Miracle-dz/UniFAR-FTUs huggingface dataset:
Glutathione S-Transferase M1 and T1 Polymorphisms in Brazilian African Descendants

ABSTRACT The glutathione S-transferase gene family has an important role in the biotransformation and detoxification of different xenobiotics and endogenous compounds. Two polymorphic genes of this family, GSTM1 and GSTT1, present null alleles that consequently do not produce the respective enzyme when the genotype is homozygous. These polymorphisms are also interesting for population dynamics studies because they have great frequency variations among different ethnic groups and have been reported worldwide. The distribution of these alleles in urban and Amerindian populations in Brazil has been described, but none of those studies reported on African-descended rural populations. The aim of this study was to analyze the genotype frequency distribution of the GSTM1 and GSTT1 null alleles in an urban sample from the Federal District (n = 91) and in four semi-isolated African-descended populations: Mocambo (n = 55), Rio das Rãs (n = 117), Riacho de Sacutiaba (n = 34), and Kalunga (n = 68). The GSTM1 and GSTT1 null genotype frequencies in these populations range from 17% to 35% for GSTM1 and from 22% to 44% for GSTT1. These values are similar to those described in other African and African-descended populations. Despite this range, there is no distribution difference among the analyzed populations. Combined GSTM1 and GSTT1 null genotype frequencies range from 6% to 13% and are similar to European-derived populations, suggesting admixture with this ethnic group. This can be interpreted as a European contribution to these African-descended populations. Regarding the urban population in the Federal District, our results suggest an important African and European contribution.
Kinematics and Mechanics of Jumping Lizards: the Modulation of Jump Power

Author(s): Olberding, Jeffrey Paul | Advisor(s): Higham, Timothy E | Abstract: In order to understand the evolution of locomotion, lizards are often used to study the relationships between morphology and locomotor performance. However, the mechanisms by which himblimb morphology results in jumping performance are not well understood, despite the fact that jumping may be important for fitness in many lizard species.Here I investigate the ways in which mechanical power is generated by the hindlimbs of jumping collared lizards, Crotaphytus collaris. I examine the contribution of each hindlimb joint to total power output. I also test the hypothesis that these lizards utilize elastic power amplification.I found a high degree of individual variation in the relationships between joint kinematics and jump power, suggesting multiple strategies for controlling jump performance and highlighting the importance for considering individual variation in biomechanical studies. I also found peak power outputs exceeding the physiological limits of lizard muscle suggesting the presence of a power amplification mechanism. Additionally, the use of countermovements may enhance jump power, though possibly through mechanisms other than elastic energy storage.
Health Maintenance of Cultured Fishes: Principal Microbial Diseases

Aiming to increase the understanding of the relationship between the aquatic environment and the development of infectious fish diseases, this book applies 22 health maintenance principles of food animal management to aquaculture and discusses how these principles improve the health of cultured fish. Viral and bacterial diseases are organized according to the species, families or groups of fish most affected by the pathogens. The text covers diseases that affect cultured fish in North America,as well as diseases of international concern. It emphasizes the management and therapeutic treatment of diseases.
New transcriptional roles for the classic Drosophila insulator protein Suppressor of Hairy-wing

The Drosophila Su(Hw) protein is a multi-zinc finger DNA binding factor required for the gypsy insulator function. At the gypsy element, Su(Hw) recruits partners Centrosomal Protein of 190 kD (CP190) and Modifier of mdg4 67.2 kD isoform (Mod67.2), which are required for the enhancer blocking and barrier functions of the insulator. Our genome-wide studies have identified thousands of endogenous non-gypsy Su(Hw) binding sites (SBSs) in the Drosophila genome, constitutively occupied throughout development. Yet, only a third of these SBSs are associated with CP190 and Mod67.2, suggesting that the endogenous function of Su(Hw) may not necessarily involve the formation of a gypsy-like chromatin insulator. To understand the function of endogenous SBSs, we investigated the requirement for Su(Hw) during female germline development. To this end, we performed genomewide transcriptional analyses in su(Hw) mutant ovaries coupled with the genome-wide definition of ovary SBSs. We identified 93 direct targets of Su(Hw) regulation in the ovary, with 68% of these genes showing increased RNA accumulation when Su(Hw) is lost. Derepressed Su(Hw) targets are normally highly expressed in central nervous system, suggesting that Su(Hw) has a critical role in silencing neural genes in the nonneural tissues. We find that a single upregulated target gene is largely responsible for the female sterility of su(Hw) mutants. This gene encodes an elav family factor RNA binding protein 9 (Rbp9), and Su(Hw)-mediated repression of Rbp9 is required at a specific stage of oogenesis. Decreasing the levels of Rbp9 restores female fertility of su(Hw) null mutants. Further, we demonstrate that Su(Hw) is required for transcriptional activation of
Pharmacokinetics and tissue disposition of urolithin A, an ellagitannin‐derived metabolite, in mice

