Miracle-dz/UniFAR-FTUs huggingface dataset:
A Na2CO3-responsive chitinase gene from Chinese wildrye improve pathogen resistance and saline-alkali stress tolerance in transgenic tobacco and maize

Salinity and microbial pathogens are the major limiting factors for crop production. Although the manipulation of many genes could improve plant performance under either of these stresses, few genes have reported that could improve both pathogen resistance and saline-alkali stress tolerance. In this study, we identified a new chitinase gene CHITINASE 2 (LcCHI2) that encodes a class II chitinase from a Chinese wildrye (Leymus Chinensis), which grows naturally on alkaline-sodic soil. Overexpression of LcCHI2 increased chitinase activity in transgenic plants. The transgenic tobacco and maize exhibited improved pathogen resistance and enhanced both neutral salt and alkaline salt stress tolerance. Overexpression of LcCHI2 reduced sodium (Na+) accumulation, malondialdehyde content and relative electrical conductivity in transgenic tobacco under salt stress. In addition, the transgenic tobacco showed diminished lesion against bacterial and fungal pathogen challenge, suggesting an improved disease resistance. Similar improved performance was also observed in LcCHI2-overexpressed maize under both pathogen and salt stresses. It is worth noting that this genetic manipulation does not impair the growth and yield of transgenic tobacco and maize under normal cultivation condition. Apparently, application of LcCHI2 provides a new train of thought for genetically engineering saline-alkali and pathogen resistant crops of both dicots and monocots.
AgROS: A Robot Operating System Based Emulation Tool for Agricultural Robotics

This research aims to develop a farm management emulation tool that enables agrifood producers to effectively introduce advanced digital technologies, like intelligent and autonomous unmanned ground vehicles (UGVs), in real-world field operations. To that end, we first provide a critical taxonomy of studies investigating agricultural robotic systems with regard to: (i) the analysis approach, i.e., simulation, emulation, real-world implementation; (ii) farming operations; and (iii) the farming type. Our analysis demonstrates that simulation and emulation modelling have been extensively applied to study advanced agricultural machinery while the majority of the extant research efforts focuses on harvesting/picking/mowing and fertilizing/spraying activities; most studies consider a generic agricultural layout. Thereafter, we developed AgROS, an emulation tool based on the Robot Operating System, which could be used for assessing the efficiency of real-world robot systems in customized fields. The AgROS allows farmers to select their actual field from a map layout, import the landscape of the field, add characteristics of the actual agricultural layout (e.g., trees, static objects), select an agricultural robot from a predefined list of commercial systems, import the selected UGV into the emulation environment, and test the robot’s performance in a quasi-real-world environment. AgROS supports farmers in the ex-ante analysis and performance evaluation of robotized precision farming operations while lays the foundations for realizing “digital twins” in agriculture.
ARABIDOPSIS NITRATE REGULATED 1 acts as a negative modulator of seed germination by activating ABI3 expression

Seed germination is a crucial transition point in plant life and is tightly regulated by environmental conditions through the coordination of two phytohormones, gibberellin and abscisic acid (ABA). To avoid unfavorable conditions, plants have evolved safeguard mechanisms for seed germination. Here, we report a novel function of the Arabidopsis MADS-box transcription factor ARABIDOPSIS NITRATE REGULATED 1 (ANR1) in seed germination. ANR1 knockout mutant is insensitive to ABA, salt, and osmotic stress during the seed germination and early seedling development stages, whereas ANR1-overexpressing lines are hypersensitive. ANR1 is responsive to ABA and abiotic stresses and upregulates the expression of ABI3 to suppress seed germination. ANR1 and ABI3 have similar expression pattern during seed germination. Genetically, ABI3 acts downstream of ANR1. Chromatin immunoprecipitation and yeast-one-hybrid assays showed that ANR1 could bind to the ABI3 promoter to regulate its expression. In addition, ANR1 acts synergistically with AGL21 to suppress seed germination in response to ABA as evidenced by anr1 agl21 double mutant. Taken together, our results demonstrate that the ANR1 plays an important role in regulating seed germination and early post-germination growth. ANR1 and AGL21 together constitutes a safeguard mechanism for seed germination to avoid unfavorable conditions.
Phenotypic clines across an unstudied hybrid zone in Woodhouse’s Scrub-Jay (Aphelocoma woodhouseii)

