Miracle-dz/UniFAR-FTUs huggingface dataset:
The molecular phylogeny of placental mammals and its application to uncovering signatures of molecular adaptation.

Considerable conflict remains in the literature as to the position of the root of placental mammals, and the placement of several intra-ordinal groups. Debate continues over the use of DNA or amino acids datasets and over the use of Supertree or Supermatrix approaches. Known phenomena exist within mammal data that complicate the reconstruction of phylogeny. These include (but are not limited to), variation in longevity, body size, metabolic rates, and germ-line generation time that result in variation in mutation rates and composition biases. Previous attempts to resolve the placental mammal phylogeny have used homogeneous evolutionary models that cannot capture and adequately describe these features across the species sampled. In this thesis I explore the properties of different datasets and data types and their suitability to the resolution of the mammal phylogeny at different depths: (i) the position of the root of the placental mammals, and (ii), the intraordinal placements within the Laurasiatheria. The datasets tested were (i) mitochondrial and nuclear data types, (ii) previously published datasets for mammals, and (iii), datasets I assembled specifically for analyses at different phylogenetic depths. I propose and apply the use of heterogeneous models to resolve the position of the root of the placental mammal phylogeny to these datasets. Reconstruction of a robust mammal phylogeny provides us with an essential framework for understanding the molecular underpinnings of adaptation to environment. The placental mammals display a huge variations in life traits such longevity, body size and DNA repair efficiency, since they emerged ~100 million years ago. With this robust phylogeny, I set out to determine the level of adaptive and non-adaptive processes acting on a set of mammal genes that are linked with longevity and cancer. The results of these analyses yield important insights into data and model suitability, and provide strong evidence for a single hypothesis for the rooting of placental mammals. These results also show that Laurasiatheria intra-ordinal placements are not fully resolved and additional sampling from this diverse clade is required. Using this resolved phylogeny, specific molecular adaptations and non-adaptive mechanisms were identified in the mammalia for a set of telomere-associated genes.
Surto de aflatoxicose em bezerros no Rio Grande do Sul

An outbreak of chronic aflatoxicosis is reported in dairy calves. Forty 4-month-old male Holstein calves of approximately 100kg were kept in individual cages of 1.5 x 1.5m and were fed a ration constituted by alfalfa hay, broken corn and milk substitute. Six calves (15%) died after presenting a disease characterized by general unthriftiness, diarrhea, rough hair coats, abdominal pain, prolapsed rectum, grinding of teeth, and lying down and rolling. The clinical course, as observed by the owners, was 2-3 days; however many calves in this lot that did not die, remained underdeveloped. Three calves were necropsied. Necropsy findings included firm, light tan livers and marked hydrothorax, ascites and edema of the mesentery, mesocolon and of the mucosal folds of the abomasum. Main histopathological changes were restricted to the liver and consisted of fibrosis, moderate megalocytosis, biliary duct hyperplasia and veno-occlusive disease. The search for Senecio spp. contamination in the alfalfa hay resulted negative. The analysis by thin layer chromatography of the corn fed to calves revealed 5,136 ppb of aflatoxin B1. A diagnosis of aflatoxicosis was made based on the characteristic clinical signs and pathology, on the absence of Senecio spp. in the food and on the presence of high levels of aflatoxin in the corn fed to the calves.
A NEW SPECIES OF THE GENUS HELIX FROM THE LESSER CAUCASUS (SW GEORGIA)

