Miracle-dz/UniFAR-FTUs huggingface dataset:
Label-free in vivo imaging of Drosophila melanogaster by multiphoton microscopy

The fruit fly Drosophila melanogaster is one of the most valuable organisms in genetic and developmental biology studies. Drosophila is a small organism with a short life cycle, and is inexpensive and easy to maintain. The entire genome of Drosophila has recently been sequenced (cite the reference). These advantages make fruit fly an attractive model organism for biomedical researches. Unlike humans, Drosophila can be subjected to genetic manipulation with relative ease. Originally, Drosophila was mostly used in classical genetics studies. In the model era of molecular biology, the fruit fly has become a model organ for developmental biology researches. In the past, numerous molecularly modified mutants with well defined genetic defects affecting different aspects of the developmental processes have been identified and studied. However, traditionally, the developmental defects of the mutant flies are mostly examined in isolated fixed tissues which preclude the observation of the dynamic interaction of the different cell types and the extracellular matrix. Therefore, the ability to image different organelles of the fruit fly without extrinsic labeling is invaluable for Drosophila biology. In this work, we successfully acquire in vivo images of both developing muscles and axons of motor neurons in the three larval stages by using the minimially invasive imaging modality of multiphoton (SHG) microscopy. We found that while SHG imaging is useful in revealing the muscular architecture of the developing larva, it is the autofluorescence signal that allows label-free imaging of various organelles to be achieved. Our results demonstrate that multiphoton imaging is a powerful technique for investigation the development of Drosophila.
A role for a conserved kinase in the transcriptional control of methionine biosynthesis in Escherichia coli experiencing sustained nitrogen starvation

The initial adaptive transcriptional response to nitrogen (N) starvation in Escherichia coli involves large-scale alterations to the transcriptome mediated by the transcription activator, NtrC. One of the NtrC-activated genes is yeaG, which encodes a conserved bacterial kinase. Although it is known that YeaG is required for optimal survival under sustained N starvation, the molecular basis by which YeaG benefits N starved E. coli remains elusive. By combining transcriptomics with targeted metabolomics analyses, we demonstrate that the methionine biosynthesis pathway becomes transcriptionally dysregulated in ΔyeaG bacteria experiencing sustained N starvation. This results in the aberrant and energetically costly biosynthesis of methionine and associated metabolites under sustained N starvation with detrimental consequences to cell viability. It appears the activity of the master transcriptional repressor of methionine biosynthesis genes, MetJ, is compromised in ΔyeaG bacteria under sustained N starvation, resulting in transcriptional derepression of MetJ-regulated genes. The results suggest that YeaG is a novel regulatory factor and functions as a molecular brake in the transcriptional control of both the NtrC-regulon and methionine biosynthesis genes in E. coli experiencing sustained N starvation.
Seasonal biodiversity and ecological studies on the epiphytic microalgae communities in polluted and unpolluted aquatic ecosystem at Assiut, Egypt

Abstract A qualitative and quantitative study on epiphytic microalgae was carried out seasonally from November 2015 to August 2016 to follow up their community structures on aquatic macrophytes related to some physico-chemical properties of two polluted and unpolluted water bodies at Assiut, Egypt. A total of 169 species related to 64 genera of epiphytic microalgae were recorded. The most dominant algal group was Bacillariophyceae (43.2%), followed by Chlorophyceae (34.91%), Cyanophyceae (20.71%) and Euglenophyceae (1.18%). The total number of epiphytic algae fluctuated between 11.1 × 104 ind.g-1 plant dry wt. on Phragmites australis in summer at Nazlet Abdellah (polluted site) and 10.02 × 107 ind.g-1 plant dry wt. on Myriophyllum spicatum in winter at El-Wasta (unpolluted site). Some epiphytic microalgae were dominant as Pseudanabaena limnetica, Calothrix braunii, Scenedesmus acutus, and Ulnaria ulna. Others were specific on certain macrophytes as Aphanocapsa thermalis and Ulothrix sp. , which grow on Phragmites australis, while Synechocystis minuscula attached itself on Myriophyllum spicatum. Analysis of PERMANOVA showed that the most important factors that induced the variation in epiphytic microalgae were the temporal variation and host plant. Water temperature, pH, nitrate, chloride, phosphate and total dissolved salts were the highest abiotic factors correlated with the variation in composition of epiphytic microalgae.
Analysis of albumen gland proteins suggests survival strategies of developing embryos of Pomacea canaliculata

