uterine wall. Results. The study compared 108 trials of labor in patients with a previous cesarean delivery at a mean gestation of 29.8 weeks±2.0 SD and 137 trials of labor in patients with a previous cesarean delivery at a mean gestation of 39.2 weeks±2.3 SD. Mode of delivery did not differ between groups. Two uterine ruptures (1.9%, 95% CI: 0.0–4.4) occurred in the case group and none in the control group (p = 0.16). Uterine ruptures caused no serious maternal or neonatal complications. The condition of the neonates was similar in the two groups. Conclusion. In view of the small number of uterine ruptures and the absence of severe maternal and fetal consequences over an 8‐year period, a trial of labor may be proposed to women with a history of cesarean delivery before 32 weeks, when obstetrical conditions are optimal.
No Need for a Body Model: Positive Velocity Feedback for the Control of an 18‐DOF Robot Walker
Authors: Schmitz Josef , Schneider Axel , Schilling Malte , Cruse Holk
Published: October 2008

In a multilegged walking robot several legs usually have ground contact and thereby form a closed kinematic chain. The control of such a system is generally assumed to require the explicit calculation of the body kinematics. Such a computation requires knowledge concerning all relevant joint angles as well as the segment lengths. Here, we propose a biologically inspired solution that does not need such a body model. This is done by using implicit communication through the body mechanics (embodiment) and a local positive velocity feedback strategy (LPVF) on the single joint level. In this control scheme the locally measured joint velocity of an elastic joint is fed into the same joint during the next time step to maintain the movement. At the same time, an additional part of this joint controller observes the mechanical joint power to confine the positive feedback. This solution does not depend on changes of the geometry, e.g. length of individual segments, and allows for a simple solution of negotiation of curves. The principle is tested in a dynamics simulation on a six‐legged walker and, for the first time, also on a real robot.
Antimicrobial-Resistant Pathogens Associated With Healthcare-Associated Infections: Annual Summary of Data Reported to the National Healthcare Safety Network at the Centers for Disease Control and Prevention, 2006–2007
Authors: Hidron Alicia I. , Edwards Jonathan R. , Patel Jean , Horan Teresa C. , Sievert Dawn M. , Pollock Daniel A. , Fridkin Scott K. ,   National Healthcare Safety Network Team and Participating National Healthcare Safety Network Facilities
Published: October 2008

Objective.

To describe the frequency of selected antimicrobial resistance patterns among pathogens causing device-associated and procedure-associated healthcare-associated infections (HAIs) reported by hospitals in the National Healthcare Safety Network (NHSN).

Methods.

Data are included on HAIs (ie, central line-associated bloodstream infections, catheter-associated urinary tract infections, ventilator-associated pneumonia, and surgical site infections) reported to the Patient Safety Component of the NHSN between January 2006 and October 2007. The results of antimicrobial susceptibility testing of up to 3 pathogenic isolates per HAI by a hospital were evaluated to define antimicrobial-resistance in the pathogenic isolates. The pooled mean proportions of pathogenic isolates interpreted as resistant to selected antimicrobial agents were calculated by type of HAI and overall. The incidence rates of specific device-associated infections were calculated for selected antimicrobial-resistant pathogens according to type of patient care area; the variability in the reported rates is described.

Results.

Overall, 463 hospitals reported 1 or more HAIs: 412 (89%) were general acute care hospitals, and 309 (67%) had 200-1,000 beds. There were 28,502 HAIs reported among 25,384 patients. The 10 most common pathogens (accounting for 84% of any HAIs) were coagulase-negative staphylococci (15%), Staphylococcus aureus (15%), Enterococcus species (12%), Candida species (11%), Escherichia coli (10%), Pseudomonas aeruginosa (8%), Klebsiella pneumoniae (6%), Enterobacter species (5%), Acinetobacter baumannii (3%), and Klebsiella oxytoca (2%). The pooled mean proportion of pathogenic isolates resistant to antimicrobial agents varied significantly across types of HAI for some pathogen-antimicrobial combinations. As many as 16% of all HAIs were associated with the following multidrug-resistant pathogens: methicillin-resistant S. aureus (8% of HAIs), vancomycin-resistant Enterococcus faecium (4%), carbapenem-resistant P. aeruginosa (2%), extended-spectrum cephalosporin-resistant K. pneumoniae (1%), extended-spectrum cephalosporin-resistant E. coli (0.5%), and carbapenem-resistant A. baumannii, K. pneumoniae, K. oxytoca, and E. coli (0.5%). Nationwide, the majority of units reported no HAIs due to these antimicrobial-resistant pathogens.
Novel Control of S Phase of the Cell Cycle by Ubiquitin-conjugating Enzyme H7
Authors: Whitcomb Elizabeth A. , Dudek Edward J. , Liu Qing , Taylor Allen
Published: October 2008

