Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessment of functional characteristics of small GTPases using small molecules

Rab and Rho subfamilies of GTPases are functionally linked to intracellular trafficking and organization of the cytoskeleton respectively. Despite their roles, use of small molecule inhibitors or activators to map the functionality of these GTPases remains largely underexplored due to lack of suitable compounds. In this dissertation, we report on the functional characterization of Rab7 and Rac1 GTPases using small molecules. 2(benzoylcarbamothioylamino)-5,5-dimethyl-4,7dihydrothieno[2,3-c]pyran-3-carboxylic acid (PubChem #: CID1067700) has been used to characterize Rab7. Using bead based flow cytometry, CID1067700 was found to have significant inhibitory potency on Rab7 nucleotide binding with a respective inhibitory efficacy of 80% for BODIPY-GTP and viii 60% for BODIPY-GDP binding. Rac1 has been functionally characterized by nonsteroidal anti-inflammatory drug (NSAID), R-Naproxen in the context of ovarian cancer. R-Naproxen isoform functionally inhibited Rac1 in the cell lines assayed relative to SNaproxen and structurally similar 6-methoxy-2-naphthylacetic Acid (6-MNA). Inhibition is based on interference with membrane distribution of Rac1 rather than overall protein levels. Taken together, this study has identified the first competitive GTPase inhibitor (CID1067700) and also demonstrated the potential utility of the compound for dissecting GTPase enzymology. The study has also shown that R-Naproxen blocks activation of Rac1 small GTPase in ovarian cancer cells with implications for the inhibition of ovarian cancer cell proliferation, migration, and invasion.
Effect of variable and constant thermal conditions on embryonic and early larval development of fish from the genus Leuciscus (Cyprinidae, Teleostei)

The aim of this study was to determine the effects of variable and constant thermal conditions on embryonic development of three endangered fish species from the genus Leuciscus. Wild living spawners of dace Leuciscus leuciscus (L.), ide L. idus (L.) and chub L. cephalus (L.) were obtained from rivers belong - ing to the Pasleka River basin (northeastern Poland) and next transported to a hatchery for the purpose of conducting artificial reproduction. The obtained eggs were fertilized and next incubated under a variety of thermal protocols: slow gradual heating of water (M1), rapid increase in temperature at the end of incuba tion (M2), fluctuating temperature (M3) and two constant temperatures (optimum and sublethal). Variable thermal changes of water were also continued after hatching, up to the yolk sac resorption by larvae. During the study it was shown that relative to incubation at optimal temperatures (12.3°C for dace, 15.7°C for ide and 19.0°C for chub), thermal modifications had no clear influence on a decrease in survival rates (differences among regimes did not exceed 5%) and increase in developmental deformations (differences below 1.0%) observed among the hatched embryos. The duration of egg incubation and developmental rate increased with increasing temperature . In the systems with modified temperature the embryonic development of dace (from fertilisation to commencement of exogenous food intake) took from 9.5 to 22.5 days, for ide from 6.1 to 12 days and for chub from 5.0 to 10.5 days. The yolk sac resorption stage in the particular species occurred from 11.7 to 23 days for dace, 7.5 to 13.2 days for ide and 5.5 to 12.8 days for chub. Different time of hatch - ing was also reflected in the level of ontogeny of hatched embryos. Among the fish hatched at modified temperatures the largest sizes, similar to those characteristic of fish incubated at optimum temperatures, were observed in individuals originating from variants where the temperature fluctuated. The developmental disproportions among the embryos of studied species originating from different thermal regimes observed at the time of leaving the egg shells were definitely larger than during the following development stages. This study also confirmed that the embryos of studied species can adapt to increasing water temperature due to global warming up to 19.0 (dace), 23.0°C (ide) and 27.5°C (chub). The obtained results are very important not only for practical purposes but also from physiological and ecological aspects.
Individual-based modeling of environmental quality effects on early life stages of fish: A case study using striped bass

