Miracle-dz/UniFAR-FTUs huggingface dataset:
A complex virome that includes two distinct emaraviruses is associated to virus-like symptoms in Camellia japonica

Camellia japonica plants manifesting a complex and variable spectrum of viral symptoms like chlorotic ringspots, necrotic rings, yellowing with necrotic rings, yellow mottle, leaves and petals deformations, flower color-breaking were studied since 1940 essentially through electron microscopic analyses; however, a strong correlation between symptoms and one or more well characterized viruses was never verified. In this work samples collected from symptomatic plants were analyzed by NGS technique and a complex virome composed by viruses members of the Betaflexiviridae and Fimoviridae families was identified. In particular, the genomic fragments typical of the emaravirus group were organized in the genomes of two new emaraviruses species, tentatively named Camellia japonica associated emaravirus 1 and 2. They are the first emaraviruses described in camellia plants and were always found solely in symptomatic plants. On the contrary, in both symptomatic and asymptomatic plants, we detected five betaflexiviruses isolates that, based on aa identitiy comparisons, can be classified in two new putative species called Camellia japonica associated betaflexivirus 1 and Camellia japonica associated betaflexivirus 2. Together with other recently identified betaflexiviruses associated to Camellia japonica disease, the betaflexiviruses characterized in this study show an unusual hyper-conservation of the coat protein at aminoacidic level.
Microtubule-dependent protein trafficking promotes apical constriction during tissue invagination

The formation of an epithelial tube is a fundamental process for organogenesis. Coordination between actomyosin and microtubule (MT) networks is critical for tube formation, but its underlying mechanisms are still unclear. During Drosophila embryonic salivary gland (SG) invagination, Folded gastrulation (Fog)-dependent Rho-associated kinase (Rok) promotes contractile apical myosin formation to drive apical constriction. MTs are also crucial for the effective change in apical area and are required for forming and maintaining apicomedial myosin. Here, we show that MT-dependent intracellular trafficking has a role in regulating apical constriction during SG invagination. Key components involved in protein trafficking, including dynein heavy chain, Rab11 and Nuclear fallout (Nuf), are apically enriched near the invagination pit in a MT-dependent manner during SG invagination. This enrichment is crucial for apical constriction as disruption of the MT networks or intracellular trafficking impairs formation of apicomedial myosin. We show that apical transport of several proteins along MTs, either in a Rab11-dependent or independent manner, mediates clustered apical constriction during SG invagination. Key proteins that are transported include the Fog ligand, the apical determinant protein Crumbs (Crb), the key adherens junction protein E-Cadherin (E-Cad) and the scaffolding protein Bazooka/Par3, and knockdown of these genes in the SG results in apical constriction defects. These results define a role of MT-dependent intracellular trafficking in regulating actomyosin networks and cell junctions to coordinate cell behaviors during tubular organ formation.
Motif Based Community Discovery

Complex networks are all around us and they are present in every system we interact with in the real world. By understanding the network we gain knowledge about the real system. One of the most important and difficult tasks in complex networks is the detection of community structures. A community is a set of nodes that are related to each other by some attribute, function or characteristic. One example of a community is, in a social network of football fans, all the fans of a specific team. The classic definition for community detection is to find a group of nodes with dense connections between each other and few connections to nodes that do not belong to that community. The most popular metric for community detection is modularity, a quality function that favors this definition. Community detection methods rely on the optimization of this metric. This metric is however not bullet proof: it has a known resolution limit and it relies on the classic definition of community which is limiting. In 2008, the novel concept of motif modularity was introduced, as a generalization of the modularity metric. It aims to replace the edge in the standard modularity with a motif a general subgraph. In the original work, the authors tested their ideas with some specific motifs. In this thesis our goal is precisely to offer contributions towards the discovery of motif based communities. We extended the original model by adding the possibility of adding new restrictions, namely specifying classes of communities for each node. We also implemented a framework that will accept any general motif and tries to find a node partition that maximizes the new metric in both directed or undirected unweighted networks. Finally, we tested the model in real networks, showcasing its potential and paving the way for new discoveries.
Local climatic changes affect biodiversity responses to land use: A review

