Miracle-dz/UniFAR-FTUs huggingface dataset:
BCMV-ukr: isolate of bean common mosaic virus revealed in Ukraine

SUMMARY Bean common mosaic virus (BCMV) is distributed worldwide and causes a serious disease in bean reducing growth and crops yield. The aim of this study was to investigate the occurrence of BCMV and Bean common mosaic necrotic virus (BCMNV) in Ukraine, to characterise host range and reactions of indicator plants to mechanical inoculation with the isolate and to differentiate it by using Drijfhout’s differentials. Leaf samples were positive for BCMV infection in RT-PCR assay employing specific primers with amplification of a 340-bp product. Based on a biological test on bean differentials, the isolate was assigned to pathogroup VII despite the fact that strain differed markedly from the standard strains in symptoms producing on differential groups IV and V. Partial sequence data of the coat protein region show 100% identity with BCMV 125 sequences tested. To our knowledge, this is the first attempt to characterise the BCMV circulating in Ukraine.
Selection of Bangka Local Groundnut (Arachis hypogaea L.) Germplasm Tolerant to Drought Stress

Bangka Belitung is dominated by marginal lands, such as dry land, which can affect the productivity of groundnut by reducing groundnut yield. Increased groundnut yield in Bangka Belitung could be done by using drought tolerance genotypes. The objective of this study is to obtain groundnut genotypes tolerant to drought stress. This research was conducted at Experimental and Research Garden, University of Bangka Belitung, from January to March 2018. This research used experimental method with Split Plot Complete Randomized Design. It consisted of 2 main plot and 8 subplot levels. The main plot consists of 100% and 40% of field capacity used in drought stress assessment. Subplot consist of eight groundnut genotypes. These genotypes were Bangka local groundnuts (Belimbing, Arung Dalam, Air Ketimbai 1, Bedeng Akeh, and Lubuk Kelik accession), and national varieties (Tuban, Hypoma and Kancil varieties). Research result showed Bangka local groundnut genotypes tolerant to drought stress was Belimbing accession for 100 seeds weight character. National varieties tolerant to drought stress were Tuban and Hypoma varieties. Tuban variety showed drought tolerance through the following characters: root length, number of seeds per pod, root dry weight, and seed weight per plant. Hypoma variety showed drought tolerance on root length and number of seeds per pod characters. Tuban, Hypoma and Belimbing could be recommended for groundnut cultivation on dry land. Keywords—germplasm, groundnut, drought stress, field capacity, Bangka.
Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication in Brassica rapa

Many crops are polyploid or have a polyploid ancestry. Recent phylogenetic analyses have found that polyploidy often preceded the domestication of crop plants. One explanation for this observation is that increased genetic diversity following polyploidy may have been important during the strong artificial selection that occurs during domestication. To test the connection between domestication and polyploidy, we identified and examined candidate genes associated with the domestication of the diverse crops of Brassica rapa. Like all “diploid” flowering plants, B. rapa has a diploidized paleopolyploid genome and experienced many rounds of whole genome duplication (WGD). We analyzed transcriptome data of more than hundred cultivated B. rapa accessions. Using a combination of approaches, we identified more than 3,000 candidate genes associated with the domestication of four major B. rapa crops. Consistent with our expectation, we found that the candidate genes were significantly enriched with genes derived from the Brassiceae mesohexaploidy. We also observed that paleologs contained significantly more genetic diversity than non-paleologs, suggesting that elevated genetic variation may explain why paleologs are enriched among domestication candidate genes. Our analyses demonstrate the key role of polyploidy in the domestication of B. rapa and provide support for its importance in the success of modern agriculture.
New sawflies from the mid-Cretaceous Myanmar amber (Insecta: Hymenoptera: Syspastoxyelidae)

