Miracle-dz/UniFAR-FTUs huggingface dataset:
Etiologia das Mastites em Cabras e Ovelhas de Raças Naturalizadas Criadas no Semiárido Nordestino (Etiology of Mastitis in native goats and sheeps born and raised in Brazilian semi-arid biom)

Goats are important species of livestock for Brazil especially at the Northeast Region. Because of that Native goats breeds represent important genetic resources for conservation and breeding programs. Although there are some of infectious diseases that may affect to the conservation of this endangered breeds, particularly mastitis. The goal of this study study was to investigate the frequency and the etiology of mastitis in native goats and sheep born and raised in Brazilian semi-arid biom of Paraiba and Pernambuco state. A total of 480 fresh milk samples from of twelve native breeds of goat, from January to July 2012. All of the biological material were plated on Sheep blood supplemented with Agar Base, and incubated at 37oC for 72 h.Gram-staining followed by biochemical tests were made for identification of bacteria. The results of bacteriological examinations showed 13.54% (65/480) of positive samples and the most frequent microorganisms isolated and identified were Staphylococcus spp. , followed by Micrococcus spp. This is the first report of isolation of bacteria that may produce mastitis in native goats and sheep from the northeast semiarid region of Brazil. The results obtained in this study will allow authorities to implement preventive measures for this disease.
Effects of Organic Acids on Escherichia coli O157:H7 Independent of pH under Acidified Food Conditions

BJORNSDOTTIR, KRISTIN. Effects of organic acids on Escherichia coli O157:H7 independent of pH under acidified food conditions. (Under the direction of Dr. Fred Breidt.) Outbreaks of illness caused by acid-tolerant bacterial pathogens in acid foods have raised questions about the safety of acidified foods. However, acidified foods have an excellent safety record which is in part due to the presence of organic acids. The objective of this research was to (1) a develop method that allowed rapid comparison of test acids on E. coli, (2) measure the effectiveness of acetic, malic, citric, and lactic acids to kill Escherichia coli O157:H7 independent of pH effects and (3) examine the mechanism of protection of D-lactic acid and on E. coli O157:H7. Gluconic acid (20 mM), which has been shown to be noninhibitory to E. coli, was used to buffer solutions with 0 mM to 420 mM fully protonated concentrations of the test acids at various pHs and temperatures, with ionic strength adjusted to 0.60-0.68. The effect of anaerobic incubation during acid challenges was examined. We found that using the 96 well microplate and determining viability by plating before and after acid challenge was consistent reproducible and efficient method which allowed us to evaluate up to 96 solution simultaneously. Compared to pH, acetic, malic, pyruvate, and particularly D-lactic acids had a significant protective effect on E. coli O157:H7 at low (120 mM) protonated acid concentrations. Citric acid was not found to exhibit any protective effect at similar concentrations. At higher concentrations L-lactic acid was the most lethal acid followed by acetic, citric and malic acids which had about equal degree of lethality against the O157:H7 strains. To our knowledge this is the first time organic acids have been observed to have a protective effect on pathogenic bacteria. D-lactic acid and pyruvate protected cells against 40 mM protonated acetic acid which has previously shown to reduce cells beyond detection during the acid challenge. These acids may protect the cells by inactivation of reactive oxygen radical species. These results showed that oxygen may play a major role in the effect of organic acids on E. coli O157:H7. It is important to understand the mechanism of this protective effect to be able to assure safety of acid and acidified foods. Additional research will be needed to understand acid specific effects on the survival of E. coli O157:H7 and other acid-resistant food pathogens in acid and acidified foods. In order to reliably and efficiently eliminate acid tolerant pathogens from acid and acidified foods we should have a clear understanding of the environmental factors that affect killing of these microorganisms. Thus, the role of oxygen during acid challenge studies must be determined to assure the safety of acid and acidified products. EFFECTS OF ORGANIC ACIDS ON ESCHERICHIA COLI O157:H7 INDEPENDENT OF pH UNDER ACIDIFIED FOOD CONDITIONS
아시아에서 분리된 viral haemorrhagic septicaemia virus (VHSV) isolates의 계통분석학적 비교

