Sequence

Acinetobacter baumannii is an opportunistic pathogen that presents a serious clinical challenge due to its increasing resistance to all available antibiotics. Phage therapy has been introduced recently to treat antibiotic-incurable A. baumannii infections. In search for new A. baumannii specific bacteriophages, 20 clinical A. baumannii strains were used in two pools in an attempt to enrich phages from sewage. The enrichment resulted in induction of resident prophage(s) and three temperate bacteriophages, named vB_AbaS_fEg-Aba01, vB_AbaS_fLi-Aba02 and vB_AbaS_fLi-Aba03, all able to infect only one strain (#6597) of the 20 clinical strains, were isolated. Morphological characteristics obtained by transmission electron microscopy together with the genomic information revealed that the phages belong to the family Siphoviridae. The ca. 35 kb genomic sequences of the phages were >99% identical to each other. The linear ds DNA genomes of the phages contained 10 nt cohesive end termini, ...

Background: DNA replication and transcription are dynamic processes regulating plant development that are dependent on the chromatin accessibility. Proteins belonging to the Agenet/Tudor domain family are known as histone modification "readers" and classified as chromatin remodeling proteins. Histone modifications and chromatin remodeling have profound effects on gene expression as well as on DNA replication, but how these processes are integrated has not been completely elucidated. It is clear that members of the Agenet/Tudor family are important regulators of development playing roles not well known in plants. Methods: Bioinformatics and phylogenetic analyses of the Agenet/Tudor Family domain in the plant kingdom were carried out with sequences from available complete genomes databases. 3D structure predictions of Agenet/ Tudor domains were calculated by I-TASSER server. Protein interactions were tested in two-hybrid, GST pulldown, semi-in vivo pulldown and Tandem Affinity Purification assays. Gene function was studied in a T-DNA insertion GABI-line. Results: In the present work we analyzed the family of Agenet/Tudor domain proteins in the plant kingdom and we mapped the organization of this family throughout plant evolution. Furthermore, we characterized a member from Arabidopsis thaliana named AIP1 that harbors Agenet/Tudor and DUF724 domains. AIP1 interacts with ABAP1, a plant regulator of DNA replication licensing and gene transcription, with a plant histone modification "reader" (LHP1) and with non modified histones. AIP1 is expressed in reproductive tissues and its down-regulation delays flower development timing. Also, expression of ABAP1 and LHP1 target genes were repressed in flower buds of plants with reduced levels of AIP1. Conclusions: AIP1 is a novel Agenet/Tudor domain protein in plants that could act as a link between DNA replication, transcription and chromatin remodeling during flower development.

Eulophidae is a hyper-diverse family of chalcidoid wasps with 324 genera, about 5300 described species and probably thousands of others to be described. Until now, the absence of unequivocal morphological apomorphies and the low resolution provided by the handful of Sanger sequenced genes have hampered the reconstruction of phylogenetic relationships within the family. Here, we used ultra-conserved elements and their flanking regions to resolve relationships among 84 species of eulophids included in 63 genera representing all subfamilies and most tribes, plus 15 outgroups. Our analyses recover all traditional Eulophidae subfamilies and tribes with high support and globally agree with the traditional classification of the family. Our results confirm that Eulophinae + Tetrastichinae is the sister group of (Opheliminae + Entiinae) + Entedoninae. At the generic level, our analyses provide high support for intergeneric relationships for which morphology and Sanger markers previously failed to provide resolution. Our results also confirm that Trisecodes does not group with Eulophidae and may not belong to this family; however, its correct classification still awaits a large-scale phylogenomic hypothesis for Chalcidoidea. This work opens new avenues towards a better understanding of the evolutionary history, biogeography and evolution of host-parasitoid associations in this hyper-diverse family of chalcidoid wasps.

