Miracle-dz/UniFAR-FTUs huggingface dataset:
Replication of Severe Acute Respiratory Syndrome Coronavirus 2 in Human Respiratory Epithelium

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged by the end of 2019 and rapidly spread in 2020. At present, it is of utmost importance to understand the biology of the virus, rapidly assess the treatment potential of existing drugs, and develop new active compounds. While some animal models for such studies are under development, most of the research is carried out in Vero E6 cells. Here, we propose fully differentiated human airway epithelium cultures as a model for studies on SARS-CoV-2. ABSTRACT Currently, there are four seasonal coronaviruses associated with relatively mild respiratory tract disease in humans. However, there is also a plethora of animal coronaviruses which have the potential to cross the species border. This regularly results in the emergence of new viruses in humans. In 2002, severe acute respiratory syndrome coronavirus (SARS-CoV) emerged and rapidly disappeared in May 2003. In 2012, Middle East respiratory syndrome coronavirus (MERS-CoV) was identified as a possible threat to humans, but its pandemic potential so far is minimal, as human-to-human transmission is ineffective. The end of 2019 brought us information about severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emergence, and the virus rapidly spread in 2020, causing an unprecedented pandemic. At present, studies on the virus are carried out using a surrogate system based on the immortalized simian Vero E6 cell line. This model is convenient for diagnostics, but it has serious limitations and does not allow for understanding of the biology and evolution of the virus. Here, we show that fully differentiated human airway epithelium cultures constitute an excellent model to study infection with the novel human coronavirus SARS-CoV-2. We observed efficient replication of the virus in the tissue, with maximal replication at 2 days postinfection. The virus replicated in ciliated cells and was released apically. IMPORTANCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged by the end of 2019 and rapidly spread in 2020. At present, it is of utmost importance to understand the biology of the virus, rapidly assess the treatment potential of existing drugs, and develop new active compounds. While some animal models for such studies are under development, most of the research is carried out in Vero E6 cells. Here, we propose fully differentiated human airway epithelium cultures as a model for studies on SARS-CoV-2.
Variation of flour colour in Western Australia adapted wheat: comparative genomics, molecular markers and QTL analysis

The yellowness of flour colour ranges is an important quality trait in wheat for end-use products and is determined by the accumulation of carotenoids in the endosperm. The aims of this study were to develop EST-based molecular markers for genes encoding enzymes of the carotenoid biosynthetic pathway leading to xanthophyll accumulation and identify quantitative trait loci for flour colour (b*) and xanthophyll content in Western Australian adapted germplasm. A novel bioinformatic strategy was developed to identify rice genes encoding key enzymes of the carotenoid biosynthetic pathway and to predict wheat orthologues on the short arm of chromosome 3 or long arm of chromosome 7. The bioinformatic strategy involved the identification of rice carotenoid genes on BAC/PAC contigs aligned to wheat mapped ESTs. Rice genes predicted to have wheat orthologues were selected based on ESTs mapping to regions on wheat homoeologous chromosomes 3 and 7 known to be involved in flour colour. The rice genes predicted to have wheat orthologues were Geranylgeranyltransferase I beta-subunit (GGT-Ibeta) and Rab geranylgeranyltransferase component A (RGGT-A) on the short arm of chromosome 3, Lycopene beta-cylcase (LBC) on the long arm of chromosome 3 and Lycopene epsilon-cylcase (LEC) on the long arm of chromosome 7. The prediction of these wheat orthologues provided the basis for development of EST-based molecular markers for detecting variation in xanthophyll content. Wheat ESTs with unknown chromosomal locations and having the highest similarity to GGT-Ibeta, RGGT-A and LBC were selected for the development of molecular markers. No EST homologues were identified for LEC and therefore this gene was not further considered. Orthology was confirmed by sequencing and deletion lines were used to confirm chromosomal locations. Two partial orthologues of GGT-Ibeta were identified on the short arms of chromosomes 3B and 3D. A partial orthologue of RGGT-A was mapped to the proximal regions of the short and long arms of chromosome 3B. At least two or more orthologues of LBC were identified from nullisomic-tetrasomic lines. An EST-based molecular marker for GGT-Ibeta was found to be involved in minor variation of xanthophyll content in a Westonia*2/Janz doubled haploid population. QTL analysis from three doubled haploid populations indicated variation in WA-adapted germplasm may be due to different alleles controlling flour colour. QTLs for b* and xanthophyll content were found to coincide on the short arms of chromosomes 3A, 4D, and 7B and the long arm of chromosomes 7A and 7B in WA-adapted germplasm. Homoeologous expression of regions controlling variation in b* and xanthophyll content on the long arm of chromosomes 7A and 7B suggests the shut-down of genes in the same region on chromosome 7D. The main outcome of this study is flour colour and identification of gene orthologues in wheat controlling variation in xanthophyll content is complex most likely because of the interaction of the carotenoid biosynthetic pathway with other pathways.
Id Proteins Promote a Cancer Stem Cell Phenotype in Mouse Models of Triple Negative Breast Cancer via Negative Regulation of Robo1