바이러스성 출혈성 패혈증을 일으키는 VHSV는 국내의 넙치양식에 심각한 피해를 주고 있다. 본 연구에서는 우리나라에서 분리한 8종의 VHSV 분리주들의 glycoprotein (G)의 염기서열을 분석하여 KoreanVHSV 분리주들과 기보고된 일본 및 중국의 분리주들을 계통발생학적으로 비교하여 G-protein의 8 부위(G34, C528, A755, T834, T951, T1147, T1221, T1336)에서 국내 VHSV 분리주들의 특이적인 서열을 확인하였고, 전 세계적으로 분리된 VHSV의 분리주들과의 비교결과 8 부위 중 3 부위 (A755, T834, T1221)의 국내VHSV 분리주 특이적 염기서열들을 확인하였다. 또한 중국 유래 VHSV 분리주의 특이적 염기서열11 부위 (C498, C545, C548, C642, G648, T678, A738, C804, C834, G851, C1139)와 일본 유래 VHSV 분리주의 특이적 염기서열 1부위 (C179)를 확인하였다. 이상의 연구결과는 국내 특이적인 염기서열을 확보하여, 구역화된 수산생물 질병의 예찰, 모니터링 및 질병 관리에 유용하게 사용될 것으로 사료된다.
Cataloging the Brassica napus seed metabolome

Abstract The allotetraploid Brassicales member canola (Brassica napus L.) is an oil-seed crop sought primarily for vegetable oil, animal feed, and biofuel. With the advent of -omics (genomics, transcriptomics, proteomics, and metabolomics) technologies, numerous studies have focused on deciphering the functional genes, proteins, and metabolites in canola. However, the oil-yielding seeds are of commercial interest and only a handful of studies using mass-spectrometry (MS) or spectroscopy based platforms have attempted to characterize and quantify metabolites of the seed. Baring metabolite profiling approaches which study groups of chemicals, metabolomic insights into the seeds are very recent. Canola seeds are enriched in fatty acids, glucosinolates, phenylpropanoids (i.e. sinapoyl cholines), flavonoids, and phytohormones among others as has become evident from MS and spectroscopy-based recent studies. Thus, cataloging of the seed metabolome is essential before gaining further insights into their roles in seed biology and plant physiology in order to further understand the qualitative traits and products obtainable from the seeds.
Influenza C incidence and herd immunity in Lancaster, UK, in the winter of 2014-2015

Influenza C is not included in the annual seasonal influenza vaccine, and has historically been regarded as a minor respiratory pathogen. However, recent work has highlighted its potential role as a cause of pneumonia in infants. We performed nasopharyngeal or nasal swabbing and/or serum sampling (n=148) in Lancaster, UK, over the winter of 2014-2015. Using enzyme-linked immunosorbent assay (ELISA), we estimated a seropositivity of 77%. By contrast, only 2 individuals, both asymptomatic adults, were influenza C-positive by polymerase chain reaction (PCR). Deep sequencing of nasopharyngeal samples produced partial sequences for 4 genome segments in one of these patients. Bayesian phylogenetic analysis demonstrated that the influenza C genome from this individual is evolutionarily distant to those sampled in recent years and represents a novel genome constellation, indicating that it is a product of a decades-old reassortment event. Although we find no evidence that influenza C was a significant respiratory pathogen during the winter of 2014-2015 in Lancaster, we confirm previous observations of seropositivity in the majority of the population. We calculate that this level of herd immunity would be sufficient to suppress epidemics of influenza C and restricts the virus to sporadic endemic spread.
Patterns of thermotolerance, chlorophyll fluorescence, and heat shock gene expression vary among four Boechera species and Arabidopsis thaliana

Thermotolerance is a property of all organisms, but owing to their sessile nature, this trait is particularly important in plants. Basal thermotolerance is based on inherent tolerance to heat stress. Acquired thermotolerance is attained through stress-induced gene expression, often of those genes encoding heat shock proteins (HSPs). Both basal and acquired thermotolerance have been extensively studied in model species such as Arabidopsis thaliana (L.) Heynh. , but much less is known about thermotolerance in wild plant species. The aims of this study were to examine the basal and acquired thermotolerance of four species of Boechera, and of A. thaliana. Four species of Boechera native to California were collected and used for this study: B. arcuata (Nutt.) Windham & Al-Shehbaz, B. californica (Rollins) Windham & Al-Shehbaz, B. depauperata (A.Nelson & P.B.Kenn.) Windham & Al-Shehbaz, and B. perennans (S.Watson) W.A. Weber. Seedlings were exposed to both basal and acquired heat stress and then monitored for lea.
Production System for Horticultural Crops Grown in the Penn State High Tunnel