Este produto educacional é resultado da dissertação de Dionei Cardozo, intitulada Do átomo de carbono às grandes populações: o ensino de funções exponenciais sob a perspectiva da Resolução de Problemas, orientada por Janaína Poffo Possamai, pertencente a linha de

We compared the genomes of nine dog rabies virus isolates using two molecular methods. The viruses used in the comparison included three Ethiopian rabies strains from carrier dogs, a street strain from a rabid dog from the same geographic area, two saliva isolates made from an experimentally infected carrier dog, the virus isolated from the tonsil of this carrier dog at necropsy, and two laboratory strains. We produced overlapping polymerase chain reaction (PCR) segments spanning 97% of the genome. Restriction analysis of these PCR products with Avail, BclI, and BamHI detected 39 variable sites representing 668 nucleotides (nt) or 5.5% of the genome. We also compared the DNA and the deduced peptide sequences of a 200-nt segment of the 3' end of the rabies nucleoprotein gene. Previous work with these Ethiopian carrier viruses and the endemic street strain had failed to show any differences among them. Both restriction mapping and sequence analysis of 200 nt of the nucleoprotein gene allowed us to individually identify these isolates. Phylogenetic analyses of these data sets showed only the two saliva isolates of the experimentally infected carrier dog to be identical. Each of the viruses in this study, including the one isolated from the tonsil of the experimentally infected carrier dog, could be distinguished by these techniques.

We present detailed modeling of the disk around the TW Hydrae Association (TWA) brown dwarf 2MASSW J1207334-393254 (2M1207), using Spitzer observations from 3.6 to 24 µm. The spectral energy distribution (SED) does not show a high amount of flaring. We have obtained a good fit using a flat disk of mass between 10 −4 and 10 −6 M ⊙ ,Ṁ 10 −11 M ⊙ yr −1 and a large inclination angle between 60 • and 70 •. We have used three different grain models to fit the 10 µm Si emission feature, and have found the results to be consistent with ISM-like dust. In comparison with other TWA members, this suggests lesser dust processing for 2M1207 which could be explained by mechanisms such as aggregate fragmentation and/or turbulent mixing. We have found a good fit using an inner disk radius equal to the dust sublimation radius, which indicates the absence of an inner hole in the disk. This suggests the presence of a small K-L ′ excess, similar to the observed K-[3.6] excess.

We present Spitzer/IRAC observations of the L5 dwarf, 2MASSI J1315309-264951 (2M1315). This ultracool dwarf is known to display strong emission in the Hα line. The SED for this object does not show any IR excess, that would indicate the presence of an accretion disk. Although the IRAC colors for 2M1315 are consistent with other L dwarfs, they seem to be redder by ∼0.1 mag compared to the other L5 dwarfs, and more like the late-type L dwarfs. The existing six epochs of spectroscopy suggest that the emission in Hα is not persistent, but shows long-term variability between a flare value of ∼100Å and a quiescent value of ∼25Å. Chromospheric activity seems to be the most likely cause, which is also indicated by the detection of Na I D lines in emission (Fuhrmeister et al.). We have measured a proper motion of 0.79 ′′ ± 0.06 ′′ /yr, that corresponds to a tangential velocity of ∼81 km/s, at a distance of ∼22 pc. The high V tan for this object suggests an old age. Evolutionary models indicate lower limits of 3.3 Gyr (Chabrier et al.) or 1.4 Gyr (Burrows et al.) for this magnetically active L dwarf to be a stable hydrogen-burning star. There seem to be no observational differences between this old L dwarf that has Hα emission and the other field L dwarfs without it.

Agent based modelling is nowadays widely used in transport and the social science. Forecasting population evolution and analysing the impact of hypothetical policies are often the main goal of these developments. Such models are based on sub-models defining the interactions of agents either with other agents or with their environment. Sometimes, several models represent phenomena arising at the same time in the real life. Hence, the question of the order in which these sub-models need to be applied is very relevant for simulation outcomes. This paper aims to analyse and quantify the impact of the change in the order of sub-models on an evolving population modelled using TransMob. This software simulates the evolution of the population of a metropolitan area in South East of Sydney (Australia). It includes five principal models: ageing, death, birth, marriage and divorce. Each possible order implies slightly different results mainly driven by how agents' ageing is defined with respect to death. Furthermore, we present a calendar-based approach for the ordering that decreases the variability of final populations. Finally, guidelines are provided proposing general advices and recommendations for researchers designing discrete time agent-based models.

