Miracle-dz/UniFAR-FTUs huggingface dataset:
Trade-offs in response to environmental constraints among strains of Scenedesmus dimorphus - eScholarship

Trade-offs, or negative functional associations among traits that affect fitness, are fundamental to ecological and evolutionary processes and are the basis for non- neutral species diversity through niche differentiation. Recent studies indicate that trade-offs occur in multiple dimensions involving population limitation by alternative resources or abiotic constraints and may drive species interactions and structure ecological communities. I tested for multivariate trade-offs among 32 natural populations of the freshwater algae Scenedesmus dimorphus in response to light, phosphorus, salinity, nitrogen source (nitrate vs. ammonium) and the presence of pathogenic fungi. Surprisingly, no evidence of trade-offs was found and positive or neutral correlations were observed among strains in response to the treatments. Strains that grew the fastest and reached the highest density at steady state tended to be least affected by light limitation, phosphorus limitation, increased salinity, and switching to ammonium as the nitrogen source. This may suggest an absence of functional constraints in S. dimorphus that limit intraspecific variation in response to several important environmental factors, nutrients and energy availability. Trade-offs may occur with other potential limiting factors such as grazers or temperature. Further research is needed to identify important axes of differentiation that constrain diversification and coexistence among Scenedesmus genotypes
The Effect of Very Virulent Infectious Bursal Disease Virus on Immune Organs of Broilers Fed Moringa Oleifera Supplemented Feed

A study was conducted to evaluate the immune modulating effect of Moringa Oleifera Leave (MOL) feed supplementation in broilers. 240 day old Ross 308 hybrid broiler chicks were assigned into four groups (A, B, C and D) of 60 chicks each in a deep litter house. Groups A and B were fed with formulated broiler starter and broiler finisher feeds containing 5% MOL for 28 and 21 days, respectively, while groups C and D were fed with formulated broiler starter and broiler finisher feed without MOL for 28 and 21 days, respectively. Broilers in groups A and C were vaccinated intramuscularly with 0.5 ml of an inactivated vaccine of intermediate strain of Infectious Bursal Disease (IBD) at 14 and 21 days of age, respectively. Broilers in groups A, B and C were challenged intraocularly at 35 days of age with 0.05 ml of a live very virulent Infectious Bursal Disease Virus (vvIBDV). The Thymus to Body Index (TBI) of birds in group A was 1.09, 1.05 and 1.03 at 35, 38 and 42 days of age respectively, while those in group B had a TBI of 0.84, 1.02 and 0.89 at 35, 38 and 42 days of age respectively. The TBI of birds in group C were 1.04, 1.22 and 1.29 at 35, 38 and 42 days of age respectively, however, there was significant difference between group B and C (P < 0.02). Moringa oleifera leaves feed supplementation improved the bursa, spleen, harderian and thymus to body weight index of broilers. The MOL feed supplementation and inactivated vaccine did not prevent the atrophy of bursa, spleen and harderian gland against the negative effect of vvIBDV 7 days post infection.
Adaptation to a Space-variant Visuomotor Delay can Cause Neglect-like Effects on Drawing Symmetry

In daily interactions, our sensorimotor system accounts for spatial and temporal discrepancies between the senses. Functional lateralization between hemispheres causes differences in attention and control of action. In addition, differences in transmission delays between modalities affects motor control. Studies on hemispatial neglect syndrome suggest a link between temporal processing and lateral spatial biases. To understand this link, we studied participants who performed lateral reaching, and adapted to delayed visual feedback in either left, right, or both workspaces. We tested transfer of adaptation to blind drawing, and found that adaptation to left or both delay caused selective leftward elongation. In contrast, adaptation to right delay caused elongation in both directions. Arm dynamics alone cannot explain these findings, but a model of a combined attentional-motor asymmetry across the hemispheres explains our observations. This suggests a possible connection between laterality in delay processing and motor performances observed in cases of hemispatial neglect.
Changes in emergence parameters as a result of transporting sterile Queensland fruit fly 'Bactrocera tryoni' (Froggatt) (Diptera: Tephritidae) pupae