Timely degradation of regulatory proteins by the ubiquitin proteolytic pathway (UPP) is an established paradigm of cell cycle regulation during the G2/M and G1/S transitions. Less is known about roles for the UPP during S phase. Here we present evidence that dynamic cell cycle–dependent changes in levels of UbcH7 regulate entrance into and progression through S phase. In diverse cell lines, UbcH7 protein levels are dramatically reduced in S phase but are fully restored by G2. Knockdown of UbcH7 increases the proportion of cells in S phase and doubles the time to traverse S phase, whereas UbcH7 overexpression reduces the proportion of cells in S phase. These data suggest a role for UbcH7 targets in the completion of S phase and entry into G2. Notably, UbcH7 knockdown was coincident with elevated levels of the checkpoint kinase Chk1 but not Chk2. These results argue that UbcH7 promotes S phase progression to G2 by modulating the intra-S phase checkpoint mediated by Chk1. Furthermore, UbcH7 levels appear to be regulated by a UPP. Together the data identify novel roles for the UPP, specifically UbcH7 in the regulation of S phase transit time as well as in cell proliferation.
An Internal Domain of Exo70p Is Required for Actin-independent Localization and Mediates Assembly of Specific Exocyst Components
Authors: Hutagalung Alex H. , Coleman Jeff , Pypaert Marc , Novick Peter J.
Published: October 2008

The exocyst consists of eight rod-shaped subunits that align in a side-by-side manner to tether secretory vesicles to the plasma membrane in preparation for fusion. Two subunits, Sec3p and Exo70p, localize to exocytic sites by an actin-independent pathway, whereas the other six ride on vesicles along actin cables. Here, we demonstrate that three of the four domains of Exo70p are essential for growth. The remaining domain, domain C, is not essential but when deleted, it leads to synthetic lethality with many secretory mutations, defects in exocyst assembly of exocyst components Sec5p and Sec6p, and loss of actin-independent localization. This is analogous to a deletion of the amino-terminal domain of Sec3p, which prevents an interaction with Cdc42p or Rho1p and blocks its actin-independent localization. The two mutations are synthetically lethal, even in the presence of high copy number suppressors that can bypass complete deletions of either single gene. Although domain C binds Rho3p, loss of the Exo70p-Rho3p interaction does not account for the synthetic lethal interactions or the exocyst assembly defects. The results suggest that either Exo70p or Sec3p must associate with the plasma membrane for the exocyst to function as a vesicle tether.
The Yeast HtrA Orthologue Ynm3 Is a Protease with Chaperone Activity that Aids Survival Under Heat Stress
Authors: Padmanabhan Nirmala , Fichtner Lars , Dickmanns Achim , Ficner Ralf , Schulz Jörg B. , Braus Gerhard H.
Published: October 2008

Ynm3 is the only budding yeast protein possessing a combination of serine protease and postsynaptic density 95/disc-large/zona occludens domains, a defining feature of the high temperature requirement A (HtrA) protein family. The bacterial HtrA/DegP is involved in protective stress response to aid survival at higher temperatures. The role of mammalian mitochondrial HtrA2/Omi in protein quality control is unclear, although loss of its protease activity results in susceptibility toward Parkinson's disease, in which mitochondrial dysfunction and impairment of protein folding and degradation are key pathogenetic features. We studied the role of the budding yeast HtrA, Ynm3, with respect to unfolding stresses. Similar to Escherichia coli DegP, we find that Ynm3 is a dual chaperone-protease. Its proteolytic activity is crucial for cell survival at higher temperature. Ynm3 also exhibits strong general chaperone activity, a novel finding for a eukaryotic HtrA member. We propose that the chaperone activity of Ynm3 may be important to improve the efficiency of proteolysis of aberrant proteins by averting the formation of nonproductive toxic aggregates and presenting them in a soluble state to its protease domain. Suppression studies with Δynm3 led to the discovery of chaperone activity in a nucleolar peptidyl-prolyl cis-trans isomerase, Fpr3, which could partly relieve the heat sensitivity of Δynm3.
Human Discs Large Is a New Negative Regulator of Human Immunodeficiency Virus-1 Infectivity
Authors: Perugi Fabien , Muriaux Delphine , Ramirez Bertha Cecilia , Chabani Sabah , Decroly Etienne , Darlix Jean-Luc , Blot Vincent , Pique Claudine
Published: October 2008

