bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolution of MDA-5/RIG-I-dependent innate immunity: Independent evolution by domain grafting
Authors: Sarkar Devanand , DeSalle Rob , Fisher Paul B.
Published: October 2008

Type I Interferons (IFNs) are requisite components in antiviral innate immunity. Classically, a Toll-like receptor-dependent pathway induces type I interferons. However, recent recognition of melanoma differentiation associated gene-5 (MDA-5) and retinoic acid inducible gene-I (RIG-I) as primary sensors of RNA viruses for type I interferon induction highlights a potentially unique pathway for innate immunity. Our present investigation tracing the phylogenetic origin of MDA-5 and RIG-I domain arrangement (CARD1-CARD2-helicase-DEAD/DEAH) indicates that these proteins originated specifically in mammals, firmly linking this family of proteins with interferons in a highly derived evolutionary development of innate immunity. MDA-5, but not RIG-I, orthologs are found in fish, indicating that MDA-5 might have evolved before RIG-I. Our analyses also reveal that the MDA-5 and RIG-I domain arrangement evolved independently by domain grafting and not by a simple gene-duplication event of the entire four-domain arrangement, which may have been initiated by differential sensitivity of these proteins to viral infection.
Protein kinase PKR mutants resistant to the poxvirus pseudosubstrate K3L protein
Authors: Seo Eun Joo , Liu Furong , Kawagishi-Kobayashi Makiko , Ung Tekly L. , Cao Chune , Dar Arvin C. , Sicheri Frank , Dever Thomas E.
Published: October 2008

As part of the mammalian cell innate immune response, the double-stranded RNA activated protein kinase PKR phosphorylates the translation initiation factor eIF2α to inhibit protein synthesis and thus block viral replication. Poxviruses including vaccinia and smallpox viruses express PKR inhibitors such as the vaccinia virus K3L protein that resembles the N-terminal substrate-targeting domain of eIF2α. Whereas high-level expression of human PKR was toxic in yeast, this growth inhibition was suppressed by coexpression of the K3L protein. We used this yeast assay to screen for PKR mutants that are resistant to K3L inhibition, and we identified 12 mutations mapping to the C-terminal lobe of the PKR kinase domain. The PKR mutations specifically conferred resistance to the K3L protein both in yeast and in vitro. Consistently, the PKR-D486V mutation led to nearly a 15-fold decrease in K3L binding affinity yet did not impair eIF2α phosphorylation. Our results support the identification of the eIF2α-binding site on an extensive face of the C-terminal lobe of the kinase domain, and they indicate that subtle changes to the PKR kinase domain can drastically impact pseudosubstrate inhibition while leaving substrate phosphorylation intact. We propose that these paradoxical effects of the PKR mutations on pseudosubstrate vs. substrate interactions reflect differences between the rigid K3L protein and the plastic nature of eIF2α around the Ser-51 phosphorylation site.
High sensitivity of BRCA1-deficient mammary tumors to the PARP inhibitor AZD2281 alone and in combination with platinum drugs
Authors: Rottenberg Sven , Jaspers Janneke E. , Kersbergen Ariena , van der Burg Eline , Nygren Anders O. H. , Zander Serge A. L. , Derksen Patrick W. B. , de Bruin Michiel , Zevenhoven John , Lau Alan , Boulter Robert , Cranston Aaron , O'Connor Mark J. , Martin Niall M. B. , Borst Piet , Jonkers Jos
Published: October 2008

Whereas target-specific drugs are available for treating ERBB2-overexpressing and hormone receptor-positive breast cancers, no tailored therapy exists for hormone receptor- and ERBB2-negative (“triple-negative”) mammary carcinomas. Triple-negative tumors account for 15% of all breast cancers and frequently harbor defects in DNA double-strand break repair through homologous recombination (HR), such as BRCA1 dysfunction. The DNA-repair defects characteristic of BRCA1-deficient cells confer sensitivity to poly(ADP-ribose) polymerase 1 (PARP1) inhibition, which could be relevant to treatment of triple-negative tumors. To evaluate PARP1 inhibition in a realistic in vivo setting, we tested the PARP inhibitor AZD2281 in a genetically engineered mouse model (GEMM) for BRCA1-associated breast cancer. Treatment of tumor-bearing mice with AZD2281 inhibited tumor growth without signs of toxicity, resulting in strongly increased survival. Long-term treatment with AZD2281 in this model did result in the development of drug resistance, caused by up-regulation of
Abcb1a
/
b
genes encoding P-glycoprotein efflux pumps. This resistance to AZD2281 could be reversed by coadministration of the P-glycoprotein inhibitor tariquidar. Combination of AZD2281 with cisplatin or carboplatin increased the recurrence-free and overall survival, suggesting that AZD2281 potentiates the effect of these DNA-damaging agents. Our results demonstrate in vivo efficacy of AZD2281 against BRCA1-deficient breast cancer and illustrate how GEMMs of cancer can be used for preclinical evaluation of novel therapeutics and for testing ways to overcome or circumvent therapy resistance.
Ozone production by amino acids contributes to killing of bacteria
Authors: Yamashita Kouhei , Miyoshi Takashi , Arai Toshiyuki , Endo Nobuyuki , Itoh Hiroshi , Makino Keisuke , Mizugishi Kiyomi , Uchiyama Takashi , Sasada Masataka
Published: October 2008

