Miracle-dz/UniFAR-FTUs huggingface dataset:
Keeping an Eye on Wild Brown Trout (Salmo trutta) Populations: Correlation Between Temperature, Environmental Parameters, and Proliferative Kidney Disease

Proliferative kidney disease (PKD) is an emerging disease of salmonids caused by the myxozoan parasite Tetracapsuloides bryosalmonae, which plays a major role in the decrease of wild brown trout (Salmo trutta) populations in Switzerland. Strong evidence demonstrated that water temperature modulates parasite infection. However, less knowledge exists on how seasonal water temperature fluctuations influence PKD manifestation under field conditions, how further environmental factors such as water quality may modulate the disease, and whether these factors coalesce with temperatures role possibly giving rise to cumulative effects on PKD. The aims of this study were to (1) determine the correlation between seasonal course of water temperature and PKD prevalence and intensity in wild brown trout populations, (2) assess if other factors such as water quality or ecomorphology correlate with the infection, and (3) quantitatively predict the implication of these factors on PKD prevalence with a statistical model. Young-of-the-year brown trout were sampled in 45 sites through the Canton of Vaud (Switzerland). For each site, longitudinal time series of water temperature, water quality (macroinvertebrate community index, presence of wastewater treatment plant effluent) and ecomorphological data were collected and correlated with PKD prevalence and intensity. 251 T. bryosalmonae-infected trout of 1,118 were found (overall prevalence 22.5%) at 19 of 45 study sites (42.2%). Relation between PKD infection and seasonal water temperature underlined that the mean water temperature for June and the number of days with mean temperature ≥15°C were the most significantly correlated parameters with parasite prevalence and intensity. The presence of a wastewater treatment plant effluent was significantly correlated with the prevalence and infection intensity. In contrast, macroinvertebrate diversity and river ecomorphology were shown to have little impact on disease parameters. Linear and logistic regressions highlighted quantitatively the prediction of PKD prevalence depending on environmental parameters at a given site and its possible increase due to rising temperatures. The model developed within this study could serve as a useful tool for identifying and predicting disease hot spots. These results support the importance of temperature for PKD in salmonids and provides evidence for a modulating influence of additional environmental stress factors.
Prevalence of beta thalassemia mutations in population of Gujarat using amplification-refractory mutation system–polymerase chain reaction

Background: Beta thalassemia is the most common genetic disorder in India. Its trait, coinheritance and mutations vary from mild to severe condition, resulting in thalassemia minor (heterozygous), intermediate and major depending upon many factors. The objective of this study was to find out the prevalence rate and the carrier of beta thalassemia in population of Gujarat using molecular genetic analysis of beta thalassemia patients by targeted mutation assay (ARMS-PCR). Methods: A total 105 samples for beta thalassemia were analysed for IVS 1-5 (G→C) and CD 15 (G→A) mutations. These two common mutations of thalassemia in Gujarat were carried out using amplification refractory mutation system–polymerase chain reaction (ARMS-PCR) and gel electrophoresis method.Results: A total 105 samples referred to us for molecular genetic analysis. The occurrence of positive mutations of IVS 1-5 (G→C) and CD 15 (G→A) were found in 48 and 15 samples respectively. The rest were negatives.Conclusions: Present study concludes that the prevalence rate of Beta thalassemia was widespread among the Gujarat population. The identification of IVS 1-5 (G→C) and CD 15 (G→A) mutations was carried out. The analysis revealed that, mutational patterns of IVS 1-5 (G→C) was the most frequent among other mutations in Gujarat region.
Altered brain-wide auditory networks in fmr1-mutant larval zebrafish

Altered sensory processing is characteristic of several psychiatric conditions, including autism and fragile X syndrome (FXS). Here, we use whole-brain calcium imaging at cellular resolution to map sensory processing in wild type larval zebrafish and mutants for fmr1, which causes FXS in humans. Using functional analyses and graph theory, we describe increased transmission and reduced filtering of auditory information, resulting in network-wide hypersensitivity analogous to the auditory phenotypes seen in FXS.
Modelling the Presence-Absence of Multiple Species

