Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of sensory experience in intrinsic biophysical diversity of glomerular interneurons of the olfactory bulb

Investigating the adaptive properties of neuronal circuits is central to understanding the operations of the brain. The mouse olfactory bulb is a structure well suited for studying these processes, since it is composed of relatively simple excitatory and inhibitory networks. Recently, it has been shown that principal neurons (mitral cells) of the olfactory bulb that participate in the same glomerular circuit exhibit similar biophysical properties based on their Ih-mediated membrane potential sag. In many cell types, including mitral cells, Ih is known to profoundly influence excitability and thus impact the input/output function of individual neurons and networks. Like principal cells, inhibitory neurons are known to exhibit Ih that influences their integrative properties. In the olfactory bulb, interneurons of the glomerular layer can receive input from one or more glomerular networks and are thought to mediate lateral or centre-surround inhibition. The regulation of Ih in these cells could thus be used as a gain-control mechanism to facilitate contrast enhancement. During my project, I therefore investigated the diversity of Ih in GAD65+ and TH+ juxtaglomerular cells belonging to the same or different glomeruli to determine the diversity of Ih-mediated membrane potential sag within and across different inhibitory circuits. I found that the two juxtaglomerular populations differed substantially in their levels of membrane potential sag. Contrary to TH+ juxtaglomerular cells, the similarity in the amount of sag recorded in GAD65+ juxtaglomerular cells was high when two neurons were found to participate in the same glomerular circuit. Furthermore, the sag amplitude of interneurons affiliated to a specific glomerular circuit was upregulated when mice were exposed to odour stimuli. This indicates that, at least for GAD65+ juxtaglomerular cells, the amount of Ih membrane sag reflects local network processing of odour information.
Climate change impacts modeling on winter wheat yield under full and deficit irrigation in Myandoab-Iran

ABSTRACT In this research, impact of climate change on wheat yield was simulated using SWAP in Myandoab, Iran. Field data of wheat in 2004–2005 and 2005–2006 periods were used for calibration and validation of the SWAP, respectively. The HadCM3 outputs, for A1B, A2 and B1 scenarios and 2046–2065 periods, were used in SWAP and wheat yield in mentioned period was compared with base period. Three irrigation levels, based on meeting 100, 70 and 50% of the crop ET demand, were used to study the climate change effects on wheat yield in full and deficit irrigation conditions. The results showed that temperature and reference evapotranspiration will increase in 2055s. Temperature increase cause to decrease crop growing period and crop evapotranspiration. The results showed that the negative impact of temperature increase has dominated to the positive impact of CO2 concentration and the yield is reduced. For full irrigation situation, the reduction will be 24.1, 22.4 and 20.8% in A1B, A2 and B1, respectively. Reduction in yield can be related to the shorter maturity period of the crop. The results showed that under deficit irrigation, the yield is also decreased but this decrease rate of yield is higher in full irrigation.
HPTLC and bioautography analysis of Casuarina equisetifolia L. and Sphaeranthus indicus extracts against Salmonella spp.

Plants have been used for medicinal purpose since ancient times. Secondary metabolites of medicinal plants have shown to possess curing activity against different ailments as well as infections caused by microorganisms. Salmonellosis, a foodborne infection, is emerging as a life threatening disease because of drug resistant strains of Salmonella spp. In present investigations, plants Casuarina equisetifolia and Sphaeranthus indicus were found to possess significant inhibitory activity against Salmonella species. HPTLC and bioautography assay of methanolic extracts of C. equisetifolia indicated polyphenols as major active compounds against S. typhi. The present study indicates that the polyphenols of this plant can be used as a potential drug against infectious disease caused by S. typhi.
Integrated analysis for identifying Portulaca oleracea and its sub-species based on chloroplastic and nuclear DNA barcoding

