Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular mechanisms regulating embryonic cerebral cortex development.

Cerebral cortex development is a complex process that integrates both extrinsic and intrinsic mechanisms. The surrounding cellular environment triggers receptor activation, which in turn initiates components of different signalling cascades and subsequently gene transcription, influencing cell survival, proliferation, and differentiation. Genetic mutations causing a loss-of-function or gain-of-function of signalling pathways elements can lead to cortical abnormalities and result in cognitive dysfunctions. In this thesis, I examined the receptor tyrosine kinase (RTK) TrkB and TrkC, the small GTPase Ras, and the C/EBP family of transcription factors, investigating their roles during cerebral cortex development. First, I looked at the role of C/EBPs during cortical cell fate determination. I determined that inhibition of C/EBPs decrease neurogenesis, keeping precursors in an undifferentiated state and later promoting their differentiation into astrocytes, while expression of an activated form of C/EBP promoted neurogenesis and reduced astrogenesis. Moreover, the inhibition of MEK, a mediator of C/EBPβ phosphorylation, also caused a decrease in neurogenesis. Thus, activation of the MEK-C/EBP pathway biases precursor cells to become neurons rather than astrocytes, thereby acting as a differentiation switch. Second, I examined the involvement of Trk signalling during cortical development. I showed that genetic knockdown using shRNA, or inhibition using dominant negative of TrkB and TrkC lead to a decrease in proliferation and later to postnatal precursor cells depletion. Moreover, it caused a reduction in number of neurons combined with mislocalization of the generated neurons to the different cortical layers. Thus, Trk signalling plays an essential role in the regulation of cortical precursor cell proliferation and differentiation during embryonic development. Third, I elucidated the effect of Costello syndrome H-Ras mutations during cerebral cortex formation. I determined that these mutations promoted cell proliferation and astrogenesis, while reducing neurogenesis. Together, these data support a model where proper Trks/Ras/MEK/C/EBP signalling is essential for normal genesis of neurons and astrocytes and show that cortical development perturbations can ultimately lead to cognitive dysfunction as seen in Costello syndrome patients.
Effekten av Bisfenol A (BPA) på hanråttors (Rattus norvegicus) reproduktion

Today evidence exist that environmental chemicals deteriorate male sperm quality and that testicular cancer is increasing. Bisphenol A (BPA) is a chemical with estrogenic effects used in the manufacture of polycarbonate plastic and are found in, for instance, plastic boxes, feeding bottles and food containers. Much of the research on how men's reproductive ability is influenced are performed on rats. This review article complies how male rat reproduction is affected by BPA as a model for humans. Studies have investigated how sperm are affected, hormonal changes during reproduction and how reactive oxygen species (ROS) affects sperm. The results show that sperm quality and sperm motility is deteriorating if rats are exposed to BPA. The negative feedback regulation of testosterone decrease, leading to an increase of luteinizing hormone (LH), which in turn leads to a decrease of testicular function. A decrease of LH is also found that indicate a decrease of pituitary secretion of LH. Increased ROS production after exposure to BPA is making sperm unable to protect themselves and they end up in oxidative stress. Thus, there is evidence that male rats have an impaired fertility caused by exposure to BPA. Through further research the effects of BPA can be clarified in more detail, give us a better understanding of how BPA can cause deterioration of sperm quality and if there is a link to the increase in testicular cancer that is seen in humans.
Influence of different factors on the effectivity of fungal bioagents to manage rice sheath blight, in nursery

The present investigation was undertaken to select the most promising isolate(s) of Trichoderma sp. and to observe the effect of different rate and time of application of bioagents(s) on sheath blight. Soil treatment with Trichoderma harzianum ( rice leaf isolate) was found more effective in reducing sheath blight as compared to other isolates of Trichoderma spp and commercial formulations of the bioagents. Application of T.harzianum, 7 days before inoculation of Rhizoctonia solani resulted in maximum reduction (78.98%) of the disease. Higher rates of T.harzianum (4 or 8 g/kg. of soil) with lower rate of pathogen inoculum was found highly effective in reducing disease severity (61.93-73.32%) and incidence (50.45-81.26%) of the disease.
Facilitating the collaboration of practitioner and scientific knowledge: experiences from an Australian action research intervention.

