Miracle-dz/UniFAR-FTUs huggingface dataset:
Dissecting the Effects of Anthrax Toxins on Dendritic Cells and Potential Reversal by Chemically Modified Tetracyclines

Stony Brook University Libraries, Department of Molecular and Cellular Biology. Lawrence Martin (Dean of Graduate School), Sanford R. Simon (Thesis Advisor, Professor of Biochemistry and Pathology), Nisson Schechter (Chairperson of Defense, Professor, Department of Molecular and Cell Biology), Dale Deutsch (Professor, Department of Molecular and Cellular Biology).
Patterns of variation in spring emergence by black rat snakes (Elaphe obsoleta obsoleta)

Substantial individual variation in timing of emergence from hibernation has been reported among reptiles, although few studies have addressed the causes of that variation. Here we report patterns of spring emergence by black rat snakes (Elaphe obsoleta obsoleta) observed at 13 communal hibernacula in eastern Ontario from 1992-1997. Because our study area is at the northern extreme of the species' range, we expected synchronous emergence given the very short active season (about 5 months). Despite these apparent time constraints, however, the emergence period lasted an average of 40 days. Although we found significant variation in timing of emergence among years and among hibernacula, we found no evidence of a simple latitudinal gradient in mean emergence dates. Within hibernacula, significantly more snakes emerged on days with high maximum air temperatures, but maximum air temperature explained only a small amount of the variation among years in emergence dates. Larger individuals emerged earlier than smaller individuals, as predicted if early spring predation risk is higher for smaller snakes. Females tended to emerge slightly earlier than males. Condition was not a significant factor determining timing of emergence in our population. Individuals demonstrated significant repeatability between years in their time of emergence relative to other snakes in the same bibernaculum.
Impact of increasing dietary oil concentrations with a constant energy level on the tolerance of broiler chickens to a high ambient temperature

Broiler males (n= 140) were used in a straight-run experimental design and distributed randomly among four treatment groups with seven replicates per treatment and five broilers per replicate. During 21–42 d old, the chickens were fed iso-caloric and iso-nitrogenous diets containing four levels of dietary vegetable oils (DVO), of 2.7, 4, 6 and 8%. During d 25–27, 31–33, and 38–40 of age, broilers were exposed to heat stress for 4 h a day (1000–1400 h) at 34 oC, 70–75 % relative humidity. Feeding an 8% DVO diet significantly increased body weight gain compared to the other DVO levels. The feed conversion ratio, protein conversion ratio, metabolizable energy conversion ratio and European production index were significantly enhanced due to feeding an 8% DVO diet compared to a diet containing 6% DVO. Feeding 8% DVO significantly increased the meat protein and lipid percentages, compared to the control group (2.7 % DVO), but decreased the plasma low-density lipoprotein, very-low-density lipoprotein and lymphocytes. Feeding 8% DVO significantly increased the mean cell volume and mean cell hemoglobin, and bursa weight and percentage compared to the control. In addition, 6 and 8% DVO significantly increased the plasma total antioxidant capacity compared to the control group, but decreased the malondialdehyde. Thus, broilers fed a diet containing 8% DVO have an increased tolerance to heat stress, as evidenced by increasing the productive performance, meat quality, blood hematological and biochemical traits, antioxidants and immunity.
The Gene Ontology Differs in Bursa of Fabricius Between Two Breeds of Ducks Post Hatching by Enriching the Differentially Expressed Genes

The bursa of Fabricius (BF) is the central humoral immune organ unique to birds. The present study investigated the possible difference on a molecular level between two duck breeds. The digital gene expression profiling (DGE) technology was used to enrich the differentially expressed genes (DEGs) in BF between the Jianchang and Nonghua-P strains of ducks. DGE data identified 195 DEGs in the bursa. Gene Ontology (GO) analysis suggested that DEGs were mainly enriched in the metabolic pathways and ribosome components. Pathways analysis identified the spliceosome, RNA transport, RNA degradation process, Jak-STAT signaling pathway, TNF signaling pathway and B cell receptor signaling pathway. The results indicated that the main difference in the BF between the two duck strains was in the capabilities of protein formation and B cell development. These data have revealed the main divergence in the BF on a molecular level between genetically different duck breeds and may help to perform molecular breeding programs in poultry in the future.
Tuberculosis in cattle caused by IS901+ Mycobacterium avium subsp. avium -a case report

