Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA barcoding of freshwater fishes from the transboundary river of Indo-Bhutan: multiple clades and cryptic diversity

Abstract The species diversity of freshwater fishes from the transboundary river, Jaldhaka is still unknown to the scientific communities. We generated 40 DNA barcode sequences of 16 morphologically identified freshwater fishes and compared genetically with the database sequences. Ten species (Acanthocobitis botia, Barilius bendelisis, Crossocheilus latius, Channa punctata, Channa quinquefasciata, Garra gotyla, Garra kempi, Opsarius barna, Psilorhynchus balitora, and Pseudecheneis sulcata) showed unique haplotypes in the studied riverine system. Further, the estimated genetic divergences, BA tree topology, and ABGD species delimitation methods revealed the presence of cryptic diversity in Badis badis, Garra annandalei, G. gotyla, G. kempi, P. balitora, Rasbora daniconius, and Pethia ticto. The study suggested more exhaustive sampling and generation of more molecular data to strengthen the fact. The aimed integrated approach will be helpful to detect the extant species diversity, helps to reevaluate the checklist and promote sustainable conservation management to protect this unparalleled ecosystem.
Cytospora chrysosperma causing branch dieback and canker of black walnut in China

Abstract A severe branch dieback and canker was observed on black walnut (Juglans nigra L.) in Yili county, Xinjiang, China, during the spring and summer, 2016. A fungus was consistently isolated from infected branches. Pathogenicity tests showed that the fungus could infect branches, and produced the same symptoms under artificial inoculation conditions as those observed in the field. The fungus was identified based on morphological and cultural characteristics as Cytospora chrysosperma. Identification was confirmed by combining multi-locus phylogenetic analyses based on the internal transcribed spacer regions (ITS 1 and 2) and intervening 5.8S nrDNA, the partial translation elongation factor (TEF-1) gene, and partial gene regions of β-tubulin (TUB 2). Morphological and cultural characteristics, as well as the sequences of the ITS, tef and β-tubulin regions and pathogenicity tests, showed that the causal agent of the disease was C. chrysosperma. This is the ﬁrst report of branch dieback and canker of black walnut caused by C. chrysosperma (Pers.) Fr. worldwide.
A neural model for the prediction of pathogenic genomic variants in Mendelian diseases

The detection of pathogenic genomic variants associated with genetic or cancer diseases represents an open problem in the context of the Genomic Medicine. In particular the detection of mutations in the non-coding regions of human genome represents a particularly challenging machine learning problem, since the number of neutral variants largely outnumber the pathogenic ones, thus resulting in highly imbalanced classification problems. We applied neural networks to the detection of pathogenic regulatory genomic variants in Mendelian diseases and we showed that leveraging imbalance-aware techniques and deep learning algorithms, we can obtain state-of-the-art results, using a less complex model than those proposed in literature for this challenging prediction task.
The world’s largest breeding colony of Leach’s Storm-petrel Hydrobates leucorhous has declined

Summary Despite the global significance of the Leach’s Storm-petrel Hydrobates leucorhous colony on Baccalieu Island, Newfoundland and Labrador, Canada, the estimate of 3.36 million breeding pairs reported for 1984 by Sklepkovych and Montevecchi stands as the single published population estimate for the world’s largest colony. This study increases knowledge of this population by analysing data from additional independent surveys conducted in 1984 and 1985, and by updating the population status with a survey conducted in 2013. Population estimates were derived by extrapolating occupied burrow densities to the estimated occupied area of four main habitat types (heath, forest, grass and fern), which in turn were based on proportions of habitats observed in plots (1984 and 1985) or by using a Geographic Information System approach (2013). Based on these surveys, the Leach’s Storm-petrel breeding population size on Baccalieu Island was estimated at 5.12 ± 0.73 (SE) and 4.60 ± 0.42 (SE) million pairs in 1984 and 1985 respectively, representing estimates 37–51% greater than the original 1984 survey. While discrepancies among these estimates were largely driven by the way occupied areas were estimated, our study confirms that Baccalieu Island hosts the largest Leach’s Storm-petrel colony in the world. Results from the 2013 survey estimate the current breeding Leach’s Storm-petrel population at 1.95 ± 0.14 (SE) million pairs, representing a 42% decline over 29 years (-1.4% per year), relative to the original published estimate of 3.36 ± 0.12 (SE) million pairs. The most prominent change has occurred in the density of storm-petrel burrows found in forest habitat which dropped by 70% despite forest remaining the second most abundant habitat available to nesting storm-petrels on Baccalieu Island. The cause of this decline remains unknown and is likely multi-faceted. Future research focusing on demographic studies is required to understand what is driving the population decline of this internationally important colony.
Polyandry and genetic diversity in populations of Pholidoptera griseoaptera along an environmental gradient