We demonstrate an individual-based approach to population modeling to evaluate environmental quality effects on early life stages of fishes. We believe that, regardless of the modeling approach, environmental quality effects ultimately must be evaluated at the population level. Determining population-level consequences of changes in environmental quality is critical because the population is the relevant endpoint of interest with respect to success of the species and its availability for harvest. It offers a common metric upon which to compare among different environmental factors, effects, and life stages.
Complete genome nucleotide sequence of Pepper mild mottle virus isolated in the Federal District, Brazil

Occurrence of Pepper mild mottle virus (PMMoV) on Capsicum plants has become common in Brazil. Despite the importance of this virus, genome information is still lacking for South American isolates. In this report, the first complete genome sequence of a Brazilian isolate of PMMoV (BR-DF01) was elucidated and compared with other PMMoV sequences. The nucleotide sequence of the complete genome of BR-DF01 isolate shared the highest nucleotide identity (99.54%) with the Japanese isolate JP-J, which does not overcome L3 resistance gene of Capsicum plants, as also observed for BR-DF01. The coat protein (CP) amino acid sequence of these two isolates was identical, which suggested that CP is the key factor for L-based resistance breaking. Phylogenetic analysis implied that BR-DF01 and PMMoV isolates belonging to Cluster I, including JP-J isolate, may share a common ancestral origin.
RICE WHITE TIP NEMATODE (APHELENCHOIDES BESSEYI) IN RICE GROWING AREAS OF TURKEY [EL NEMATODO DE LA PUNTA BLANCA DEL ARROZ (APHELENCHOIDES BESSEYI) EN ZONAS DE CULTIVO DE ARROZ DE TURQUÍA]

White tip nematode (Aphelenchoides besseyi Christie, 1942) is economically important in rice growing areas and ithas been recorded in many countries. In this study systematic sampling of rice seed samples of different region in Turkeywas done. Aphelenchoides besseyi individuals obtained were evaluated morphologically and fit the original definition ofprevious morphometric and morphological characteristics. We found Turkey specimens to have a shorter spear (8.95 μm)but Allen (1952) and Fortuner (1970) found the spear length to be 10 μm and 11.9 μm, respectively.
Investigation of leptin genotypes and economically important dairy traits in jersey cows.

Dairy farming is one of the most important agricultural industries in South Africa, and thus improving the performance of dairy cows, with respect to economically important dairy traits, would be beneficial. Selection of dairy cows has traditionally been phenotypic, but new molecular techniques have made it possible to evaluate phenotypic dairy traits at the DNA level, providing the possibility of more accurate selection. The economically important dairy traits, milk production and reproductive performance, are quantitative traits, and are therefore controlled by many genes and the environment. A number of genes have been identified that have been shown to influence economically important dairy traits, including the lep gene. This gene encodes the hormone leptin, which has been proven to regulate feed intake, energy balance, fertility and immune function. A polymorphism has been identified in the lep gene, which may be associated with economically important dairy traits. This study on a South African Jersey herd investigated the possible association of the polymorphism, RFLP-Kpn 21, with milk production and reproductive performance. The lactation records of fifty Jersey cows that completed their first lactation between 1997 and 2004 were collected, and these cows were genotyped for the RFLP-Kpn 21 polymorphism, located at exon 2 of the lep gene. This involved the extraction of DNA from venous blood, using a salting out technique. The extracted DNA was amplified using PCR primers; the reverse primer included a purposeful mismatch. The role of the purposeful mismatch was to create a recognition site for a restriction enzyme (Kpn 21), thus allowing the alleles of the polymorphism to be identified through a restriction digestion protocol. Two alleles were identified, the Cand the Tallele. The genotype of each cow was identified using PAGE. The significance of the genotype effects on the milk production traits and the reproductive performance traits were estimated using the F-statistic provided by a GLM Univariate analysis. In conclusion, no significant effect of the
Morphometrics and the comparative method: studying the evolution of biological shape

