Miracle-dz/UniFAR-FTUs huggingface dataset:
Diagnóstico molecular de factores genéticos relacionados con periodontitis en pacientes mestizos mexicanos. Estudio piloto

Periodontal disease (PD) is a complex condition caused by bacterial infection and increased host immune response, deeply involved in the loss of tooth supporting tissue. It is important to note that genetics has been considered an important factor in the etiology of periodontal disease. In the present study, we determined the contribution of certain genes to identify genetic risk markers for its future use in molecular PD diagnosis. The studied genes were adiponectin (ADIPOQ) and T-cadherin (CDH13), related to infl ammation, and the gene that codes for peroxisome proliferator-activated receptor gamma (PPARG), related to bone metabolism. In order to fi nd genetic risk markers, we analyzed allele and genotype frequency differences in three SNP polymorphisms in 31 genetically unrelated Mexican mestizos: 14 periodontitis cases and 17 periodontal healthy controls. DNA was isolated from oral epithelial cells and polymorphisms were analyzed by TaqMan ® SNP genotyping assays. Our results suggest that A allele on CDH13 gene may confer risk to PD development (OR = 2.15, 95% CI = 1.05-4.43, p ≤ 0.02). In agreement with this fi nding, the homozygous genotype for this allele (AA) was more frequent among cases (80%) than controls (50%). Regarding ADIPOQ, it showed a higher proportion of risk genotypes reported in other populations (TT), where this genotype was more frequent in cases (7%) than in controls (absent). Finally, PPARG did not show any difference between both studied groups. Although the differences found in this study were not statistically signifi cant, our results reveal interesting trends that may become evident with a higher sample size.
The Need for New Criteria to Define Disease Activity and Treatment Response Using Disease Activity Score (DAS)28-C-reactive Protein

In 1990, disease activity score (DAS) was developed for decision to start treatment with a slow acting antirheumatoic drugs (now named disease-modifying antirheumatic drugs) and to stop the treatment especially in patients with early rheumatoid arthritis (RA). It consists of Ritchie index (the sum of the grades of tenderness of 52 joints), swollen joints, erythrocyte sedimentation rate (ESR) and general health (GH). Using the DAS, rheumatologists became able to make their decision in the real practice [1]. While the validity of most single varialbes are poor and not suitable for assessment of disease activity, the combination of clinical and laboratory variables reflects disease activity in clinical practice [1,2]. Since DAS in 28 joints (DAS28) was suggested, the most clinical studies and practices have been using this score for 30 years. DAS28 was originally composed with 28 tender joints, 28 swollen joints, ESR and GH in patients with both early and established RA [3]. ESR is influenced by many confounding factors such as age, sex, abnormal red blood cells, blood viscosity and pathologic and physiologic condition. However, C-reactive protein (CRP) is independent of these conditions and has more specificity for inflammatory change and it is used as relacement of ESR in assessment of DAS28 [4]. The fomulas of each DAS28 score are as follows:
The effect of body size on the outcome of fights in burying beetles (Nicrophorus)

Chez Nicrophorus, plusieurs individus arrivant sur un cadavre mais generalement un seul couple y reste et s'y reproduit. Les interactions intersexuelles et les combats intra- et interspecifiques sont etudies chez 3 especes. La vraisemblance des differents types de combat est estime d'apres l'abondance, la preference de l'habitat et la frequence saisonniere des especes. Pour les combats intraspecifiques, l'individu de plus grande taille gagne toujours. Pour les combats interspecifiques, les individus appartenant aux 2 especes. Les plus grandes sont avantages par rapport a l'espece la plus petite, meme s'ils sont de meme taille que l'individu qui leur est oppose. Il n'y a pas de choix du partenaire sexuel
Immunolocalisation within neural tissue of MADM : a novel metalloprotease with a potential integrin-binding domain

