Miracle-dz/UniFAR-FTUs huggingface dataset:
Janzen–Connell patterns can be induced by fungal‐driven decomposition and offset by ectomycorrhizal fungi accumulated under a closely related canopy

Summary 1.Seedlings near a conspecific adult might suffer increased mortality due to pressure from enemies such as belowground pathogenic fungi (Janzen-Connell Hypothesis), however variation exists among taxa such that some experience low levels of mortality. We hypothesized that seedlings close to adults might profit, rather than suffer, from belowground fungi, notably from mycorrhiza or decomposers, in particular near large adult trees and under a closely related canopy. 2.We planted oak seedlings in a temperate forest at different distances from adults and followed seedling mortality, budburst (early budburst permitting photosynthesis during the best light conditions) and leaf herbivory. We applied fungicide on half of the seedlings for 2 years to identify the net effect of belowground fungi on seedlings. We quantified seedling mycorrhization and fungal-driven decomposition of a neighbourhood-specific and an unspecific substrate, local oak leaves and cellulose, respectively. Finally, we related mycorrhization and decomposition to seedling performance. 3.We found that, in seedlings planted close to conspecific adults, belowground fungi had a negative net effect on seedlings: elimination of fungi, surprisingly, decreased herbivory. This effect could be due to oak leaf decomposition, which related to increased seedling herbivory and was higher near a conspecific adult. Under a closely related canopy, however, the net effect of belowground fungi on nearby seedlings became positive: elimination of fungi delayed budburst. This effect could be due to colonization by the ectomycorrhizal fungus Cortinarius sp. , which related to accelerated budburst and was higher near a conspecific under a closely related canopy. Effects of belowground fungi on nearby seedlings were not dependent on the size of the conspecific and were species- but not lineage-specific. 4.Overall, our results suggest that a Janzen-Connell-like pattern, i.e. increased mortality of seedlings near conspecific adult, can be (i) induced by specialist decomposers increasing the nutritional quality of conspecific seedlings to herbivores, and (ii) offset by ectomycorrhizal fungal mutualists under a closely related canopy. Coexistence among closely related adult trees appears to change interactions between adults and nearby conspecific seedlings from conspecific inhibition to conspecific facilitation. This article is protected by copyright. All rights reserved.
Production performance of four lines of Japanese quail reared under tropical climatic conditions of Tamil Nadu, India

This research investigated the growth and other production traits of four distinct lines (L1, L2, L3, and L4) of Japanese quail (Cortunix japanoica) kept in the tropical climate of Tamil Nadu, India. The traits related to body weight at different weeks and weight gain were measured in 180 birds (90 males and 90 females) per line up to the fifth week of age, and then 90 birds (females only) from the sixth to the 16th week of age, with egg production and feed efficiency parameters measured in 10 observations per line. The traits were analysed using the General Linear Model procedure, and Tukey’s HSD was used to test for statistical differences (p < 0.05) between the means for subclasses under a specific effect. The results revealed a highly significant difference (p < 0.01) in body weight from hatch to fifth week of age. At 5th week of age, the L3 and L2 did not differ (p > 0.05) based on Tukey test; therefore, both presented the highest values and were statistically significant (p < 0.01) with L4 with a lowest value of 203.62 g. The cumulative fifth week feed conversion ratio showed non-significant difference (p > 0.05) at first and second week, and highly significant difference (p < 0.01) from third to fifth week of age. The age at 50 per cent egg production was 60.2 (L4), 61.4 (L2), 65.1 (L3) and 66.0 (L1) days and the L1 egg production differed significantly (p < 0.01) from L4 line. The highest bodyweight (g) during the laying period (at 15 weeks of age) was observed in L2 (327.08) and L3 (326.54) and differed significantly (p < 0.01) from L1 (309.24) as well as L4 (288.69) lines. The mean egg weight (g) of different lines showed non-significant difference (p > 0.05) at all weeks, except at 11th week of age (p < 0.01). The mean feed consumption (g)/bird/day differed significantly (p < 0.01) from 6th to 16th week of age, except at sixth and eighth week of age, where it was non-significant (p > 0.05). The overall feed efficiency/dozen of eggs (from 6th to 16th weeks) ranged from 1.33 (L1) to 1.98 (L3). The livability from 6 to 16 weeks of age was 100 per cent in all the lines. In order to boost Japanese quail production in the tropics, L3 and L4 may be selected for body weight and egg production, respectively.
WEED MANAGEMENT IN AEROBIC RICE: ROLE OF ESTABLISHMENT METHODS AND HERBICIDES