Climate and land‐use change, the greatest pressures on biodiversity, can directly influence each other. One key case is the impact land‐use change has on local climatic conditions: human‐altered areas are often warmer and drier than natural habitats. This can have multiple impacts on biodiversity and is a rapidly developing field of research. Here, we summarize the current state of understanding on the impact that local climatic changes have on biodiversity responses to land‐use change, in particular looking at whether human‐altered land uses favour species with certain climatic niches.
Preputial gland adenoma in a wild nutria (Myocastor coypus): a case report

Tumor incidence in wild mammals is reportedly very low. Wild nutria, a large rodent, is known to carry many infectious diseases, but rarely exhibits neoplastic diseases. We necropsied a male wild nutria and found a large nodular mass in the left inguinal region, adjacent to the penis. Histopathologically, the mass was diagnosed as preputial gland adenoma. Spontaneous preputial gland adenomas are extremely rare in all animals. Moreover, reports of tumors in nutrias have been limited to adenocarcinomas of the lungs and uterus, as well as subcutaneous fibromas. Here, we describe preputial gland adenoma in a wild nutria.
Prophase removal of chromosome-associated RNAs facilitates anaphase chromosome segregation

During mitosis, the genome is transformed from a decondensed, transcriptionally active state to a highly condensed, transcriptionally inactive state. Mitotic chromosome reorganization is marked by the general attenuation of transcription on chromosome arms, yet how the cell regulates nuclear and chromatin-associated RNAs after chromosome condensation and nuclear envelope breakdown is unknown. SAF-A/hnRNPU is an abundant nuclear protein with RNA-to-DNA tethering activity, coordinated by two spatially distinct nucleic acid binding domains. Here we show that RNA is evicted from prophase chromosomes through Aurora-B-dependent phosphorylation of the SAF-A DNA-binding domain; failure to execute this pathway leads to accumulation of SAF-A:RNA complexes on mitotic chromosomes and elevated rates of anaphase segregation defects. This work reveals a role for Aurora-B in removing chromatin-associated RNAs during prophase, and demonstrates that Aurora-B dependent relocalization of SAF-A during cell division contributes to the fidelity of chromosome segregation.
Effect of propyl isothiocyanate on antioxidant enzymes of garden cress seedlings under in vitro condition

Keyword: vitro culture, propyl isothiocyanate, oxidative stress In this study effects of different levels of propyl isothiocyanate on some physiological parameters and antioxidant enzyme activities such as ascorbate peroxidase, catalase and guaiacol peroxidase in seedlings of Lepidiun sativum L. under in vitro was investigated. The seeds of Lepidium sativum (Garden Cress) were sterilized and cultured in MS medium. After 20 days, seedlings were treated with concentrations of 0.01, 0.1 and 1 mM propyl isothiocyanate (various levels of stress) under sterile condition. After 3 days, result showed chlorophyll a, chlorophyll b, total chlorophyll, carotenoids and soluble proteins were significantly decreased, while reduced carbohydrates, proline and antioxidant enzymes activities were increased in seedlings which have been under oxidative stress. One of the major tissue damage following exposure to stress in plants is caused by the oxidative stress. Thus propyl isothiocyanate appears to cause oxidative stress and activation of the plant's defenses parameters.
Quantifying the Individual Impact of Artificial Barriers in Freshwaters: A Standardized and Absolute Index of Genetic Connectivity

