Miracle-dz/UniFAR-FTUs huggingface dataset:
Advances in biotechnology: Genomics and genome editing

Abstract Genomics, the study of genes, their functions and related techniques has become a crucial science for developing understanding of life processes and how they evolve. Since the advent of the human genome project, huge strides have been made in developing understanding of DNA and RNA sequence information and how it can be put to good use in the biotechnology sector. Newly derived sequencing and bioinformatics tools have added to the torrent of new insights gained, so that ‘sequence once and query often’ type DNA apps are now becoming reality. Genome editing, using tools such as CRISPR/Cas9 nuclease or Cpf1 nuclease, provide rapid methods for inserting, deleting or modifying DNA sequences in highly precise ways, in virtually any animal, plant or microbial system. Recent international discussions have considered human germline gene editing, amongst other aspects of this technology. Whether or not gene edited plants will be considered as genetically modified remains an important question. This will determine the regulatory processes adopted by different groups of nations and applicability to feeding the world’s ever growing population. Questions surrounding the intellectual property rights associated with gene editing must also be resolved. Mitochondrial replacement therapy leading to ‘3-Parent Babies’ has been successfully carried out in Mexico, by an international team, to correct mother to child mitochondrial disease transmission. The UK has become the first country to legally allow ‘cautious use’ of mitochondrial donation in treatment. Genomics and genome editing will continue to advance what can be achieved technically, whilst society determines whether or not what can be done should be applied.
Biodiversity patterns and ecological processes in Neotropical dry forest: the need to connect research and management for long-term conservation

Neotropical dry forests are among the most diverse and threatened ecosystems worldwide. The extent and knowledge of Neotropical dry forests are quite heterogeneous with forests located in the Ecuadorian province especially diverse, threatened and poorly studied. In this work, we review patterns and conservation status of biodiversity, ecosystem processes and human perception of tropical dry forest of the Ecuadorian province. We found that patterns of biodiversity, endemism and conservation status are generally poorly studied. Overall, these forests provide habitat for at least 900 species including trees, birds, mammals, amphibians and reptiles. On average 18% of these species (range 6–25%) are endemic to the region and 25% (3–50%) are recognized as threatened. Little is known about groups such as invertebrates, fish, fungi, or herbaceous plants, and as well as about processes generating and maintaining critical ecosystem functions. Available literature points out the importance of positive ecological interactions such us plant–frugivore and plant–plant facilitation interactions in maintaining the regeneration dynamics of these forests. Faced by the formative state of knowledge about basic biodiversity patterns and ecological functions, the implementation of ecosystem risk assessment under the IUCN criteria for the Red List of Ecosystems may offer constructive means to organize, integrate and advance existing knowledge and conservation priorities for dry forests of the Ecuadorian province. With examples of existing conflicts between people and protected areas, we emphasize the importance of consultation and involvement of local communities in the development of conservation measures including new protected areas. Lastly, we reflect on some encouraging examples where ecosystem goods and services provided by these forests may be used in a sustainable manner, contributing to local communities’ income and preserving biodiversity. In this regard, we highlight how the interaction between research and innovation together with local management may lead to sustainable development and, thus, encourage these sectors to work together for the conservation of dry forests of the Ecuadorian province.
Effects of age and nutritional status at mating on the reproductive and productive traits in Suffolk sheep kept under permanent outdoor management system

