Miracle-dz/UniFAR-FTUs huggingface dataset:
SAKE (Single-cell RNA-Seq Analysis and Klustering Evaluation) Identifies Markers of Resistance to Targeted BRAF Inhibitors in Melanoma Cell Populations

Single-cell RNA-Seq’s (scRNA-Seq) unprecedented cellular resolution at a genome wide scale enables us to address questions about cellular heterogeneity that are inaccessible using methods that average over bulk tissue extracts. However, scRNA-Seq datasets also present additional challenges such as high transcript dropout rates, stochastic transcription events, and complex population substructures. Here, we present SAKE (Single-cell RNA-Seq Analysis and Klustering Evaluation): a robust method for scRNA-Seq analysis that provides quantitative statistical metrics at each step of the scRNA-Seq analysis pipeline including metrics for: the determination of the number of clusters present, the likelihood that each cell belongs to a given cluster, and the association of each gene marker in determining cluster membership. Comparing SAKE to multiple single-cell analysis methods shows that most methods perform similarly across a wide range cellular contexts, with SAKE outperforming these methods in the case of large complex populations. We next applied the SAKE algorithms to identify drug-resistant cellular populations as human melanoma cells respond to targeted BRAF inhibitors. Single-cell RNA-Seq data from both the Fluidigm C1 and 10x Genomics platforms were analyzed with SAKE to dissect this problem at multiple scales. Data from both platforms indicate that BRAF inhibitor resistant cells can emerge from rare populations already present before drug application, with SAKE identifying both novel and known markers of resistance. In addition, we compare integrated genomic and transcriptomic markers to show that resistance can arise stochastically within multiple distinct clonal populations.
‘Columbia Sunrise’ Thornless Trailing Blackberry

‘Columbia Sunrise’ is a new, very early ripening, thornless trailing blackberry (Rubus subg. Rubus Watson) cultivar from the U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS) breeding program in Corvallis, OR, released in cooperation with Oregon State University’s Agricultural Experiment Station. ‘Columbia Sunrise’ is introduced as a very early ripening, thornless trailing blackberrywith large, firm fruit with a very good flavor and good yields that will be suited for hand-harvested fresh and machine-harvested processed markets. ‘Columbia Sunrise’ should be adapted to areas where other trailing blackberries can be grown successfully. A U.S. Plant Patent has been applied for (USPPAF 15/330,508).
Thaumatococcus daniellii leaves: its chemical compositions, antioxidant and antimicrobial activities.

The preliminary phytochemical investigation of n-hexane, ethyl acetate and methanol extracts of Thaumatococcus daniellii leaves revealed the presence of fats and oils, terpenoids, flavonoids, steroids and glycosides. The antimicrobial tests against some strains of bacteria and fungi showed inhibitions at moderate to high concentrations. Methanol extract of the plant exhibited low 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activity with IC 50 of 615.14 μg/ml. Gas chromatography-mass spectrometry (GC-MS) characterization of n-hexane, ethylacetate and methanol extracts of T. daniellii leaves identified , thirteen and fifteen compounds, with tetracontane (28.76%) and L-ascorbic acid (15.07%); hexadecanoic acid (21.62%) and γ-sitosterol (11.06%); and naphthalene-1,2,3,5,6,7,8,8a-octahydro-1,8a-dimethyl-7-(1-methylethenyl)-,1R(1.alpha.,7.beta.,8a.alpha.] (26.90%) and hexadecanoic acid (12.60%) being the major compounds respectively. The GC-MS analysis revealed various peaks of bioactive compounds of which the antioxidant and antimicrobial activities of the plant have been attributed to the prominent compounds in synergy with all the other compounds present in smaller quantities in the extracts. Keywords : Thaumatococcus daniellii, Antimicrobial activity, Antioxidant activity, GC-MS analysis, L-ascorbic acid, γ-sitosterol
Evidence of early defence to Ascochyta lentis within the recently identified Lens orientalis resistance source ILWL180

R. H. R. Dadu , R. Ford, P. Sambasivam and D. Gupta* School of Agriculture and Food, Faculty of Veterinary and Agriculture Sciences, The University of Melbourne, Dookie Campus, Vic. ; Environmental Futures Research Institute, School of Natural Sciences, Griffith University, Nathan Campus, Qld; and Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville Campus, Vic. , Australia
Vertical distribution of foliar biomass in western larch (Larix occidentalis)