Reactive oxygen species produced by phagocytosing neutrophils are essential for innate host defense against invading microbes. Previous observations revealed that antibody-catalyzed ozone formation by human neutrophils contributed to the killing of bacteria. In this study, we discovered that 4 amino acids themselves were able to catalyze the production of an oxidant with the chemical signature of ozone from singlet oxygen in the water-oxidation pathway, at comparable level to antibodies. The resultant oxidant with the chemical signature of ozone exhibited significant bactericidal activity in our distinct cell-free system and in human neutrophils. The results also suggest that an oxidant with the chemical signature of ozone produced by neutrophils might potentiate a host defense system, when the host is challenged by high doses of infectious agents. Our findings provide biological insights into the killing of bacteria by neutrophils.
HCO
3
−
/Cl
−
anion exchanger SLC4A2 is required for proper osteoclast differentiation and function
Authors: Wu Jing , Glimcher Laurie H. , Aliprantis Antonios O.
Published: October 2008

As the only cell capable of bone resorption, the osteoclast is a central mediator of skeletal homeostasis and disease. To efficiently degrade mineralized tissue, these multinucleated giant cells secrete acid into a resorption lacuna formed between their apical membrane and the bone surface. For each proton pumped into this extracellular compartment, one bicarbonate ion remains in the cytoplasm. To prevent alkalinization of the cytoplasm, a basolateral bicarbonate/chloride exchanger provides egress for intracellular bicarbonate. However, the identity of this exchanger is unknown. Here, we report that the bicarbonate/chloride exchanger, solute carrier family 4, anion exchanger, member 2 (SLC4A2), is up-regulated during osteoclast differentiation. Suppression of
Slc4a2
expression by RNA interference inhibits the ability of RAW cells, a mouse macrophage cell line, to differentiate into osteoclasts and resorb mineralized matrix
in vitro
. Accordingly,
Slc4a2
-deficient mice fail to remodel the primary, cartilaginous skeletal anlagen. Abnormal multinucleated giant cells are present in the bone marrow of
Slc4a2
-deficient mice. Though these cells express the osteoclast markers CD68, cathepsin K, and NFATc1, compared with their wild-type (WT) counterparts they are larger, fail to express tartrate-resistant acid phosphatase (TRAP) activity, and display a propensity to undergo apoptosis.
In vitro Slc4a2
-deficient osteoclasts are unable to resorb mineralized tissue and cannot form an acidified, extracellular resorption compartment. These data highlight SLC4A2 as a critical mediator of osteoclast differentiation and function
in vitro
and
in vivo
.
Membrane proteomics of phagosomes suggests a connection to autophagy
Authors: Shui Wenqing , Sheu Leslie , Liu Jun , Smart Brian , Petzold Christopher J. , Hsieh Tsung-yen , Pitcher Austin , Keasling Jay D. , Bertozzi Carolyn R.
Published: October 2008

Phagocytosis is the central process by which macrophage cells internalize and eliminate infectious microbes as well as apoptotic cells. During maturation, phagosomes containing engulfed particles fuse with various endosomal compartments through the action of regulatory molecules on the phagosomal membrane. In this study, we performed a proteomic analysis of the membrane fraction from latex bead-containing (LBC) phagosomes isolated from macrophages. The profile, which comprised 546 proteins, suggests diverse functions of the phagosome and potential connections to secretory processes, toll-like receptor signaling, and autophagy. Many identified proteins were not previously known to reside in the phagosome. We characterized several proteins in LBC phagosomes that change in abundance on induction of autophagy, a process that has been previously implicated in the host defense against microbial pathogens. These observations suggest crosstalk between autophagy and phagocytosis that may be relevant to the innate immune response of macrophages.
Differential effects of central fructose and glucose on hypothalamic malonyl–CoA and food intake
Authors: Cha Seung Hun , Wolfgang Michael , Tokutake Yuka , Chohnan Shigeru , Lane M. Daniel
Published: October 2008

The American diet, especially that of adolescents, contains highly palatable foods of high-energy content and large amounts of high-fructose sweeteners. These factors are believed to contribute to the obesity epidemic and insulin resistance. Previous investigations revealed that the central metabolism of glucose suppresses food intake mediated by the hypothalamic AMP-kinase/malonyl–CoA signaling system. Unlike glucose, centrally administered fructose increases food intake. Evidence presented herein indicates that the more rapid initial steps of central fructose metabolism deplete hypothalamic ATP level, whereas the slower regulated steps of glucose metabolism elevate hypothalamic ATP level. Consistent with effects on the [ATP]/[AMP] ratio, fructose increases phosphorylation/activation of hypothalamic AMP kinase causing phosphorylation/inactivation of acetyl–CoA carboxylase, whereas glucose has the inverse effects. The changes provoked by central fructose administration reduce hypothalamic malonyl–CoA level and thereby increase food intake. These findings explain the paradoxical fructose effect on food intake and lend credence to the malonyl–CoA hypothesis.
Human exonuclease 1 and BLM helicase interact to resect DNA and initiate DNA repair
Authors: Nimonkar Amitabh V. , Özsoy A. Zeynep , Genschel Jochen , Modrich Paul , Kowalczykowski Stephen C.
Published: October 2008