Nowadays, a wide range of microsimulations are performed thanks to agent based simulations. This frame-work allows to model the interactions between agents and environment in a flexible way. Such models should be initialised with a given set of agents representing the initial population, and their interactions rules should be set. Very often the initial population of agents is obtained using a synthetic population generator. TransMob is an agent-based model that aims to simulate transport and land use interdependencies for urban planning. TransMob contains two types of modules responsible for: the dynamics of the social structure within the population (ageing, divorces,...); and the travel behaviour of the individuals (assigning diaries, ...). In the current version of TransMob, the processes happening in the agents everyday life are modelled and performed in a specific order: first ageing, then death, divorce, marriage and finally giving birth. This work focus on the impact of the ...

Background Genome-wide repeat sequences, such as LINEs, SINEs and LTRs share a considerable part of the mammalian nuclear genomes. These repeat elements seem to be important for multiple functions including the regulation of transcription initiation, alternative splicing and DNA methylation. But it is not possible to study all repeats and, hence, it would help to shortlist before exploring their potential functional significance via experimental studies and/or detailed in silico analyses. Result We developed the 'Genomic Repeat Element Analyzer for Mammals' (GREAM) for analysis, screening and selection of potentially important mammalian genomic repeats. This web-server offers many novel utilities. For example, this is the only tool that can reveal a categorized list of specific types of transposons, retro-transposons and other genome-wide repetitive elements that are statistically over-/under-represented in regions around a set of genes, such as those expressed differentially in a disease condition. The output displays the position and frequency of identified elements within the specified regions. In addition, GREAM offers two other types of analyses of genomic repeat sequences: a) enrichment within chromosomal region(s) of interest, and b) comparative distribution across the neighborhood of orthologous genes. GREAM successfully short-listed a repeat element (MER20) known to contain functional motifs. In other case studies, we could use GREAM to shortlist repetitive elements in the azoospermia factor a (AZFa) region of the human Y chromosome

We combined new sequence data for more than 300 muroid rodent species with our previously published sequences for up to five nuclear and one mitochondrial genes to generate the most widely and densely sampled hypothesis of evolutionary relationships across Muroidea. An exhaustive screening procedure for publically available sequences was implemented to avoid the propagation of taxonomic errors that are common to supermatrix studies. The combined data set of carefully screened sequences derived from all available sequences on GenBank with our new data resulted in a robust maximum likelihood phylogeny for 900 of the approximately 1,620 muroids. Several regions that were equivocally resolved in previous studies are now more decisively resolved, and we estimated a chronogram using 28 fossil calibrations for the most integrated age and topological estimates to date. The results were used to update muroid classification and highlight questions needing additional data. We also compared the results of multigene supermatrix studies like this one with the principal published supertrees and concluded that the latter are unreliable for any comparative study in muroids. In addition, we explored diversification patterns as an explanation for why muroid rodents represent one of the most species-rich groups of mammals by detecting evidence for increasing net diversification rates through time across the muroid tree. We suggest the observation of increasing rates may be due to a combination of parallel increases in rate across clades and high average extinction rates. Five increased diversification-rate-shifts were inferred, suggesting that multiple, but perhaps not independent, events have led to the remarkable species diversity in the superfamily. Our results provide a phylogenetic framework for comparative studies that is not highly dependent upon the signal from any one gene.

Significance Snakes of the genus Thermophis are endemic to the Tibetan plateau and occur at elevations over 3,500 m and present an opportunity to study the genetics mechanisms of adaptation to high-elevation conditions in ectotherms. Here, we provide a de novo genome of the Tibetan hot-spring snake, Thermophis baileyi , and conduct a series of comparisons with other reptiles. We identify genes under positive selection and test properties of allelic variants of proteins that are involved in DNA damage repair and responses to hypoxia. Functional assays reveal convergent genetic mechanisms that underlie high-elevation adaptation in both endotherms and ectotherms.