Predicting which species will be present (or absent) across a geographical region remains one of the key problems in ecology. Numerous studies have suggested several ecological forces that can determine species presence-absence: environmental factors (i.e. abiotic environments), interactions among species (i.e. biotic interactions), dispersal and demographic stochasticity. While various ecological forces have been considered, less attention has been given to the problem of understanding how dispersal processes, in interaction with other ecological factors, shape community assembly in the presence of priority effects (i.e. initial abundances determine the presence-absence of species). In this thesis, we investigate the consequences of different dispersal patterns and stochasticity on the occurrence of priority effects and species coexistence in multi-species competitive systems. By employing deterministic and stochastic models in one-dimensional space, our study shows the conditions under which priority effects occur and disappear as local dispersal strength changes. Without dispersal, priority effects emerge in the presence of intense biotic interactions, with only one species surviving at any given location (i.e. coexistence is impossible). For moderate dispersal levels, dispersal enhances priority effects and promotes multiple species coexistence. Further increasing dispersal strength leads to the disappearance of priority effects and causes extinction of some species. We also demonstrate contrasting observations of stochasticity on priority effects: while priority effects are more prevalent in the stochastic individual-based models (IBM) than in the deterministic models for large populations, we observe fewer occurrences of priority effects in IBM for small populations. When non-local dispersal is incorporated into the models, priority effects are more pronounced than in the local dispersal models. We also investigate the effects of different dispersal patterns on species coexistence: although very long-range dispersal leads to species extinctions, intermediate-range dispersal permits more outcomes where multispecies coexistence is possible than short-range dispersal (or purely local dispersal). Finally, we extend our model to consider community dynamics in two-dimensional space. We find that knowledge of species’ environmental requirements is also crucial
Complete Genome Sequencing and Comparative Genome Characterization of Lactobacillus johnsonii ZLJ010, a Potential Probiotic With Health-Promoting Properties

Lactobacillus johnsonii ZLJ010 is a probiotic strain isolated from the feces of a healthy sow and has putative health-promoting properties. To determine the molecular basis underlying the probiotic potential of ZLJ010 and the genes involved in the same, complete genome sequencing and comparative genome analysis with L. johnsonii ZLJ010 were performed. The ZLJ010 genome was found to contain a single circular chromosome of 1,999,879 bp with a guanine–cytosine (GC) content of 34.91% and encoded 18 ribosomal RNA (rRNA) genes and 77 transfer RNA (tRNA) genes. From among the 1,959 protein coding sequences (CDSs), genes known to confer probiotic properties were identified, including genes related to stress adaptation, biosynthesis, metabolism, transport of amino acid, secretion, and the defense machinery. ZLJ010 lacked complete or partial biosynthetic pathways for amino acids but was predicted to compensate for this with an enhanced transport system and some unique amino acid permeases and peptidases that allow it to acquire amino acids and other precursors exogenously. The comparative genomic analysis of L. johnsonii ZLP001 and seven other available L. johnsonii strains, including L. johnsonii NCC533, FI9785, DPC6026, N6.2, BS15, UMNLJ22, and PF01, revealed 2,732 pan-genome orthologous gene clusters and 1,324 core-genome orthologous gene clusters. Phylogenomic analysis based on 1,288 single copy genes showed that ZLJ010 had a closer relationship with the BS15 from yogurt and DPC6026 from the porcine intestinal tract but was located on a relatively standalone branch. The number of clusters of unique, strain-specific genes ranged from 42 to 185. A total of 219 unique genes present in the genome of L. johnsonii ZLJ010 primarily encoded proteins that are putatively involved in replication, recombination and repair, defense mechanisms, transcription, amino acid transport and metabolism, and carbohydrate transport and metabolism. Two unique prophages were predicted in the ZLJ010 genome. The present study helps us understand the ability of L. johnsonii ZLJ010 to better adapt to the gut environment and also its probiotic functionalities.
Bayesian transfer in a complex spatial localization task

