Irreducible Representations of Diperiodic Groups

The irreducible representations of all of the 80 diperiodic groups, being the symmetries of the systems translationally periodical in two directions, are calculated. To this end, each of these groups is factorized as the product of a generalized translational group and an axial point group. The results are presented in the form of the tables, containing the matrices of the irreducible representations of the generators of the groups. General properties and some physical applications (degeneracy and topology of the energy bands, selection rules, etc.) are discussed.Comment: 30 pages, 5 figures, 28 tables, 18 refs, LaTex2.0

HIV-Specific Probabilistic Models of Protein Evolution

Comparative sequence analyses, including such fundamental bioinformatics techniques as similarity searching, sequence alignment and phylogenetic inference, have become a mainstay for researchers studying type 1 Human Immunodeficiency Virus (HIV-1) genome structure and evolution. Implicit in comparative analyses is an underlying model of evolution, and the chosen model can significantly affect the results. In general, evolutionary models describe the probabilities of replacing one amino acid character with another over a period of time. Most widely used evolutionary models for protein sequences have been derived from curated alignments of hundreds of proteins, usually based on mammalian genomes. It is unclear to what extent these empirical models are generalizable to a very different organism, such as HIV-1–the most extensively sequenced organism in existence. We developed a maximum likelihood model fitting procedure to a collection of HIV-1 alignments sampled from different viral genes, and inferred two empirical substitution models, suitable for describing between-and within-host evolution. Our procedure pools the information from multiple sequence alignments, and provided software implementation can be run efficiently in parallel on a computer cluster. We describe how the inferred substitution models can be used to generate scoring matrices suitable for alignment and similarity searches. Our models had a consistently superior fit relative to the best existing models and to parameter-rich data-driven models when benchmarked on independent HIV-1 alignments, demonstrating evolutionary biases in amino-acid substitution that are unique to HIV, and that are not captured by the existing models. The scoring matrices derived from the models showed a marked difference from common amino-acid scoring matrices. The use of an appropriate evolutionary model recovered a known viral transmission history, whereas a poorly chosen model introduced phylogenetic error. We argue that our model derivation procedure is immediately applicable to other organisms with extensive sequence data available, such as Hepatitis C and Influenza A viruses

Etiological Profile and Treatment Outcome of Epistaxis at a Tertiary Care Hospital in Northwestern Tanzania: A Prospective Review of 104 Cases.

Epistaxis is the commonest otolaryngological emergency affecting up to 60% of the population in their lifetime, with 6% requiring medical attention. There is paucity of published data regarding the management of epistaxis in Tanzania, especially the study area. This study was conducted to describe the etiological profile and treatment outcome of epistaxis at Bugando Medical Centre, a tertiary care hospital in Northwestern Tanzania. This was a prospective descriptive study of the cases of epistaxis managed at Bugando Medical Centre from January 2008 to December 2010. Data collected were analyzed using SPSS computer software version 15. A total of 104 patients with epistaxis were studied. Males were affected twice more than the females (2.7:1). Their mean age was 32.24 ± 12.54 years (range 4 to 82 years). The modal age group was 31-40 years. The commonest cause of epistaxis was trauma (30.8%) followed by idiopathic (26.9%) and hypertension (17.3%). Anterior nasal bleeding was noted in majority of the patients (88.7%). Non surgical measures such as observation alone (40.4%) and anterior nasal packing (38.5%) were the main intervention methods in 98.1% of cases. Surgical measures mainly intranasal tumor resection was carried out in 1.9% of cases. Arterial ligation and endovascular embolization were not performed. Complication rate was 3.8%. The overall mean of hospital stay was 7.2 ± 1.6 days (range 1 to 24 days). Five patients died giving a mortality rate of 4.8%. Trauma resulting from road traffic crush (RTC) remains the most common etiological factor for epistaxis in our setting. Most cases were successfully managed with conservative (non-surgical) treatment alone and surgical intervention with its potential complications may not be necessary in most cases and should be the last resort. Reducing the incidence of trauma from RTC will reduce the incidence of emergency epistaxis in our centre

Probing a Complex of Cytochromecand Cardiolipin by Magnetic Circular Dichroism Spectroscopy: Implications for the Initial Events in Apoptosis

