Miracle-dz/UniFAR-FTUs huggingface dataset:
FtsK in motion reveals its mechanism for double-stranded DNA translocation

Significance DNA motors are widespread molecular machines that hydrolyze ATP to generate movement. Among them, the bacterial protein FtsK is unusual in that it translocates on double-stranded DNA and is also the fastest known translocase. However, its translocation mechanism is poorly characterized, and there is currently no structural data of an active double-stranded DNA translocase bound to its substrate. We reveal FtsK’s mechanism to be related to hexameric helicases that move on single-stranded DNA, but uniquely adapted to the double-stranded substrate. Our work also highlights the concomitant conformational changes occurring all around the hexameric ring for each step of the reaction cycle. FtsK protein contains a fast DNA motor that is involved in bacterial chromosome dimer resolution. During cell division, FtsK translocates double-stranded DNA until both dif recombination sites are placed at mid cell for subsequent dimer resolution. Here, we solved the 3.6-Å resolution electron cryo-microscopy structure of the motor domain of FtsK while translocating on its DNA substrate. Each subunit of the homo-hexameric ring adopts a unique conformation and one of three nucleotide states. Two DNA-binding loops within four subunits form a pair of spiral staircases within the ring, interacting with the two DNA strands. This suggests that simultaneous conformational changes in all ATPase domains at each catalytic step generate movement through a mechanism related to filament treadmilling. While the ring is only rotating around the DNA slowly, it is instead the conformational states that rotate around the ring as the DNA substrate is pushed through.
The complete mitochondrial genome of Propsilocerus akamusi (Diptera, Chironomidae)

Abstract Propsilocerus akamusi is one of the most important genera of Chironomidae. However, the systemically classification and taxonomic studies have so far been limited. In this study, we report the complete mitochondrial genome sequence of P. akamusi. The mitogenome has 15,632 base pairs (77.58% A + T content) and made up of total of 37 genes (13 protein-coding, 22 transfer RNAs, and 2 ribosomal RNAs). This study will provide useful genetic information for future phylogenetic and taxonomic classification of Chironomidae.
The plastid genome of Pentadiplandra brazzeana Baillon (Pentadiplandraceae)

Abstract Pentadiplandra brazzeana is the only species of Pentadiplandraceae. This species is shrubs or tuberous liana with a natural distribution in tropical West Africa. This study firstly determined its complete plastome. The plastome is totally 156,625 bp in length, which contains a pair of 26,751-bp-long inverted repeat regions (IRs), a large single copy region of 85,318 bp, and a small single copy region of 17,805 bp. A total of 112 unique genes were identified in this plastome, of which 78 are protein-coding genes, 30 are tRNA genes, and 4 are rRNA genes. Phylogenetic analysis based on 82 genes fully resolved relationships among sampled families of Brassicales, which are consistent with previous studies.
Complete genome sequence of Oryctes rhinoceros Nudivirus isolated from Coconut Rhinoceros Beetle in the Solomon Islands

Oryctes Nudivirus (OrNV) has been an effective biocontrol agent against the insect pest Oryctes rhinoceros (Coleoptera: Scarabaeidae) for decades, but there is evidence that resistance could be evolving in some host populations. We detected OrNv infection in O. rhinoceros from the Solomon Islands and used Oxford Nanopore Technologies (ONT) long-read sequencing to determine the full length of the virus genomic sequence isolated from an individual belonging to a mitochondrial lineage (CRB-G) that was previously reported as resistant to OrNV. The complete circular genome of the virus consisted of 125,917 nucleotides, encoding 130 open reading frames (ORFs) for proteins in the range ~5 kDa (51aa) to ~140 kDa (1280aa). This Solomon Islands isolate has high (99.85%) nucleotide sequence identity to the previously sequenced isolate PV505 from Southern Luzon, Philippines, and has 138 amino acid modifications when compared with the originally described full genome sequence of the Ma07 strain from Malaysia.
Characterisation of the complete mitochondrial genome of the Jinchuan Yak (Bos grunniens)