ABSTRACT The albumen gland of Pomacea canaliculata secretes the perivitelline fluid (PVF) surrounding the developing embryo which gives its eggs a highly effective defence against environmental factors and predators. Although previous studies have determined the functions of some PVF proteins extracted from P. canaliculata eggs, knowledge of the protein composition of PVF is still limited. In this study we use LC-MS/MS to identify 87 proteins from the albumen gland of P. canaliculata, 53 of which (60.9%) were annotated using the KEGG database. These classified into five functional groups: metabolism (54.7%); genetic information processing (9.4%); environmental information processing (3.8%); cellular processes (11.3%); and organismal systems (20.8%). The analyses found 12 proteins related to innate immunity and three proteins linked to defence against predation, providing important information for studies on embryo survival strategies and the invasive capabilities of P. canaliculata.
Deciphering signaling specificity with interpretable deep neural networks

Protein kinase phosphorylation is a prevalent post-translational modification (PTM) regulating protein function and transmitting signals throughout the cell. Defective signal transductions, which are associated with protein phosphorylation, have been revealed to link to many human diseases, such as cancer. Defining the organization of the phosphorylation-based signaling network and, in particular, identifying kinase-specific substrates can help reveal the molecular mechanism of the signaling network. Here, we present DeepSignal, a deep learning framework for predicting the substrate specificity for kinase/SH2 sequences with or without mutations. Empowered by the memory and selection mechanism of recurrent neural network, DeepSignal can identify important specificity-defining residues to predict kinase specificity and changes upon mutations. Evaluated on several public benchmark datasets, DeepSignal significantly outperforms current methods on predicting substrate specificity on both kinase and SH2 domains. Further analysis in The Cancer Genome Atlas (TCGA) demonstrated that DeepSignal is able to aggregate mutations on both kinase/SH2 domains and substrates to quantify binding specificity changes, predict cancer genes related to signaling transduction, and identify novel perturbed pathways. Availability Implementation of DeepSignal is at https://github.com/luoyunan/DeepSignal
Systematic palaeontology (Vertebrate palaeontology) A new ground sloth (Mammalia: Xenarthra) from the Quaternary of Brazil

The record of South-American Pleistocene Megalonychidae is scarce. Of the species described for intertropical Brazil, including Megalonyx sp. , Ocnopus gracilis, Valgipes deformis, Xenocnus cearensis and Ahytherium aureum, only the last, recently described, is valid. The new megalonychid species described here was recovered from the same locality as Ah. aureum. The latter is apparently more closely linked to the North-American Pleistocene forms whereas Australonyx aquae may be more closely related to the Antillean sloths. The fossil remains of extant taxa recovered in association with the new sloth species suggest that the region, currently within the Caatinga biome, was a mosaic of the Atlantic Forest and Savannah biomes during the final stages of the
Unrecognized species diversity and new insights into colour pattern polymorphism within the widespread Malagasy snake Mimophis (Serpentes: Lamprophiidae)

Although many wide-ranging taxa occur in Madagascar, phylogeographic studies for most of these species are still lacking. This is especially the case for snakes, where of more than 100 endemic species, the population structure of only two species has so far been examined. Here, we examine genetic population structure of one of the most common snakes of Madagascar, Mimophis mahfalensis (Grandidier, 1867). This taxon is the only representative of Psammophiinae in Madagascar, where the majority of species in this subfamily is distributed throughout mainland Africa. Applying an integrative approach, where both morphological data and genetic results from coalescent species delimitation analyses are considered, we determine that Mimophis mahfalensis is composed of two distinct taxa: M. mahfalensis in the central montane and southern parts of Madagascar, and a second new species restricted to the north and north-west, which we describe here. We also examine the colour pattern polymorphism exhibited in Mimophis, which has been previously hypothesized as sexually dimorphic and/or geographically correlated. However, we find all three colour morphs in both sexes, and both species of Mimophis. Our work highlights the importance of phylogeographic studies that examine wide-ranging taxa to detect cryptic species diversity, even amongst species that are common, or have been previously considered to be well known. www.zoobank.org/lsid:zoobank.org:pub:9791DC0B-49E5-4571-884C-4AA85EAF2472
Single Cell Molecular Heterogeneity In Musculoskeletal Differentiation