Phylogenetic comparative methods are one of the most important parts of the morphometric toolkit for studies of morphological evolution. The assessment of repeated independent events of evolution of phenotypic and associated ecological-functional traits is still a starting point for the study of adaptation, but modern comparative approaches go beyond correlative methods, allowing for the modeling of evolutionary scenarios and analyses of trait evolution patterns. The evidence for adaptive change due to ecological diversification is stronger (even if still circumstantial) if models that predict increases in diversification rate fit the data well and the morphological changes are associated with ecological and functional changes. A large body of literature is dedicated to methodological and theoretical aspects of comparative methods, but in the context of univariate traits. On the other hand, biological shape is a complex trait, and morphometric data is essentially multivariate. Whereas most comparative methods allow for direct multivariate extensions, dimension reduction is an almost certain requirement due to the high dimensionality of morphometric data sets and the large number of evolutionary parameters that need to be estimated by comparative methods. Objective methods with considerable statistical support to determine data dimensionality exist, but the applied literature usually relies on subjective criteria to how many shape dimensions should be retained. The most appropriate calculation and interpretations of principal components, the most popular dimension reduction method, are also topics that should be considered more carefully in applications. The maturity of comparative methods and the development of model-based approaches linking macroevolutionary patterns and microevolutionary processes provide an exciting perspective for the study of morphological evolution. Download the complete "Yellow Book" on "Virtual Morphology and Evolutionary Morphometrics in the new millenium". 6283
Description of Neolamprologus timidus, new species, and review of N. furcifer from Lake Tanganyika (Teleostei: Cichlidae)

Neolamprologus timidus, new species, is described from Ulwile Island and adjacent localities on the Tanzanian coast of Lake Tanganyika. The species was observed or collected along about 100 km of coastline from KolwePoint, Cape Mpimbwe, south to Kisi Island. It is distinguished from the most similar species, N. furcifer, by presenceof scales on most of the cheek, long pectoral fin and pelvic fin with the second ray longer than the first. Neolamprologus timidus is sympatric with N. furcifer at Kolwe Point and south to Kampempa Point, and at Lupitaand Ulwile Islands south to Kisi Island, but N. furcifer is otherwise absent from the range of N. timidus. Two morphologically distinct forms are recognized in N. furcifer. Samples of N. furcifer from Ulwile Island and slightly more southern localities possess a caudal fin with rounded lobes and long middle rays, appearing onlyslightly emarginate. Samples of N. furcifer from Udachi and nearby localities possess pointed caudal-fin lobeswith greatly elongated streamers, similar to N. timidus and to N. furcifer from other parts of Lake Tanganyika, including the type specimens from the southern part of the lake. The variation in caudal-fin shape may be an expression of character displacement as it occurs in the area of sympatry between N. timidus and N. furcifer. MitochondrialDNA sequences are nearly identical in samples of N. furcifer with pointed or rounded caudal fin. A molecular phylogenetic analysis of a large set of lamprologin cichlids using two mitochondrial genes corroborates earlier analyses and places N. furcifer and N. timidus in different clades with different species of Neolamprologus, Julidochromis, Chalinochromis, and Telmatochromis despite sharing a unique combination of fin and bodyshape, and colour pattern. A 4648 base-pair multiloci analysis of a smaller number of species using fragments ofthree mitochondrial and two nuclear genes resolves N. furcifer and N. timidus in sister clades, but the N. timidus clade also includes Telmatochromis brachygnathus, and N. furcifer is sister species of Chalinochromis brichardi.
Gene expression profiling of chicken intestinal host responses

