First fungus gnats of genus Manota Williston (Diptera: Mycetophilidae) from Japan

The genus Manota is recorded from Japan for the first time. Three new species, Manota satoyamanis, Manota indahae and Manota tunoae spp. nov., are described, based on specimens collected in an ecological sampling program of arthropods in the “satoyama” landscape of Ishikawa Prefecture. “Satoyama” represents the traditional rural landscape of Japan, which is characterized by a mosaic of secondary forests, plantations, ponds and rice paddy fields. The new species raise the number of Palearctic Manota species from five to eight.     

Utilizing rabbit immunoglobulin G protein for mark-capture studies on the desert subterranean termite, Heterotermes aureus (Snyder)

Mark-capture dispersal studies were conducted to investigate the feasibility of marking the southwestern desert subterranean termite, Heterotermes aureus (Snyder) with rabbit immunoglobulin G (IgG). In turn, short-range dispersal patterns of H. aureus were measured across a 20-m diameter desert landscape at three distinct field locations. Each location consisted of 51 termite feeding stations containing corrugated cardboard. The central feeding station (CFS) at each location was impregnated with rabbit IgG. A circular grid was then constructed around each CFS that consisted of 50 additional unmarked cardboard feeding stations strategically placed around the CFS at distances of 1.5, 2.0, 4.0, 7.0 or 10.0 m. Termites self-marked with rabbit IgG by feeding on the marked bait. The CFS and the 50 peripheral feeding stations were sampled for marked termites twice at each location 17–65 days after the marked bait was placed at the CFS to determine the spatial dispersal patterns of H. aureus within each research grid. Termites that self marked by feeding on rabbit IgG marked bait were detected by an anti-rabbit IgG enzyme-linked immunosorbent assay (ELISA). Generally, the CFSs contained the highest frequency of marked termites with 28.0% of the individuals assayed from the CFSs containing rabbit IgG. Over the course of the study, 39 of the unmarked peripheral feeding stations contained at least one marked termite. Of the termites assayed from the peripheral stations (n = 2,955), 124 or 4.2% of the individuals contained the mark. The average distance traveled by the marked termites collected at the peripheral feeding stations was 5.7 ± 3.3 m from the CFSs. We also examined single nucleotide polymorphisms (SNPs) from termites collected at each field site. Data indicated that each field site were genetically distinct and therefore non-related termites. We discuss the advantages and limitations of marking termites with rabbit IgG for dispersal studies.     

Manufacturing and <Emphasis Type="Italic">in vivo</Emphasis> inner ear visualization of MRI traceable liposome nanoparticles encapsulating gadolinium

Background  

Treatment of inner ear diseases remains a problem because of limited passage through the blood-inner ear barriers and lack of control with the delivery of treatment agents by intravenous or oral administration. As a minimally-invasive approach, intratympanic delivery of multifunctional nanoparticles (MFNPs) carrying genes or drugs to the inner ear is a future therapy for treating inner ear diseases, including sensorineural hearing loss (SNHL) and Meniere's disease. In an attempt to track the dynamics and distribution of nanoparticles in vivo, here we describe manufacturing MRI traceable liposome nanoparticles by encapsulating gadolinium-tetra-azacyclo-dodecane-tetra-acetic acid (Gd-DOTA) (abbreviated as LPS+Gd-DOTA) and their distribution in the inner ear after either intratympanic or intracochlear administration.     

Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms

Background

Complete genome annotation is a necessary tool as Anopheles gambiae researchers probe the biology of this potent malaria vector.

Results

We reannotate the A. gambiae genome by synthesizing comparative and ab initio sets of predicted coding sequences (CDSs) into a single set using an exon-gene-union algorithm followed by an open-reading-frame-selection algorithm. The reannotation predicts 20,970 CDSs supported by at least two lines of evidence, and it lowers the proportion of CDSs lacking start and/or stop codons to only approximately 4%. The reannotated CDS set includes a set of 4,681 novel CDSs not represented in the Ensembl annotation but with EST support, and another set of 4,031 Ensembl-supported genes that undergo major structural and, therefore, probably functional changes in the reannotated set. The quality and accuracy of the reannotation was assessed by comparison with end sequences from 20,249 full-length cDNA clones, and evaluation of mass spectrometry peptide hit rates from an A. gambiae shotgun proteomic dataset confirms that the reannotated CDSs offer a high quality protein database for proteomics. We provide a functional proteomics annotation, ReAnoXcel, obtained by analysis of the new CDSs through the AnoXcel pipeline, which allows functional comparisons of the CDS sets within the same bioinformatic platform. CDS data are available for download.

Conclusion

Comprehensive A. gambiae genome reannotation is achieved through a combination of comparative and ab initio gene prediction algorithms.     