Ptáček M. , Ducháček J., Stádník L. , Fantová M. (2017): Effects of age and nutritional status at mating on the reproductive and productive traits in Suffolk sheep kept under permanent outdoor management system. Czech J. Anim. Sci., 62, 211–218. This study examined the variability of reproductive and productive traits in Suffolk sheep (a commercial flock, n = 316 ewes) with regard to the dams’ age or the nutritional status of sheep at mating under a year-round outdoor management. Data were collected across a 3-year monitoring period (totally 655 observations). The fixed effects of dam’s age (dams grouped as: 2, 3, 4, 5, 6 years and older), ewe’s live weight (LW; ewes grouped as: < 72 kg; 72–83 kg; > 83 kg), and backfat thickness at mating (BT; ewes grouped as: < 7.9 mm; 7.9–10.5 mm; > 10.5 mm) were evaluated. The dam’s age influenced reproductive and productive traits such that 2and 6-year and older ewes reached the lowest values. Ewes with LW > 83 kg had significantly higher lambing rate (11.8%) compared to those with LW < 72 kg. The group of ewes with LW < 72 kg gave birth to a significantly lower number of live lambs in litter (–8.9%) in comparison with LW < 83 kg group. An increase (9.9%; P < 0.01) of total litter weight at birth or an increase (12.5%; P < 0.05) of total litter weight at 100 days of age were detected in LW > 83 kg group compared to LW < 72 kg group. BT > 10.5 mm ewes had by 8.9% lower lambing rate (P < 0.05), by 6.8% lower litter size (P < 0.05), by 14.5% lower number of live lambs in litter (P < 0.01), and by 8.6% lower total litter weight at birth compared to BT < 7.9 mm ewes. A significantly lower total litter weight at 100 days of age (–10.8%) and a significantly lower total litter gain from birth to 100 days of age (–11.5%) were detected in BT > 10.5 mm ewes in comparison to BT 7.9–10.5 mm ewes.
Seaweed liquid extracts effect on Salvia officinalis growth, biochemical compounds and water deficit tolerance

The foliar spray of seaweed liquid extracts (SLE) (Fucus spiralis and Ulva rigida) was applied at three different concentrations (12.5, 25 and 50) to the plants of Salvia plants (Salvia officinalis L.) submitted or not to water stress (moderate and severe stress). The application of seaweed extract significantly enhanced growth parameters. The highest plant height was obtained with application of 50% concentration of U. rigida,followed by 25% concentration of F. spiralis that resulted in 40 and 15% increases, respectively, compared to the control plants. The maximum dry weight was also achieved with the same concentration of seaweed extract. Improved photosynthetic pigment content such as chlorophyll a and chlorophyll b was also observed with seaweed extracts application. Total chlorophyll amount was enhanced to 2.15 and 1.62 times when the plants were sprayed with U. rigida (50%) and F. spiralis (25%) extracts, respectively. Water deficit effect on S. officinalis L was notably reduced by the application of seaweed extracts. Thus, under moderate stress, the plant showed an important reduction of total chlorophyll (55.34%) compared to plant treated with U. rigida extract (32%) and F. spiralis (33%). The lipid peroxidation was low pronounced in plants stressed and treated by seaweed extract. Hence, low content ofmalondialdehyde (MDA) (7.30 µM g-1 FW. and 5.7 µM g-1 FW.) was exhibited in plant stressed and treated with 50% of U. rigida extract and 25% of F. spiralis extract, respectively, compared to plant controls (13.99 µM g-1 FW). In conclusion, these data suggests that seaweed extract can be applied as natural fertilizer in agricultural sector. Key words: Fucus spiralis, growth parameters, Morocco, peroxidation, proline, Salvia officinalis, seaweed extract, Ulva rigida, chlorophyll.
A cell-topography based mechanism for ligand discrimination by the T-cell receptor

The T-cell receptor (TCR) triggers the elimination of pathogens and tumors by T lymphocytes. In order for this to avoid damage to the host, the receptor has to discriminate between thousands of peptide ligands presented by each host cell. Exactly how the TCR does this is unknown. In resting T-cells, the TCR is largely unphosphorylated due to the dominance of phosphatases over kinases expressed at the cell surface. When agonist peptides are presented to the TCR by major histocompatibility complex (MHC) proteins expressed by antigen-presenting cells (APCs), very fast receptor triggering occurs, leading to TCR phosphorylation. Recent work suggests that this depends on the local exclusion of the phosphatases from regions of contact of the T cells with the APCs. Here, we develop and test a quantitative treatment of receptor triggering reliant only upon TCR dwell-time in phosphatase-depleted cell-cell contacts constrained in area by cell topography. Using the model and experimentally-derived parameters, we find that ligand discrimination is possible but that it depends crucially on individual contacts being 400 nm in diameter or smaller, i.e. the size generated by microvilli. The model not only correctly predicts the relative signaling potencies of known agonists and non-agonists, but achieves this in the absence of conventional, multi-step kinetic proof-reading. Our work provides a simple, quantitative and predictive molecular framework for understanding why TCR triggering is so selective and fast, and reveals that for some receptors, cell topography crucially influences signaling outcomes. Significance statement One approach to testing biological theories is to determine if they are predictive. A simple, theoretical treatment of TCR triggering suggests that ligand discrimination by the receptor relies on just two physical principles: (1) the time TCRs spend in cell-cell contacts depleted of large tyrosine phosphatases; and (2) constraints on contact size imposed by T cells using finger-like protrusions to interrogate their targets. The theory not only allows agonistic and non-agonistic TCR ligands to be distinguished but predicts the relative signalling potencies of agonists with remarkable accuracy. This suggests that the theory captures the essential features of receptor triggering.
Seasonal Survey in Content of Aflatoxin M1 and Somatic Cell Count in Collected Raw Milk Samples from Qazvin Province, Iran