This paper presents results from an action research intervention aimed at strengthening the role of private sector advisers in the Australian agricultural extension system. Private sector advisers participating in the research identified a number of barriers to their effective inclusion in this system. For example, in the traditionally science-centric Australian extension system, persisting industry-led funding structures and processes are perceived as having a ‘gatekeeping function’ when it comes to the setting of practice-based research priorities and therefore the further development and uptake of potential innovations from practice. Issues also arise around linking private sector advisers with current research and development and translating it into relevant on-farm extension practice (Nettle et al, IFSA 2018). In Australia, the privatisation of the Extension and Advisory system has been varied across industries, resulting in a complex system with different models of engagement between researchers, advisory practitioners and industry-based decision-makers. This has implications for the Australian agricultural knowledge and innovation system. Against this background, the paper focusses on the question of how integration of practitioner and scientific-based knowledge can be implemented towards innovative solutions for complex problems. The paper describes the implementation of a shared knowledge management intervention. Based on principles of action research and collaborative design, participants jointly developed knowledge management processes aimed at breaking sectoral silos (public, private; research and practice) by bringing together a variety of actors in the agricultural knowledge system in two specific case study settings. The findings from these interactions emphasise the importance of transparent communication and other trust building exercises, particularly the need to be inclusive of all actors and perspectives when collaboratively defining the ‘problem’ or ‘knowledge gap’ that is to be addressed. Historical tensions and expectations around roles and responsibilities between researchers, advisory practitioners and industry-based decision-makers can easily jeopardise any collaborative knowledge management efforts and therefore need to be made explicit. In this context, the findings indicate, first, that there is a role for agricultural industry bodies to strategically broker, support and enhance such cross-sector dialogue, and, second, that definition of this role will depend on the industry bodies’ willingness to commit to and adequately resource their uptake of such a role in the system. The research results make a contribution to theories of (inter)organisational collaboration and social learning in agricultural knowledge and innovation systems and have resulted in strategic and policy recommendations to participating industry bodies.
Influence of Botrytis cinerea (Helotiales: Sclerotiniaceae) infected leaves of Vitis vinifera (Vitales: Vitaceae) on the preference of Epiphyas postvittana (Lepidoptera: Tortricidae)

Herbivorous insects use sensory cues to choose their host plants for feeding and/or oviposition by assessing host quality. Olfactory, contact and visual cues of the host mediate such choices. The right‐host choice for oviposition by a lepidopteran is essential for the performance of its progeny. In natural conditions, plants are often and concurrently attacked by both herbivorous insects and pathogenic fungi. In such a three‐way relationship, the interaction between the plant and insect is usually influenced by the fungal population, and such an influence can be either mutualistic or antagonistic. In the present study, we tested the three‐way relationship using the system, Epiphyas postvittana–Vitis vinifera–Botrytis cinerea. We sought answers to the questions: (1) whether the females of E. postvittana prefer to oviposit on V. vinifera leaves infected by B. cinerea; and (2) whether the larvae of E. postvittana prefer to feed on V. vinifera leaves infected by B. cinerea. We found that the host‐seeking gravid females of E. postvittana ‘tested’ the infection status of the host plant using olfactory, visual, and tactile cues; in consequence, they laid significantly fewer eggs on the moderately (30–60%) and intensely (90–100%) infected leaves of V. vinifera. The neonate larvae preferred to feed on mildly (5–10%) and moderately (30–60%) infected leaves, as against the uninfected (control) leaves, and showed no preference for intensely (90–100%) infected leaves. External and internal examination of the larvae established that the larvae fed on B. cinerea‐infected leaf because viable conidia of B. cinerea occurred on the body surface and within the gut of the neonate larvae.
Richness and diversity of ants and beetles in genetically modified cotton field in Brazil.