Woodhouse’s Scrub-Jay (Aphelocoma woodhouseii) comprises 7 subspecies, ranging from the Rocky Mountains to southern Mexico. We quantified the phenotype of specimens throughout Mexico and found support for significant phenotypic differences between “Sumichrast’s group” in southern Mexico (A. w. sumichrasti and A. w. remota) and the 2 subspecies in northern Mexico, or “Woodhouse’s group” (A. w. grisea and A. w. cyanotis). Despite significant differentiation in body size and mantle color, we found no clear geographic boundary between the groups, suggesting either a geographic cline or hybridization upon secondary contact. We tested for selection against hybridization by fitting models to geographic clines for both body size and back color, and found support for a stable contact zone centered near Mexico City, with selection against intermediate back color. Based on these results, we infer that Sumichrast’s and Woodhouse’s groups diverged during a period of geographic and genetic isolation. The phenotypic introgression between Sumichrast’s and Woodhouse’s groups near Mexico City likely represents a case of recent secondary contact, with selection against hybridization maintaining a geographically stable contact zone.
Generating Hierarchical Paths of Chinese Text from Wikipedia

: [ Objective ] Generate hierarchical semantic paths of texts from Wikipedia. [ Methods ] We first establish article concept vector of Chinese texts from Wikipedia through explicit semantic analysis. And then, we mapped the vector to the category nodes of hierarchical-tree-like graph. Finally, we generated the hierarchical paths with the help of seed node information diffusion and top-down path selection, as well as optimization technology. [ Results ] The average relevance degree of the first generated hierarchical path was 54.10% on the test dataset
Seasonal Variation of Essential Oil in Rosmarinus officinalis Leaves in Sardinia

Rosmarinus officinalis L. is an aromatic plant belonging to the Lamiaceae family widely distributed in the Mediterranean area. The interest on this species is related to the multiple uses of the plant as a food ingredient, in the pharmaceutical and cosmetic industries. The chemical composition of essential oil (EO) from 5 accessions of R. officinalis L. , collected monthly through a full year in Sardinia, has been studied by gas chromatography (GC) and GC-mass spectrometry technique. The EO ranged from 0.29% to 0.89%. The qualitative determinations revealed the presence of 27 compounds belonging to 6 chemical groups (hydrocarbon monoterpene, alcohols, aldehydes, ketones, esters, hydrocarbon sesquiterpene). Overall the GC-flame ionization detector analysis showed the presence of 7 major compounds: α-pinene (26%-28%), camphene (5%-8%), 1,8-cineole (15%-25%), borneol (5%-11%), camphor (3%-12%), verbenone (6%-15%), and bornyl acetate (4%-7%). Chromatographic data were also subjected to a chemometric approach that evidenced discrimination of the samples according to the site of collection.
Efficacy of botanical insecticides against pod borer (Maruca vitrata) on cowpea (Vigna unguiculata)

The field experiment was conducted during kharif 2016-17 to evaluation of botanical insecticides against pod borer on cowpea. Two rounds of insecticides were sprayed at fifteen days interval. The most effective treatment evaluated against pod borer was chlorpyriphos 20 EC@ 300g a.i. ha during first spray (1.97, 1.74 and 1.53 larvae /m at 3, 5, and 7 days after spray, respectively) and second spray (1.51, 1.54 and 1.93 larvae /m at 3, 5 and 7days after spray, respectively) followed by neem oil @ 2 % first spray (4.30, 4.08 and 3.52 larvae /m ) second spray (3.00, 2.85 and 3.28 larvae /m ) and NSKE @ 5 % during first spray (4.62, 4.18 and 3.81 larvae /m ) second spray (3.12, 3.09 and 3.37 larvae /m ) respectively. The maximum larval population was found in untreated plot. The highest green pod yield of cowpea was recorded in Chlorpyriphos 20 EC@300g a.i. ha (53.12 qha followed by neem oil @ 2% (43.53 qha) and NSKE @ 5% (42.11 qha) while lowest yield recorded in untreated control plot (32.16 qha).
Distribution models for Ascia monuste and the host Brassica oleracea var. capitata

