Miracle-dz/UniFAR-FTUs huggingface dataset:
The anatomy, organisation and development of contralateral callosal projections of the mouse somatosensory cortex

Background: Alterations in the development of neuronal connectivity can result in dramatic outcomes for brain function. In the cerebral cortex, most sensorimotor and higher-order functions require coordination between precise regions of both hemispheres through the axons that form the corpus callosum. However, little is known about how callosal axons locate and innervate their contralateral targets. Methods: Here, we use a combination of in utero electroporation, retrograde tracing, sensory deprivation and high-resolution axonal quantification to investigate the development, organisation and activity dependence of callosal axons arising from the primary somatosensory cortex of mice. Results: We show that distinct contralateral projections arise from different neuronal populations and form homotopic and heterotopic circuits. Callosal axons innervate the contralateral hemisphere following a dorsomedial to ventrolateral and region-specific order. Furthermore, we identify two periods of region- and layer-specific developmental exuberance that correspond to initial callosal axon innervation and subsequent arborisation. Early sensory deprivation affects only the latter of these events. Conclusion: Taken together, these results reveal the main developmental events of contralateral callosal targeting and may aid future understanding of the formation and pathologies of brain connectivity.
The Central Role of the Matrix Protein in Nipah Virus Assembly and Morphogenesis

Abstract : Nipah virus (NiV) is an emerging paramyxovirus distinguished by its ability to cause fatal disease in both animal and human hosts. Together with Hendra virus (HeV), they comprise the genus Henipavirus in the Paramyxoviridae family. NiV and HeV are restricted to Biosafety Level-4 (BSL-4) containment and this has hampered progress towards examining the details of their replication and morphogenesis mechanisms. Here, recombinant gene expression systems to study NiV particle assembly and budding through the formation of virus-like particles (VLPs) have been established to circumvent these obstacles. When expressed by recombinant Modified Vaccinia virus Ankara (rMVA) or by plasmid vector transfection, individual NiV matrix (M), fusion (F) and attachment (G) proteins were released into cell culture supernatants in a membrane associated state as determined by sucrose density gradient flotation and immunoprecipitation analysis. However, co-expression of F and G along with M revealed a shift in their distribution across the gradient, indicating association with M in VLPs.
Relative importance of anthropogenic landscape characteristics for Neotropical frugivores at multiple scales

Frugivores are key components of Neotropical forests, regulating plant communities, forest structure, and plant diversity; however, they are highly threatened by human impacts worldwide. To effectively conserve this group, maintain their ecological functions, and plan management actions or establish future protected areas, we need to gather information about their relationship with the landscape attributes. Here, we used camera traps and call surveys (April 2013 to March 2014) to estimate the occupancy of seven frugivores (a rodent, two ungulates, two primates and two ground‐dwelling birds) at 45 sampling sites distributed within a protected area of Atlantic Forest (35 000 ha) in south‐east Brazil. We evaluated the relative effects of anthropogenic landscape variables, environmental attributes and geomorphometry on their occupancy at multiple scales. To achieve this, we measured landscape metrics at three spatial scales (200, 500 and 1000 m) around each sampling site and used multi‐season occupancy modeling. Factors related to human presence or disturbance, such as human accessibility, proximity to the reserve, and forest cover, were the main predictors of occupancy by frugivorous game species (paca – Cuniculus paca; brocket deer – Mazama sp.; and collared peccary – Pecari tajacu). Strictly environmental and geomorphometric variables were weaker determinants of frugivore occupancy. Our results also suggest that weather, season and habitat‐related variables can equally influence animal detection probability. Moreover, different species of frugivores responded differently to landscape attributes, and their response depended on the spatial landscape scale at which they perceive their habitat. This highlights the importance of a multi‐taxa and multi‐scale approach when assessing species‐habitat relationships and planning wildlife management actions.
Expression Analysis of Droughtinduced Genes in Wild Tomato Line ( Solanum habrochaites )