Oxidation of cardiolipin (CL) by its complex with cytochrome c (cyt c) plays a crucial role in triggering apoptosis. Through a combination of magnetic circular dichroism spectroscopy and potentiometric titrations, we show that both the ferric and ferrous forms of the heme group of a CL:cyt c complex exist as multiple conformers at a physiologically relevant pH of 7.4. For the ferric state, these conformers are His/Lys- and His/OH–-ligated. The ferrous state is predominantly high-spin and, most likely, His/–. Interconversion of the ferric and ferrous conformers is described by a single midpoint potential of -80 ± 9 mV vs SHE. These results suggest that CL oxidation in mitochondria could occur by the reaction of molecular oxygen with the ferrous CL:cyt c complex in addition to the well-described reaction of peroxides with the ferric form

Impact flux on Jupiter: From superbolides to large-scale collisions

Context. Regular observations of Jupiter by a large number of amateur astronomers have resulted in the serendipitous discovery of short bright flashes in its atmosphere, which have been proposed as being caused by impacts of small objects. Three flashes were detected: one on June 3, 2010, one on August 20, 2010, and one on September 10, 2012. Aims. We show that the flashes are caused by impacting objects that we characterize in terms of their size, and we study the flux of small impacts on Jupiter. Methods. We measured the light curves of these atmospheric airbursts to extract their luminous energy and computed the masses and sizes of the objects. We ran simulations of impacts and compared them with the light curves. We analyzed the statistical significance of these events in the large pool of Jupiter observations. Results. All three objects are in the 5-20 m size category depending on their density, and they released energy comparable to the recent Chelyabinsk airburst. Model simulations approximately agree with the interpretation of the limited observations. Biases in observations of Jupiter suggest a rate of 12-60 similar impacts per year and we provide software tools for amateurs to examine the faint signature of impacts in their data to increase the number of detected collisions. Conclusions. The impact rate agrees with dynamical models of comets. More massive objects (a few 100 m) should impact with Jupiter every few years leaving atmospheric dark debris features that could be detectable about once per decade

Evolution of Parallel Spindles Like genes in plants and highlight of unique domain architecture#

<p>Abstract</p> <p>Background</p> <p>Polyploidy has long been recognized as playing an important role in plant evolution. In flowering plants, the major route of polyploidization is suggested to be sexual through gametes with somatic chromosome number (2<it>n</it>). <it>Parallel Spindle1 </it>gene in <it>Arabidopsis thaliana </it>(<it>AtPS1</it>) was recently demonstrated to control spindle orientation in the 2nd division of meiosis and, when mutated, to induce 2<it>n </it>pollen. Interestingly, <it>AtPS1 </it>encodes a protein with a FHA domain and PINc domain putatively involved in RNA decay (i.e. Nonsense Mediated mRNA Decay). In potato, 2<it>n </it>pollen depending on parallel spindles was described long time ago but the responsible gene has never been isolated. The knowledge derived from <it>AtPS1 </it>as well as the availability of genome sequences makes it possible to isolate potato <it>PSLike </it>(<it>PSL</it>) and to highlight the evolution of <it>PSL </it>family in plants.</p> <p>Results</p> <p>Our work leading to the first characterization of <it>PSLs </it>in potato showed a greater <it>PSL </it>complexity in this species respect to <it>Arabidopsis thaliana</it>. Indeed, a genomic <it>PSL </it>locus and seven cDNAs affected by alternative splicing have been cloned. In addition, the occurrence of at least two other <it>PSL </it>loci in potato was suggested by the sequence comparison of alternatively spliced transcripts.</p> <p>Phylogenetic analysis on 20 <it>Viridaeplantae </it>showed the wide distribution of <it>PSLs </it>throughout the species and the occurrence of multiple copies only in potato and soybean.</p> <p>The analysis of PSL^FHAand PSL^PINcdomains evidenced that, in terms of secondary structure, a major degree of variability occurred in PINc domain respect to FHA. In terms of specific active sites, both domains showed diversification among plant species that could be related to a functional diversification among <it>PSL </it>genes. In addition, some specific active sites were strongly conserved among plants as supported by sequence alignment and by evidence of negative selection evaluated as difference between non-synonymous and synonymous mutations.</p> <p>Conclusions</p> <p>In this study, we highlight the existence of PSLs throughout <it>Viridaeplantae</it>, from mosses to higher plants. We provide evidence that <it>PSLs </it>occur mostly as singleton in the analyzed genomes except in soybean and potato both characterized by a recent whole genome duplication event. In potato, we suggest the candidate <it>PSL </it>gene having a role in 2<it>n </it>pollen that should be deeply investigated.</p> <p>We provide useful insight into evolutionary conservation of FHA and PINc domains throughout plant PSLs which suggest a fundamental role of these domains for PSL function.</p