Polyandry is a common mating pattern in different insect species and it leads to increased genetic diversity in the offspring and prevents inbreeding in populations. According to the theory of mate choice, mates should choose a partner that will increase heterozygosity in their offspring. In this way females will increase their reproductive success and offspring will have higher fitness and be good competitors. Phenotypic traits such as large body size is preferred by both females and males crickets according to earlier studies. The environment can also have an influence on mating pattern as sexual selection could vary depending on the environment. I used the dark bush-cricket, Pholidop-tera griseoaptera in an experiment to examine the mechanisms behind polyandry and the correlation between phenotypic, genetic and environmental factors. My general aim was to broaden the knowledge about the mating system in this insect species. The study was placed at Slovak Academy of sciences in Slovakia. Bush-crickets from five different altitudes were collected, and mating experiments was performed using the offspring of these animals. Eleven mating groups were used with 5 females and 5 males in each group. The bush-crickets were kept in either warm or cold temperatures in open-air cages. Microsatellites was used to identify genetic diversity of populations to examine if there was a correlation with the frequency of copulations. Measurement of body-size were performed on each cricket and estimation of number of copulations were done for each female.I found that in warm temperature, females of P. grisoptera had the highest frequency of copulations and there males choose high quality females. In cold temperature there were less copulations, indicating that the environmental condition restrict the ability for mate choice. This study is only a snapshot of the pattern of polyandry and the behaviour needs to be studied further, but it has broadened the knowledge about the mating system in this nuptial gift-giving insect species.
A Meier-Gorlin Syndrome Mutation in Orc4 Causes Tissue-Specific DNA Replication Defects in Drosophila melanogaster

Meier-Gorlin syndrome is a rare recessive disorder characterized by a number of distinct developmental defects, including primordial dwarfism, small ears, and small or missing patella. Genes encoding members of the origin recognition complex (ORC) and additional proteins essential for DNA replication (CDC6, CDT1, GMNN, CDC45, and MCM5) are mutated in individuals diagnosed with MGS. The primary role of ORC is to license origins during the G1 phase of the cell cycle, but it also plays roles in cilia development, heterochromatin formation, and other cellular processes. Because of its essential role in DNA replication, ORC is required for every cell division during development. Thus, it is unclear how the Meier-Gorlin syndrome mutations in ORC lead to the tissue-specific defects associated with the disease. To address this question, we have used Cas9-mediated genome engineering to generate a Drosophila melanogaster model of individuals carrying a mutation in ORC4. Like the people with Meier-Gorlin syndrome, these flies reach adulthood, but have several tissue-specific defects. Genetic analysis revealed that this allele is a hypomorph and that mutant females are sterile. We demonstrated that this sterility is caused by a failure in DNA replication. By leveraging the well-studied Drosophila system, we showed that a disease-causing mutation in orc4 disrupts DNA replication, and we propose that in individuals with MGS defects arise preferentially in tissues with a high-replication demand.
Physico-chemical and sensory properties of strawberries (Fragaria x ananassa) grown in conventional and hydroponic systems

