Miracle-dz/UniFAR-FTUs huggingface dataset:
Virulence prediction model (virprob) using amino acid and dipeptide composition for human pathogens

Pathogenic bacteria that cause infectious disease are operated by various virulence mechanisms. Hence, it is important to develop a reliable system for predicting bacterial virulent proteins aiming at discovering novel drug/vaccine and for understanding virulence mechanisms in pathogens. On the basis of features like amino acid and dipeptide composition, it tried to identify the virulence potential in the given biological protein sequence of bacteria using statistical methods like regression analysis, which is of great use in the prediction strategies of the virulence protein. In this work a bacterial virulent protein prediction model, virprob, is proposed based on classifiers, where the features are extracted directly from the amino acid sequence of a given protein. It is a probabilistic model which predicts the virulence potential of the corresponding human pathogenic bacterial protein. An extensive evaluation according to a blind testing protocol, where the parameters of the system are calculated using the training set and the system is validated in independent dataset, has demonstrated the validity of virprob with 53.6% of accuracy. The statistical analysis method may increase the prediction accuracy when combined with machine learning techniques. The results of this analysis might help in rapidly advancing knowledge of infectious agents. Key words: Virulence, proteins, virprob, pathogen.
Desenvolvimento de um sistema de expressão em Metarhizium anisopliae baseado no promotor homólogo do gene tef-1 α

XII 1 INTRODUÇÃO. 1 1.1 O fungo Metarhizium anisopliae . 3 1.1.1 Morfologia, classificação e importância. 3 1.1.2 O processo de infecção . 5 1.2 Sistema de expressão em Metarhizium anisopliae . 6 1.2.1 Vetores de expressão em Metarhizium anisopliae . 6 1.3 Fator de alongamento de cadeia 1 α. 8 2 OBJETIVOS . 11 2.1 Geral . 11 2.2 Específicos . 11 3 MATERIAIS E MÉTODOS. 13 3.1 Linhagens de Escherichia coli . 13 3.2 Linhagem de Metarhizium anisopliae . 13 3.3 Meios de cultivo e manutenção de microrganismos.13 3.4 Extração de ácidos nucléicos . 14 3.4.1 Extração de DNA de plasmídeos. 14 3.4.2 Extração de DNA de M. anisopliae . 14 3.4.3 Extração de RNA de M. anisopliae . 15 3.5 “Screening” de banco de cDNA.16 3.6 “Screening” de banco genômico. 16 3.7 PCR inverso (iPCR) . 17 3.8 Hibridização de ácidos nucléicos . 18 3.8. 1 Hibridização de DNA (Southern Blot). 18 VI 3.8. 2 Hibridização de RNA (Northern Blot) . 19 3.9 Vetores, enzimas de restrição, enzimas de modifição, marcadores de tamanho molecular e soluções. 19 3.10 Sequenciamento e análise das seqüências . 20 3.11 Transformação de Metarhizium anisopliae . 20 3.12 Bioensaios de transformantes em carrapato Boophilus microplus . 21 4 RESULTADOS . 22 4.1 Isolamento e caracterização do cDNA do gene tef1-α de Metarhizium anisopliae.22 4.2 Isolamento e caracterização do gene tef1-α de Metarhizium anisopliae.26 4.3 Análise filogenética de genes orthologos a tef1-α . 33 4.4 Análise da expressão do gene tef-1α de Metarhizium anisopliae . 35 4.5 Construção de um vetor de expressão para Metarhizium anisopliae.36 4.6 Bioensaio dos transformantes.40 5 DISCUSSÃO. 43 6 CONCLUSÕES. 54 7 REFERÊNCIAS BIBLIOGRAFICAS . 56 8 APÊNDICE 1 . 71 9 APÊNDICE 2 . 73 10 APÊNDICE 3 . 73 Dutra V, Nakazato L, Broetto L, Silveira Schrank I, Henning Vainstein M, Schrank A. (2004) Application of representational difference analysis to identify sequence tags expressed by Metarhizium anisopliae during the infection process of the tick Boophilus microplus cuticle. Research in Microbiology. 155(4):245-51. 11 APÊNDICE 4 . 81 Manuscrito: Luciano Nakazato, Valéria Dutra, Leonardo Broetto, Charley Christian Staats, Marilene, Henning Vainstein, Augusto Schrank (submetido AMB-05-12707) Development of an expression vector for Metarhizium anisopliae based on the tef-1α homologous promoter. Applied Microbiology and Biotechnology.
Characterization of a highly conserved microsatellite marker with utility potentials in cyprinid fishes