Fragmentation by artificial barriers is an important threat to freshwater biodiversity. Mitigating the negative aftermaths of fragmentation is of crude importance, and it is now essential for environmental managers to benefit from a precise estimate of the individual impact of weirs and dams on river connectivity. Although the indirect monitoring of connectivity using molecular data constitutes a promising approach, it is still plagued with several constraints preventing a standardized and individual quantification of barrier effects. Indeed, observed levels of genetic differentiation depend on both the age of the obstacle and the effective size of the populations it separates, making difficult comparisons among obstacles. Here, we developed a standardized index of genetic connectivity (CINDEX), allowing an absolute and independent assessment of the individual effects of obstacles on connectivity. The CINDEX is the standardized ratio (expressed as a percentage) between the observed genetic differentiation between pairs of populations located on either side of an obstacle and the genetic differentiation expected if this obstacle completely prevented gene flow. The expected genetic differentiation is calculated from simulations taking into account both the age of the barrier and the effective size of the targeted populations. Using both simulated and published empirical datasets, we explored and discussed the validity and the limits of the CINDEX. We demonstrated that it allows quantifying genetic effects of fragmentation only a few generations after barrier creation and provides valid comparisons among populations (or species) of different effective populations sizes and obstacles of different ages. The computation of the CINDEX requires a minimum amount of fieldwork and genotypic data, and solves some of the difficulties inherent to the study of artificial fragmentation in rivers and potentially in other ecosystems. This makes the CINDEX a promising and objective tool for managers aiming at restoring connectivity and at evaluating the efficiency of restoration programs.
Effect of pre-exercise single dose arginine ingestion on plasma amino acid profile during exhaustive exercise in elite male wrestlers (Elit erkek güreşçilerde egzersiz öncesi tek doz arjinin aliminin tüketici egzersiz sirasinda plazma amino asit profiline etkisi)

Aim: The aim of this study was to investigate the possible effects of pre-exercise single dose arginine ingestion on plasma amino acid profile during incremental exercise to exhaustion. Methods: Ten volunteer elite male wrestlers (age: 24.7±3.8) participated in this study. Testretest protocol was done on the same subjects. Exercise protocol started at 90 watts on bicycle ergometry and the load was increased 30 watts in every 3 min till the exhaustion. Arginine (1.5gr/10 kg body weight) or placebo were given to the subjects after 12 h fasting (during the night) and venous blood samples were collected 1 h after the supplementation (right before exercise protocol) and right after the exercise protocol for both test and retest. Plasma amino acid profiles were determined by HPLC. Results: Pre- and post-exercise arginine, ornithine and citrulline concentrations were significantly higher in arginine vs. placebo trial (p<0.05). Glutamine, tyrosine, methionine, phenylalanine, isoleucine and leucine concentrations increased following exercise only in arginine trial (p<0.05). Citrulline and tryptophan levels decreased while alanine levels increased after exercise in both trials (p<0.05). There was an increase following exhaustive exercise in total branched chain amino acid concentrations in arginine trial (p<0.05) whereas there is no significant change in placebo trial. Total amino acid concentrations were increased with exercise in both trials but post-exercise concentrations was higher in arginine trial compared to placebo trial (p<0.05). Conclusion: Results suggest that pre-exercise arginine supplementation can promote an amino acid profile that could be favorable for performance; however, further investigation is
TSLP Promotes Interleukin-3-independent Basophil Haematopoiesis and Type 2 Inflammation

MC Siracusa, SA Saenz, DA Hill. Nature. 2011;477(7363):229–233 Allergic diseases involve epithelial surfaces, and the epithelial cytokine thymic stromal lymphopoietin (TSLP) has been described as the “master switch” for allergic inflammation. The purpose of this study was to determine how TSLP contributes to allergic disease pathogenesis. Most studies were performed in mice. Human studies were performed with the use of basophils from patients with eosinophilic esophagitis or from healthy controls. TSLP-treated mice were evaluated for changes in circulating immune cells and cytokine secretion. The effect of tissue-specific TSLP production …
Keragaman Genetik Penduduk Papua: Polimorfime pada Daerah 3’UTR Gen Reseptor Lipoprotein Densitas Rendah (LDLR)