Ellagitannins (ETs) are bioactive polyphenols present in some fruits (pomegranates, strawberries, red and black raspberries) and nuts (almonds, walnuts). Once consumed, ETs hydrolyze and are absorbed as ellagic acid which rapidly clears from plasma over 5 h. Ellagic acid is further metabolized by liver enzymes and gut microflora into 1,6‐hydroxybenzopyran derivatives (or urolithins). However the pharmacokinetics and tissue disposition of urolithins has not been reported. Therefore we synthesized and intraperitoneally (i.p.) or orally administered urolithin A (UA) to B6 mice. Blood (over 24 h) and tissues (prostate, liver, kidney, lung, colon, intestine, brain) were collected and analyzed for UA and its conjugates by high performance liquid chromatography mass spectrometry. Metabolite levels were UA >UA‐sulphate>UA‐glucuronide>methylated‐UA; all metabolites cleared by 24 h. UA concentration was highest in mouse prostate tissues by the oral route, and in colon and prostate tissues by the i.p. route. Only methlyated‐UA was detected in brain tissues. Administration by i.p. resulted in shorter Tmax (2 h) and higher concentrations than oral administration (Tmax, 4 h). Given that the mouse prostate gland was a main target tissue of concentration by UA, and the previous report of the effects of pomegranate juice on prostate cancer patients, further human bioavailability studies are warranted.
Highly Active Yeast MnSOD has a Novel Mechanism Involving Six-coordinate Mn(3+) Species

Author(s): Sheng, Yuewei | Advisor(s): Valentine, Joan S | Abstract: Manganese-bound superoxide dismutase (MnSOD) is a very important antioxidant enzyme. The mechanism by which MnSOD removes O2— involves product inhibition, that is, reduction of O2— occurs through either a "prompt protonation" pathway, or an "inner-sphere" pathway, with the latter leading to formation of an observable Mn-peroxo complex. Human MnSOD is more gated toward the "inner-sphere" pathway than bacterial enzymes. To study whether product inhibition is a common feature to eukaryotic MnSODs, we studied a mitochondrial MnSOD from the eukaryote model organism Saccharomyces cerevisiae (ScMnSOD). To our surprise, ScMnSOD was found to display the highest catalytic efficiency at high levels of O2— among MnSODs that had been characterized. To understand further the mechanism of product inhibition, we compared ScMnSOD with another yeast MnSOD, the cytosolic MnSOD from Candida albicans (CaMnSODc). CaMnSODc, like ScMnSOD, is less inhibited than human and bacterial MnSODs. Although the active site of yeast MnSODs closely resembles that of MnSODs from other organisms, spectroscopic studies suggest the presence of a six-coordinate Mn3+ species in oxidized yeast MnSODs. To explore further the origin of the fast catalysis by yeast MnSODs, the Y34F (a strictly conserved second-sphere residue) form of ScMnSOD was created. Y34F ScMnSOD has a novel catalytic mechanism, in which protonation of the Mn-peroxo complex occurs through a fast pathway at neutral pH, leading to a putative six-coordinate Mn3+ species, which actively oxidizes O2— in the catalytic cycle. Because wild-type and the mutant yeast MnSOD both rest in the 2+ state and become six-coordinate when oxidized up from Mn2+, six-coordinate Mn3+ species could also actively function in the mechanism of wild-type yeast MnSODs. ScMnSOD is a tetramer, while CaMnSODc is a dimer or loose tetramer, even though they are similar in many ways. Investigations of their crystal structures suggest that when CaMnSODc is in the dimeric form, its N-terminal regions are highly disordered, hindering it from forming a tetramer in solution. To further investigate the physiological significance of the tetramer structure, we mutated two residues (Lys182/Ala183 in ScMnSOD, Lys184/Leu185 in CaMnSODc) at the dimer interface in the two yeast MnSODs. We find that the dimer interface, which is critical for MnSOD activity, is reinforced by tetramer formation.
Nutrigenomics: Emerging face of molecular nutrition to improve animal health and production -