At the Pennsylvania State University (Penn State) High Tunnel Research and Education Facility, a system of production of high-value horticultural crops in high tunnels has been developed that uses plastic mulch and drip irrigation. The Penn State system involves small-scale, plasticapplication equipment that prepares and applies plastic mulch and dripirrigation tape to individual raised beds. It differs from the production system developed by researchers at the University of New Hampshire in which drip-irrigation tape is manually applied to the soil surface and then the entire soil surface in the high tunnel is covered with a black plastic sheet. An overview of the production system used in the Penn State high tunnels is presented in this report.
XVI.—On the Development of the Cranial Muscles in Protopterus and Lepidosiren

The cranial structures of Protopterus and Lepidosiren are now fairly well known, and especially owing to the investigations of Bischoff, Bridge, Fürbringer, Göppert, Humphry, Hyrtl, Jaquet, Luther, Maurer, Owen, Pinkus, Ruge, and Wiedersheim, on their adult anatomy, and to those of Kerr and Agar on their development. Some papers on the development of Ceratodus, which I have recently published, suggested the advisability of obtaining further information on certain points, and this became possible owing to the generosity of Professor Graham Kerr, who gave me both larval and adult stages for the purpose.
Modeling morphogenesis in living matter

Among the fundamental processes involved in the development of an organism, morphogenesis is one of the most complex. During the past centuries, an amount of experimental studies have improved our actual knowledge of the mechanisms which drive many morphogenetic processes in living organisms. Only recently, experiments have been complemented with mathematical modeling as a tool for proving novel insights on morphogenesis in soft tissues. In this context, this thesis aims at developing new mathematical models for the formation of patterns and forms in soft tubular organs. A macroscopic approach is adopted, where the tissue is considered as a continuum body undergoing growth and remodeling. The main idea behind the proposed models is that during growth and remodeling, residual stresses can arise and once they exceed a critical value, an elastic instability can occur in the tissue and lead to a morphological change. Therefore, the morphoelastic models are developed integrating the modern theories of growth and remodeling within the framework of the thermo-mechanics of open systems. The occurrence of the elastic instability is investigated using the method of incremental deformations superposed on finite deformations. The critical thresholds for the onset of the instability are determined together with the modes of the associated instability pattern. The morphoelastic theory is applied to the modeling of different morphogenetic processes occurring in soft tubular organs and gives useful insights in two interesting problems: the formation of the wide range of patterns in the gastro-intestinal system and the occurrence of torsional instabilities in pre-stressed tubular organs.
The effect of nitrogen level on rice growth, carbon-nitrogen metabolism and gene expression

Abstract As one of the essential macroelements, nitrogen (N) plays an important role in plant growth and development. In order to know the effect of different N levels on the rice plant growth and carbon-nitrogen metabolism, we analyzed the rice growth phenotype, leaf SPAD value, photosynthesis, carbon-nitrogen metabolic status and gene expression profile under four different N levels (0×N, 0.1×N, 1×N and 5×N). The plant height and dry weight increased with increasing N levels, whereas an opposite trend was observed for the root length, which decreased with increasing N levels. The leaf SPAD value, stem nitrate concentration, soluble proteins, photosynthetic rate, stomatal conductance and total nitrogen concentration increased with increasing N levels, whereas an opposite trend was observed for soluble carbohydrates and carbon/nitrogen ratio which decreased with increasing N levels. Metabolite profile analysis revealed that the low N treatment caused visible decreases in the concentrations of total sugars and organic acids in the leaves, while caused visible increases in the concentrations of total sugars, organic acids and free amino acids in the roots. Gene expression analysis showed that the transcriptional levels of 5 genes (GS1;3, NADH-GOGAT1, NADH-GOGAT2, PEPC4 and PEPC7) altered significantly under four different N levels.
Dinosaur eggs: gas conductance through the shell, water loss during incubation and clutch size

The conductance of water vapor and respiratory gases by diffusion through the eggshells of Upper Cretaceous dinosaurs has been estimated from measurements of shell and pore geometry in fossil specimens. When compared to recent reptile and bird eggs for which nest environments are known, the highly porous eggshells of three dinosaur species indicate that the dinosaur nests were high in humidity and probably low in oxygen and high in carbon dioxide. Such conditions most likely occurred underground or within an incubation mound. By isolating the eggs from the atmosphere, however, some large sauropods may have been forced to limit their clutch size to numbers small enough to prevent depletion of oxygen and elevation of carbon dioxide to intolerable levels in the nest. Fossil evidence supports this and suggests that one sauropod actually divided her large eggs into several clutches. Each small clutch probably had a metabolic rate similar to those of clutches produced by recent reptiles and mound nesting birds.
Induction of defence-related enzymes in tomato (Solanum lycopersicum) plants treated with Bacillus subtilis CBR05 against Xanthomonas campestris pv. vesicatoria

