Horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein S4

Background  

The universal ribosomal protein S4 is essential for the initiation of small subunit ribosomal assembly and translational accuracy. Being part of the information processing machinery of the cell, the gene for S4 is generally thought of as being inherited vertically and has been used in concatenated gene phylogenies. Here we report the evolution of ribosomal protein S4 in relation to a broad sharing of zinc/non-zinc forms of the gene and study the scope of horizontal gene transfer (HGT) of S4 during bacterial evolution.     

MultiSeq: unifying sequence and structure data for evolutionary analysis

Background  

Since the publication of the first draft of the human genome in 2000, bioinformatic data have been accumulating at an overwhelming pace. Currently, more than 3 million sequences and 35 thousand structures of proteins and nucleic acids are available in public databases. Finding correlations in and between these data to answer critical research questions is extremely challenging. This problem needs to be approached from several directions: information science to organize and search the data; information visualization to assist in recognizing correlations; mathematics to formulate statistical inferences; and biology to analyze chemical and physical properties in terms of sequence and structure changes.     

Systematic characterization of mutations altering protein degradation in human cancers

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From reaction kinetics to dementia: A simple dimer model of Alzheimer’s disease etiology

Oligomers of the amyloid β-protein (Aβ) have been implicated in the pathogenesis of Alzheimer’s disease (AD) through their toxicity towards neurons. Understanding the process of oligomerization may contribute to the development of therapeutic agents, but this has been difficult due to the complexity of oligomerization and the metastability of the oligomers thus formed. To understand the kinetics of oligomer formation, and how that relates to the progression of AD, we developed models of the oligomerization process. Here, we use experimental data from cell viability assays and proxies for rate constants involved in monomer-dimer-trimer kinetics to develop a simple mathematical model linking Aβ assembly to oligomer-induced neuronal degeneration. This model recapitulates the rapid growth of disease incidence with age. It does so through incorporation of age-dependent changes in rates of Aβ monomer production and elimination. The model also describes clinical progression in genetic forms of AD (e.g., Down’s syndrome), changes in hippocampal volume, AD risk after traumatic brain injury, and spatial spreading of the disease due to foci in which Aβ production is elevated. Continued incorporation of clinical and basic science data into the current model will make it an increasingly relevant model system for doing theoretical calculations that are not feasible in biological systems. In addition, terms in the model that have particularly large effects are likely to be especially useful therapeutic targets.     

Safety of over Twelve Hundred Infant Male Circumcisions Using the Mogen Clamp in Kenya

Background

Several sub-Saharan African countries plan to scale-up infant male circumcision (IMC) for cost-efficient HIV prevention. Little data exist about the safety of IMC in East and southern Africa. We calculated adverse event (AE) rate and risks for AEs associated with introduction of IMC services at five government health facilities in western Kenya.

Methods

AE data were analyzed for IMC procedures performed between September, 2009 and November, 2011. Healthy infants aged ≤2 months and weighing ≥2.5 kg were eligible for IMC. Following parental consent, trained clinicians provided IMC services free of charge under local anesthesia using the Mogen clamp. Odds ratios and 95% confidence intervals were used to explore AE risk factors.

Findings

A total of 1,239 IMC procedures were performed. Median age of infants was 4 days (IQR = 1, 16). The overall AE rate among infants reviewed post-operatively was 2.7% (18/678; 95%CI: 1.4, 3.9). There was one severe AE involving excision of a small piece of the lateral aspect of the glans penis. Other AEs were mild or moderate and were treated conservatively. Babies one month of age or older were more likely to have an AE (OR 3.20; 95%CI: 1.23, 8.36). AE rate did not differ by nurse versus clinical officer or number of previous procedures performed.

Conclusion

IMC services provided in Kenyan Government hospitals in the context of routine IMC programming have AE rates comparable to those in developed countries. The optimal time for IMC is within the first month of life.     