The error-free repair of double-stranded DNA breaks by homologous recombination requires processing of broken ends. These processed ends are substrates for assembly of DNA strand exchange proteins that mediate DNA strand invasion. Here, we establish that human BLM helicase, a member of the RecQ family, stimulates the nucleolytic activity of human exonuclease 1 (hExo1), a 5′→3′ double-stranded DNA exonuclease. The stimulation is specific because other RecQ homologs fail to stimulate hExo1. Stimulation of DNA resection by hExo1 is independent of BLM helicase activity and is, instead, mediated by an interaction between the 2 proteins. Finally, we show that DNA ends resected by hExo1 and BLM are used by human Rad51, but not its yeast or bacterial counterparts, to promote homologous DNA pairing. This in vitro system recapitulates initial steps of homologous recombination and provides biochemical evidence for a role of BLM and Exo1 in the initiation of recombinational DNA repair.
Crystal structure and activity of
Bacillus subtilis
YoaJ (EXLX1), a bacterial expansin that promotes root colonization
Authors: Kerff Frédéric , Amoroso Ana , Herman Raphaël , Sauvage Eric , Petrella Stéphanie , Filée Patrice , Charlier Paulette , Joris Bernard , Tabuchi Akira , Nikolaidis Nikolas , Cosgrove Daniel J.
Published: October 2008

We solved the crystal structure of a secreted protein, EXLX1, encoded by the
yoaJ
gene of
Bacillus subtilis
. Its structure is remarkably similar to that of plant β-expansins (group 1 grass pollen allergens), consisting of 2 tightly packed domains (D1, D2) with a potential polysaccharide-binding surface spanning the 2 domains. Domain D1 has a double-ψ β-barrel fold with partial conservation of the catalytic site found in family 45 glycosyl hydrolases and in the MltA family of lytic transglycosylases. Domain D2 has an Ig-like fold similar to group 2/3 grass pollen allergens, with structural features similar to a type A carbohydrate-binding domain. EXLX1 bound to plant cell walls, cellulose, and peptidoglycan, but it lacked lytic activity against a variety of plant cell wall polysaccharides and peptidoglycan. EXLX1 promoted plant cell wall extension similar to, but 10 times weaker than, plant β-expansins, which synergistically enhanced EXLX1 activity. Deletion of the gene encoding EXLX1 did not affect growth or peptidoglycan composition of
B. subtilis
in liquid medium, but slowed lysis upon osmotic shock and greatly reduced the ability of the bacterium to colonize maize roots. The presence of EXLX1 homologs in a small but diverse set of plant pathogens further supports a role in plant–bacterial interactions. Because plant expansins have proved difficult to express in active form in heterologous systems, the discovery of a bacterial homolog opens the door for detailed structural studies of expansin function.
Structure of ratcheted ribosomes with tRNAs in hybrid states
Authors: Julián Patricia , Konevega Andrey L. , Scheres Sjors H. W. , Lázaro Melisa , Gil David , Wintermeyer Wolfgang , Rodnina Marina V. , Valle Mikel
Published: October 2008

During protein synthesis, tRNAs and mRNA move through the ribosome between aminoacyl (A), peptidyl (P), and exit (E) sites of the ribosome in a process called translocation. Translocation is accompanied by the displacement of the tRNAs on the large ribosomal subunit toward the hybrid A/P and P/E states and by a rotational movement (ratchet) of the ribosomal subunits relative to one another. So far, the structure of the ratcheted state has been observed only when translation factors were bound to the ribosome. Using cryo-electron microscopy and classification, we show here that ribosomes can spontaneously adopt a ratcheted conformation with tRNAs in their hybrid states. The peptidyl-tRNA molecule in the A/P state, which is visualized here, is not distorted compared with the A/A state except for slight adjustments of its acceptor end, suggesting that the displacement of the A-site tRNA on the 50S subunit is passive and is induced by the 30S subunit rotation. Simultaneous subunit ratchet and formation of the tRNA hybrid states precede and may promote the subsequent rapid and coordinated tRNA translocation on the 30S subunit catalyzed by elongation factor G.
Mechanism of thermal decomposition of carbamoyl phosphate and its stabilization by aspartate and ornithine transcarbamoylases
Authors: Wang Qin , Xia Jiarong , Guallar Victor , Krilov Goran , Kantrowitz Evan R.
Published: October 2008

Carbamoyl phosphate (CP) has a half-life for thermal decomposition of <2 s at 100 °C, yet this critical metabolic intermediate is found even in organisms that grow at 95–100 °C. We show here that the binding of CP to the enzymes aspartate and ornithine transcarbamoylase reduces the rate of thermal decomposition of CP by a factor of >5,000. Both of these transcarbamoylases use an ordered-binding mechanism in which CP binds first, allowing the formation of an enzyme·CP complex. To understand how the enzyme·CP complex is able to stabilize CP we investigated the mechanism of the thermal decomposition of CP in aqueous solution in the absence and presence of enzyme. By quantum mechanics/molecular mechanics calculations we show that the critical step in the thermal decomposition of CP in aqueous solution, in the absence of enzyme, involves the breaking of the C

O bond facilitated by intramolecular proton transfer from the amine to the phosphate. Furthermore, we demonstrate that the binding of CP to the active sites of these enzymes significantly inhibits this process by restricting the accessible conformations of the bound ligand to those disfavoring the reactive geometry. These results not only provide insight into the reaction pathways for the thermal decomposition of free CP in an aqueous solution but also show why these reaction pathways are not accessible when the metabolite is bound to the active sites of these transcarbamoylases.
Risk of gynecologic cancers in Danish hereditary non‐polyposis colorectal cancer families
Authors: BOILESEN ASTRID ELISABETH BRUUN , BISGAARD MARIE LUISE , BERNSTEIN INGE
Published: October 2008