In small cattle herd an eight-year-old cow showed a reaction to bovine tuberculin in two consecutive skin tests. The animal showing clinical signs related to tuberculin was slaughtered for diagnostic purpose. The lungs were completely coverred with disseminate tubercles of different sizes and the mediastinal lymph nodes were enlarged. Pneumonia granulomatosa tuberculosa and lymphadenitis hyperplastica chronica were diagnosed histologically.Mycobacterium avium susp.avium of IS901+ and IS1245+ genotype was also isolated from lungs and from lymph node. Six weeks after the affected animal has been eliminated from the herd, the skin test in other animals on the farm was performed: single test with avian tuberculin in extensively poultry (n=12), comparative test with bovine and avian tuberculin in catlle (n=7). Concluding from the results of negative skin testing of other animals on the farm, it is very likely that the cow did not transmit M.a. avium into the environment.
Navigating on a chemical radar: Usage of root exudates by foraging Diabrotica virgifera virgifera larvae

In the darkness of the soil matrix, the larva of the western corn rootworm (WCR) Diabrotica virgifera virgifera LeConte relies on chemical cues to locate and accept its host plant roots. For almost 40 years, entomologists and chemical ecologists have tackled the challenge of isolating and identifying active chemical compounds emitted by host plant roots (most of the research has been conducted on maize Zea mays L.) and used by the foraging insect pest larvae. A number of molecules of interest have been documented but have so far only been implemented with little success in the current arms race to manage WCR (and soil‐dwelling pests). An in‐depth understanding of the mechanisms underlying the insect foraging behaviour is certainly critical to the development of highly effective and sustainable pest control strategies. This contribution reviews the progress and highlights the gaps in our current knowledge on the chemical ecology of WCR larvae. An individual‐based model of the larval behaviour in response to root volatiles has been developed based on data from the literature. It also proposes avenues (tested or theoretical) to eventually implement this knowledge in integrated pest management of this major maize pest, a critical approach as WCR has evolved resistance to several control strategies.
Task errors contribute to implicit remapping in sensorimotor adaptation

Perturbations of sensory feedback evoke sensory prediction errors (discrepancies between predicted and actual sensory outcomes of movements), and reward prediction errors (discrepancies between predicted rewards and actual rewards). Sensory prediction errors result in obligatory remapping of the relationship between motor commands and predicted sensory outcomes. The role of reward prediction errors in sensorimotor adaptation is less clear. When moving towards a target, we expect to obtain the reward of hitting the target, and so we experience a reward prediction error if the perturbation causes us to miss it. These discrepancies between desired task outcomes and actual task outcomes, or “task errors”, are thought to drive the use of strategic processes to restore success, although their role is not fully understood. Here, we investigated the role of task errors in sensorimotor adaptation: during target-reaching, we either removed task errors by moving the target mid-movement to align with cursor feedback of hand position, or enforced task error by moving the target away from the cursor feedback of hand position. Removing task errors not only reduced the rate and extent of adaptation during exposure to the perturbation, but also reduced the amount of post-adaptation implicit remapping. Hence, task errors contribute to implicit remapping resulting from sensory prediction errors. This suggests that the system which implicitly acquires new sensorimotor maps via exposure to sensory prediction errors is also sensitive to reward prediction errors.
The role of yeast culture (Saccharomyces cerevisiae) on performance, egg yolk fatty acid composition, and fecal microflora of laying hens

ABSTRACT This study investigated the effects of different levels (0.05, 0.1, and 0.2%) of yeast culture supplementation on body weight, feed intake, feed conversion ratio, egg production, egg weight, egg quality traits, egg yolk fatty acid composition, and microbiological flora in feces. A total of 240 laying hens at 18-19 weeks of age were divided into four groups and fed a basal diet containing 2750 kcal/kg metabolizable energy and 16% crude protein for 16 weeks. The basal diet was supplemented [. ]
Experimental Approaches to Understand and Control Salmonella Infection in Poultry