Genetic engineering has created many genetically modified (GM) crop varieties that express the cry toxin from the bacterium Bacillus thuringiensis (Bt). The cry toxin, synthesized during plant growth, has insecticidal properties, and can be expressed anywhere in the plant. This study aimed to ascertain the richness and species diversity of edaphic Formicidae and Coleoptera in GM cotton fields compared with the conventional non-transformed cotton crop. We analyzed data from commercial cotton fields located in the municipality of Maracaju, Mato Grosso do Sul, Brazil. The experiment was conducted during the reproductive period of cotton, employed two treatments: Bt cotton and non-Bt cotton. Samples were collected with pitfall traps. Formicidae species richness in the Bt area was lower than in the non-Bt area, but species composition did not differ between the two treatments. Species composition of Coleoptera communities also differed between the treatments because some species were more abundant in the Bt cotton area. On the other hand, the species richness of this group was similar in both areas.
Mining large collections of gene expression data to elucidate transcriptional regulation of biological processes

A vast amount of gene expression data is available to biological researchers. As of October 2010, the GEO database has 45,777 chips of publicly available gene expression profiling data from the Affymetrix (HGU133v2) GeneChip platform, representing 2.5 billion numerical measurements. Given this wealth of data, ‘meta-analysis’ methods allowing inferences to be made from combinations of samples from different experiments are critically important. This thesis explores the application of localized pattern-mining approaches, as exemplified by biclustering, for large-scale gene expression analysis. Biclustering methods are particularly attractive for the analysis of large compendia of gene expression data as they allow the extraction of relationships that occur only across subsets of genes and samples. Standard correlation methods, however, assume a single correlation relationship between two genes occurs across all samples in the data. There are a number of existing biclustering methods, but as these did not prove suitable for large scale analysis, a novel method named ‘IslandCluster’ was developed. This method provided a framework for investigating the results of different approaches to biclustering meta-analysis. The biclustering methods used in this work involve preprocessing of gene expression data into a unified scale in order to assess the significance of expression patterns. A novel discretisation approach is shown to identify distinct classes of genes’ expression values more appropriately than approaches reported in the literature. A Gene Expression State Transformation (‘GESTr’) introduced as the first reported modelling of the biological state of expression on a unified scale and is shown to facilitate effective meta-analysis. Localised co-dependency analysis is introduced, a paradigm for identifying transcriptional relationships from gene expression data. Tools implementing this analysis were developed and used to analyse specificity of transcriptional relationships, to distinguish related subsets within a set of transcription factor (TF) targets and to tease apart combinatorial regulation of a set of targets by multiple TFs. The state of pluripotency, from which a mammalian cell has the potential to differentiate into any cell from any of the three adult germ layers, is maintained by forced expression of Nanog and may be induced from a non-pluripotent state by the expression of Oct4, Sox2, Klf4 and cMyc. Analysis of cMyc regulatory targets shed light on a recent proposition that cMyc induces an ‘embryonic stem cell like’ transcriptional signature outside embryonic stem (ES) cells, revealing a cMyc-responsive subset of the signature and identifying ES cell expressed targets with evidence of broad cMyc-induction. Regulatory targets through which cMyc, Oct4, Sox2 and Nanog may maintain or induce pluripotency were identified, offering insight into transcriptional mechanisms involved in the control of pluripotency and demonstrating the utility of the novel analysis approaches presented in this work.
Predicting susceptibility to future declines in the world's frogs