Prior knowledge can help observers across a range of tasks. Adults can simultaneously learn two location priors and integrate these with sensory information to locate hidden objects. Importantly, observers weight prior and sensory (likelihood) information differently depending on their respective reliabilities, in line with principles of Bayesian inference. Yet, there is limited evidence that observers actually perform Bayesian inference, rather than a heuristic, such as forming a look-up table. To distinguish these possibilities, we ask whether previously-learnt priors will be immediately integrated with a new, untrained likelihood. If observers use Bayesian principles, they should immediately put less weight on the new, less reliable, likelihood (“Bayesian transfer”). In an initial experiment, observers estimated the position of a hidden target, drawn from one of two distinct distributions (priors), using sensory and prior information. The sensory cue consisted of dots drawn from a Gaussian distribution centred on the true location with either low, medium, or high variance; the latter introduced after block three of five to test for evidence of Bayesian transfer. Observers did not place significantly less weight on the cue relative to the prior in the high compared to medium variance condition, counter to Bayesian predictions. However, when explicitly informed of the different prior variabilities, observers placed less weight on the new high variance likelihood (“Bayesian transfer”), yet substantially diverged from the ideal observer, placing too much weight on the medium and high variance likelihoods in all reported experiments. These results emphasise the limits of Bayesian models in complex tasks.
Apple Scion and Rootstock Contribute to Nutrient Uptake and Partitioning under Different Belowground Environments

Soil environment strongly contributes to tree growth and development, affecting nutrient and water uptake. Composite woody perennials, like apple, are a combination of two genetically different parts: a rootstock and a scion, and yet, the role of each part on nutrient uptake and distribution under differing soil environments has not been previously studied. We tested how water limitations and elevated soil temperatures, applied to different apple rootstocks and scions, affected mineral nutrient uptake and distribution on young apple trees. Two one-year-old potted apple cultivars were grown in a greenhouse, ‘Honeycrisp’ and ‘Gala,’ combined with four rootstocks: G890, G41, M9, and B9. Belowground abiotic environmental treatments were imposed for 60 days after trees reached approximately 45 cm height. Water limitations reduced aboveground biomass and, to a lesser extent, root biomass. ‘Gala’ and the rootstock G890 showed elevated mineral nutrient uptake compared to ‘Honeycrisp’ and the other rootstock genotypes. Additionally, G890 showed a greater plasticity for both biomass and mineral nutrient accumulation. Elevated soil temperatures increased the ratios of K:Ca, N:Ca, Mg:Ca, and (N + K + Mg):Ca in leaf tissue of rootstock G41 and ‘Honeycrisp’. These findings highlight the importance of the use of scion and rootstock genotypes that are adapted to specific soil environments to ensure optimal nutrient uptake.
Phenotypic and Genotypic Diversity Among Symbiotic and Non-symbiotic Bacteria Present in Chickpea Nodules in Morocco

Environmental pollution problems and increased demand for green technologies in production are forcing farmers to introduce agricultural practices with a lower impact on the environment. Chickpea (Cicer arietinum) in arid and semi-arid environments is frequently affected by harsh environmental stresses such as heat, drought and salinity, which limit its growth and productivity and affect biological nitrogen fixation ability of rhizobia. Climate change had further aggravated these stresses. Inoculation with appropriate stress tolerant rhizobia is necessary for an environmentally friendly and sustainable agricultural production. In this study, endophytic bacteria isolated from chickpea nodules from different soil types and regions in Morocco, were evaluated for their phenotypic and genotypic diversity in order to select the most tolerant ones for further inoculation of this crop. Phenotypic characterization of 135 endophytic bacteria from chickpea nodules showed a wide variability for tolerance to heavy metals and antibiotics, variable response to extreme temperatures, salinity, pH and water stress. 56% of isolates were able to nodulate chickpea. Numerical analysis of rep-PCR results showed that nodulating strains fell into 22 genotypes. Sequencing of 16S rRNA gene of endophytic bacteria from chickpea nodules revealed that 55% of isolated bacteria belong to Mesorhizobium genus. Based on MLSA of core genes (recA, atpD, glnII and dnaK), tasted strains were distributed into six clades and were closely related to Mesorhizobium ciceri, Mesorhizobium opportunistum, Mesorhizobium qingshengii, and Mesorhizobium plurifarium. Most of nodulating strains were belonging to a group genetically distinct from reference Mesorhizobium species. Three isolates belong to genus Burkholderia of the class β- proteobacteria, and 55 other strains belong to the class γ- proteobacteria. Some of the stress tolerant isolates have great potential for further inoculation of chickpea in the arid and semiarid environments to enhance biological nitrogen fixation and productivity in the context of climate change adaptation and mitigation.
Assessment of the Utility of Gene Positioning Biomarkers in the Stratification of Prostate Cancers