Salmonella is a major foodborne pathogen around the world and chickens are the major reservoir to transmit Salmonella into the human food chain. For decreasing the infection of Salmonella, we developed six attenuated live vaccines based on Salmonella Enteritidis (SE) and Typhimurium (ST) for testing the cross-serovar and cross-serogroup protection from the challenge of Salmonella Heidelberg and Campylobacter jejuni. One of the constructed vaccine strain showed ability to protect against challenge from Salmonella Heidelberg. Even though some preventive approaches are able to decrease Salmonella colonization in the gastrointestinal tract of chickens or other farm animals, Salmonella transmission mechanisms remain unclear. For analyzing Salmonella transmission routes and dynamics, we designed a series of Salmonella isogenic barcode-tagged strains by inserting six random nucleotides into a functionally neutral region on the chromosome of Salmonella Enteritidis. These barcode-tagged strains can be used as a tool for quantitative tracking of Salmonella transmission in the chicken flock by profiling the barcode regions using high-throughput sequencing. The efficiency of this novel approach has been estimated by chicken experiments and can be applied for further studies about Salmonella transmission and population dynamics. Due to the increasing pressure of using antibiotics as the growth promoter in the farm animals, probiotics is a suitable alternative to replace antibiotics by providing beneficial effects, such as promotion of animal health, decreased infection by pathogens, and improval of growth performance in poultry. In this study, 90 probiotic candidate strains were isolated and evaluated for decreasing the gut permeability in Caco-2 cell lines. The result from animal experiments indicated that a combined batch culture of 3 selected strains showed significant efficacy in controlling intestinal colonization of ST in neonatal turkey poults.
Evolution of patterned plumage as a sexual signal in estrildid finches

Animals are often covered with stripy or dotty patterns on their body surface, which can help them to hide or to signal. Estrildid finches are especially rich in species with plumage patterns but their geometric features show great variations. Our comparative study revealed that conspicuous plumage patterns are possessed by species with an elaborate courtship dance, suggesting that plumage patterns in estrildid finches work as sexual signals in both sexes.
Expression of a glucomannan mannosyltransferase gene (GMMT) from Aloe vera is induced by water deficit and abscisic acid

GMMT (a possible CSLA9) from Aloe vera is upregulated during water stress. Aloe vera GMMT expression is also induced by exogenous application of the plant stress hormone abscisic acid (ABA) in non-water-stressed plants. Summary In Aloe barbadensis Miller (Aloe vera), a xerophytic crassulacean acid metabolism (CAM) plant, the main polysaccharide of the gel present in the leaves is an acetylated glucomannan named acemannan. This polysaccharide is responsible for the plant succulence, helping it to retain water. In this study we determined using polysaccharide analysis by carbohydrate gel electrophoresis (PACE) that the acemannan is a glucomannan without galactose side branches. We also investigated the expression of the gene responsible for acemannan backbone synthesis, encoding a glucomannan mannosyltransferase (GMMT). It was found by in silico analyses that the GMMT gene belongs to the cellulose synthase like A type-9 (CSLA9) subfamily. Using RT-qPCR it was found that the expression of GMMT increased in Aloe vera plants subjected to water stress. This expression correlates with an increase of endogenous ABA levels, suggesting that the gene expression could be regulated by ABA. To corroborate this hypothesis, exogenous ABA was applied to non-water-stressed plants, increasing the expression of GMMT significantly 48 h after ABA treatment.
DNA fingerprinting based on SSR amplification profiles for Piper species identification (Piperaceae)

DNA fingerprinting based on SSR amplification profiles was applied to native species of Piper from the Atlantic Forest to compare the utility of this type of molecular marker with the morphological characters traditionally applied in Piper taxonomy and identification. Fifty-one SSR markers developed for four species of Piper native to Asia and Mesoamerica were applied to 16 species, together with 63 morphological characters, for species characterization. Molecular and morphological data were analysed by cluster analysis, followed by a cluster sharpness test and the construction of a heat map to visualize the association of characters with species groups. A multivariate regression tree determined the number of loci needed for species identification. Forty-five primers were transferable to at least four species. Molecular data were more efficient in detecting sharp groups than morphological data. Species groups delimited by a set of shared morphological characters were differentiated based on molecular data. The sixteen studied species could be separated by nine primers, demonstrating the cross-species transferability of SSR markers and the usefulness of DNA fingerprinting for both the delimitation and the identification of species of Piper.
Using step‐selection functions to model landscape connectivity for African elephants: accounting for variability across individuals and seasons

