Miracle-dz/UniFAR-FTUs huggingface dataset:
The re-sequencing and re-assembly of complete chloroplast genome of Melastoma dodecandrum (Melastomataceae) from Fujian, China

Abstract The plant genus Melastoma of the family Melastomataceae is comprised of nine species and one variety in China. Melastoma dodecandrum is the only creeping species of this genus. Previous study has reported the complete chloroplast genome of M. dodecandrum from Guangzhou, China, but there may be some differences between plant populations from different regions. Herein, we reported the complete chloroplast genome of M. dodecandrum from Fuzhou, China, which was assembled from Pacbio and whole genome data was sequenced. The sequence has a circular molecular length of 156,598 bp and contained 129 genes. Phylogenetic analysis indicated that M. dodecandrum was closely related to M. candidum in Melastomataceae. The study aims to provide insights for the future studies on the differences in molecular evolution level between plant populations of M. dodecandrum and taxonomy of Melastoma.
Streamlined production, purification, and comparison of recombinant extracellular polyhydroxybutyrate depolymerases

Heterologous production of extracellular polyhydroxybutyrate (PHB) depolymerases (PhaZs) has been of interest for over 30 years, but implementation is sometimes difficult and can limit the scope of research. With the constant development of tools to improve recombinant protein production in Escherichia coli, we propose a method that takes characteristics of PhaZs from different bacterial strains into account. Recombinant His-tagged versions of PhaZs (rPhaZ) from Comamonas testosteroni 31A, Cupriavidus sp. , Marinobacter algicola DG893, Pseudomonas stutzeri, and Ralstonia sp. were successfully produced with varying expression, solubility, and purity levels. PhaZs from C. testosteroni and P. stutzeri were more amenable to heterologous expression in all aspects; however, strategies were developed to circumvent low expression and purity for the other PhaZs. Degradation activity of the rPhaZs was compared using a simple PHB plate-based method, adapted to test for various pH and temperatures. rPhaZ from M. algicola presented the highest activity at 15 °C, and rPhaZs from Cupriavidus sp. and Ralstonia sp. had the highest activity at pH 5.4. The methods proposed herein can be used to test the production of soluble recombinant PhaZs, and to perform preliminary evaluation for applications that require PHB degradation.
Constraints on fruit tracking by birds at the range edge

Biotic interactions may be disrupted at the range boundary if the involved species are rare in the most distant sectors. This study assesses fruit tracking by seed‐dispersing birds wintering on the border of the Palaearctic, a region where many species become scarcer before reaching the limits of their distribution in the Sahara. As vagrancy improves fruit tracking, this study tests if vagrant birds track fruit resources better than non‐vagrant birds and if their tracking ability is reduced at the range edge.
Bacterial and Archaeal Communities in Sediments from the Adjacent Waters of Rushan Bay (China) Revealed by Illumina Sequencing

Abstract In this study, bacterial and archaeal communities in sediments from the adjacent waters of Rushan Bay were studied based on 16S ribosomal RNA (rRNA) gene. Illumina sequencing and quantitative PCR (qPCR) analyses were used to analyze the bacterial and archaeal community characteristics. The ecological analyses of sequences revealed that the diversity of bacterial communities was higher than that of archaeal communities. The abundance of bacterial 16S rRNA genes was observed to be greater than that of archaeal 16S rRNA genes. Proteobacteria and Piscirickettsiaceae were the most abundant bacterial phylum and family; Thaumarchaeota dominated the archaeal communities, and MGI in Thaumarchaeota and Halobacteria in Euryarchaeota were prevalent and the predominant archaeal class in this study. Temperature and ammonium concentration were related to the bacterial communities, whereas the nitrite concentration and ammonium concentration had a correlation with the archaeal communities; meanwhile, a complex combination of environmental factors might shape the bacterial and archaeal communities in this dynamic environment. Functional Annotation of Prokaryotic Taxa (FAPROTAX) analysis showed that most bacterial sequences were involved in chemoheterotrophy, sulfate respiration, respiration of sulfur compounds, aerobic nitrite oxidation and nitrification; for the archaeal communities, the essential ecological functions were chemoheterotrophy, other ecological functions such as aerobic ammonia oxidation and methanogenesis, were also predicted to be present in this study. The comparison of bacterial and archaeal communities in different environments suggest that similar conditions are hypothesized to give rise to similar microbial communities, and environmental conditions may contribute significantly to the bacterial and archaeal community structure.
The HSP90 paralog TRAP1 oligomerizes into an OXPHOSregulated protein complex that may be essential for maintaining mitochondrial metabolic homeostasis