Breast cancers display phenotypic and functional heterogeneity and several lines of evidence support the existence of cancer stem cells (CSCs) in certain breast cancers, a minor population of cells capable of tumor initiation and metastatic dissemination. Identifying factors that regulate the CSC phenotype is therefore important for developing strategies to treat metastatic disease. The Inhibitor of Differentiation Protein 1 (Id1) and its closely related family member Inhibitor of Differentiation 3 (Id3) (collectively termed Id) are expressed by a diversity of stem cells and are required for metastatic dissemination in experimental models of breast cancer. In this study, we show that ID1 is expressed in rare neoplastic cells within ER-negative breast cancers. To address the function of Id1 expressing cells within tumors, we developed independent murine models of Triple Negative Breast Cancer (TNBC) in which a genetic reporter permitted the prospective isolation of Id1+ cells. Id1+ cells are enriched for self-renewal in tumorsphere assays in vitro and for tumor initiation in vivo. Conversely, depletion of Id1 and Id3 in the 4T1 murine model of TNBC demonstrates that Id1/3 are required for cell proliferation and self-renewal in vitro, as well as primary tumor growth and metastatic colonization of the lung in vivo. Using combined bioinformatic analysis, we have defined a novel mechanism of Id protein function via negative regulation of the Roundabout Axon Guidance Receptor Homolog 1 (Robo1) leading to activation of a Myc transcriptional programme.
POSSIBILITY OF EARLY COMMENCEMENT OF TAPPING IN RUBBER (HEVEA BRASILIENSIS) USING DIFFERENT GENOTYPES AND TAPPING SYSTEMS

The feasibility of commencing tapping (‘opening’) of rubber trees for latex extraction at a lower stem girth (40 and 45 cm) than the currently recommended 50 cm was investigated in three different genotypes. The possibility of combining early opening with low frequency tapping and yield stimulation using Ethrel (LFT + E) was also examined. One of the genotypes tested, RRIC 121, gave a higher dry rubber yield, both per tapping and cumulatively over a given period, when opened at 40 cm than at 50 cm. Of the other two genotypes, one (RRISL 211) showed a clear reduction in yield with early opening, while the other (RRIC 102) did not show a significant yield response. Among the three genotypes tested, RRIC 121 showed the minimum depression in trunk girth increment. Analysis of yield components showed that the response of a given genotype to early opening and LFT + E is determined by the interaction between latex volume per tapping and dry rubber content (DRC), which were negatively correlated. RRIC 121 had a significantly greater DRC, which enabled it to maintain a higher dry rubber yield under early opening and LFT + E despite producing a lower latex volume than both the other genotypes. In contrast, despite producing a substantially greater latex volume than the other two genotypes, RRISL 211 did not produce a higher dry rubber yield because of its lower DRC. The higher DRC was also responsible for the greater response of RRIC 121 to yield stimulation with Ethrel, which reduced the plugging index and increased the initial latex flow rate. Early commencement of tapping in combination with LFT + E is therefore possible in rubber when amenable genotypes are selected, offering the potential of improving the economics of rubber production, especially for smallholders, in West Asia.
Stannic Oxide Nanoparticle Regulates Proliferation, Invasion, Apoptosis, and Oxidative Stress of Oral Cancer Cells