Many plant genes are regulated in response to abiotic stresses such as drought, high salinity, heat and cold, and their gene products function in stress response and tolerance. The whole process of plant adaptation to these environmental stresses is controlled by orchestration of complex molecular networks. In the present study, eight genes showing significant difference of expression on exposure to artificial drought stress in tomato, were selected from the previously performed microarray experiment. Expression analysis of the genes was done semi-quantitatively as well as quantitatively under artificially imposed drought stress and the results were almost similar to those of microarray experiment. Tissue-specific analysis of the genes, performed on tolerant line, revealed fairly a similar pattern of expression in root, stem and leaf with notable differences in flower, which experienced the least influence of drought. The results confirmed that SIPRP16, SICYP51-17, SIMCPI19 and SIGDSL20 were downregulated in both the lines with stronger downregulation in sensitive line. SIWRKY4 was downregulated in both the lines with more folds of downregulation in tolerant line . SIEFH12 and SISNF4-15 were upregulated in tolerant line. SlUSPA9 was upregulated in both the lines with relatively more folds of upregulation in sensitive line.
Differences in Bacterial Communities on Decaying Leaf Litter of Different Tress in Response to Burning as a Forest Restoration Technique

Decomposition is the process by which organic matter gets degraded into basic components to provide energy for decomposer microorganisms and to also make nutrients available for plant uptake. Leaf litter decomposition is an important process and influences the nutrient cycling and the productivity and structure of the entire ecosystem; however, few studies have examined the bacterial communities on decomposing litter, especially how they may vary between tree species or in woodlands subject to ecological restoration. Such restoration has become important, as fire suppression beginning in the 1920s has impacted the structure of forest ecosystems through the process of mesophication, diminishing the abundance of fire-dependent species and favoring more shade-tolerant, fire-intolerant trees. These changes likely influence the composition of the litter microbial community. This study used next generation sequencing of 16S rRNA genes to characterize the bacterial communities on litter from six different tree species, including representatives of upland oak woodlands (oaks) and mesophytic species (non-oaks), in a north Mississippi forest undergoing restoration. Results suggest that the bacterial community on leaf litter changes significantly as decomposition proceeds, and that there are differences in bacterial communities present on litter from oak versus non-oak species. Comparing the bacterial communities on leaf litter collected from a site that experienced a prescribed burn within the collection year, to a non-burned site suggested that fire did affect the bacterial community present on the decaying leaf litter. Together, these results indicate that both ecological restoration (fire) and the effects of restoration (a change in tree species) are likely to influence the composition of the litter bacterial community.
Effect of germination on antioxidant activity, total phenolics, β-carotene, ascorbic acid and α-tocopherol contents of lead tree sprouts (Leucaena leucocephala (lmk.) de Wit).

This study aims to determine the effect of germination time on the antioxidant activity of Leucaena leucocephala (lmk.) de Wit (lead tree) sprouts. Determination of antioxidant activity was carried out on ethanol extract of germinated seeds using β-carotene bleaching assay. The results showed that the antioxidant activity of germinated seeds were affected by germination time. Germination for 4 days affected the greatest enhancement in antioxidant activity by 2.78 fold and caused a significant increment in total phenolic content by 7.29, β-carotene by 3.27, ascorbic acid by 3.81 and α-tocopherol by 4.58 fold, respect to imbibed seeds. The total phenolics content was 53.42±0.22 mg CAE/g dw, β-carotene was 530.99±71.13 10-3 mg/100 g, ascorbic acid was 152.37±2.06 mg/100 g, and α-tocopherol was 59.27±0.10 mg/100 g sample. The findings suggested that the L. leucocephala sprouts could be considered as a source of natural antioxidant.
Genome Functional Annotation using Deep Convolutional Neural Networks

