Miracle-dz/UniFAR-FTUs huggingface dataset:
Toxicity Assessment of Sub Lethal Doses of Chlorpyrifos on the Kidney and Liver Organs of Male Wistar Rats

Chlorpyrifos, an organophosphate pesticide is an important neurotoxic and tissue damage agent. It is one of the most heavily used pesticides in domestic and agricultural applications globally. Repeated doses of chlorpyrifos have been able to cause significant disturbances on the biochemical and physiological functions of the blood, and histological abnormalities in livers and kidneys exposed to this insecticide. The toxicities of sub lethal oral administration of chlorpyrifos daily for 28 days were assessed using a completely randomized design. Twenty five albino Wistar rats weighing between 150-200 g divided into five groups containing five rats each were housed in the Central Animal house of College of Medicine, University of Ibadan. Chlorpyrifos at 0 (control), 18.9, 25.9, 32.2 and 39.2 mg/kg were orally administered to male rats, respectively for four weeks, between the months of May and June, 2014. At the end of the experimental period, the toxicities of chlorpyrifos were assessed in rats using haematology, serum liver enzymes and histopathological assays. Results revealed significant reduction in body weights compared to control. The packed cell volume (PCV), hemoglobin (Hb) and lymphocytes (Lymp) also showed significant reduction at Original Research Article Fayinminnu et al.; IJBCRR, 17(3): 1-15, 2017; Article no.IJBCRR. 31349 2 39.2, 25.9 and 32.2 mg/kg (39.33, 45.40 and 44.80%), respectively compared to control (49.67%). Insecticide administration to rats resulted in significant elevation of serum transaminases (AST and ALT) and alkaline phosphatase (ALP) from 32.2, 39.2 and 25.9 mg/kg dosages, (ranged from 294.94-542.00 u/L for AST and from 96.25-130.77 u/L for ALT), respectively. Also, experimental treated groups exhibited marked of total protein and altered albumin and globulin contents compared to control. Studies revealed dose dependent increase of histopathological alterations. The livers showed moderate vacuolar change of hepatocytes, having a finely reticulated cytoplasmic and congestion of central veins. The kidneys showed mild focal sloughing off of tubular epithelium of renal cortex, fluid in tubular lumen, tubules appearing dilated and cystic (nephrosis) and proteinaeceous fluid in Bowman`s capsule and compressing the glomerulus tufts (Esinophilic). Different concentrations of chlorpyrifos including the lowest tested dose produced marked alterations in the exposed animals in this study and thereby affecting the overall performance in terms of health and wellbeing. Thus, this could cause similar health and environmental risks to humans even at the lowest dose.
Analysing genebank collections using "R": making trait information widely available to users.

Genebanks provide important conservation and distribution systems for the delivery of genetic diversity. Despite the importance of access to information by plant breeders and other germplasm users, backlogs in characterization and evaluation, as well as analysis, are widespread. At the Nordic Genetic Resource Center a process was initiated in which researchers, technicians and statisticians were invited to a series of workshops to identify and analyse current and old data with the open source R software. This article summarizes our results by emphasizing three selected datasets, namely those of pea, barley and red clover. The objective was the process itself, rather than producing a specific scientific output. We demonstrate how summary statistics can be used to note problems. Thereafter, we discuss how graphical tools can be applied in the type of multivariate analysis of data commonly found in genebanks.
Prophylactic immunity in the mealworm beetle Tenebrio molitor.