Objective To explore the effects of SnO2 nanoparticles (NPs) on proliferation, invasion, apoptosis, and oxidative stress of oral cancer. Methods SnO2 NPs were prepared and characterized. Oral cancer cell lines CAL-27 and SCC-9 were cultured in vitro. We detected the effects of various concentrations of SnO2 NPs (0, 5, 25, 50, 100, 200 μg/mL) on the proliferation of oral cancer cells, and observed the morphological changes, and measured the cells ability of migration, invasion and apoptosis condition, and the levels of oxidative stress were measured by detecting malondialdehyde (MDA) and reactive oxygen species (ROS). Besides, we also measured the changes of mRNA and protein levels of factors related to cell proliferation, migration, invasion, apoptosis, and oxidative stress. Results SnO2 NPs inhibited the proliferation of oral cancer cells in a concentration-dependent manner (all P < 0.05). And SnO2 NPs treatment could reduce the migration and invasion ability of cells (all P < 0.05), induce apoptosis, and those effects were better when treated for 48 h than 24 h (all P < 0.05). And SnO2 NPs could induce oxidative stress in cells (all P < 0.05). Besides, the concentrations of cyclin-D1, C-myc, matrix MMP-9, and MMP-2 in SnO2 NPs treated group was decreased (all P < 0.05), and the expression levels of cleaved Caspase-3, cleaved Caspase-9, and Cytochrome C were increased (all P < 0.05). Conclusion In the present study, we found that SnO2 NPs could play a cytotoxic role in oral cancer cells, and inhibit cell proliferation, migration, and invasion, and induce oxidative stress and apoptosis, which suggests that SnO2 NPs may have the effects of anti-oral cancer. However, a more in-depth study is needed to determine its roles.
Acid phosphatase activity of intact roots and phosphorus nutrition in plants. 2. Variations among wheat roots.

Variation in phosphatase activity (E.C. 3.1.3.41) in some cultivated wheats and wild progenitors was examined and a comparison made. The limits likely to occur in wheat were estimated, and the usefulness of phosphatase activity as an indicator of plant potential for exploiting low phosphorus status situations was explored. Under the test conditions, within the cultivated wheats, the phosphatase activity varied in optical density from 4.6 to 9.3 per g fresh weight (P < 0.001), and selections among wheats on this basis could be made. Phosphorus uptake and total dry matter yield were negatively related to phosphatase activity (r = - 0.80 and - 0.82 respectively, each P < 0. OOl), providing further supportive evidence of the proposition that plants with lower phosphatase activities may gain and use phosphorus more readily than plants with higher ones. The phosphatase activity of wild and cultivated progenitors of modern wheats ranged in optical density from 15.5 to 45.4 per g fresh weight. All the cultivated species had low phosphatase activities which, on the basis of the proposition, suggests that some unconscious selection for ability to use low fertility situations may have occurred with the domestication of wheat. On the other hand, there was no apparent grouping according to geographic origin of earlier cultivars used in Australia with respect to phosphatase activity to suggest any conscious selection for ability to grow well on low phosphorus status soils.
Reproductive biology, ecology and historic biogeography of selected rare and endagered Oxalis L. (Oxalidaceae) species

19 INTRODUCTION . 20 MATERIALS AND METHODS . 23 RESULTS . : . 27 DISCUSSION . 37 CONCLUSION . 46 REFERENCES . 46 APPENDIX 1 . 50 Stellenbosch University https://scholar.sun.ac.za
Use of Human Dental Pulp and Endothelial Cell Seeded Tyrosine-Derived Polycarbonate Scaffolds for Robust in vivo Alveolar Jaw Bone Regeneration

The ability to effectively repair craniomaxillofacial (CMF) bone defects in a fully functional and aesthetically pleasing manner is essential to maintain physical and psychological health. Current challenges for CMF repair therapies include the facts that craniofacial bones exhibit highly distinct properties as compared to axial and appendicular bones, including their unique sizes, shapes and contours, and mechanical properties that enable the ability to support teeth and withstand the strong forces of mastication. The study described here examined the ability for tyrosine-derived polycarbonate, E1001(1K)/β-TCP scaffolds seeded with human dental pulp stem cells (hDPSCs) and human umbilical vein endothelial cells (HUVECs) to repair critical sized alveolar bone defects in an in vivo rabbit mandible defect model. Human dental pulp stem cells are uniquely suited for use in CMF repair in that they are derived from the neural crest, which naturally contributes to CMF development. E1001(1k)/β-TCP scaffolds provide tunable mechanical and biodegradation properties, and are highly porous, consisting of interconnected macro- and micropores, to promote cell infiltration and attachment throughout the construct. Human dental pulp stem cells/HUVECs seeded and acellular E1001(1k)/β-TCP constructs were implanted for one and three months, harvested and analyzed by micro-computed tomography, then demineralized, processed and sectioned for histological and immunohistochemical analyses. Our results showed that hDPSC seeded E1001(1k)/β-TCP constructs to support the formation of osteodentin-like mineralized jawbone tissue closely resembling that of natural rabbit jaw bone. Although unseeded scaffolds supported limited alveolar bone regeneration, more robust and homogeneous bone formation was observed in hDPSC/HUVEC-seeded constructs, suggesting that hDPSCs/HUVECs contributed to enhanced bone formation. Importantly, bioengineered jaw bone recapitulated the characteristic morphology of natural rabbit jaw bone, was highly vascularized, and exhibited active remodeling by the presence of osteoblasts and osteoclasts on newly formed bone surfaces. In conclusion, these results demonstrate, for the first time, that E1001(1K)/ β-TCP scaffolds pre-seeded with human hDPSCs and HUVECs contributed to enhanced bone formation in an in vivo rabbit mandible defect repair model as compared to acellular E1001(1K)/β-TCP constructs. These studies demonstrate the utility of hDPSC/HUVEC-seeded E1001(1K)/β-TCP scaffolds as a potentially superior clinically relevant therapy to repair craniomaxillofacial bone defects.
High Light Induced Alka(e)ne Biodegradation for Lipid and Redox Homeostasis in Cyanobacteria