Objective. Women in hereditary non‐polyposis colorectal cancer (HNPCC) families have an elevated risk of endometrial and ovarian cancer. The risk in Lynch syndrome families with known mutations in mismatch repair genes (MMR genes) seems to be higher than in familial colorectal cancer (CRC) families. Data in the Danish HNPCC register on the frequency and lifetime risk of gynecologic cancers were analyzed and the actual surveillance strategy discussed in relation to the results. Design. Register‐based retrospective study. Method. A total of 1,780 at‐risk women were identified and epidemiological, clinical and MMR gene mutation data were retrieved. Results. In a total of 105 cases of endometrial cancer, there was no significant difference in MSH2, MSH6 and MLH1 mutation carrier frequency. Compared to the general population, mutation carriers had a 20 times increase in lifetime risk of endometrial cancer. Lifetime risk was elevated four times in familial CRC families. In these families, frequency was correlated to the pedigree phenotype, with significantly higher frequency demonstrated in Amsterdam II families compared to Amsterdam I families and families suspected of HNPCC. A total of 39 cases of ovarian cancer were identified with a lifetime risk of three to four times the general population. No significant correlation was found between the frequency of ovarian cancer and MMR gene mutation status in the families. Conclusion. The benefit of surveillance concerning gynecological cancers seems to be less well founded in familial CRC families than in Lynch syndrome families. Modifying the surveillance strategy may be relevant in the future, but before changing existing guidelines concerning surveillance, further research is recommended.
Hepatocellular enzyme glutathione S‐transferase alpha and intrahepatic cholestasis of pregnancy
Authors: JOUTSINIEMI TITTA , LEINO RIITTA , TIMONEN SUSANNA , PULKKI KARI , EKBLAD ULLA
Published: October 2008

Objective. To evaluate and compare plasma glutathione S‐transferase alpha (GSTA) concentrations in the third trimester of pregnancy in patients with intrahepatic cholestasis of pregnancy (ICP) and in healthy pregnant women.Design. Non‐randomized clinical study.Setting.Maternity unit and Department of Clinical Chemistry, Turku University Central Hospital, Turku, Finland.Population. Twenty‐seven women with ICP and 49 healthy pregnant women.Methods. GSTA concentrations were assessed in plasma samples in the third trimester of pregnancy using an enzyme‐linked immunoassay (HEPKIT™ Alpha, Biotrin, Sinsheim‐Reihen, Germany).Main outcome measures. Plasma GSTA, serum alanine and bile acid concentrations were compared between study and control group. Correlation between plasma GSTA levels and serum alanine aminotransferase and bile acid levels in the ICP patients were tested by Spearman correlation coefficients. Main perinatal outcome was compared between the groups.Results. GSTA concentration in the control group was 1.62 μg/l (range: 0.25–6.1). In the ICP patients, the mean plasma GSTA concentration was 51.0 μg/l (range: 2.1–183.5), the mean serum alanine aminotransferase concentration was 145.70 U/l (range: 6–393) and the mean bile acid concentration was 19.2 μmol/l (range: 3–63). There was a statistically significant correlation in ICP patients between plasma GSTA concentration and serum alanine aminotransferase concentration (r= 0.694,p= 0.0001), but not with serum bile acid concentration. Nor was there any statistically significant correlation between gestational weeks and plasma GSTA concentration in the study group.Conclusion. Plasma GSTA measurements may provide a more sensitive and specific diagnostic tool for diagnosis of ICP than the evaluation of transaminases or bile acid concentrations alone. Further studies are needed to evaluate the role of GSTA in the follow‐up of patients with ICP and its prognostic value for threatening fetal distress in patients with ICP.
Highly Resistant Microorganisms in a Teaching Hospital: The Role of Horizontal Spread in a Setting of Endemicity
Authors: Willemsen Ina , Mooij Marlies , van der Wiel Marsha , Bogaers Diana , van der Bijl Madelon , Savelkoul Paul , Kluytmans Jan
Published: October 2008

Objective.

To determine the incidence density of highly resistant organisms (HROs) and the relative contribution of horizontal spread in a setting of endemicity.

Methods.

Prospective surveillance was performed among hospitalized patients during an 18-month period. Enterobacteriaceae, non-fermentative gram-negative bacilli,Staphylococcus aureus, Streptococcus pneumoniae,andEnterococcus faecium—all considered highly resistant, according to Dutch guidelines—were included. Epidemiological linkage and nosocomial transmission were determined on the basis of molecular typing and hospital admission data.

Results.

From 119 patients, we recovered a total of 170 unique HRO isolates, as follows:Escherichia coli,96 isolates;Klebsiellaspecies, 11 isolates;Enterobacterspecies, 8 isolates;Proteusspecies, 9 isolates;Citrobacterspecies, 5 isolates;Pseudomonasspecies, 5 isolates;Aci-netobacterspecies, 3 isolates;Morganellaspecies, 2 isolates;Salmonellaspecies, 1 isolate;Serratiaspecies, 1 isolate;S. pneumoniae,20 isolates; andS. aureus,9 isolates. No vancomycin-resistantE. faeciumwas found. The incidence density was 4.3 HRO isolates per 10,000 patient-days. The majority of HRO isolates were unique, and nosocomial transmission was observed 4 times for highly resistant gram-negative bacilli (case reproduction rate, 0.05) and 4 times for penicillin-nonsusceptibleS. pneumoniae(case reproduction rate, 0.29). A stay on the intensive care unit was the main determinant for the recovery of an HRO.

Conclusion.

Nosocomial transmission of HROs was observed 8 times during the 18-month period. The intensive care unit was identified as the main reservoir of horizontal spread of HROs. This study shows that nosocomial transmission of HROs is largely preventable using transmission precautions.
Outcomes of Carbapenem-Resistant Klebsiella pneumoniae Infection and the Impact of Antimicrobial and Adjunctive Therapies
Authors: Patel Gopi , Huprikar Shirish , Factor Stephanie H. , Jenkins Stephen G. , Calfee David P.
Published: October 2008

Background.