In eukaryotic cells, the genome is spatially organized in a non-random fashion within the confines of the interphase nucleus, and most genes occupy preferred nuclear positions. For some genomic loci these positioning patterns are context specific, reflected in the distinct location of certain genes and chromosomes in different cell types and in disease. Disease-related differential spatial positioning of genes has led to the hypothesis that the spatial reorganization of the genome may be utilized as a diagnostic biomarker. In keeping with this possibility, the positioning patterns of specific genes can be used to reproducibly discriminate benign tissues from cancerous ones. In addition to the use of spatial genome organization for diagnostic purposes, we explore here the potential use of spatial genome organization as a prognostic tool. This is a pressing need since in many cancer types there is a lack of accurate markers to predict the aggressiveness of individual tumors. We find that directional repositioning of SP100 and TGFB3 gene loci stratifies prostate cancers of differing Gleason scores. A more peripheral position of SP100 and TGFB3 in the nucleus, compared to benign tissues, is associated with low Gleason score cancers, whereas more internal positioning correlates with higher Gleason scores. Conversely, LMNA is more internally positioned in many non-metastatic prostate cancers, while its position is indistinguishable from benign tissue in metastatic cancer. Our findings of subtype-specific gene positioning patterns in prostate cancer provides a proof-of-concept for the potential usefulness of spatial gene positioning as a prognostic biomarker.
EFFICIENCY OF TWO MOLECULAR TOOLS BASED ON DNA USED FOR DIFFERENTIATING SOME MICROBIAL STRAINS

In the present study, two molecular biology tools based on DNA were compared in the differentiating between some microbial strains isolated from soil. Two types (16SrRNA and 18SrRNA) of ribosomal RNA genes were used for identification of the four bacterial and three fungal isolates, respectively. The identified microbial isolates were submitted in GenBank as strains of Escherichia coli MSL-19 (LC455952.1); Bacillus sp. MSLB-1 (LC455953.1); Bacillus sp. MSLB2 (LC455954.1); Bacillus sp. MSLB3 (LC455955.1); Penicillium sp. MLSP1 (LC455956.1); Aspergillus niger MLSAs1 (LC455958.1); Aspergillus sp. MLSAs2 (LC455959.1). The DNA obtained from the seven microbial strains was used as templates for RAPDPCR differentiating in the presence of eight random primers. Electrophoresis analysis was performed, and on scoring, the identity percentages between the bacterial and fungal strains were separately analyzed. A percentage of 82-83% was recorded between the E. coli and the three Bacillus strains, while, identities of 93-98% were recorded between the three Bacillus strains. Similar trend (90-96%) was observed between the Penicillium and Aspergillus strains. Results confirmed that identities based on the two ribosomal RNA genes (82-98%) was higher than that of RAPD-PCR (70.0-79.7%), and this is because of ribosomal RNA genes are in limited sizes (~1500-1600 bp) and specific for differentiating species, while RAPD-PCR tool depends on using some random primers could be recorded on the whole genome. The phylogenetic trees based on the two molecular tools supported the obtained results. As a conclusion, tools of RAPD-PCR and ribosomal RNA genes were successfully used to identify and detect the genetic variability of microbial strains isolated from soil.
Dynamics of activating and repressive histone modifications in Drosophila neural stem cell lineages and brain tumors