Cyanobacteria are the oldest photosynthetic microorganisms with good environmental adaptability. They are ubiquitous in light-exposed habitats on Earth. In recent years, cyanobacteria have become an ideal platform for producing biofuels and biochemicals from solar energy and carbon dioxide. Alka(e)nes are the main constituents of gasoline, diesel, and jet fuels. Alka(e)ne biosynthesis pathways are present in all sequenced cyanobacteria. Most cyanobacteria biosynthesize long chain alka(e)nes via acyl-acyl-carrier proteins reductase (AAR) and aldehyde-deformylating oxygenase (ADO). Alka(e)nes can be biodegraded by a variety of cyanobacteria, which lack a β-oxidation pathway. However, the mechanisms of alka(e)ne biodegradation in cyanobacteria remain elusive. In this study, a cyanobacterial alka(e)ne biodegradation pathway was uncovered by in vitro enzyme assays. Under high light, alka(e)nes in the membrane can be converted into alcohols and aldehydes by ADO, and aldehyde dehydrogenase (ALDH) can then convert the aldehydes into fatty acids to maintain lipid homeostasis in cyanobacteria. As highly reduced molecules, alka(e)nes could serve as electron donors to further reduce partially reduced reactive oxygen species (ROS) in cyanobacteria under high light. Alka(e)ne biodegradation may serve as an emergency mechanism for responding to the oxidative stress generated by excess light exposure. This study will shed new light on the roles of alka(e)ne metabolism in cyanobacteria. It is important to reduce the content of ROS by optimization of cultivation and genetic engineering for efficient alka(e)ne biosynthesis in cyanobacteria.
Effect of acetylated retrograded starch (resistant starch RS4) on the nutritional value and microstructure of the crumb (SEM) of wheat bread.

The objective of this study was to evaluate nutritional value and the microstructure of crumb of bread baked with three types of wheat flour with acetylated retrograded resistant starch preparation (RS4) obtained in the laboratory. The research material was three wheat flour type 550, 750 and 2000 incorporated with acetylated retrograded starch obtained in the laboratory with a degree of substitution DS = 0,16. Content of RS4 preparations in the achieved flour samples was 10, 20, 30and 40%. The control sample was wheat flour without additives (0%). The study assessed the nutritional value of bread on the basis of energy value, the total amount of digested starch (TDS) and total dietary fiber (TDF). Also carried pictures of bread crumb investigated using scanning electron microscopy (SEM). Breads baked with whole meal flour type 2000 were characterized by higher energy than breads made from flour lower type. Increasing the type of wheat flour resulted in a gradual decrease in the total amount of digested starch (TDS) in the breads. The consequence of increasing the share of resistant starch in the samples was a gradual increase in total dietary fiber (TDF). With the increase in the share of resistant starch in the samples were reduced energy value, and the total amount of digested starch (TDS). In the photograph of the control bread crumb made using a scanning electron microscope is shown forming the gluten network of pores of medium and large.
Effects of contaminated sediment on the epidermis of mummichog, Fundulus heteroclitus