ABSTRACT Bacterial spot disease caused by Xanthomonas campestris pv. vesicatoria is one of the most important destructive diseases of tomato in many parts of the agricultural world. Therefore, the present study aims to determine the effects of Bacillus subtilis CBR05 inoculation on bacterial spot disease severity and the induction of defence-related enzymes response in tomato. Tomato leaves were evaluated to determine the activities of antioxidant enzymes (superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and polyphenol oxidase (PPO)) and the content of malondialdehyde (MDA). A reduction in bacterial spot severity was observed in plants inoculated with B. subtilis, compared with those of uninoculated controls. A significant increase in SOD, CAT, POD, and PPO activities was observed in plants treated with B. subtilis after 24 h inoculation compared with non-inoculated pathogen control and mock-inoculated controls. Moreover, the MDA content was induced by pathogen infection, and its amount in B. subtilis inoculated plants was significantly lower than that in pathogen control. Our results suggest that early increases in antioxidant enzymes and the reduction in MDA content with B. subtilis inoculation may play a pivotal role in mitigating oxidative stress, thereby induced systemic resistance against bacterial spot disease in tomato.
Relative Attractiveness of Different Pollens to Honeybees when Foraging in a Flight Room and when Fed in the Hive

SummaryAlthough the pigments of pollen responsible for its yellow colour, and also for the absorption of long-wave UV light, attracted foraging honeybees to pollen sources in the flight room, they appeared not to be directly associated with the substance(s) that attracted bees in the hive to eat the pollen fed to them.
A survey of gastrointestinal helminth of stray dogs in Zabol city, southeastern of Iran

Canids are reservoir for some zoonoses helminthic disease. They are one of main public health problem. The aim of this study was to ascertain frequency of gastrointestinal helminthic infection of stray dogs in Zabol city, southeaster of Iran. In this descriptive study, 30 stray dogs were euthanized, intestine was removed by necropsy. Then, the intestines was opened by scalpel and their contents passed through mesh sieve. The helminth were collected. The nematodes were preserved in 70% ethanol with 5% glycerin and cestodes were preserved in 70% ethanol. The cestodes were stained by acetocarmine. The nematodes were cleared by lactophenol. The genus and species of helminth were identified by identification keys. Twenty two (73.3%) of stray dogs had at least one intestinal helminthic infection. Recovered helminth from stray dogs include: Taenia hydatigena (53.3% ), Taenia ovis (20%), Taenia multiceps (6.6%), Mesocestoides spp (10%), Toxocara canis (23.3%), Toxocara cati (3.3%). Data showed that the stray dogs in Zabol city harbor some important zoonoses helminth parasite like Toxocara .
Grizzly bears without borders: Spatially explicit capture–recapture in southwestern Alberta