Landscape connectivity is an important component of systematic conservation planning. Step‐selection functions (SSFs) is a highly promising method for connectivity modeling. However, differences in movement behavior across individuals and seasons are usually not considered in current SSF‐based analyses, potentially leading to imprecise connectivity models. Here, our objective was to use SSFs to build functional connectivity models for African elephants Loxodonta africana in a seasonal environment to illustrate the temporal variability of functional landscape connectivity. We provide a methodological framework for integrating detected inter‐individual variability into resistance surface modeling, for assessing how landscape connectivity changes across seasons, and for evaluating how seasonal connectivity differences affect predictions of movement corridors. Using radio‐tracking data from elephants in the Borderland area between Kenya and Tanzania, we applied SSFs to create seasonal landscape resistance surfaces. Based on seasonal models, we predicted movement corridors connecting major protected areas (PAs) using circuit theory and least‐cost path analysis. Our findings demonstrate that individual variability and seasonality lead to substantial changes in landscape connectivity and predicted movement corridors. Specifically, we show that the models disregarding seasonal resource fluctuations underestimate connectivity for the wet and transitional seasons, and overestimate connectivity for the dry season. Based on our seasonal models, we predicted a connectivity network between large PAs and highlight seasonal and consistent patterns that are most important for effective management planning. Our findings reveal that elephant movements in the borderland between Kenya and Tanzania are essential for maintaining connectivity in the dry season, and that existing corridors do not protect these movements in full extent.
The truncated bell: an enigmatic but pervasive elevational diversity pattern in Middle American ants

272 –––––––––––––––––––––––––––––––––––––––– © 2018 The Authors. This is an Online Open article This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. Subject Editor: Michael Kaspari Editor-in-Chief: Miguel Araújo Accepted 18 May 2018 42: 272–283, 2019 doi: 10.1111/ecog.03871 doi: 10.1111/ecog.03871 42 272–283
In situ structures of periplasmic flagella reveal a distinct cytoplasmic ATPase complex in Borrelia burgdorferi

Periplasmic flagella are essential for the distinct morphology and motility of spirochetes. A flagella-specific Type III secretion system (fT3SS) composed of a membrane-bound export apparatus and a cytosolic ATPase complex is responsible for the assembly of the periplasmic flagella. Here, we combine cryo-electron tomography and mutagenesis approaches to characterize the fT3SS machine in the Lyme disease spirochete Borrelia burgdorferi. We define the fT3SS machine by systematically characterizing mutants lacking key component genes. We discover that a distinct cytosolic ATPase complex is attached to the flagellar C-ring through multiple spoke-like linkers. The ATPase complex not only strengthens structural rigidity of the C-ring, but also undergoes conformational changes in concert with flagellar rotation. Our studies provide structural framework to uncover the unique mechanisms underlying assembly and rotation of the periplasmic flagella and may provide the bases for the development of novel therapeutic strategies against several pathogenic spirochetes.
Substituição da farinha de peixe por hidrolisado proteico de peixe em rações para o camarão marinho Litopenaeus vannamei na fase de berçário

