Phylogenetic relationships of African Caecilians (Amphibia: Gymnophiona): insights from mitochondrial rRNA gene sequences

Africa (excluding the Seychelles) has a diverse caecilian fauna, including the endemic family Scolecomorphidae and six endemic genera of the more cosmopolitan Caeciliidae. Previous molecular phylogenetic studies have not included any caecilians from the African mainland. Partial 12S and 16S mitochondrial gene sequences were obtained for two species of the endemic African Scolecomorphidae and five species and four genera of African Caeciliids, aligned against previously reported sequences for 16 caecilian species, and analysed using parsimony, maximum likelihood, Bayesian and distance methods. Results are in agreement with traditional taxonomy in providing support for the monophyly of the African Caeciliid genera Boulengerula and Schistometopum and for the Scolecomorphidae. They disagree in indicating that the Caeciliidae is paraphyletic with respect to the Scolecomorphidae. Although more data from morphology and/or molecules will be required to resolve details of the interrelationships of the African caecilian genera, the data provide strong support for at least two origins of caecilians in which the eye is reduced and covered with bone, and do not support the hypotheses that the caecilian assemblages of Africa, and of East and of West Africa are monophyletic

Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V'DJer

Motivation: B-cell receptor (BCR) repertoire profiling is an important tool for understanding the biology of diverse immunologic processes. Current methods for analyzing adaptive immune receptor repertoires depend upon PCR amplification of VDJ rearrangements followed by long read amplicon sequencing spanning the VDJ junctions. While this approach has proven to be effective, it is frequently not feasible due to cost or limited sample material. Additionally, there are many existing datasets where short-read RNA sequencing data are available but PCR amplified BCR data are not. Results: We present here V'DJer, an assembly-based method that reconstructs adaptive immune receptor repertoires from short-read RNA sequencing data. This method captures expressed BCR loci from a standard RNA-seq assay. We applied this method to 473 Melanoma samples from The Cancer Genome Atlas and demonstrate V'DJer's ability to accurately reconstruct BCR repertoires from short read mRNA-seq data

The genetic hallmarks of dog breed development reveal shared patterns of historical human-dog interactions

Each Approximately 15,000 years ago, the wild grey wolf gave rise to the first domestic dogs. Multiple domestication events likely took place throughout modern day Eurasia, though the precise times and locations are a hotly debated topic among researchers. Distinct populations of dogs, varying in physical appearance and behavior, developed to reflect the needs or desires of the human cultures in which they were formed. Rich in history, Italy is home to at least 24 unique dog breeds. Genetic analysis of these breeds, in relation to global dog breeds, has highlighted key technological advancements and movements of the region\u2019s people. We have analyzed DNA from 1,609 dogs, representing 182 breeds, and 16 wild canids, on a panel of 142,840 markers genomewide. Twenty-four of these breeds are native to Italy, with 3 represented by both Italian and American populations. Through analysis of phylogeny and identity-by-descent haplotype sharing, patterns of breed formation have emerged that parallel the developmental progression of humans. Selection for common physical and behavioral phenotypes in hunting sighthounds, without evidence of recent shared genetic history, reveals shared human needs and biologically ideal forms. Identification of breed relationships to the isolated Fonni\u2019s Dog of Sardinia exposes geographic regions of development and tracks shared migration with human cultures. Finally, molecular evidence of historic agricultural practices is observed in the shared genetics of livestock guardian breeds

A Monolayer of Primary Colonic Epithelium Generated on a Scaffold with a Gradient of Stiffness for Drug Transport Studies

Animal models are frequently used for in vitro physiologic and drug transport studies of the colon, but there exists significant pressure to improve assay throughput as well as to achieve tighter control of experimental variables than can be achieved with animals. Thus, development of a primary in vitro colonic epithelium cultured as high resistance with transport protein expression and functional behavior similar to that of a native colonic would be of enormous value for pharmaceutical research. A collagen scaffold, in which the degree of collagen cross-linking was present as a gradient, was developed to support the proliferation of primary colonic cells. The gradient of cross-linking created a gradient in stiffness across the scaffold, enabling the scaffold to resist deformation by cells. mRNA expression and quantitative proteomic mass spectrometry of cells growing on these surfaces as a monolayer suggested that the transporters present were similar to those in vivo. Confluent monolayers acted as a barrier to small molecules so that drug transport studies were readily performed. Transport function was evaluated using atenolol (a substrate for passive paracellular transport), propranolol (a substrate for passive transcellular transport), rhodamine 123 (Rh123, a substrate for P-glycoprotein), and riboflavin (a substrate for solute carrier transporters). Atenolol was poorly transported with an apparent permeability (Papp) of < 5 × 10-7 cm s-1, while propranolol demonstrated a Papp of 9.69 × 10-6 cm s-1. Rh123 was transported in a luminal direction (Papp,efflux/Papp,influx = 7) and was blocked by verapamil, a known inhibitor of P-glycoprotein. Riboflavin was transported in a basal direction, and saturation of the transporter was observed at high riboflavin concentrations as occurs in vivo. It is anticipated that this platform of primary colonic epithelium will find utility in drug development and physiological studies, since the tissue possesses high integrity and active transporters and metabolism similar to that in vivo