Tridimensional model structure and patterns of molecular evolution of Pepino mosaic virus TGBp3 protein

<p>Abstract</p> <p>Background</p> <p><it>Pepino mosaic virus </it>(PepMV) is considered one of the most dangerous pathogens infecting tomatoes worldwide. The virus is highly diverse and four distinct genotypes, as well as inter-strain recombinants, have already been described. The isolates display a wide range on symptoms on infected plant species, ranging from mild mosaic to severe necrosis. However, little is known about the mechanisms and pattern of PepMV molecular evolution and about the role of individual proteins in host-pathogen interactions.</p> <p>Methods</p> <p>The nucleotide sequences of the triple gene block 3 (TGB3) from PepMV isolates varying in symptomatology and geographic origin have been analyzed. The modes and patterns of molecular evolution of the TGBp3 protein were investigated by evaluating the selective constraints to which particular amino acid residues have been subjected during the course of diversification. The tridimensional structure of TGBp3 protein has been modeled <it>de novo </it>using the Rosetta algorithm. The correlation between symptoms development and location of specific amino acids residues was analyzed.</p> <p>Results</p> <p>The results have shown that TGBp3 has been evolving mainly under the action of purifying selection operating on several amino acid sites, thus highlighting its functional role during PepMV infection. Interestingly, amino acid 67, which has been previously shown to be a necrosis determinant, was found to be under positive selection.</p> <p>Conclusions</p> <p>Identification of diverse selection events in TGB3p3 will help unraveling its biological functions and is essential to an understanding of the evolutionary constraints exerted on the <it>Potexvirus </it>genome. The estimated tridimensional structure of TGBp3 will serve as a platform for further sequence, structural and function analysis and will stimulate new experimental advances.</p

Evolution and Survival on Eutherian Sex Chromosomes

Since the two eutherian sex chromosomes diverged from an ancestral autosomal pair, the X has remained relatively gene-rich, while the Y has lost most of its genes through the accumulation of deleterious mutations in nonrecombining regions. Presently, it is unclear what is distinctive about genes that remain on the Y chromosome, when the sex chromosomes acquired their unique evolutionary rates, and whether X-Y gene divergence paralleled that of paralogs located on autosomes. To tackle these questions, here we juxtaposed the evolution of X and Y homologous genes (gametologs) in eutherian mammals with their autosomal orthologs in marsupial and monotreme mammals. We discovered that genes on the X and Y acquired distinct evolutionary rates immediately following the suppression of recombination between the two sex chromosomes. The Y-linked genes evolved at higher rates, while the X-linked genes maintained the lower evolutionary rates of the ancestral autosomal genes. These distinct rates have been maintained throughout the evolution of X and Y. Specifically, in humans, most X gametologs and, curiously, also most Y gametologs evolved under stronger purifying selection than similarly aged autosomal paralogs. Finally, after evaluating the current experimental data from the literature, we concluded that unique mRNA/protein expression patterns and functions acquired by Y (versus X) gametologs likely contributed to their retention. Our results also suggest that either the boundary between sex chromosome strata 3 and 4 should be shifted or that stratum 3 should be divided into two strata

Telomeric expression sites are highly conserved in trypanosoma brucei

Subtelomeric regions are often under-represented in genome sequences of eukaryotes. One of the best known examples of the use of telomere proximity for adaptive purposes are the bloodstream expression sites (BESs) of the African trypanosome Trypanosoma brucei. To enhance our understanding of BES structure and function in host adaptation and immune evasion, the BES repertoire from the Lister 427 strain of T. brucei were independently tagged and sequenced. BESs are polymorphic in size and structure but reveal a surprisingly conserved architecture in the context of extensive recombination. Very small BESs do exist and many functioning BESs do not contain the full complement of expression site associated genes (ESAGs). The consequences of duplicated or missing ESAGs, including ESAG9, a newly named ESAG12, and additional variant surface glycoprotein genes (VSGs) were evaluated by functional assays after BESs were tagged with a drug-resistance gene. Phylogenetic analysis of constituent ESAG families suggests that BESs are sequence mosaics and that extensive recombination has shaped the evolution of the BES repertoire. This work opens important perspectives in understanding the molecular mechanisms of antigenic variation, a widely used strategy for immune evasion in pathogens, and telomere biology