A metalloprotease previously isolated from bovine brain was shown to be a member of a family which includes both mammalian proteins and snake venom metalloproteases containing a potential integrin-binding (disintegrin) domain. The bovine enzyme was named MADM for Mammalian-Disintegrin Metalloprotease (Howard et al., 1996; Biochemical Journal 371; 45-50). The present studies were undertaken to generate antibodies reactive with the rat MADM homologue and to use these for immunolocalisation of the protein in rat central nervous system (CNS). A truncated rat MADM homologue was initially isolated from a commercial brain cDNA library, and the sequence encoding the mature protein was completed using the technique of 5’-RACE (rapid amplification of cDNA ends). It was found that the rat MADM sequence had a very high degree of identity at both the nucleic acid and the amino acid level with bovine MADM, possibly implying a critical function for this protein. An antigenicity plot of the mature rat protein was used to design peptides for antiMADM antibody production. Although the level of immunogenicity was generally low, two specific polyclonal antisera were produced in rabbits, and used in Western blotting experiments to demonstrate the presence of MADM protein in a range of rat tissues and cultured cell lines. Within adult rat CNS, the MADM protein was localised by immunohistochemistry to microglial cells of the white matter. The patterns of expression of p i, p2, P3, and p4-integrin subunits within the CNS were also examined, with the intention of identifying potential candidates for MADM’s cognate integrin; only P2 integrins have been shown to co-localise with MADM to microglia. Ramified microglia of normal adult rat brain were shown to express low levels of MADM, and the protease was not demonstrated to be upregulated by reactive microglia either during early postnatal development or in the vicinity of a cerebral stab wound. Fluorescent confoeal microscopy used to examine MADM expression by isolated microglia demonstrated that in vitro, MADM was found intraeellularly, and could not be induced to move to a cell surface location even on microglia activated by cytokines; this intracellular' localisation is in direct contradiction of the structural evidence pointing to a transmembrane position for MADM. However, MADM was found to be expressed on the surface of cultured mouse NSO myeloma cells, a result which may reflect a facet of the immoi'talisation process, or may imply that MADM is dependent on specific integrin expression for its surface localisation.
EFFECTS OF INSECTICIDE TREATMENTS FOR NAVEL ORANGEWORM ON POPULATIONS OF PACIFIC SPIDER MITE IN ALMOND, 2010

In 2010 we conducted a navel orangeworm trial at the University of California West Side Research and Extension Center in Five Points, Fresno Co., CA. The trial evaluated the populations of spider mites at harvest approximately 4 wk after treatments for navel orangeworm at hull split. A total of 84 nonpareil trees were organized into a RCBD with six blocks of 13 treatments and an untreated check. Trees were 3 years old and planted in a spacing of 22 ft × 15 ft. Treatments were applied to individual trees with a hand gun using 200 gpa at 150 PSI on 22 Jul. This corresponded with the second flight of navel orangeworm and the initiation of hull split. Mite densities were evaluated on 17 Aug. A total of twenty random leaves were collected from each individual tree. Leaves were transported to a laboratory where the numbers of motile Pacific spider mites (larvae, nymphs, and adults) per leaf were counted. Avg number of mites per leaf were analyzed by ANOVA with means separated by Fisher’s Protected LSD (P = 0.05).
A High-throughput Screen for Novel Genes Involved in Maintaining Genome Stability and the DNA Damage Response Pathway in Saccharomyces cerevisiae

Oncogenesis is frequently accompanied by rampant genome instability, which fuels genetic heterogeneity and resistance to targeted cancer therapy. I have developed an approach that allows precise, quantitative measurement of genome instability in a high-throughput format in Saccharomyces cerevisiae. My approach takes advantage of the strongly DNA damage-inducible gene RNR3, in conjunction with the Reporter Synthetic Genetic Array methodology, to infer mutants exhibiting genome instability by assaying for increased Rnr3 abundance. We screen for genome instability across ~4200 non-essential mutant yeast alleles in untreated conditions and in the presence of the DNA damaging agent MMS. Our results provide broad insights into the cellular processes and pathways required for genome maintenance. Preliminary follow-up work suggests that several genes have bona fide roles in the maintenance of genome stability. In addition, I conducted both screens in their entirety on two, highly orthogonal fluorescence imaging platforms and compared their reproducibility and sensitivity.
Extinction of an lmmunoglobutin K Promoter in Cell Hybrids Is Mediated by the Octame Car&&s with Suppression of W-2 Ex