Traditional research related to animal nutrition is mainly deals with either deficiency or excess of the particular nutrient which leads to ill health as well as decreased animal production. But genomic revolution has propelled the development of several new technologies that can be applied in nutritional sciences (Collins,et.al., 2003). New techniques like genomic, proteomic, metabolomic, and bioinformatic are now making their ways to solve the intervening puzzle between nutrient and genes (Daniel, 2002). This era of newer technologies have the potential to improve the nutritional assessment and measures of bioavailability of various nutrients to get sustainable livestock production. The application of these innovative tools and the concepts developed from genomic studies assures to revise the thinking of researches engaged in nutritional science to improve animal health and ultimately the production. (Dawson, 2006) Since, recently various clinical trials deals with nutritional research have proved the relationship among diet, health, disease and production. Its well known fact that dietary deficiency, imbalance of nutrients and or excess of diet has a profound effect leads to ill health indicative of that dietary compound have direct effects on molecular processes which ultimately change the gene expression. Advancement in nutritional science discovered that nutrients or their metabolites can regulate the various bodily functions directly or by stimulating or inactivating specific regulators. Hence, to study the nutrient gene relationship or interaction between genomics and nutrition, nutrigenomics has been introduced in the nutrition research (Mariman, 2006).
Changing trends of carbapenem resistance of escherichia coli and klebsiella pneumoniae strains isolated from intensive care units, inpatient services and outpatient’s clinics: a five years retrospective analysis

Background: Carbapenem resistance (CR) was rarely reported in Klebsiella pneumoniae and Escherichia coli strains until ten years ago. In recent years, increasing carbapenem resistance in gram negative bacteria is a substantial concern. Objectives: In this study; we aimed to evaluate the changing frequency of CR in K.pneumoniae and E.coli strains that were isolated from the patients from intensive care units, inpatient services and outpatientsÂ’ clinics in the last five years. Methods: Data of antimicrobial susceptibility belonging to clinical isolates of K.pneumoniae and E.coli strains determined between 2013 and 2017 were retrospectively collected from Laboratory Information System. Results were statistically analyzed. Results: A total 4002 K.pneumoniae and 13462 E.coli strains were included. The CR of K.pneumoniae strains were found as 11.6%; while of E.coliÂ’s were found as 0.6%. The highest CR frequency was detected among intensive care unitsÂ’ isolates of K. pneumoniae as 20.1%. We determined that CR significantly increased in intensive care unit isolates of E.coli and K.pneumoniae about 5-10 folds throughout the study period; however, there was no remarkable change in the CR of E.coli strains from the outpatientsÂ’ clinics. Conclusion: We determined that the resistances of K.pneumoniae and E.coli strains to carbapenems were progressively increasing by years, especially in intensive care units and inpatient services. Therefore, appropriate antimicrobial use policies sought to be considered against to this growing problem.
Penile urethral stricture disease

Patients affected by a urethral stricture account for a considerable cost to all healthcare systems. The estimated prevalence of all urethral stricture in the UK is 10/100,000 men during youth, increasing to about 40/100,000 by age 65 years and to more than 100/100,000 thereafter. A penile urethral stricture is a narrowing of the lumen of the urethra due to ischaemic fibrosis of the urethral epithelium and/or spongiofibrosis of the corpus spongiosum occurring within the penile urethra. Its aetiology is largely idiopathic but other important causes are failed hypospadias repair and lichen sclerosus, which account for 60% of all cases. Strictures of the anterior urethra account for 92% of cases: bulbar strictures are more frequent (46.9%), followed by penile (30.5%) and combined bulbar/penile (9.9%), that is, 40.4% of all men presenting with stricture will have a penile urethral stricture alone or in combination with a bulbar urethral stricture. There are several options for the treatment of penile urethral strictures ranging from less invasive treatments, including urethral dilatation and direct vision internal urethrotomy, to more complex augmentation graft and flap urethroplasty. The aim of the present review is to describe the aetiology and epidemiology of anterior urethral strictures and the available options reported in literature for their treatment. Level of evidence: 1a
Diagnostic Tools and Management Strategies used by Specialized Dentists and Physical Therapists for Patients with Bruxism: a Delphi Procedure