Abstract The taxonomy of Portulaca oleracea has been considered as being complex since the aggregate is composed of many subspecies or a group of micro-species based on seed-coat characters, seed size, and chromosome number. In order to enlarge the background of the extent of genetic variability between and within Tunisian P. oleracea accessions, a combined morphological and molecular approach was adapted, in the present survey. The morphological analyses of the spontaneous Tunis population display high intra population variability characterized by two distinct morphotypes corresponding to the botanical forms (wild and cultivated plant). Furthermore, the molecular approach based on sequences data related to chloroplastic and ribosomal DNA, was used to understand this variability. The obtained results highlighted the greater molecular variability of this plant and allowed to segregate between morphotypes and genotypes of Portulaca. Mostly, this work shows the important contribution of DNA barcoding approach in resolving low-level-taxonomy problems to distinguish between natural populations and varieties.
PRELIMINARY PHYTOCHEMICAL SCREENING OF VARIOUS EXTRACTS OF PUNICA GRANATUM PEEL, WHOLE FRUIT AND SEEDS

Herbal medicines as the major remedy in traditional system of medicine have been used in medical practices since antiquity. In addition to its ancient historical uses, pomegranate is used in several systems of medicine for a variety of ailments. The objective of the present study was to investigate the presence of various phytochemicals from the ethanolic, aqueous and chloroform extracts of Punica granatum peel, whole fruit and seeds. The three different extracts from peel were found to contain Triterpenoids, Steroids, Glycosides, Flavonoids, Tannins, Carbohydrate & Vitamin C. The three different extracts from whole fruit were found to contain Triterpenoids, Steroids, Glycosides, Saponins, Alkaloids, Flavonoids, Tannins, Carbohydrate & Vitamin C. The three different extracts from seeds were found to contain Triterpenoids, Steroids, Glycosides, Saponins, Alkaloids, Tannins, Carbohydrate & Vitamin C. The generated data from the three different extracts of Punica granatum peel, whole fruit & seeds provided the basis for its wide uses in the traditional & folk medicines.
Characterizing Excluded Strand DNA Interactions with Hexameric Helicases and Determining Roles in Unwinding Mechanisms

DNA replication is an essential process for all living organisms, and errors in this process can lead to genetic mutations and disease. An assembly of protein machinery, termed the replisome, coordinates enzymatic activities at the replication fork. The DNA helicase is the heart of the replisome unwinding double-strand DNA at the head of the progressing replisome and providing single-strand templates for DNA polymerases. Replicative helicases are composed of six subunits, and arranged in a ring-like structure where ATP hydrolysis events provide the energy to translocate upon and unwind the DNA. The mechanism of helicase unwinding has been widely studied, but there are still many aspects that remain unknown. It is generally thought that these helicases encircle one strand of DNA while the other is excluded from the central channel of the helicase. Our lab has previously identified an interaction between the excluded strand and the helicase exterior that was important for unwinding in the archaeal MCM helicase. The steric exclusion model of replicative helicase unwinding was expanded to include the excluded strand interactions in this newly proposed steric exclusion and wrapping (SEW) model. Here, we present work that expands on the SEW model by revealing that the bacterial DnaB and mitochondrial Twinkle replicative helicases also interact with the excluded strand. We have also developed a new single-molecule FRET analysis program to characterize these excluded strand interactions. Although the excluded strand interaction is seen in multiple replicative helicases, we propose distinct roles for the interaction based on functional assays and known differences in replisome architecture across the various organisms. We have also begun to characterize the helicase-excluded strand wrapping interaction in the presence of other replisome components, namely the single-strand binding (SSB) protein. We further characterized the archaeal SSB protein from Sulfolobus solfataricus and provide evidence for a novel DNA-helicase-SSB ternary complex. Overall, this thesis makes significant contributions to the understanding of replicative helicase unwinding mechanisms by expanding upon the current steric exclusion and wrapping model and introduces a novel single-molecule FRET analysis program that we anticipate will be adopted and utilized by others in the field.
Process for the production of triglycerides