Immune systems are thought to be costly to maintain and express in a variety of taxa. Evidence for this comes from observations that mechanisms which deal with pathogenic challenge are often extremely variable and are induced in the presence of an immune challenge, rather than being constitutively active. This thesis presents work aimed at testing predictions arising from these ideas, using the mealworm beetle T. molilor (Coleoptera: Tenebrionidae) as a model system. Assays were developed which reflected three specific aspects of immunity (haemocyte count, phenoloxidase levels and resistance to a generalist fungal pathogen), thereby allowing aspects of immune function to be quantified. It was shown that the level of fungal resistance differed in beetles reared gregariously (higher resistance) and solitarily (lower resistance). Conspecifics are a source of disease (Freeland 1983), so this is an example of immune defences being induced in situations with a higher risk of pathogenesis (density dependent prophylaxis). A strong predictor of fungal resistance was the degree of melanisation of the adults' cuticles. This trait was shown to be highly heritable (59%), as was the total haemocyte count of an individual: an important aspect of general invertebrate immunity. Selection for cuticular melanisation resulted in a rapid response, confirming the existence of large amounts of additive genetic variance for this trait. Fungal resistance showed a correlated 111 response to selection for cuticular melanisation, indicating that this too has additive genetic variance. Lines selected for darker cuticles showed higher levels of fungal resistance than those selected for lighter cuticles. Cuticular melanisation and fungal resistance are therefore genetically correlated, and the former can be used as an indicator of the latter in T. molitor. No specific costs of cuticular melanisation or fungal resistance were identified. A correlated response to selection for cuticular melanisation on larval competitive ability was investigated, but no such response was seen. Thus the mechanisms maintaining variability and inducibility in cuticular melanisation and fungal resistance are unknown. This thesis has therefore identified patterns of immune expression consistent with the hypothesis that immunity has associated costs, although these costs have not been shown. It has also identified a potentially novel role for cuticular melanisation, as an indicator of immunity to fungal pathogens.
Crossing system application and its effect on lambs growth traits.

: Success of crossing depends on the breeds used and the genetic distance among them, as well the combining ability of maternal and individual heterosis to make the proper choice of breeds employed in a crossing system. The aim of this study is to find the effect of genotype and crossing system on early weights and daily gain of lambs. The lambs of purebred Pirot Pramenka ( P) got the lowest body weight at birth, at 30 days, at 60 days and 90 days with a value of 3.65 kg, 9.48 kg, 14.99 kg and 21.96 kg while purebred Wurttemberg attained the highest body weight at birth of 4.48 kg. The lambs of three bred crossing (PxWxF) highest on BW30, BW60 and BW90 days. The results showed a highly significant difference on average daily gain (ADG) among genotypes (P ˂0.01) except on the difference between W – PxW of which belongs to the lower border of significant level (P ˂0.05). The highest difference on ADG was between P – PxWxF (105.950 g), wherein the lowest difference was between W– PxW (9.290 g). It can close that the attained value between pure bred Wurttemberg (W) and two-bred crossing (PxW) was almost equal. Genotype and crossing system have significant effect on body weight and average daily gain of lambs. Based on the results obtained, it shows an advantage effect of crossing system (PxWxF) when it comes on growth and daily gain of lambs.
Computational Methods For Analyzing Rna Folding Landscapes And Its Applications

Non-protein-coding RNAs play critical regulatory roles in cellular life. Many ncRNAs fold into specific structures in order to perform their biological functions. Some of the RNAs, such as riboswitches, can even fold into alternative structural conformations in order to participate in different biological processes. In addition, these RNAs can transit dynamically between different functional structures along folding pathways on their energy landscapes. These alternative functional structures are usually energetically favored and are stable in their local energy landscapes. Moreover, conformational transitions between any pair of alternate structures usually involve high energy barriers, such that RNAs can become kinetically trapped by these stable and local optimal structures. We have proposed a suite of computational approaches for analyzing and discovering regulatory RNAs through studying folding pathways, alternative structures and energy landscapes associated with conformational transitions of regulatory RNAs. First, we developed an approach, RNAEAPath, which can predict low-barrier folding pathways between two conformational structures of a single RNA molecule. Using RNAEAPath, we can analyze folding
Exploring the Role of Biofilms in the Transport and Establishment of Invasive Marine Macrofoulers