The genus Helix Linnaeus, 1758 includes the largest snails of the family Helicidae, and prob-ably the largest terrestrial pulmonates in western Eurasia. It is distributed in northern Africa and Eurasia. Three species of Helix have been so far recorded from Georgia: H. lucorum (Linnaeus, 1758) and H. vulgaris (Rossmassler, 1839), both widely distributed in western Eurasia, and H. buchi (L. Pfeiffer, 1853) which is endemic to the western part of the Caucasus Ecoregion sensu Mittermeier et al. (2004). A further five species are known from Asia Minor, the region south-west of the southern Caucasus: H. figulina (Ross, 1839), H. pericalla (Kobelt et Rolle, 1896), H. cheikliensis (Zilch, 1952), H. cincta (Muller, 1774), and H. pomatia (Linnaeus, 1758) (Schutt, 2001; http://www.biolib.cz/en/taxon/id269332); none of those, however, have been recorded from the north-eastern part of Turkey adjacent to Georgia.Three very large helicid snails were collected on June 25th, 2006 by two of the authors (LM and DT) in south-western Georgia, at an elevation of between 1540 and 1595 m. a.s. l. (Fig. 1). Helix buchi or other known Caucasian representatives of the genus have never been recorded from this area. Our specimens differ from all other large members of the genus found in the Caucasus and Asia Minor and represent a new species which we describe below.Helix goderdziana sp. nov. (Figs 2-4)Holotype 1 shell (n10), Zoological Research Institute (ZRI), Tbilisi, Georgia.Paratypes 2 specimens: subadult shell (n8) and shell + soft parts (n9): Zoological Research Institute (ZRI), Tbilisi, Georgia.Type locality South-Western Georgia, just east of the Goderdzi Pass (see Fig. 1, 41
Response of Rice to p(CO2) Enrichment

SUMMARY Rice (Oryza sativa L.) is grown in many different agro-ecological zones and it assimilates CO2 directly through C3 photosynthesis. At current CO2 partial pressure [p(CO2)], rice is not photosynthetically saturated but immediately after exposure to 100 p(CO2), photosynthetic rates are increased by 48 percent on an average. However, this increase is not sustained during prolonged exposure and is associated with reduced amounts of ribulose-1-5-bisphospate carboxylase/oxygenase (Rubisco) content and its maximum potential activity (Vcmax). Rubisco content and Vcmax were reduced by 33 and 22%, respectively, at elevated p(CO2) and this has an additive effect on leaf photosynthesis. Activation state of the Rubisco is also decreased by elevated p(CO2) but no deactivation of Rubisco occurs in rbc S antisense rice with 40% wild type Rubisco suggesting that deactivation is an optimize response. Large amounts of Rubisco (about 80–90%) is synthesized prior to full expansion of leaf when sugar accumulation is minimal. After the leaf has fully expanded, very little Rubisco (about 10-20%) is synthesized and a large amount of sugar accumulates during this period. Therefore, it is unlikely that downregulation of Rubisco at elevated p(CO2) is caused by decreasing the mRNA transcripts for Rubisco small subunit (rbcS) and Rubisco large subunit (rbcL) through soluble sugars. It is more likely that elevated p(CO2) mediated decline in Rubisco is due to rapid degradation of protein and lower nitrogen (N) allocation to Rubisco due to reduced N afflux. Leaf N content was reduced by 16% in plants grown at elevated p(CO2) though leaf N to Rubisco ratio remained consistently unchanged regardless of growth p(CO2) suggesting that N assimilation, distribution and remobilization at the whole plant level is tightly controlled at elevated p(CO2). Further, changes in N and C metabolisms at elevated p(CO2) are likely to reduce the critical N concentration by 30% at elevated p(CO2).
Sequence Variation in the APOA1 and APOA4 Genes and their Relationship with Plasma HDL-Cholesterol Levels