Carbapenem-resistant Klebsiella pneumoniae is an emerging healthcare-associated pathogen.

Objective.

To describe the epidemiology of and clinical outcomes associated with carbapenem-resistant K. pneumoniae infection and to identify risk factors associated with mortality among patients with this type of infection.

Setting.

Mount Sinai Hospital, a 1,171-bed tertiary care teaching hospital in New York City.

Design.

Two matched case-control studies.

Methods.

In the first matched case-control study, case patients with carbapenem-resistant K. pneumoniae infection were compared with control patients with carbapenem-susceptible K. pneumoniae infection. In the second case-control study, patients who survived carbapenem-resistant K. pneumoniae infection were compared with those who did not survive, to identify risk factors associated with mortality among patients with carbapenem-resistant K. pneumoniae infection.

Results.

There were 99 case patients and 99 control patients identified. Carbapenem-resistant K. pneumoniae infection was independently associated with recent organ or stem-cell transplantation (P = .008), receipt of mechanical ventilation (P = .04), longer length of stay before infection (P = .01), and exposure to cephalosporins (P = .02) and carbapenems (P < .001). Case patients were more likely than control patients to die during hospitalization (48% vs 20%; P < .001) and to die from infection (38% vs 12%; P < .001). Removal of the focus of infection (ie, debridement) was independently associated with patient survival (P = .002). The timely administration of antibiotics with in vitro activity against carbapenem-resistant K. pneumoniae was not associated with patient survival.

Conclusions.

Carbapenem-resistant K. pneumoniae infection is associated with numerous healthcare-related risk factors and with high mortality. The mortality rate associated with carbapenem-resistant K. pneumoniae infection and the limited antimicrobial options for treatment of carbapenem-resistant K. pneumoniae infection highlight the need for improved detection of carbapenem-resistant K. pneumoniae infection, identification of effective preventive measures, and development of novel agents with reliable clinical efficacy against carbapenem-resistant K. pneumoniae.
Prevalence of Markers for Hepatitis B Virus and Vaccination Compliance Among Medical School Students in Italy
Authors: Trevisan Andrea , Bruno Alberto , Mongillo Michele , Morandin Marta , Pantaleoni Anna , Borella-Venturini Matteo , Giraldo Monica
Published: October 2008

The prevalence of markers for hepatitis B virus (HBV) and the rate of compliance with HBV vaccination laws were investigated in a study at Padua University Medical School (Italy). Of 2,361 students, 385 (16.3%) tested negative for antibody to hepatitis B surface antigen. When vaccination was actively offered to these students, there was a low rate of compliance (47.0% [181 students]) but a good rate of seroconversion (93.1% [95 of 102 students]). Screening for HBV markers appears to be crucial to efforts to increase rates of vaccination coverage.
Certain components of Springer fibers and associated cycles for discrete series representations of 𝑆𝑈(𝑝,𝑞)
Authors: Barchini L. , Zierau R.
Published: October 2008

An explicit geometric description of certain components of Springer fibers for

S
L
(
n
,
C
)

SL(n,C)

s given in this article. These components are associated to closed

S
(
G
L
(
p
)
×
G
L
(
q
)
)

S(GL(p)\times GL(q))

-orbits in the flag variety. The geometric results are used to compute the associated cycles of the discrete series representations of

S
U
(
p
,
q
)

SU(p,q)

. A discussion of an alternative, and more general, computation of associated cycles is given in the appendix.
Multiple Regulatory Steps Control Mammalian Nonmuscle Myosin II Assembly in Live Cells
Authors: Breckenridge Mark T. , Dulyaninova Natalya G. , Egelhoff Thomas T.
Published: October 2008

To better understand the mechanism controlling nonmuscle myosin II (NM-II) assembly in mammalian cells, mutant NM-IIA constructs were created to allow tests in live cells of two widely studied models for filament assembly control. A GFP-NM-IIA construct lacking the RLC binding domain (ΔIQ2) destabilizes the 10S sequestered monomer state and results in a severe defect in recycling monomers during spreading, and from the posterior to the leading edge during polarized migration. A GFP-NM-IIA construct lacking the nonhelical tailpiece (Δtailpiece) is competent for leading edge assembly, but overassembles, suggesting defects in disassembly from lamellae subsequent to initial recruitment. The Δtailpiece phenotype was recapitulated by a GFP-NM-IIA construct carrying a mutation in a mapped tailpiece phosphorylation site (S1943A), validating the importance of the tailpiece and tailpiece phosphorylation in normal lamellar myosin II assembly control. These results demonstrate that both the 6S/10S conformational change and the tailpiece contribute to the localization and assembly of myosin II in mammalian cells. This work furthermore offers cellular insights that help explain platelet and leukocyte defects associated with R1933-stop alleles of patients afflicted with human MYH9-related disorder.
The Unfolded Protein Response Is Induced by the Cell Wall Integrity Mitogen-activated Protein Kinase Signaling Cascade and Is Required for Cell Wall Integrity inSaccharomyces cerevisiae
Authors: Scrimale Thomas , Didone Louis , de Mesy Bentley Karen L. , Krysan Damian J.
Published: October 2008