The molecular chaperone TRAP1 has been studied for almost two decades, yet, the mechanistic basis underlying its function in the mitochondria still remains poorly understood. Recent studies have presented it as an inhibitor of OXPHOS and an inducer of the Warburg phenotype, but multiple reports have conflicted with this paradigm. This study seeks to reconcile previous reports in a cohesive model by proposing that TRAP1 does not necessarily down or upregulate OXPHOS, but, is actually required to maintain OXPHOS homeostasis. Using multiple CRISPR KO cell lines, real time OCR analyses with different carbon sources, metabolomics and various proteomic approaches to understand interactions, this study provides a platform to understand TRAP1 function in mitochondria. We show that TRAP1 induces a metabolic rewiring independent of its ATPase activity, requires an ATP-bound state to interact with various mitochondrial proteins and forms an oligomerized protein complex that may be the functional unit of TRAP1.
AquaCropR: Crop Growth Model for R

The Food and Agriculture Organization (FAO) AquaCrop model, run either via a standalone graphical user interface (GUI) or via a matlab application programming interface (API) (AquaCrop-OS), has been successfully tested on many crop species and under multiple scenarios. However, with these current versions, it is difficult for users to adapt formulae, add functionality or incorporate the model into other applications such as decision support tools. Here, we report on the release of a version of AquaCrop written in R. Performance of the model was tested using published datasets of wheat (Triticum aestivum L.) and maize (Zea mays L.), comparing output from AquaCropR with these other versions of AquaCrop. Our goal in developing this version was to widen the use and improvement of AquaCrop through open access.
The C. elegans RIG-I homolog drh-1 mediates the Intracellular Pathogen Response upon viral infection

Mammalian RIG-I-like receptors detect viral dsRNA and 5’ triphosphorylated RNA to activate transcription of interferon genes and promote antiviral defense. The C. elegans RIG-I-like receptor DRH-1 promotes defense through antiviral RNA interference, but less is known about its role in regulating transcription. Here we describe a role for drh-1 in directing a transcriptional response in C. elegans called the Intracellular Pathogen Response (IPR), which is associated with increased pathogen resistance. The IPR includes a set of genes induced by diverse stimuli including intracellular infection and proteotoxic stress. Previous work suggested that the proteotoxic stress caused by intracellular infections might be the common trigger of the IPR, but here we demonstrate that different stimuli act through distinct pathways. Specifically, we demonstrate that DRH-1/RIG-I is required for inducing the IPR in response to Orsay virus infection, but not in response to other triggers like microsporidian infection or proteotoxic stress. Furthermore, drh-1 appears to be acting independently of its known role in RNAi. Interestingly, expression of the replication competent Orsay virus RNA1 segment alone is sufficient to induce most of the IPR genes in a manner dependent on RNA dependent RNA polymerase activity and on drh-1. Altogether, these results suggest that DRH-1 is a pattern-recognition receptor that detects viral replication products to activate the IPR stress/immune program in C. elegans. Importance C. elegans lacks homologs of most mammalian pattern recognition receptors, and how nematodes detect pathogens is poorly understood. We show that the C. elegans RIG-I homolog drh-1 mediates induction of the Intracellular Pathogen Response (IPR), a novel transcriptional defense program, in response to infection by the natural C. elegans viral pathogen Orsay virus. drh-1 appears to act as a pattern-recognition receptor to induce the IPR transcriptional defense program by sensing the products of viral RNA-dependent RNA polymerase activity. Interestingly, this signaling role of drh-1 is separable from its previously known role in antiviral RNAi. In addition, we show that there are multiple host pathways for inducing the IPR, shedding light on the regulation of this novel transcriptional immune response.
Multidimensional stable isotope analysis illuminates resource partitioning in a sub‐Antarctic island bird community