A process for the production of triglycerides comprising: (a) subjecting a first triglyceride comprising at least 40 mol% oleic acid residues, based on the total acyl groups in the triglyceride, to a reaction with stearic acid , at least one ester of stearic acid or a mixture thereof, to obtain a composition comprising 1,3-distearoyl 2-dell glyceride and trioleyl glyceride; (b) treating the composition to form a first fraction with a greater weight of oleyl groups compared to said composition and a second fraction with a greater amount by weight of stearoyl groups compared to said composition; (c) hydrolyzing the first fraction to form oleic acid; (d) reacting said oleic acid or an ester thereof with a triglyceride comprising at least 50 mol% of palmitic acid residues, based on the total acyl groups, to form a composition comprising 1,3-dioleyl 2-palmitoyl glyceride.
Evaluation of wild barley species as possible sources of drought tolerance for arid environments

Abstract In this study, agro-morphological and yield-related traits associated with drought tolerance in 80 barley genotypes belonging to 15 wild species together with the cultivated one, and their potential to improve adaptation to different levels of drought stress conditions (moisture environments) were studied. There was significant genetic variation among the genotypes and species for all of the measured traits, as well as differential responses of genotypes across environments. The results indicated high variation for grain yield (GY) under drought stress among the genotypes, and that some of the wild genotypes had consistently superior specific adaptation to the water stress conditions. The genotypes belong to wild barley species, especially Hordeum murinum and Hordeum marinum had lower GY but relatively higher yield stability under different environments. Traits such as number of seed per plant and hundred kernel weight were positively correlated with GY in all of the environments. High negative correlation between GY and days to ripening was observed only under intense drought environment, showing drought escape as a strategy of wild plants under highly stressed conditions. Grouping of the genotypes by principal component analysis completely separated cultivated barley and its progenitor (Hordeum vulgare ssp. spontaneum) from other wild genotypes; however, the other wild species were slightly separated from each other. In addition, the Iranian and foreign genotypes did not completely separate from each other. The identified wild barley genotypes with favourable characters and high drought tolerance could be used in genetic studies and barley improvement programmes especially for drought stress.
Exploring the chemo-textural familiarity hypothesis for scorpion navigation

Abstract The navigation by scene familiarity hypothesis provides broad explanatory power for how bees and ants navigate from the hive to distant food sources and back. The premise is that the visual world is decomposed into pixelated matrices of information that are stored and readdressed as the insects retrace learned routes. Innate behaviors in these insects (including learning walks/flights and path integration) provide the important goal-directed views to allow the initial retracing (i.e., the insect must learn the scene while moving toward the goal because everything looks different while moving away). Scorpion navigation may use a similar premise, with the chemical and textural features of the environment substituting for visual input. Scorpion pectines support thousands of chemo- and mechano-sensitive units called peg sensilla, each containing at least 10 energetically expensive sensory neurons. We have long wondered why pectines have so many pegs and associated neurons. Many sand scorpions emerge onto the surface from their home burrows at night to pursue insect prey and somehow find their way back to their burrows. Based on the measured resolution of peg sensilla, we have calculated that sufficient information exists in sand's texture to enable scorpions to retrace previously experienced paths with little to no chance of confusion. Preliminary evidence of learning walks and path integration in scorpions is also congruent with the navigation by chemo-textural familiarity hypothesis.
Genome-wide Association Studies Reveal Similar Genetic Architecture with Shared and Unique QTL for Bacterial Cold Water Disease Resistance in Two Rainbow Trout Breeding Populations

Bacterial cold water disease (BCWD) causes significant mortality and economic losses in salmonid aquaculture. In previous studies, we identified moderate-large effect QTL for BCWD resistance in rainbow trout (Oncorhynchus mykiss). However, the recent availability of a 57K SNP array and a genome physical map have enabled us to conduct genome-wide association studies (GWAS) that overcome several experimental limitations from our previous work. In the current study, we conducted GWAS for BCWD resistance in two rainbow trout breeding populations using two genotyping platforms, the 57K Affymetrix SNP array and restriction-associated DNA (RAD) sequencing. Overall, we identified 14 moderate-large effect QTL that explained up to 60.8% of the genetic variance in one of the two populations and 27.7% in the other. Four of these QTL were found in both populations explaining a substantial proportion of the variance, although major differences were also detected between the two populations. Our results confirm that BCWD resistance is controlled by the oligogenic inheritance of few moderate-large effect loci and a large-unknown number of loci each having a small effect on BCWD resistance. We detected differences in QTL number and genome location between two GWAS models (weighted single-step GBLUP and Bayes B), which highlights the utility of using different models to uncover QTL. The RAD-SNPs detected a greater number of QTL than the 57K SNP array in one population, suggesting that the RAD-SNPs may uncover polymorphisms that are more unique and informative for the specific population in which they were discovered.
Mechanistic pathways of diversity-function relationships in Australian ants