The yeast cell wall is an extracellular structure that is dependent on secretory and membrane proteins for its construction. We investigated the role of protein quality control mechanisms in cell wall integrity and found that the unfolded protein response (UPR) and, to a lesser extent, endoplasmic reticulum (ER)-associated degradation (ERAD) pathways are required for proper cell wall construction. Null mutation of IRE1, double mutation of ERAD components (hrd1Δ and ubc7Δ) and ire1Δ, or expression of misfolded proteins show phenotypes similar to mutation of cell wall proteins, including hypersensitivity to cell wall-targeted molecules, alterations to cell wall protein layer, decreased cell wall thickness by electron microscopy, and increased cellular aggregation. Consistent with its important role in cell wall integrity, UPR is activated by signaling through the cell wall integrity mitogen-activated protein (MAP) kinase pathway during cell wall stress and unstressed vegetative growth. Both cell wall stress and basal UPR activity is mediated by Swi6p, a regulator of cell cycle and cell wall stress gene transcription, in a manner that is independent of its known coregulatory molecules. We propose that the cellular responses to ER and cell wall stress are coordinated to buffer the cell against these two related cellular stresses.
Identifying molecular markers associated with classification of genotypes by External Logistic Biplots
Authors: Demey J. R. , Vicente-Villardón J. L. , Galindo-Villardón M. P. , Zambrano A. Y.
Published: October 2008

For characterization of genetic diversity in genotypes several molecular techniques, usually resulting in a binary data matrix, have been used. Despite the fact that in Cluster Analysis (CA) and Principal Coordinates Analysis (PCoA) the interpretation of the variables responsible for grouping is not straightforward, these methods are commonly used to classify genotypes using DNA molecular markers. In this article, we present a novel algorithm that uses a combination of PCoA, CA and Logistic Regression (LR), as a better way to interpret the variables (alleles or bands) associated to the classification of genotypes. The combination of three standard techniques with some new ideas about the geometry of the procedures, allows constructing an External Logistic Biplot (ELB) that helps in the interpretation of the variables responsible for the classification or ordination. An application of the method to study the genetic diversity of four populations from Africa, Asia and Europe, using the HapMap data is included.

Availability: The Matlab code for implementing the methods may be obtained from the web site: http://biplot.usal.es.

Contact:  jhonny.demey@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Small RNA gene identification and mRNA target predictions in bacteria
Authors: Pichon Christophe , Felden Brice
Published: October 2008

Motivation: Bacterial small ribonucleic acids (sRNAs) that are not ribosomal and transfer or messenger RNAs were initially identified in the sixties, whereas their molecular functions are still under active investigation today. It is now widely accepted that most play central roles in gene expression regulation in response to environmental changes. Interestingly, some are also implicated in bacterial virulence. Functional studies revealed that a large subset of these sRNAs act by an antisense mechanism thanks to pairing interactions with dedicated mRNA targets, usually around their translation start sites, to modulate gene expression at the posttranscriptional level. Some sRNAs modulate protein activity or mimic the structure of other macromolecules. In the last few years, in silico methods have been developed to detect more bacterial sRNAs. Among these, computational analyses of the bacterial genomes by comparative genomics have predicted the existence of a plethora of sRNAs, some that were confirmed to be expressed in vivo. The prediction accuracy of these computational tools is highly variable and can be perfectible. Here we review the computational studies that have contributed to detecting the sRNA gene and mRNA targets in bacteria and the methods for their experimental testing. In addition, the remaining challenges are discussed.

Contact:  bfelden@univ-rennes1.fr
Defensins and the dynamic genome: What we can learn from structural variation at human chromosome band 8p23.1
Authors: Hollox Edward J. , Barber John C.K. , Brookes Anthony J. , Armour John A.L.
Published: October 2008

Over the past four years, genome-wide studies have uncovered numerous examples of structural variation in the human genome. This includes structural variation that changes copy number, such as deletion and duplication, and structural variation that does not change copy number, such as orientation and positional polymorphism. One region that contains all these types of variation spans the chromosome band 8p23.1. This region has been studied in some depth, and the focus of this review is to examine our current understanding of the variation of this region. We also consider whether this region is a good model for other structurally variable regions in the genome and what the implications of this variation are for clinical studies. Finally, we discuss the bioinformatics challenges raised, discuss the evolution of the region, and suggest some future priorities for structural variation research.
Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa
Authors: Zhou Xuefeng , Sunkar Ramanjulu , Jin Hailing , Zhu Jian-Kang , Zhang Weixiong
Published: October 2008

Natural antisense transcripts (NATs) have been shown to play important roles in post-transcriptional regulation through the RNA interference pathway. We have combined pyrophosphate-based high-throughput sequencing and computational analysis to identify and analyze, in genome scale, cis-NAT and trans-NAT small RNAs that are derived under normal conditions and in response to drought and salt stresses in the staple plant Oryza sativa. Computationally, we identified 344 cis-NATs and 7142 trans-NATs that are formed by protein-coding genes. From the deep sequencing data, we found 108 cis-NATs and 7141 trans-NATs that gave rise to small RNAs from their overlapping regions. Consistent with early findings, the majority of these 108 cis-NATs seem to be associated with specific conditions or developmental stages. Our analyses also revealed several interesting results. The overlapping regions of the cis-NATs and trans-NATs appear to be more enriched with small RNA loci than non-overlapping regions. The small RNAs generated from cis-NATs and trans-NATs have a length bias of 21 nt, even though their lengths spread over a large range. Furthermore, >40% of the small RNAs from cis-NATs and trans-NATs carry an A as their 5′-terminal nucleotides. A substantial portion of the transcripts are involved in both cis-NATs and trans-NATs, and many trans-NATs can form many-to-many relationships, indicating that NATs may form complex regulatory networks in O. sativa. This study is the first genome-wide investigation of NAT-derived small RNAs in O. sativa. It reveals the importance of NATs in biogenesis of small RNAs and broadens our understanding of the roles of NAT-derived small RNAs in gene regulation, particularly in response to environmental stimuli.
Suppression of 4-Coumarate-CoA Ligase in the Coniferous GymnospermPinus radiata
Authors: Wagner Armin , Donaldson Lloyd , Kim Hoon , Phillips Lorelle , Flint Heather , Steward Diane , Torr Kirk , Koch Gerald , Schmitt Uwe , Ralph John
Published: October 2008