Summary When immunoglobulin-expressing B cells are fused with fibroblasts, immunoglobulin expression is rap idly and selectively suppressed. Here we demonstrate that the conserved octamer motif of a K light chain gene promoter plays a crucial role in mediating this “extinction” phenomenon. Replacement of this octamer site by an Spl or NFl binding site is sufficient to bypasa extinction. Furthermore, in early cell hybrids, immunoglobulfn suppression is correlated with absence of the cell-specific transcription factor Ott-2 and its transcripts. Such hybrids cannot support transcription of a transiently introduced reporter plasmid, driven by an octamer-containing promoter, unless an exprersion vector encoding Ott-2 is cotransfected. Transfection of the same Ott-2 expression vector into hybrid cells is also sufficient to “reactivate” an integrated K promoter conrtruct. Thus, our data further establish the role of Ott-2 for immunoglobulin transcription and show that in B ceil x fibroblast hybrids, the lack of a necessary cell-specific transcription factor is involved in the extinction of immunoglobulin expression.
An investigation into the contrasting growth response of lodgepole pine and white spruce to harvest-related soil disturbance

Losses in forest productivity through poor soil management are typically evaluated by changes in crop production, but conflicting growth responses among co-occurring species can challenge criteria for sustainability. In this study, we evaluate species response to compaction and organic matter removal by contrasting the growth and foliar attributes at age 20 of lodgepole pine (Pinus contorta Dougl. ex Loud.) and hybrid white spruce (Picea glauca × engelmannii (Moench) Voss) in sub-boreal forests of central British Columbia. Bole volume increment was stable for lodgepole pine, averaging a 6 % difference across treatments. White spruce, in contrast, often had large growth increases on forest floor retained – compacted plots (average of 63 % gain) but reductions in productivity on the forest floor removed – compacted plots (40 % decline). Foliar nitrogen concentrations converged across treatments for both species, despite the removal of over 50 % of the site N capital. Some key differences in species traits w.
Hygienic Effects of Trimming and Washing Operations in a Beef-Carcass-Dressing Process †.

Swab samples were obtained from the surfaces of randomly selected beef carcasses passing through a high-speed dressing process. A single sample was obtained from a randomly selected site on the surface of each selected carcass. Fifty such samples were collected at each of four stages in the process. The aerobic bacteria, coliforms, and Escherichia coli recovered from each sample were enumerated. Values for the mean log units and standard deviations of each set of 50 log values were calculated on the assumption that the log values were normally distributed. The log of the arithmetic mean was estimated from the mean log and standard deviation values for each set. The results show that the average numbers of E. coli , coliforms, and aerobic bacteria which are deposited on carcasses during skinning and evisceration are not reduced by trimming, and that washing approximately halves the average numbers of those bacteria on carcasses. It is concluded that commercial trimming and washing operations are not effective means of decontaminating beef carcasses.
Quality Attributes and Storage Stability of Chicken Meat Biscuits Incorporated with Wheat and Oat Bran

Fiber-enriched chicken meat biscuits incorporated with wheat bran and oat bran at three different levels i.e., 3% (W1/O1), 5.0% (W2/O2) and 7% (W3/O3) were formulated and evaluated. On the basis of sensory quality from each group, W2 and O2 were selected for storage study at ambient temperature for 180 days. The bran incorporation resulted in a significant lowering (P < 0.05) in the pH values, fat content, water activity and calorific values whereas moisture content, ash and crude fiber content of treatment recorded an increased trend. Bran treated samples were found with improved oxidative stability as measured by free fatty acids and thiobarbituric acid reactive substances value during storage. Treated biscuits were recorded with significantly (P < 0.05) lower pH value and higher water activity during entire storage. Oat bran incorporated chicken meat biscuit were found to better maintained sensory characteristics than wheat bran incorporated meat biscuits and control throughout the storage study. Practical Applications Biscuits are generally cereal based snacks, lacking in essential amino acids and dietary fiber. The incorporation of meat and brans would increase its nutritive and functional value as well as keeping quality. It also partially fulfills the dietary requirement of dietary fiber.
Function assignment to Influenza B virus proteins using Support Vector Machine- A clue for vaccine development