Transport and establishment of macrofoulers between neighboring ports is a key step in the marine coastal bioinvasion process, and one that may be regulated by the composition of biofilms that colonize all submerged surfaces. However, it is unclear how biofilms in ports are distributed on resident and imported surfaces and how they might alter subsequent macrofouling colonization. This study establishes that the biofilms developed at and transplanted between neighboring ports harbor unique microbial assemblages. Bacteria were the primary contributors of biofilm variation among sites, while diatoms drove differences between resident and transplanted biofilms. While these biofilms were distinct from one another, they contributed to differences in macrofouling recruitment in only 25% of all species, and to community composition in just 10% of all cases. These results suggest that macrofouling larvae are resourceful and can readily recruit to and colonize biofilms that contain a wide variety of microbes. This generalist response is likely fundamental to the successful transport, establishment and global invasion success of macrofoulers in marine systems.
Methods for On-Orbit Germination of Arabidopsis thaliana for Proteomic Analysis

Abstract Large-scale omics approaches make excellent choices for research aboard the International Space Station (ISS) because they provide large amounts of data that can be continually mined even after the original research has been completed. A proteomic approach can provide information about which proteins are produced, degraded, or post-translationally modified, potentially shedding light on cellular strategies that cannot be discerned from transcriptomic data. To collect sufficient tissue from a Biological Research In Canisters (BRIC)-grown experiment on the ISS for proteomic analysis, several modifications were made to existing protocols. Approximately 800–1000 seeds were housed in each Petri Dish Fixation Units (PDFU). These were germinated up to 120 h after planting by transferring the BRIC from cold stasis to room temperature. Growth continued for only 72 h after germination to allow sufficient tissue for extraction, and to minimize the impact of ethylene and crowding stress. Seedlings were then exposed to RNAlater®. Results indicate that RNAlater® - treated Arabidopsis seedlings yield an equal amount of protein to those flash-frozen in liquid nitrogen.
Reproduction and Population Structure of Acanthocardia tuberculata (Linnaeus, 1758) (Bivalvia: Cardiidae) in Southern Spain: Implications for Stock Management

ABSTRACT The cardid bivalve Acanthocardia tuberculata is harvested in southern Spain and on the Atlantic coast of Morocco for the Spanish canning industry. The reproductive cycle and population structure of this species were studied in southern Spain from June 1999 to May 2000, using histology and condition indices, as well as modal size classes in length-frequency distribution analysis. The samples were collected monthly during autumn and winter months and fortnightly during spring and summer months. A total of 4,047 specimens were examined, from which 3,539 specimens were processed for biomass analyses and 508 for the study of the gametogenic cycle. Shell lengths of individuals ranged from 6 to 76 mm (48.15 ± 15.15 mm, mean ± SD), and the sex ratio was 1:1. The reproductive cycle of A. tuberculata showed an annual pattern, with an extended sexual activity from January to July, during which successive spawning events were observed, and with a clear-cut resting period from September to November. Small-size individuals are recruited into the population from June to December. No correlations were found between the environmental variables (sea water temperature and concentration of chlorophyll a) and the condition indices, which could be explained by the presence of upwellings in the area that introduce random fluctuations of these environmental variables. To improve management of the wild stock, a closed season during June–July was proposed together with a minimum harvest size of 45 mm.
Morphological changes with depth in the calcareous brown alga Padina pavonica

Abstract The calcareous brown alga Padina pavonica (L.) Thivy (Phaeophyceae, Dictyotales) is common worldwide in the sublittoral of warm-temperate coasts. We studied its distribution and changes of morphology and thallus anatomy along a light gradient. Specimens were collected at different depths in the Bay of Calvi (Corsica, Mediterranean) during spring and autumn. We sampled individuals for mapping and recorded a significant decrease of both coverage and number of individuals with depth, but an increase in frond size. Frond thickness and cell volumes (cell length, height, width) were measured and compared to irradiance levels and between two seasons. Fronds in spring were small and thick and contained larger cells than specimens collected in autumn. Additionally, fronds from shallow areas were thicker than those from deeper areas. Fronds always consisted of three cell layers, and both surfaces were calcified. A carbonate cover (carbonate content per unit dry mass and frond area) was present on both surfaces in both seasons, with a significantly lower cover in spring. In spring, the beginning of the growing season for Padina, the growth rates at sheltered and exposed sites and from different depths were all similar, averaging 0.45 mm day−1.
In-Season Estimation of Corn Yield Potential Using Proximal Sensing