Heart disease continues to be the leading cause of death in the United States, making it one of the foremost public health concerns. Many factors influence the risk to develop heart disease, including abnormal blood lipid levels. High levels of plasma high-density lipoprotein (HDL)-cholesterol have been shown to have a protective effect. Recent genome-wide association studies (GWAS) and candidate gene studies have identified genes thought to contribute to HDL-cholesterol levels. Two genes, APOA1 and APOA4, have been associated with HDL-cholesterol levels in multiple studies with inconsistent results. The majority of these studies focused on the "common variant-common disease" hypothesis whereas only one study by Cohen et al. (2004) evaluated APOA1 using the "rare variant-common disease" hypothesis. The aim of this study was to further investigate the role of common and rare variation in these two genes by sequencing individuals having extremely low and high HDL-cholesterol levels in two populations, U.S. Non-Hispanic Whites (NHWs), and African Blacks, and then screening the identified variants in the entire sample. In the initial sequence analysis, 54 variants were identified in APOA1 (25 of which were new), and 43 in APOA4 (21 of which were new). According to preliminary analysis of the sequencing data for APOA1 and APOA4, no striking difference was noticed between the distribution of rare variants between high and low HDL groups in either population. To date, screening data was compiled for the entire NHWs and Black samples for a total of seven common variants: 2 for APOA1 (rs5070 and rs5072), and 5 in APOA4 (rs5092, rs5100, rs5104, rs5106, and rs5109). All 7 variants were present in the Black population; five were present in NHWs (rs5070, rs5072, rs5092, rs5100, and rs5104). Modest or marginal significant p-values were observed; however, none would maintain significance after multiple testing correction in either population. Additional variants identified in sequencing remain to be screened in the entire NHWs and Black samples.
Non-ribose ligands for the human adenosine A1 receptor

This thesis describes new, non-ribose ligands for the human Adenosine A1 Receptor (hA1R). An introduction to the four adenosine receptors subtypes, their history and cloning, occurrence, functioning, trafficking and therapeutic potential is given in Chapter 1. The process of desensitization and internalization of adenosine receptors in cell systems, tissues and in vivo studies is described in Chapter 2. An overview of the current literature concerning desensitization and internalization of the adenosine receptors is given and the regulation of the different subtypes upon agonist binding is discussed. In Chapter 3, human adenosine A1 receptors fused to 351Cys mutated Giα-subunits are used as tools to study inverse agonism. In addition, the enhancing effect of the allosteric modulator PD81,723 on agonist affinity is shown. The influence of allosteric modulators on the internalization of the A1R is detailed in Chapter 4. The synthesis, affinity and activity of twelve non-ribose ligands, all ¬¬¬2-amino-4-(3 and/or 4-disubstituted phenyl)-6-(substituted)sulfanyl-pyridine-3,5-dicarbonitriles, are described in Chapter 5. Chapter 6 evaluates the characteristics of LUF6037 a representative of these 3,4-methylenedioxyphenyl substituted compounds. One of the other non-ribose agonists with high affinity for the A1R, LUF5834, was chosen to be radioactively labelled. Chapter 7 describes the evaluation of [3H]LUF5834 as a new agonist radioligand.
Phylogeny and evolution of the mollusca.

Brought together by Winston F. Ponder and David R. Lindberg, thirty-six experts on the evolution of the Mollusca provide an up-to-date review of its evolutionary history. The Mollusca are the second largest animal phylum and boast a fossil record of over 540 million years. They exhibit remarkable anatomical diversity and include the bivalves (scallops, oysters, and clams), gastropods (limpets, snails, and slugs), and cephalopods (squid, cuttlefish, and octopus). This study treats each major taxon and supplies general information as well as overviews of evolution and phylogeny using data from different sources - morphological, ultrastructural, molecular, developmental, and from the fossil record.
Cholinesterases: cholinergic biomarkers for the detection of sublethal effects of organophosphorous and carbamates in Catla catla.

Cholinergic enzyme inhibition is the most authentic tool to assess the environmental impact of pesticides on aquatic fauna. In current investigation we determined the sublethal toxic effects of carbofuran (carbamate) and profenofos (organophosphate) on acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) of various fish organs (brain, gills, kidneys, flesh, liver and blood). Fingerlings of Catla catla were exposed to three sublethal concentrations of profenofos (0.038, 0.019 and 0.012 mg/L) and carbofuran (0.198, 0.099 and 0.066 mg/L) for a period of two months. A highly significant inhibition in both of the cholinergic enzyme activities was observed even at the lowest concentrations of profenofos and carbofuran. Maximum inhibition of AChE activity was determined in the flesh (92.24%), whereas maximum inhibition of BuChE activity was determined in brain (93.10%) when exposed to profenofos. Similarly, carbofuron appeared to most detrimental for kidney (78.09%) when AChE activity was determined and it appeared to be most harmful for the liver (89.19%) when BuChE activity was assessed. Hence, profenofos proved to be the most potent inhibitor of cholinesterases (AChE and BuChE) as compared to cabofuran thus appearing to be more toxic for these aquatic animals. © 2014 Friends Science Publishers
Helminthes parasitizing Semaprochilodus Insignis Jardine, 1841 (Osteichthyes: Prochilodontidae) from the central Amazonia (Brazil) and their relationship with the host