Deep neural network application is today a skyrocketing field in almost all disciplinary domains. In genomics, the development of deep neural networks is expected to revolutionize current practice, from fundamental issues such as understanding the evolution of genomes to more specific applications such as the development of personalized medicine. Several approaches have been developed relying on deep convolutional neural networks to identify the functional role of sequences such as promoters, enhancers or protein binding sites along genomes. These approaches rely on the generation of sequences batches with known annotations for learning purpose. While they show good performance to predict annotations from a test subset of these batches, they usually perform less well when applied genome-wide (i.e., for whole genome annotation). The transcription start sites are collected in reference genomes for human (hg38) and mouse (mm10) species from UCSC and WashU EpiGenome repositories. The input of the proposed method are generated using two strategies: first, we generate balanced and imbalanced datasets; then, we opt for a data augmentation strategy to increase the examples size. An optimal method is the proposed to train deep convolutional neural networks for this specific application. We use as a case study gene transcription start sites. Through analysis of human and mouse genomes, we show that that a deep convolutional neural network model trained on one organism (human) can be used to predict transcription start sites in a different species (mouse). The proposed method optimizes the ratio between positive and negative examples. It achieves the highest prediction scores of test sets for identifying transcription start sites. Furthermore, The ability of our model is assessed by predicting potential TSS in full chromosomes. This method provides a cost-effective and optimal method to learn transcription start sites from a species to predict them in another species and vice versa. Our method provides a new tool to address the conservation of the whole nuclear machinery that interprets the sequences. Our method yields higher scores and substantially more accurate predictions than state-of-the-art methods as it is applied on a genome-wide scale. Additionally, these findings reveal the generability of the proposed method when applied on other species.
Structure and diversity of fish communities in the Hairtail Protected Area of the East China Sea.

The data of the Hairtail Protected Area in the East China Sea (ECS) are based according to the accumulated survey data of two seasons trawl, spring and autumn of 2012 and 2013. In results, we were able to identify of 138 kinds of fish species consisting of 17 orders and 57 families which belong to Chondrichthyes (2 taxa) and Osteichthyes (136 taxa). The total number of species in autumn 2012 and 2013 were 95 and 82, respectively. In addition, the total number of species in spring 2012 and 2013 were 67 and 74, respectively. The species with index of relative importance (IRI) greater than 500 were defined as dominant species, a total of 11 species in spring-autumn (2012-2013), which are: Small snakehead (Channa asiatica), Branded goby (Chaeturichthys stigmatias), Small yellow croaker (Pseudosciaena polyactis), Bombay duck (Harpadon nehereus), Largehead hairtail (Trichiurus haumela), Silver croaker (Pennahia argentata), Skinnycheek lanternfish (Benthosema pterotum), Vertical striped cardinalfish (Apogonichthys lineatus), Mi-iuy croaker (Miichthys miiuy), Japanese anchovy (Engraulis japonicus), (Odontamblyopus rubicundus) and each species are dominant only one seasons except 5 species which is dominant in both seasons annually. Abundance-Biomass Comparison (ABC) curves of the Hairtail Protected Area (HPA) fishes according to the two seasons’ fish communities showed that the abundance curve was always above (upper) the biomass curve of each year, indicating that the species composition was less diverse, the species are small size, large abundance, quick sexual maturity and short lifetime (r strategy) and the community structure tended to be unstable.
Genetic Diversity Analysis of Soursop (Annona muricata L.) in West Java Region of Indonesia Using RAPD Markers

