Genomic organization of the mouse T-cell receptor β-chain gene family

We have combined three different methods, deletion mapping of T-cell lines, field-inversion gel electrophoresis, and the restriction mapping of a cosmid clone, to construct a physical map of the murine T-cell receptor β-chain gene family. We have mapped 19 variable (Vβ) gene segments and the two clusters of diversity (Dβ) and joining (Jβ) gene segments and constant (Cβ) genes. These members of the β-chain gene family span ~450 kilobases of DNA, excluding one potential gap in the DNA fragment alignments

Junctions between i-motif tetramers in supramolecular structures

The symmetry of i-motif tetramers gives to cytidine-rich oligonucleotides the capacity to associate into supramolecular structures (sms). In order to determine how the tetramers are linked together in such structures, we have measured by gel filtration chromatography and NMR the formation and dissociation kinetics of sms built by oligonucleotides containing two short C stretches separated by a non-cytidine-base. We show that a stretch of only two cytidines either at the 3′- or 5′-end is long enough to link the tetramers into sms. The analysis of the properties of sms formed by oligonucleotides differing by the length of the oligo-C stretches, the sequence orientation and the nature of the non-C base provides a model of the junction connecting the tetramers in sms

Upper Limb Terminal Device with Force and Position Feedback

ME450 Capstone Design and Manufacturing Experience: Winter 2010Current myoelectric prostheses lack the ability to provide sensory feedback, forcing amputees to rely solely on visual feedback. We have developed a prosthetic terminal device capable of relaying grip force back to the touch (haptic) receptors on the amputee’s residual limb. Our device is elemental to an experimental apparatus to test hypotheses in the value of haptic feedback. Our terminal device interfaces with the amputee’s residual limb and will be activated by electromyographic (EMG) signals. The prototype will be used in experimentation to test an amputee’s ability to distinguish object stiffness using haptic cues, in the absence of visual and auditory cues.http://deepblue.lib.umich.edu/bitstream/2027.42/109375/1/me450w10project18_report.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/109375/2/me450w10project18_photo.jp

EST analysis of gene expression in early cleavage-stage sea urchin embryos

A set of 956 expressed sequence tags derived from 7-hour (mid-cleavage) sea urchin embryos was analyzed to assess biosynthetic functions and to illuminate the structure of the message population at this stage. About a quarter of the expressed sequence tags represented repetitive sequence transcripts typical of early embryos, or ribosomal and mitochondrial RNAs, while a majority of the remainder contained significant open reading frames. A total of 232 sequences, including 153 different proteins, produced significant matches when compared against GenBank. The majority of these identified sequences represented ‘housekeeping’ proteins, i.e., cytoskeletal proteins, metabolic enzymes, transporters and proteins involved in cell division. The most interesting finds were components of signaling systems and transcription factors not previously reported in early sea urchin embryos, including components of Notch and TGF signal transduction pathways. As expected from earlier kinetic analyses of the embryo mRNA populations, no very prevalent protein-coding species were encountered; the most highly represented such sequences were cDNAs encoding cyclins A and B. The frequency of occurrence of all sequences within the database was used to construct a sequence prevalence distribution. The result, confirming earlier mRNA population analyses, indicated that the poly(A) RNA of the early embryo consists mainly of a very complex set of low-copy-number transcripts

Building Representative Composite Items

International audienceThe problem of summarizing a large collection of homogeneous items has been addressed extensively in particular in the case of geo-tagged datasets (e.g. Flickr photos and tags). In our work, we study the problem of summarizing large collections of heterogeneous items. For example, a user planning to spend extended periods of time in a given city would be interested in seeing a map of that city with item summaries in different geographic areas, each containing a theater, a gym, a bakery, a few restaurants and a subway station. We propose to solve that problem by building representative Composite Items (CIs). To the best of our knowledge, this is the first work that addresses the problem of finding representative CIs for heterogeneous items. Our problem naturally arises when summarizing geo-tagged datasets but also in other datasets such as movie or music summarization. We formalize building representative CIs as an optimization problem and propose KFC, an extended fuzzy clustering algorithm to solve it. We show that KFC converges and run extensive experiments on a variety of real datasets that validate its effectiveness

Phylogeography, Risk Factors and Genetic History of Hepatitis C Virus in Gabon, Central Africa