Severe suppression of 4-coumarate-coenzyme A ligase (4CL) in the coniferous gymnosperm Pinus radiata substantially affected plant phenotype and resulted in dwarfed plants with a “bonsai tree-like” appearance. Microscopic analyses of stem sections from 2-year-old plants revealed substantial morphological changes in both wood and bark tissues. This included the formation of weakly lignified tracheids that displayed signs of collapse and the development of circumferential bands of axial parenchyma. Acetyl bromide-soluble lignin assays and proton nuclear magnetic resonance studies revealed lignin reductions of 36% to 50% in the most severely affected transgenic plants. Two-dimensional nuclear magnetic resonance and pyrolysis-gas chromatography-mass spectrometry studies indicated that lignin reductions were mainly due to depletion of guaiacyl but not p-hydroxyphenyl lignin. 4CL silencing also caused modifications in the lignin interunit linkage distribution, including elevated β-aryl ether (β-O-4 unit) and spirodienone (β-1) levels, accompanied by lower phenylcoumaran (β-5), resinol (β-β), and dibenzodioxocin (5-5/β-O-4) levels. A sharp depletion in the level of saturated (dihydroconiferyl alcohol) end groups was also observed. Severe suppression of 4CL also affected carbohydrate metabolism. Most obvious was an up to approximately 2-fold increase in galactose content in wood from transgenic plants due to increased compression wood formation. The molecular, anatomical, and analytical data verified that the isolated 4CL clone is associated with lignin biosynthesis and illustrated that 4CL silencing leads to complex, often surprising, physiological and morphological changes in P. radiata.
The Role of Impulse on the Initiation of Particle Movement Under Turbulent Flow Conditions
Authors: Diplas Panayiotis , Dancey Clint L. , Celik Ahmet O. , Valyrakis Manousos , Greer Krista , Akar Tanju
Published: October 2008

Fundamental to our understanding of erosional and transport phenomena in earth-surface dynamics and engineering is knowledge of the conditions under which sediment motion will begin when subjected to turbulent flow. The onset criterion currently in use emphasizes the time-averaged boundary shear stress and therefore is incapable of accounting for the fluctuating forces encountered in turbulent flows. We have validated through laboratory experiments and analytical formulation of the problem a criterion based upon the impulse imparted to a sediment grain. We demonstrate that in addition to the magnitude of the instantaneous turbulent forces applied on a sediment grain, the duration of these turbulent forces is also important in determining the sediment grain's threshold of motion, and that their product, or impulse, is better suited for specifying such conditions.
Comment on "Differential Rescue of Light- and Food-Entrainable Circadian Rhythms"
Authors: Mistlberger Ralph E. , Yamazaki Shin , Pendergast Julie S. , Landry Glenn J. , Takumi Toru , Nakamura Wataru
Published: October 2008

Fuller
et al
. (Reports, 23 May 2008, p. 1074) reported that the dorsomedial hypothalamus contains a
Bmal1
-based oscillator that can drive food-entrained circadian rhythms. We report that mice bearing a null mutation of
Bmal1
exhibit normal food-anticipatory circadian rhythms. Lack of food anticipation in
Bmal1

–
/
–

mice reported by Fuller
et al
. may reflect morbidity due to weight loss, thus raising questions about their conclusions.
Response to Comment on "Differential Rescue of Light- and Food-Entrainable Circadian Rhythms"
Authors: Fuller Patrick M. , Lu Jun , Saper Clifford B.
Published: October 2008

The points raised by Mistlberger
et al
. arise from a shortcoming in their approach, namely, that they measure the response to food restriction by using food-seeking behavior, which is confounded by homeostatic inputs. We used unrelated circadian-driven physiological responses, and we stand by our finding that the dorsomedial nucleus of the hypothalamus contains a food-entrainable oscillator that is sufficient for entrainment of circadian rhythms of body temperature and locomotor activity.
Ages for the Middle Stone Age of Southern Africa: Implications for Human Behavior and Dispersal
Authors: Jacobs Zenobia , Roberts Richard G. , Galbraith Rex F. , Deacon Hilary J. , Grün Rainer , Mackay Alex , Mitchell Peter , Vogelsang Ralf , Wadley Lyn
Published: October 2008

The expansion of modern human populations in Africa 80,000 to 60,000 years ago and their initial exodus out of Africa have been tentatively linked to two phases of technological and behavioral innovation within the Middle Stone Age of southern Africa—the Still Bay and Howieson's Poort industries—that are associated with early evidence for symbols and personal ornaments. Establishing the correct sequence of events, however, has been hampered by inadequate chronologies. We report ages for nine sites from varied climatic and ecological zones across southern Africa that show that both industries were short-lived (5000 years or less), separated by about 7000 years, and coeval with genetic estimates of population expansion and exit times. Comparison with climatic records shows that these bursts of innovative behavior cannot be explained by environmental factors alone.
Energy Uptake and Allocation During Ontogeny
Authors: Hou Chen , Zuo Wenyun , Moses Melanie E. , Woodruff William H. , Brown James H. , West Geoffrey B.
Published: October 2008