A central theme in community ecology is understanding how similar species co‐exist and how their interactions may evolve in the context of climate change. Most studies of resource partitioning among central place foragers, particularly birds, focus on the offspring‐rearing period, when they are accessible, but breeding success may be determined earlier and little is known about how such species partition resources at the onset of breeding. We used a non‐invasive approach to evaluate resource partitioning in co‐existing females at a sub‐Antarctic island during their pre‐laying periods. Three hypotheses were tested using carbon, nitrogen and oxygen stable isotope ratios measured in shells and membranes of hatched eggs as ecological tracers: 1) resource partitioning by geographic location and trophic level will exist among the 12 bird species and will be enhanced within taxonomic groups; 2) given the absence of strong oxygen gradients in the Southern Ocean we will not detect spatial structuring based on oxygen isotopes, but differences will exist between resident and oceanic species as the former may use meteoric water; 3) capital and income breeder strategies can be differentiated using stable isotopes of egg remains. Two and three dimensional isotopic data showed resource partitioning among species. As predicted, segregation was evident within the four main taxonomic groups: penguins, albatrosses, burrowing petrels and giant petrels. Unexpectedly, oxygen isotopes revealed widespread use of meteoric water among a suite of sub‐Antarctic birds. Stable isotopes allowed us to identify females of most species as income breeders at the onset of breeding, with the exception of the females of the two crested penguin exhibiting a mix of income and capital resources use. Multidimensional isotopic analyses revealed that resource partitioning exists at multiple stages of the annual cycle in ways likely to be important under global change, exhibiting wide potential for ecosystem analysis.
Studies on Genetic Variability, Association and Path Coefficient Analysis in Black Gram (Vigna mungo L. Hepper)

Black gram (Vigna mungo L. Hepper, 2n=22) is an important self-pollinated and short duration legume crop belonging to the family Leguminosae and sub-family Papilionaceae. India is the center of origin of black gram (Mehra et al., 2016) and black gram is cultivated as a sole crop or succeeding crop using residual moisture of preceding crop, normally cultivated after harvest of rice. India produces 1.5 to 1.9 million tons of black gram annually from about 3.5 million hectares of area, and an average productivity of 500 kg per hectare (Sakila et al., 2018). Black gram seeds are rich in protein (25-26 %), carbohydrate (60%), fat (1.5%), minerals, amino acids and vitamins (Parveen et al., 2011). Dried black gram seeds contain high protein and lysine content which is deficient in cereals.
Steryl Ester Formation and Accumulation in Steroid-Degrading Bacteria

Oleaginous bacteria exhibit great potential for the production of high-value neutral lipids, such as triacylglycerols and wax esters. This study describes the formation of steryl esters (SEs) as neutral lipid storage compounds in sterol-degrading oleaginous bacteria, providing a basis for biotechnological production of SEs using bacterial systems with potential applications in the functional food, nutraceutical, and cosmetic industries. We found cholesteryl ester (CE) formation in several sterol-degrading Actino- and Proteobacteria under nitrogen-limiting conditions, suggesting an important role of this process in storing energy and carbon under adverse conditions. In addition, Mycobacterium tuberculosis grown on cholesterol accumulated CEs in the presence of an additional fatty acid substrate. ABSTRACT Steryl esters (SEs) are important storage compounds in many eukaryotes and are often prominent components of intracellular lipid droplets. Here, we demonstrate that selected Actino- and Proteobacteria growing on sterols are also able to synthesize SEs and to sequester them in cytoplasmic lipid droplets. We found cholesteryl ester (CE) formation in members of the actinobacterial genera Rhodococcus, Mycobacterium, and Amycolatopsis, as well as several members of the proteobacterial Cellvibrionales order. CEs maximally accumulated under nitrogen-limiting conditions, suggesting that steryl ester formation plays a crucial role for storing excess energy and carbon under adverse conditions. Rhodococcus jostii RHA1 was able to synthesize phytosteryl and cholesteryl esters, the latter reaching up to 7% of its cellular dry weight and 69% of its lipid droplets. Purified lipid droplets from RHA1 contained CEs, free cholesterol, and triacylglycerols. In addition, we found formation of CEs in Mycobacterium tuberculosis when it was grown with cholesterol plus an additional fatty acid substrate. This study provides a basis for the application of bacterial whole-cell systems in the biotechnological production of SEs for use in functional foods and cosmetics. IMPORTANCE Oleaginous bacteria exhibit great potential for the production of high-value neutral lipids, such as triacylglycerols and wax esters. This study describes the formation of steryl esters (SEs) as neutral lipid storage compounds in sterol-degrading oleaginous bacteria, providing a basis for biotechnological production of SEs using bacterial systems with potential applications in the functional food, nutraceutical, and cosmetic industries. We found cholesteryl ester (CE) formation in several sterol-degrading Actino- and Proteobacteria under nitrogen-limiting conditions, suggesting an important role of this process in storing energy and carbon under adverse conditions. In addition, Mycobacterium tuberculosis grown on cholesterol accumulated CEs in the presence of an additional fatty acid substrate.
Fungos fitopatogênicos associados a Passiflora foetida no Brasil e o seu potencial para uso em controle biológico