Background: The most valid tool in bruxism diagnostics is considered electromyography/ polysomnography with audio/video recording. Given that this is too expensive and time-consuming for daily practice; many other tools are used to diagnose bruxism. Owing to the lack of knowledge about the etiology and (patho) physiology of bruxism, no definitive intervention exists and current management strategies mainly focus on reducing negative consequences of bruxism. This study aimed to identify diagnostic tools and management strategies that dentists and physical therapists who specialize in the orofacial region consider being the most clinically useful for patients with bruxism and which are actually used. Method: The results of a literature study were used as a starting point for a Delphi procedure. The first round (36 participants) focused on collecting preferences in diagnostics and management of bruxism. In the second round (29 participants), the number of diagnostic tools and management strategies that were rated as clinically useful were narrowed down to those that were actually used by the participants in daily practice. Results: For the diagnostics of both awake and sleep bruxism, mostly aspects of the anamnesis and the clinical examination were considered clinically useful and actually used in daily practice. Moreover, for sleep bruxism, more tools were combined to set the diagnosis than for awake bruxism. Both groups of participants valued habit reversal and lifestyle advice in the management of awake bruxism, and habit reversal, sleep hygiene advice and lifestyle advice for sleep bruxism. In addition, both groups suggested profession-specific strategies. Conclusion: The diagnostic tools and management strategies used in daily practice among specialized dentists and physical therapists in the Netherland form a colorful palette and, as expected, are determined by profession.
Investigating the role of CK2 in the DNA damage response

Casein Kinase 2 (CK2) is a ubiquitous serine/threonine kinase. Due to its pleiotropic nature CK2 is involved in a multitude of cellular pathways including cell survival, proliferation and apoptosis. Therefore it has come as no surprise that a requirement for CK2 activity has been identified during the repair of DNA damage. Here we have described a novel role for CK2 in the response to DNA double-strand breaks. We have shown the mediator of DNA damage checkpoint 1 (MDC1) is constitutively phosphorylated by CK2, which is required for an interaction with the MRE11/RAD50/NBS1 (MRN) complex, via the FHA domain of NBS1. Moreover, disruption of this interaction resulted in loss of MRN foci following ionizing radiation and a partial G2/M checkpoint defect. Furthermore, the identification of three siblings presenting NBS/Seckel-like phenotypes with a unique mutation in the BRCT domain of NBS1, that phenocopied some of our observations, provided additional evidence for the importance of phospho-dependent interactions within the cell. Lastly, the identification of putative CK2 target residues in MRE11 and our preliminary data suggest that the kinase may play further roles in regulating the activity of the MRN complex that lie outside its activity in DNA double-strand break repair.
T cell immunity to Kaposi’s sarcoma-associated herpesvirus latent proteins

T cell immunity is important for the control of Kaposi’s sarcoma-associated herpesvirus (KSHV) disease, yet little is known about KSHV-specific immunity in healthy donors. Screening PBMCs from such donors by ELISpot analysis identified weak responses to the KSHV latent antigens; antigens expressed in the virus associated pathologies. We generated T cell clones to the latent proteins LANA and vFLIP and determined whether they recognised target cells. CD8+ clones poorly recognised targets expressing vFLIP or LANA, through mechanisms which reduce target protein synthesis: vFLIP used rare codons in the mRNA encoding this protein, while deleting the acidic repeat of LANA increased its recognition. We then examined whether LANA-specific CD4+ T cells recognised B cells expressing or fed LANA protein. These were recognised, however most KSHV-infected cell lines, in the form of primary effusion lymphoma (PEL) lines, were not. PELs express vIRF3 which inhibits promoter function of the HLA class II transactivator CIITA. Expressing CIITA from a different promoter restored CD4+ T cell recognition of PELs. This study suggests CD8 recognition of the latent antigens tested is inefficient due to the innate properties of the targets but that CD4 T cells can effectively recognise targets if the immune evasion mechanisms are bypassed.
Evolutionary expansion and divergence in a large family of primate-specific zinc finger transcription factor genes