The 2004 Global Amphibian Assessment demonstrated that almost 400 anuran species have recently moved closer to extinction due to a host of threat mechanisms. Of particular concern is the role of the fungal pathogen, Batrachochytrium dendrobatidis (Bd), for which more traditional conservation management is not effective. Determining which biological and environmental factors affect a species' susceptibility to these mechanisms would greatly aid conservation prioritisation and planning. We performed phylogenetic comparative analyses to determine which biological and environmental factors predict species' susceptibility to rapid declines, both generally and in the context of Bd. Our results extend the findings of previous finer scale studies: we find that high‐altitude, restricted‐range, aquatic species with low fecundity are most likely to suffer Bd‐related declines. We use our findings to identify those species most at risk of Bd‐related declines and global extinction in the future, and identify areas where many species are predicted to be susceptible. Identifying susceptible species in advance of their decline is particularly important in setting priorities when, as here, declines are hard to arrest once underway.
RNA packaging and uncoating in simple single-stranded RNA viruses

Simple (non-enveloped) small, positive-sense single-stranded RNA viruses infect hosts from all kingdoms of life. However, their assembly and uncoating processes remain poorly understood. For turnip crinkle virus (TCV), 3D reconstructions by cryoelectron microscopy (cryo-EM) are shown for the native and the expanded form. The expanded form is a putative disassembly intermediate and exhibits pores that are large enough to allow exit of single-stranded RNA. Biochemical experiments revealed the expanded form is protease-sensitive, although the RNA genome remains protected from ribonuclease. Virus particles complexed with ribosomes are shown by negative stain EM. Proteolysis causes release of some coat protein from the capsid, while the capsid remains largely intact. Proteolysed particles have lost their icosahedral symmetry and show a protuberance in negative stain EM. Taken together, these results suggest expansion and subsequent proteolysis are essential steps in the uncoating process of TCV, and that the capsid plays multiple roles consistent with ribosome-mediated genome uncoating to avoid host anti-viral activity. Similarly, 3D cryo-EM reconstructions are presented for native equine rhinitis A virus (ERAV) an expanded particle containing no RNA. The native virus fits well with the ERAV crystal structure. The empty particle is a putative disassembly intermediate representing a stage after the release of the RNA genome. A mechanism is suggested that is consistent with the RNA release from the endosome without exposure to the endosomal contents. A crystal structure is presented of satellite tobacco necrosis virus (STNV) virus-like particles containing a small RNA fragment. The coat protein structure is identical to that of native STNV. Although density internal to the coat protein shell has been observed in the experiment that corresponds to earlier experiments, no unambiguous RNA structure can be built into the density. Together, the results presented here shed some light on the life cycle of three of these viruses.
EXPRESSION OF GASTRIN-17, PEPSINOGEN I AND II AND HELICOBACTER PYLORI IgG IN A SRI LANKAN DYSPEPTIC PATIENT POPULATION USING GASTROPANEL

Objective: This study was aimed to assess the usefulness of Gastropanel assay, an ELISA-based non-invasive diagnostic technique, in diagnosis of H. pylori infection and disease severity in a Sri Lankan population. Methods: Blood specimens were collected from dyspeptic patients attending routine upper-gastrointestinal endoscopy at a tertiary care hospital. Serum Gastrin-17, Pepsinogen I and II were measured using the Gastropanel assay (Biohit Oyj, Finland). H. pylori infection was diagnosed using Gastropanel H. pylori-IgG (Biohit Oyj, Finland), histology and H. pylori-IgG (Bioactiva Diagnostica, Germany). Antral biopsies were histologically graded to determine the disease severity. Results: Among the dyspeptic population, H. pylori infection was diagnosed in 22 patients by histology and in another 15 by H. pyloriIgG assays. The expression of G-17, PG I and II did not show a significant difference between histologically confirmed H. pyloripositive patients and H. pylori-negative patients. The PG I/II ratio were normal in the World Journal of Pharmaceutical Research SJIF Impact Factor 8.074 Volume 7, Issue 5, 48-61. Research Article ISSN 2277– 7105 Article Received on 04 Jan. 2018, Revised on 25 Jan. 2018, Accepted on 15 Feb. 2018 DOI: 10.20959/wjpr20185-11214
N-Methyl-D-Aspartate Receptors