Secretion of mucus by epidermal goblet cells protects fish against many biological, physical, and chemical insults encountered in the environment. This study monitored changes in hemoglobin concentration in epidermal mucus and in the density, diameter, and mucus quality of epidermal goblet cells in the mummichog, Fundulus heteroclitus, following exposure to creosote‐contaminated sediment from the Elizabeth River, Virginia, USA. Fish were exposed for 13 d in flow‐through aquaria to either uncontaminated (US) or contaminated (CS) sediments and were sampled periodically. The condition index was lower and the mortality rate and the occurrence of epidermal lesions were higher in CS‐exposed fish than in US‐exposed fish. Hemoglobin contents in epidermal mucus from the former group were significantly higher than from the latter. Significant reductions in both size and density of goblet cells in CS‐exposed fish suggested a mucus secretion rate exceeding its production rate. Significant changes in mucin types between treatments did not occur until day 13 and are not believed to be directly related to the creosote present in the contaminated sediment. These results all indicate that exposure to creosote‐contaminated sediment had a profound and deleterious effect on fish health.
Small RNA Deep Sequencing Identifies a Unique miRNA Signature Released in Serum Exosomes in a Mouse Model of Sjögren's Syndrome

Sjögren's Syndrome (SS) is an autoimmune disease characterized by lymphocytic infiltration and loss of function of moisture-producing exocrine glands as well as systemic inflammation. SS diagnosis is cumbersome, subjective and complicated by manifestation of symptoms that overlap with those of other rheumatic and ocular diseases. Definitive diagnosis averages 4–5 years and this delay may lead to irreversible tissue damage. Thus, there is an urgent need for diagnostic biomarkers for earlier detection of SS. Extracellular vesicles called exosomes carry functional small non-coding RNAs which play a critical role in maintaining cellular homeostasis via transcriptional and translational regulation of mRNA. Alterations in levels of specific exosomal miRNAs may be predictive of disease status. Here, we have assessed serum exosomal RNA using next generation sequencing in a discovery cohort of the NOD mouse, a model of early-intermediate SS, to identify dysregulated miRNAs that may be indicative of SS. We found five miRNAs upregulated in serum exosomes of NOD mice with an adjusted p < 0.05—miRNA-127-3p, miRNA-409-3p, miRNA-410-3p, miRNA-541-5p, and miRNA-540-5p. miRNAs 127-3p and 541-5p were also statistically significantly upregulated in a validation cohort of NOD mice. Pathway analysis and existing literature indicates that differential expression of these miRNAs may dysregulate pathways involved in inflammation. Future studies will apply these findings in a human cohort to understand how they are correlated with manifestations of SS as well as understanding their functional role in systemic autoimmunity specific to SS.
Metabolic Demands, Center of Mass Movement and Fractional Utilization of V˙O2max in Elite Adolescent Tennis Players During On-Court Drills

The aim of the study was to investigate the exercise intensity and energy expenditure during four types of on-court tennis drills. Five female and five male tennis players participated in the study (age: 17 ± 2 years; V∙O2max: 54 ± 6 ml·kg−1·min−1). Anthropometric measures were taken for each player and, on separate days, each player performed (i) treadmill running to determine V∙O2max and (ii) four different tennis drills (Drill1-4) during which V∙O2, blood lactate concentration, ratings of perceived exertion (RPE 6–20), and displacement of center of mass (m) using 3D kinematics were recorded. The drills were designed to simulate match play with 90 s of rest between each drill. A repeated two-way ANOVA was used for physiological and biomechanical data and Friedman's test for RPE using < α 0.05. Fractional utilization of V∙O2max was greatest during Drill1 81.8 ± 7.0% and lowest during Drill4 72.4 ± 5.2% (p < 0.001) with no difference between sexes (p > 0.05). The highest energy expenditure was during Drill1 and lowest during Drill4 (77 ± 15 and 49 ± 11 kcal, respectively, p < 0.05). Energy expenditure per meter for Drill1–Drill4 was subsequently reduced for each drill with 10.5 ± 2.1, 9.9 ± 2.2, 7.6 ± 1.7, and 8.0 ± 1.6 J·kg−1·m−1 (p < 0.01). There were no interaction effects for any of these variables. RPE (6–20) and blood lactate concentration post Drill1–Drill4 were 17.5, 15.5, and 13.0 (overall, legs and arms, p < 0.001) and 5.9 ± 2.0, 4.9 ± 1.9, 5.6 ± 2.0, and 5.0 ± 2.2 mmol·l−1 (p < 0.05). The findings of this study demonstrate that the on-court tennis drills performed here are suitable for high intensity training in junior tennis players. The energy expenditure per minute is comparable to similar sports whereas the energy expenditure per meter is notably greater.