SUMMARY Weed management in rice depends on establishment method and proper selection of herbicide. A field experiment was conducted during dry seasons of 2013 and 2014 to develop a robust strategy for effective weed management in aerobic rice system for tropical rice belts. The efficacy of post-emergent herbicides bispyribac-sodium, azimsulfuron and flucetosulfuron were evaluated under different rice establishment methods (row sowing, spot seeding and broadcasting). Grass weed species constituted 58–68% of the total weed density across the establishment methods in the weedy check treatment. The total weed density and weed biomass were lowest in spot seeding with azimsulfuron (35 g active ingredient (a.i.) ha−1) 30 and 60 days after sowing. Among herbicides, use of azimsulfuron caused the highest grain yield (5.2 Mg ha−1), realizing 72% increase in grain yield over the weedy check. Yields in row sowing and spot seeding were similar and the same was verified when comparing yields in plots treated with bispyribac-sodium and azimsulfuron. Based on our findings and considering both weed presence and grain yield, azimsulfuron in spot seeding can be recommended in aerobic rice.
Comparative study of size exclusion chromatography for isolation of small extracellular vesicle from cell-conditioned media, plasma, urine, and saliva

Introduction: Extracellular vesicles (EVs) are secreted from all types of cells and are involved in the trafficking of proteins, metabolites, and genetic material from cell to cell. According to their biogenesis and physical properties, EVs are often classified as small EVs (including exosomes) or large EVs, and large oncosomes. A variety of methods are used for isolated EVs; however, they have several limitations, including vesicle deformation, reduced particle yield, and co-isolate protein contaminants. Here we present an optimized fast and low-cost methodology to isolate small EVs (30–150 nm) from biological fluids comparing two SEC stationary phases, G200/120 and G200/140 columns. Methods: The optimization parameters considered were a) the selection of the stationary phase, b) the eluate volume per fraction, and c) the selection of the enriched 30–150 nm EVs-fractions. The efficiency and separation profile of each UF/SEC fraction was evaluated by Nanoparticle tracking analysis (NTA), flow cytometry, total protein quantification, and Western blot. Results: Both columns can isolate predominantly small EVs with low protein contaminants from plasma, urine, saliva, and HEK293-derived EV from collection medium. Column G200/ 40 offers a more homogeneous enrichment of vesicles between 30 and 150 nm than G200/120 [76.1 ± 4.4% with an average size of 85.9 ± 3.6 nm (Mode: 72.8 nm)] in the EV collection medium. The enrichment, estimated as the vesicle-to-protein ratio, was 1.3 × 1010 particles/mg protein for G200/40, obtaining a more significant EVs enrichment compared to G200/120. The optimized method delivers 0.8 ml of an EVs-enriched-outcome, taking only 30 min per sample. Using plasma, the enrichment of small EVs from the optimized method was 70.5 ± 0.18%, with an average size of 119.4 ± 6.9 nm (Mode: 120.3 nm), and the enrichment of the vesicle isolation was 4.8 × 1011 particles/mg protein. The average size of urine and saliva -EVs samples was 147.5 ± 3.4 and 111.9 ± 2.5 nm, respectively. All the small EVs isolated from the samples exhibit the characteristic cup-shaped morphology observed by Transmission electron microscopy (TEM). Discussion: This study suggests that the combination of methods is a robust, fast, and improved strategy for isolating small EVs.
Streptococcus pyogenes infection and the human proteome with a special focus on the IgG-cleaving enzyme IdeS

Infectious diseases are characterized by a complex interplay between host and pathogen, but how these interactions impact the host proteome is unclear. Here we applied a novel mass spectrometry based proteomics strategy to investigate how the human proteome is transiently modified by the pathogen Streptococcus pyogenes, with a particular focus on bacterial cleavage of IgG in vivo. In invasive diseases, S. pyogenes evokes a massive host response in blood, whereas superficial diseases are characterized by a local leakage of several blood plasma proteins at the site of infection including IgG. S. pyogenes produces IdeS, a protease cleaving IgG in the lower hinge region and we find highly effective IdeS-cleavage of IgG in samples from local IgG poor microenvironments. The results show that IdeS contributes to the adaptation of S. pyogenes to its normal ecological niches. Additionally, the work identifies novel clinical opportunities for in vivo pathogen detection.
Association of automatic milking systems milking frequency in primiparous and multiparous cows with their yield and milkability