Low-density lipoprotein receptors (LDL-R) play a role in transporting plasma cholesterol into cells. This protein is encoded by the LDLR gene that contains the 3'untranslated region (3'UTR). 3'UTR is known as an important regulatory element to the precision of expression in many genes. The genetic variation of the 3'UTR region in some tribal populations indicates that this area has a high diversity. So it can be used to study the evolution of genetic diversity. A total of 9 individuals from Papua from different districts were analyzed for their 3'UTR area. The results of this study indicate that the variation of nucleotides obtained ranges from 0 to 3 nucleotides with an average of 0.0611 nucleotides and nucleotide diversity (π) of 0.00105 nucleotides. In addition, two SNPs were identified in positions *315 and *540 consisting of two general haplotypes (CG and GG) and one special haplotype (CA) with a haplotype diversity of 0.556 ± 0.165. The results of this study can be concluded that the 3'UTR area has a low genetic diversity with a small number of samples.
The genome of the butternut canker pathogen, Ophiognomonia clavigignenti-juglandacearum shows an elevated number of genes associated with secondary metabolism and protection from host resistance responses in comparison with other members of the Diaporthales

Ophiognomonia clavigignentijuglandacearum (Oc-j) is a plant pathogenic fungus that causes canker and branch dieback diseases in the hardwood tree butternut, Juglans cinerea. Oc-j is a member of the order of Diaporthales, which includes many other plant pathogenic species, several of which also infect hardwood tree species. In this study, we sequenced the genome of Oc-j and achieved a high-quality assembly and delineated the phylogeny of Oc-j within the Diaporthales order using a genome-wide multi-gene approach. We also further examined multiple gene families that might be involved in plant pathogenicity and degradation of complex biomass, which are relevant to a pathogenic life-style in a tree host. We found that the Oc-j genome contains a greater number of genes in these gene families compared to other species in Diaporthales. These gene families include secreted CAZymes, kinases, cytochrome P450, efflux pumps, and secondary metabolism gene clusters. The large numbers of these genes provide Oc-j with an arsenal to cope with the specific ecological niche as a pathogen of the butternut tree.
Mitochondrial heteroplasmy in an avian hybrid form (Passer italiae: Aves, Passeriformes)

Abstract Mitochondrial heteroplasmy is the result from biparental transmission of mitochondrial DNA (mtDNA) to the offspring. In such rare cases, maternal and paternal mtDNA is present in the same individual. Though recent studies suggested that mtDNA heteroplasmy might be more common than previously anticipated, that phenomenon is still poorly documented and was mostly detected in case studies on hybrid populations. The Italian sparrow, Passer italiae is a homoploid hybrid form that occurs all across the Italian Peninsula mostly under strict absence of either of its parent species, the house sparrow (P. domesticus) and the Spanish sparrow (P. hispaniolensis). In this study, we document a new case of mitochondrial heteroplasmy from two island populations of P. italiae (Ustica and Lipari). Our analysis was based on the mitochondrial NADH dehydrogenase subunit 2 (ND2) that allows for a clear distinction between mitochondrial lineages of the two parental species. We amplified and sequenced the mitochondrial ND2 gene with specifically designed primer combinations for each of the two parental species. In two of our study populations, a single individual carried two different ND2 haplotypes from each of the two parental lineages. These findings contribute to current knowledge on the still poorly documented phenomenon of paternal leakage in vertebrates.
Enabling Mg metal anodes rechargeable in conventional electrolytes by fast ionic transport interphase

Abstract Rechargeable magnesium batteries have received extensive attention as the Mg anodes possess twice the volumetric capacity of their lithium counterparts and are dendrite-free. However, Mg anodes suffer from surface passivation film in most glyme-based conventional electrolytes, leading to irreversible plating/stripping behavior of Mg. Here we report a facile and safe method to obtain a modified Mg metal anode with a Sn-based artificial layer via ion-exchange and alloying reactions. In the artificial coating layer, Mg2Sn alloy composites offer a channel for fast ion transport and insulating MgCl2/SnCl2 bestows the necessary potential gradient to prevent deposition on the surface. Significant improved ion conductivity of the solid electrolyte interfaces and decreased overpotential of Mg symmetric cells in Mg(TFSI)2/DME electrolyte are obtained. The coated Mg anodes can sustain a stable plating/stripping process over 4000 cycles at a high current density of 6 mA cm−2. This finding provides an avenue to facilitate fast ion diffusion kinetics of Mg metal anodes in conventional electrolytes.
The complete mitochondrial genome of the Minla cyanouroptera (Passeriformes: Timaliidae)

