Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of long-term warming and enhanced nitrogen and sulfur deposition on microbial communities in a boreal peatland

With ongoing environmental change, it is important to understand ecosystem responses to multiple perturbations over long time scales at in situ conditions. Here, we investigated the individual and combined effects of 18 years of warming and enhanced nitrogen and sulfate deposition on peat microbial communities in a nutrient-poor boreal mire. The three perturbations individually affected prokaryotic community composition, where nitrogen addition had the most pronounced effect, and its combination with the other perturbations led to additive effects. The functional potential of the community, characterized by shotgun metagenomics, was strongly affected by the interactive effects in the combined treatments. The responses in composition were also partly reflected in the functional gene repertoire and in altered carbon turnover, i.e. an increase of methane production rates as a result of nitrogen addition and a decrease with warming. Long-term nitrogen addition and warming-induced changes caused a shift from Sphagnum-dominated plant communities to vascular plant dominance, which likely transact with many of the observed microbial responses. We conclude that simultaneous perturbations do not always lead to synergistic effects, but can also counteract and even neutralize one another, and thus must be studied in combination when attempting to predict future characteristics and services of peatland ecosystems.
Review of Aphidiinae parasitoids (Hymenoptera: Braconidae) of the Middle East and North Africa: key to species and host associations

In this study, a total of 108 Aphidiinae species, belonging to 18 genera, associated with 240 aphid species in 16 countries of the Middle East and North Africa are reviewed. 743 host aphid-parasitoid associations are listed. New material was collected from various regions of Saudi Arabia during 2011–2013. Three species including Aphidius avenae Haliday, 1834, Aphidius platensis Brèthes, 1913 and Praon barbatum Mackauer, 1967 are first recorded for the fauna of this country. Lysiphlebus marismortui Mescheloff & Rosen, 1990 syn. nov. is classified as the junior synonym of Lysiphlebus confusus Tremblay & Eady, 1978. An illustrated up-to-date key to all known species of Aphidiinae that occur in the Middle East and North Africa is provided. The findings are discussed in relation to the overall parasitoid-aphid associations in the target investigated region.
Disease threshold for cherry leaf spot incidence on commercial sweet cherry cultivars

The aim of this study was to demonstrate the 10% threshold level for cherry leaf spot incidence on 23 commercial sweet cherry cultivars in two training systems. Twenty three cherry cultivars were evaluated in the two training systems with a spacing of 4 x 1 m and with a spacing of 2 x 5 m. Results showed that leaves of many cultivars were heavily infected, e.g. cultivars (cvs) ’Biggareau Burlat’, ’Sunburst’, while others showed low disease incidence e.g. cvs ’Celeste’ and ’Blaze Star’. According to the 10 % threshold level, cv ’Celeste’ proved to be the most resistant cultivar to leaf infection, while cv ’Münchebergi korai’ exceeded extremely the 10% threshold level. Leaf spot incidence was affected by training system on most cultivars. Thirteen cultivars had less than 10% infection in the 4 x 1 m spacing (i.e. they did not reach the 10% disease threshold level). At the same time, only 3 cultivars showed less than 10% infection in the 5 x 2 m spacing.
A genetic and biochemical study of obesity in Egypt

gene polymorphism , biomarker Background: Numerous studies have documented the association adiponectin (ADIPOQ) gene polymorphisms with obesity but the consequences are indecisive. The purpose of this work is to study the connection between adiponectin gene polymorphisms G276T and T45G with obesity and biochemical variants in Egyptian population. Material and methods: Genotyping of G276T single nucleotide polymorphisms of adiponectin gene was performed by Alleles Refractory Mutation Systems PCR(ARMS PCR) method, while Genotyping of T45G single nucleotide polymorphism of adiponectin gene was performed by RFLP PCR method. The analysis was done in 172 matched person; 89 obese patients, 43 overweight patients, and 40 normal healthy controls. Biochemical parameters were calculated through standard procedures. Results: For adiponectin polymorphism G276T, it was related to overweight under Co dominant and recessive models (P= 0.010, P= 0.036) respectively, also it was associated with obesity under recessive model (P= 0.048). Higher BMI was associated with heterozygous GT and homozygous GG carriers of G276T (P= 0.032) compared to TT carriers, For adiponectin gene polymorphism T45 G, it was associated with Obesity under Co dominant and dominance models (P= 0.046, P= 0.045) respectively. Heterozygous GT and homozygous GG carriers of T45G were related higher BMI (P= 0.029), triglyceride (P= 0.029), and VLDL (P= 0.026) compared to TT carriers at adiponectin polymorphism T45G. Conclusion: The study suggests that the ADIPOQ 276G>T and ADIPOQ 45T>G polymorphisms may be vital indicators of obesity and associated complications in several population. © 2017 Publisher All rights reserved. 249 Noha Mohamed Said et al, 2017 Biochemistry letters, 12(20) 2017, Pages 248-264
Pivotal involvement of the CX3CL1-CX3CR1 axis for the recruitment of M2-TAMs in skin carcinogenesis