i Table of contents . iv Acknowledgements . vii Authorship declaration . ix Chapter 1 General introduction . 1 1.1 Biodiversity and ecosystem function in the modern world . 2 1.2 Diversity-function theory . 3 1.3 Diversity-multifunction theory . 5 1.4 Multi-functionality in the context of ecological trade-offs . 7 1.5 Ants as a model consumer level taxon for testing BD-EF theory . 8 1.6 Study region . 12 1.7 Thesis structure . 12 1.8 Key research questions and thesis outline . 12 Chapter 2 Woody plant richness does not influence invertebrate community reassembly trajectories in a tree diversity experiment . 17 2.1 Abstract . 18 2.2 Introduction . 19 2.3 Methods . 22 2.3. 1 Experimental design . 22 2.3. 2 Statistical Analysis . 27 2.4 Results . 31 2.4. 1 Higher taxa responses . 33 2.4. 2 Ant species richness, abundance and evenness responses . 33 2.4. 3 Ant community compositional responses . 37 2.4. 4 Differing trajectories of functional groups . 37 2.5 Discussion . 39 2.5. 1 Woody plant presence promotes invertebrate diversity . 39 2.5. 2 Woody plant diversity does not influence invertebrate diversity . 41 2.5. 3 Removal of weedy understory leads to biodiversity gains . 43 2.5. 4 Implications for conservation and restoration practices . 44 2.6 Supplementary Information . 46 2.6. 1 Validation of dropping nitrogen treatment from the final analyses . 46
A new genus for the eastern dwarf galagos (Primates: Galagidae)

1African Primate Initiative for Ecology and Speciation, Department of Zoology & Entomology, University of Fort Hare, Alice 5700, South Africa 2Africa Earth Observatory Network – Earth Systems Science Research Institute, Nelson Mandela Metropolitan University, Port Elizabeth 6031, South Africa 3Biogéosciences, UMR CNRS 6282, Université de Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000 Dijon, France 4EPHE, PSL Research University, 75014 Paris, France 5School of Archaeology and Anthropology, Australian National University, Canberra, ACT 2601, Australia 6Conservation International, 10 Bayles Avenue, Stony Brook, NY 11790-2122, United States of America. 7Dipartimento di Scienze della Vita e Biologia dei Sistemi Life Sciences and Systems Biology, Università degli Studi di Torino, Via Accademia Albertina, 13, 10123 Torino, Italy 8Behavioral Ecology and Sociobiology Unit, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany 9Department of Anthropology, The University of Texas at San Antonio, TX 78249, United States of America
Genomic integrative analysis to improve fusion transcript detection, liquid association and biclustering

More data provide more possibilities. Growing number of genomic data provide new perspectives to understand some complex biological problems. Many algorithms for single-study have been developed, however, their results are not stable for small sample size or overwhelmed by study-specific signals. Taking the advantage of high throughput genomic data from multiple cohorts, in this dissertation, we are able to detect novel fusion transcripts, explore complex gene regulations and discovery disease subtypes within an integrative analysis framework. In the first project, we evaluated 15 fusion transcript detection tools for paired-end RNA-seq data. Though no single method had distinguished performance over the others, several top tools were selected according to their F-measures. We further developed a fusion meta-caller algorithm by combining top methods to re-prioritize candidate fusion transcripts. The results showed that our meta-caller can successfully balance precision and recall compared to any single fusion detection tool. In the second project, we extended liquid association to two meta-analytic frameworks (MetaLA and MetaMLA). Liquid association is the dynamic gene-gene correlation depending on the expression level of a third gene. Our MetaLA and MetaMLA provided stronger detection signals and more consistent and stable results compared to single-study analysis. When applied our method to five Yeast datasets related to environmental changes, genes in the top triplets were highly enriched in fundamental biological processes corresponding to environmental changes. In the third project, we extended the plaid model from single-study analysis to multiple cohorts for bicluster detection. Our meta-biclustering algorithm can successfully discovery biclusters with higher Jaccard accuracy toward large noise and small sample size. We also introduced the concept of gap statistic for pruning parameter estimation. In addition, biclusters detected from five breast cancer mRNA expression cohorts can successfully select genes highly associated with many breast cancer related pathways and split samples with significantly different survival behaviors. In conclusion, we improved the fusion transcripts detection, liquid association analysis and bicluster discovery through integrative-analysis frameworks. These results provided strong evidence of gene fusion structure variation, three-way gene regulation and disease subtype detection, and thus contribute to better understanding of complex disease mechanism ultimately.
Field observations of the ecology and habitsof mangrove rivulus (Rivulus marmoratus)in Belize and Florida(Teleostei: Cyprinodontiformes: Rivulidae)