Emergence of sterile Queensland fruit fly was assessed at the Camden mass-production facility and at the Yanco release centre in New South Wales between November 2002 and January 2005. Pupal weight was positively and significantly related to the percentage emergence at both Camden and at Yanco. However, average emergence rates fell from 82.1% at Camden to 68.4% at Yanco. The date of larval hopping at Camden influenced percentage emergence. Pupal weights for the 4th, 5th and 6th days of larval hopping were more likely to significantly influence the percentage emergence of flies than it did on the first three days of hopping.
Estimating the age of western grey kangaroos (Macropus fuliginosus ocydromus)

Scientific studies and population management may benefit from knowledge of the age structure of a target population. We evaluated traditional and newly developed methods of estimating the age of kangaroos with data from 336 western grey kangaroos (Macropus fuliginosus) culled from a wild population in south-western Australia. We compared their ages based on molar progression with data on head, leg, and foot length, a balanced sum of all three measures, dried eye-lens weight, and molar wear score, and derived formulae to estimate age from each variable. Molar wear score has a linear relationship to molar progression and therefore leads to similar estimations of age, but requires only one complete arcade of molars. Because the relationships between age and the lengths of head, foot and leg are curvilinear, these become less reliable indicators of age with increasing age but the accuracy can be improved by considering a combination of the lengths of head, foot, and leg. Estimation of age from dried lens weight is more accurate than estimation from morphometry. The use of morphometry to estimate the age of kangaroos older than two years is more reliable than previously thought and requisite data can be collected from live animals. Where lethal methods are needed to collect samples, a largely intact skull, a single arcade of molars, or the lens extracted from one eye can reliably be used to estimate age.
Investment patterns and kinship cues in a cooperatively breeding bird

In cooperatively breeding species, ‘helpers’ provide care for other individuals’ offspring. Research into cooperative breeding, which initially asked the deceptively simple question ‘why? ’, has continued to provide insights in behavioural ecology thanks to the opportunities for adaptation and coevolution that are generated in these unusual societies. I explore some of these potential adaptations in detail, mainly through studying a population of riflemen Acanthisitta chloris, which are passerine birds endemic to New Zealand. Previous work showed that riflemen are kin-based, facultative cooperative breeders. Most help is provided by adult birds, who have dispersed from their natal territory, but commute short distances to provision at the nests of relatives. Help is associated with enhanced recruitment of related offspring, and thus considered likely to confer indirect fitness benefits. These conclusions are substantiated by my results. Provisioning by helpers is a special case of parental investment, and in Chapter 2 I characterise investment by rifleman carers. I find that sealed-bid and conditional cooperation models are inappropriate to describe investment in riflemen, and discuss possible reasons for this. I also demonstrate the validity of provisioning rate as a measure of food delivery in riflemen. In the following two chapters I test the hypothesis that helping drives adaptive sex allocation in cooperative breeders, first using data from riflemen, and then across 26 bird species. Surprisingly, the hypothesis is not supported in either case. In chapters 5 and 6 I consider how riflemen recognise their relatives in order to direct help to them. I identify candidate vocal and chemical kinship cues and test the responses of provisioning riflemen to olfactory manipulations and call playback. My findings have implications for measuring parental investment in birds; show interesting discrepancies with evolutionary theory, and illustrate opportunities and challenges in sensory ecology. These themes are discussed in the final chapter.
Tomato Grafting: A Global Perspective

Grafting of vegetable seedlings is a unique horticultural technology practiced for many years in East Asia to overcome issues associated with intensive cultivation using limited arable land. This technology was introduced to Europe and other countries in the late 20th century along with improved grafting methods suitable for commercial production of grafted vegetable seedlings. Tomato grafting is becoming a well-developed practice worldwide with many horticultural advantages. The primary motiva- tion for grafting tomato has been to prevent the damage caused by soilborne pathogens under intensive production system. However, recent reports suggest that grafting onto suitable rootstocks can also alleviate the adverse effects of abiotic stresses such as salinity, water, temperature, and heavy metals besides enhancing the efﬁciency of water and nutrient use of tomato plants. This review gives an overview of the scientiﬁc literatures on the various aspects of tomato grafting including important steps of grafting, grafting methods, scion–rootstock interaction, and rootstock-derived changes in vegetative growth, fruit yield, and quality in grafted plants under different growing conditions. This review also highlights the economic signiﬁcance of grafted tomato cultivation and offers discussion on the future thrust and technical issues that need to be addressed for the effective adoption of grafting.
Total phenolic content, antioxidant activity, and anthocyanin profile of sprouted onion powder