Purpose: Identification of protein functions of Influenza B virus to understand the biological processes and networks of the virus which lead to novel way of diagnostics and vaccine designing. Methods: The protein sequences of Influenza B virus was retrieved from NCBI and Swiss Protein Databank. Prediction and analysis of different protein function family of proteins of Influenza B virus was done by the software, SVMProt, Support vector machine which classifies a protein into functional families from its primary sequence based on physico-chemical properties of amino acids.Results: The studies from SVMProt on Influenza B proteins suggest quite disparity of protein functions between structural and non-structural classes of proteins. ATP Binding cassette is a protein function shared by both the classes of proteins. Functions performed exclusively by Structural proteins are aptamer binding, these proteins belong to major facilitator family and transferasestransferring one carbon groups, whereas non-structural proteins performs functions like nuclear receptor and zinc-binding.Discussion and Conclusion: Protein function predictied by SVMProt is different for structural and non-structural protein of Influenza B virus, some of which may be responsible for virulence or pathogenicity of the virus and others for replication of the virus in the host. Functional classification of the proteins helps to facilitate the study of various biological processes and search for new therapeutic targets for vaccine designing.
Farming and Foraging: indirect effects of management on bird biology through changing distributions of food and predators

Farmland songbirds have shown dramatic population declines that have been linked to agricultural intensification. Populations have been impacted via three key factors: a reduction in available nesting habitat, a reduction in the availability of food for nestlings, and a reduction in over-winter food availability. The abundance of nest predators such as corvids, and the presence of sub-clinical disease may also play a part, and this thesis investigates the inter-relationships of some of these five factors along with their potential impacts upon farmland bird populations, using the yellowhammer Emberiza citrinella as a model species. It appears that the quality, not the quantity of fledglings has declined, possibly due to delayed life-history effects following on from conditions experienced in the nest. Increases in corvid abundance are associated with declines in chick growth and condition, mediated by behavioural compensation by provisioning adults: these effects are especially marked in large broods and where invertebrate food supply is low; where food supply is high a slightly positive effect of corvid abundance on condition and growth is found, implying an adaptive response by adults to maximise food provisioning in order for chicks to fledge more quickly and thus reduce their risk of predation in the nest. High territory densities, found where the availability of suitable nesting habitat is high, are associated with apparent density-dependent competition for high quality food and reduced chick growth, probably reducing fledgling quality and potentially leading to population sinks in areas of good nesting habitat, or in areas with high corvid densities. Survival analysis from a yellow hammer population sampled over four successive winters indicates that survival is male-biased, probably due to the higher work rates of females during breeding. Survival probability increases with increasing wing length, although analysis of 21 years of ringing data from the same site indicate a significant trend towards decreasing wing length, when controlling for the effects of age and sex. This apparent paradox is likely to have arisen from a decline in wing length of fledglings recruiting into the population as a result of a decline in habitat quality or food availability, both of which have been shown to influence feather growth. Infection by blood parasites showed associations with reduced feather growth and may indirectly influence survival, possibly by compounding food stress over-winter.
The development of peptide-based vaccine for leptospirosis: In Silico approach / Salwana Binti Othman

Leptospirosis is a worldwide zoonosis infection caused by Gram-negative bacteria from the genus of Leptospira. Eight pathogenic species of Leptospira have been identified and there are more than 250 serovars that can cause leptospirosis to human and animals. Due to the indistinguishable symptoms of the disease, leptospirosis is often misdiagnosed, resulting to death if antibiotic treatment is not given immediately. Prophylactic vaccine can reduce the mortality rate resulting from the late treatment. However, the existing vaccines for leptospirosis are serovar-specific and can only provide limited protection to human. Therefore, a new and more effective vaccine is urgently needed. The vaccine can be developed in shorter time with reduced cost through rational design and in silico approach by maximizing the use of the abundant information on the sequences of leptospiral antigenic proteins and the growing number of bioinformatics tools. The objective of this research is to perform an in silico analysis to develop a vaccine from the peptide sequence of leptospiral outer membrane protein, LigB. The predicted peptide-based vaccine, which requires experimental validation in the future, is hoped to be effective against all pathogenic serovars of Leptospira and ultimately provide us immunity to leptospirosis.
Purification and TEM of Afp and Its Variants