Abstract The blue-winged minla (Minla cyanouroptera) belongs to Timaliidae, which is a near threatened species in the IUCN Red List. In this study, the complete mitochondrial genome of Minla cyanouroptera was sequenced and characterized. The genome is 17,862 bases in length (GenBank accession no. MK940810). The overall base composition of M. cyanouroptera mitogenome is 30.9% for A, 31.5% for C, 13.8% for G, and 23.8% for T. The nucleotide sequence data of 13 protein-coding genes of 12 Passeriformes species were used for phylogenetic analyses. Trees constructed by using Bayesian and maximum-likelihood methods demonstrated that Minla ignotincta was closest to M. cyanouroptera.
Qualitative and quantitative analyses of tree forking habit with single-image photogrammetry: a case study of old-growth temperate oaks in a mixed, deciduous forest remnant near Krakow, Poland

Tree forking is both ecologically and economically relevant, but remains much understudied. Here, thirty old-growth temperate oaks (Quercus robur or Q. petraea) forking habit was analysed with the single-image photogrammetry (SIP); in a north-exposed mixed, deciduous forest remnant (near Krakow; Poland). A new classification of mature oak architectures was proposed, based on the original Hallé-Oldeman model, with modified locations of the main branches and presence or absence of bifurcation in the main stem. Two of the models were most clearly represented by the studied oaks. It was found that the trees tended to either keep branches at varying heights, with no forks; or to iterate forking, with no major (non-fork) branches below the first fork. The quantitative analysis confirmed the applicability of the branch to parent stem diameter ratio to define a fork. Branching ratio was positively correlated with both tree diameter and height of a branch above the ground, which is consistent with a previous study, based on much younger trees. It is concluded, that most probably the tree-level factors and phenomena, such as water supplies and posture control, played the key role in the studied oaks forking habit. The SIP method enabled valuable insights into the large oaks’ forking, both at the tree and branch levels; and may be further employed to study mature trees’ bifurcation patterns. Based on this study, some possible improvements to the methodology were discussed.
Combining physiology and genetics to dissect source-sink relationships in wheat

The growth and yield of wheat is subject to constant attempts at improvement. Recent technology has allowed us to speed this process up by utilising genetic markers. Previous work has had to concentrate on small groups of traits at any one time due to the limited allelic representation in bi-parental populations. The aim of this project was to identify and study the genetic underpinnings of source and sink related traits in field conditions. The crop was measured throughout the full season to observe how these traits interact with each other continuously. To this end, the National Institute of Agricultural Botany (NIAB) eight-parent population was studied in two field seasons. The allelic diversity and high level of recombination present in this population gives us an unprecedented opportunity to identify novel Quantitative Trait Loci (QTL) that control varying aspects that impact the final yield. All traits measured exhibited a much greater range of diversity in the progeny compared to that of the founder lines. Using that diversity, we were able to identify QTL on every chromosome, with multiple major effect, stable, QTL occurring on 1B, 4B, 4D, 5A and 6A. Some of these have been described in previous literature, while others such as 1B appear to be novel. Further to this, there were two noteworthy QTL for yield that were not co-locating with any of the other measured traits. One of these QTL was stably located on 7B and explains on average 1.6% of the total phenotypic variation, while the other is located on 5B, explaining 6.02% of the total variation in a single environment.
Ecological quality and conservation status of inland waters

ABSTRACT Assessment of freshwater ecosystems is crucial for measuring their ecological status and providing primary information for their conservation. This editorial introduces a special section of Inland Waters regarding the study of ecological monitoring and biodiversity conservation of inland waters. Papers in this special section of Inland Waters are briefly described and a synthesis of the topic is provided to offer a summary of contents and an overview of the subject matter.