A microsatellite locus, MFW1, originating from common carp is highly conserved in flanking nucleotides but variable in repeat length in some fishes from different families of the Cypriniformes. This orthologous locus is polymorphic in approximately 58% of the species tested in the order and is inherited by Mendelian law. It proved to be a potentially good marker in population genetics and in the cyprinid species-breeding programme in which no microsatellite markers were available.
Occurrence of tolerance mechanism of resistance in some maize varieties to Chilo partellus (Swinhoe) (Pyralidae: Lepidoptera)

Out of nine mazie varieties evaluated for tolerance mechanism of resistance to the maize stalk borer, Chilo partellus, only Antigua Gr. 1 and Ganga 5 resisted the attack of this pest and registered lower mean damage grade (4.7 and 4.9) than Basi local (7.8) and lower mean per cent yield loss (9.7 and 16.9) than Basi local (92.1). The resistance In these two former varieties could be attributed more to the predominant mechanism i.e., antibiosis, rather than to tolerance. In spite of 2–3 repeated releases of newly hatched larvae, these two varieties showed low larval survival (2.4 and 3.1 larvae/plant) as compared to the susceptible variety Basi local (5.4 larvae/plant). Obviously, the tolerance mechanism was rather masked, particularly in the internal feeder, C. partellus, where it was difficult to maintain the equal pest population on the resistant and susceptible varieties.
RUNX1 Transcription Repression and Stability: Interplay Between Phosphorylation and O-GlcNAc Modification

RUNX1 is a transcription factor that plays major role in hematopoeisis. RUNX1 activation is dependent on phosphorylation in its transactivation domain. Ser 249 and 276 are the potential sites for phosphorylation that lead to transcriptionally active RUNX1 which has transient action and is prone to proteasome mediated degradation. We propose that Ser 249 and 276 have the highest potential for O-GlcNAc modification, and are the Yin Yang sites (potential for both phosphorylation and O-GlcNAc modifications). In contrast to phosphorylation modification, O-glycosylation modification of RUNX1 leads to its transcriptional repression. This novel O-GlcNAc modification on RUNX1 provides a mechanism for regulation of transcription activity and stability of RUNX1. OGT mediated O-GlcNAc modified RUNX1 is more stable and is resistant to proteasome mediated degradation.
Successful Use of a Strain and Counterstrain Technique with Physical Therapy: Myofascial Pain Unresponsive to Standard Treatment

&NA; Chronic pain disorders, including fibromyalgia and myofascial pain syndrome often do not respond adequately to standard therapy. The cases reviewed herein suggest the strain and counterstrain (SCS) technique, described in 1981 by Jones, may be helpful in reducing pain and improving function in patients with localized myofascial pain syndromes. This was a case study and retrospective review of 20 patients who had had chronic pain for an average of 2.7 years and were treated with SCS for pain relief. For all these patients, prior medical treatment had failed to provide pain relief or return of function. The procedure is a fairly common osteopathic and chiropractic technique, which to our knowledge has not received any systematic evaluation. A reduction in pain and an increase in function of 50%‐100% occurred in 19 of 20 patients immediately after SCS therapy. Partial improvement was maintained for 6 months in 11 of 20 patients, and 4 were still pain free. We believe that SCS techniques should be considered and evaluated further as adjunctive therapy for patients previously unresponsive to standard treatment for myofascial pain syndrome.
Micropropagation of Plumbago zeylanica L.

vitro propagation of Plumbago zeylanica was investigated to develop reliable protocols for direct and indirect shoot regeneration. Axillary shoot multiplication, callus induction and shoot regeneration from callus culture was obtained on Murashige and Skoog (MS) medium supplemented with different concentrations and combinations of plant growth regulators. A maximum number of shoots (38 ± 1.3 per explant) was obtained from nodal explants when cultured on MS liquid medium supplemented with 1.0 mg·L -1 BAP, 0.5 mg·L -1 IBA and 2.0 mg·L -1 adenine sulfate. The highest percentage of callus induction was obtained when stem explants cultured on MS medium supplemented with 2.0 mg·L -1 BAP and 1.5 mg·L -1 IAA. The greatest percentage of shoot induction (100%) with a mean of 34.2 shoots obtained from callus was cultured on MS medium supplemented with 0.75 mg·L -1 BAP, 1.0 mg·L -1 IAA, NAA and adenine sulfate each. Regenerated shoots were rooted best on half-strength MS medium containing 0.5 mg·L -1 NAA and 3% (w/v) sucrose. The regenerated plantlets were acclimatized in the culture room and successfully transferred in soil.
BY PIERRE-FRAN(~OIS PIGUET, CLAUDE IRLE, EVELYNE KOLLATTE,