ABSTRACT The aim of the study was to determine the association of automatic milking systems milking frequency (≤2.40, 2.41–2.80 and >2.80 times/day) in primiparous and multiparous cows with their daily milk yield and milkability. The analysis included of the milk production level and the interaction between milking frequency per day and daily milk yield. Regardless of the daily production level, most primiparous cows were milked 2.41–2.80 times/day and most multiparous cows >2.80 times/day. Higher daily milk yield and a more favourable effect of increasing milking frequency on this parameter were observed in multiparous cows, with an increase from 29.7 kg (milking frequency ≤2.40 times/day) to 31.1 kg milk (>2.80 times/day). In primiparous cows, this increase was smaller and amounted to 0.8 kg milk (from 29.2 to 30.0 kg).
A new species of Murina (Chiroptera: Vespertilionidae) from sub-Himalayan forests of northern Myanmar

A new species of Murina of the suilla- type is described from the Hkakabo Razi Landscape, Kachin, Upper Myanmar, an area that is currently being nominated as a World Heritage Site. The new species is a small vespertilionid, with a forearm length of 29.6 mm, and is very similar to M. kontumensis , which was recently described from Vietnam. However, it is distinguishable by a combination of external and craniodental morphology and genetics. The DNA Barcode reveals that the new species clusters sisterly to M. kontumensis but with a genetic distance of 11.5%. A single known specimen of the new species was collected from a lowland forest area in the plains of the Hkakabo Razi landscape, south-eastern Himalaya. Additional information on ecology, echolocation, and conservation are included. The high cryptic diversity of the genus Murina in Southeast Asia, as well as the Hkakabo Razi Landscape being a bat diversity hotspot, is highlighted.
Spatial Genetic Structure under Limited Dispersal: Theory, Methods and Consequences of Isolation-by-Distance

Isolation-by-distance is a specific type of spatial genetic structure that arises when parentoffspring dispersal is limited. Many natural populations exhibit localized dispersal, and as a result, individuals that are geographically near each other will tend to have greater genetic similarity than individuals that are further apart. It is important to identify isolation-by-distance because it can impact the statistical analysis of population samples and it can help us better understand evolutionary dynamics. For this dissertation I investigated several aspects of isolation-by-distance. First, I looked at how the shape of the dispersal distribution affects the observed pattern of isolation-by-distance. If, as theory predicts, the shape of the distribution has little effect, then it would be more practical to model isolation-by-distance using a simple dispersal distribution rather than replicating the complexities of more realistic distributions. Therefore, I developed an efficient algorithm to simulate dispersal based on a simple triangular distribution, and using a simulation, I confirmed that the pattern of isolationby-distance was similar to other more realistic distributions. Second, I developed a Bayesian method to quantify isolation-by-distance using genetic data by estimatingWright’s neighborhood size parameter. I analyzed the performance of thismethod using simulated data and amicrosatellite data set from two populations of Maritime pine, and I found that the neighborhood size estimates had good coverage and low error. Finally, one of the major consequences of isolation-by-distance is an increase in inbreeding. Plants are often particularly susceptible to inbreeding, and as a result, they have evolved many inbreeding avoidance mechanisms. Using a simulation, I determined which mechanisms are more successful at preventing inbreeding associated with isolation-by-distance.
Cool-Season Weed Control Using Ammonium Nonanoate and Cultivation in Organic Vidalia® Sweet Onion Production

Abstract Ammonium nonanoate is registered for weed control in certified organic cropping systems and may be useful to control cool-season weeds in organic Vidalia® sweet onion production. Ammonium nonanoate combined with tine-weeder cultivation was evaluated for weed control in organic onion in Georgia. There were no statistical interactions between main effects of herbicides and cultivation with a tine weeder for cool-season weed control and onion yield, indicating that ammonium nonanoate does not improve weed control compared with cultivation. Ammonium nonanoate at 4% and 6% did not adequately control weeds and onion yields were reduced. Ammonium nonanoate at 8% and 10% controlled cutleaf evening-primrose and lesser swinecress equal to the standard of d-limonene (14%), but the degree of control did not consistently protect onion yields from losses due to weeds. These results are in agreement with previous studies using clove oil and pelargonic acid. There is no advantage to using ammonium nonanoate for cool-season weed control in organic Vidalia® sweet onion production. Nomenclature: Ammonium nonanoate; clove oil; d-limonene; pelargonic acid; cutleaf evening-primrose, Oenothera laciniata Hill; lesser swinecress, Coronopus didymus (L.) Sm. ; dry-bulb onion, Allium cepa L.
Environment and dispersal influence changes in species composition at different scales in woody plants of the Western Ghats, India