ABSTRACT Many insects have been described from the mid-Cretaceous Myanmar (Burmese) amber in recent years, including about 50 families of wasps. However, only two species of sawfly, Syspastoxyela rhaphidia and Striaexyela longicornis (Syspastoxyelidae), have been described in Myanmar amber, in contrast to more than 100 species of sawflies from the Mesozoic of Kazakhstan and China. Herein, we describe three new taxa of sawflies, Deltoxyela engeli gen. et sp. nov., Syspastoxyela pinguis sp. nov. and Syspastoxyela simpla sp. nov., based on six amber pieces with 21 specimens of sawflies from the mid-Cretaceous Myanmar amber. The new findings suggest that syspastoxyelids were speciose and prosperous in the ecosystem, even though only one family of sawflies, Syspastoxyelidae, has been reported hitherto.
Host fruit as a suitable bacteria growth substrate that promotes larval development of Bactrocera dorsalis (Diptera: Tephritidae)

The ability of a host plant to act as a substrate or media for larval development may depend on how good it is at offering suitable nutrients for bacterial growth. In this study, we hypothesized that the suitability of a fruit type for fruit fly larval development is positively correlated with the ability of that fruit to act as a substrate/media for fruit fly symbiotic bacterial growth. We allowed a single female fruit fly to lay eggs on five different host fruits, then we monitored the larval development parameters across five generations and analyzed the bacterial community structure of larvae developing in 2 of these hosts (apple and banana) at the first and fifth generations. Results indicate that the larval length and dry weight did not vary significantly across experimental generations, but were greatly affected by fruit types and larval stages. The larval development time was extended considerably in apple and tomato but shortened in banana and mango. There was a significant shift in bacterial community structure and composition across fruits and generations. The bacterial community of larvae within the same fruit (apple and banana) clustered and was similar to the parental female (with the predominance of Proteobacteria), but there was a shift at the fifth generation (dominance of Firmicutes). Banana offered a suitable better development and growth to larvae and bacteria, respectively, compared to apple in which reduced larval development and bacterial growth were recorded. Although additional experiments are needed to adequately show that the differences in microbiome seen in fruit fly larval guts are the actual driver of different developmental outcomes of larvae on the different fruits, at the very least, our study has provided intriguing data suggesting interaction between the diets and gut microbial communities on insect development. Importance and Significance of the study Tephritid fruit flies entertain complex interactions with gut bacteria. These bacteria are known to provide nutritional benefits to their hosts, by supplementing missing nutrients from the host diets and regulating energy balance. Foraging for food is a risky exercise for the insect which is exposed to ecological adversities, including predators. Therefore, making beneficial choice among available food substrates is a question of survival for the flies and bacteria as well. Our study demonstrates interactions between the host fly and its intestinal bacteria in sustaining the larval development while foraging optimally on different fruit types. These findings add a novel step into our understanding of the interactions between the gut microbial communities and B. dorsalis and provide avenues for developing control strategies to limit the devastative incidence of the fly.
The complete chloroplast genome of Houttuynia cordata Thunb. (Family: Saururaceae)

Abstract The chloroplast genome sequence of Houttuynia cordata has been characterized from Illumina pair-end sequencing. The complete chloroplast genome was 161,090 bp in length, containing a large single-copy (LSC) region of 88,180 bp and a small single-copy (SSC) region of 19,204 bp, which were separated by a pair of 26,853 bp inverted repeat regions. Furthermore, phylogenetic analysis revealed that H. cordata is a sister of Piper cenocladum.
The complete chloroplast genome sequence of Mytilaria laosensis

Abstract The first complete chloroplast genome (cpDNA) sequence of Mytilaria laosensis was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 159,941 bp in length, contains a large single-copy region (LSC) of 89,016 bp and a small single-copy region (SSC) of 18,127 bp, which were separated by a pair of inverted repeats (IR) regions of 26,399 bp. The genome contains 130 genes, including 85 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 37.9%, and the corresponding values of the LSC, SSC, and IR regions are 35.9, 32.8, and 43.1%, respectively. Further phylogenomic analysis showed that M. laosensis and Chunia bucklandioides clustered in a clade in family Hamamelidaceae.
Isolation and molecular identification of pectinase producing Aspergillus species from different soil samples of Bhubaneswar regions