Human immunodeficiency virus (HIV)-1 replication is positively or negatively regulated through multiple interactions with host cell proteins. We report here that human Discs Large (Dlg1), a scaffold protein recruited beneath the plasma membrane and involved in the assembly of multiprotein complexes, restricts HIV-1 infectivity. The endogenous Dlg1 and HIV-1 Gag polyprotein spontaneously interact in HIV-1-chronically infected T cells. Depleting endogenous Dlg1 in either adherent cells or T cells does not affect Gag maturation, production, or release, but it enhances the infectivity of progeny viruses five- to sixfold. Conversely, overexpression of Dlg1 reduces virus infectivity by ∼80%. Higher virus infectivity upon Dlg1 depletion correlates with increased Env content in cells and virions, whereas the amount of virus-associated Gag or genomic RNA remains identical. Dlg1 knockdown is also associated with the redistribution and colocalization of Gag and Env toward CD63 and CD82 positive vesicle-like structures, including structures that seem to still be connected to the plasma membrane. This study identifies both a new negative regulator that targets the very late steps of the HIV-1 life cycle, and an assembly pathway that optimizes HIV-1 infectivity.
Competitive Nuclear Export of Cyclin D1 and Hic-5 Regulates Anchorage Dependence of Cell Growth and Survival
Authors: Mori Kazunori , Hirao Etsuko , Toya Yosuke , Oshima Yukiko , Ishikawa Fumihiro , Nose Kiyoshi , Shibanuma Motoko
Published: October 2008

Anchorage dependence of cell growth and survival is a critical trait that distinguishes nontransformed cells from transformed cells. We demonstrate that anchorage dependence is determined by anchorage-dependent nuclear retention of cyclin D1, which is regulated by the focal adhesion protein, Hic-5, whose CRM1-dependent nuclear export counteracts that of cyclin D1. An adaptor protein, PINCH, interacts with cyclin D1 and Hic-5 and potentially serves as an interface for the competition between cyclin D1 and Hic-5 for CRM1. In nonadherent cells, the nuclear export of Hic-5, which is redox-sensitive, was interrupted due to elevated production of reactive oxygen species, and cyclin D1 was exported from the nucleus. When an Hic-5 mutant that was continuously exported in a reactive oxygen species-insensitive manner was introduced into the cells, cyclin D1 was retained in the nucleus under nonadherent conditions, and a significant population of cells escaped from growth arrest or apoptosis. Interestingly, activated ras achieved predominant cyclin D1 nuclear localization and thus, growth in nonadherent cells. We report a failsafe system for anchorage dependence of cell growth and survival.
RanBP2 and SENP3 Function in a Mitotic SUMO2/3 Conjugation-Deconjugation Cycle on Borealin
Authors: Klein Ulf R. , Haindl Markus , Nigg Erich A. , Muller Stefan
Published: October 2008

The ubiquitin-like SUMO system controls cellular key functions, and several lines of evidence point to a critical role of SUMO for mitotic progression. However, in mammalian cells mitotic substrates of sumoylation and the regulatory components involved are not well defined. Here, we identify Borealin, a component of the chromosomal passenger complex (CPC), as a mitotic target of SUMO. The CPC, which additionally comprises INCENP, Survivin, and Aurora B, regulates key mitotic events, including chromosome congression, the spindle assembly checkpoint, and cytokinesis. We show that Borealin is preferentially modified by SUMO2/3 and demonstrate that the modification is dynamically regulated during mitotic progression, peaking in early mitosis. Intriguingly, the SUMO ligase RanBP2 interacts with the CPC, stimulates SUMO modification of Borealin in vitro, and is required for its modification in vivo. Moreover, the SUMO isopeptidase SENP3 is a specific interaction partner of Borealin and catalyzes the removal of SUMO2/3 from Borealin. These data thus delineate a mitotic SUMO2/3 conjugation–deconjugation cycle of Borealin and further assign a regulatory function of RanBP2 and SENP3 in the mitotic SUMO pathway.
Extracellular Cleavage of Cadherin-11 by ADAM Metalloproteases Is Essential forXenopusCranial Neural Crest Cell Migration
Authors: McCusker Catherine , Cousin Hélène , Neuner Russell , Alfandari Dominique
Published: October 2008

Cell adhesion molecules such as cadherins alternate their expression throughout cranial neural crest (CNC) development, yet our understanding of the role of these molecules during CNC migration remains incomplete. The “mesenchymal” cadherin-11 is expressed in the CNC during migration yet prevents migration when overexpressed in the embryo, suggesting that a defined level of cadherin-11–mediated cell adhesion is required for migration. Here we show that members of the meltrin subfamily of ADAM metalloproteases cleave the extracellular domain of cadherin-11 during CNC migration. We show that a fragment corresponding to the putative shed form of cadherin-11 retains biological activity by promoting CNC migration in vivo, in a non-cell–autonomous manner. Additionally, cleavage of cadherin-11 does not affect binding to β-catenin and downstream signaling events. We propose that ADAM cleavage of cadherin-11 promotes migration by modifying its ability to support cell–cell adhesion while maintaining the membrane-bound pool of β-catenin associated with the cadherin-11 cytoplasmic domain.
A Lipid-signaled Myosin Phosphatase Surge Disperses Cortical Contractile Force Early in Cell Spreading
Authors: Du Guangwei , Frohman Michael A.
Published: October 2008