Question What are the relative roles of environmental and spatial factors in influencing variation in species composition of tropical woody plants at different spatial scales? Location Tropical evergreen forests of the Western Ghats, South India. Methods Using a plot-based species inventory spanning the entire latitudinal extent (1200 km) of the Western Ghats’ wet evergreen forests, we collected primary data on spatial variation in species composition of woody plants. Each plot was characterized by a set of environmental descriptors consisting of topographic, edaphic and climatic variables, while eigenvector-based spatial variables and plot coordinates were used as spatial descriptors. We used ordination-based as well as distance-based variation partitioning techniques to partition the variation in species composition into components uniquely and jointly explained by environmental and spatial factors. Results The compositional similarity of woody plants largely showed a linear decline with log-geographic distance. However, this relationship was spatially structured. After controlling for the differences in environment, compositional similarity was found to be strongly associated with geographic distance only at the smallest spatial scale. Variation partitioning analysis revealed that environmental variables explained a much larger proportion of variation in species composition overall compared to spatial variables. Among environmental variables, climatic variables emerged as the most important predictors of variation in species composition at regional and landscape scales. Conclusions Strong association between compositional similarity and geographic distance at local scales indicates the influence of dispersal limitation, while niche differentiation seems to be a more important driver of variation in species composition at larger spatial scales. Overall, our results provide evidence for scale-dependent shifts in the relative importance of factors that are responsible for variation in species composition. This article is protected by copyright. All rights reserved.
Inherited arrhythmia syndromes From genotype to phenotype in hiPSC-derived cardiomyocytes

Brugada syndrome (BrS) is a rare cardiac rhythm disorder associated with sudden cardiac death. Mutations in the sodium channel gene SCN5A are found in ~20 % of cases while mutations in other genes collectively account for < 5 %. In the remaining patients the genetic defect and the underlying pathogenic mechanism remain obscure. To provide insight into the mechanism of BrS in individuals without identified mutations, we here studied electrophysiological properties of cardiomyocytes (CMs) generated from human induced pluripotent stem cells (hiPSCs) from 3 BrS patients who tested negative for mutations in the known BrS-associated genes. Patch clamp studies revealed no differences in sodium current (I Na ) in hiPSC-CMs from the 3 BrS patients compared to 2 unrelated controls. Moreover, action potential upstroke velocity (V max ), reflecting I Na , was not different between hiPSC-CMs from the BrS patients and the controls. hiPSC-CMs harboring the BrS-associated SCN5A-1795insD mutation exhibited a reduction in both I Na and V max , demonstrating our ability to detect reduced sodium channel function. hiPSC-CMs from one of the BrS lines demonstrated a mildly reduced action potential duration, however, the transient outward current (I to ) and the L-type calcium current (I Ca,L ), both implicated in BrS, were not different compared to the controls. Our findings indicate that ion channel dysfunction, in particular in the cardiac sodium channel, may not be a prerequisite for BrS.
Coronavirus proteins and their directed evolution to inhibit virus replication