With the significant improvement of human civilization there is a spur in the urban, rural and industrial development, which has a profound effect on the surrounding natural environment. Increased utilization of natural resources is often associated with accumulation of waste materials whose management is crucial for sustainable development of life. Availability of different microorganisms in the soil facilitates the degradation of wastes through their potential enzymatic activities. Pectinase seems to be one of the important enzymes produced by a wide variety of microorganisms contained in the soil. It is mainly involved in maceration and rotting of plant extracts and debris by hydrolysis of 1,4-alpha glycosidic bonds of de-esterified pectate of plant call wall. In this paper we report molecular identification of some pectinase producing Aspergillus species selected from soil samples of five different zones of Bhubaneswar city using molecular biology and computational techniques. Among fifteen fungal isolates studied from these five zones Aspergillus parvisclerotigenus was potent for pectinase production next to Aspergillus niger in form of halozone of 0.6 mm. It’s 28S rDNA sequence also had some significant identity (>90%) with different subspecies of Aspergillus. We hope that our findings will helpful in genetic manipulation for improvement of fungal strains of isolates. Again large scale use of the improved Aspergillus strains can degrade plant biomass & diverse industrial wastes which will reduce environmental pollution of capital urban like Bhubaneswar.
Apcdd1 is a dual BMP/Wnt inhibitor in the developing nervous system and skin

Animal development and homeostasis depend on precise temporal and spatial intercellular signaling. Components shared between signaling pathways, generally thought to decrease specificity, paradoxically can also provide a solution to pathway coordination. Here we show that the Bone Morphogenetic Protein (BMP) and Wnt signaling pathways share Apcdd1 as a common inhibitor and that Apcdd1 is a taxon-restricted gene with novel domains and signaling functions. Previously, we showed that Apcdd1 inhibits Wnt signaling, here we find that Apcdd1 potently inhibits BMP signaling in body axis formation and neural differentiation in chicken, frog, zebrafish, and humans. Our results from experiments and modeling suggest that Apcdd1 may coordinate the outputs of two signaling pathways central to animal development and human disease. Significance Statement Apcdd1 is a taxon-restricted gene that inhibits both BMP and Wnt intercellular signaling pathways in multiple organisms including mice, frog, zebrafish, and chicken. It encodes a bi-functional protein with a novel protein domain that can bind to Wnt and BMP receptors and block downstream signaling.
KSn4(PO4)(3)

The crystal structure of potassium tetratin(II) tris­(ortho­phosphate), KSn4(PO4)3, obtained by hydro­thermal synthesis, has been determined from single-crystal X-ray diffraction data. The structure consists of [Sn4(PO4)3] units sharing common corners, which leads to a three-dimensional network structure and generates cages along the c direction. The cages are occupied by K atoms on threefold axes.
Assessing the capacity of endemic alpine water beetles to face climate change

Accurate assessments of species' vulnerability to climate change require integrated measurements of its different drivers, including extrinsic (the magnitude and rate of climate change) and intrinsic factors (organisms' sensitivity and adaptive capacity). According to these factors, aquatic insects restricted to alpine ponds may be especially threatened by climate change. However, vulnerability predictions based on such an integrative approach are scarce for alpine pond taxa. We combined distributional, climatic data and experimental measurements of heat tolerance and acclimation capacity of two water beetles endemic to Sierra Nevada National Park (Spain) to evaluate different components of their vulnerability to climate change. We estimated: (i) changes in climatically suitable habitat under different scenarios of climate change and (ii) thermal safety margins (the difference between species upper thermal limits and the maximum temperatures in their current localities), for current and future conditions, and acclimation capacity, as measures of the physiological capacity to persist in situ. Species distribution models predicted a virtual loss of climatically suitable area under different climate change scenarios. Nonetheless, both taxa showed heat tolerance limits above the predicted maximum temperatures in their current localities (but no capacity to adjust such limits through acclimation). Therefore, these beetles could have the physiological capacity to deal with warming conditions in situ. We recommend concentrating conservation efforts in current localities as the most efficient management strategy for both taxa. Our results stress the importance of accounting for physiological tolerances when predicting the vulnerability to climate change in alpine freshwater biota.
Skull shape variation in extant pangolins (Pholidota: Manidae): allometric patterns and systematic implications