Mesenchymal stem cells (MSCs) display substantial cell-to-cell variation that manifests across many aspects of cell phenotype and complicates the use of MSCs in regenerative applications. However, most conventional assays measure MSC properties in bulk and, as a consequence, mask this cell-to-cell variation. To better understand MSC heterogeneity and its underlying mechanisms, we quantitatively assessed MSC phenotype within the context of chondrogenesis, amongst clonal populations and single cells. Clonal MSCs differed in their contractility, ability to transmit extracellular strain the nucleus, capacity to form cartilage-like matrix, and transcriptomic signature. RNA FISH measurements of single cell gene expression found that both primary chondrocytes and chondrogenically-induced MSCs showed substantial mRNA expression heterogeneity. Surprisingly, variation in differentiation marker transcript levels only weakly associated with cartilage-like matrix production at the single cell level. This finding suggested that, although canonical markers have very clear functional roles in differentiation and matrix formation, their instantaneous mRNA abundance is only tenuously linked to the chondrogenic phenotype and matrix accumulation at the single cell level. One possible explanation for the apparent disconnect between gene and protein expression is that mRNA and protein exhibit different temporal dynamics. Using stochastic models of single cell behavior, we explored the impact of transcriptional stochasticity and temporal matrix dynamics on the perceived relationship between single cell mRNA and protein abundance. Simulations suggested that considering recent temporal fractions of protein (vs. total protein) increased the correlation between mRNA and protein abundance, and illustrated that mRNA stability was a crucial determinant of the timescale over which any such correlation persisted. Experimentally, non-canonical amino acid tagging was used to visualize and quantify temporal fractions of nascent extracellular matrix with high fidelity. The organization and temporal dynamics of the proteinaceous matrix depended on the biophysical features of the microenvironment, including the biomaterial scaffold and the niche constructed by cells themselves. Both chondrocytes and MSCs demonstrated marked cell-to-cell heterogeneity in nascent matrix production, consistent with model predictions. Ongoing work aims to combine these experimental measurements of nascent protein expression with instantaneous measures of mRNA abundance to better understand the mRNA-protein relationship, and to harness this understanding to improve regenerative therapies. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Bioengineering First Advisor Robert L. Mauck
Immunodeficient pigs for biomedical research

One requirement for regenerative medicine is the test of function of human cells and tissues in a physiologically relevant animal models prior to transplantation into humans. To avoid rejection, recipient animals must be immunodeficient. The goal of this doctoral project was to derive a genetically modified pig line suitable for investigation of human xeno-transplants, to be achieved by inactivation of key immunoregulatory genes in somatic cells and generation of whole animals by nuclear transfer. Janus kinase 3 (JAK3) knockout pigs were generated. Such animals will be of interest in other biomedical areas such as cancer and research on infectious diseases.
Precise excitation-inhibition balance controls gain and timing in the hippocampus

Excitation-inhibition (EI) balance controls excitability, dynamic range, and input gating in many brain circuits. Subsets of synaptic input can be selected or 'gated' by precise modulation of finely tuned EI balance, but assessing the granularity of EI balance requires combinatorial analysis of excitatory and inhibitory inputs. Using patterned optogenetic stimulation of mouse hippocampal CA3 neurons, we show that hundreds of unique CA3 input combinations recruit excitation and inhibition with a nearly identical ratio, demonstrating precise EI balance at the hippocampus. Crucially, the delay between excitation and inhibition decreases as excitatory input increases from a few synapses to tens of synapses. This creates a dynamic millisecond-range window for postsynaptic excitation, controlling membrane depolarization amplitude and timing via subthreshold divisive normalization. We suggest that this combination of precise EI balance and dynamic EI delays forms a general mechanism for millisecond-range input gating and subthreshold gain control in feedforward networks.
Selective loading of exosomal HULC and miR-372 is responsible for chondrocyte death during OA pathogenesis