The butterfly Ascia monuste L. (Lepidoptera: Pieridae) is a specialist pest of brassica crops in neotropical regions where it significantly impacts crop production. Understanding the actual and potential distribution of the pest and its hosts in current and future climates may help government agencies to mitigate and manage potential incursions. Here, we use MaxEnt algorithm to model the current distribution of both A. monuste and its host, Brassica oleracea var. capitata L. (cabbage) and then model the likely impact of projected climate change (RCP 4.5 and 8.5 scenarios) on their potential future distributions. While A. monuste is currently restricted to the American continent, we show that under current conditions the potential distribution of both the butterfly and cabbage includes areas of Africa, Asia, Oceania and Europe to some extent. The annual temperature range and mean annual temperature were the strongest predictors of the distribution of both species. Under a projected climate change scenario, suitable areas in the tropical climate zone are expected to decrease for both species. However, in temperate regions, the suitable area for cabbage is expected to increase but will remain unsuitable for the pest. Our results highlight the need for strategies to prevent the introduction of A. monuste to other areas of the tropical climate zone and for the development of management practices in the neotropical region.
Development of a DNA Barcoding Protocol for Fungal Specimens from the E.C. Smith Herbarium (ACAD)

Abstract Many field-collected fungal specimens are maintained in herbaria worldwide. These specimens contain an untapped wealth of taxonomic and ecological fungal biodiversity information. However, DNA can be difficult to obtain from preserved specimens. We present a DNA barcoding protocol specifically for preserved fungal specimens (ascomycetes and basidiomycetes). The E.C. Smith Herbarium at Acadia University houses 20,000 fungal specimens representative of northeastern North America. We achieved a DNA barcoding success rate of 18% from pre-1980 specimens (n = 39) using a kit-based DNA extraction protocol and sequencing of the full internal transcribed spacer (ITS) region of ribosomal DNA. This result surpassed success rates of previous protocols. We also explored the use of mini-barcodes from the ITS1 region only. Mini-barcodes (n = 13) demonstrated a 92% success rate in post-1980 specimens compared to full barcodes (46% success rate, n = 13) while retaining all the identification power of full barcodes in the examined specimens. Our approach will enable herbarium collections to be used more efficiently to populate DNA sequence databases such as GenBank. This approach will expand the number of reference DNA barcode sequences from vouchered fungal specimens within publicly available databases.
Effects of global warming on reproduction and potential dispersal of Mediterranean Cnidarians

Abstract Water temperature directly affects life cycles, reproductive periods, and metabolism of organisms living the oceans, especially in the surface zones. Due to the ocean warming, changes in water stratification and primary productivity are affecting trophic chains in sensitive world areas, such as the Mediterranean Sea. Benthic and pelagic cnidarians exhibit complex responses to climatic conditions. For example, the structure and phenology of the Mediterranean hydrozoan community displayed marked changes in species composition, bathymetric distribution, and reproductive timing over the last decades. The regional species pool remained stable in terms of species numbers but not in terms of species identity. When the Scyphozoa group is considered, we observe that Pelagia noctiluca (among the most abundant jellyfish in the Mediterranean Sea and eastern Atlantic waters) has increasingly frequent massive outbreaks associated to warmer winters. Variations in metabolic activities, such as respiration and excretion, are strongly temperature-dependent, with direct increment of energetic costs with jellyfish size and temperature, leading to growth rate reduction. Water temperature affects sexual reproduction through changes in the energy storage and gonad development cycles. Anthozoan life cycles depend also on primary productivity and temperature: gonadal production and spawning are tightly related in shallow populations (0–30 m depth) with the spring-summer temperature trends and autumn food availability. Overall, the energy transferred from the mother colonies to the offspring may decrease, negatively affecting their potential to settle, metamorphose and feed during the first months of their lives, eventually impairing the dominance of long-living cnidarian suspension feeders in shallow benthic habitats. In this review, we describe the already ongoing effects of sea warming on several features of cnidarian reproduction, trying to elucidate how reproductive traits and potential dispersion will be affected by the cascade effects of increasing temperature in the Mediterranean Sea.
Key Problems of Data Management in Data Center in Big Data Context