Abstract Jinchuan yak was a newly discovered yak breed, not only possesses a large proportion of multi-ribs but also exhibits many good characteristics. However, there is limited information about its overall genetic structure. In this study, we assembled the mitochondrial genome for Jinchuan yak (Bos grunniens), the results show that the mitochondrial genome is 16,324bp long with an A + T-biased base composition (61.0% A + T) and harbours the typical set of 37 mitochondrial genes and 1 non-coding control region. The PCGs start with the typical ATA or ATG codons and are terminated with TAA, TAG or the incomplete stop codon T. Phylogenetic analysis suggests that Jinchuan yak is most closely related to Datong yak and Sunan yak.
Coriandrum sativum l. (apiaceae) and elettaria cardamomum (l.) maton (zingiberaceae) for antioxidant and antimicrobial protection

Spice plants are known for their compounds that are useful as foods flavoring, food preservatives, and medicines. This due to the presence of secondary metabolite compounds in plants such as terpenoids, flavonoids, phenols, and saponins. These compounds are known to be potential to inhibit microorganism’s growth causing decay in food and oxidation. The use of these sources for applications in the food sector is relatively safer and environmentally friendly than the use of antibiotics in general. This study was conducted to determine the antimicrobial and antioxidant activities from Coriandrum sativum L. (coriander) and Elettaria cardamomum (L.) Maton (cardamom). The essential oil extract from these plants was tested for phytochemical content qualitatively for terpenoid screening and by using Gas Chromatography-Mass Spectroscopy (GC/MS). Furthermore, the antioxidant activity from the oil extracts was tested by DPPH method. Meanwhile, their ability to inhibit gram-positive bacteria Staphylococcus aureus and Gram-negative bacteria Escherichia coli were tested by paper disc method. The phytochemical characterization showed a positive result of terpenoid and GC/MS result showed dominant of monoterpenes compounds, such as α-pinene and ß-pinene. The DPPH results revealed that the essential oils have different antioxidant and antimicrobial potential, whereas Coriander tends to have a higher antimicrobial activity, while Cardamom superior in antioxidant activity. These results will become the basis for the development of potential essential oil with the best antimicrobial activity for food active packaging materials.
The complete plastome genome and its inference on the phylogenetic position of Bletilla formosana (Orchidaceae)

Abstract Bletilla formosana is a traditional Chinese medicinal herb and recently threatened by overexploitation owing to the increasing demand. In present study, we sequenced and assembled the complete chloroplast (cp) genomes of this species. The plastome genome is a typical quadripartite circle molecule with the total lenth of 158,968 bp and overall GC content of 37.3%. We predicted 104 genes in the cp genome, including 80 protein coding gens, 20 tRNA and 4 rRNA. Phylogenetic analysis shows that B. formosana is sister to B. striata.
Gonad transcriptome of golden mussel Limnoperna fortunei reveals potential sex differentiation genes

The golden mussel Limnoperna fortunei is an Asian invasive bivalve that threats aquatic biodiversity and causes economic damage, especially to the hydroelectric sector in South America. Traditional control methods have been inefficient to stop the advance of the invasive mollusk, which currently is found in 40% of Brazilian hydroelectric power plants. In order to develop an effective strategy to stop golden mussel infestations, we need to better understand its reproductive and sexual mechanisms. In this study, we sequenced total RNA samples from male and female golden mussel gonads in the spawning stage. A transcriptome was assembled resulting in 200,185 contigs with 2,250 bp N50 and 99.3% completeness. Differential expression analysis identified 3,906 differentially expressed transcripts between the sexes. We searched for genes related to the sex determination/differentiation pathways in bivalves and model species and investigated their expression profiles in the transcriptome of the golden mussel gonads. From a total of 187 genes identified in the literature, 131 potential homologs were found in the L. fortunei transcriptome, of which 15 were overexpressed in males and four in females. To this group belong gene families relevant to sexual development in various organisms, from mammals to invertebrates, such as Dmrt (doublesex and mab3-related-transcription factor), Sox (SRY-related HMG-box) and Fox (forkhead box).
Inferring competitive outcomes, ranks and intransitivity from empirical data: A comparison of different methods