Chicken lines differ in genetic disease susceptibility. The scope of the research described in this thesis was to identify genes involved in genetic disease resistance in the chicken intestine. Therefore gene expression in the jejunum was investigated using a microarray approach. An intestine specific cDNA microarray was generated from a normalized and subtracted library. Gene expression in young chickens was studied using two different disease models, malabsorption syndrome and Salmonella enteritidis . For each model two different chicken lines were studied, which differed in susceptibility to the specific diseases. Gene expression differences between the chicken lines were found under control and under infected conditions. In the studies described here the main focus was on genes that could be involved in disease susceptibility. Large differences between the chicken lines with different genetic backgrounds were found in their gene expression responses to the infections. After malabsorption syndrome the more susceptible chicken line regulated immune related genes, genes involved in food absorption and genes with unknown functions. The chicken line most susceptible for salmonella upregulated genes involved in inflammation, or with unknown functions, whereas the more resistant chicken line regulated genes involved in acute phase response, the fibrinogen system, actin polymerisation, and also genes with unknown functions. Most gene expression responses to both infection models were found 1 day post infection. Gene expression differences between the two chicken lines lead to the hypothesis that immunological differences could be the basis of differences in susceptibility for Salmonella . Therefore the two chicken lines were studied for the phagocytic properties of intestinal mononuclear cells and these properties were different for the two chicken lines. Also, a decrease in the number of CD4 + T-cells and macrophages in response to the Salmonella infection was found only in one chicken line. In both chicken lines the number of CD8 + T-cells increased, but faster in the susceptible chicken line. So genetic background influences intestinal gene expression responses and immunological responses.
Human impacts on connectivity in marine and freshwater ecosystems assessed using graph theory: a review

Human activities are altering the processes that connect organisms within and among habitats and populations in marine and freshwater (aquatic) ecosystems. Connectivity can be quantified using graph theory, where habitats or populations are represented by ‘nodes’ and dispersal is represented by ‘links’. This approach spans discipline and systemic divides, facilitating identification of generalities in human impacts. We conducted a review of studies that have used graph theory to quantify spatial functional connectivity in aquatic ecosystems. The search identified 42 studies published in 2000–14. We assessed whether each study quantified the impacts of (1) habitat alteration (loss, alteration to links, and gain), (2) human movements causing species introductions, (3) overharvesting and (4) climate change (warming temperatures, altered circulation or hydrology, sea-level rise) and ocean acidification. In freshwater systems habitat alteration was the most commonly studied stressor, whereas in marine systems overharvesting, in terms of larval dispersal among protected areas, was most commonly addressed. Few studies have directly assessed effects of climate change, suggesting an important area of future research. Graph representations of connectivity revealed similarities across different impacts and systems, suggesting common strategies for conservation management. We suggest future research directions for studies of aquatic connectivity to inform conservation management of aquatic ecosystems.
Development of assays for therapeutic screening in myotonic dystrophy

Myotonic dystrophy (DM) is an autosomal dominant inherited multisystemic neuromuscular disease. The molecular mechanism for DM is mediated by toxic RNAs containing expanded repeat units. DMI is caused by a CTG repeat expansion in 3'-UTR of the DMPK gene while DM2 is caused by CCTG repeat in intronl of the ZNF9 gene. The molecular features of DM are formation of RNA foci, co-localisation of MBNL proteins with ribonuclear foci, splicing defects of a subset of pre-mRNAs with elevation ofCUGBPI in DMl. In order to develop therapy for DM, assays were designed based on the molecular characteristics of the disease to screen compounds. Two primary assays were based on disruption of nuclear foci and on correction of misregulated splicing involving intron2 CLCNI. The first part of this report deals with the development of a nuclear foci assay and splicing construct assay. Both assays were optimised in HTS and utilized in screens for molecules that clear nuclear foci from DM cells and correct misregulated splicing in intron2 of CLCNI respectively. High throughput screens of kinase and phosphatase inhibitor libraries using the nuclear foci assay and CLCNI splicing construct assay yielded two positive hits: protein kinase C inhibitors designated in the compound library as D8 (hypericin) and D9 (Ro-31-8220). The second part of this thesis deals with the confirmation of compound hits obtained from the primary screen. I examined two aspects: mutant DMPKtranscript entrapment in nucleus and splicing defects associated with the disease. A BpmJ restriction assay was used to test the effect of compounds on mutant DMPK transcripts showed that both D8 and D9 were unable to release the mutant transcript into the cytoplasm. D8 demonstrated efficacy in reversing spliceopathy in alternative splicing assays of JR, SERCAI MBNLI and MBNL2 while D9 did not have this effect except on MBNLI which showed a very minor efficacy.
Order parameters of unsaturated phospholipids in membranes and the effect of cholesterol: a 1 H- 13 C solid-state NMR study