Western larch (Larix occidentalis Nutt.) is an endemic pioneer species in northwestern North America and unique as a deciduous conifer and the most shade-intolerant, fastest growing, and most fire-resistant species in the northwestern United States. To better understand its production ecology, we used a multilevel modeling approach to analyze the intrinsic dynamics of western larch vertical foliage distribution and compared it with other species. We found that western larch allocates foliage into a more diffuse distribution as the crown lengthens, whereas shade-tolerant evergreens concentrate foliage into a more monolayered distribution higher within the crown as it lengthens. Crown foliar biomass scaled linearly with diameter at breast height, indicating that western larch does not fill volume in the crown with foliage at an increasing rate like other conifers. Our model supports the hypothesis that foliar shade intolerance and water stress jointly influence foliage allocation in this deciduous conifer.
SOMATIC EMBRYOGENESIS AND IN-VITRO REGENERATION OF RICE (ORYZA SATIVA L.) CULTIVARS UNDER ONE-STEP AND MULTIPLE-STEP SALINITY STRESSES

The present study aimed to examine the effect of one-step and multiple-step salinity stress on the somatic embryogenesis of rice cultivars within the solid and liquid (cell suspension) culture media conditions. Five rice cultivars, including Puteh Perak, Mahsuri, Basmati-370, Nona Bokra and Khari Gunja were used in this study. The callus cultures were induced from the rice seed embryo using solid MS media containing 10 µM 2,4-D and 2 µM Kinetin. The results indicated that in the one-step NaCl treatment, the growth of the control calli and cell suspensions of the cultivars was decreased, and significant morphological changes were observed. In contrast, the multiple-step NaCl treatment of the calli and cell suspensions led to higher growth of the cultures in the presence of NaCl compared to the controls. The solid MS media, containing 3 µM IAA and 40 µM Kinetin performed as the best media for plant regeneration in both calli and cell suspensions. The regeneration capacity of the one-step treated calli and cell suspensions were decreased with the increased concentration of NaCl in the media. Higher regeneration frequencies occurred in the multiple-step treated calli of Pueth Perak and Nona Bokra compared to their controls while the other cultivars showed a lower regeneration under the same trend of salinity. The plant regeneration capacity of the multiple-step treated, as well as the control cultures, was decreased with increasing the cultures age. However, the NaCl-treated cultures maintained higher regeneration capacity under the both modes of treatment (one-step and multi-step) for up to 48 weeks compared to the control treatments.
Diversity and mesoscale spatial changes in the planktonic cnidarian community under extreme warm summer conditions

Knowing the variations of planktonic cnidarians under climate change conditions is of importance due to the key role of carnivorous gelatinous zooplankton in the pelagic ecosystem. We investigated the abundance, spatial distribution, species richness and community structure of planktonic cnidarians in a temperate area, the NW Mediterranean, during the extremely warm summer of 2003 and the average summer of 2004. The surveys covered a broad and heterogeneous area. During the warm summer, the cnidarian community was half as abundant as during 2004, whereas its diversity was higher. The mesoscale spatial distribution of several species varied between the years. The structure of the community had a coastal-offshore ordination in the typical summer, but a north–south one in the warm summer when the temperature gradient prevailed instead of the bathymetry. Only hydromedusae were more abundant during the warm summer. The dominant siphonophore, Muggiaea atlantica, exhibited one of the greatest abundance decreases in 2003. Our results emphasize that exceptionally warm summer conditions could reduce gelatinous zooplankton abundance and change their latitudinal distribution and community composition. We stress the importance of mesoscale plankton surveys, including detailed taxonomic identification, as a critical tool for better understanding marine ecosystem responses to climatic variability.
Décryptage du Polymorphisme de Compatibilité dans l’interaction entre Biomphalaria glabrata et Schistosoma mansoni : une approche intégrative