The inference of pairwise competitive outcomes (PCO) and multispecies competitive ranks and intransitivity from empirical data is essential to evaluate how competition shapes plant communities. Three categories of methods, differing in theoretical background and data requirements, have been used: (a) theoretically sound coexistence theory‐based methods, (b) index‐based methods, and (c) ‘process‐from‐pattern’ methods. However, how they are related is largely unknown. In this study, we explored the relations between the three categories by explicitly comparing three representatives of them: (a) relative fitness difference (RFD), (b) relative yield (RY), and (c) a reverse‐engineering approach (RE). Specifically, we first conducted theoretical analyses with Lotka–Volterra competition models to explore their theoretical linkages. Second, we used data from a long‐term field experiment and a short‐term greenhouse experiment with eight herbaceous perennials to validate the theoretical findings. The theoretical analyses showed that RY or RE applied with equilibrium data indicated equivalent, or very similar, PCO respectively to RFD, but these relations became weaker or absent with data further from equilibrium. In line with this, both RY and RE converged with RFD in indicating PCO over time in the field experiment as the communities became closer to equilibrium. Moreover, the greenhouse PCO (far from equilibrium) were only similar to the field PCO of earlier rather than later years. Intransitivity was more challenging to infer because it could be reshuffled by even a small competitive shift among similar competitors. For example, the field intransitivity inferred by three methods differed greatly: no intransitivity was detected with RFD; intransitivity detected with RY and RE was poorly correlated, changed substantially over time (even after equilibrium) and failed to explain coexistence. Our findings greatly help the comparison and generalization of studies using different methods. For future studies, if equilibrium data are available, one can infer PCO and multispecies competitive ranks with RY or RE. If not, one should apply RFD with density gradient or time‐series data. Equilibria could be evaluated with T tests or standard deviations. To reliably infer intransitivity, one needs high quality data for a given method to first accurately infer PCO, especially among similar competitors.
GNMFLMI: Graph Regularized Nonnegative Matrix Factorization for Predicting LncRNA-MiRNA Interactions

Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have been involved in various biological processes. Emerging evidence suggests that the interactions between lncRNAs and miRNAs play an important role in regulating of genes and the development of many diseases. Due to the limited scale of known lncRNA-miRNA interactions, and expensive time and labor costs for identifying them by biological experiments, more accurate and efficient lncRNA-miRNA interactions computational prediction approach urgently need to be developed. In this work, we proposed a novel computational method, GNMFLMI, to predict lncRNA-miRNA interactions using graph regularized nonnegative matrix factorization. More specifically, the similarities both lncRNA and miRNA are calculated based on known interaction information and their sequence information. Then, the affinity graphs for lncRNAs and miRNAs are constructed using the p-nearest neighbors, respectively. Finally, a graph regularized nonnegative matrix factorization model is developed to accurately identify potential interactions between lncRNAs and miRNAs. To evaluate the performance of GNMFLMI, five-fold cross validation experiments are carried out. GNMFLMI achieves the AUC value of 0.9769 which outperforms the compared methods NMF and CNMF. In the case studies for lncRNA nonhsat159254.1 and miRNA hsa-mir-544a, 20 and 16 of the top-20 associations predicted by GNMFLMI are confirmed, respectively. Rigorous experimental results demonstrate that GNMFLMI can effectively predict novel lncRNA-miRNA interactions, which can provide guidance for relevant biomedical research.
Detection of Somaclonal Variation in Aquatic Plant Pearl Grass (Hemianthus micranthemoides)

