Miracle-dz/UniFAR-FTUs huggingface dataset:
New seed collections of North American pitseed goosefoot (Chenopodium berlandieri) and efforts to identify its diploid ancestors through whole-genome sequencing

Pitseed goosefoot ( Chenopodium berlandieri ) is an ecologically diverse wild/weedy North American species within the primary gene pool for improving South American quinoa ( Chenopodium quinoa ). Both taxa are 36-chromosome allotetraploids with subgenomes AA and BB. The A genome is found in a large number of diploids in the Americas, along with one Northeast Asian taxon, and was recently shown to be the maternal ancestor, while the paternal B genome is closely related to several extant Eurasian diploids. Two of our primary objectives were 1) to determine the extent of genetic diversity in the allotetraploid C. berlandieri-quinoahircinum complex and 2) to characterize the evolutionary path from polyploidization to domestication in these taxa. In an effort to survey genetic diversity, in 2018, we made seed collections of southern Texas, southern Great Plains, and New England coastal ecotypes of C. berlandieri as well as sympatric diploids. With respect to the second goal, we performed wholegenome sequencing of two Sonoran Desert Chenopodium A-genome diploids in subsection Cellulata and Andean cultivated C. pallidicaule in subsection Leiosperma . When paired reads were aligned to the whole-genome reference of C. quinoa strain ‘QQ74’, the match percentages were 99.31, 99.23, and 98.53 for C. watsonii , C. sonorense , and C. pallidicaule , respectively. These data strongly support C. watsonii as being the most closely related of these three species to the A-genome ancestor of quinoa. Ongoing sequencing efforts with a larger panel of diploids are aimed at identifying the maternal ancestor of C. quinoa and C. berlandieri , if extant.
Analysis of Septum Defects in Arabidopsis Organ Boundary Mutants

Arabidopsis thaliana, a model plant species, has been heavily studied to determine the genetic contributions that lead to gynoecium development. The Arabidopsis fruit is created from two carpels that form a gynoecium, which contains the stigma, style, and ovary. The ovary is divided into two sub-compartments by a septum, and the ovules develop within the ovary. The fruit’s purpose is to protect, nurture, and eventually disperse the mature ovules, or seeds, and if the septum does not fuse properly, the plant’s fertility will be impacted. SHOOT MERISTEMLESS (STM) and ARABIDOPSIS THALIANA HOMEOBOX GENE1 (ATH1) are two genes that are known to be involved in fruit development, specifically meristem maintenance and organ boundary specification. Plants with mutations in both STM and ATH1 produce fruit with multiple developmental defects. To investigate the effects of stm and ath1 mutations on septum development, I analyzed the septa of stm, ath1, stm/+ ath1, and stm ath1 fruit in comparison to wild-type fruit. Because STM maintains the stem cell population in flower meristems and induces the biosynthesis of cytokinin in the carpel margin meristem (which includes the septum), I hypothesized that stm mutant fruit would display moderate septum defects. Also, because previous studies have shown that ATH1 and STM act redundantly in promoting fruit development, I hypothesized that the stm ath1 double mutant fruit would have enhanced septum defects compared to the stm single mutant. To evaluate the septum fusion defects, I measured the amount of septum surface area missing in relation to the total potential septum surface area for each fruit. This study revealed that 50 of the 51 stm single mutant fruit had septa fusion defects, while none of the ath1-5 fruit had abnormal septa. In addition, I found that the fusion defects present in the stm ath1-5 double mutant were not significantly enhanced relative to the stm single mutant. These results suggest that STM alone plays a critical role in fusion of the septum during fruit development.
Forage quality and productivity of barley (Hordeum vulgare L.) as influenced by cutting management under staggered sowing in North-West India