Pangolins are among the most endangered groups of mammals, comprising eight extant species delineated into three genera. Despite several studies dedicated to their skeletal anatomy, the potential taxonomic insight from cranial morphological variation in extant Pholidota is yet to be assessed with modern geometric morphometric methods. We present the first comprehensive study on the cranial morphology of extant pangolins and discuss its implications for the taxonomy and evolution of the group. We performed landmark-based morphometric analyses on 241 museum specimens to describe the variation in skull shape in seven of the eight extant species. Our analyses revealed genus- and species-level morphological discrimination, with Asian species (Manis spp.) being grouped together, whereas African pangolins present distinct skull shapes between small (Phataginus spp.) and large (Smutsia spp.) species. Analyses of allometry also identified a set of traits whose allometric trajectories distinguish Asian from African specimens. Finally, we uncovered intraspecific variation in skull shape in white-bellied pangolins (Phataginus tricuspis) that partly corroborates recent DNA-based differentiation among biogeographically distinct populations. Overall, our results shed light on the morphological diversity of the skull of these enigmatic myrmecophagous mammals and confirm the genus-level classification and cryptic diversity within the white-bellied pangolin revealed by molecular phylogenetics.
Comparison of Arm-Trunk Movement between Complete Paraplegic and Able-Bodied Subjects during Circle Drawing

Abstract Study design : This study was a cross sectional, controlled trial. Objectives: To examine the performance of repetitive circle drawing on dynamic sitting balance between subject with spinal cord injury (SCI) and age-matched able-bodied (AB) adults. Summary of background data : Previous studies showed that the dynamic sitting balance is impaired in SCI. However, the arm-trunk coordinated movement for different directions in seated SCI has not been examined yet. Methods: Twelve subjects with complete T7-T12 thoracic cord injury (mean age: 36.3 ± 3.0 years) and 12 age- matched AB adults were recruited. Subjects performed 10 repetitive circle drawing at seated position. The three- dimensional motion system (Vicon) was used to measure shoulder, trunk and pelvic angles at sitting position. Results : The SCI group displayed an arm-trunk movement with a significantly larger shoulder adduction/ abduction angle (p<0.001), but less trunk flexion/extension, pelvic anterior/posteriortilt and pelvic rotation angles than AB controls (p<0.05, p<0.001, and p<0.001, respectively). Conclusions: The small circle drawing is feasible to detect the compensatory movement of shoulder for the impairment of trunk and pelvic control in thoracic SCI. Furthermore, the assistance and guidance of trunk and pelvic movements is important for the arm-trunk coordinated movement in thoracic SCI.
Transmission network reconstruction for foot-and-mouth disease outbreaks incorporating farm-level covariates

Transmission network modelling to infer ‘who infected whom’ in infectious disease outbreaks is a highly active area of research. Outbreaks of foot-and-mouth disease have been a key focus of transmission network models that integrate genomic and epidemiological data. The aim of this study was to extend Lau’s systematic Bayesian inference framework to incorporate additional parameters representing predominant species and numbers of animals held on a farm. Lau’s Bayesian Markov chain Monte Carlo algorithm was reformulated, verified and pseudo-validated on simulated outbreaks populated with demographic data Japan and Australia. The modified model was then implemented on genomic and epidemiological data from the 2010 outbreak of foot-and-mouth disease in Japan, and outputs compared to those from the SCOTTI model implemented in BEAST2. The modified model achieved improvements in overall accuracy when tested on the simulated outbreaks. When implemented on the actual outbreak data from Japan, infected farms that held predominantly pigs were estimated to have five times the transmissibility of infected cattle farms and be 49% less susceptible. The farm-level incubation period was 1 day shorter than the latent period, the timing of the seeding of the outbreak in Japan was inferred, as were key linkages between clusters and features of farms involved in widespread dissemination of this outbreak. To improve accessibility the modified model has been implemented as the R package ‘BORIS’ for use in future outbreaks.
Computational Prediction of Ubiquitination Proteins Using Evolutionary Profiles and Functional Domain Annotation