VII INTRODUÇÃO . 1 MATERIAIS E MÉTODOS . 5 LEVANTAMENTO DE FUNGOS ASSOCIADOS A PASSIFLORA FOETIDA . 5 PROCESSAMENTO GERAL DE AMOSTRAS . 5 EXAME MORFOLÓGICO . 6 TESTE DE PATOGENICIDADE 1 . 6 TESTE DE PATOGENICIDADE 2 . 7 TESTE DE PATOGENICIDADE 3 . 7 ANÁLISE MOLECULAR . 8 RESULTADOS . 9 LEVANTAMENTO DE FUNGOS ASSOCIADOS A PASSIFLORA FOETIDA . 9 TESTES DE PATOGENICIDADE 1 . 12 TAXONOMIA . 15 DISCUSSÃO . 19 REFERÊNCIAS . 28
Wildfire alters the structure and seasonal dynamics of nocturnal pollen‐transport networks

Wildfires drive global biodiversity patterns and affect plant–pollinator interactions, and are expected to become more frequent and severe under climate change. Post‐fire plant communities often have increased floral abundance and diversity, but the effects of wildfires on the ecological process of pollination are poorly understood. Nocturnal moths are globally important pollinators, but no previous study has examined the effects of wildfire on nocturnal pollination interactions. We investigated the effects of wildfire on nocturnal pollen‐transport networks. We analysed the abundance and species richness of moths and flowers, and the structure of these networks, at three burned and three unburned sites in Portugal for two years, starting eight months after a large fire. Nocturnal pollen‐transport networks had lower complexity and robustness following the fire than at nearby unburned sites. Overall, 70% of individual moths carried pollen, and moths were found to be transporting pollen from 83% of the flower species present. Burned sites had significantly more abundant flowers, but less abundant and species‐rich moths. Individual moths transported more pollen in summer at burned sites, but less in winter; however, total pollen transport by the moth assemblage at burned sites was just 20% of that at unburned sites. Interaction turnover between burned and unburned networks was high. Negative effects of fire upon moths will likely permeate to other taxa through loss of mutualisms. Therefore, if wildfires become more frequent under climate change, community resilience may be eroded. Understanding the responses of ecological networks to wildfire can inform management that promotes resilience and facilitates whole‐ecosystem conservation.
Boiling Acid Mimics Intracellular Giant Virus Genome Release

Since their discovery, giant viruses have expanded our understanding of the principles of virology. Due to their gargantuan size and complexity, little is known about the life cycles of these viruses. To answer outstanding questions regarding giant virus infection mechanisms, we set out to determine biomolecular conditions that promote giant virus genome release. We generated four metastable infection intermediates in Samba virus (lineage A Mimiviridae) as visualized by cryo-EM, cryo-ET, and SEM. Each of these four intermediates reflects a stage that occurs in vivo. We show that these genome release stages are conserved in other, diverse giant viruses. Finally, we identified proteins that are released from Samba and newly discovered Tupanvirus through differential mass spectrometry. Our work revealed the molecular forces that trigger infection are conserved amongst disparate giant viruses. This study is also the first to identify specific proteins released during the initial stages of giant virus infection.
Source of additive genetic variance of important traits