ABSTRACT The regrowth ability of barley can be put to use by taking one cutting during the active vegetative growth stage and then leaving the regenerated crop for grain production. The effects of three sowing dates (October 15; October 30 and November 15) and five cutting management (control; cut at 50 days after sowing (DAS); cut at 60 DAS; cut at 50 DAS + N application and cut at 60 DAS + N application) on forage quality and productivity of barley was evaluated over a 2-year period (2015–2017). November 15 sowing with early fodder cutting, taken at 50 DAS produced significantly higher ether extract, digestibility (in vitro), nitrate content and leaf stem ratio, while crude protein of October 30 and November 15 sowing with cut at 50 DAS were statistically similar. October 15 sowing and cut at 60 DAS gave highest crude fibre, neutral detergent fibre and digestible dry matter. Early sowing i.e. October 15 with cut at 60 DAS gave significantly higher green fodder yield. October 15 and cut at 50 DAS produced significantly higher grain yield than other treatments but was statistically similar with control crops that sown on October 15 and October 30.
Biological growth model as a new selection strategy for improvement of feed efficiency in swine

Biological growth models are of increasing interest in animal breeding. One possible application is their use to optimise selection for feed intake capacity. For this to be achieved the input parameters of maximum protein deposition rate and minimum lipid to protein deposition ratio have to be known. Different methods can be used for measuring protein and lipid deposition rate on live animals (e.g. deuterium dilution technique, magnetic resonance tomography (MRT)) or on slaughter animals in a serial slaughter trial with the entire body chemically analysed. All these techniques are very expensive and can be obtained only in an experimental trial. Therefore, a trial that addresses these needs and also allows a comparison of the methods will be of great value. Correlation between protein or lipid deposition and indicator carcass cuts varied substantially during growth. The combinations of carcass cuts to predict protein and lipid deposition generally provided higher values. The number and kind of predicted variable varied during the growth, so it is necessary to measure protein also by direct methods.
Sequencing and analysis of the complete mitochondrial genome of Crocidura tanakae from China and its phylogenetic analysis

Abstract The complete mitogenome sequence of Crocidura tanakae was determined using long PCR. The genome was 16,969 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, 1 origin of L strand replication and 1 control region. The overall base composition of the heavy strand is A (32.5%), C (22.3%), T (31.9%), and G (13.3%). The base compositions present clearly the A–T skew, which is most obviously in the control region and protein-coding genes. Mitochondrial genome analyses based on MP, ML, NJ, and Bayesian analyses yielded identical phylogenetic trees. The five Crocidura species formed a monophyletic group with the high bootstrap value (100%) in all examinations. This study verifies the evolutionary status of C. tanakae in Soricidae at the molecular level. The mitochondrial genome would be a significant supplement for the C. tanakae genetic background.
Biological characteristics and population status of steelhead ( Oncorhynchus mykiss ) in southeast Alaska.

We reviewed existing data to determine the range and distribution of steelhead (Oncorhynchus mykiss) in southeast Alaska, summarized biological characteristics, and determined population status of steelhead stocks. Unique or sensitive stocks that may require consideration in planning land management activities are identified within the data reviewed. Data sources were personal communications, reports, and unpublished data files of State and Federal agencies. Only eight winter-run stocks in southeast Alaska and two summer-run stocks in southwest Alaska had sufficient data to evaluate biological characteristics. Age structure, sex ratio, incidence and frequency of repeat spawning, and body length were similar among winter-run stocks, and consistent with coastwide trends of increasing freshwater age and body size of steelhead stocks in the northern portion of their range. Winter-run stocks appeared to have a greater proportion of repeat spawners (kelts) than summer-run stocks, and juvenile steelhead in the summer-run stocks generally spent 1 year less in both fresh water and the ocean. Assessment of escapement trends, run timing, and stock status is hindered by lack of adequate data both in number of stocks with sufficient data and the number of years of data available. Incomplete weir counts during immigration and emigration of adult fish and low sample sizes of escapement indices, both within and among years, decrease the reliability of estimates. Although stocks with sufficient data are not at risk, small run sizes that are typical of most steelhead stocks may be more susceptible to poor land management practices and overharvest than larger stocks. Abstract 1 Introduction
Time‐series metatranscriptomes reveal conserved patterns between phototrophic and heterotrophic microbes in diverse freshwater systems