* This paper analysed the challenges of data management in data center, such as big data volume, data heterogeneous, high time requirement of data processing, and widely separated data sources. We discussed the disadvantages of traditional data management technologies to deal with these problems. We also highlighted the key problems of data management in data center including data integration, data analysis, and representation of data analysis results.
Phased Diploid Genome Assemblies for Three Strains of Candida albicans from Oak Trees

Although normally a harmless commensal, Candida albicans, it is also one of the most common causes of bloodstream infections in the U.S. Candida albicans has long been considered an obligate commensal, however, recent studies suggest it can live outside animal hosts. Here, we have generated PacBio sequences and phased genome assemblies for three C. albicans strains from oak trees (NCYC 4144, NCYC 4145, and NCYC 4146). PacBio datasets are high depth (over 400 fold coverage) and more than half of the sequencing data are contained in reads longer than 15 kb. Primary assemblies showed high contiguity with several chromosomes for each strain recovered as single contigs, and greater than half of the alternative haplotype sequence was assembled in haplotigs at least 174 kb long. Using these assemblies we were able to identify structural polymorphisms, including a polymorphic inversion over 100 kb in length. These results show that phased de novo diploid assemblies for C. albicans can enable the study of genomic variation within and among strains of an important fungal pathogen.
Métodos de Extração de Compostos Fenólicos das Folhas de Corchorus olitorius

Corchorus olitorius é uma planta alimentícia não convencional (PANC) conhecidapopularmente como jute nalta, jute tossa, moroheiya, mishti paat e malokhieh.A folha e a semente de Corchorus olitorius vem sendo pesquisadas como potencialfármaco para o tratamento de diabetes melito tipo 2 e suas complicações. Oobjetivo deste trabalho é identificar e comparar os métodos de extração para oscompostos fenólicos de Corchorus olitorius já testados em trabalhos de pesquisa.Dentre os reveladores analisados estão, acetato de potássio, água, cloreto de alumínio,etanol, éter dietílico, metanol, butanol, hexano. Devido os fenóis existentes no Corchorusolitorius ser de forma polar, faz-se necessário uma extração preferível emágua e metanol, onde, para futura pratica é necessária preparação de extrato hidrofílicocomo o realizado pela metodologia de Oboh (2009). As folhas deverão ser lavadasem água destilada, levadas ao sol e moídas. O extrato aquoso da folha deve ser prepa -rado embebendo o vegetal em água por cerca de 24 h e a mistura filtrada. O filtradodeve ser evaporado sob pressão negativa a 408 ºC. O extrato poderá ser armazenadono refrigerador para posterior análise com rendimento calculado em 16,6%.
TANGLED1 mediates interactions between microtubules that may promote spindle organization and phragmoplast guidance to the division site in maize

The microtubule cytoskeleton serves as a dynamic structural framework for mitosis in eukaryotic cells. TANGLED1 (TAN1) is a microtubule-binding protein that localizes to the division site and mitotic microtubules and plays a critical role in division plane orientation in plants. Here, in vitro experiments demonstrate that TAN1 directly binds microtubules, mediating microtubule zippering or end-on microtubule interactions, depending on their contact angle. Maize tan1 mutant cells improperly position the preprophase band (PPB), which predicts the future division site. However, cell-shape-based modeling indicates that PPB positioning defects are likely a consequence of abnormal cell shapes and not due to TAN1 absence. Spindle defects in the tan1 mutant suggest that TAN1-mediated microtubule zippering may contribute to metaphase spindle organization. In telophase, co-localization of growing microtubules ends from the phragmoplast with TAN1 at the division site suggests that TAN1 interacts with microtubule tips end-on. Together, our results suggest that TAN1 contributes to spindle and phragmoplast microtubule organization to ensure proper division plane orientation.
Phenotypic detection of methicillin-resistant Staphylococcus aureus in village chickens from poultry markets in Maiduguri, Nigeria