The presence of aflatoxin M1 (AFM1) and somatic cell (Sc) in milk and milk products is a public health concern; also, it is an important index for evaluating the quality and safety of milk. Therefore, monitoring their level in milk has high health importance. The aim of this study was to determine the content AFM1 and somatic cell count )Scc( in raw cow milk samples in Qazvin province during various seasons (warm and cold). In this cross sectional study, 92 raw cow milk samples (produced by six semi industrial farms) was randomly collected from milk collection centers in Qazvin province (Iran) during the warm and the cold seasons in 2016 (23samples for each season). All samples were examined by Enzyme-linked immunosorbent assay (ELISA) and somatic cell counter; the archived data were analyzed using ANOVA and Chi-square test. The results showed that all collected samples were contaminated with AFM1 and AFM1 in raw cow milk samples that were above the maximum residue limits (MRL) (Iran legal limit = 100 ng L-1) in %36.95 samples; in addition, the SCC was above the MRL (Iran legal limit = 500000 cell ml-1) in 45.65 % of milk samples. AFM1 Contamination in warm seasons (%52.17) was significantly higher than in cold seasons (%21.73) (P 0.05). According to the results of this research, comprehensive and careful supervising of the production and supply of milk and evaluation of AFM1 and Scc are necessary.
Dosimetric Comparison of Different Planning Techniques in Left-sided Whole-Breast Irradiation: A Planning Study

Purpose: This planning study compared the various dosimetric parameters of different types of intensity-modulated radiotherapy (IMRT) and volumetric-modulated arc therapy (VMAT) techniques for left-sided breast cancer radiotherapy. Materials and Methods: Treatment of 22 left-sided breast cases was planned using two IMRT and VMAT techniques for the prescription of 40 Gy in 15 fractions. For tangential IMRT (Tan_IMRT), five beams were placed as conventional tangential beams. For equally spaced IMRT (Equi_IMRT), six beams were placed equidistantly at 40° interval from 300° to 140°. For tangential VMAT (Tan_VMAT), two arcs were used with the avoidance sector in such a way that the beam covered like tangential fields. For full-arc VMAT (Full_VMAT), similar arcs as Tan_VMAT were used, without avoidance sector. All treatment plans were generated using Eclipse planning system for TrueBeam STx linear accelerator. For planning target volume (PTV), dose parameters including D95%,D99%,V105%,homogeneity index (HI), and conformity index (CI) were analyzed. Different dose parameters for the left lung, heart, left anterior descending artery (LAD), right lung, and right breast were also analyzed. In addition, low-dose spillage in the normal tissues and the number of monitor units (MUs) required for the treatment were compared. Results: IMRT technique exhibited superior D95%and D99%for PTV compared with VMAT techniques. VMAT plans provided more V105%(6%) compared with that of IMRT plans (approximately 1%). HI was better in IMRT plans (Tan_IMRT, 0.085 ± 0.015; Equi_IMRT, 0.094 ± 0.011) than in VMAT plans. CI was better in VMAT plans. The mean lung dose (7.7 Gy ± 1.788 Gy) and V5Gy(34.99% ± 6.799%) were better achieved in Tan_IMRT plan than other plans. Right lung, heart, and right breast sparing were better achieved in Tan_IMRT plan. Moreover, low-dose spillage was very less in the Tan_IMRT compared with all other techniques. Conclusion: Dosimetric comparison in this study showed that tangential IMRT technique is superior in terms of target coverage, sparing of lung, heart, and right breast, and low-dose spillage control in the left-sided breast-only radiotherapy.
Thrombosis Management and Challenges in COVID-19 Patients Presenting with Acute Coronary Syndromes