Crop sensing is a promising approach for predicting corn (Zea mays L.) yield. Yield prediction is the first step in development of algorithms for sensor-based N management. Here, we evaluated the impact of (i) timing of sensing (growth stage), and (ii) method of reporting sensor data on estimations of corn grain and silage yield in New York. Sensor data were reported as the normalized difference vegetation index (NDVI), in-season estimated yield (INSEY) expressed as NDVI divided by days after planting (DAP; INSEYDAP), growing degree days (GGD; INSEYGGD), and the inverse simple ratio (ISR; [1–NDVI]/[1+NDVI]) divided by DAP (INSEYISR). To evaluate timing of sensing, corn of six fertility trials was scanned at every growth stage between V4 and V11. The replicated trials had up to six N rates (0, 56, 112, 168, 224, and 336 kg ha–¹). The V7 sensor and yield data from zero-N plots of nine additional on-farm trials (varying histories) were added to derive yield algorithms for New York. Drought at three sites in 2016 negatively impacted the accuracy of sensor-based grain yield estimates (R² 0.70 (grain) and >0.77 (silage). We conclude that INSEY data obtained at V7 can be used to accurately predict corn grain and silage yields in non-drought conditions in New York.
Reviewing biomedical role of Plasma Gelsolin

Gelsolin is circulating in human plasma in extremely high concentrations that is exhausted by intermediaries of inflammation and largely produced by skeletal muscles. Gelsolin is a Ca2+ dependant actin-binding and an actin-depolymerizing protein. Owing to capability of gelsolin to swiftly severe F-actin, plasma gelsolin has become a very important injury healing protein in various pathological conditions. Decreased levels of the plasma gelsolin have been reported in human diseases as well as in animal models of diseases. Therefore, pGSN deficiency appears to be a powerful biomarker and a potential therapeutic target in diseases. Here, we review the biomedical functions of gelsolin and impact of gelsolin levels in different disease conditions.
Computational Interrogation of Transcriptional and Post-Transcriptional Mechanisms Regulating Dendritic Development

The specification and modulation of cell-type specific dendritic morphologies plays a pivotal role in nervous system development, connectivity, structural plasticity, and function. Regulation of gene expression is controlled by a wide variety of cellular and molecular mechanisms, of which two major types are transcription factors (TFs) and microRNAs (miRNAs). In Drosophila, dendritic complexity of dendritic arborization (da) sensory neurons of the peripheral nervous system are known to be regulated by two transcription factors Cut and Knot, although much remains unknown about the molecular mechanisms and regulatory networks via which they regulate the final arbor shape through spatio-temporal modulation of dendritic development and dynamics. Here we use bioinformatics analysis of transcriptomic data to identify putative genomic targets of these TFs with a particular emphasis on those that effect neuronal cytoskeletal architecture. We use transcriptomic, as well as data from various genomic and protein interaction databases, to build a weighted functional gene regulatory network for Knot, to identify the biological pathways and downstream genes that this TF regulates. To corroborate bioinformatics network predictions, knot putative targets, which classify into neuronal and cytoskeletal functional groups, have been experimentally validated by in vivo genetic perturbations to elucidate their role in Knot-mediated Class IV (CIV) dendritogenesis. MicroRNAs (miRNAs) have emerged as key post-transcriptional regulators of gene expression, however identification of biologically-relevant target genes for this epigenetic regulatory mechanism remains a significant challenge. To address this knowledge gap, we have developed a novel R based tool, IntramiR-ExploreR, that facilitates integrated discovery of miRNA targets by incorporating target databases and novel target prediction algorithm to arrive at high confidence intragenic miRNA target predictions. We have explored the efficacy of this tool using D.melanogaster as a model organism for bioinformatics analyses and functional validation, and identified targets for 83 intragenic miRNAs. Predicted targets were validated, using in vivo genetic perturbation. Moreover, we are constructing interaction maps of intragenic miRNAs focusing on neural tissues to uncover regulatory codes via which these molecules regulate gene expression to direct cellular development. INDEX WORDS: gene regulatory networks, microRNA target predictions, dendrite development, bioinformatics, transcription factors. COMPUTATIONAL INTERROGATION OF TRANSCRIPTIONAL AND POSTTRANSCRIPTIONAL MECHANISMS REGULATING DENDRITIC DEVELOPMENT
The prioritisation of a short list of alien plants for risk analysis within the framework of the Regulation (EU) No. 1143/2014