Microbial communities form the base of food webs in freshwater ecosystems, yet the interactions within these diverse assemblages are poorly understood. Based on evidence showing that primary production and respiration follow diurnal trends in lakes, we hypothesized that gene expression in freshwater microbes would have similar diel cycles. We used three 2‐d time series of metatranscriptomes to test this hypothesis in a eutrophic lake, an oligotrophic lake, and a humic lake. We identified prominent diel cycles in all three lakes, particularly in genes related to photosynthesis, sugar transport, and carbon fixation. The maximal time of expression for sugar transport genes tended to trail that of photosynthesis genes by several hours, indicating possible metabolic exchange between co‐occurring microbial lineages. These results provide an initial step in understanding sophisticated multispecies transcriptional organization within freshwater microbial communities.
Systematic identification of factors bound to isolated metaphase ESC chromosomes reveals a role for chromatin repressors in compaction

Epigenetic information is transmitted from mother to daughter cells through mitosis. To identify trans-acting factors and cis-acting elements that might be important for conveying epigenetic memory through cell division, we isolated native (unfixed) chromosomes from metaphase-arrested cells using flow cytometry and performed LC-MS/MS to determine the repertoire of chromosome-bound proteins. Quantitative proteomic comparisons between metaphase-arrested cell lysates and chromosome-sorted samples revealed a cohort of proteins that were significantly enriched on mitotic ESC chromosomes. These include pluripotency-associated transcription factors, repressive chromatin-modifiers (such as PRC2 and DNA methyl-transferases) and proteins governing chromosome architecture. We showed that deletion of PRC2, DNMT1/3a/3b or Mecp2 provoked an increase in the size of individual mitotic chromosomes consistent with de-condensation, as did experimental cleavage of cohesin complexes. These data provide a comprehensive inventory of chromosome-bound factors in pluripotent stem cells at mitosis and reveal an unexpected role for chromatin repressor complexes in preserving mitotic chromosome compaction.
EBV-miR-BART7-3p Imposes Stemness in Nasopharyngeal Carcinoma Cells by Suppressing SMAD7

Cancer stem-like cells, possessing “stemness” properties, play crucial roles in progression, metastasis, and drug resistance in various cancers. Viral microRNAs (such as EBV-miR-BART7-3p), as exogenous regulators, have been discovered to regulate malignant progression of nasopharyngeal carcinoma (NPC), suggesting a possible role of viral microRNAs in imposing stemness. In this study, we found that EBV-miR-BART7-3p induce stemness of NPC cells. We firstly reported that EBV-miR-BART7-3p increased the percentage of side population cells, the development of tumor spheres, and the expression level of stemness markers in vitro. This viral microRNA also enhanced stem-like or cancer-initiating properties of NPC cells in vivo. Besides, we identified SMAD7 as a novel target gene of EBV-miR-BART7-3p in addition to PTEN gene we previously reported; this viral microRNA suppressed SMAD7, led to activation of TGF-β signaling, and eventually enhanced the stemness of NPC cells. Silencing of SMAD7 resembled the effects generated by EBV-miR-BART7-3p in NPC cells. After reconstitution of SMAD7, EBV-miR-BART7-3p-expressing cells underwent a phenotypic reversion. EBV-positive NPC cells were used to enable experimental validation. Finally, we further discovered that EBV-miR-BART7-3p increased chemo-resistance of NPC in vitro and in vivo, supporting that EBV-miR-BART7-3 resulted in increased stemness of NPC cells and lead to drug resistance and cancer recurrence. Overall, this study uncovered a novel mechanism underlying viral microRNA-associated stemness of NPC cells. This viral microRNA and its associated cellular genes may be potential therapeutic targets for restraining chemo-resistance and recurrence of NPC.
Correlative single‐molecule localization microscopy and electron tomography reveals endosome nanoscale domains