ABSTRACT During central nervous system development, spatiotemporal gene expression programs mediate specific lineage decisions to generate neuronal and glial cell types from neural stem cells (NSCs). However, little is known about the epigenetic landscape underlying these highly complex developmental events. Here, we perform ChIP-seq on distinct subtypes of Drosophila FACS-purified NSCs and their differentiated progeny to dissect the epigenetic changes accompanying the major lineage decisions in vivo. By analyzing active and repressive histone modifications, we show that stem cell identity genes are silenced during differentiation by loss of their activating marks and not via repressive histone modifications. Our analysis also uncovers a new set of genes specifically required for altering lineage patterns in type II neuroblasts (NBs), one of the two main Drosophila NSC identities. Finally, we demonstrate that this subtype specification in NBs, unlike NSC differentiation, requires Polycomb-group-mediated repression. Highlighted Article: A FACS-based method for sorting different cell types and their ChIP-seq have provided an in vivo dataset that reveals dynamic histone modifications during neuronal differentiation in Drosophila.
Effect of Organic Manures, Biofertilizers and NPK on Vegetative Growth, Yield, Fruit Quality and Soil Fertility of Eureka Lemon Trees (Citrus limon (L.) Burm).

A field experiment was carried out during the years 2013, 2014 and 2015 on Eureka lemon at El-Nubaria region, El-Beheira governorate, to study the effect of farmyard manure and biofertilizers with NPK dose on soil fertility, growth, yield, fruit quality and leaf nutrient content of Eureka lemon trees. Eleven treatments were arranged in a randomized complete block design with three replicates. Results revealed significant differences amongst various growth attributes, fruit yield, fruit quality, leaf mineral content and soil nutrients availability due to farmyard manure and biofertilizers application. Also, farmyard manure and biofertilizers could compensate for the 50% reduction of chemical fertilizers, and increasing yield compared to chemical fertilizers with significant differences. Therefore, treatment of 50% NPK + 55 kg farmyard manure + biofertilizers is recommended for growers. This treatment gave the best growth, yield and fruit quality of Eureka lemon trees. Moreover, this treatment improved the nutritional status of the trees, through the beneficial effects of organic and biofertilizers which enhanced the availability of most nutrients in the soil.
Pine Pitch Canker and Insects: Regional Risks, Environmental Regulation, and Practical Management Options

Pine pitch canker (PPC), caused by the pathogenic fungus Fusarium circinatum (Nirenberg and O’ Donnell), is a serious threat to pine forests globally. The recent introduction of the pathogen to Southern Europe and its spread in Mediterranean region is alarming considering the immense ecological and economic importance of pines in the region. Pines in forests and nurseries can be infected, resulting in severe growth losses and mortality. The pathogen is known to spread in plants for planting and in seeds, and results from recent studies have indicated that F. circinatum may also spread through phoretic associations with certain insects. With this review, we aim to expand the current understanding of the risk of insect-mediated spread of PPC in different parts of Europe. Through the joint action of a multinational researcher team, we collate the existing information about the insect species spectrum in different biogeographic conditions and scrutinize the potential of these insects to transmit F. circinatum spores in forests and nurseries. We also discuss the impact of environmental factors and forest management in this context. We present evidence for the existence of a high diversity of insects with potential to weaken pines and disseminate PPC in Europe, including several common beetle species. In many parts of Europe, temperatures are projected to rise, which may promote the activity of several insect species, supporting multivoltinism and thus, further amplifying the risk of insect-mediated dissemination of PPC. Integrated pest management (IPM) solutions that comply with forest management practices need to be developed to reduce this risk. We recommend careful monitoring of insect populations as the basis for successful IPM. Improved understanding of environmental control of the interaction between insects, the pathogen, and host trees is needed in order to support development of bio-rational strategies to safeguard European pine trees and forests against F. circinatum in future.