In this study, we took advantage of the rather similar compositions of adult and NB lymph node cells (LNC), both of which are devoid of hematopoiesis and which have a proportion of T lymphocytes of ~60 and 80% of the cells, respectively, to compare the various T cell functions on a per T cell basis. We found that the peripheral T lymphocytes of 5-d-old mice have some phenotypic features of cortical thymocytes (peanut leetin binding, high frequency of cells in S phase), and that many of the functional characteristics of LNC from 5-d-old mice are also comparable to those of cortical thymocytes: lectin responsiveness, capacity to induce a lethal graft vs. host reaction (GVHR), and ability to help B lymphocytes in a humoral response. In contrast, the in vitro induction of cytotoxic T lymphocytes (CTL) from NB LNC was comparable in magnitude to that of adult LNC. These results are relevant not only for the understanding of the immunoincompetence of the NB and young mice but also for the maturation of T lymphocytes during ontogenesis.
Life cycle versus systematic placement: phylogenetic and cytogenetic studies in annual Artemisia (Asteraceae, Anthemideae)

Artemisia L. comprises ca. 20 annual species out of ca. 500, which are distributed mainly across the Old World grades, accounting for multiple independent acquisitions of annual habit throughout the evolutionary history of the genus. This makes Artemisia an interesting subject for the study of plant life cycle evolution in a phylogenetic context and its consequences at genomic level. The main aim of this phylogenetic analysis was to circumscribe 17 of the annual representatives within the major lineages of Artemisia. Genome size has been assessed and ancestral values reconstructed on the tree. Fluorescent in situ hybridisation (FISH) has also been performed to characterise the physical distribution of ribosomal DNA loci. Our results show that annual Artemisia have been especially misassigned at subgeneric level and confirm that they are phylogenetically restricted to basal grades, while absent from the derived ones. Annuals display great diversity of genomic traits; however, although most of them show genome downsizing with respect to their most recent common ancestors, no apparent correlation exists between this trait, the number of rDNA sites, and the phylogenetic placement. Nonetheless, such diversity suggests that higher rates of genome restructuring may have been key in governing genome evolution in annual species.
A AND B GENOME HOMOEOLOGIES IN TETRAPLOID AND OCTOPLOID CYTOTYPES OF BROMUS INERMIS

Homoeology between the A and B genomes of allotetraploid (2n = 4x = 28) AiAiBiBi and autoallooctoploid (2n = 8x = 56) AIAIAIAIBIBIBIBI cytotypes of B. inermis Leyss. was studied in a tetraploid F1 .
Ecological Characteristics of Small Mammal Communities at a Superfund Site

Abstract Wildlife species can serve as biomonitors of environmental health and are prognostic of ecotoxicological consequences when contaminants are introduced into the environment. Small mammals, particularly rodents, comprise the majority of indicator species used in terrestrial biomonitoring studies; however, many biomonitoring studies address acute effects over relatively short periods. We still know little regarding effects of chronic exposure to contaminants on small mammals. The overall goal of this study was to determine ecological characteristics of small mammal communities inhabiting a heavy metal contaminated site, Tar Creek Superfund Site, compared to reference sites located in northeastern Oklahoma over a 2 y timeframe. Primary hazardous materials present at Tar Creek Superfund Site include lead, zinc and cadmium. Mark-recapture techniques were employed to test the hypothesis that structure and composition of small mammal communities inhabiting this contaminated site would be significantly altered compared to uncontaminated reference sites. Contaminated and reference sites were similar in vegetation compositional characteristics. Small mammal communities inhabiting Tar Creek Superfund Site had reduced species diversity, including richness and evenness, compared to reference sites. Furthermore, communities within Tar Creek Superfund Site were dominated by a single species, Peromyscus leucopus (white-footed mouse). Species composition was different between contaminated sites and reference sites as evidenced by detrended correspondence analysis, with contaminated sites being more similar to each other than to either reference site. No direct link between site contamination and disparities among most ecological characteristics could be established.
TcZFP8, a novel member of the Trypanosoma cruzi CCHC zinc finger protein family with nuclear localization.