A deplecao dos estoques pesqueiros associada a crescente demanda da aquicultura por farinha de peixe para fabricacao de racoes tem ocasionado a elevacao de seu custo. Na busca de meios para tornar a aquicultura menos dependente da pesca, diversas materias primas alternativas estao sendo utilizadas na fabricacao de racoes para peixes e crustaceos. No presente estudo foram utilizadas carcacas de tilapia provenientes de industrias de filetamento de pescado na fabricacao de hidrolisados proteicos de peixe e sua posterior incorporacao em racoes para pos-larvas de camaroes marinhos. Foram produzidos dois hidrolisados de peixe (HPP) com tempos de hidrolise de uma (HPP 1) e duas horas (HPP 2). Foi utilizada a protease comercial alcalase na reacao. Os hidrolisados produzidos foram caracterizados estruturalmente e nutricionalmente. Foram determinados os graus de hidrolise, os perfis eletroforeticos, zimograma, composicao centesimal e teores de aminoacidos e acidos graxos. Os graus de hidrolise obtidos variaram de 34,01 a 48 %. Foram detectados peptidios de 10 a 250 kDa e foram observados 4 bandas no zimograma, para cada hidrolisado, cujos pesos variaram de 75 a 250 kDa. Os teores de proteina bruta dos hidrolisados foram de 68,04% (HPP 1) e 70,69 % (HPP 2). Em seguida foram elaboradas 7 racoes experimentais que continham substituicoes graduais de farinha de peixe nas proporcoes de 0% (controle), 10, 20 e 30 % pelos hidrolisados HPP1 e HPP2 totalizando sete dietas formuladas (0%, H110%, H120%, H130%, H210%, H220% e H230%). Essas racoes foram fornecidas para camaroes marinhos na fase inicial de pos-larva 12 durante 45 dias. Ao termino do cultivo foi avaliado o desempenho zootecnico dos camaroes alimentados com as racoes formuladas. Foi constatado que os camaroes alimentados com as racoes contendo o HPP 2 tiveram melhores crescimentos que os demais tratamentos, provando que o hidrolisado pode ser utilizado em racoes para pos larvas de Litopenaeus vannamei substituindo em 15 % a farinha de peixe.
Invasão biológica por Cryptostegia madagascariensis: uma abordagem voltada para estresses abióticos

A introdução, acidental ou deliberada, de espécies exóticas por diferentes vetores é atualmente uma das principais mudanças globais, resultando em uma série de problemas. Embora nem todas as introduções de espécies não nativas possuam efeitos negativos, muitos desses táxons podem desencadear efeitos indesejáveis sobre a biodiversidade, desde o nível genético até o nível de paisagens. Este trabalho visou apresentar o conhecimento atual sobre as invasões biológicas por espécies vegetais, particularmente, sobre a invasora Cryptostegia madagascariensis Bojer ex Decne. Novas introduções são feitas anualmente em todo o mundo e apenas uma pequena parte desses táxons se tornam invasores, mesmo assim, causam sérios danos aos ecossistemas invadidos. O sucesso das plantas infestantes deve-se às características intrínsecas dessas espécies, que garantem as mesmas vantagens competitivas com as espécies nativas e ao nível de perturbação dos novos nichos, que torna os ambientes totalmente favoráveis ao estabelecimento de novas espécies e ao surgimento de áreas monodominadas. Nesse contexto, encontra-se C. madagascariensis, trepadeira de origem da ilha de Madagascar, na África, que foi introduzida no Brasil com fins ornamentais, tornando-se invasora de ecossistemas naturais, principalmente em ambientes de mata ciliar e baixadas úmidas, no domínio da Caatinga e ecossitemas associados.Palavras chave: Espécies exóticas, Caatinga, salinização, déficit hídrico. Abstract: The introduction, accidental or deliberate, of exotic species by different vectors is currently a major global changes, resulting in a number of local and global problems. Although not all introductions of non-native species have negative effects, many of the non-native species can have undesirable effects on biodiversity from the genetic level to the landscape. This work aimed to present the current knowledge on biological invasions by species and particularly on invasive Cryptostegia madagascariensis Bojer ex Decne. New introductions are made every year around the world and only a small part of these taxa become invasive, yet cause serious damage to ecosystems invaded. The success of weed plants is due to the intrinsic characteristics of these species that ensures the same competitive advantages with native species and the level of disruption in new niches which makes them totally supportive environments to establish new species and the emergence of monodominadas areas. In this context is C. madagascariensis, origin of climbing on the island of Madagascar in Africa, which was introduced in Brazil with ornamental purposes, becoming invasive in natural ecosystems, especially in riparian environments and humid lowlands, in the field of savanna and associated ecosystems.Key words: Exotic species, Caatinga, salination, deficit hydride.