The effect of sprouting of onions on total phenolic content, antioxidant activity, and anthocyanin profile of freeze dried powders produced from Indian onion cultivars was examined. Sprouting was carried out at an average light intensity of 64 Lumen, average relative humidity of 80.2%, and average temperature of 15.22 °C for three weeks. Two way analyses of data revealed significant (P<0.05) effect of sprouting and cultivar on functional composition of freeze dried powders. In all sprouted powder samples, there were significant (P<0.05) enhancements in total phenolic content, total flavonoid content, vitamin C content, antioxidant activity, and colour due to increase in anthocyanin contents. The anthocyanin profile depicted an increase in total anthocyanin concentration in powders developed from all four cultivars with the highest increase in powder from PRO-6 (23.87–27.15 mg kg−1), followed by Punjab Naroya (9.97–12.92 mg kg−1), commercial (7.15–8.43 mg kg−1), and Punjab White cultivar (3.45–4.09 mg kg−1).
Brain Region Specificity of Mitochondrial Biogenesis and Bioenergetics Response to Nrf2 Knockdown: A Comparison Among Hippocampus, Prefrontal Cortex and Amygdala of Male Rat Brain

Nuclear factor (erythroid-derived 2)-like 2 (Nrf2) has been identified as the well-known coordinator of intracellular antioxidant defense system. Herein, we aimed to evaluate the effects of Nrf2 silencing on mitochondrial biogenesis markers peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α), nuclear respiratory factor-1(NRF-1), mitochondrial transcription factor A (TFAM) and cytochrome c as well activities of two enzymes citrate synthase (CS) and malate dehydrogenase (MDH) in three brain regions hippocampus, amygdala, and prefrontal cortex of male Wistar rats. Small interfering RNA (siRNA) targeting Nrf2 was injected in dorsal third ventricle. Next, western blot analysis and biochemical assays were used to evaluation of protein level of mitochondrial biogenesis factors and CS and MDH enzymes activity, respectively. Based on findings, whilst Nrf2-silencing led to notably reduction in protein level of mitochondrial biogenesis upstream PGC-1α in three brain regions compared to the control rats, the level of NRF-1, TFAM and cytochrome c remained unchanged. Furthermore, although Nrf2 silencing increased CS activity, activity of MDH significantly decreased in hippocampus and prefrontal cortex areas. Interestingly, CS and MDH activities in amygdala did not change after Nrf2 knockdown. In conclusion, the present findings highlighted complexity of interaction of Nrf2 and mitochondrial functions in a brain region-specific manner. However, by outlining the exact interaction between Nrf2 and mitochondria, it would be possible to find a new therapeutic strategies for neurological disorders related to oxidative stress.
Effect of age and sex on carcass characteristics and internal organ weights of scavenging chickens and helmeted guinea fowls

ABSTRACT The objective of the study was to determine the effect of age and sex on carcass characteristics and internal organ weights in scavenging guinea fowls and chickens. Ninety-six scavenging birds, purchased from farmers, were used comprising 48 guinea fowls and 48 chickens from communal farmers. Guinea fowls comprised 25 females and 23 males, with 21 growers and 27 adults. Chickens had 18 females and 30 males with 19 growers and 29 adults. Guinea fowls had heavier body weight and relative hot carcass and cold dressed weight than chickens and which increased with age. Breast and wing relative weights were higher in guinea fowls. Chickens recorded the higher weight of leg and drumstick than guinea fowls. The neck, feet and head weights were heavier in chickens except for the back which was similar to guinea fowls. Chickens had significantly higher abdominal fat than guinea fowls. Relative weights of the heart, liver, kidney, lung and gizzard were higher in chickens. Relative total intestinal weight and lengths of total intestines, small and large intestines were higher in chickens than in guinea fowls. Relative lengths of the intestines decreased with age. Chickens and guinea fowls could have different capacities to utilize scavengeable feed resources.
Avances sobre nutrición y fertilidad en ganado lechero: Revisión