Background: Ubiquitination, as a post-translational modification, is a crucial biological process in cell signaling, apoptosis, and localization. Identification of ubiquitination proteins is of fundamental importance for understanding the molecular mechanisms in biological systems and diseases. Although high-throughput experimental studies using mass spectrometry have identified many ubiquitination proteins and ubiquitination sites, the vast majority of ubiquitination proteins remain undiscovered, even in well-studied model organisms. Objective: To reduce experimental costs, computational methods have been introduced to predict ubiquitination sites, but the accuracy is unsatisfactory. If it can be predicted whether a protein can be ubiquitinated or not, it will help in predicting ubiquitination sites. However, all the computational methods so far can only predict ubiquitination sites. Methods: In this study, the first computational method for predicting ubiquitination proteins without relying on ubiquitination site prediction has been developed. The method extracts features from sequence conservation information through a grey system model, as well as functional domain annotation and subcellular localization. Results: Together with the feature analysis and application of the relief feature selection algorithm, the results of 5-fold cross-validation on three datasets achieved a high accuracy of 90.13%, with Matthew’s correlation coefficient of 80.34%. The predicted results on an independent test data achieved 87.71% as accuracy and 75.43% of Matthew’s correlation coefficient, better than the prediction from the best ubiquitination site prediction tool available. Conclusion: Our study may guide experimental design and provide useful insights for studying the mechanisms and modulation of ubiquitination pathways. The code is available at: https://github.com/Chunhuixu/UBIPredic_QWRCHX
Two human Mitochondrial Pyruvate Carrier mutations reveal distinct mechanisms of molecular pathogenesis

The uptake of pyruvate into the liver mitochondria is an important step in carbohydrate utilization for energy production and gluconeogenesis. Pyruvate is a major TCA cycle substrate and requires import into the mitochondrial matrix for channeling into gluconeogenesis. The identification of the genes encoding the MPC now enables molecular-genetic studies on MPC function. We generated mice with liver-specific deletion of Mpc1 and investigated the importance of the MPC for hepatic gluconeogenesis. Using both genetic and chemical MPC disruption we found that the MPC gates pyruvate-driven hepatic gluconeogenesis in mouse and rat primary hepatocytes. We also observed that disruption of MPC activity induced alternative pathways for gluconeogenesis utilizing pyruvate-alanine cycling and glutaminolysis.
Preliminary results on antifungal activity of donkey milk

Donkey milk is being increasingly studied for its use in the human medicine and its antimicrobial activity has been reported in the literature. However, there have been only few studies on milk's inhibiting activity against fungi. Donkey milk is currently used in the personal healthcare industry, thus evaluating its antifungal activity against some dermatophytes is of interest in relation to the natural prevention or control of dermatophyte infections. This preliminary study evaluated the in vitro antifungal activity of donkey milk. Four fresh pasteurized bulk milk samples were collected from a donkey farm. Pasteurized donkey bulk milk samples were analysed in relation to gross composition, individual mineral content (Ca, P, Mg, K, Na, and Zn mg/L), fatty acid profile, and lysozyme activity. The milk samples were tested against isolates of Microsporum canis, Microsporum gypseum, and Trichophyton mentagrophytes. Sensitivity testing was assessed by a microdilution test, starting by a milk concentration of 90%. To calculate minimal inhibitory concentration values, 80%, 70%, 60% 50%, 40%, 30%, 20%, and 10% dilutions were tested. Donkey milk was proven to inhibit mycotic growth. In particular, M. canis and T. mentagrophytes failed to grow in 60% donkey milk and M. gypseum appeared to be sensitive to 70%. The antidermatophyte effect could be related to the milk content of some fatty acids with reported antifungal activities. In the analysed donkey milk, C10:0 on average constituted 70% of the short chain fatty acids and the milk fat showed a relatively high content of linoleic and alpha linolenic acid (15.34 and 4.87 g/100f of the total fatty acids respectively). We also found a high lysozyme activity (1402.50 U/mL of milk). In conclusion, donkey milk showed an overall antidermatophytic effect. On the basis of the promising results obtained in this preliminary report, further studies are needed to evaluate the in vivo use of donkey milk against dermatophytosis.