This report provides a synopsis of fil. '1d studil'S of RiI'll/liS man1l0ralllS from two population surveys of mangro\'C islands adjacent to the Belize barrier fl'Cf and observations made over fifteen years at several sites in South Florida. Florida populations consist ne.uly exclusively of hermaphrodites (> 99%), while the Belize populations containl'<i a significant proportion (10·25%) of males. Our combined observations demonstrate that this species is not "rare" as previously thought, but elusive and highly adapted to microhabitats within mangrove forests. Standard ichthyo· logical collecting techniques are indfl'Ctive in this habitat and have previously failed to reveal the strength of the association of R. mllrm"mllls with the mangral ecosystem.
Different leaf extracts from Brunfelsia uniflora in mice

portuguesNo Brasil, pelo menos 16 especies de plantas toxicas podem afetar o sistema nervoso central dos bovinos. Recentemente no estado do Piaui, no Nordeste do Brasil, Brunfelsia uniflora foi relatada como causadora de sinais nervosos em jumentos, bovinos e pequenos ruminantes. Para avaliar a toxicidade de B. uniflora, 20 camundongos foram distribuidos em quatro grupos de cinco animais recebendo diferentes extratos da planta. Os extratos de alcaloides, flavonoides, saponinas ou solucao salina (grupo controle) foram administrados por gavagem. Apos a administracao dos extratos, em dose unica (5g kg-1), todos os animais foram observados diariamente. Os camundongos que receberam os extratos de B. uniflora apresentaram sinais clinicos moderados a graves, incluindo piloeracao, vocalizacao e convulsoes. Todos os camundongos que receberam extrato de saponinas morreram entre 10 e 20 minutos apos. A avaliacao bioquimica serica dos animais que receberam saponinas, revelou discretos aumentos nos niveis de proteina total e diminuicao nos niveis de magnesio e cloro. Conclui-se que, as saponinas presentes nas folhas de B. uniflora induzem efeitos neurologicos toxicos agudos e, morte em camundongos. Palavras-chave: toxicidade; alcaloides; saponinas; flavonoides; Brunfelsia; Solanaceae EnglishIn Brazil, at least 16 poisonous plant species can affect the central nervous system of livestock. Recently in the state of Piaui, Northeastern Brazil, Brunfelsia uniflora was reported as a cause of nervous signs in donkeys, cattle, and small ruminants. In order to assess the toxicity of B. uniflora extracts, 20 Swiss mice were distributed into four groups (n=5) receiving by gavage alkaloids, flavonoids, saponins, or saline (control group). After administration of the extracts in a single dose (5g kg-1), all mice were observed daily for clinical signs. Mice that received the extracts showed moderate to severe clinical signs, including piloerection, vocalization, and seizures. All mice dosed with saponins died between 10 and 20min after administration. Serum biochemical evaluation of animals that received saponins revealed slight increases in total protein levels and decreased magnesium and chlorite levels. In conclusion, saponins of B. uniflora leaves induced acute toxic neurological effects and death in mice. Key words: toxicity; alkaloids; saponins; flavonoids; Brunfelsia; Solanaceae