Strawberry is considered a fruit of great commercial interest in many countries due to its color, aroma, flavor, and nutritional properties. However, it is possible that the differences among the cultivation systems could affect the production of photoassimilates in the plant and, consequently, their partitioning into the fruits composition, influencing its quality. Therefore, the aim of this work was to evaluate the influence of the cultivation systems (hydroponics in gutters and slabs, and conventional) and genotype on the physicochemical properties, antioxidant and sensory activity in strawberry fruits. The experiment was carried out using a completely randomized design in a factorial 4 × 3 scheme with four replications, represented by trays of approximately 200 g of fruit. In the Laboratory, the strawberries (cv. Oso Grande, Festival, Camarosa, and Albion) were analyzed for their physicochemical properties and sensory variables: titratable acidity (TA), soluble solids (SS), SS/TA ratio, soluble sugars, vitamin C, polyphenol, and antioxidant activity. It was observed that cultivation systems and genotype studied influence the antioxidant activity, physicochemical and sensory properties of strawberries. The conventional system shows higher values for physicochemical variables and antioxidant activity, with cultivar variation within each system. The antioxidant activity attributed to strawberry is strongly related to the content of extractable polyphenols and vitamin C. Regarding the sensory properties, cultivars show good overall acceptability in all production systems studied, no presenting difference among systems.
Evolutionary history and classification of Micropia retroelements in Drosophilidae species

Current knowledge indicates TEs have been shaping the evolution of genomes and host species, contributing to the creation of new genes and promoting rearrangements frequently associated with new regulatory networks. Support for these hypothesis frequently result from studies with model species, and Drosophila detaches as a great model organism to the study of TEs. Micropia belongs to the Ty3/Gypsy group of LTR retroelements, and comprises one of the least studied Drosophila transposable elements. In this study, we assessed the evolutionary history of Micropia within Drosophilidae, while trying to assist in the classification of this TE. At first, we analyzed its presence in the genome of several species from natural populations and then, based on searches within genomic databases, we retrieved Micropia-like sequences from distinct Drosophilidae species genomes. We expanded the knowledge of Micropia distribution within Drosophila, and detected an array of divergent sequences, which allowed subdividing this retroelement in 20 subfamilies. Even so, a patchy distribution of Micropia sequences within the Drosophilidae phylogeny could be identified combined with incongruences of the species and the Micropia phylogenies. Comparing dS values between Micropia and host nuclear sequences, we found several cases of unexpected high levels of similarity between Micropia sequences found in divergent species. All these findings propose a hypothesis to the evolution of Micropia within Drosophilidae, including several VTTs and HTTs events, associated to ancestral polymorphisms and recurrent Micropia sequences diversification.
CHAPTER 19:Automated Identification and Scoring of Micronuclei

Micronucleus (MN) assays are used as a measure of cellular damage, and are often preferred over other chromosomal aberration assays since they possess similar statistical robustness for detection of genotoxins and require less technical expertise, making them easier to perform. However, the traditional visual scoring methods are tedious and prone to scorer subjectivity. A number of techniques to automate the MN assays have been developed using a variety of technologies. This chapter will provide an overview of several current methods used to automate MN assays, including automated slide-scoring and laser scanning cytometry, as well as conventional and imaging flow cytometry techniques.
A direct role for SNX9 in the biogenesis of filopodia

Filopodia are finger-like actin-rich protrusions that extend from the cell surface and are important for cell-cell communication and pathogen internalization. The small size and transient nature of filopodia combined with shared usage of actin regulators within cells confounds attempts to identify filopodial proteins. Here, we used phage display phenotypic screening to isolate antibodies that alter the actin morphology of filopodia-like structures in vitro. We found that all of the antibodies that cause shorter FLS interact with SNX9, an actin regulator that binds phosphoinositides during endocytosis and in invadopodia. In cells, we discover SNX9 at specialised filopodia in Xenopus development and that SNX9 is an endogenous component of filopodia that are hijacked by Chlamydia entry. We show the use of antibody technology to identify proteins used in filopodia-like structures, and a role for SNX9 in filopodia.
Atlas of transcriptionally active transposable elements in human adult tissues