En esta revision se analizan los ultimos antecedentes sobre la relacion entre la nutricion y fertilidad en ganado lechero. Se establece la importancia de los niveles de glucosa en el postparto temprano y su relacion con la fisiologia de algunas hormonas tales como la insulina, IGF-I y somatotrofina. Se resalta la importancia de la inmunosupresion durante el periparto y su relacion con el exceso de tejido adiposo que establece un estado pro-inflamatorio caracteristico asociado a la aparicion de enfermedades metabolicas y reproductivas que afectan el rendimiento productivo y la fertilidad del rodeo lechero.
Evaluation, Antioxidant, Antimitotic and Anticancer Activity of Iron Nanoparticles Prepared by Using Water Extract of Vitis Vinifera L. Leaves

The water extract of Vitis vinifera was used for the rapid synthesis of the iron nanoparticle, which is very simple and eco-friendly in nature. The UV-visible spectroscopy technique was employed to establish the formation of which inhibition onion root growth in a dose-dependent manner. A decrease in the mitotic index may indicate its genotoxic effect on Allium cepa root assay. Nanoparticle was studied for its in vitro anti-inflammatory and antioxidant activity using different models, all the testing, gave significant correlation existed between concentrations of the nanoparticle and percentage inhibition of protein denaturation and scavenging free radicals.n These results clearly indicate that iron nanoparticle is effective against inflammation and free radical-mediated disease.
Phytochimic Screening and characterization of the substances present in the extracts of two marine algas: Sargassum muticum (Yendo) Fensholt, 1955 and Cystoseira tamariscifolia (Hudson); Harvested from the bay of the star in Mauritania

Algaes are widely used products globally as medicinal products, cosmetic, and food condiment products. The natural substances derived have multiple interests. Among these compounds, secondary metabolites are to a large extent found. Phytochemical screening enabled us to demonstrate the presence of secondary metabolites in the plant tissues of our algae. The detection of these chemical compounds is based on tests of component solubility, precipitation and turbidity reactions, specific color change or ultraviolet light examination. In the present work, phytochemical characterizations of two macroalgae of the Mauritanian Atlantic coast (Baie de l'étoile) Have been carried out, to know; Sargassum muticum; Cystoseira tamariscifolia. The results obtained demonstrated the presence of several secondary metabolites which may be responsible for important biological properties.
Coalescent Species Tree Inference of Coluber and Masticophis

The genus-level taxonomy of the New World racers and whipsnakes (Coluber and Masticophis) has long been contentious regarding whether the two genera are mutually exclusive clades. This argument is based on morphological characters and largely single-locus analyses. Herein we examine the phylogenetic history of this group using multi-locus data in a coalescent framework, where paraphyly of Masticophis would result in support for the recognition of only a single genus (Coluber) for these species. We sample all currently recognized species and incorporate broad geographic sampling for the more widespread species groups to explore biogeographic patterns across North America. Our analyses suggest that Masticophis is monophyletic with respect to Coluber constrictor, albeit with low support. These results also demonstrate that there is undescribed cryptic diversity in this group, and we underscore additional avenues of study to further delimit unrecognized species in this clade. The biogeography of the island endemic, Masticophis anthonyi, is discussed with respect to what is known about other codistributed vertebrates. Lastly we provide an overview of the history of the arguments for or against the use of the generic name Masticophis and suggest its continued use.
Evolutionary insights into the host-­‐specific adaptation and pathogenesis of group B Streptococcus

Streptococcus agalactiae (group B Streptococcus, GBS) is a commensal of the intestinal and genitourinary tracts in the human population, while also a leading cause of neonatal infections. Likewise, GBS remains a serious concern in many countries as frequently responsible for bovine mastitis. Therefore, the purpose of my PhD project was to use state-of-the-art whole-genome approaches to decipher the host-specific adaptation and pathogenesis of GBS in both humans and bovines. By comparing the genomic profile of strains from infected newborns and their mothers we showed that the transmission of GBS from mother to child is accompanied in particular instances by the acquisition of specific pathoadaptive mutations. Moreover, from the study of the evolutionary forces acting on the human-specific and hypervirulent clonal complex (CC) 17, we reveal that various systems can evolve to improve the ability of GBS to survive in the human host. Functions related to metabolism, cell adhesion, regulation and immune evasion were among the most preferentially affected in GBS strains from human origin. Conversely, colonization of Portuguese dairy farms by one single CC61 clone for over 20 years highlighted that the specific regulation of iron/manganese uptake is a recurrent adaptive strategy in the bovine environment.
REGULATION OF STEM CELL FUNCTION IN THE ADULT BODY