Aims: The aim of this study was determine the genetic diversity of Annona muricata L. using molecular random amplified polymorphic DNA (RAPD) markers. Amplification of genomic DNA of 9 samples using RAPD analysis yielded 57 fragment, of which 30 were polymorphic, with an average of 6 polymorphic fragment per primer. Study Design: The data was analysed with SIMQUAL program of NTSYS-pc (Version 2.02), and similarities between accessions were estimated using the Jaccard’s coefficient calculated as J = A / (N - D), where A is the number of positive matches (that is, presence of band in both samples), D is the number of negative matches (that is, absence of band in both samples) and N is the total sample size including both the number of matches and unmatches. Dendrogram was created from the resultant similarity matrices using the UPGMA method following SAHN function of NTSYS-pc (Version 2.02). Place and Duration of Study: The study was conducted from September 2014 to March 2015. The analysis of genetic diversity was done in the Biochemistry Laboratory and the Molecular Biology Laboratory of Plant II, Agronomy and Horticulture Faculty of Agriculture Bogor Agricultural University. Methodology: Plant material from West Java, DNA extraction after that primer screening and DNA amplification. Data analysis and Electrophoresis of amplified product. Results: The genetic distance was calculated based on Jaccard’s similarity coefficient using SIMQUAL program in NTSYS-pc software to clarify the genetic relationships. An UPGMA dendrogram was constructed using NYSYSpc 2.10 software. A clear divergence between the two related species was found from the cluster analysis. Jaccard similarity coefficient of soursop ranged from 0.451 to 0.902 which revealed a wide range of genetic identity. Based on this value it was noticed that the relationship between soursop sample was closely. High similarity coefficient of 0.902 was measured between; the sample GRT3 with CJR2 and CJR3. According to analysis of the Jaccard similarity coefficient, the sample SKB2 with SKB1 had low similarity coefficient (0.451). This indicated that both the accessions were genetically distant. Conclusion: Primary elected to amplify DNA Annona muricata L. produces two main groups. Group A consists of 4 samples (GRT1, CJR1, SKB1, GRT 2) and group B consisted of 5 samples (GRT3, CJR2, CJR3, SKB2, SKB3).
Is GPS telemetry location error screening beneficial?

The accuracy of global positioning system (GPS) locations obtained from study animals tagged with GPS monitoring devices has been a concern as to the degree it influences assessments of movement patterns, space use, and resource selection estimates. Many methods have been proposed for screening data to retain the most accurate positions for analysis, based on dilution of precision (DOP) measures, and whether the position is a two dimensional or three dimensional fix. Here we further explore the utility of these measures, by testing a Telonics GEN3 GPS collar's positional accuracy across a wide range of environmental conditions. We found the relationship between location error and fix dimension and DOP metrics extremely weak (r2adj ∼ 0.01) in our study area. Environmental factors such as topographic exposure, canopy cover, and vegetation height explained more of the variance (r2adj = 15.08%). Our field testing covered sites where sky-view was so limited it affected GPS performance to the degree fix attempts failed frequently (fix success rates ranged 0.00–100.00% over 67 sites). Screening data using PDOP did not effectively reduce the location error in the remaining dataset. Removing two dimensional fixes reduced the mean location error by 10.95 meters, but also resulted in a 54.50% data reduction. Therefore screening data under the range of conditions sampled here would reduce information on animal movement with minor improvements in accuracy and potentially introduce bias towards more open terrain and vegetation.
Gyrinicola chabadamsoni n. sp. and G. tba (Dinnik 1933) (Nematoda, Oxyuroidea) from tadpoles of the hybridogenetic complex Rana lessonae-esculenta (Amphibia, Ranoidea)