Biomphalaria glabrata est un mollusque d’eau douce, vivant en Amerique latine. Ce planorbe est principalement connu pour etre l’hote intermediaire de Schistosoma mansoni, vers plat parasite responsable de la bilharziose intestinale, seconde endemie parasitaire humaine mondiale derriere le paludisme.Dans ce contexte, il apparait clairement qu’une meilleure comprehension de l’interaction entre le parasite et le mollusque, hote intermediaire, represente une voie de recherche prometteuse. La comprehension des interactions immunologiques entre l’escargot et le parasite ainsi que des mecanismes moleculaires par lesquels les deux partenaires interagissent apparait comme un pre-requis a la decouverte de nouvelles cibles ou de nouvelles strategies afin de developper desmoyens de lutte contre le pathogene.Le projet de cette these s’inscrit dans cette optique et vise a une meilleure comprehension des interactions immunologiques entre le mollusque Biomphalaria glabrata et le trematode Schistosoma mansoni. Differents aspects de l’interaction entre B.glabrata et S.mansoni ont ete explores, des bases moleculaires et cellulaires a l’interaction tripartite entre l’immunite du mollusque, son microbiote et le pathogene. Dans un premier temps nous avons pu demontrer ungradient d’infectivite des parasites et de susceptibilite des mollusques de differents provenances geographiques. De plus, l’interaction immunologique entre le mollusque et le parasite est supportee par une adaptation locale, a l’echelle moleculaire. Nous avons egalement pu montrer qu’une opsonine, la BgTEP, jouait un role cle dans l’interaction entre B.glabrata et ses differents pathogenes. Enfin, l’existence d’une veritable interaction tripartite entre la reponse immunitaire du mollusque, son microbiote et son parasite a pu etre mise en evidence.
Diversity and abundance of litter-dwelling arthropods increase with time-since-burn in a Florida scrub ecosystem

Abstract Fire is an important disturbance that can impact biodiversity and ecosystem functions. Although fire impacts have been well studied in plants and some animals, the effects of fire on litter-dwelling arthropods remain poorly documented. I investigated the effect of time-since-burn on litter-dwelling arthropods in a Florida scrub ecosystem. I measured total arthropod richness and diversity as well as arachnid detritivore and predator abundance along a time-since-burn chronosequence. Arthropod richness and diversity and arachnid abundance significantly increased within 8 years post-burn. Arthropod richness and diversity and arachnid abundance did not differ between 8 and 89 years since last burn. These results demonstrate that litter-dwelling arthropods can quickly re-establish their community composition within 8 years after a burn, which may have important consequences for litter decomposition and nutrient cycling rates over successional time.
Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences

Sequence specific RNA-binding proteins (RBPs) control many important processes affecting gene expression. They regulate RNA metabolism at multiple levels, by affecting splicing of nascent transcripts, RNA folding, base modification, transport, localization, translation and stability. Despite their central role in most aspects of RNA metabolism and function, most RBP binding specificities remain unknown or incompletely defined. To address this, we have assembled a genome-scale collection of RBPs and their RNA binding domains (RBDs), and assessed their specificities using high throughput RNA-SELEX (HTR-SELEX). Approximately 70% of RBPs for which we obtained a motif bound to short linear sequences, whereas ~30% preferred structured motifs folding into stem-loops. We also found that many RBPs can bind to multiple distinctly different motifs. Analysis of the matches of the motifs on human genomic sequences suggested novel roles for many RBPs in regulation of splicing, and revealed RBPs that are likely to control specific classes of transcripts. Global analysis of the motifs also revealed an enrichment of G and U nucleotides. Masking of G and U by proteins increases the specificity of RNA folding, as both G and U can pair to two other RNA bases via canonical Watson-Crick or G-U base pairs. The collection containing 145 high resolution binding specificity models for 86 RBPs is the largest systematic resource for the analysis of human RBPs, and will greatly facilitate future analysis of the various biological roles of this important class of proteins.
PRESTO, a new tool for integrating large-scale -omics data and discovering disease-specific signatures

