PHYLOGEOGRAPHY OF THE ASIAN ELEPHANT (ELEPHAS MAXIMUS) BASED ON MITOCHONDRIAL DNA

Abstract Populations of the Asian elephant (Elephas maximus) have been reduced in size and become highly fragmented during the past 3000 to 4000 years. Historical records reveal elephant dispersal by humans via trade and war. How have these anthropogenic impacts affected genetic variation and structure of Asian elephant populations? We sequenced mitochondrial DNA (mtDNA) to assay genetic variation and phylogeography across much of the Asian elephant's range. Initially we compare cytochrome b sequences (cyt b) between nine Asian and five African elephants and use the fossil‐based age of their separation (～5 million years ago) to obtain a rate of about 0.013 (95% CI = 0.011–0.018) corrected sequence divergence per million years. We also assess variation in part of the mtDNA control region (CR) and adjacent tRNA genes in 57 Asian elephants from seven countries (Sri Lanka, India, Nepal, Myanmar, Thailand, Malaysia, and Indonesia). Asian elephants have typical levels of mtDNA variation, and coalescence analyses suggest their populations were growing in the late Pleistocene. Reconstructed phylogenies reveal two major clades (A and B) differing on average by HKY85/Γ‐corrected distances of 0.020 for cyt b and 0.050 for the CR segment (corresponding to a coalescence time based on our cyt b rate of ～1.2 million years). Individuals of both major clades exist in all locations but Indonesia and Malaysia. Most elephants from Malaysia and all from Indonesia are in well‐supported, basal clades within clade A, thus supporting their status as evolutionarily significant units (ESUs). The proportion of clade A individuals decreases to the north, which could result from retention and subsequent loss of ancient lineages in long‐term stable populations or, perhaps more likely, via recent mixing of two expanding populations that were isolated in the mid‐Pleistocene. The distribution of clade A individuals appears to have been impacted by human trade in elephants among Myanmar, Sri Lanka, and India, and the subspecies and ESU statuses of Sri Lankan elephants are not supported by molecular data.     

Unique roles of SK and Kv4.2 potassium channels in dendritic integration

Focal activation of glutamate receptors in distal dendrites of hippocampal pyramidal cells triggers voltage-dependent Ca(2+) channel-mediated plateau potentials that are confined to the stimulated dendrite. We examined the role of dendritic K(+) conductances in determining the amplitude, duration, and spatial compartmentalization of plateau potentials. Manipulations that blocked SK-type Ca(2+)-activated K(+) channels, including apamin and BAPTA dialysis, increased the duration of plateau potentials without affecting their amplitude or compartmentalization. Manipulations that blocked Kv4.2 A-type K(+) channels, including a dominant-negative Kv4.2 construct and 4-aminopyridine, increased the amplitude of plateau potentials by allowing them to recruit neighboring dendrites. Prolongation of plateau potentials or block of Kv4.2 channels at branch points facilitated the ability of dendritic excitation to trigger fast action potentials. SK channels thus underlie repolarization of dendritic plateau potentials, whereas Kv4.2 channels confine these potentials to single dendritic branches, and both act in concert to regulate synaptic integration.     

Exploring the interaction energies for the binding of hydroxydiphenyl ethers to enoyl-acyl carrier protein reductases

It is now well established that the potent anti-microbial compound, triclosan, interrupts the type II fatty acid synthesis by inhibiting the enzyme enoyl-ACP reductase in a number of organisms. Existence of a high degree of similarity between the recently discovered enoyl-ACP reductase from P. falciparum and B. napus enzyme permitted building of a satisfactory model for the former enzyme that explained some of the key aspects of the enzyme such as its specificity for binding to the cofactor and the inhibitor. We now report the interaction energies between triclosan and other hydroxydiphenyl ethers with the enzymes from B. napus, E. coli and P. falciparum. Examination of the triclosan-enzyme interactions revealed that subtle differences exist in the ligand binding sites of the enzymes from different sources i.e., B. napus, E. coli and P. falciparum. A comparison of their binding propensities thus determined should aid in the design of effective inhibitors for the respective enzymes.     

An Analysis of Sponsors/Collaborators of 69,160 Drug Trials Registered with ClinicalTrials.gov

Background

Clinical trials have been criticized on various counts. Any attempt to improve how trials are conducted or reported requires—amongst other things—an understanding of the number, the nature and the location of those that sponsor them or collaborate on them. Here we sought to identify the nature and location of each sponsor/collaborator.

Methods and Findings

We examined the ''sponsor/collaborator'' field for the 69,160 drug trials that were registered with ClinicalTrials.gov over a 9-year period (2005–2014). Of the 12,823 unique sponsors, 56% had sponsored only one and 27% had sponsored 2–5 trials each. Just 18% were involved with six or more trials each, and we have (arbitrarily) labeled these organizations as ''more experienced'' in sponsoring/collaborating on trials. These 18% (2,266 sponsors/collaborators) were analyzed further: (a) 951 were corporate organizations and (b) 1,145 were non-corporates (including 31 individuals) with (c) 170 unclassified. Further, we identified the location of each organization in (a) and (b).