Many cellular organelles, including endosomes, show compartmentalization into distinct functional domains, which however cannot be resolved by diffraction-limited light microscopy. Single molecule localization microscopy (SMLM) offers nanoscale resolution but data interpretation is often inconclusive when the ultrastructural context is missing. Correlative light electron microscopy (CLEM) combining SMLM with electron microscopy (EM) enables correlation of functional sub-domains of organelles in relation to their underlying ultrastructure at nanometer resolution. However, the specific demands for EM sample preparation and the requirements for fluorescent single-molecule photo-switching are opposed. Here, we developed a novel superCLEM workflow that combines triple-colour SMLM (dSTORM & PALM) and electron tomography using semi-thin Tokuyasu thawed cryosections. We applied the superCLEM approach to directly visualize nanoscale compartmentalization of endosomes in HeLa cells. Internalized, fluorescently labelled Transferrin and EGF were resolved into morphologically distinct domains within the same endosome. We found that the small GTPase Rab5 is organized in nano-domains on the globular part of early endosomes. The simultaneous visualization of several proteins in functionally distinct endosomal sub-compartments demonstrates the potential of superCLEM to link the ultrastructure of organelles with their molecular organization at nanoscale resolution. Synopsis Suborganelle compartmentalization cannot be resolved by diffraction limited light microscopy and not interpreted without knowledge of the underlying ultrastructure. This work shows a novel superCLEM workflow that combines multi-colour single-molecule localization-microscopy with electron tomography to map several functional domains on early endosomes. superCLEM reveals that the small GTPase Rab5 is organized in nano-domains largely devoid from cargo molecules Transferrin and EGF and opens new possibilities to perform structure-function analysis of organelles at the nanoscale.
Mummified fossil of Keteleeria from the Late Pleistocene of Maoming Basin, South China, and its phytogeographical and paleoecological implications

Keteleeria is a small genus of Pinaceae now mainly restricted to eastern Asia. Although this genus has been documented with a wide distribution in the geologic record of Europe, North America, and Asia, its history in low‐latitude areas (including South China) has remained obscure. In this paper, a fossil wood of Keteleeria sp. is described from the Late Pleistocene (29–27 ka BP) of the Maoming Basin, South China. This wood is the most ancient megafossil evidence of Keteleeria within the modern distribution area of this genus. The fossil records of Keteleeria suggests that this thermophyllous genus migrated into South China by the Middle Pleistocene escaping from glacial cooling and became widespread over this region in the Late Pleistocene beginning from the interglacial stage preceding the Last Glacial Maximum. The analysis of growth rings in the fossil wood and its comparison with those of modern Keteleeria davidiana (Bertrand) Beissner indicates that in the Late Pleistocene of Maoming Basin (29–27 ka BP) there was a humid climate with less pronounced seasonality of precipitation than that seen in the subtropical monsoonal climate of modern northeastern Vietnam. Apparently, the Maoming Basin was influenced by interglacial regime with summer–monsoon circulation. The previously proposed method to distinguish between evergreen and deciduous conifers based on growth ring anatomy, is not reliable because of the wide variance and ambiguity in its results.
Transmission analysis of a large TB outbreak in London: mathematical modelling study using genomic data

Outbreaks of tuberculosis- such as the large isoniazid-resistant outbreak centered on London, United Kingdom, which originated in 1995- provide excellent opportunities to model transmission of this devastating disease. Transmission chains for tuberculosis are notoriously difficult to ascertain, but mathematical modelling approaches, combined with whole-genome sequencing (WGS) data, have strong potential to contribute to transmission analyses. Using such data, we aimed to reconstruct transmission histories for the outbreak using a Bayesian approach, and to use machine learning techniques with patient-level data to identify the key covariates associated with transmission. By using our transmission reconstruction method that accounts for phylogenetic uncertainty, we are able to identify 24 transmission events with reasonable confidence, 11 of which have zero single nucleotide polymorphism (SNP) distance, and as maximum distance of 3. Patient age, alcohol abuse and history of homelessness were found to be the most important predictors of being credible tuberculosis transmitters.
Contribution of cytosine desaminases of AID/APOBEC family to carcinogenesis