An update on cardiovascular malformations in congenital rubella syndrome

BACKGROUND : Congenital rubella syndrome (CRS) has long been characterized by the triad of deafness, cataract, and cardiovascular malformations (CVMs). While initial reports identified patent ductus arteriosus (PDA) as the primary CVM in CRS, the exact nature of the CVMs found in CRS has not been well established. METHODS : We searched the English literature from 1941 through 2008 to identify studies that used cardiac catheterization or echocardiography to evaluate the CVMs in CRS. RESULTS : Of the 121 patients in the 10 studies with catheterization data, 78% had branch pulmonary artery stenosis, and 62% had a PDA. In 49% of cases, both branch pulmonary artery stenosis and PDA were present, whereas isolated branch pulmonary artery stenosis and isolated PDA were found in 29 and 13% of cases, respectively. Of the 12 patients in the 10 studies with echocardiographic data, PDA was more common than branch pulmonary artery stenosis, but this finding is greatly limited by the small numbers of patients and limitations of echocardiography. Although published studies of CVMs in CRS have in general reported PDA as the CVM phenotype most commonly associated with CRS, among CRS cases evaluated by catheterization, branch pulmonary artery stenosis was actually more common than PDA. Moreover, although the combination of branch pulmonary artery stenosis and PDA was more common than either branch pulmonary artery stenosis or PDA alone, isolated branch pulmonary artery stenosis was twice as common as isolated PDA. CONCLUSION : Among children with suspected CRS, clinical evaluations for the presence of CVMs should include examinations for both branch pulmonary artery stenosis and PDA. Birth Defects Research (Part A), 2010. © 2009 Wiley‐Liss, Inc.     

Preventing and troubleshooting artefacts in saturation labelled fluorescence 2-D difference gel electrophoresis (saturation DiGE)

Saturation DiGE is a powerful but challenging technique for the characterisation of changes in protein expression between two or more scarce samples. In this paper, measures to prevent and troubleshoot artefacts in the saturation DiGE workflow are discussed, with illustration of some examples as they may be encountered in gel images or analysis.     

A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy

While current major national research efforts (i.e., the NIH Human Microbiome Project) will enable comprehensive metagenomic characterization of the adult human microbiota, how and when these diverse microbial communities take up residence in the host and during reproductive life are unexplored at a population level. Because microbial abundance and diversity might differ in pregnancy, we sought to generate comparative metagenomic signatures across gestational age strata. DNA was isolated from the vagina (introitus, posterior fornix, midvagina) and the V5V3 region of bacterial 16S rRNA genes were sequenced (454FLX Titanium platform). Sixty-eight samples from 24 healthy gravidae (18 to 40 confirmed weeks) were compared with 301 non-pregnant controls (60 subjects). Generated sequence data were quality filtered, taxonomically binned, normalized, and organized by phylogeny and into operational taxonomic units (OTU); principal coordinates analysis (PCoA) of the resultant beta diversity measures were used for visualization and analysis in association with sample clinical metadata. Altogether, 1.4 gigabytes of data containing >2.5 million reads (averaging 6,837 sequences/sample of 493 nt in length) were generated for computational analyses. Although gravidae were not excluded by virtue of a posterior fornix pH >4.5 at the time of screening, unique vaginal microbiome signature encompassing several specific OTUs and higher-level clades was nevertheless observed and confirmed using a combination of phylogenetic, non-phylogenetic, supervised, and unsupervised approaches. Both overall diversity and richness were reduced in pregnancy, with dominance of Lactobacillus species (L. iners crispatus, jensenii and johnsonii, and the orders Lactobacillales (and Lactobacillaceae family), Clostridiales, Bacteroidales, and Actinomycetales. This intergroup comparison using rigorous standardized sampling protocols and analytical methodologies provides robust initial evidence that the vaginal microbial 16S rRNA gene catalogue uniquely differs in pregnancy, with variance of taxa across vaginal subsite and gestational age.     

Heritability of cortisol response to confinement stress in European sea bass dicentrarchus labrax

Background

In fish, the most studied production traits in terms of heritability are body weight or growth, stress or disease resistance, while heritability of cortisol levels, widely used as a measure of response to stress, is less studied. In this study, we have estimated heritabilities of two growth traits (body weight and length) and of cortisol response to confinement stress in the European sea bass.

Findings

The F1 progeny analysed (n = 922) belonged to a small effective breeding population with contributions from an unbalanced family structure of just 10 males and 2 females. Heritability values ranged from 0.54 (±0.21) for body weight to 0.65 (±0.22) for standard body length and were low for cortisol response i.e. 0.08 (±0.06). Genetic correlations were positive (0.94) between standard body length and body weight and negative between cortisol and body weight and between cortisol and standard body length (−0.60 and −0.55, respectively).

Conclusion

This study confirms that in European sea bass, heritability of growth-related traits is high and that selection on such traits has potential. However, heritability of cortisol response to stress is low in European sea bass and since it is known to vary greatly among species, further studies are necessary to understand the reasons for these differences.     

Diverged Alleles of the Anopheles gambiae Leucine-Rich Repeat Gene APL1A Display Distinct Protective Profiles against Plasmodium falciparum

Functional studies have demonstrated a role for the Anopheles gambiae APL1A gene in resistance against the human malaria parasite, Plasmodium falciparum. Here, we exhaustively characterize the structure of the APL1 locus and show that three structurally different APL1A alleles segregate in the Ngousso colony. Genetic association combined with RNAi-mediated gene silencing revealed that APL1A alleles display distinct protective profiles against P. falciparum. One APL1A allele is sufficient to explain the protective phenotype of APL1A observed in silencing experiments. Epitope-tagged APL1A isoforms expressed in an in vitro hemocyte-like cell system showed that under assay conditions, the most protective APL1A isoform (APL1A²) localizes within large cytoplasmic vesicles, is not constitutively secreted, and forms only one protein complex, while a less protective isoform (APL1A¹) is constitutively secreted in at least two protein complexes. The tested alleles are identical to natural variants in the wild A. gambiae population, suggesting that APL1A genetic variation could be a factor underlying natural heterogeneity of vector susceptibility to P. falciparum.