We previously revealed the crucial roles of CX3CL1-CX3CR1 axis in skin wound healing. Although repeated wounds frequently develop into skin cancer, the roles of CX3CL1 in skin carcinogenesis remain elusive. Here, we proved that CX3CL1 protein expression and CX3CR1+ macrophages were observed in human skin cancer tissues. Similarly, we observed the enhancement of CX3CL1 expression and the abundant accumulation of CX3CR1+ tumor-associated macrophages (TAMs) with M2 phenotypes in the skin carcinogenesis process induced by the combined treatment with 7,12-dimethylbenz-(a)anthracene (DMBA) and 12-O-tetradecanoylphorbol-13-acetate (TPA). In this mouse skin carcinogenesis process, CX3CR1+ TAMs exhibited M2 phenotypes with the expression of Wnt3a and angiogenic molecules including vascular endothelial growth factor (VEGF) and matrix metalloproteinase (MMP)-9. Compared to wild-type mice, CX3CR1-deficient mice showed fewer numbers of skin tumors with a lower incidence. Concomitantly, M2-macrophage numbers and neovascularization reduced with the depressed expression of angiogenic factors and Wnt3a. Thus, the CX3CL1-CX3CR1 axis can crucially contribute to skin carcinogenesis by regulating the accumulation and functions of TAMs. Thus, this axis can be a good target for preventing and/or treating skin cancers.
Comparative metagenomics of microbial mats from hypersaline lakes at Rottnest Island (WA, Australia), advancing our understanding of the effect of mat community and functional genes on microbialite accretion

Microbial mats are organosedimentary structures organized as multilayered carpets of microbial communities. Within the microbial mat microenvironment, the occurrence of different metabolic processes can lead to local chemistry alterations, inducing carbonate precipitation. Carbonate accretion in lithifying microbial mats typically induces microbialite formation, a poorly understood process, but studies have suggested that taxonomic composition of lithifying mats and their predominant metabolic pathways contribute. In contrast to lithifying mats, non‐lithifying mats, which do not form microbialites, can sporadically trap carbonate sand grains that are actively bound to the microbial mat through the production of extracellular polymeric substances. Both mat types occur in hypersaline lakes at Rottnest Island (Western Australia) and are currently under threat due to pollution and thus are being managed by the relevant government agency. Characterizing the microbial communities and functional genes of both mat types may help to develop strategies to better manage their ecosystem and elucidate microbialite formation processes. Metagenomics was used to compare the taxonomic and functional diversity of both mat types to determine whether differences in their taxonomy and functional capacity may influence their ability to form microbialites. Results revealed that both mat types harbor taxa (e.g., Firmicutes and Archaea), and functional genes (e.g., associated with photosynthesis, carbon, and sulfur cycles) that are known to play important roles in microbialite formation. This suggests that although non‐lithifying mats are not accreting carbonate, they have the potential to form microbialites. Further investigation is needed to determine whether environmental factors could be inhibiting carbonate precipitation within these mats.
The Laboratory Domestication of Zebrafish: From Diverse Populations to Inbred Substrains

The zebrafish (Danio rerio) is a model vertebrate widely used to study disease, development and other aspects of vertebrate biology. Most of the research is performed on laboratory strains, one of which has been fully sequenced in order to derive a reference genome. It is known that the laboratory strains differ genetically from each other, but so far no genome-scale survey of variation between the laboratory and wild zebrafish populations exists. Here we use Restriction-Associated DNA sequencing (RAD-seq) to characterize three different wild zebrafish lineages from a population genetic viewpoint, and to compare them to four common laboratory strains. For this purpose we combine new genome-wide sequence data obtained from natural samples in India, Nepal and Bangladesh with a previously published dataset. We measured nucleotide diversity, heterozygosity, allele frequency spectra and patterns of gene conversion, and find that wild fish are much more diverse than laboratory strains. Further, in wild zebrafish there is a clear signal of GC-biased gene conversion that is missing in laboratory strains. We also find that zebrafish populations in Nepal and Bangladesh are distinct from all the other strains studied, making them an attractive subject for future studies of zebrafish population genetics and molecular ecology. Finally, isolates of the same strains kept in different laboratories show a clear pattern of ongoing differentiation into genetically distinct substrains. Together, our findings broaden the basis for future genetic and evolutionary studies in Danio rerio.
Extension of the Action Verb Corpus for Supervised Learning