When cells cease migrating through the vasculature, adhere to extracellular matrix, and begin to spread, they exhibit rapid changes in contraction and relaxation at peripheral regions newly contacting the underlying substrata. We describe here a requirement in this process for myosin II disassembly at the cell cortex via the action of myosin phosphatase (MP), which in turn is regulated by a plasma membrane signaling lipid. Cells in suspension exhibit high levels of activity of the signaling enzyme phospholipase D2 (PLD2), elevating production of the lipid second messenger phosphatidic acid (PA) at the plasma membrane, which in turn recruits MP and stores it there in a presumed inactive state. On cell attachment, down-regulation of PLD2 activity decreases PA production, leading to MP release, myosin dephosphorylation, and actomyosin disassembly. This novel model for recruitment and restraint of MP provides a means to effect a rapid cytoskeletal reorganization at the cell cortex upon demand.
The Anaphase Promoting Complex Targeting Subunit Ama1 Links Meiotic Exit to Cytokinesis during Sporulation inSaccharomyces cerevisiae
Authors: Diamond Aviva E. , Park Jae-Sook , Inoue Ichiro , Tachikawa Hiroyuki , Neiman Aaron M.
Published: October 2008

Ascospore formation in yeast is accomplished through a cell division in which daughter nuclei are engulfed by newly formed plasma membranes, termed prospore membranes. Closure of the prospore membrane must be coordinated with the end of meiosis II to ensure proper cell division. AMA1 encodes a meiosis-specific activator of the anaphase promoting complex (APC). The activity of APCAma1is inhibited before meiosis II, but the substrates specifically targeted for degradation by Ama1 at the end of meiosis are unknown. We show here that ama1Δ mutants are defective in prospore membrane closure. Ssp1, a protein found at the leading edge of the prospore membrane, is stabilized in ama1Δ mutants. Inactivation of a conditional form of Ssp1 can partially rescue the sporulation defect of the ama1Δ mutant, indicating that an essential function of Ama1 is to lead to the removal of Ssp1. Depletion of Cdc15 causes a defect in meiotic exit. We find that prospore membrane closure is also defective in Cdc15 and that this defect can be overcome by expression of a form of Ama1 in which multiple consensus cyclin-dependent kinase phosphorylation sites have been mutated. These results demonstrate that APCAma1functions to coordinate the exit from meiosis II with cytokinesis.
Multiple Rab GTPase Binding Sites in GCC185 Suggest a Model for Vesicle Tethering at theTrans-Golgi
Authors: Hayes Garret L. , Brown Frank C. , Haas Alexander K. , Nottingham Ryan M. , Barr Francis A. , Pfeffer Suzanne R.
Published: October 2008

GCC185, a trans-Golgi network-localized protein predicted to assume a long, coiled-coil structure, is required for Rab9-dependent recycling of mannose 6-phosphate receptors (MPRs) to the Golgi and for microtubule nucleation at the Golgi via CLASP proteins. GCC185 localizes to the Golgi by cooperative interaction with Rab6 and Arl1 GTPases at adjacent sites near its C terminus. We show here by yeast two-hybrid and direct biochemical tests that GCC185 contains at least four additional binding sites for as many as 14 different Rab GTPases across its entire length. A central coiled-coil domain contains a specific Rab9 binding site, and functional assays indicate that this domain is important for MPR recycling to the Golgi complex. N-Terminal coiled-coils are also required for GCC185 function as determined by plasmid rescue after GCC185 depletion by using small interfering RNA in cultured cells. Golgi-Rab binding sites may permit GCC185 to contribute to stacking and lateral interactions of Golgi cisternae as well as help it function as a vesicle tether.
Genetic Hypervariability in Two Distinct Deuterostome Telomerase Reverse Transcriptase Genes and their Early Embryonic Functions
Authors: Wells Trystan B. , Zhang Guanglei , Harley Zenon , Vaziri Homayoun
Published: October 2008