In a 17-kb genomic fragment of Trypanosoma cruzi chromosome XX, we identified three tandemly linked genes coding for CX 2 CX 4 HX 4 C zinc finger proteins. We also showed that similar genes are present in T. brucei and Leishmania major, sharing three mono- phyletic groups among these trypanosomatids. In T. cruzi, TcZFP8 cor- responds to a novel gene coding for a protein containing eight zinc finger motifs. Molecular cloning of this gene and heterologous expression as a fusion with a His-tag were performed in Escherichia coli. The purified recombinant protein was used to produce antibody in rabbits. Using Western blot analysis, we observed the presence of this protein in all three forms of the parasite: amastigote, trypomastigote and epimasti- gote. An analysis of cytoplasmic and nuclear cell extracts showed that this protein is present in nuclear extracts, and indirect immunofluores- cence microscopy confirmed the nuclear localization of TcZFP8. Ho-
Proanthocyanidins, anthocyanins and phenolic acids in food barleys of diverse origin

Phytochemicals found in grains complement those found in fruits and vegetables. These phytochemicals, though minor compounds, contribute to the antioxidant properties which are related to the health benefits associated with the consumption of whole grain. In this thesis project, nine barley genotypes of diverse origin namely CI2230 from Nepal, CI1248 from Israel, 3 Peruvian genotypes; Peru 3, Peru 16 and Peru 35, Hokuto Hadaka from Japan, EX116; a cross between Moroccan and Canadian genotype, EX83; a cross between two Canadian genotypes and EX127; a cross between Canadian and German genotypes were studied. The genotypes were categorized based on appearance into purple, black and yellow grains. Phenolic acids and flavonoids were identified and quantified in these diverse genotypes using HPLC-ESI-MS analysis. The main classes of dietary flavonoids studied in the barleys were anthocyanins and flavan-3-ols. Phenolic acids were identified and quantified (p-coumaric, ferulic, sinapic, caffeic, vanillic). Three ferulic acid dehydrodimers (8-0-4â DFA, 8-5â benzofuran form and 5-5â DFA) were also identified. The most abundant dimeric flavan-3-ols were procyanidins B3 and prodelphinidin B3. The monomeric unit, (+)-catechin, was the most abundant while catechin glucoside (m/z 451) was also identified. Among the Peruvian genotypes, Peru 16 and Peru 35 exhibited relatively high levels of total PA content. Total phenolic content and antioxidant activities of methanolic, acetone and alkali hydrolyzed extracts of the nine barley genotypes was determined by the Folin- Ciocalteau assay, DPPH radical scavenging assay and oxygen radical absorbance capacity (ORAC assay). The acetone extract exhibited the highest antioxidant capacity using all the methods of analysis. Furthermore, dark colored grains were found to exhibit higher contents of phenolic compounds. The phenolic acids, PAs and anthocyanins identified and quantified had significant contribution to the overall antioxidant capacity of the barley whole grain. Four hull-less genotypes namely CI2230, EX127, CI1248 and Peru 35 were further partially sprouted to establish the effects of sprouting on phenolic acid composition. Partial sprouting was observed to significantly increase the soluble conjugated phenolic acids. The barley genotypes studied were found to contain different quantities of phytochemicals and had high proanthocyanidin content thereby rendering them as alternative sources of antioxidants. Barley sprouts present a possible novel food ingredient with improved properties such as phenolic acid composition and other benefits such as easier incorporation into food products under development.
Review HUMAN GENOME PROJECT AND ITS IMPACT ON DIABETES MELLITUS

The human genome project (HGP) has made available the draft sequence of 3.1 billion nucleotide bases of human DNA, through a confluence of diverse fields. It marks the historic beginning of a new era when health and disease would be understood on the basis of genetic susceptibility. Post HGP, advances in diabetes can be expected in understanding its etiology and management. Putative susceptibility genes were localized to chromosomes 2q37, 12q, 3q and 20. A hitherto unsuspected gene for calpain 10 protein, may be a new marker. Ultimately, it would be possible to identify genes as the most 'proximal phenotype. ' Armed with this information, interventions can be planned to favorably alter the gene-protein expression.
Ecology of feeding nile tilapia under Azolla cover in earthen ponds: an assessment using structural equation modelling