Background Cohesive visualization and interpretation of hyperdimensional, large-scale -omics data is an ongoing challenge, particularly for biologists and clinicians involved in current highly complex sequencing studies. Multivariate studies are often better suited towards non-linear network analysis than differential expression testing. Here, we present PRESTO, a ‘PREdictive Stochastic neighbor embedding Tool for Omics’, which allows unsupervised dimensionality reduction of multivariate data matrices with thousands of subjects or conditions. PRESTO is intuitively integrated into an interactive user interface that helps to visualize the multidimensional patterns in genome-wide transcriptomic data from basic science and clinical studies. Results PRESTO was tested with multiple input omics’ platforms, including microarray and proteomics from both mouse and human clinical datasets. PRESTO can analyze up to tens of thousands of genes and shows no increase in processing time with a large number of samples or patients. In complex datasets, such as those with multiple time points, several patient groups, or diverse mouse strains, PRESTO outperformed conventional methods. Core co-expressed gene networks were intuitively grouped in clusters, or gates, after dimensionality reduction and remained consistent across users. Networks were identified and assigned to physiological and pathological functions that cannot be gleaned from conventional bioinformatics analyses. PRESTO detected gene networks from the natural variations among mouse macrophages and human blood leukocytes. We applied PRESTO to clinical transcriptomic and proteomic data from large patient cohorts and detected disease-defining signatures in antibody-mediated kidney transplant rejection, renal cell carcinoma, and relapsing acute myeloid leukemia (AML). In AML, PRESTO confirmed a previously described gene signature and found a new signature of 10 genes that is highly predictive of patient outcome. Conclusions PRESTO offers an important integration of powerful bioinformatics tools with an interactive user interface that increases data analysis accessibility beyond bioinformaticians and ‘coders’. Here, we show that PRESTO out performs conventional methods, such as DE analysis, in multi-dimensional datasets and can identify biologically relevant co-expression gene networks. In paired samples or time points, co-expression networks could be compared for insight into longitudinal regulatory mechanisms. Additionally, PRESTO identified disease-specific signatures in clinical datasets with highly significant diagnostic and prognostic potential.
Age, growth, and reproductive biology, of the winter skate, Leucoraja ocellata, in the western Gulf of Maine

This study describes the age, growth and reproductive biology of the winter skate, Leucoraja ocellata, in the Western Gulf of Maine. Age was estimated by enumerating annular bands within the vertebral centra. Precision of the age estimates was evaluated using the Index of Average Percent Error and the annual nature of growth band formation was documented using marginal increment analyses. Growth was assessed with the use of the von Bertalanffy growth equation. Age and size at maturity was estimated by measuring morphological and histological changes in the reproductive tract and circulating steroid hormone concentrations. Maturity ogives for males predict that 50% maturity occurs at a total length of 730 mm and at 11 years. For females, maturity ogives predict that 50% maturity occurs at a total length of 760 mm and between 11 and 12 years of age. To elucidate the reproductive cycle of the winter skate, plasma concentrations of the sex steroids testosterone (T), 17beta-estradiol (E2), and progesterone (P4) were determined by radio immunoassay and compared to morphological and histological changes occurring in the reproductive tract over a complete reproductive cycle for mature individuals. Overall, when the results of my dissertation are combined, they indicate that the winter skate is a late maturing, slow growing, long lived species, with an apparent succinct reproductive cycle. Like many other elasmobranchs, these characteristics make L. ocellata 's populations highly susceptible to exploitation by commercial fisheries.
Phylogeny and the colourful history of jewel bugs (Insecta: Hemiptera: Scutelleridae)

Members of the family Scutelleridae (Heteroptera: Pentatomomorpha: Pentatomoidea) are also called shield bugs because of the greatly enlarged scutellum, or jewel bugs because of the brilliant colours of many species. All scutellerids are phytophagous, feeding on various parts of their host plants. Due to lack of obvious synapomorphies and the failure to apply rigorous phylogenetic methods, the higher classification of Scutelleridae has been disputed for more than 150 years. Here we reconstructed a phylogeny of Scutelleridae based on complete sequences of 18S and 28S nuclear rDNAs and all 13 protein‐coding genes of the mitochondrial genome, with the sampled taxa covering all of the currently recognized subfamilies. The monophyly of Scutelleridae was confirmed by the congruence of the results of analyses conducted using Bayesian inference, maximum likelihood and maximum parsimony. The phylogenetic relationships among subfamilies were well resolved for the first time. Furthermore, time‐divergence studies estimated that the time of origin of Scutelleridae was in the Early Cretaceous (142.1–122.8 Ma), after the origin of the angiosperms. The diversification between the extant subfamilies of Scutelleridae and within the subfamilies occurred from the late Palaeocene to the late Miocene, simultaneously with the rise of the major groups of angiosperms and other phytophagous insects.
Morphophysiological Responses of Common Bean (Phaseolus vulgaris L.) Genotypes to Water Stress