ABSTRACT Exosomes are membranous vesicles containing various biomolecules, including non-coding RNAs (ncRNAs). ncRNAs are secreted from several cell types and are involved in various biological functions, including cellular communication. The aim of this study was to identify and illustrate the significance of the osteoarthritis (OA)-specific packaging of exosomal ncRNAs. In this study, we hypothesized that selective packaging of ncRNAs into exosomes would reflect the cellular response to chondrocyte death during OA pathogenesis. Exosomal HULC level significantly decreased in OA exosomes, whereas exosomal miR-372-3p level significantly increased in OA exosomes. In addition, chondrocytes with high HULC levels in the cytosol showed lower overall proliferation and higher apoptotic cell death than normal chondrocytes, whereas chondrocytes with high miR-372-3p in the cytosol showed higher overall proliferation and lower cell death than OA chondrocytes. Among the signaling molecules known to be involved in OA pathogenesis, GSK is one of the regulators of the selective exosomal packaging observed in OA chondrocytes. Inhibition of GSK observed in OA chondrocytes was responsible for enriched uploading of miR-372-3p and suppressed uploading of HULC during OA pathogenesis. In conclusion, we show that selective ncRNAs observed in OA play a critical role in chondrocyte proliferation/apoptosis.
Close Genetic Relatedness of Chromis Fish (Abudefduf sp.) Between Indonesia and Korea Population

The purpose of our study was to look closely relationship of Chromis fish taken from Korean waters and Indonesia based on Deoxyribose Nukleid Acid (DNA) mitochondrial marker. Samples of data taken from each of the 21 identified samples of the Abudefduf vaigiensis species, Abudefduf sexfasciatus and Abudefduf bengalensis . The samples taken were then extracted, amplified, and sequenced based on the mitochondrial DNA marker from the CYTB locus. The DNA sequence result is processed in MEGA 6.06 software to analyze the phylogenetic tree for determine close relatedness. The result showed there were 4 main clades including one clade outgrup explaining the chromis fish close relatedness i.e. 1) Abudefduf vaigiensis group , Abudefduf sexfasciatus and Abudefduf bengalensis , 2) Abudefduf Bengalensis group and 3) Abudefduf vaigiensis group from Buton waters location. The closest relatedness between Chromis fish found in Korea and Indonesia in the A. vaigiensis Korea and A. vaigiensis species in Sorong waters, ie, by the genetic distance of 0.0008. This genetic distance value in pairs of 10000 pairs of nucleotide have 8 pairs of different nucleotide.
Identifying sustainable forest management research narratives: a text mining approach

ABSTRACT Although it is obvious that research regarding Sustainable Forest Management (SFM) is context specific and developed over time, not many research papers yet intended to investigate these changes. As a matter of fact, the number of scientific publications addressing SFM is relatively high. Hence, such a wide field cannot be sufficiently covered by traditional literature review approaches. With this paper, we aim at identifying the most convergent narratives within the SFM-research landscape by applying a text mining methodology to recent scientific literature. By doing so, we generated results that indicate that there may have been three phases in the evolution of SFM-research: the early phase covers in particular issues regarding land use in tropical and developing countries. Furthermore, papers in this phase tend to focus on general concepts or policy issues. In contrast, the second phase is characterized by a larger share of publications in forestry focused journals. This process is seemingly connected with issues like forest management, certification, forest stand management and the development of sustainability indicators. A third phase can be observed by the relative downturn of publications in forest-focused journals between 2005 and 2010. A new focus in this period is climate change.
Interferon tau stimulated gene expression and proinflammatory cytokine profile relative to insemination in dairy cows