Discovered more than 70 years ago due to advances in electrophysiology and cell culture techniques, N-methyl-D-aspartate (NMDA) receptors remain the target of assiduous basic and clinical research. This interest flows from their intimate engagement with fundamental processes in the mammalian central nervous system and the resulting natural desire to understand how this receptor’s genetically encoded structural properties generate their distinctive functional features and how in turn these unique functional attributes play into the larger opus of physiological and pathological processes. From the overwhelming literature on the subject, the authors briefly outline contemporary understanding of the receptor’s evolutionary origins, molecular diversity, and expression patterns; sketch hypothesized correlations between structural dynamics, signal kinetics, and pathophysiological consequences; and highlight the breadth of processes in which NMDA receptors are implicated, many of which remain poorly understood. Continued developments in cryo-electron microscopy, whole-genome sequencing and editing, imaging, and other emerging technologies will likely confirm some of the current hypotheses and challenge others to produce a more accurate reflection of these receptors’ complex operation and myriad roles in health and disease.
A survey on Nosema apis infection in apiaries of Urmia, North-West of Iran.

The microsporidium Nosema apis is a protozoan parasite specific for the epithelial cells of the ventricles of adult bees. Nosemosis occurs throughout the world. Between February and May 2002-2003, samples were randomly collected twice from 20 apiaries in Urmia region North-West of Iran. During this survey total of 487 hives were examined for infection with N. apis. In the first stage of study (February 2002), no infection was seen in hives samples, but in second stage of same year (May 2002) the infection was seen in one apiary with 131 hives. In third and forth stage of study (February and May 2003) the infection was seen in one and 4 apiaries respectively. The results showed the low infection rate in the early months of the first year of study that it was increased in next year. The reason of high infection rate in the second year of the study can be the result of more rainy and cloudy days in this period comparing to the first year. This has caused the hone bees to stay more often in the hives and increase spores excreted and subsequently spore intake were raised.
Whole-transciptome analysis of [psi+] budding yeast via cDNA microarrays

Introduction: Prions of yeast present a novel analytical challenge in terms of both initial characterization and in vitro manipulation as models for human disease research. Presently, few robust analysis strategies have been successfully implemented which enable the efficient study of prion behavior in vivo. This study sought to evaluate the utilization of conventional dual-channel cDNA microarrays for the surveillance of transcriptomic regulation patterns by the [PSI+] yeast prion relative to an identical prion deficient yeast variant, [psi-]. Methods: A data analysis and normalization workflow strategy was developed and applied to cDNA array images, yielded quality-regulated expression ratios for a subset of genes exhibiting statistical congruence across multiple experimental repetitions and nested hybridization events. The significant gene list was analyzed using classical analytical approaches including several clustering-based methods and singular value decomposition. To add biological meaning to the differential expression data in hand, functional annotation using the Gene Ontology as well as several pathway-mapping approaches was conducted. Finally, the expression patterns observed were queried against all publicly curated microarray data performed using S. cerevisiae in order to discover similar expression behavior across a vast array of experimental conditions. Results: These data collectively implicate a low-level of overall genomic regulation as a result of the [PSI+] state, where the maximum statistically significant degree of differential expression was less than ±1 Log2(FC) in all cases. Notwithstanding, the [PSI+] differential expression was localized to several specific classes of structural elements and cellular functions, implying under homeostatic conditions significant up or down regulation is likely unnecessary but possible in those specific systems if environmental conditions warranted. As a result of these findings additional work pertaining to this system should include controlled insult to both yeast variants of differing environmental properties to promote a potential [PSI+] regulatory response coupled with co-surveillance of these conditions using transcriptomic and proteomic analysis methodologies.