Yield of common bean (Phaseolus vulgaris L.) is highly constrained by water deficit especially when this occurs during the reproductive development. The purpose of the study was to determine the association of the morphophysiological traits with water stress and how this affects grain yield in common beans. A field experiment involving eight common bean genotypes and three water regimes (50 %, 75 %, and 100 % of crop evapotranspiration) was conducted at National Irrigation Research Station, Mazabuka district during the 2012 growing season. A Split plot design with four replications was used; with soil moisture regime (main plot) and the genotypes (subplot). Based on variation in water stress tolerances, 8 test genotypes - Gadra, KE 3, KE 4, ZM 4488, SER 76 SER 180, SER 89 and CAR-ZAR were used. Water stress treatments were imposed at pre-flowering stage and was discontinued after 43 days when the crop was in its late reproductive stage. Significant differences were found among genotypes for Chlorophyll a (Chl a), Chlorophyll b (Chl b), Total Chlorophyll, Relative water content, Grain yield, Number pods per, Seed weight, Seeds per pod and Days to 50 % flowering under the three water stress conditions. The grain yield in normally irrigated condition (2191.3 kg ha-1) was 60 % higher than in high water stress condition (866.2 kg ha-1), while in the low water stress condition (1078.3 kg ha-1), the reduction in grain yield was 50.8 %. There were significant genotype by environment showing that the genotypes behaved differently under the different growing conditions. Results suggested that Gadra, KE 4, ZM 4488, and SER 180 were water stress tolerant while the SER 89, CAR-ZAR, KE 3 and SER 76 were water stress sensitive genotypes. These results suggest that a selection method based on 100 SW, Chl a, Chl b, and NPP can be used in breeding for bean genotypes to water stress.
Body-shape diversity in Triassic–Early Cretaceous neopterygian fishes: sustained holostean disparity and predominantly gradual increases in teleost phenotypic variety

Abstract. Comprising Holostei and Teleostei, the ∼ 32,000 species of neopterygian fishes are anatomically disparate and represent the dominant group of aquatic vertebrates today. However, the pattern by which teleosts rose to represent almost all of this diversity, while their holostean sister-group dwindled to eight extant species and two broad morphologies, is poorly constrained. A geometric morphometric approach was taken to generate a morphospace from more than 400 fossil taxa, representing almost all articulated neopterygian taxa known from the first 150 million years—roughly 60%—of their history (Triassic-Early Cretaceous). Patterns of morphospace occupancy and disparity are examined to: (1) assess evidence for a phenotypically “dominant” holostean phase; (2) evaluate whether expansions in teleost phenotypic variety are predominantly abrupt or gradual, including assessment of whether early apomorphy-defined teleosts are as morphologically conservative as typically assumed; and (3) compare diversification in crown and stem teleosts. The systematic affinities of dapediiforms and pycnodontiforms, two extinct neopterygian clades of uncertain phylogenetic placement, significantly impact patterns ofmorphological diversification. For instance, alternative placements dictate whether or not holosteans possessed statistically higher disparity than teleosts in the Late Triassic and Jurassic. Despite this ambiguity, all scenarios agree that holosteans do not exhibit a decline in disparity during the Early Triassic–Early Cretaceous interval, but insteadmaintain their Toarcian–Callovian variety until the end of the Early Cretaceouswithout substantial further expansions.After a conservative Induan–Carnian phase, teleosts colonize (and persistently occupy) novel regions of morphospace in a predominantly gradual manner until the Hauterivian, after which expansions are rare. Furthermore, apomorphy-defined teleosts possess greater phenotypic variety than typically assumed. Comparison of crown and stem teleost partial disparity indicates that, despite a statistically significant increase in crown teleost disparity between the Late Jurassic and earliest Cretaceous, stem teleosts remained important long-term contributors to overall teleost disparity during this time.