Functional proteins of complex eukaryotes within the same species are rather invariant. A single catalytic component of telomerase TERT is essential for an active telomerase complex that maintains telomeres. Surprisingly, we have identified two paralogous SpTERT-L and SpTERT-S genes with novel domains in Strongylocentrotus purpuratus (purple sea urchin). The SpTERT-S and SpTERT-L genes were differentially expressed throughout embryogenesis. An unusual germline nucleotide substitution and amino acid variation was evident in these TERTs. The hypervariability of SpTERT-S haplotypes among different individuals reached unprecedented levels of π > 0.2 in exon 11 region. The majority of nucleotide changes observed led to nonsynonymous substitutions creating novel amino acids and motifs, suggesting unusual positive selection and rapid evolution. The majority of these variations were in domains involved in binding of SpTERT to its RNA component. Despite hypervariability at protein level, SpTERT-S conferred telomerase activity, and its suppression during early embryogenesis led to arrest at late mesenchymal blastula. Domain exchange and embryo rescue experiments suggested that SpTERT may have evolved functions unrelated to classic telomerase activity. We suggest that telomerase has a specific and direct function that is essential for integration of early polarity signals that lead to gastrulation. Identification of these unique hypervariable telomerases also suggests presence of a diversity generation mechanism that inculcates hypervariable telomerases and telomere lengths in germline.
Localization of Double-stranded Small Interfering RNA to Cytoplasmic Processing Bodies Is Ago2 Dependent and Results in Up-Regulation of GW182 and Argonaute-2
Authors: Jagannath Aarti , Wood Matthew J.A.
Published: October 2008

Processing bodies (P-bodies) are cytoplasmic foci implicated in the regulation of mRNA translation, storage, and degradation. Key effectors of microRNA (miRNA)-mediated RNA interference (RNAi), such as Argonaute-2 (Ago2), miRNAs, and their cognate mRNAs, are localized to these structures; however, the precise role that P-bodies and their component proteins play in small interfering RNA (siRNA)-mediated RNAi remains unclear. Here, we investigate the relationship between siRNA-mediated RNAi, RNAi machinery proteins, and P-bodies. We show that upon transfection into cells, siRNAs rapidly localize to P-bodies in their native double-stranded conformation, as indicated by fluorescence resonance energy transfer imaging and that Ago2 is at least in part responsible for this siRNA localization pattern, indicating RISC involvement. Furthermore, siRNA transfection induces up-regulated expression of both GW182, a key P-body component, and Ago2, indicating that P-body localization and interaction with GW182 and Ago2 are important in siRNA-mediated RNAi. By virtue of being centers where these proteins and siRNAs aggregate, we propose that the P-body microenvironment, whether as microscopically visible foci or submicroscopic protein complexes, facilitates siRNA processing and siRNA-mediated silencing through the action of its component proteins.
Amelioration of Muscular Dystrophy by Transgenic Expression of Niemann-Pick C1
Authors: Steen Michelle S. , Adams Marvin E. , Tesch Yan , Froehner Stanley C.
Published: October 2008

Duchenne muscular dystrophy (DMD) and other types of muscular dystrophies are caused by the loss or alteration of different members of the dystrophin protein complex. Understanding the molecular mechanisms by which dystrophin-associated protein abnormalities contribute to the onset of muscular dystrophy may identify new therapeutic approaches to these human disorders. By examining gene expression alterations in mouse skeletal muscle lacking α-dystrobrevin (Dtna−/−), we identified a highly significant reduction of the cholesterol trafficking protein, Niemann-Pick C1 (NPC1). Mutations in NPC1 cause a progressive neurodegenerative, lysosomal storage disorder. Transgenic expression of NPC1 in skeletal muscle ameliorates muscular dystrophy in the Dtna−/−mouse (which has a relatively mild dystrophic phenotype) and in the mdx mouse, a model for DMD. These results identify a new compensatory gene for muscular dystrophy and reveal a potential new therapeutic target for DMD.
CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data
Authors: Cesaroni Matteo , Cittaro Davide , Brozzi Alessandro , Pelicci Pier Giuseppe , Luzi Lucilla
Published: October 2008

Summary: CARPET (collection of automated routine programs for easy tiling) is a set of Perl, Python and R scripts, integrated on the Galaxy2 web-based platform, for the analysis of ChIP-chip and expression tiling data, both for standard and custom chip designs. CARPET allows rapid experimental data entry, simple quality control, normalization, easy identification and annotation of enriched ChIP-chip regions, detection of the absolute or relative transcriptional status of genes assessed by expression tiling experiments and, more importantly, it allows the integration of ChIP-chip and expression data. Results can be visualized instantly in a genomic context within the UCSC genome browser as graph-based custom tracks through Galaxy2. All generated and uploaded data can be stored within sessions and are easily shared with other users.