This study describes the parasitic fauna and the host-parasite relationship of Semaprochilodus insignis Jardine, 1841 from Coari Lake, a tributary of the middle Solimoes River (state of Amazonas, Brazil) in Central Amazonia. Of 56 fish examined, 23.2% had gills parasitized by Gyrodactylus Gemini Ferraz, Shinn & Sommerville 1994 (Monogenoidea: Gyrodactylidae), and the intestine by Procamallanus inopinatus Travassos, Artigas & Pereira, 1928 (Nematoda: Camallanidae). The highest rates of infection were caused by G. gemini. Even though the relative condition factor (Kn) was not affected by parasitism, there was a positive correlation between the intensity of both helminthes, the Kn and the total length of the hosts. This is the first report on the parasitic fauna of S. insignis with occurrences of G. gemini and P. inopinatus for this Neotropical host fromthe Amazonia.
TECHNIQUES TO FINE-TUNE REPRODUCTION

When an analysis of herd records indicates relatively good fertility, there may still be room for further improvements. Herd output can be measured as weaned pig production. However, while the average number of pigs weaned per week may be good, weekly production may not be consistent (e.g. +/- 10%). Fine-tuning reproduction may allow increases in pig production, or just improve consistency of production. This may be achieved by consistently meeting breeding targets, or by improvements in farrowing rate or litter size. This paper will examine the potential to fine-tune the control of estrus and breeding management to aid the achievement of maximum reproductive output.
The NPL clean up.

The article discusses the efforts by banks around the world as of mid-September 2016 to clean up their non-performing loans (NPL) to improve their balance sheets. Also cited are the percentage of NPLs of banks in such countries as Italy, Cyprus, and Portugal, the purchase by investment firm Cerberus of the NPL portfolios of the banks Van Lanschot and UK Asset Resolution, and the effectiveness of securitisation as possible solution in cleaning up NPLs.
Intestine Homeostasis and the Role of Tumor Suppressor Gene 101 in Drosophila Melanogaster: A Dissertation

Tissue homeostasis in the adult Drosophila melanogaster intestine is maintained by controlling the proper balance of stem cell self-renewal and differentiation. In the adult fly midgut, intestinal stem cells (ISCs) are the only dividing cells and their identity maintenance is crucial to the proper functioning of the fly gut. Various pathways such as Notch, JAK-STAT and Wingless are known to regulate ISC division and differentiation. Here I used a pathogen feeding model to study conditions that accelerate ISC division and guide intestinal cell differentiation favoring enterocyte development. I also examined the role of Tumor Suppressor Gene 101 (TSG101) in ISC maintenance and function. TSG101, a part of the ESCRT1 complex. It is known to stimulate the Notch pathway and to play a role in endocytic trafficking. TSG101 loss-of-function mutants show developmental defects in various fly and mammalian tissues. The protein also plays a role in virus abscission from host cells. In my experiments I have observed that TSG101 is required for ISC maintenance. TSG101 knockdown and loss of function mutant clones have defects in ISC proliferation that hinder the normal intestinal responses to oral pathogen ingestion. Based on these results I conclude that TSG101 is needed in the adult fly intestine for proper ISC maintenance and function, thereby being an important player in intestinal homeostasis.
Epitopes, aggregation and membrane binding: investigating the protein structure-function relationship