Conclusions

Clinical trials are an important part of a nation''s research endeavors, and ultimately contribute to the health of its people. Thus, understanding the clinical trial landscape—including the number and nature of sponsors, and how active they are—is important for every country. We believe that policy makers in particular should be interested in this study to understand the current situation, and to use the numbers as a baseline for the evolving landscape, to assess the impact of their strategies in future.     

Characterizations of candidate genes for IDD susceptibility from the diabetes-prone NOD mouse strain

The nucleotide sequences of the NOD and C57BL/6J alleles of Glut-2, Sod-2, and Il-2 were determined by RT-PCR sequencing. Each of these loci is located in intervals that strongly correlated with susceptibility to diabetes in an (NOD/Uf x C57BL/6J)F₁ x NOD/Uf backcross. No significant variations in the alleles of Glut-2 at 16 cM on Chromosome (Chr) 3 or Sod-2 at 8 cM on Chr 17 were detected. However, the Il-2 allele in NOD at 20 cM on Chr 3 was found to differ from that in C57BL/6J by a complex mutation involving the contraction of a simple sequence repeat (SSR). Il-2 in NOD differs from the allele in C57BL/6J via a complex mutation involving a deletion of four CAG codons from the SSR together with a length-compensatory four-codon duplication of a segment 5 from the SSR. Two nonsynonymous mutations in the coding region 5 to the SSR were also detected. Only these two allelic forms of Il-2 were detected in a survey of 13 standard inbred lines and 4 wild mouse strains. We propose to designate these alleles as Il-2 ^a (for alleles such as C57BL/6J that contain 12 CAG repeats) and Il-2 ^b (for alleles such as NOD), which occurred in a variety of standard inbred strains and in all four wild Mus musculus domesticus tested. The distribution of these Il-2 alleles among inbred strains correlated with the detection of Chr 3 as an interval effecting diabetes susceptibility in three separate genetic crosses. However, functional characterizations of the quantity and functional characteristics of Il-2 produced by Il-2 ^a and Il-2 ^b failed to reveal any allele-specific variations.     

A facile preparation of α-hydroxy fatty acids

A convenient, one-step synthesis of α-hydroxy long chain, very long-chain and branched chain fatty acids from non-oxygenated fatty acids is described. The procedure involves preparation of fatty acid dianion using lithium diisopropylamide and oxygenation of the dianion by molecular oxygen.     

Species discrimination through DNA barcoding in the genus Salacia of the Western Ghats in India

The genus Salacia (Celastraceae) is a source of many important pharmaceutical chemicals used in the Ayurvedic system of medicine in India. Owing to morphological similarities between species, the taxonomy of Salacia is complex and not fully settled. To ensure quality and assured therapeutic effects in the raw drugs from the genus, proper identification at the species level is critical. The main objective of this study was to find suitable DNA barcodes that can accurately and efficiently identify the potential medicinal species of the genus. Among the barcode loci analyzed, ITS2 exhibited the highest interspecific divergence, followed by trnH‐psbA, matK and rbcL. A clear barcoding gap was evident for the ITS2 barcode region whereas it was less conspicuous for trnH‐psbA and matK. The ITS2 barcode could discriminate all the eight analyzed Salacia species with 100% accuracy. We therefore propose barcoding with ITS2 to confirm the taxonomic identity of the raw drugs in the market. Further, the ITS2 region can be recommended for biosystematic studies in the genus.     

Emergence of carbapenem non‐susceptible multidrug resistant Acinetobacter baumannii strains of clonal complexes 103B and 92B harboring OXA‐type carbapenemases and metallo‐β‐lactamases in Southern India

The molecular epidemiology and carbapenem resistance mechanisms of clinical isolates of Acinetobacter baumannii obtained from a south Indian tertiary care hospital were investigated by repetitive extragenic palindromic sequence PCR (REP‐PCR) and multi‐locus sequence typing (MLST). Analysis of resistant determinants was achieved by PCR screening for the presence of genes encoding OXA‐carbapenemases, metallo‐β‐lactamases (MBLs) and efflux pumps. REP‐PCR generated around eight clusters of high heterogeneity; of these, two major clusters (I and V) appeared to be clonal in origin. Analysis of representative isolates from different clusters by MLST revealed that most of the isolates belonged to sequence type 103 of CC103^B. Second most prevalent ST belonged to clonal complex (CC) 92^B which is also referred to as international clone II. Most of the isolates were multi‐drug resistant, being susceptible only to polymyxin‐B and newer quinolones. Class D β‐lactamases such as bla_{OXA‐51‐like} (100%), bla_{OXA‐23‐like} (56.8%) and bla_{OXA‐24‐like} (14.8%) were found to be predominant, followed by a class B β‐lactamase, namely bla_IMP‐1 (40.7%); none of the isolates had bla_OXA‐58 like, bla_NDM‐1 or bla_SIM‐1. Genes of efflux‐pump adeABC were predominant, most of isolates being biofilm producers that were PCR‐positive for autoinducer synthase gene (>94%). Carbapenem non‐susceptible isolates were highly diverse and present throughout the hospital irrespective of type of ward or intensive care unit. Although previous reports have documented diverse resistant mechanisms in A. baumannii, production of MBL and OXA‐type of carbapenamases were found to be the predominant mechanism(s) of carbapenem resistance identified in strains isolated from Southern India.