Hemianthus micranthemoides is an ornamental plan used for foreground plant in aquarium decorations. In Malaysia, the plant available on market is regenerated through tissue culture techniques which expose the risk for somaclonal variation. The objectives of this study are to identify suitable Random Amplified Polymorphic DNA (RAPD) markers for determining somaclonal variation rate in micropropagated plantlets of H. micranthemoides and to observe the effects of somaclonal variation on the plantlet growth (area of spreadability, shoot and root length). Out of 20 RAPD primers screened by polymerase chain reaction (PCR) using mother plant, one was selected as a suitable marker to detect somaclonal variation of H. micranthemoides which was P15. Somaclonal variation rate of the H. micranthemoides was determined by analyzing the RAPD-PCR bands. The results showed somaclonal variation was observed at the fifth subculture (S5) with the percentage of polymorphic bands of 50 % when compared to mother plant. Repeated subclutures has affected the growth of the regenerates negatively. It was shown that as the number of subculture increased, the growth of plantlet decreased in terms of decreasing shoot and root length as well as area of spreadability. This findings serves as a guide especially for tissue culturist to minimize subculture numbers when micropropagating H. micranthemoides.
RNA recognition by the E2 subunit of the chloroplast pyruvate dehydrogenase complex from Chlamydomonas

The dihydrolipoamide acetyltransferase subunit (DLA2) of the chloroplast puruvate dehydrogenase complex (cpPDC) from the green alga Chlamydomonas reinhardtii has previously been shown to possess a moonlighting activity in chloroplast gene expression. Exclusively under mixotrophic growth conditions, DLA2 forms part of an RNP particle with the psbA mRNA that encodes the D1 protein of the photosystem II reaction center. Here, we report on the further characterization of DLA2’s RNA-binding activity. Size-exclusion chromatography and Western analyses revealed that DLA2 is the only cpPDC subunit that shuttles between the metabolic cpPDC and the RNP complex. Microscale thermophoresis-based determination of RNA-binding affinities demonstrated that two DLA2 regions are crucial for RNA recognition, the peripheral E3-binding domain (E3BD) and the C-terminus of the catalytic domain. Specificity for the psbA RNA probe is conferred by the E3BD in vitro, as verified by competitive binding assays in the presence of an excess of the E3 (DLD2) of cpPDC. The data support a model in which an environmental trigger induces release of DLA2 from the cpPDC and its subsequent association with the psbA mRNA.
Muscle synergies are associated with intermuscular coherence in an isometric upper limb task

To elucidate the underlying physiological mechanism of muscle synergies, we investigated the functional corticomuscular and intermuscular binding during an isometric upper limb task in 14 healthy participants. Cortical activity was recorded using 32-channel encephalography (EEG) and muscle activity using 16-channel electromyography (EMG). Using non-negative matrix factorization (NMF), we calculated muscle synergies from two different tasks. A preliminary multidirectional task was used to identify synergy preferred directions. A subsequent coherence task, consisting of generating forces isometrically in the synergy PDs, was used to assess the functional connectivity properties of synergies. Functional connectivity was estimated using corticomuscular coherence (CMC) and intermuscular coherence (IMC). Overall, we were able to extract four different synergies from the multidirectional task. A significant alpha band IMC was present consistently in all extracted synergies. Moreover, alpha band IMC was higher between muscles with higher weights within a synergy. In contrast, no significant CMC was found between the motor cortex area and synergy muscles. In addition, there is a relationship between a synergy muscle weight and the level of IMC. Our findings suggest the existence of a consistent shared input between muscles of each synergy. Finally, the existence of a shared input onto synergistic muscles within a synergy supports the idea of neurally-derived muscle synergies that build human movement.
Isolation and identification of rhizospheric fungus under Mahoni (Swietenia mahagoni) stands and its ability to produce IAA (Indole Acetid Acid) hormones

Rhizosphere is a part of the soil that is in the roots of plants in which there are many soil microorganisms. One of the microorganisms found in the rhizosphere is fungi. Rhizosphere fungus plays an important role in increasing plant growth by various mechanisms that are carried out such as increasing nutrient absorption, as a bilogical control of pathogenic attacks and can produce growth hormones for plants. This study aims to identify and get the information of the diversity of rhizosphere fungi from mahogany stands in two provenances, and get information on IAA level production. The research methods include isolation of fungi and identification of rhizosphere fungi, as well as test of IAA production capability qualitatively and quantitatively. The results showed 17 rhizosphere fungus isolates were found under the mahogany stand in Takalar District those were included in the genus Rhizopus, Fusarium, Aspergillus, Penicillium and Gliocladium, whereas 11 Mahogany stands in the Maros Regency were included in the genus Trichoderma, Gliocladium, Rhizopus and Aspergillus. The whole genus is capable of producing IAA hormone, but the genus capable of producing the highest IAA is the Trichoderma genus.
Direct selection for phenotypic traits in carrot genotypes