Thrombotic complications in patients with coronavirus disease 2019 (COVID-19) infection have been increasingly recognized, particularly those affecting the cardiovascular system. Patients with COVID-19 infection can suffer from increased coagulopathy as well as myocardial injury. In this review, we discuss these complications with special focus on management challenges in patients with acute coronary disease based on the available evidence from published literature.
Beneficial aspects of autism stemming from enhanced visuospatial skills: Result from a comparative study in India

Background: Autism spectrum disorder (ASD) is a relatively common neurodevelopmental disorder characterized by impairments in social interaction and communication, associated with restrictive and repetitive behaviors, interests, and activities. However, there are various positive character traits among individuals suffering from ASD – they are generally honest, decisive, and nonjudgmental. They are also reported to have excellent attention to details, which have been ascribed to their enhanced visual search skills. Aim: Our study was undertaken to assess these visuospatial perception skills among children with autism and compare the results with that of typically developing (TD) children in the Indian population. Materials and Methods: A total of 47 children with ASD and 47 age-, gender-, and education-matched TD children were assessed using tests for disjunctive and conjunction search, real-world visual search, and visual working memory. Results: Children with ASD performed significantly better than the TD children in tests for visual search and were comparable in the test for visual working memory. Conclusion: Our study showed that children with autism have enhanced visual skills, and this quality can be honed further and be utilized in jobs that require good observation skills and attention to details.
Expanding the language network: Domain-specific hippocampal recruitment during high-level linguistic processing

Language processing requires us to encode linear relations between acoustic forms and map them onto hierarchical relations between meaning units. Such relational binding of linguistic elements might recruit the hippocampus given its engagement by similar operations in other cognitive domains. Historically, hippocampal engagement in online language use has received little attention because patients with hippocampal damage are not aphasic. However, recent studies have found that these patients exhibit language impairments when the demands on flexible relational binding are high, suggesting that the hippocampus does, in fact, contribute to linguistic processing. A fundamental question is thus whether language processing engages domain-general hippocampal mechanisms that are also recruited across other cognitive processes or whether, instead, it relies on certain language-selective areas within the hippocampus. To address this question, we conducted the first systematic analysis of hippocampal engagement during comprehension in healthy adults (n=150 across three experiments) using fMRI. Specifically, we functionally localized putative “language-regions” within the hippocampus using a language comprehension task, and found that these regions (i) were selectively engaged by language but not by six non-linguistic tasks; and (ii) were coupled in their activity with the cortical language network during both “rest” and especially story comprehension, but not with the domain-general “multiple-demand (MD)” network. This functional profile did not generalize to other hippocampal regions that were localized using a non-linguistic, working memory task. These findings suggest that some hippocampal mechanisms that maintain and integrate information during language comprehension are not domain-general but rather belong to the language-specific brain network. Significance statement According to popular views, language processing is exclusively supported by neocortical mechanisms. However, recent patient studies suggest that language processing may also require the hippocampus, especially when relations among linguistic elements have to be flexibly integrated and maintained. Here, we address a core question about the place of the hippocampus in the cognitive architecture of language: are certain hippocampal operations language-specific rather than domain-general? By extensively characterizing hippocampal recruitment during language comprehension in healthy adults using fMRI, we show that certain hippocampal subregions exhibit signatures of language specificity in both their response profiles and their patterns of activity synchronization with known functional regions in the neocortex. We thus suggest that the hippocampus is a satellite constituent of the language network.
First record of Pseudopaludicola pocoto Magalhães, Loebmann, Kokubum, Haddad & Garda, 2014 (Anura, Leptodactylidae, Leiuperinae) in Bahia state, northeastern Brazil, with further data on its advertisement call

We report the first record of Pseudopaludicola pocoto from Bahia state, Brazil. In addition to the new distributional record, which fill gaps in the species distribution, new data and brief comments on its advertisement call are also provided. We also provide a map of the localities reported in the literature.
Natural killer cell responses to Plasmodium falciparum-infected red blood cells