Approximately half of the human genome consists of mobile repetitive DNA sequences known as transposable elements (TEs). They are usually silenced by epigenetic mechanisms, but a few are known to escape silencing at embryonic stages, affecting early human development by regulating nearby protein-coding genes. To investigate transcriptional activity in human adult tissues we systematically investigate the expression landscape of about 4.2 million non-coding TEs in 8,051 RNA-Seq datasets from up to 49 adult tissues and 540 individuals. We show that approximately 79,558 individual TEs (2%). belonging to 856 subfamilies escape epigenetic silencing in adult tissues and become transcriptionally active, often in a very tissue-specific manner. Supporting a role for TEs in the regulation of expression of nearby genes, we found the expression of TEs often correlated with the expression of nearby genes, and significantly stronger when the TEs include eQTLs for the genes. We identified thousands of tissue-elevated, sex-associated TEs in the breast, ethnicity-associated in the skin and age-associated in the tibial artery, where we found a potential implication of two TE subfamilies in atherosclerosis. Our results suggest a functional role of TEs in the regulation of gene expression, support their implication in human phenotypes, and also serve as a comprehensive resource of transcriptionally active TEs in human adult tissues.
Diffusive Flux Analysis of Tumor Vascular Permeability for 3-Helix-Micelles in Comparison to Other Nanoparticles

Understanding the complex interplay of factors affecting nanoparticle accumulation in solid tumors is a challenge that must be surmounted to develop effective cancer nanomedicine. The tumor microenvironment is unique in comparison to healthy tissue, possessing elevated interstitial pressure that limits convective transport, hence leaving diffusive processes to predominate especially in the tumor’s necrotic core. Certain tumor types such as glioblastoma multiforme and pancreatic tumor are known to be poorly permeable, making them less accessible for nanoparticle drug delivery. Evidence indicates that small and long-circulating nanoparticles are ideal for taking advantage of the enhanced permeability and retention effect, even in such intractable tumor models. Three-helix-micelle (3HM) self-assembled nanoparticles possess these characteristics, and previous studies have shown that 3HM can achieve more favorable tumor accumulation and penetration than liposomes in several tumor models. The reason for its superior performance had yet to be determined, and thus we sought to examine its passive transport into tumors. In this paper we present a simple mathematical model based on diffusive flux to describe particle accumulation in tumors with respect to particle plasma pharmacokinetics. Fitting the diffusive flux equation to in vivo particle tumor concentration yields the particle effective permeability value, which for 3HM is 2.31 ± 0.18 x 10−8 cm/s in U87MG glioblastoma and 4.25 ± 0.91 x 10−8 cm/s in HT29 colon cancer murine models. Applying this diffusive flux model to other nanoparticles reported in literature enables the effect of plasma half-life to be decoupled from particle permeability in influencing tumor accumulation, reinforced trends reported in the field regarding the impact of particle size, and provided a semi-quantitative means of comparing various tumor models. This work is also the first demonstration, to the best our knowledge, of extracting particle permeability values from bulk biodistribution data obtained via positron emission tomography, as opposed to laborious tumor optical window intravital microscopy experiments. As such the analysis provided here presents a simple and accessible tool to further enhance nanomedicine development. Graphical abstract
Effects of silver nitrate (AgNO3) on growth and anatomical structure of vegetative organs of liquorice (Glycyrrhiza glabra L.) under in vitro condition