Revision of the Paridris nephtaspecies group (Hymenoptera, Platygastroidea, Platygastridae)

The Paridris nephta group is revised (Hymenoptera: Platygastridae). Fifteen species are described, 14 of which are new: Paridris atroxTalamas, sp. n.(Yunnan Province, China), Paridris bununTalamas, sp. n.(Taiwan), Paridris ferusTalamas, sp. n.(Thailand), Paridris kagemonoTalamas, sp. n.(Japan), Paridris minatorTalamas, sp. n.(Laos, Thailand), Paridris mystaxTalamas, sp. n.(Laos, Thailand), Paridris nephta(Kozlov) (Japan, North Korea, South Korea, Far Eastern Russia), Paridris nilakaTalamas, sp. n.(Thailand), Paridris reptilisTalamas, sp. n.(Taiwan), Paridris rugulosusTalamas, sp. n.(Laos, Vietnam), Paridris solarisTalamas, sp. n.(Laos, Thailand, Vietnam), Paridris teresTalamas, sp. n.(Vietnam), Paridris toketokiTalamas, sp. n.(Taiwan), Paridris verrucosusTalamas, sp. n.(Guangdong Province, China), Paridris yakTalamas, sp. n.(Thailand).     

Analysis of alien introgression in coffee tree (<Emphasis Type="Italic">Coffea</Emphasis><Emphasis Type="Italic">arabica</Emphasis> L.)

The transfer of desired traits from related wild diploid Coffea species into the cultivated allotetraploid C. arabica is essential in coffee breeding to develop pest/disease-resistant cultivars. The present work is an attempt to gain insights into alien introgression in C. arabica. An F2 population derived from a cross between T5296 and Et6 was analysed with simple sequence repeat (SSR; microsatellite) and amplified fragment length polymorphism (AFLP) molecular markers. The T5296 is a derivative of an interspecific hybrid introgressed by the diploid C. canephora species and Et6 is a wild Ethiopian accession of C. arabica. The origin of the revealed polymorphism was determined by comparisons using representative accessions from C. arabica and its two diploid parental species, C. eugenioides and C. canephora. The number and mode of inheritance of canephora-introgressed segments were investigated, as well as their sub-genome localisation and rate of recombination. The results suggested that the transfer of desirable genes into C. arabica from C. canephora is not limited by the ploidy level differences or the suppression of recombination between the different genomes.     

Back from extinction: Rediscovery of the Canterbury knobbled weevil Hadramphus tuberculatus (Pascoe 1877) (Coleoptera: Curculionidae), with a review of its historical distribution

Abstract

The Canterbury knobbled weevil, Hadramphus tuberculatus (Coleoptera: Curculionidae: Molytini), was once widespread in the Canterbury plains, foothills and fringing ranges, ranging from Oxford in the north to Waimate in the south. Habitat degradation, reduction in host plant numbers through grazing and predation by rodents are thought to be responsible for the decline in its numbers and distribution. In December 2004, more than 80 years since the last sighting of H. tuberculatus in 1922, a single individual was found at Burkes Pass Scenic Reserve. This paper records the rediscovery of H. tuberculatus, reviews the historical distribution records for H. tuberculatus, discusses them with respect to changes in host plant habitat in the eastern South Island, and suggests conservation strategies to protect this and other relictual populations that might be found in future.     

Nucleic Acid Template and the Risk of a PCR-Induced HIV-1 Drug Resistance Mutation

Background

The HIV-1 nucleoside RT inhibitor (NRTI)-resistance mutation, K65R confers intermediate to high-level resistance to the NRTIs abacavir, didanosine, emtricitabine, lamivudine, and tenofovir; and low-level resistance to stavudine. Several lines of evidence suggest that K65R is more common in HIV-1 subtype C than subtype B viruses.

Methods and Findings

We performed ultra-deep pyrosequencing (UDPS) and clonal dideoxynucleotide sequencing of plasma virus samples to assess the prevalence of minority K65R variants in subtype B and C viruses from untreated individuals. Although UDPS of plasma samples from 18 subtype C and 27 subtype B viruses showed that a higher proportion of subtype C viruses contain K65R (1.04% vs. 0.25%; p<0.001), limiting dilution clonal sequencing failed to corroborate its presence in two of the samples in which K65R was present in >1.5% of UDPS reads. We therefore performed UDPS on clones and site-directed mutants containing subtype B- and C-specific patterns of silent mutations in the conserved KKK motif encompassing RT codons 64 to 66 and found that subtype-specific nucleotide differences were responsible for increased PCR-induced K65R mutation in subtype C viruses.

Conclusions

This study shows that the RT KKK nucleotide template in subtype C viruses can lead to the spurious detection of K65R by highly sensitive PCR-dependent sequencing techniques. However, the study is also consistent with the subtype C nucleotide template being inherently responsible for increased polymerization-induced K65R mutations in vivo.