ABSTRACT Selection of more productive carrot genotypes is fundamental for crop breeding programs aiming to increase productivity and reduce cost production. Thus, the aim of this work was to evaluate gains from direct selection and to measure its effects on other agronomic traits of interest in carrots. Thirty six carrot genotypes were evaluated in two experiments: the first, sown in the second half of November 2016 and the second one in the first week of March 2017. The experimental plots covered a useful area of 1.5 m2, in transversal rows and 0.10-m double spacing between single rows x 0.20-m between double rows in a randomized block design with 3 replicates. At 90 days, the incidence of leaf blight was evaluated using a note scale and 100 days after sowing, roots were harvested measuring the number and mass of total, commercial and non-commercial roots of each plot. The direct selection of commercial root mass allowed to estimate indirect and expressive gains for most evaluated traits, allowing to select seven genotypes (populations 758, 751, 737, 736, 735, 744 and 742) which can be released as cultivar or for the formation of a broader genetic-based population.
Induced phenological avoidance: A neglected defense mechanism against seed predation in plants

Flowering phenology is an important life‐history trait affecting plant reproductive performance and is influenced by various abiotic and biotic factors. Pre‐dispersal seed predation and pollination are expected to impose counteracting selection pressure on flowering phenology, with pre‐dispersal seed predation expected to favour off‐peak flowering and pollination to favour synchronous flowering. Here we studied the effect of pre‐dispersal seed predation by the beetle Byturus ochraceus, a specialist seed herbivore, on the flowering phenology of Geum urbanum. This forest understorey plant species is self‐pollinating, so that the influence of seed predation can be studied independent from pollination. We measured in detail the timing and predation rate of individual flowers during two consecutive years in more than 60 individuals. We tested the hypotheses that pre‐dispersal seed predation exerts selection for within‐season compensatory flowering as well as for induced phenological avoidance in the following season. We found no indication for compensatory flowering within a growing season, but plants that experienced predation shifted their flowers to the end of the flowering season the subsequent year. This induced phenological avoidance points to a plastic response to pre‐dispersal seed predation that may be adaptive. Importantly, the delay in flower production came at a cost, since flowers later in the season had a reduced seed output, presumably because of increasing light limitation following forest canopy closure. Synthesis. Herbivory by specialist enemies can cause serious fitness decline in hosts. We here show that induced shifts in phenology can form an important defense strategy against pre‐dispersal seed predation. The induced mismatches between herbivore and host phenology are anticipated to be adaptive when herbivory is predictable across successive flowering periods.
Loss of m1acp3Ψ ribosomal RNA modification is a major feature of cancer

The ribosome is an RNA-protein complex essential for translation in all domains of life. The structural and catalytic core of the ribosome is its ribosomal RNA (rRNA). While mutations in ribosomal protein (RP) gene are known drivers of oncogenesis, oncogenic rRNA variants have remained elusive. We discovered a cancer-specific single nucleotide variation at 18S.1248U in the 18S rRNA of up to 45.9% colorectal carcinoma (CRC) patients and across >22 cancer types. This is the site of a unique hyper-modified base, 1-methyl-3-α-amino-α-carboxyl-propyl pseudouridine (m1acp3Ψ), a modification that is >1 billion years conserved at the ribosome’s peptidyl decoding-site. A sub-set of CRC tumors we term ‘hypo-m1acp3Ψ’, show sub-stoichiometric m1acp3Ψ-modification unlike normal control tissues. Our m1acp3Ψ knockout model and hypo-m1acp3Ψ patient tumors share a translational signature, characterized by highly abundant ribosomal proteins. Thus, m1acp3Ψ-deficient rRNA forms an uncharacterized class of ‘onco-ribosome’ which may serve as an innovative chemotherapeutic target for treating cancer patients.