The Action Verb Corpus (AVC) is a multimodal dataset of simple actions for robot learning. The extension introduced here is especially geared to supervised learning of actions from human motion data. Recorded are RGB-D videos of the test scene, grayscale videos from the user’s perspective, human hand trajectories, object poses and speech utterances. The three actions TAKE, PUT and PUSH are annotated with labels for the actions in different granularity.
[Embargoed] Confirmation of the barley vacuolar pyrophosphatase HvHVP10 as a candidate gene for salinity tolerance

xix CERTIFICATION OF DISSERTATION . xxi ACKNOWLEDGEMENTS . xxii 1 Background and Literature Review . 1 1.1 Barley . 1 1.2 Salinity as a limitation on crop production . 1 1.3 Mechanisms of salinity tolerance . 3 1.4 Sodium exclusion QTL (HvNax3) in barley . 5 1.4. 1 Vacuolar proton pumps . 9 1.4. 2 Vacuolar H-Pyrophosphatase (V-PPase). 11 1.4. 3 Other candidate genes within the HvNax3 QTL . 21 1.5 Research Questions . 23 1.6 Aims/Objectives of the project. 23 1.7 Significance/Contribution to the discipline . 24 2 Confirmation of the barley V-PPase HvHVP10 as a candidate gene for the HvNax3 sodium exclusion QTL in barley . 25 2.
Effect of Crop Sequenceof Rice, Maize and Fahll Berseem Residues on Wheat Productivity and Soil Fertility

A two years' field trial was conducted at Gemmaiza Agricultural Research Station, during 2013/14 and 2014/15 seasons to study the effect of plant residues; rice straw, corn stover and fahal berseem as a cash crop on wheat production and soil properties. The experimental design was strip-plot design in three replications. Where rice and maize were occupied the vertical stripplots, while the plant residues were occupied the horizontalstrip plots. Rice straw treatments were: untreated soil with rice straw, treated soil with chopped rice straw output of 33 % from the previous crop and fahal berseem one cut residues incorporated in soil followed by wheat. The same treatments were repeated with corn residues. Results showed that available N, P and K in soil were increased resulting from the decomposition of rice straw and corn stover. This improved soil fertility which is reflected in increasing the productivity of wheat crop compared with the other treatments. Also, application of different treatments significantly influenced the yield and its attributes of wheat crop in both seasons. The highest values of cereal units, economic evaluation and net return were resulted from the crop sequence corn followed by fahal berseem one cut followed by wheat, compared to other treatments in both seasons, respectively.
Genetic variants influence the response of body composition and insulin resistance to dietary monounsaturated fatty acids consumption

ii ACKNOWLEDGMENT . iv DEDICATION. vii TABLE OF CONTENTS . viii LIST OF TABLES . xv LIST OF FIGURES . xvii ABBREVIATIONS . xix CHAPTER I . 1 GENERAL INTRODUCTION . 1 1.
Detection of Some SalmonellaEnteritidisVirulence Genes by Multiplex-PCR Assay Using Two Different DNA Extraction Methods

The aim of this study was screeningsome Salmonella genus-specific virulence genes by multiplex-PCR technique using a group of primers targeting InvA,SipB,SpiA,CdtB,PefA genes using two different DNA extraction methods. A total of fifteen Salmonella isolates from patient's stool samples were collected. Suspected colonies onHiChromeRajhans (HCR) Medium and XLD medium were selected, and biochemical and serological tests were then performed for identification of Salmonella. Identification of Salmonella serotypes was done in Central Public Health Laboratory (CPHL) with O and H antisera. Extraction of bacterial genome was down by boiling method and salting out method using commercial kit (WizardÂ® Genomic DNA purification Kit). The results showed that all screened genes (chromosomally and plasmid-mediated) were found in all tested SalmonellaEnteritidis strains except cdtB gene which is thought to be limited only to certain SalmonellaTyphi andS.Paratyphi A strains. Moreover,the presence of pefA gene could be depending on host-adapted serovars. Boiling extraction method and commercial kit both gave a good result in multiplex-PCR technique. In conclusion, the results from this study of occurrence of SPIs genes support previous studies suggesting that these virulence genes are widely distributed among Salmonella and required for full Salmonella virulence, in addition, the boiling method was good, easy and specific method for multiplex-PCR technique.
Expressão do receptor c-MET, seu ligante HGF e VEGF como marcadores tumorais no câncer gástrico dos tipos intestinal e difuso na população brasileira: estudo piloto para padronização da técnica de PCR quantitativo