Objective: The study was carried out to detect the carriage of methicillin-resistant Staphylococcus aureus (MRSA) and their antimicrobial susceptibilities in village chickens sold at Maiduguri poultry markets using phenotypic characterization. Materials and Methods: This was a cross-sectional study where 120 samples comprised 50% each of Nasal and cloacal swabs, were, respectively, collected from live village chickens sold at Maiduguri poultry markets and examined for the presence MRSA based on bacterial culture, biochemical characteristics, growth on oxacillin resistant screening agar base, and antimicrobial susceptibility tests. Results: The study revealed an overall occurrence of 38.33% S. aureus and 32.60% MRSA, respectively. Antimicrobial susceptibility test was carried out on MRSA positive isolates against seven antimicrobials. All the isolates (100%) exhibited resistance against cefoxitin, whereas the least antimicrobial resistance was recorded against erythromycin and streptomycin each with 26.6%, respectively. In the same way, the highest antibiotic susceptibility in this study was observed against erythromycin (60%) and least susceptibility was against vancomycin and streptomycin with 20% each. A varying intermediate antibiotic susceptibility ranging from 13.33% to 53.33% was observed. Multiple-drug resistance patterns were exhibited by MRSA isolates from this study with 73.3% of the isolates exhibiting resistance to two or more antibiotics. Conclusion: This study has shown the carriage of MRSA by village chickens which calls for serious public health concern and concludes that these birds might have acquired these pathogens from the environment or infected humans since they normally receive no less medical attention.
CBP80/20-dependent translation initiation factor (CTIF) inhibits HIV-1 Gag synthesis by targeting the function of the viral protein Rev

Translation initiation of the human immunodeficiency virus type-1 (HIV-1) unspliced mRNA has been shown to occur through cap-dependent and IRES-driven mechanisms. Previous studies suggested that the nuclear cap-binding complex (CBC) rather than eIF4E drives cap-dependent translation of the unspliced mRNA and we have recently reported that the CBC subunit CBP80 supports the function of the viral protein Rev during nuclear export and translation of this viral transcript. Ribosome recruitment during CBC-dependent translation of cellular mRNAs relies on the activity CBP80/20 translation initiation factor (CTIF), which bridges CBP80 and the 40S ribosomal subunit through interactions with eIF3g. Here, we report that CTIF restricts HIV-1 replication by interfering with Gag synthesis from the unspliced mRNA. Our results indicate that CTIF associates with Rev through its N-terminal domain and is recruited onto the unspliced mRNA ribonucleoprotein complex in order to block translation. We also demonstrate that CTIF induces the cytoplasmic accumulation of Rev impeding the association of the viral protein with CBP80. We finally show that CTIF restricts HIV-2 but not MLV Gag synthesis indicating an inhibitory mechanism conserved in Rev-expressing human lentiviruses.
Distribution of lethal yellowing and associated phytoplasma strains in Jamaica, Mexico and other countries in the region

The relentless spread of the fatal disease lethal yellowing (LY) throughout the coconut growing areas is having a serious impact on many vulnerable communities. Phytoplasmas from the 16SrIV group are the associated agents. These obligated phytopathogenic mollicutes systemically colonize phloem tissues inducing numerous biochemical and physiological changes leading to symptom development and ultimate death of coconut palms. Large numbers of coconut trees succumbed to the disease over the past three decades. There are different subgroups of the 16SrIV phytoplasmas affecting palms in the Americas. It is important for these to be properly identified along with the epidemiology of the disease. The effective molecular tools used to identify these subgroups show variations in some conserved genomic regions. In the Americas the subgroups have been identified, the current distribution of LY in Jamaica and Mexico and the 16SrIV subgroups occurring in these countries and in other Caribbean countries are described.