The Escherichia coli SRP Receptor Forms a Homodimer at the Membrane

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Helicobacter pylori ABC transporter: effect of allelic exchange mutagenesis on urease activity.

Helicobacter pylori urease requires nickel ions in the enzyme active site for catalytic activity. Nickel ions must, therefore, be actively acquired by the bacterium. NixA (high-affinity nickel transport protein)-deficient mutants of H. pylori retain significant urease activity, suggesting the presence of alternate nickel transporters. Analysis of the nucleotide sequence of the H. pylori genome revealed a homolog of NikD, a component of an ATP-dependent nickel transport system in Escherichia coli. Based on this sequence, a 378-bp DNA fragment was PCR amplified from H. pylori genomic DNA and used as a probe to identify an H. pylori lambda ZAPII genomic library clone that carried these sequences. Four open reading frames of 621, 273, 984, and 642 bp (abcABCD) were revealed by sequencing and predicted polypeptides of 22.7, 9.9, 36.6, and 22.8 kDa, respectively. The 36.6-kDa polypeptide (AbcC) has significant homology (56% amino acid sequence identity) to an E. coli ATP-binding protein component of an ABC transport system, while none of the other putative proteins are significantly homologous to polypeptides in the available databases. To determine the possible contribution of these genes to urease activity, abcC and abcD were each insertionally inactivated with a kanamycin resistance (aphA) cassette and allelic exchange mutants of each gene were constructed in H. pylori UMAB41. Mutation of abcD resulted in an 88% decrease in urease activity to 27 +/- 31 mumol of NH3/min/mg of protein (P < 0.0001), and a double mutant of nixA and abcC resulted in the near abolishment of urease activity (1.1 +/- 1.4 mumol of NH3/min/mg of protein in the double mutant versus 228 +/- 92 mumol of NH3/min/mg of protein in the parent [P < 0.0001]). Synthesis of urease apoenzyme, however, was unaffected by mutations in any of the abc genes. We conclude that the abc gene cluster, in addition to nixA, is involved in production of a catalytically active urease.     

Digging through the Obstruction: Insight into the Epithelial Cell Response to Respiratory Virus Infection in Patients with Cystic Fibrosis

Respiratory virus infections are common but generally self-limiting infections in healthy individuals. Although early clinical studies reported low detection rates, the development of molecular diagnostic techniques by PCR has led to an increased recognition that respiratory virus infections are associated with morbidity and acute exacerbations of chronic lung diseases, such as cystic fibrosis (CF). The airway epithelium is the first barrier encountered by respiratory viruses following inhalation and the primary site of respiratory viral replication. Here, we describe how the airway epithelial response to respiratory viral infections contributes to disease progression in patients with CF and other chronic lung diseases, including the role respiratory viral infections play in bacterial acquisition in the CF patient lung.     

Persistence of genetic variation in recolonized Tsuga canadensis (Eastern hemlock) populations following historic forest clearance

The recovery of genetic variation in newly recolonized populations is an important concern in forest conservation genetics. We examined the potential recovery of genetic diversity and changes to genetic structure in populations of the wind‐pollinated species Tsuga canadensis that naturally regenerated following the extensive 19th century regional forest clearance for agriculture in west‐central Massachusetts. We genotyped 264 individuals across six microsatellite loci and compared levels and patterns of genetic variation between primary forests (forests that were logged but never cleared) and secondary forests (stands that were recolonized following agricultural abandonment). We found no significant reductions in genetic diversity in secondary forests (A_R = 5.450; H_S = 0.718) compared to primary forests (A_R = 5.742; H_S = 0.730). Moreover, the population genetic differentiation was also not significantly reduced in secondary compared to primary forests, with no significant genetic structure observed among all populations. These results suggest rapid genetic recovery of T. canadensis populations in recolonized forests compared with other late‐successional temperate tree species.     

Progress in methods for rare variant association

Empirical studies and evolutionary theory support a role for rare variants in the etiology of complex traits. Given this motivation and increasing affordability of whole-exome and whole-genome sequencing, methods for rare variant association have been an active area of research for the past decade. Here, we provide a survey of the current literature and developments from the Genetics Analysis Workshop 19 (GAW19) Collapsing Rare Variants working group. In particular, we present the generalized linear regression framework and associated score statistic for the 2 major types of methods: burden and variance components methods. We further show that by simply modifying weights within these frameworks we arrive at many of the popular existing methods, for example, the cohort allelic sums test and sequence kernel association test. Meta-analysis techniques are also described. Next, we describe the 6 contributions from the GAW19 Collapsing Rare Variants working group. These included development of new methods, such as a retrospective likelihood for family data, a method using genomic structure to compare cases and controls, a haplotype-based meta-analysis, and a permutation-based method for combining different statistical tests. In addition, one contribution compared a mega-analysis of family-based and population-based data to meta-analysis. Finally, the power of existing family-based methods for binary traits was compared. We conclude with suggestions for open research questions.     

The Effect of Social Parasitism by Polyergus breviceps on the Nestmate Recognition System of Its Host,Formica altipetens

Highly social ants, bees and wasps employ sophisticated recognition systems to identify colony members and deny foreign individuals access to their nest. For ants, cuticular hydrocarbons serve as the labels used to ascertain nest membership. Social parasites, however, are capable of breaking the recognition code so that they can thrive unopposed within the colonies of their hosts. Here we examine the influence of the socially parasitic slave-making ant, Polyergus breviceps on the nestmate recognition system of its slaves, Formica altipetens. We compared the chemical, genetic, and behavioral characteristics of colonies of enslaved and free-living F. altipetens. We found that enslaved Formica colonies were more genetically and chemically diverse than their free-living counterparts. These differences are likely caused by the hallmark of slave-making ant ecology: seasonal raids in which pupa are stolen from several adjacent host colonies. The different social environments of enslaved and free-living Formica appear to affect their recognition behaviors: enslaved Formica workers were less aggressive towards non-nestmates than were free-living Formica. Our findings indicate that parasitism by P. breviceps dramatically alters both the chemical and genetic context in which their kidnapped hosts develop, leading to changes in how they recognize nestmates.     