Availability:  http://bio.ifom-ieo-campus.it/galaxy

Contacts:  matteo.cesaroni@ifom-ieo-campus.it; lucilla.luzi@ifom-ieo-campus.it
Integrated search and alignment of protein structures
Authors: Sacan Ahmet , Toroslu I. Hakki , Ferhatosmanoglu Hakan
Published: October 2008

Motivation: Identification and comparison of similar three-dimensional (3D) protein structures has become an even greater challenge in the face of the rapidly growing structure databases. Here, we introduce Vorometric, a new method that provides efficient search and alignment of a query protein against a database of protein structures. Voronoi contacts of the protein residues are enriched with the secondary structure information and a metric substitution matrix is developed to allow efficient indexing. The contact hits obtained from a distance-based indexing method are extended to obtain high-scoring segment pairs, which are then used to generate structural alignments.

Results: Vorometric is the first to address both search and alignment problems in the protein structure databases. The experimental results show that Vorometric is simultaneously effective in retrieving similar protein structures, producing high-quality structure alignments, and identifying cross-fold similarities. Vorometric outperforms current structure retrieval methods in search accuracy, while requiring com-parable running times. Furthermore, the structural superpositions produced are shown to have better quality and coverage, when compared with those of the popular structure alignment tools.

Availability: Vorometric is available as a web service at http://bio.cse.ohio-state.edu/Vorometric

Contact:  sacan@cse.ohio-state.edu
SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology
Authors: Viklund Håkan , Bernsel Andreas , Skwark Marcin , Elofsson Arne
Published: October 2008

Summary: SPOCTOPUS is a method for combined prediction of signal peptides and membrane protein topology, suitable for genome-scale studies. Its objective is to minimize false predictions of transmembrane regions as signal peptides and vice versa. We provide a description of the SPOCTOPUS algorithm together with a performance evaluation where SPOCTOPUS compares favorably with state-of-the-art methods for signal peptide and topology predictions.

Availability: SPOCTOPUS is available as a web server and both the source code and benchmark data are available for download at http://octopus.cbr.su.se/

Contact:  arne@bioinfo.se

Supplementary information:  Supplementary data are available at Bioinformatics online.
Diel vertical migration of Arctic zooplankton during the polar night
Authors: Berge Jørgen , Cottier Finlo , Last Kim S , Varpe Øystein , Leu Eva , Søreide Janne , Eiane Ketil , Falk-Petersen Stig , Willis Kate , Nygård Henrik , Vogedes Daniel , Griffiths Colin , Johnsen Geir , Lorentzen Dag , Brierley Andrew S
Published: October 2008

High-latitude environments show extreme seasonal variation in physical and biological variables. The classic paradigm of Arctic marine ecosystems holds that most biological processes slow down or cease during the polar night. One key process that is generally assumed to cease during winter is diel vertical migration (DVM) of zooplankton. DVM constitutes the largest synchronized movement of biomass on the planet, and is of paramount importance for marine ecosystem function and carbon cycling. Here we present acoustic data that demonstrate a synchronized DVM behaviour of zooplankton that continues throughout the Arctic winter, in both open and ice-covered waters. We argue that even during the polar night, DVM is regulated by diel variations in solar and lunar illumination, which are at intensities far below the threshold of human perception. We also demonstrate that winter DVM is stronger in open waters compared with ice-covered waters. This suggests that the biologically mediated vertical flux of carbon will increase if there is a continued retreat of the Arctic winter sea ice cover.
Infrared radiation from hot cones on cool conifers attracts seed-feeding insects
Authors: Takács Stephen , Bottomley Hannah , Andreller Iisak , Zaradnik Tracy , Schwarz Joseph , Bennett Robb , Strong Ward , Gries Gerhard
Published: October 2008

Foraging animals use diverse cues to locate resources. Common foraging cues have visual, auditory, olfactory, tactile or gustatory characteristics. Here, we show a foraging herbivore using infrared (IR) radiation from living plants as a host-finding cue. We present data revealing that (i) conifer cones are warmer and emit more near-, mid- and long-range IR radiation than needles, (ii) cone-feeding western conifer seed bugs,Leptoglossus occidentalis(Hemiptera: Coreidae), possess IR receptive organs and orient towards experimental IR cues, and (iii) occlusion of the insects' IR receptors impairs IR perception. The conifers' cost of attracting cone-feeding insects may be offset by occasional mast seeding resulting in cone crops too large to be effectively exploited by herbivores.
Either or neither, but not both: locating the effects of masked primes
Authors: Schlaghecken Friederike , Klapp Stuart T , Maylor Elizabeth A
Published: October 2008