Liquorice (Glycyrrhiza glabra L.) has been used worldwide as a medicine for a long time. In this research, the effect of silver nitrate (AgNO3) as a growth regulator and anti-ethylene in in vitro culture was investigated on growth and anatomical structure of vegetative organs (root, hypocotyl, shoot, leaf) as well as the number of stomata and trichomes in the leaves of liquorice under in vitro culture condition. The seeds were cultured in MS culture media containing different concentrations of AgNO3 (0, 2, 4, 8, and 10 mg L-1). Investigations on 20-day seedlings after three replications showed a significant increase in length and growth of roots, hypocotyls and shoots, and decreased number of stomata and trichomes in the samples treated with AgNO3 (P≤0.05). The effects of AgNO3 on anatomical structures of the organs included the increased cell division in root and shoot tips, reduced vascular tissues and sclerenchyma-fiber (with lignified cell walls), increased thickness of Casparian strip and cell walls of endodermis, reduced thickness of epidermis and increased intercellular spaces in mesophyll. The leaf area was measured in the 4-month plantlets, showing a significant increase in the samples treated with AgNO3. Furthermore, there was significant difference in increased leaf area applying 10 mg L-1 treatment and other concentrations as well as between the concentrations of 2 and 8 mg L-1. It seems that these results are due to the inhibitory effects of AgNO3 on the production and function of ethylene and the plant strategy to increase the tolerance against silver metal.
Wheat Straw Return Influences Nitrogen-Cycling and Pathogen Associated Soil Microbiota in a Wheat–Soybean Rotation System

Returning straw to soil is an effective way to sustain or improve soil quality and crop yields. However, a robust understanding of the impact of straw return on the composition of the soil microbial communities under field conditions has remained elusive. In this study, we characterized the effects of wheat straw return on soil bacterial and fungal communities in a wheat–soybean rotation system over a 3-year period, using Illumina-based 16S rRNA, and internal transcribed region (ITS) amplicon sequencing. Wheat straw return significantly affected the α-diversity of the soil bacterial, but not fungal, community. It enhanced the relative abundance of the bacterial phylum Proteobacteria and the fungal phylum Zygomycota, but reduced that of the bacterial phylum Acidobacteria, and the fungal phylum Ascomycota. Notably, it enriched the relative abundance of nitrogen-cycling bacterial genera such as Bradyrhizobium and Rhizobium. Preliminary analysis of soil chemical properties indicated that straw return soils had significantly higher total nitrogen (TN) contents than no straw return soils. In addition, the relative abundance of fungal genera containing pathogens was significantly lower in straw return soils relative to control soils, such as Fusarium, Alternaria, and Myrothecium. These results suggested a selection effect from the 3-year continuous straw return treatment and the soil bacterial and fungal communities were moderately changed.
Dispersal of mahogany seeds and seedlings (Swietenia macrophylla) in open ombrophilous forest with palm trees from southeastern Pará, Brazil

We performed a study of dispersal of mahogany seeds and seedlings (Swietenia macrophylla King, Meliaceae) in open ombrophilous forest with palm trees from southeastern Pará. For this study, we placed four transects of 2x50m, each subdivided in 25 blocs of 2x2m, in the directions N, S, E, W of four mahogany matrices. We found that: seeds dispersed according to the direction of prevailing winds that favored higher density and dispersal distance in the W - N direction; the intact seeds have reached greater dispersal distances than the aborted ones and can be dispersed beyond the matrix tree 50 m distance in the west direction; the greatest abundance of seeds and seedlings was found between 10 and 20 m distance from the matrices; seedling density was considered low, however, it increases from the east to west direction of the matrices, and can be found beyond the 50m distance in the N and W directions; the size of mahogany seeds is more important in determining the weight than width, which is a more conservative variable; the recruitment and growth of seedlings seem to be associated with clearings - where the highest heights were observed - which are quite disturbed sites with a higher incidence of light and other environmental seasonality. The information provide here may contribute to enhance the management actions for the use of the species included in the Appendix II of CITES.
Design of Quaternary Logical Circuit Using Voltage and Current Mode Logic

In VLSI technology, designers main concentration were on area required and on performance of the device. In VLSI design power consumption is one of the major concerns due to continuous increase in chip density and decline in size of CMOS circuits and frequency at which circuits are operating. By considering these parameter logical circuits are designed using quaternary voltage mode logic and quaternary current mode logic. Power consumption required for quaternary voltage mode logic is 51.78 % less as compared to binary . Area in terms of number of transistor required for quaternary voltage mode logic is 3 times more as compared to binary. As quaternary voltage mode circuit required large area as compared to quaternary current mode circuit but power consumption required in quaternary voltage mode circuit is less than that required in quaternary current mode circuit .