Fisher’s fundamental theorem of natural selection predicts no additive variance of fitness in a natural population. Consistently, observations in a variety of wild populations show virtually no narrow-sense heritability (h2) for traits closely related to fitness. However, counterexamples are also reported, calling for a deeper understanding on the evolution of additive variance. In this study we propose adaptive divergence followed by population mixture as a source of additive variance of fitness-related traits. We experimentally tested the proposal by examining a panel of ∼1,000 yeast segregants produced by a hybrid of two yeast strains subject to adaptive divergence. We measured over 400 yeast cell morphological traits and found a strong positive correlation between their h2 and their relatedness to fitness. This pattern, being a counterexample of the prediction of Fisher’s theorem, well supports our proposal. Because adaptive divergence followed by population mixture could happen constantly, particularly in some species including humans and domesticated animals or crops, the proposal provides a framework for reconciling the availability of abundant additive variances of important traits with Fisher’s fundamental theorem of natural selection.
Do pioneer species enhance early performance of native species in subtropical shrublands? An examination involving six native species in South China

This paper examines the following questions: (1) Do early pioneer species have a greater impact on the survival and growth of different successional native trees compared to the shrub Rhodomyrtus tomentosa? (2) Do canopy treatments affect soil nutrients and light availability? (3) What is the mechanism underlying the interaction between nurse species and target species? Degraded shrubland sites (Heshan, Guangdong, China), under moist subtropical conditions were studied. About 1-year-old seedlings of Pinus massoniana, Schima wallichii, Schefflera heptaphylla, Castanopsis hystrix, Cryptocarya chinensis and Castanea chinensis were transplanted under the canopy of R. tomentosa, Dicranopteris dichotoma and in open interspaces without vegetation. Survival and growth were recorded from the first growing season after planting. Leaf gas exchange, water potential, soil physicochemical characters and irradiation were then measured. Canonical redundancy analyses (RDA) were used to evaluate the relationships between environmental factors and seedling survival and growth conditions. Both R. tomentosa and D. dichotoma canopy treatment facilitated seedling survival and growth either directly or indirectly. Irradiance/radiation was considered the most important resource (factor) for seedling growth in subtropical regions, however, soil nutrients and species are yet to be examined simultaneously with irradiance/radiation under field conditions. We conclude that early successional species facilitates the survival and growth of late successional species in subtropical shrublands. However, further predictions of successional trajectories remain elusive and are influenced by stochastic processes, including arrival order, shade tolerance, physiological character of the colonizing species and their competitive interactions.
A molecular investigation of the dynamics of piscine orthoreovirus in a wild sockeye salmon community on the Central Coast of British Columbia

Field surveillance for RNA viruses often requires RNA isolation from multiple tissue types, each presenting different challenges. Here I compare three RNA isolation approaches for salmonid blood and pooled organ tissues across seven metrics of performance. I find that isolation methods have different strengths and weaknesses depending on the tissue. Trizol reagent performs best for adult salmonid blood, while an updated acidic phenol guanidinium chloroform method produces higher yields and purer RNA from mixed organ pools. Silica filter spin columns produce high quality RNA from juvenile sockeye blood, but Trizol produces higher yields. A trade-off is also found on the time-cost continuum. RTqPCR analysis with silica filter spin columns and Trizol-isolated RNA indicates impurities resulting from suboptimal extraction methods influence measured expression levels, thus, RNA purity and yield are important to standardize across tissue types and studies. Collectively these results indicate that there are tradeoffs in the different methodologies used for RNA extraction from field-collected tissues.
Complete mitochondrial genome of green shrimp, Chlorotocus crassicornis (Crustacea: Decapoda: Pandalidae) in Korean water

Abstract The complete mitochondrial genome of green shrimp, Chlorotocus crassicornis (Costa, 1871) was generated by the combination of next-generation sequencing platform and long PCR technique. The mitochondrial genome of C. crassicornis was 16,500 bp, in which 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and a putative control region was encoded. Based on the 13 protein-coding genes region, the phylogenetic tree was clearly demonstrated that C. crassicornis is closest to Pandalopsis japonica and Pandalus borealis with 77% identity. This mitogenome information will be helpful for the further studies of deep-sea fisheries resources management strategies in Korea including C. crassicornis species.