Execution of a response that has been primed by a backward-masked stimulus is inhibited (negative compatibility effect; NCE). Three experiments investigated the locus of this inhibition. Masked primes (left- or right-pointing arrows) were followed either by an arrow or a circle target. Arrow targets always required a left- or right-hand response, but the experiments differed in the response required to circles: press neither, either or both response keys (i.e. nogo, free choice and bimanual, respectively). Arrow targets showed the usual NCEs. Circle targets showed NCEs in the form of a response bias away from the primed response in the nogo and free-choice tasks; primes and targets differed on these trials, ruling out a perceptual explanation of the NCE. The bimanual task showed no such bias, suggesting that the NCE is located at a level of abstract response codes rather than specific muscle commands.
Migration strategy and divergent sexual selection on bird song
Authors: Collins Sarah A , de Kort Selvino R , Pérez-Tris Javier , Luis Tellería José
Published: October 2008

Migratory birds are assumed to be under stronger sexual selection pressure than sedentary populations, and the fact that their song is more complex has been taken as confirmation of this fact. However, this assumes that sexual selection pressure due to both male competition and female choice increase together. A further issue is that, in many species, songs become less complex during competitive encounters; in contrast, female choice selects for more complex song, so the two selection pressures may drive song evolution in different directions. We analysed song in two sedentary and two migratory populations of blackcaps (
Sylvia atricapilla
), a species in which different song parts are directed to males and females. We found that migratory populations produce longer, female-directed warbles, indicating sexual selection through female choice is the strongest in these populations. However, the part of the song directed towards males is shorter and more repetitive (as observed in individual competitive encounters between males) in non-migratory populations, indicating sedentary populations, are under stronger selection due to male competition. We show for the first time that the intensity of selection pressure from male competition and female choice varies independently between populations with different migratory behaviours. Rapid alterations in the migration patterns of species are thus likely to lead to unexpected consequences for the costs and benefits of sexual signals.
Human adaptations for the visual assessment of strength and fighting ability from the body and face
Authors: Sell Aaron , Cosmides Leda , Tooby John , Sznycer Daniel , von Rueden Christopher , Gurven Michael
Published: October 2008

Selection in species with aggressive social interactions favours the evolution of cognitive mechanisms for assessing physical formidability (fighting ability or resource-holding potential). The ability to accurately assess formidability in conspecifics has been documented in a number of non-human species, but has not been demonstrated in humans. Here, we report tests supporting the hypothesis that the human cognitive architecture includes mechanisms that assess fighting ability—mechanisms that focus on correlates of upper-body strength. Across diverse samples of targets that included US college students, Bolivian horticulturalists and Andean pastoralists, subjects in the US were able to accurately estimate the physical strength of male targets from photos of their bodies and faces. Hierarchical linear modelling shows that subjects were extracting cues of strength that were largely independent of height, weight and age, and that corresponded most strongly to objective measures of upper-body strength—even when the face was all that was available for inspection. Estimates of women's strength were less accurate, but still significant. These studies are the first empirical demonstration that, for humans, judgements of strength and judgements of fighting ability not only track each other, but accurately track actual upper-body strength.
Hippocampal volumes and neuron numbers increase along a gradient of environmental harshness: a large-scale comparison
Authors: Roth Timothy C , Pravosudov Vladimir V
Published: October 2008

Environmental conditions may provide specific demands for memory, which in turn may affect specific brain regions responsible for memory function. For food-caching animals, in particular, spatial memory appears to be important because it may have a direct effect on fitness via the accuracy of cache retrieval. Animals living in more harsh environments should rely more on cached food, and thus theoretically should have better memory to support cache retrieval, which may be crucial for survival. Consequently, animals in harsh environments may benefit from more neurons within a larger hippocampus (Hp), a part of the brain involved in spatial memory. Here, we present the first large-scale test of the hypothesis that Hp structure is related to the severity of the environment within a single food-caching species (the black-capped chickadee,
Poecile atricapillus
) with a large range encompassing a great diversity of climatic conditions. Hp size in birds collected at five locations along a gradient of environmental harshness from Alaska to Kansas ranked perfectly with climatic severity. Birds from more harsh northern climates (defined by lower ambient temperature, shorter day length and more snow cover) had significantly larger Hp volumes and more Hp neurons (both relative to telencephalon volume) than those from more mild southern latitudes. Environmental pressures therefore seem capable of influencing specific brain regions independently, which may result in enhanced memory, and hence survival, in harsh climates.
Reproductive skew in female common marmosets: what can proximate mechanisms tell us about ultimate causes?
Authors: Saltzman Wendy , Digby Leslie J , Abbott David H
Published: October 2008