A beige-coloured, Gram-staining negative, aerobic, non-motile, moderately thermophilic, rod-shaped bacterium, CC-MHSW-1T, was isolated on Marine Agar 2216 from a water sample from a coastal hot spring on Green Island (Lutao), located off Taituang, Taiwan. 16S rRNA gene sequence analysis demonstrated that the novel strain shared <94 % sequence similarity with members of the genera Lutimaribacter, Maritimibacter and Oceanicola. Ubiquinone (Q-10) was the major respiratory quinone and C18 : 1ω7c was the predominant fatty acid. The predominant polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and unidentified phospholipids and aminolipids. The DNA G+C content of strain CC-MHSW-1T was 64.7 mol%. On the basis of 16S rRNA gene sequence analysis and the chemotaxonomic and physiological data, strain CC-MHSW-1T represents a new genus and species in the family Rhodobacteraceae for which the name Jhaorihella thermophila gen. nov., sp...

Symptoms associated with infection by Ornithogalum mosaic virus (OMV) were documented among horticulturally important Ornithogalum spp. grown in commercial greenhouses and open fields in Israel. OMV was mechanically transmitted to Chenopodium quinoa and C. amaranticolor. The virus was purified from infected C. quinaa using CsCl step gradient centrifugation. Virus yield of 18-24 mg kg-' were obtained. Antiserum produced to the purified virus was highly specific in immunoblots and immunosorbent electron microscopy. Reverse transcriptionpolymerase chain reaction (RT-PCR) utilising potyvirus-specific primers and the viral RNA resulted in the amplification of a DNA product of 1275 nucleotides. This PCR product was cloned and sequenced; it encoded an open reading frame of 333 codons and a 3' non-coding region of 275 nucleotides. Analysis of the amino acid sequences of the putative CP of the Israeli isolate of OMV showed 95% similarities to the South African isolate.

This diploma thesis presents a development of web application for variability detection in the DNA sequence called Amplicode 2018. DNA consists of four nucleotides adenine (A), cytosine (C), guanine (G) and thymine (T) which are interconnected into sequence. The phenotype level differences are related to genetic code at the genotype level. Sequences with different variations can determine particular attributes, for example height, hair colour, pigmentation of the iris, predispositions to specific diseases, etc. Web application Amplicode 2018 enables detection of sequence variations within a gene of choice using different open source tools. The entire tool and parameter selection is carried out using the user-friendly website, that can be used by users with limited knowledge of Linux operating system, commands and switches of open source tools. The end result is consistently provided in the same format, regardless the various intermediate steps. It offers the ability to analyse the q...

The concise, enantioselective total syntheses of (-)-citrinadin A and (+)-citrinadin B in a total of only 20 and 21 steps, respectively, from commercially available starting materials are described. Our strategy, which minimizes refunctionalization and protection/deprotection operations, features the highly diastereoselective, vinylogous Mannich addition of a dienolate to a chiral pyridinium salt to set the first chiral center. The absolute stereochemistry of this key center was then relayed by a sequence of substrate-controlled reactions, including a highly stereoselective epoxidation/ring opening sequence and an oxidative rearrangement of an indole to furnish a spirooxindole to establish the remaining stereocenters in the pentacyclic core of the citrinadins. An early stage intermediate in the synthesis of (-)-citrinadin A was deoxygenated to generate a dehydroxy compound that was elaborated into (+)-citrinadin B by a sequence of reaction identical to those used to prepare (-)-citr...

The present work involves the study of the Asmari Formation from the viewpoint of the stratigraphy, microfacies, and depositional environment. The Khorramabad area, Zagros basin, west Iran, has been investigated for the first time. For this purpose, seventy-three samples were taken from the Shurab section. Eight microfacies have been identified in the Asmari Formation: Sandy wackestone (MF1), Peloidal Mudstone (MF2), Bioclastic milina Wackestone-Packstone (MF3), Bioclastic imperforate foraminifera Wackestone-Packstone (MF4), Coral boundstone (MF5), Bioclastic packstone-grainstone (MF6), Bioclastic imperforate foraminifera grainstone (MF7), Mudstone microfacies (MF8). Two benthic foraminiferal biozones were recognized, which are Archaias asparagus-Archaias Henson Assemblage Zone, which is restricted to Chattian, and the Eulepidina-Miogypsina Assemblage Zone, which is restricted to Aquitanian. The biostratigraphic correlation with other studies in and outside Iran, executed across the studied section, enveloping the Chattian to Aquitanian, divulges a progression in the biozone thickness, indicating a migration of the depositional center towards the northwest of the basin. The Asmari Formation is deposited from an outer ramp and open shelf lagoon and is defined as a tropical environment.