The three-dimensional structure of a protein, formed as a result of amino-acid sequences folding into compact domains, is regarded as a key factor in its biological function. How and why proteins fold into specific topologies, remain the key focus of scientific research in the field of biophysics. By stripping down complex reactions down to the most basic elements, biophysicists aim to develop simplified models for biological phenomena such as antibody discrimination, viral fusion or self-assembly. Focusing on small model peptide systems, rather than the full proteins from which they were derived, was hoped to result in accurate structural measurements and provide a more transparent comparison between simulation and experiment. The aim of this research was therefore to investigate how accurate these models were when compared against experiment. Furthermore, while breaking down the complex biological phenomena into simple models, there was also a conscious effort to ensure that the models were representative of real biological systems, and a major focus was therefore aimed at determining whether any meaningful biomedical insight may be extrapolated from such models. Peptides found in hormones (human chorionic gonadotropin, luteinizing hormone), viruses (HIV) and amyloid diseases (transthyretin) were selected in order to probe a variety of questions in relation to the aforementioned biological phenomena. Namely, how the primary sequence influenced the three-dimensional structure (and thus its biological function), how its environment could influence such a confirmation, and how these systems aggregated. This doctoral study has made use of a combination of computer simulations and experimental techniques to investigate a selection of biologically relevant peptides; utilising classical atomistic molecular dynamics (MD) simulations to characterise the free-energy landscapes of the chosen peptides, and compare these findings with the secondary structure content predicted by spectroscopic methods such as circular dichroism and infrared spectroscopy. The peptide systems studied within, were found to be characterised by rugged free-energy landscapes unlike their protein counterparts (defined by singular, deep minima). Furthermore, these landscapes were found to be highly plastic and sensitive to changes in the local environment.
Theoretical investigation of intra- and inter-cellular spatiotemporal calcium patterns in microcirculation

Part of the Biochemical and Biomolecular Engineering Commons, Biomechanics and Biotransport Commons, Biophysics Commons, Cell Biology Commons, Cellular and Molecular Physiology Commons, Molecular, Cellular, and Tissue Engineering Commons, Non-linear Dynamics Commons, Ordinary Differential Equations and Applied Dynamics Commons, Partial Differential Equations Commons, Systems Biology Commons, and the Transport Phenomena Commons
Bacterial abundance in modified extensive and semi-intensive shrimp culture ponds of Penaeus monodon.

A study was carried out to analyse the bacterial abundance in the brackishwater culture ponds of Penaeus monodon situated along coastal Andhra Pradesh (India). The physico-chemical characteristics of the pond water and the bacterial counts of pond water, pond sediment and muscle and hepatopancreas (HP) of the shrimps were estimated at intervals of 15 days for one crop cycle during 1996. The physico-chemical characteristics of the pond water in all the ponds were within normal limits. The semi-intensive ponds recorded higher bacterial loads as compared to modified-extensive ponds. In pond water, the bacterial loads fluctuated erratically, and showed no definite trend with the progress of culture period. The pond sediment with its high organic load recorded higher values than pond water and demonstrated a general trend of increase of bacterial load with the progress of the culture. The bacterial load in HP of shrimp was found to be higher than that in muscle and both showed an increasing trend with shrimp age but the overall load remained within the safe level. The high bacterial loads noted in semi-intensive ponds prior to crop harvest are found to be associated with poor water quality, exaggerated by low D.O. , high ammonia, algal blooms and high organic content in the bottom. Relationship could not be found between water quality parameters and the bacterial load in the pond water and also there was no relationship between the bacterial load of shrimp and that of the pond environment.
Towards the management of hypertension: Modulation of the renin-angiotensin system by food protein hydrolysates and peptides

In response to the side effects of antihypertensive drugs, dietary and lifestyle modification approaches have become alternative strategies for prevention and modulation of mild hypertension. Moreover, the use of low molecular size bioactive peptides (BAPs) as antihypertensive agents has gained particular attention as a result of the safety, low cost, and consumer preference for natural health products compared to drugs. BAPs are produced by enzymatic hydrolysis of food proteins followed by post-hydrolysis processing to fractionate the active peptides. Antihypertensive BAPs exert their effect mostly by modulating the renin-angiotensin system pathway leading to decrease in vasoactive peptides with concomitant reduction of elevated blood pressure associated with hypertension in animal models and humans. This review revisits the prevalence of hypertension and the molecular basis of activity, bioavailability and safety of BAPS as well as contradictions and controversies on the use of peptides as antihypertensive agents.