Change in Obesity Prevalence across the United States Is Influenced by Recreational and Healthcare Contexts,Food Environments,and Hispanic Populations

Objective

To examine change in county-level adult obesity prevalence between 2004 and 2009 and identify associated community characteristics.

Methods

Change in county-level adult (≥20 years) obesity prevalence was calculated for a 5-year period (2004–2009). Community measures of economic, healthcare, recreational, food environment, population structure, and education contexts were also calculated. Regression analysis was used to assess community characteristics associated (p<0.01) with change in adult obesity prevalence.

Results

Mean±SD change in obesity prevalence was 5.1±2.4%. Obesity prevalence decreased in 1.4% (n = 44) and increased in 98% (n = 3,060) of counties from 2004–2009. Results showed that both baseline levels and increases in physically inactive adults were associated with greater increases in obesity prevalence, while baseline levels of and increases in physician density and grocery store/supercenter density were related to smaller increases in obesity rates. Baseline levels of the Hispanic population share were negatively linked to changing obesity levels, while places with greater Hispanic population growth saw greater increases in obesity.

Conclusions

Most counties in the U.S. experienced increases in adult obesity prevalence from 2004 to 2009. Findings suggest that community-based interventions targeting adult obesity need to incorporate a range of community factors, such as levels of physical inactivity, access to physicians, availability of food outlets, and ethnic/racial population composition.     

Structure of the cuticle of the common house cricket with reference to the location of lipids

Cuticle segments from the thorax, abdomen, and jumping legs of the house cricket. Acheta domesticus, were examined using histological techniques for light microscopy, scanning and transmission electron microscopy, and direct examination of frozen-fractured cuticle. The surface of untreated cuticle is covered by a lipid film which obscures fine surface detail. Standard EM preparative procedures, as well as washing the cuticle with ethanol before examination, remove this film exposing previously covered openings to dermal gland ducts and wax canals. An epicuticle, exocuticle, mesocuticle, endocuticle, and a deposition layer were present in all transverse sections of cuticle. Light microscopy showed that the exocuticle and mesocuticle are heavily impregnated with lipids, whereas there is little lipid associated with the endocuticle. Frozen-fractured cuticle clearly shows the ‘plywood’ structure of the meso- and endocuticle, while the exocuticle fractures as if it were a solid sheet. The epicuticle is composed of a dense homogeneous layer, cuticulin, outer epicuticle, and the outer membrane. Superficial wax was detected only in cuticle samples prepared using vinylcyclohexane dioxide as a polar dehydrant. The results were used to construct a comprehensive model of the cuticle of A. domesticus.     

Proficiencies of two artificial substrates in collecting stream macroinvertebrates

Proficiencies in collecting stream macroinvertebrates by two types of artificial substrates, #200 3M conservation webbing and cone-shaped concrete blocks, were compared with bottom net collections. Conservation webbing collected more individuals than cone substrates, but fewer taxa than either cone substrates or bottom nets. Diversity indices calculated for collections made with the three techniques were lowest for webbing collections, highest for net collections and intermediate for cone collections. It was concluded that collections made with webbing substrates gave an extremely distorted view of macroinvertebrate community balance due to a preponderance of net spinning and case building forms, and that cone substrates were better suited for use in the particular situation studied.Department of Biology, Virginia Polytechnic Institute and State University.Center for Environmental Studies, Virginia Polytechnic Institute and State University.     

Single intraamniotic injections of prostaglandin F-2-alpha as an abortifacient agent: size of effective dose and effect of parity

This report discusses the authors' experience with intraamniotic administration of single doses of the prostaglandin PGF2alpha as an abortifacient agent. 98 healthy women between the 12th and 26th week of pregnancy admitted to the Clinical Research Unit of the North Carolina Memorial Hospital were given a single intraamniotic dose of PGF2a administered through an indwelling polyethelene catheter inserted either transabdominally or transvaginally. The drug was given as Tham salt with the first 5 mg of any dose being given at the rate of 1 mg/minute for 5 minutes, followed by more rapid administration of the balance of the dose. Abortion which did not occur within 48 hours was considered a failure. Each patient received 1 of the following dosages: 25, 40, 50, and 75. 9 (64%) of 14 patients given 25 mg PGF2a aborted within the 48-hour period. The percentages of abortion in the doses 40, 50, and 75 mg were 88.9% (9 patients), 96.7% (60 patients) and 93.3% (15 patients) respectively. As these figures were almost similar, the 84 patients were combined as a single group (84 patients) relative to the injection-abortion time, effect of parity, and stage of gestation at which the abortion was carried out. Half of the patients in this combined group aborted in approximately 21 hours; more than 90% at the end of 32 hours; and 95% at the end of the 48 hours post-injection. For comparison, the cumulative abortion curve of 552 patients who had intraamniotic saline for abortion showed that 50% of the women aborted within 31 hours, 84% within 48 hours, and 97% within 72 hours. Prostaglandin induced abortions thus are shown to reach the 50% level 10 hours before the saline patients, and the 90% level about 21 hours before the saline patients. Significant side effects (presented elsewhere) were observed in all groups, with the incidence increasing at higher dosages. Mean induction-abortion time for nulliparas at all dosages was 17.4 hours; for multiparas, 20.4 hours. There was no clear relationship between gestational age and parity. The study shows that the effective dose for inducing abortion with PGF2a lies within the 40 to 50 mg dose range.