Abstract A profitable and scientific dairy farming can be achieved by identifying the non-pregnant animals at an early date post-insemination. The present study was executed to identify the genes for early pregnancy diagnosis in bovine. The blood samples were collected from the Karan Fries cows on days 0, 4, 8, 12, 14, 16, 18, 21, 24, 28, 35 and 42 relative to the date of insemination. The experimental animals were grouped into pregnant (P), conception failure/early embryonic mortality (EEM) and late embryonic mortality cows (LEM), based on progesterone assay, ultrasonography and per-rectal palpation. Each group comprised of 6 cows. The plasma TNF-α concentration was higher in pregnant than EEM and LEM cows. The IL-8 concentration was higher in EEM than pregnant and LEM cows. The mRNA expression of CXCL17 and IFIT2 was significantly (p < 0.05) higher from day 4–35 than day 0 in pregnant and LEM cows. The degree of expression of Interferon-tau stimulated genes was higher in pregnant and LEM cows than EEM cows. The experiment reveals that the time-dependent changes in the IFNτ stimulated gene expression in blood neutrophils coupled with proinflammatory cytokine profile could be useful biomarkers for bovine gestation.
Monitoring fruit-feeding butterfly assemblages in two vertical strata in seasonal Atlantic Forest: temporal species turnover is lower in the canopy

Abstract: To address how seasonality affects the richness and abundance of tropical insects, we compared the canopy and understorey communities of fruit-feeding butterflies in a seasonal Atlantic forest in south-eastern Brazil. Butterflies were sampled over 1 y using a standardized design with baited traps. A total of 2047 individuals in 69 species were recorded (1415 in the canopy, 632 in the understorey). Clear differences were found between canopy and understorey, with significantly higher butterfly abundances in the canopy. We observed two marked peaks of abundance and richness in both strata; one at the transition from dry to the wet seasons, and the other at the transition from wet to dry seasons. We found lower species turnover throughout the year in the canopy. We interpret this as evidence that temperature is more important than rainfall in explaining the yearly variation of abundance in vertical strata. The higher temperatures found in the canopy may allow butterflies to maintain activity in this stratum all year round, whereas the understorey is subject to colder temperatures, thus presenting a higher species turnover. These results improve our understanding of diversity gradients between evergreen and seasonal tropical forests, allowing insights into how climate and beta diversity gradients interact.
The VT GAL4, LexA, and split-GAL4 driver line collections for targeted expression in the Drosophila nervous system

In studying the cellular interactions within complex tissues, it is extremely valuable to be able to reproducibly and flexibly target transgene expression to restricted subsets of cells. This approach is particularly valuable in studying the nervous system, with its bewildering diversity of neuronal cell types. We report here the generation of over 18,000 driver lines (the VT collection) that exploit the GAL4, LexA, and split-GAL4 systems to express transgenes in distinct and highly specific cell types in Drosophila. We document the expression patterns of over 14,000 of these lines in the adult male brain.
Survey of the response of 82 domestic landraces of Zea mays to cucumber mosaic virus (CMV) reveals geographical region‐related resistance to CMV in Japan

Zea mays has been historically imported to Japan via two independent geographical routes: into southern Japan by trading with Europe in the 16th century and into northern Japan by import from North America in the 19th century. Breeding to genetically improve on quality traits and high yields has led to the current domestic landraces in each region. In a survey of 82 domestic landraces, nine out of 38 landraces originating from southern Japan showed complete immunity to cucumber mosaic virus yellow strain (CMV(Y)) without the formation of necrotic local lesions (NLLs). In contrast, three out of 44 landraces originating from northern Japan developed NLLs, but revealed no systemic spread of the virus. Due to the absence of good documentation on NLL formation in Z. mays, the response of domestic landraces Aso-1 and Aso-3, originating from Ibaraki in northern Japan, to a challenge with CMV(Y) and CMV(Ma-1) was further analysed. Aso-3 only formed NLL in response to CMV(Y) but not to CMV(Ma-1). Moreover, in CMV(Y)-inoculated Aso-3, virus spread was restricted to the primary infection site and the expression of defence-related genes was up-regulated, whereas Aso-1 became systemically infected with either CMV(Y) or CMV(Ma-1). The response of Aso-3 to CMV(Y) was inherited as a single dominant trait. Together, these results pointed towards the induction of hypersensitive response (HR)-mediated resistance to CMV(Y) in Aso-3. Although HR-mediated resistance to viruses has been studied mainly in dicots, the pathosystem CMV-Z. mays may provide a model to investigate HR-mediated resistance to viruses in monocot plants.