Most biological phospholipids contain at least one unsaturated alkyl chain. However, few order parameters of unsaturated lipids have been determined because of the difficulty associated with isotopic labeling of a double bond. Dipolar recoupling on axis with scaling and shape preservation (DROSS) is a solid-state nuclear magnetic resonance technique optimized for measuring 1 H- 13 C dipolar couplings and order param- eters in lipid membranes in the fluid phase. It has been used to determine the order profile of 1,2-dimyristoyl-sn- glycero-3-phosphocholine hydrated membranes. Here, we show an application for the measurement of local order parameters in multilamellar vesicles containing unsaturated lipids. Taking advantage of the very good 13 C chemical shift dispersion, one can easily follow the segmental order along the acyl chains and, particularly, around the double bonds where we have been able to determine the previously misassigned order parameters of each acyl chain of 1,2-dioleoyl-sn-glycero-3-phos- phocholine (DOPC). We have followed the variation of such order profiles with temperature, unsaturation content and cholesterol addition. We have found that the phase formed by DOPC with 30% cholesterol is analogous to the liquid-ordered (lo) phase. Because these experiments do not require isotopic enrichment, this technique can, in principle, be applied to natural lipids and biomembranes.
Extraction of trypsin inhibitor from three legume seeds of the Royal Project Foundation.

Trypsin inhibitor was isolated from navy bean (Phaseoulus vulgaris), red kidney bean (Phaseoulus vulgaris L) and adzuki bean (Vigna angularis) from the Royal Project Foundation, Thailand. Extraction of navy bean and red kidney bean with 0.02 M NaOH showed the highest recovery of trypsin inhibitor, while water was the best extractant for adzuki bean. The extraction time significantly affected the trypsin inhibitor recovery (p<0.05). Two hours of extraction gave the highest yield of trypsin inhibitor from three legumes. The trypsin inhibitors were estimated to have molecular weight of 132, 118 and 13 kDa under non-reducing conditions for navy bean, red kidney bean and adzuki bean, respectively. The inhibitory activities of the inhibitor from these legumes were lost when they were treated with β-mercaptoethanol, indicating the subunit of polypeptide in its composition.
Are Managers 'Under-the-Weather' During Earnings Conference Calls?

Earnings conference calls represent an important communication channel between managers and investors. We examine the impact of weather-induced mood on manager behavior during these calls. Using a large sample of earnings conference calls from 2006 to 2017, we find managers speak more negatively and with less (more) quantitative information (uncertainty) when local weather conditions are bad. We further identify that this negative relation is less pronounced for CFOs than CEOs. Financial expertise mitigates negative behavior bias induced by weather and we confirm with subgroups of CEOs with previous financial experience. We document a significantly negatively market reaction to weather-induced behavior that cannot be explained by existing textual analysis methods. Our results remain significant after adding controls for investor mood, separating firms into those from big and small states, mediation tests, firm fixed effects, and propensity score matching. Taken together, our findings suggest that exogenous effects of bad weather significantly impact manager behavior that the market views negatively.
The Routing Structure of Questionnaires

Increasingly, survey data are collected by means of computer-assisted interviewing (CAI) systems. The expanding capacities of computer hardware and software have made it possible to develop very large and complex electronic questionnaires. Unfortunately, it has also become more and more difficult for developers, interviewers, supervisors and managers to keep control of the content and structure of CAI instruments. Therefore, tools are needed for producing a readable and understandable presentation of an electronic questionnaire. One aspect of such documentation is the routing structure of questionnaires. This paper discusses a number of ways to document the routing structure.