Thirty-seven alien plant species, pre-identified by horizon scanning exercises were prioritised for pest risk analysis (PRA) using a modified version of the EPPO Prioritisation Process designed to be compliant with the EU Regulation 1143/2014. In Stage 1, species were categorised into one of four lists – a Residual List, EU List of Minor Concern, EU Observation List and the EU List of Invasive Alien Plants. Only those species included in the latter proceeded to the risk management stage where their priority for PRA was assessed. Due to medium or high spread potential coupled with high impacts twenty-two species were included in the EU List of Invasive Alien Plants and proceeded to Stage 2. Four species (Ambrosia trifida, Egeria densa, Fallopia baldschuanica and Oxalis pes-caprae) were assigned to the EU Observation List due to moderate or low impacts. Albizia lebbeck, Clematis terniflora, Euonymus japonicus, Lonicera morrowii, Prunus campanulata and Rubus rosifolius were assigned to the residual list due to a current lack of information on impacts. Similarly, Cornus sericea and Hydrilla verticillata were assigned to the Residual List due to unclear taxonomy and uncertainty in native status, respectively. Chromolaena odorata, Cryptostegia grandiflora and Sphagneticola trilobata were assigned to the Residual List as it is unlikely they will establish in the Union under current climatic conditions. In the risk management stage, Euonymus fortunei, Ligustrum sinense and Lonicera maackii were considered a low priority for PRA as they do not exhibit invasive tendencies despite being widely cultivated in the EU over several decades. Nineteen species were identified as having a high priority for a PRA (Acacia dealbata, Ambrosia confertiflora, Andropogon virginicus, Cardiospermum grandiflorum, Celastrus orbiculatus, Cinnamomum camphora, Cortaderia jubata, Ehrharta calycina, Gymnocoronis spilanthoides, Hakea sericea, Humulus scandens, Hygrophila polysperma, Lespedeza cuneata, Lygodium japonicum, Pennisetum setaceum, Prosopis juliflora, Sapium sebiferum, Pistia stratiotes and Salvinia molesta).
Regulation of cytochrome c in respiration, apoptosis, neurodegeneration and cancer: The good, the bad and the ugly

Despite the fact that over 200 phosphorylation sites have been mapped on the mitochondrial oxidative phosphorylation (OxPhos) complexes, very little is known about the relevant cell signaling pathways and the terminal kinases and phosphatases that control these phosphorylations. Within OxPhos, cytochrome c (Cytc) plays a special role because it is not only involved in electron transport but is also a key executer of apoptosis when it is released from the mitochondria. It is therefore not surprising that Cytc is regulated by phosphorylation. Four phosphorylation sites have been mapped on mammalian Cytc, two of which have been studied functionally, demonstrating that both respiration and apoptosis are under the control of signaling pathways that have yet to be identified. We here review the regulation and multiple functions of mammalian Cytc, including respiration, reactive oxygen species (ROS) scavenging under healthy conditions, ROS production via p66, and cardiolipin oxidation during apoptosis. We propose targeting Cytc by manipulation of signaling cascades as a therapeutic avenue in conditions including neurodegeneration and cancer. Abbreviations: Apaf-1, apoptotic protease-activating factor 1; CPP, cell-penetrating peptide; COX, cytochrome c oxidase; Cytc, cytochrome c; Cytc-T, testes cytochrome c; ΔΨm, mitochondrial membrane potential; ETC, electron transport chain; OxPhos, oxidative phosphorylation; ROS, reactive oxygen species.