NK cells are known to respond in vitro to P. falciparum-infected red blood cells (iRBCs), although responses are highly heterogeneous between donors. Although their role during malaria infection is not fully understood, they may play a role in cytokine production during early infection, and furthermore may interact with and kill iRBCs. The work described in this thesis examines the role of NK cell receptors in determining the functional outcomes of NK cell activation by iRBCs, focusing on NK cell responses to exogenous cytokines and the phenotypic and functional profiles of NK cells from malaria naive (LSHTM) and malaria exposed (Ugandan) subjects. In a model of early activation of NK cells by accessory cell-derived cytokines, I have shown a key role for IL-18 in mediating NK cell responses during both primary and secondary immune responses as IL-18 synergises with cytokines from the common gamma chain family. NK cells from LSHTM donors showed low background expression of IFN- and CD25, but responded to iRBCs by secretion of IFN-, which was potentiated by exogenous IL-15. By contrast, NK cells from Ugandan donors showed higher background CD25 expression and signs of in vivo/ex vivo preactivation and enhanced responsiveness to IL-15, but did not make any appreciable response to iRBCs. Potential explanations for these findings are explored and discussed. KIR genotype and KIR expression also varied between LSHTM and Ugandan donors. Specifically, expansions of KIR2DL1+ CD57+ NKG2C+ NK cell populations (possibly driven by human cytomegalovirus (HCMV) infection) were observed in the Ugandan donors. Conversely, percentages of KIR2DL3+ and 2DS4+ NK cells were higher among LSHTM donors, indicating that HLA genotype or allelic KIR polymorphisms may influence KIR expression. Finally, the formation of NK-iRBC conjugates, which may be a precursor to NK cellmediated killing of iRBCs, was observed in cells from nearly all donors, but did not correlate with other functional responses. Analysis of KIR expression and NK cell functional responses indicated that donors expressing inhibitory KIR2DL5 had reduced numbers of conjugates. Further experiments indicated that KIR2DL5 might be specifically upregulated after incubation with iRBCs, and that individuals carrying a normally non-expressed KIR2DL5 gene may be able to express this gene under certain circumstances. This tentatively suggests a role for KIR2DL5 during NK cell responses to malaria infection, and suggests a possible function for a common but frequently non-expressed gene. In summary, my work suggests that NK cell responses are strongly influenced by cytokine receptor and KIR expression, which in turn depend on NK cell maturation status. KIR expression patterns may in part explain differential NK responses to iRBCs between LSHTM and Ugandan donors. I also propose a possible role for KIR2DL5 in malaria infection, and a reason for the low expression of this gene in African populations.
Expression And Functions Of Il-24 And Socs3 In Pseudomonas Aeruginosa Keratitis In A C57bl/6 Mouse Model

EXPRESSION AND FUNCTIONS OF IL-24 AND SOCS3 IN PSEUDOMONAS AERUGINOSA KERATITIS IN A C57BL/6 MOUSE MODEL by BING XU August 2016 Advisor: Dr. Fu-shin Yu Major: Anatomy and Cell Biology Degree: Doctor of Philosophy The aim of this study was to elucidate the expression and functions of interleukin (IL)-24 and suppressor of cytokine signaling 3 (SOCS3), and their regulatory relationship in C57BL/6 mouse corneas in response to Pseudomonas aeruginosa (PA) infection. Among IL-20R cytokines, only IL-24 was induced at both mRNA and protein levels by the infection, and this upregulation was dampened by flagellin pretreatment. Time course studies revealed that IL-24 expression was markedly elevated, followed by a subsidence and second elevation, a pattern shared with SOCS3 but not IL-1β or IL-6. Silencing of IL-24 enhanced S100A8/A9 expression, and suppressed SOCS3, IL-1β, IL1RN, and MMP13 expression during an early stage of infection. Downregulation of IL-24 signaling pathway significantly reduced the severity of keratitis, bacterial burden, and neutrophil infiltration; while recombinant IL-24 exacerbated PA keratitis. Furthermore, SOCS3 knockdown impaired the control of PA keratitis. In vitro, while IL-1β induced the expression of SOCS3, IL-24, IL-1β, and IL-6, IL-24 only elicited robust expression of SOCS3 in primarily cultured human corneal epithelial cells. In conclusion, IL-24 promotes PA keratitis by inducing SOCS3 expression, resulting in the suppression of