Decoherence of molecular wave packets in an anharmonic potential

The time evolution of anharmonic molecular wave packets is investigated under the influence of the environment consisting of harmonic oscillators. These oscillators represent photon or phonon modes and assumed to be in thermal equilibrium. Our model explicitly incorporates the fact that in the case of a nonequidistant spectrum the rates of the environment induced transitions are different for each transition. The nonunitary time evolution is visualized by the aid of the Wigner function related to the vibrational state of the molecule. The time scale of decoherence is much shorter than that of dissipation, and gives rise to states which are mixtures of localized states along the phase space orbit of the corresponding classical particle. This behavior is to a large extent independent of the coupling strength, the temperature of the environment and also of the initial state.Comment: 7 pages, 4 figure

Mutual Events in the Cold Classical Transneptunian Binary System Sila and Nunam

Hubble Space Telescope observations between 2001 and 2010 resolved the binary components of the Cold Classical transneptunian object (79360) Sila-Nunam (provisionally designated 1997 CS29). From these observations we have determined the circular, retrograde mutual orbit of Nunam relative to Sila with a period of 12.50995 \pm 0.00036 days and a semimajor axis of 2777 \pm 19 km. A multi-year season of mutual events, in which the two near-equal brightness bodies alternate in passing in front of one another as seen from Earth, is in progress right now, and on 2011 Feb. 1 UT, one such event was observed from two different telescopes. The mutual event season offers a rich opportunity to learn much more about this barely-resolvable binary system, potentially including component sizes, colors, shapes, and albedo patterns. The low eccentricity of the orbit and a photometric lightcurve that appears to coincide with the orbital period are consistent with a system that is tidally locked and synchronized, like the Pluto-Charon system. The orbital period and semimajor axis imply a system mass of (10.84 \pm 0.22) \times 10^18 kg, which can be combined with a size estimate based on Spitzer and Herschel thermal infrared observations to infer an average bulk density of 0.72 +0.37 -0.23 g cm^-3, comparable to the very low bulk densities estimated for small transneptunian binaries of other dynamical classes.Comment: In press in Icaru

A latent class analysis of risk factors for acquiring HIV among men who have sex with men: implications for implementing pre-exposure prophylaxis programs

Current Centers for Disease Control and Prevention (CDC) guidelines for prescribing pre-exposure prophylaxis (PrEP) to prevent HIV transmission are broad. In order to better characterize groups who may benefit most from PrEP, we reviewed demographics, behaviors, and clinical outcomes for individuals presenting to a publicly-funded sexually transmitted diseases (STD) clinic in Providence, Rhode Island, from 2012 to 2014. Latent class analysis (LCA) was used to identify subgroups of men who have sex with men (MSM) at highest risk for contracting HIV. A total of 1723 individuals presented for testing (75% male; 31% MSM). MSM were more likely to test HIV positive than heterosexual men or women. Among 538 MSM, we identified four latent classes. Class 1 had the highest rates of incarceration (33%), forced sex (24%), but had no HIV infections. Class 2 had <5 anal sex partners in the previous 12 months, the lowest rates of drug/alcohol use during sex and lower HIV prevalence (3%). Class 3 had the highest prevalence of HIV (7%) and other STDs (16%), > 10 anal sex partners in the previous 12 months (69%), anonymous partners (100%), drug/alcohol use during sex (76%), and prior STDs (40%). Class 4 had similar characteristics and HIV prevalence as Class 2. In this population, MSM who may benefit most from PrEP include those who have >10 sexual partners per year, anonymous partners, drug/alcohol use during sex and prior STDs. LCA is a useful tool for identifying clusters of characteristics that may place individuals at higher risk for HIV infection and who may benefit most from PrEP in clinical practice

Studies of modern Italian dog populations reveal multiple patterns for domestic breed evolution

Through thousands of years of breeding and strong human selection, the dog (Canis lupus familiaris) exists today within hundreds of closed populations throughout the world, each with defined phenotypes. A singular geographic region with broad diversity in dog breeds presents an interesting opportunity to observe potential mechanisms of breed formation. Italy claims 14 internationally recognized dog breeds, with numerous additional local varieties. To determine the relationship among Italian dog populations, we integrated genetic data from 263 dogs representing 23 closed dog populations from Italy, seven Apennine gray wolves, and an established dataset of 161 globally recognized dog breeds, applying multiple genetic methods to characterize the modes by which breeds are formed within a single geographic region. Our consideration of each of five genetic analyses reveals a series of development events that mirror historical modes of breed formation, but with variations unique to the codevelopment of early dog and human populations. Using 142,840 genome-wide SNPs and a dataset of 1,609 canines, representing 182 breeds and 16 wild canids, we identified breed development routes for the Italian breeds that included divergence from common populations for a specific purpose, admixture of regional stock with that from other regions, and isolated selection of local stock with specific attributes

Particle interactions with single or multiple 3D solar reconnecting current sheets

The acceleration of charged particles (electrons and protons) in flaring solar active regions is analyzed by numerical experiments. The acceleration is modelled as a stochastic process taking place by the interaction of the particles with local magnetic reconnection sites via multiple steps. Two types of local reconnecting topologies are studied: the Harris-type and the X-point. A formula for the maximum kinetic energy gain in a Harris-type current sheet, found in a previous work of ours, fits well the numerical data for a single step of the process. A generalization is then given approximating the kinetic energy gain through an X-point. In the case of the multiple step process, in both topologies the particles' kinetic energy distribution is found to acquire a practically invariant form after a small number of steps. This tendency is interpreted theoretically. Other characteristics of the acceleration process are given, such as the mean acceleration time and the pitch angle distributions of the particles.Comment: 18 pages, 9 figures, Solar Physics, in pres