Two morphological types of the viviparous oxyurid nematode Gyrinicola were recovered from waterfrog tadpoles in France (Ain department, Rhone-Alpes region) and assigned to two species: G. tba (Dinnik 1930), redescribed, and G. chabadamsoni n. sp. Gyrinicola tba is close to G. batrachiensis (Walton 1929) and G. chabaudi Araujo and Artigas 1982 in that the female possesses a long tail and few cuticular buccal flaps. The new species, type host Rana kl. esculenta, is distinct by several characters: in females, by the 12 cuticular buccal flaps with internal crests, short caudal filament, short ovary producing embryonated eggs and large uterine pouch containing males and embryos, like in G. japonica Yamaguti 1938, and narrower thick-shelled eggs with subapical elongated operculum; in males, by the round genital cone, the third caudal pair of papillae at mid tail, length of the body and caudal part. Gyrinicola tba and the new species were found in R. lessonae and in the hybrid R. kl. esculenta but each with different seasonal infection rates. Comparative analyses of the data from the five Gyrinicola species were done. All females have one genital tract producing thick-shelled female eggs. The second genital tract is one of four types corresponding to different reproductive patterns: i) it forms a uterine pouch containing males in G. chabadamsoni and G. japonica; ii) it forms a slender uterus containing numerous autoinfective larval stages in G. batrachiensis from R. clamitans; iii) it forms a slender uterus containing only a few embryos in G. tba and G. chabaudi; and iv) it has regressed in G. batrachiensis from Bufo americanus. Haplodiploidy is expected or proved for types i) and ii) and thelytoky for types iii) and iv).
Running title: HLA-A disruption in donor cells

Long-term engraftment of allogeneic cells necessitates eluding immune-mediated rejection which is currently achieved by matching for human leukocyte antigen (HLA) expression, immunosuppression, and/or delivery of donor-derived cells to sanctuary sites. Genetic engineering provides an alternative approach to avoid clearance of cells that are recognized as “non-self” by the recipient. To this end, we developed designer zinc finger nucleases (ZFNs) and employed a “hit-and-run” approach to genetic editing for selective elimination of HLA expression. Electro-transfer of mRNA species coding for these engineered nucleases completely disrupted expression of HLA-A on human T-cells, including CD19-specific T-cells. The HLA-A neg T-cell pools can be enriched and evade lysis by HLA-restricted cytotoxic T-cell clones. Recognition by NK-cells of cells that had lost HLA expression was circumvented by enforced expression of non-classical HLA molecules. Furthermore, we demonstrate that ZFNs can eliminate HLA-A expression from embryonic stem cells which broadens the applicability of this strategy beyond infusing HLA-disparate immune cells. These findings establish that clinically-appealing cell types derived from donors with disparate HLA expression can be genetically edited to evade an immune response and provide a foundation whereby cells from one donor can be administered to multiple recipients. Although these post-transcriptional approaches reduce antigen levels, they require sustained transgene expression and moreover reduce but do not completely eliminate HLA expression. Given that an αβ T-cell receptor (TCR) response can be triggered by just a small number of cell-surface HLA molecules, 14 we sought an alternative to achieve complete elimination of HLA. Here we show that transient expression of zinc finger nucleases (ZFNs) 15 targeting the HLA-A locus can permanently and completely eliminate HLA-A expression from (i) a model cell line, (ii) primary and genetically modified human T-cells used in clinical trials, and (iii) human embryonic stem cells (hESC). These results highlight a path toward rapid human application as circulating NK-cells could be prevented from recognizing cells engineered to lose HLA expression. Fok I domain variants. mRNA species encoding ZFN-L and heterodimeric Fok I mutants EL:KK targeting HLA-A HLA-A2 expression after
Effects of cytoplasm, male and female parents on biomass productivity in sorghum (Sorghum bicolor L. Moench)

ABSTRACT Production of renewable fuel requires biomass sources. To meet this need, energy sorghum was identified as a potential biomass source. Hybrid sorghum development involves the use of cytoplasmic male sterility (CMS) and since there are multiple CMS systems, it is important to determine if any of the CMS systems has an effect on agronomic performance and biomass composition. Energy sorghum hybrids were produced using four seed and four pollinator lines, resulting in 16 hybrid genotypes in three different cytoplasms (A1, A2, and A3). These hybrids were evaluated in three environments across 2 years for agronomic and biomass composition traits. For most traits, differences among hybrids and environments accounted for most of the variation, cytoplasm did not in any trait. These results indicated that different CMS systems can be used for energy sorghum hybrids without affecting yield or composition.