Local perceptions of grizzly bear (Ursus arctos) numbers in southwestern Alberta, Canada are incongruent with their threatened status. We used non-invasive genetic sampling to estimate grizzly bear density and abundance in southwestern Alberta. We established 899 bear rub objects (e.g., tree, power pole, fence post) for hair sample collection across the study area by surveying trail networks, using geographic information system layers, and working with >70 landowners to identify priority sampling areas. The study area included 2 management zones: the Recovery Zone where the objective was to recover the grizzly bear population, and a Support Zone intended to maintain those bears not exclusively within the Recovery Zone. We visited rub objects every 3 weeks from late May through early November for 8 visits (7 sampling occasions) per field season. We also allowed for opportunistically collected hair samples (e.g., trapped bears, hair at agricultural bear-conflict sites). We identified species, individual identity, and sex based on nuclear DNA extracted from hair follicles. From 2013 through 2014, we identified 164 individual grizzly bears. Using spatially explicit capture–recapture models (SECR), we estimated density in 2 ways. First, we estimated density for each sex and year separately (2013: M = 9.2/1,000 km2 in the Recovery Zone and 8.1/1,000 km2 in the Support Zone, F = 14.9/1,000 km2 in the Recovery Zone and 13.6/1,000 km2 in the Support Zone; 2014: M = 7.2/1,000 km2 in the Recovery Zone and 5.7/1,000 km2 in the Support Zone, F = 9.0/1,000 km2 in the Recovery Zone and 8.5/1,000 km2 in the Support Zone). Second, we did not allow density to vary across years and instead estimated a single density for the study area (M = 8.0/1,000 km2 in the Recovery Zone and 7.1/1,000 km2 in the Support Zone, F = 12.4/1,000 km2 in the Recovery Zone and 10.0/1,000 km2 in the Support Zone). Though yearly variation occurred, we derived from our density estimates an expected abundance of approximately 67.4 resident grizzly bears, indicating a 4% per year increase since a 2007 estimate of 51 bears. These SECR density estimates pertain only to bears with home ranges that were centered within the study area. Using traditional capture-mark-recapture (CMR) models with the same data yielded a higher estimate of bears because it included all bears that were using the study area (2013: F = 68.9, M = 102.6; 2014: F = 63.0, M = 108.6), including >50% of bears previously genotyped in Montana or British Columbia. In contrast with the SECR estimates, the CMR estimates represent the number of bears that southwestern Alberta residents could have encountered (i.e., the population of bears that had potential to have been involved in conflict). Shifts in grizzly bear distribution resulted in large changes in our SECR density estimates between years, whereas our estimate of the number of bears using the area remained constant. We recommend increased inter-jurisdictional monitoring and management of this international grizzly bear population. © 2016 The Wildlife Society.
Bioaccumulation and changes in the photosynthetic apparatus of Prosopis juliflora exposed to copper

The effect of copper toxicity on the photosynthetic activities and bioaccumulation in different tissues of Prosopis juliflora was investigated using three CuSO 4 concentrations (10, 50 and 100 mM) added under hydroponic conditions. Copper concentration and chlorophyll fluorescence were measured after 48 h of copper stress. The results obtained in this study show that increasing levels of 50 and 100 mM Cu 2+ resulted in a significant accumulation of this metal mainly in roots compared with control roots. On the other hand, our result showed a significant reduction of maximum photochemical efficiency of photosystem II (F v /F m ) and the activity of photosystem II (F v /F 0 ) ratios in P. juliflora leaf treated with 100 mM Cu 2+ with respect to control after 4h of exposure. These changes suggested that the photosynthetic apparatus of P. juliflora was the primary target of the Cu 2+ action. Therefore the information provided by this short-term (48 h) experiment in P. juliflora showed that several physiological processes are activated, in which the copper uptake by roots and their accumulation in tissues play a central role. In conclusion, the chlorophyll fluorescence parameters can be used as a useful physiological tool to assess early changes in photosynthetic performance of P. juliflora in response to copper pollution in short-term. Finally, the present study showed that P. juliflora is a promising prospect for heavy metals phytoremediation purposes occurring in arid and semi-arid climates in the northwest Mexico.
Inhibition of Foodborne Bacterial Pathogens by Bacteriocins from Lactococcus lactis and Pediococcus pentosaceous 1.

The objective of this study was to develop an appropriate method for detecting specific bacteriocin-mediated inhibition. This method could be used to determine the effectiveness of known bacteriocin-producing lactic acid bacteria against foodborne pathogens. Lactococcus lactis subsp. lactis 11454, Pediococcus pentosaceous FBB61, and P. pentosaceous FBB63-DG2 were evaluated for their ability to inhibit a variety a foodborne pathogens. Of the three procedures used, the agar spot method was chosen as the most reproducible and reliable assay method. After optimization of the plate agar media composition, and the time and temperature of the assay, the three bacteriocin-producing strains were screened against a broad range of Gram-positive and Gram-negative foodborne pathogens. The three bacteriocin-producing organisms inhibited the following Gram-positive foodborne pathogens: Bacillus cereus , Clostridium perfringens . Staphylococcus aureus , and 22 representatives of 5 species of Listeria including L. monocytogenes , L. ivanovii , L. innocua , L. seeligeri , and L. welshimeri . Additionally, strain 11454 slightly inhibited several Gram-negative foodborne pathogens, including Aeromonas hydrophila AH2, Escherichia coli 0157:H7, Vibrio cholerae 851, and V. parahaemolyticus A865957. Gram-negative organisms not inhibited by any of the bacteriocin-producing organisms included Campylobacter jejuni , several serovars of Salmonella enteriditis , and species of Yersinia and Vibrio .