Common marmosets are cooperatively breeding monkeys that exhibit high reproductive skew: most subordinate females fail to reproduce, while others attempt to breed but produce very few surviving infants. An extensive dataset on the mechanisms limiting reproduction in laboratory-housed and free-living subordinate females provides unique insights into the causes of reproductive skew. Non-breeding adult females undergo suppression of ovulation and inhibition of sexual behaviour; however, they receive little or no aggression or mating interference by dominants and do not exhibit behavioural or physiological signs of stress. Breeding subordinate females receive comparable amounts of aggression to non-breeding females but are able to conceive, gestate and lactate normally. In groups containing two breeding females, however, both dominant and subordinate breeders kill one another's infants. These findings suggest that preconception reproductive suppression is not imposed on subordinate females by dominants, at a proximate level, but is instead self-imposed by most subordinates, consistent with restraint models of reproductive skew. In contrast to restraint models, however, this self-suppression probably evolved not in response to the threat of eviction by dominant females but in response to the threat of infanticide. Thus, reproductive skew in this species appears to be generated predominantly by subordinate self-restraint, in a proximate sense, but ultimately by dominant control over subordinates' reproductive attempts.
Transcriptional Modulation of Ethylene Response Factor Protein JERF3 in the Oxidative Stress Response Enhances Tolerance of Tobacco Seedlings to Salt, Drought, and Freezing
Authors: Wu Lijun , Zhang Zhijin , Zhang Haiwen , Wang Xue-Chen , Huang Rongfeng
Published: October 2008

Abiotic stresses such as drought, cold, and salinity affect normal growth and development in plants. The production and accumulation of reactive oxygen species (ROS) cause oxidative stress under these abiotic conditions. Recent research has elucidated the significant role of ethylene response factor (ERF) proteins in plant adaptation to abiotic stresses. Our earlier functional analysis of an ERF protein, JERF3, indicated that JERF3-expressing tobacco (Nicotiana tabacum) adapts better to salinity in vitro. This article extends that study by showing that transcriptional regulation of JERF3 in the oxidative stress response modulates the increased tolerance to abiotic stresses. First, we confirm that JERF3-expressing tobacco enhances adaptation to drought, freezing, and osmotic stress during germination and seedling development. Then we demonstrate that JERF3-expressing tobacco imparts not only higher expression of osmotic stress genes compared to wild-type tobacco, but also the activation of photosynthetic carbon assimilation/metabolism and oxidative genes. More importantly, this regulation of the expression of oxidative genes subsequently enhances the activities of superoxide dismutase but reduces the content of ROS in tobacco under drought, cold, salt, and abscisic acid treatments. This indicates that JERF3 also modulates the abiotic stress response via the regulation of the oxidative stress response. Further assays indicate that JERF3 activates the expression of reporter genes driven by the osmotic-responsive GCC box, DRE, and CE1 and by oxidative-responsive as-1 in transient assays, suggesting the transcriptional activation of JERF3 in the expression of genes involved in response to oxidative and osmotic stress. Our results therefore establish that JERF3 activates the expression of such genes through transcription, resulting in decreased accumulation of ROS and, in turn, enhanced adaptation to drought, freezing, and salt in tobacco.
Arabidopsis Casein Kinase 1-Like 6 Contains a Microtubule-Binding Domain and Affects the Organization of Cortical Microtubules
Authors: Ben-Nissan Gili , Cui Weier , Kim Dong-Jin , Yang Yaodong , Yoo Byung-Chun , Lee Jung-Youn
Published: October 2008

Members of the casein kinase 1 (CK1) family are evolutionarily conserved eukaryotic protein kinases that are involved in various cellular, physiological, and developmental processes in yeast and metazoans, but the biological roles of CK1 members in plants are not well understood. Here, we report that an Arabidopsis (Arabidopsis thaliana) CK1 member named casein kinase 1-like 6 (CKL6) associates with cortical microtubules in vivo and phosphorylates tubulins in vitro. The unique C-terminal domain of CKL6 was shown to contain the signal that allows localization of CKL6 to the cortical microtubules. This domain on its own was sufficient to associate with microtubules in vivo and to bind tubulins in vitro. CKL6 was able to phosphorylate soluble tubulins as well as microtubule polymers, and its endogenous activity was found to associate with a tubulin-enriched subcellular fraction. Two major in vitro phosphorylation sites were mapped to serine-413 and serine-420 of tubulin β. Ectopic expression of wild-type CKL6 or a kinase-inactive mutant form induced alterations in cortical microtubule organization and anisotropic cell expansion. Collectively, these results demonstrate that CKL6 is a protein kinase containing a novel tubulin-binding domain and plays a role in anisotropic cell growth and shape formation in Arabidopsis through the regulation of microtubule organization, possibly through the phosphorylation of tubulins.