BACKGROUND: The epidemiological and molecular characteristics of hepatitis C virus (HCV) infection in the general population have been poorly investigated in Africa. The aim of this study was to determine the prevalence, genotype distribution and epidemic history of HCV in the Gabonese general population. METHODS/PRINCIPAL FINDINGS: A total of 4042 sera collected from adults in 220 villages in all nine administrative areas of the country were screened for antibodies to HCV. HCV NS5B region sequencing was performed for molecular characterization and population genetic analyses. Of 4042 tested sera, 455 (11.2%) were positive. The seroprevalence of HCV varied significantly by administrative area, with the highest rate in Ogooue-Lolo province (20.4%) and the lowest in Ogooue-Maritine province (3.7%). History of parenteral injections, past hospital admission and age over 55 years were independent risk factors for HCV infection (p<0.0001). Phylogenetic analyses showed that 91.9% of the strains were genotype 4 (HCV-4), 5.7% genotype 1 and 2.2% genotype 2. HCV-4 strains were highly heterogeneous, with more than eight subtypes; subtype 4e predominated (57.3%). Coalescence analyses indicated that subtype 4e was the oldest, with an estimated most recent common ancestor of 1702 [95% CI, 1418-1884]. The epidemic profile indicated that it spread exponentially during the first part of the 20th century, probably by iatrogenic transmission. CONCLUSIONS/SIGNIFICANCE: These results confirm the endemicity of HCV subtype 4e in Gabon and show that its spread is due to a cohort effect, with previous, possibly iatrogenic events. More extensive epidemiological studies are needed to better characterize the route of transmission and the dissemination of HCV in Gabon

Kinetic of biobased bitumen synthesis from microalgae biomass by hydrothermal liquefaction

The current worldwide consumption of bitumen is about 100 million tons. A remarkable combination of properties (adhesion, impermeability to water, specific thermo-rheological behavior) makes it a key material in road construction. Today’s bitumen is mostly obtained from petroleum refining, so bioabased alternatives have to be explored for the future. The ALGOROUTE project funded by the French National Agency for Research (ANR) focuses on the use of hydrothermal liquefaction (HTL) process for the production of bitumen mimicking binders from microalgae biomass. HTL applied to microalgae is inspired by the geological process of petroleum formation, but on a very short time scale: For conditions around 260 °C / 50 bar, bitumen like products have been obtained by our consortium for residence times of about 1 hour [1] [2]. Beside temperature and pressure, the key parameters are the reaction time, algae/water ratio and loading level of reactor. Please click Additional Files below to see the full abstract

Bat flies (Diptera: Nycteribiidae and Streblidae) infesting cave-dwelling bats in Gabon: Diversity, dynamics and potential role in Polychromophilus melanipherus transmission

Background Evidence of haemosporidian infections in bats and bat flies has motivated a growing interest in characterizing their transmission cycles. In Gabon (Central Africa), many caves house massive colonies of bats that are known hosts of Polychromophilus Dionisi parasites, presumably transmitted by blood-sucking bat flies. However, the role of bat flies in bat malaria transmission remains under-documented. Methods An entomological survey was carried out in four caves in Gabon to investigate bat fly diversity, infestation rates and host preferences and to determine their role in Polychromophilus parasite transmission. Bat flies were sampled for 2–4 consecutive nights each month from February to April 2011 (Faucon and Zadie caves) and from May 2012 to April 2013 (Kessipoughou and Djibilong caves). Bat flies isolated from the fur of each captured bat were morphologically identified and screened for infection by haemosporidian parasites using primers targeting the mitochondrial cytochrome b gene. Results Among the 1,154 bats captured and identified as Miniopterus inflatus Thomas (n = 354), Hipposideros caffer Sundevall complex (n = 285), Hipposideros gigas Wagner (n = 317), Rousettus aegyptiacus Geoffroy (n = 157, and Coleura afra Peters (n = 41), 439 (38.0 %) were infested by bat flies. The 1,063 bat flies recovered from bats belonged to five taxa: Nycteribia schmidlii scotti Falcoz, Eucampsipoda africana Theodor, Penicillidia fulvida Bigot, Brachytarsina allaudi Falcoz and Raymondia huberi Frauenfeld group. The mean infestation rate varied significantly according to the bat species (ANOVA, F (4,75) = 13.15, P < 0.001) and a strong association effect between bat fly species and host bat species was observed. Polychromophilus melanipherus Dionisi was mainly detected in N. s. scotti and P. fulvida and less frequently in E. africana, R. huberi group and B. allaudi bat flies. These results suggest that N. s. scotti and P. fulvida could potentially be involved in P. melanipherus transmission among cave-dwelling bats. Sequence analysis revealed eight haplotypes of P. melanipherus. Conclusions This work represents the first documented record of the cave-dwelling bat fly fauna in Gabon and significantly contributes to our understanding of bat fly host-feeding behavior and their respective roles in Polychromophilus transmission. (Résumé d'auteur