SummaryThe recent completion of the horse genome and commercial availability of an equine SNP genotyping array has facilitated the mapping of disease genes. We report putative localization of the gene responsible for dwarfism, a trait in Friesian horses that is thought to have a recessive mode of inheritance, to a 2‐ MB region of chromosome 14 using just 10 affected animals and 10 controls. We successfully genotyped 34 429 SNPs that were tested for association with dwarfism using chi‐square tests. The most significant SNP in our study, BIEC2‐239376 (P2df = 4.54 × 10−5, Prec = 7.74 × 10−6), is located close to a gene implicated in human dwarfism. Fine‐mapping and resequencing analyses did not aid in further localization of the causative variant, and replication of our findings in independent sample sets will be necessary to confirm these results.

Mortalidad por influenza y neumonía en el adulto mayor. Impacto de la vacunación anti influenza en este grupo poblacional. Matanzas 2001-2008 Mortality for influenza and pneumonia in elder people. Impact of the anti-influenza vaccination in this population group. Matanzas 2001-2008

The present work involves the study of the Asmari Formation from the viewpoint of the stratigraphy, microfacies, and depositional environment. The Khorramabad area, Zagros basin, west Iran, has been investigated for the first time. For this purpose, seventy-three samples were taken from the Shurab section. Eight microfacies have been identified in the Asmari Formation: Sandy wackestone (MF1), Peloidal Mudstone (MF2), Bioclastic milina Wackestone-Packstone (MF3), Bioclastic imperforate foraminifera Wackestone-Packstone (MF4), Coral boundstone (MF5), Bioclastic packstone-grainstone (MF6), Bioclastic imperforate foraminifera grainstone (MF7), Mudstone microfacies (MF8). Two benthic foraminiferal biozones were recognized, which are Archaias asparagus-Archaias Henson Assemblage Zone, which is restricted to Chattian, and the Eulepidina-Miogypsina Assemblage Zone, which is restricted to Aquitanian. The biostratigraphic correlation with other studies in and outside Iran, executed across the studied section, enveloping the Chattian to Aquitanian, divulges a progression in the biozone thickness, indicating a migration of the depositional center towards the northwest of the basin. The Asmari Formation is deposited from an outer ramp and open shelf lagoon and is defined as a tropical environment.

The present work involves the study of the Asmari Formation from the viewpoint of the stratigraphy, microfacies, and depositional environment. The Khorramabad area, Zagros basin, west Iran, has been investigated for the first time. For this purpose, seventy-three samples were taken from the Shurab section. Eight microfacies have been identified in the Asmari Formation: Sandy wackestone (MF1), Peloidal Mudstone (MF2), Bioclastic milina Wackestone-Packstone (MF3), Bioclastic imperforate foraminifera Wackestone-Packstone (MF4), Coral boundstone (MF5), Bioclastic packstone-grainstone (MF6), Bioclastic imperforate foraminifera grainstone (MF7), Mudstone microfacies (MF8). Two benthic foraminiferal biozones were recognized, which are Archaias asparagus-Archaias Henson Assemblage Zone, which is restricted to Chattian, and the Eulepidina-Miogypsina Assemblage Zone, which is restricted to Aquitanian. The biostratigraphic correlation with other studies in and outside Iran, executed across the studied section, enveloping the Chattian to Aquitanian, divulges a progression in the biozone thickness, indicating a migration of the depositional center towards the northwest of the basin. The Asmari Formation is deposited from an outer ramp and open shelf lagoon and is defined as a tropical environment.