Coronaviruses are enveloped, positive sense, RNA viruses that infect many species of animals, including humans. Of the six coronaviruses that can infect humans, SARS-CoV and MERS-CoV are the etiological agents of most concern currently. Coronaviruses possess the most complex and largest RNA genomes among all RNA viruses. The genome contains up to 15 genes with multiple open reading frames (ORFs) encoding both structural and non-structural proteins. Coronaviruses encode about 30 proteins that play specific, and often essential, roles in viral replication and assembly. This thesis presents work done to express Murine hepatitis virus strain A59 (MHVA59) proteins such as Nucleoprotein and membrane genes, non-structural proteins (5,6,7,8,9,10,16) from gene1, part of non-structural proteins (Plpro, Y-domain from nsp3 and N-terminal from nsp12) and RdRp from C-terminal part of nsp12 in E. coli BL21 cells and mammalian 17clone-1 cells, the latter of which are permissive for MHV-A59. The efficiency of transfection and expression of the proteins in mammalian cells was evaluated. SUMOStar (small ubiquitin-like modifier) fusion technology was used to enhance protein expression in the eukaryotic system. Expressed proteins were detected by Western blot with an anti-His tag antibody. The ability of virus-expressed proteins to interfere with virus infection was tested and an inhibitory effect was detected by plaque assay. The coronavirus nucleoprotein (N) is an important component for both viral replication and transcription. Error-prone PCR (ep-PCR) was used with the N protein as template to introduce random error and the number of mutations introduced was calculated after 100 random colonies were sequenced to validate the mutagenesis. Transient expression of N protein was shown to increase the efficiency of infection and virus yield. The function of N was investigated by screening for dominant-negative N mutants, using a library of N variants constructed using ep-PCR. The cytotoxicity of N variants was tested by MTT assay. Expressed N variants showed a range of effects ranging from a 10-fold increase in virus yield associated with the wild type N to 10-fold inhibition of virus growth. One particular N variant, mut38, was non-toxic, but reproducibly inhibited virus growth. The potential to screen for dominant-negative N variants using cell survival was also assessed using different N libraries. The thesis also investigated different strategies aimed at purification of non-structural protein 16 (nsp16). The overall findings suggest an ability of virus-expressed proteins in eukaryotic cells to interfere with virus infection and demonstrate that such antiviral activity can be generated by mutating an important viral protein.
Functional annotation of selected Theileria parva hypothetical proteins without known sequence descriptions and pathway associations

ii DECLARATION . iii ACKNOWLEDGEMENTS . iv TABLE OF CONTENTS . v LIST OF FIGURES . vii LIST OF TABLES . viii LIST OF OUTPUTS . ix CHAPTER 1 . 1 1.1. BACKGROUND . 1 1.2. LITERATURE REVIEW . 3 1.2.1. Theileria parasites . 4 1.2.2. Disease Syndromes Resulting From Theileria parva Infections . 6 1.2.2.1. East Coast fever (ECF) . 6 1.2.2.2. Corridor Disease . 6 1.2.2.3. January disease . 7 1.2.3. Life Cycle of Theileria parva . 7 1.2. 4. Control and Treatment of Theileria parva Infections . 9 1.2. 5. Whole-Genome Sequencing of Theileria parva . 10 1.2. 6. Analysis of Theileria parva Transcriptome . 12 1.2. 7. Hypothetical Proteins . 13 1.2. 8. Computational Biology . 13 1.2. 8.1. Biological features exploited in in silico methods for protein function prediction . 14 1.3 PROBLEM STATEMENT/HYPOTHESIS. 27 1.3.1. Project Objectives . 28 CHAPTER 2 . 29 2.0 MATERIALS AND METHODS . 29 2.1. Experimental Design . 32 2.2 Experimental Procedures . 33 2.2.1. Selection and retrieval of sequences . 33 2.2.2. Classification of proteins into canonical functional families . 33 2.2.3. Characterisation of the physicochemical properties . 34 2.2. 4. Sub-cellular localisation prediction . 34 2.2. 5. Identification of secreted proteins . 36 2.2. 6. Sequence comparisons . 37 © University of Pretoria vi 2.2. 7. Predictions of domains . 38 2.2. 8. Detection of virulence factors . 38 2.2. 9. Protein-protein interaction network . 39 2.2.10. Prediction of 3D-structures the of HPs . 39 2.2.11. Performance assessment . 40 CHAPTER 3 . 41 3.0. RESULTS . 41 3.1. Selection of HPs . 41 3.2. Predicted Functional Families . 41 3.3. Physiochemical Properties Characterisation . 49 3.4. Subcellular Localisation . 51 3.4. 1. Confirmation of the nuclear, mitochondrial and membrane-associated proteins . 51 3.4. 1.1. Nuclear proteins . 51 3.4. 1.2. Mitochondrial proteins . 51 3.4. 1.3. Membrane-associated proteins . 51 3.4. 1.4. Detection of secreted/secretome analysis . 53 3.5. Sequence Comparisons . 53 3.5. 1. Detection of homologs of hypothetical protein sequences . 53 3.5. 1.1. Homology confirmation . 55 3.5. 2. Orthology analysis . 66 3.6. Prediction of Domains . 68 3.7. Virulence factors detection. 69 3.8. Protein-Protein Network Predictions . 75 3.9. Prediction of 3D-structures . 76 3.10 Performance Assessment . 76 CHAPTER 4 . 77 4.0 DISCUSSION . 77 CONCLUSION . 90 STUDY LIMITATIONS . 91 FUTURE RECOMENDATIONS . 93 REFERENCES . 94 APPENDIX . 109 © University of Pretoria