Author(s): Peiris, Tanuja Harshani | Advisor(s): Oviedo, Nestor J | Abstract: Stem cells (SCs) distributed along the body have the capability to divide upon physiological demand and further differentiate into specialized cells that repair injured tissues. Thus, understanding regulatory mechanisms that control SC behavior during tissue repair and physiological demand is crucial for biomedical applications. Here we perform analysis of SCs in vivo, during tissue regeneration and physiological cellular turnover by using the planarian flatworm, Schmidtea mediterranea. Planarians provide an excellent model to explore fundamental aspects of cell regulation in their natural environment during adult tissue maintenance, regeneration and repair. In particular, I analyze components of (1) the TOR (Target of Rapamycin) and AKT pathway: an evolutionary conserved signaling system that has been implicated in cell cycle progression, metabolism, protein synthesis and cell growth. (2) DNA repair mechanisms. I have identified homologs for members of these pathways and designed a strategies to study their function with RNA interference (RNAi). Obtained results indicate that the TOR and AKT signaling is involved with controlling systemic SC behavior and can participate in physiological cell turnover but are unable to form regenerative blastema upon damage. Uniquely, TOR-independent SCs are capable of repairing damage by remodeling pre-existing tissue, which does not require active cell proliferation. Regional differences in cellular proliferation, migration and tissue repair exist along the anteroposterior (AP) axis in vertebrate and invertebrate animals. Despite years of research, the basic mechanisms controlling cell division and tissue repair along the body remain poorly understood. Loss-of-function genetic approaches allowed to identify mechanisms controlling regional differences in cell proliferation along the planarian AP axis. These results suggest interplay between DNA repair mechanisms and tumor suppressor genes as capable of regulating cell behavior in specific areas of the adult body. Here I explored the possibility of controlling tissue regeneration and repair by exploring interactions between DNA double-strand break repair mechanisms through Rad51, and the tumor suppressors p53 and the retinoblastoma pathways. We hope to expand these results to understand stem cell-directed regeneration of particular tissues to enable the implementation of effective biomedical approaches.
Novel inhibitors of dihydrodipicolinate synthase

ii ACKNOWLEDGMENTS . iii DEDICATION . iv TABLE OF CONTENTS . v LIST OF TABLES . viii LIST OF FIGURES . ix LIST OF SCHEMES. xiv LIST OF ABBREVIATIONS . xv CHAPTER 1.INTRODUCTION . 1 1.1 DHDPS as a herbicidal and antibiotic target . 1 1.2 Structure of DHDPS . 2 1.2.1 Active site and proposed catalytic mechanism . 2 1.2.2 Allosteric site and putative mechanisms of signal transduction . 4 1.3 Feedback inhibition of DHDPS by lysine in bacteria and plants . 6 1.3. 1 Kinetic models of lysine inhibition . 6 1.3. 2 DHDPS lacking lysine inhibition . 6 1.4 Inhibitors of DHDPS targeting the active site and the allosteric site . 7 1.5 Proposal and research objectives . 9 1.6 Contributions of the author to the work presented in this thesis . 11 1.7 References . 12 CHAPTER 2.DIHYDRODIPICOLINATE SYNTHASE FROM CAMPYLOBACTER JEJUNI: KINETIC MECHANISM OF COOPERATIVE ALLOSTERIC INHIBITION AND INHIBITOR-INDUCED SUBSTRATE COOPERATIVITY . 15 2.1 Permission to use this manuscript . 15 2.2 Abstract . 16 2.3 Introduction . 17 2.4 Materials and methods . 19 2.4. 1 ASA synthesis . 19 2.4. 2 Cloning of the dapA and dapB genes . 19 2.4. 3 Expression and purification of enzymes . 20 2.4. 4 Enzyme assays . 21 2.5 Results . 22 2.5. 1 Ping-pong mechanism . 22 2.5. 2 Lysine inhibition . 23 2.5. 3 Calculation of cooperativity coefficient for lysine . 24