Cytosine deaminases of the AID/APOBEC family have a weighty influence on human health. These enzymes are part of the innate and humoral immunity; they participate in lipid metabolism and muscle development, protect cells from viruses and regulate retrotransposition. If the activity of AID/APOBEC deaminases is misregulated, they can become “weapons of mass destruction,” causing deaminations in unprotected single-stranded DNA regions leading to genome-wide mutagenesis. Ultimately, mutations contribute to cell malignancy and rapid evolution of cancer cells, helping them to evade the organism’s defense. Also, hypermutable tumor cells develop resistance to anti-cancer drugs. Here we overview current understanding of the structure, functions, and regulation of AID/APOBEC cytosine deaminases in connection to carcinogenesis.
Reactivation of chromosome signalling induces reversal of the meiotic program

Chromosome movements and programmed DNA double-strand breaks (DSBs) promote homologue pairing and initiate recombination at meiosis onset. Meiotic progression involves checkpoint-controlled termination of these events when all homologue pairs achieve synapsis and form crossover precursors. We show that termination of chromosome movement and DSB formation is reversible and is continuously implemented by the synaptonemal complex (SC), which silences chromosome signals that promote CHK-2 activity. Forced removal of the SC or different meiosis-specific cohesin complexes, which are individually required for SC stability, causes rapid CHK-2-dependent reinstallation of the DSB-formation and chromosome-movement machinery. This nuclear reorganization occurs without transcriptional changes, but requires signalling from HORMA protein HTP-1. Conversely, CHK-2 inactivation causes rapid disassembly of the DSB-formation and chromosome-movement machinery. Thus, nuclear organization is constantly controlled by the level of CHK-2 activity. Our results uncover an unexpected plasticity of the meiotic program and show how chromosome signalling integrates nuclear organization with meiotic progression.
Germination et croissance des plantules d’une espèce fruitière indigène au Niger : Balanites aegyptiaca (L.) Del.

Balanites aegyptiaca est l’une des plantes a usages multiples au Niger tres appreciee par les populations. Cette etude conduite au Centre Regional de Recherche Agronomique de Zinder, vise a etudier la germination et l’evolution des plantules de cette espece. Les essais de germination ont ete effectues dans des planches rectangulaires sur six types de traitements pendant 3 mois et le suivi de croissance des plantules dans des pots plastiques enfouis dans le sol pendant 6 mois. L’etude a montre que l’ingestion des fruits de Balanites aegyptiaca par les chevres reduit significativement la dormance tegumentaire. Les graines extraites des noyaux qui ont transite par le tractus digestif des chevres ont le taux de germination le plus eleve (76,87%) et le taux de germination le plus faible a ete obtenu avec les fruits entiers (38,12%). Apres 6 mois de suivi, la croissance du pivot racinaire des plantules (78,59±9,04 cm) est plus importante que celle de la partie aerienne (61,8±6,2 cm). Cette etude permet d’envisager la production des plants de Balanites aegyptiaca en vue de sa conservation durable. © 2019 International Formulae Group. All rights reserved Mots cles: Balanites aegyptiaca , germination, ingestion par chevres, dormance, croissance, Niger English Title: Germination and seedling growth of an indigenous fruit species in Niger : Balanites aegyptiaca (L.) Del. English Abstract Balanites aegyptiaca is one of multipurpose plants in Niger very appreciated by the populations. This study conducted at Zinder’s Regional Center for Agricultural Research, aims to study the germination and evolution of seedlings of this species. The germination tests were carried into rectangular plates on six types of treatment for 3 months and the growth monitoring of seedlings in plastic pots buried in the soil for 6 months. The study showed that ingestion of Balanites aegyptiaca fruits by goats significantly reduces tegumentary dormancy. Seeds extracted from cores that have passed into the digestive tract of goats have the highest germination rate (76.87%) and the lowest germination rate was obtained with intact fruits (38.12%). After 6 months of monitoring, the pivot root growth of seedlings (78.59±9.04 cm) is greater than the aerial part (61.8±6.2 cm). This study allows envisaging the production of Balanites aegyptiaca plants for its sustainable conservation. © 2019 International Formulae Group. All rights reserved Keywords: Balanites aegyptiaca , germination, goat ingestion, dormancy, growth, Niger