All organisms face the problem of how to fuel ontogenetic growth. We present a model, empirically grounded in data from birds and mammals, that correctly predicts how growing animals allocate food energy between synthesis of new biomass and maintenance of existing biomass. Previous energy budget models have typically had their bases in rates of either food consumption or metabolic energy expenditure. Our model provides a framework that reconciles these two approaches and highlights the fundamental principles that determine rates of food assimilation and rates of energy allocation to maintenance, biosynthesis, activity, and storage. The model predicts that growth and assimilation rates for all animals should cluster closely around two universal curves. Data for mammals and birds of diverse body sizes and taxa support these predictions.
Wolbachia
and Virus Protection in Insects
Authors: Hedges Lauren M. , Brownlie Jeremy C. , O'Neill Scott L. , Johnson Karyn N.
Published: October 2008

Wolbachia pipientis bacteria are common endosymbionts of insects that are best known for their ability to increase their prevalence in populations by manipulating host reproductive systems. However, there are examples of Wolbachia that exist in nature that seem to induce no reproductive parasitism trait and yet are able to invade populations. We demonstrate a fitness benefit for Wolbachia-infected insects that may explain this paradox. Drosophila melanogaster flies infected with Wolbachia are less susceptible to mortality induced by a range of RNA viruses. The antiviral protection associated with Wolbachia infection might be exploited in future strategies to reduce transmission of pathogens by insects.
Glia Are Essential for Sensory Organ Function in
C. elegans
Authors: Bacaj Taulant , Tevlin Maya , Lu Yun , Shaham Shai
Published: October 2008

Sensory organs are composed of neurons, which convert environmental stimuli to electrical signals, and glia-like cells, whose functions are not well understood. To decipher glial roles in sensory organs, we ablated the sheath glial cell of the major sensory organ of
Caenorhabditis elegans
. We found that glia-ablated animals exhibit profound sensory deficits and that glia provide activities that affect neuronal morphology, behavior generation, and neuronal uptake of lipophilic dyes. To understand the molecular bases of these activities, we identified 298 genes whose messenger RNAs are glia-enriched. One gene,
fig-1
, encodes a labile protein with conserved thrombospondin TSP1 domains. FIG-1 protein functions extracellularly, is essential for neuronal dye uptake, and also affects behavior. Our results suggest that glia are required for multiple aspects of sensory organ function.
Experimental Evidence for Spatial Self-Organization and Its Emergent Effects in Mussel Bed Ecosystems
Authors: van de Koppel Johan , Gascoigne Joanna C. , Theraulaz Guy , Rietkerk Max , Mooij Wolf M. , Herman Peter M. J.
Published: October 2008

Spatial self-organization is the main theoretical explanation for the global occurrence of regular or otherwise coherent spatial patterns in ecosystems. Using mussel beds as a model ecosystem, we provide an experimental demonstration of spatial self-organization. Under homogeneous laboratory conditions, mussels developed regular patterns, similar to those in the field. An individual-based model derived from our experiments showed that interactions between individuals explained the observed patterns. Furthermore, a field study showed that pattern formation affected ecosystem-level processes in terms of improved growth and resistance to wave action. Our results imply that spatial self-organization is an important determinant of the structure and functioning of ecosystems, and it needs to be considered in their conservation.
Why Rich States Aren't Republican
Authors: Clark Terry Nichols , Graziul Christopher
Published: October 2008

Red State, Blue State, Rich State, Poor State
. Why Americans Vote the Way They Do.
By Andrew Gelman, David Park, Boris Shor, Joseph Bafumi, and Jeronimo Cortina
. Princeton University Press, Princeton, NJ, 2008. 247 pp. $27.95, £16.95. ISBN 9780691139272.

Beginning with the paradox that while rich states have tilted toward the Democratic Party, rich voters still tend to favor the Republicans, the authors explore voting patterns in recent U.S. elections and their implications for American politics.
Antibodies against Glucan, Chitin, and
Saccharomyces cerevisiae
Mannan as New Biomarkers of
Candida albicans
Infection That Complement Tests Based on
C. albicans
Mannan
Authors: Sendid B. , Dotan N. , Nseir S. , Savaux C. , Vandewalle P. , Standaert A. , Zerimech F. , Guery B. P. , Dukler A. , Colombel J. F. , Poulain D.
Published: October 2008

Antibodies against
Saccharomyces cerevisiae
mannan (ASCA) and antibodies against synthetic disaccharide fragments of glucans (ALCA) and chitin (ACCA) are biomarkers of Crohn's disease (CD). We previously showed that
Candida albicans
infection generates ASCA. Here, we explored ALCA and ACCA as possible biomarkers of invasive
C. albicans
infection (ICI). ASCA, ALCA, ACCA, and
Candida
mannan antigen and antibody detection tests were performed on 69 sera obtained sequentially from 18 patients with ICIs proven by blood culture, 59 sera from CD patients, 47 sera from hospitalized subjects colonized by
Candida
species (CZ), and 131 sera from healthy controls (HC). ASCA, ALCA, and ACCA levels in CD and ICI patients were significantly different from those in CZ and HC subjects (
P
< 0.0001). In ICI patients, these levels increased as infection developed. Using ASCA, ALCA, ACCA, and Platelia
Candida
tests, 100% of ICIs were detected, with the kinetics of the antibody response depending on the patient during the time course of infection. A large number of sera presented with more than three positive tests. This is the first evidence that the detection of antibodies against chitin and glucans has diagnostic value in fungal infections and that these tests can complement more specific tests. Future trials are necessary to assess the value of these tests in multiparametric analysis, as well as their pathophysiological relevance.