INTRODUCAO: O carcinoma gastrico (CG) e a terceira causa de morte, entre os tumores malignos, no mundo, provocando, aproximadamente, 900.000 mortes/ano. Alteracoes em oncogenes que codificam receptores tirosina-quinase desempenham papel importante napatogenese do CG. O gene MET e um proto-oncogene que codifica o receptor tirosina-quinase c-MET e se faz necessario para desenvolvimento embrionario e reparo tecidual. O Fator de Crescimento Hepatocitico (HGF) e o unico ligante conhecido para o receptor c-MET. Aativacao oncogenica de MET suprime a apoptose e promove a sobrevivencia da celula, proliferacao, migracao, diferenciacao e angiogenese. Dentre os fatores angiogenicos, o VEGF e o regulador principal. Sua funcao biologica inclui promover a mitose de celulas endoteliais e estimular sua proliferacao. A expressao desses biomarcadores no CG e relativamente recente e estudos de base populacional sao necessarios para definicao do padrao de expressao.OBJETIVOS: Padronizar a tecnica qPCR para avaliar, quantitativamente, em amostras teciduais parafinadas, a presenca de expressao dos genes MET, HGF e VEGF no CG dos tipos difuso e intestinal. METODOS: Foram estudados 20 pacientes com CG, sendo dez do tipo intestinal (idade media 72,1 anos) e dez do tipo difuso (idade media 50,1 anos). Em todos os pacientes foram analisadas amostras teciduais provenientes do tumor e de areas distantes do tecido tumoral. A expressao relativa dos marcadores tumorais c-Met, HGF e VEGF foirealizada pela tecnica de qPCR, atraves da comparacao entre amostras tumorais e nao tumorais, quando normalizados com o gene de referencia constitutivo GAPDH. RESULTADOS: Para c-Met, 18/20 (90%) pacientes expressaram esse marcador e 9/20 (45%) superexpressaram esse gene, sendo tres pacientes com CG tipo intestinal e seis comCG tipo difuso. Para o HGF, apenas 7/20 (35%) expressaram esse gene, sendo o mesmo superexpresso em 4/20 (20%) pacientes, sendo dois pacientes com CG tipo intestinal e dois pacientes com CG do tipo difuso. Para o VEGF, 20/20 (100%) pacientes expressaram esse marcador e em 12/20 (60%) pacientes foi observada superexpressao, sendo oito pacientes com CG tipo difuso e quatro com CG tipo intestinal. CONCLUSOES: A tecnica de qPCR foi padronizada e se mostrou viavel para analise de expressao dos genes MET, HGF e VEGF nas amostras parafinadas de CG do tipo intestinal e difuso. A continuidade desse estudo, com maior amostragem, sera conduzida para a caracterizacao do padrao de expressao desses biomarcadores no CG humano na populacao brasileira.
An Economic Assessment of Genetic Information: Leptin Genotyping of Breeding Cattle

Mitchell, Jay Douglas; M.S.; Department of Agribusiness aod Applied Economics; College of Agriculture, Food Systems, and Natural Resources; North Dakota State University; October 2006. An Economic Assessment of Genetic Information: Leptin Genotyping of Breeding Cattle. Major Professor: Dr. Eric A. De Vuyst. Recent studies show polymorphisms in the leptin gene significantly impact milk production in dairy cattle. If the leptin gene were to have a similar impact on beef cattle, calf weaning weights would be expected to increase from the increased milk production in the cows. Since weaning weight is a key component of profitability in a cow-calf operation, leptin genotyping may prove to have ao economic impact in breeding cattle. However, no research has been done to link the economic impact of increased milk production to breeding cattle. Using 595 observations from genotyped cows spaoning 11 years (1995-2005), calf weaoing weight by genotype is estimated as a function of calf and dam characteristics and environmental effects. A MIXED procedure, utilizing data from 89 culled cows, is used to determine statistical differences in average cull age by genotype. A simulation model calculates mean annualized equivalent return by genotype and breed using the regression coefficients aod residuals and 16 years of price data. Results show that at least one T-allele in breeding cows increases calf weaoing weight, average cull age, and annualized equivalent return compared to cows with homozygous C-alleles. These results indicate that there may be future premiums and discounts for breeding cattle based on genotype. Seedstock producers could potentially begin to segregate herds based upon genotype so that they could sell genotypic registered products. Cow-calf producers may also benefit from this knowledge by increasing the amount of TT genotype breeding cattle in their herd to maximize profits.
Cooperative DNA binding by proteins through DNA shape complementarity