[Abstract] The Serratia entomophila antifeeding prophage (Afp), forms a phage-tail-like particle (tailocin) that causes cessation of feeding activity of the New Zealand grass grub, Costelytra zealandica. Here, we describe the more detailed purification protocol for Afp particles and its variants which is based on the procedure described in our original publication (Rybakova et al., 2013). The purification procedure includes inducing Escherichia coli (E. coli) cells harbouring afp genes under arabinose-inducible promoter for 24 h. The cells are harvested and sonicated on ice followed by DNAse treatment and centrifugation. The supernatant is then filter sterilised and applied to the size exclusion chromotography (SEC) column. The fractions containing Afp or its variants are pooled and ultracentrifuged. The supernatant is removed and the transparent pellet is resuspended in the residual buffer. The procedure results in Afp particles or variants thereof that are approximately 70% pure. The Afp particles are negatively stained and visualized using Transmission electron microscopy (TEM).
Implication of Epigenetic Modifications in Neurodegenerative Disorders:Traces and Imprints

Neurodegenerative disorders like Alzheimer’s, Parkinson’s, Huntington’s and ALS; present a complex biological disorder resulting loss of synaptic connections, neuronal damage and decay in old and elderly persons. Such a degrading process of neurons affects the central nervous system and results in loss of cognitive abilities, memory, sensory abilities and impairs the motor neuron functions. Thus, understanding the biology of neurodegenerative diseases has been crucial in ensuring healthy aged life. Although several cases of familial neurodegenerative disorders have been reported, yet the mechanism for sporadic neuronal degeneration remains largely unknown. Therefore, in this review we aim to understand the role of environmental triggers, i.e. epigenetics in affecting the normal functioning and coordination of host nervous system. A distinct signature mark of neurodegenerative disorders involves misfolding and structural aberration in native proteins leading to formation of intracellular fibrillary tangles, Lewy bodies, extracellular plaques, to name a few. This paper focusses primarily on four kinds of neurodegenerative disorders as mentioned above and reviewed the role of DNA/histone methylation, acetylation, ubiquitination along with mutational changes to the native protein product.
Apport de la génétique dans le concept de terrain à risque pour l'alcoolo-dépendance

Les variations du risque individuel pour l'alcoolo-dependance sont multifactorielles, complexes et pour la plupart, mal connues. Neanmoins, les facteurs genetiques ont un role important dans cette vulnerabilite individuelle, le poids des facteurs genetiques additifs etant estime entre 30 % et 50 % de ce qui explique l'alcoolo-dependance. Les etudes de concentration familiale soulignent la difficulte de la delimitation phenotypique de l'alcoolo-dependance, puisque certains sous-groupes d'alcoolisme ont un determinisme beaucoup plus dependant des facteurs genetiques que d'autres (formes precoces, severes, avec conduites sociopathiques.). Compliquant encore les choses, plusieurs etudes d'agregation familiale ont souligne que les facteurs genetiques en cause etaient assez peu dependants de la substance consommee, la vulnerabilite etant essentiellement axee sur le concept d' « addiction ». La substance consommee serait alors de determinisme plus familial et/ou environnemental. La mise en evidence de genes de vulnerabilite a surtout servi a mieux delimiter le phenotype « alcoolo-dependance» qu'a proposer de nouveaux traitements. Trois exemples sont ici detailles. Tout d'abord le role du gene codant pour le deuxieme recepteur dopaminergique qui semble implique dans la dependance severe et comorbide. Ensuite le role du gene codant pour le transporteur de la serotonine qui accroit le risque suicidaire chez les sujets alcoolo-dependants. Enfin la participation de polymorphismes genetiques du transporteur de la dopamine expliquant 20 % de la variance de la qualite du sevrage alcoolique (epilepsie, delirium tremens versus pas de symptome).