The mechanisms by which Nile tilapia (Oreochromis niloticus) grow under Azolla cover (AC) in semi-intensive system was evaluated for 90 days using structural equation modelling and pathway analysis. The following Azolla cover (AC) extensions were applied: 0%, 15%, 30%, 45%, 60%, 75% and 90% of the surface. Fingerlings (initial mean weight: 15.8 ± 0.2 g) were additionally fed with the same diet formulated with local ingredients and containing 20% of Azolla meal. To quantify the relative contribution of AC and artificial feed in growth of fish, two models were defined, in which: (1): Azolla in ponds was considered as direct food for fish and a macrophyte on water surface; (2): Azolla acts as macrophyte only. Pathway analysis was done using standardized fortnight data and a coefficient was calculated for each causal relationship.Survival rate did not show any significant difference and values were higher than 84%. From the two competing models, indirect effects of AC on fish growth via phytoplankton biomass was similar and was the most important in the first month of experiment, the average ratio calculated being -0.68. As fish size increases, phytoplankton becomes limited and feeding on artificial food progressively grows in importance and influences growth. The coefficient of this direct effect on fish growth can reach 1.36, whilst the indirect effects from AC was -0.58 at the same period. The ratio of the relative contribution of the direct effect of feed versus the indirect effect of AC on Nile tilapia growth was therefore 1.36/0.58. Summary, in ponds covered with Azolla, fingerlings of Nile tilapia fed agricultural by-products feed primarily on phytoplankton at the beginning, and artificial food gains prominence with time, beneficially in tropical aquaculture where there is a need to reduce the feed cost in that enterprise.
Rufous owl (Ninox rufa) diet and breeding in an urban forest remnant in North-Eastern Queensland

Information on the diet of the Rufous Owl (Ninox rufa) was gathered from the regurgitated pellets and prey remains from a pair that used the habitat surrounding Centenary Lakes, Cairns, north-east Queensland. Mammals comprised the largest portion of the diet during the 2010 breeding period, but passerine birds were also a major food source. Some new prey items are identified and the regular use of invertebrate prey, such as beetles, is further confirmed. Historical prey items recorded at the site and in adjoining suburbia are also mentioned. The results support the view that the diet of this species is likely determined by diverse foraging behaviours and differences in prey availability across the species' range.
ARRAYED CAPTURE, ASSAYING AND BINARY COUNTING OF CELLS IN A STOPPED-FLOW SEDIMENTATION MODE

In this work we present a centrifugal microfluidic platform for highly efficient trapping, staining and identification of biological cells. V-shaped geometric traps are used to captured mixed populations of cells under stagnant flow conditions. We demonstrate the capability to discriminate cells based on surface markers (EpCAM) as well as on intracellular markers (ESR1). Captured cells are arrayed in single cell ordered pattern and align in a well-defined focal plane which greatly facilitates the readout of cell-based assays.
Redescription of Difflugia tuberspinifera Hu, Shen, Gu et Gong, 1997 (Protozoa : Rhizopoda : Arcellinida : Difflugiidae) from China

The freshwater testate amoeba Difflugia tuberspinifera Hu et al. 1997 collected from pond and lake in China, is investigated by light and scanning electron microscopy. This little known taxon is redescribed and its morphology, biometry and ecology are supplied. After carefully comparison with other six similar species including Difflugia bartosi Stepanek, D. corona Wallich, D. corona cashi Deflandre, D. corona tuberculata Vucetich, D. muriformis Gauthier-Lievre et Thomas and Netzelia tuberculata (Wallich) Netzal we believe that the sub-spherical to spherical shell, the mulberry-shaped appearance, the 7-10 apertural tooth-like structures, the short collar and the conical spines numbering from 4 to 8 at the upper equatorial region in D. tuberspinifera set it apart from other species. Besides, statistical analysis indicates that D. tuberspinifera is a size-monomorphic species characterized by a main-size class and a small size range and the shell height is significant correlated with other morphometric characters at p < 0.05 excepting the number of aperture tooth-like structures and the number of spines. Moreover, D. tuberspinifera inhabits not only lotic but also lentic environment.
A Rapid Procedure for the Isolation of RNA from High-phenolic-containing Tissues of Pecan

A simple and efficient protocol is reported for the isolation of RNA from embryos and leaves of pecan ( Carya illinoinensis (Wangenh.) K. Koch). The method relies on suppression of the polyphenols from interaction with the RNA and their rapid removal from the homogenate by chloroform extraction. This method produced abun- dant amounts of high-quality RNA. This protocol is likely to be useful for Juglanda- ceous species and other recalcitrant plants with high levels of phenolic compounds.