Abstract Localized arrays of proteins cooperatively assemble onto chromosomes to control DNA activity in many contexts. Binding cooperativity is often mediated by specific protein–protein interactions, but cooperativity through DNA structure is becoming increasingly recognized as an additional mechanism. During the site-specific DNA recombination reaction that excises phage λ from the chromosome, the bacterial DNA architectural protein Fis recruits multiple λ-encoded Xis proteins to the attR recombination site. Here, we report X-ray crystal structures of DNA complexes containing Fis + Xis, which show little, if any, contacts between the two proteins. Comparisons with structures of DNA complexes containing only Fis or Xis, together with mutant protein and DNA binding studies, support a mechanism for cooperative protein binding solely by DNA allostery. Fis binding both molds the minor groove to potentiate insertion of the Xis β-hairpin wing motif and bends the DNA to facilitate Xis-DNA contacts within the major groove. The Fis-structured minor groove shape that is optimized for Xis binding requires a precisely positioned pyrimidine-purine base-pair step, whose location has been shown to modulate minor groove widths in Fis-bound complexes to different DNA targets.
Studies on Association between Yield and Yield Attributing Traits in Cluster Bean [Cyamopsis tetragonoloba (L.) TAUB.] Genotypes

Cluster bean [Cyamopsis tetragonoloba (L.) Taub] is also known as guar bean, has a chromosome number of 2n= 2x=14. It is an arid legume crop, mostly cultivated in the arid and semi-arid areas as it is drought tolerant. The long deep taproot system enables the plant to grasp maximum water from the soil making it an ultimate drought resistant crop. It has the freedom from serious pests and diseases and long storage life of the harvested pods.
Evidence for a deep, distributed and dynamic semantic code in human ventral anterior temporal cortex

How does the human brain encode the meanings of words and objects? Most theories propose that local neural populations independently encode various semantic features. Alternatively, meanings may arise as distributed neural patterns that change radically in real time as a stimulus is processed. We introduce a technique for revealing a dynamically-changing distributed code in simulated neural data, then apply it to neural signals collected from human cortex while participants named line drawings of common items. The data reveal a dynamic semantic code along ventral temporal cortex possessing stable elements posteriorly and rapidly-changing elements anteriorly. The results challenge the established view of semantic representation, resolve conflicting findings from past research, and provide a new framework for understanding the time-course of distributed representation in the brain. One Sentence Summary The brain’s code for semantic information changes rapidly in real time as a stimulus is recognized.
Observaciones sobre las chisas (Coleóptera: Scarabaeidae) en Nariño

Durante los anos 1986-1988 se realizaron observaciones periodicas en los municipios de Yacuanquer y Ospina (departamento de Narino), en lotes de cebada infestados con chisas con el objeto de conocer las especies, su comportamiento en el campo y dano. Los muestreos se realizaron cada quince dias y en cada lote se analizaron cinco sitios de 30 x 30 cm cada uno. Los resultados indican que en el municipio de Yacuanquer existen las especies Ancognatha scarabaeoides Burmeister, A. nigriventris Otoya, A. vu/garis Arrow (Scarabaeidae-Dynastinae) Astaena sp. y PhyIlophaga sp. (Scarabaeidae-Meloionthinae), mientras que en Ospina predomina Astaena sp. Cuando las larvas de tercer instar ocurren desde Ia germinacion hasta los 30 dias el dano se manifiesta como trozador de plantulas y Si se presentan en Ia epoca de espigamiento y lineado de grano, actuan como comedores de ra(ces, por Ia cual Ia planta pierde anclaje, hay vaneamiento y volcamiento. De todas las especies de chisas encontradas, las mas abundantes y que mayores perdidas causan son: A. scarabaeoides, Astaena sp. y Phyllophaga sp. La especie A. scarabaeoides presenta una generacion al ano, mientras que una generacion de Astaena sp. representa cada dos anos.