We present the results of a multidisciplinary study of the M s = 6.2, 1995, June 15, Aigion earthquake (Gulf of Corinth, Greece). In order to constrain the rupture geometry, we used all available data from seismology (local, regional and teleseismic records of the mainshock and of aftershocks), geodesy (GPS and SAR interferometry), and tectonics. Part of these data were obtained during a postseismic field study consisting of the surveying of 24 GPS points, the temporary installation of 20 digital seismometers, and a detailed field investigation for surface fault break. The Aigion fault was the only fault onland which showed detectable breaks (<4 cm). We relocated the mainshock hypocenter at 10 km in depth, 38 21.7 0 N, 22 12.0 0 E, about 15 km NNE to the damaged city

Rotavirus virus-like particles (RV-VLPs) are potential alternative non-live vaccine candidates due to their high immunogenicity. They mimic the natural conformation of native viral proteins but cannot replicate because they do not contain genomic material which makes them safe. To date, most RV-VLPs have been derived from cell culture adapted strains or common G1 and G3 rotaviruses that have been circulating in communities for some time. In this study, chimaeric RV-VLPs were generated from the consensus sequences of African rotaviruses (G2, G8, G9 or G12 strains associated with either P[4], P[6] or P[8] genotypes) characterised directly from human stool samples without prior adaptation of the wild type strains to cell culture. Codon-optimised sequences for insect cell expression of genome segments 2 (VP2), 4 (VP4), 6 (VP6) and 9 (VP7) were cloned into a modified pFASTBAC vector, which allowed simultaneous expression of up to four genes using the Bac-to-Bac Baculovirus Expression System (BEVS; Invitrogen). Several combinations of the genome segments originating from different field strains were cloned to produce double-layered RV-VLPs (dRV-VLP; VP2/6), triplelayered RV-VLPs (tRV-VLP; VP2/6/7 or VP2/6/7/4) and chimaeric tRV-VLPs. The RV-VLPs were produced by infecting Spodoptera frugiperda 9 and Trichoplusia ni cells with recombinant baculoviruses using multi-cistronic, dual co-infection and stepwise-infection expression strategies. The size and morphology of the RV-VLPs, as determined by transmission electron microscopy, revealed successful production of RV-VLPs. The novel approach of producing tRV-VLPs, by using the consensus insect cell codon-optimised nucleotide sequence derived from dsRNA extracted directly from clinical specimens, should speed-up vaccine research and development by bypassing the need to adapt rotaviruses to cell culture. Other problems associated with cell culture adaptation, such as possible changes in epitopes, can also be circumvented. Thus, it is now possible to generate tRV-VLPs for evaluation as non-live vaccine candidates for any human or animal field rotavirus strain.

Resumen: Introducción. Las enfermedades causadas por virus se han convertido en un factor limitante para los cultivos de tomate de árbol presentes en diferentes regiones de Colombia, incluyendo aquellos del departamento de Nariño. Estudios previos apuntan a ...

Cyclic lipopeptides including surfactin, iturin and fengycin families are important metabolites produced by Bacillus having significant role in disease control, agriculture, medicine, cosmetics, pharmaceuticals, food and petroleum industry. Some of these lipopeptides have been reported to show biosurfactant activities with surfactin being the most studied biosurfactant possessing growth inhibition activity for phytopathogenic bacteria, fungi, virus or mycoplasma. srfA operon of surfactin is essential for competence development and the presence of this operon is confined to Bacillus subtilis, B. amyloliquefaciens and B. circulans only. In the present project, three different Bacillus species i.e. Bacillus subtilis, Bacillus thuringiensis and Bacillus sphaericus were screened for the presence of srfAA ORF1 of surfactin synthetase using PCR. Specific primers were designed against this ORF1 region for PCR amplification with the help of online bioinformatics tools and by using already re...

The present study was carried out from January to June 2016 in Rajasthan that aimed to sequence the 16S rRNA gene of S. hardwickii to trace genetic variation. Non-invasive molecular techniques were used to isolate DNA from fecal matter. The sequences were edited and assembled using SeqMan computer program, aligned with six global sequences following Clustal W algorithm to ascertain single nucleotide polymorphisms (SNPs). Maximum-likelihood phylogenetic tree was constructed using MEGA v6.0 with 1000 bootstrap replicates. Multiple sequence alignment with global sequences showed single bp changes at four positions in Indian and two global samples. Phylogenetic analysis revealed shared ancestry between Indian and these two global samples with indels at seven bp positions 126-128 (insertion) and 249-252 (deletion), and largely due to the movement of specimens involved in illegal trading. The study though short term, quite promising and revealed monomorphic nature of Indian isolates that ...