Although most genes are conserved as one-to-one orthologs in different mammalian orders, certain gene families have evolved to comprise different numbers and types of protein-coding genes through independent series of gene duplications, divergence and gene loss in each evolutionary lineage. One such family encodes KRAB-zinc finger (KRAB-ZNF) genes, which are likely to function as transcriptional repressors. One KRAB-ZNF subfamily, the ZNF91 clade, has expanded specifically in primates to comprise more than 110 loci in the human genome, yielding large gene clusters in human chromosomes 19 and 7 and smaller clusters or isolated copies at other chromosomal locations. Although phylogenetic analysis indicates that many of these genes arose before the split between old world monkeys and new world monkeys, the ZNF91 subfamily has continued to expand and diversify throughout the evolution of apes and humans. The paralogous loci are distinguished by sequence divergence within their zinc finger arrays indicating a selection for proteins with different DNA binding specificities. RT-PCR and in situ hybridization data show that some of these ZNF genes can have tissue-specific expression patterns, however many KRAB-ZNFs that are near-ubiquitous could also be playing very specific roles in halting target pathways in all tissues except for a few, wheremore » the target is released by the absence of its repressor. The number of variant KRAB-ZNF proteins is increased not only because of the large number of loci, but also because many loci can produce multiple splice variants, which because of the modular structure of these genes may have separate and perhaps even conflicting regulatory roles. The lineage-specific duplication and rapid divergence of this family of transcription factor genes suggests a role in determining species-specific biological differences and the evolution of novel primate traits. « less
Epidemiological Aspects of Malaria in Pregnant Women: Prevalence and Risk Factors in Mwene Ditu, DR Congo

Introduction: Malaria in pregnancy induces significant risks for the mother and the foetus. The objective of this study was to determine the prevalence of malaria and the risk factors among pregnant women in the Health District of Mwene Ditu in DR Congo. Methods: A cross-sectional descriptive study based on household survey was carried out in June 2016 in the Health District of Mwene Ditu. The calculated sample size was 461 pregnant women selected through a stratified random sampling. A structured interview using a pre-established questionnaire was administered to and peripheral blood samples were collected for laboratory tests in all pregnant women presenting malaria symptoms or fever history. The following statistics were used: Chi square test and Odds ratio with a confidence interval at 95%. Results: The prevalence of malaria in pregnant women was 14.97%. The following parameters proved to be risk factors for malaria illness in pregnant women in Mwene Ditu: low socio-economic level of the couple [AOR = 6.48 (1.51; 27.78)], agrarian activities [AOR = 5,56 (2.47; 12.50)], facts of not sleeping under ITBN each night [AOR = 17.39 (8.38; 36.10)] as well as of not getting SP for intermittent preventive treatment (IPT) in pregnancy [AOR = 4.08 (1.32; 12.59)] and financially supporting all interventions for fighting against malaria [AOR = 3.43 (1.42; 8.29)]. Conclusion: Malaria is frequent among the pregnant women of Mwene Ditu. The ANC frequentation and an appropriate organization prove to be paramount interest.
The scent of death: Chemosensory assessment of predation risk by prey animals

AbstractIt is well documented that animals take risk of predation into account when making decisions about how to behave in particular situations, often trading-off risk against opportunities for mating or acquiring energy. Such an ability implies that animals have reliable information about the risk of predation at a given place and time. Chemosensory cues are an important source of such information. They reliably reveal the presence of predators (or their presence in the immediate past) and may also provide information on predator activity level and diet. In certain circumstances (e.g., in the dark, for animals in hiding) they may be the only cues available. Although a vast literature exists on the responses of prey to predator chemosensory cues (or odours), these studies are widely scattered, from marine biology to biological control, and not well known or appreciated by behavioural ecologists. In this paper, we provide an exhaustive review of this literature, primarily in tabular form. We highlight so.