Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional studies of the interstrand cross-link repair protein, SNM1A and its beta-CASP domain

v ACKNOWLEDGEMENTS . vi DEDICATION . vii TABLE OF CONTENTS . viii LIST OF FIGURES . x LIST OF TABLES . xii LIST OF ABBREVIATIONS . xiii CHAPTER 1: INTRODUCTION . 1 1.1 ICL damage . 1 1.2 ICL damage in chemotherapy . 3 1.3 ICL damage repair in humans . 6 1.4 Function of SNM1A in ICL repair . 10 1.5 Additional functions of SNM1A . 13 1.6 Structure and Function of SNM1A . 14 1.7 The beta-CASP domain. 17 1.8 Thesis Objective . 24 CHAPTER 2: MATERIALS AND METHODS . 26 2.1 Cloning of SNM1A variants . 26 2.2 SNM1A expression in S. cerevisiae and purification . 27 2.3 SNM1A and beta-CASP domain expression in E. coli . 28 2.4 Inclusion body isolation . 28 2.5 Inclusion body solubilization assay . 29 2.6 Screening for aggregation of inclusion body material . 30 2.7 IMAC purification of protein from inclusion bodies under denaturing conditions . 30 2.8 Refolding of protein purified from inclusion bodies . 31 2.9 Assays for determining nuclease activity of SNM1A . 32 2.10 Assays for determining nuclease activity of the beta-CASP domain of SNM1A . 32 2.11 Enzyme kinetics determination . 33 2.12 Complementation assays . 34 M.Sc. Thesis – B. Buzon; McMaster University – Biochemistry and Biomedical Sciences ix CHAPTER 3: RESULTS . 37 3.1 Results for SNM1A. 37 3.1.1 Expression and purification of SNM1A . 37 3.1.2 Refolding SNM1A from solubilized inclusion body preparations . 41 3.1.3 Exonuclease activity assay for SNM1A . 43 3.2 Results for the beta-CASP domain of SNM1A . 48 3.2.1 Expression of the beta-CASP domain . 48 3.2.2 Optimization of conditions for beta-CASP domain inclusion body isolation . 48 3.2.3 Solubilization of the beta-CASP domain . 53 3.2.4 Refolding of beta-CASP domain inclusion bodies . 57 3.2.5 Purification of the beta-CASP domain under denaturing conditions . 60 3.2.6 Nuclease activity of the beta-CASP domain . 63 3.2.7 Enzyme kinetics of the beta-CASP domain . 66 3.3 Complementation of pso2 null strains with SNM1A variants . 70 CHAPTER 4: DISCUSSION. 74 4.1 Discussion of SNM1A . 74 4.1.1Expression of human SNM1A in S. cerevisiae . 74 4.1.2 Expression of human SNM1A in E. coli . 75 4.1.3 Refolding SNM1A from inclusion bodies . 76 4.1.4 5’ Exonuclease activity of SNM1A . 78 4.2 Discussion of the beta-CASP domain of SNM1A . 79 4.2.1 Expression of the beta-CASP domain of human SNM1A in E. coli. 79 4.2.2 Optimization of isolation of beta-CASP domain inclusion bodies . 79 4.2.3 Beta-CASP domain inclusion body solubilization . 81 4.2.4 Refolding of beta-CASP domain inclusion bodies . 83 4.2.5 Exonuclease activity of the beta-CASP domain . 85 4.2.6 Enzyme kinetics of purified, refolded beta-CASP domain . 88 4.3 In vivo activity of a minimal beta-CASP domain . 95 CHAPTER 5: CONCLUSIONS AND FUTURE DIRECTIONS . 97 APPENDIX . 102 REFERENCES . 105 M.Sc. Thesis – B. Buzon; McMaster University – Biochemistry and Biomedical Sciences
Bioactive substances in meat and meat products.

In addition to the traditional essential nutrients, meat and meat products contain a number of bioactive substances which have potential beneficial effects on human health. L-Carnitine, coenzyme Q 10 , carnosine, anserine, taurine, creatine, glutathione, alpha lipoic acid, conjugated linoleic acid (CLA) and bioactive peptides are among these substances and are described in this publication.
Estimation of Genetic Parameters on Pre-weaning Growth Traits in Hanwoo

A total of 4,627 records on pre-weaning growth traits, birth weight(BW), weaning weight(WW) and pre-weaning daily gain(ADG) of Hanwoo’s born form 1970 to 2005 were collected from Hanwoo Experiment Station, National Livestock Research Institute. Variance components and heritabilities of BW, WW and ADG were estimated with two models; Model 1 included only direct genetic effect while Mode1 2 included direct genetic, maternal genetic and permanent environmental effects. Direct herit- ability estimates of BW, WW and ADG estimated by model 1 were 0.34, 0.26 and 0.20, respectively. In model 2, direct heritability and maternal genetic heritability estimates were 0.14 and 0.06 for BW, 0.07 and 0.04 for WW and 0.05 and 0.04 for ADG. Estimates of genetic correlation between direct and maternal effect for BW, WW and ADG were 0.58, 0.75 and 0.61, respectively. Genetic correlation coefficients between BW and WW, between BW and ADG, and between WW and ADG were 0.76, 0.62 and 0.99, respectively.
Genetical genomics in Arabidopsis: from natural variation to regulatory networks

In Arabidopsis Recombinant Inbred Line (RIL) populations are widely used for Quantitative Trait Locus (QTL) analyses. However, mapping analyses with this type of populations can be limited because of masking effects of major QTLs and epistatic interactions of multiple QTLs. An alternative type of immortal experimental population commonly used in plant species are sets of introgression lines. Here we introduce the development of a genome wide coverage Near Isogenic Line (NIL) population of Arabidopsis thaliana, by introgressing genomic regions from the Cape Verde Islands (Cvi) accession into the Landsberg erecta (Ler) genetic background. We have empirically compared the QTL mapping power of this new population with an already existing RIL population derived from the same parents. For that, we analyzed and mapped QTLs affecting six developmental traits with different heritability. Overall, in the NIL population smaller effect QTLs than in the RIL population could be detected although the localization resolution was lower. Furthermore, we estimated the effect of population size and of the number of replicates on the detection power of QTLs affecting the developmental traits. In general, population size is more important than the number of replicates to increase the mapping power of RILs, whereas for NILs, several replicates are absolutely required. These analyses are expected to facilitate experimental design for QTL mapping using these two common types of segregating populations.
Identification of drugs of Madhuraskandha of Charakasamhita

In the classical text, Rasa oriented group of drugs were mentioned called as Rasaskandha. Acharya Sushruta, Vagbhata have mentioned these groups in the context of description of Rasa (Taste). But Acharya Charaka quoted these groups in Vimanasthana while describing drugs for Asthapana Basti (Corrective enema). Drugs having predominantly of Madhura rasa (sweet taste) and Vipaka (Final transformation of drug) or that can produce effect similar to that of Madhura Rasa or Vipaka ( Prabhava- specific action) are included under Madhuraskandha . In total 85 drugs are mentioned. In this group 68 are identified, 14 are unidentified and 3 are found to be controversial drugs. Among them 56 drugs are Madhura rasa (sweet taste) dominant, 53 are Madhura vipaka (final transformation into sweet) dominant and 18 are categorized under Madhura prabhava (specific action). The drugs included in Madhuraskandha (group of the drugs having Sweet taste or potential), irrespective of Madhura Rasa or Vipaka , are capable of attributed to functions Madhura Rasa or Vipaka like Jeevaniya (invigorating) , Preenana (soothing) , Balya (promotes strength) , Brihmana (nourishing), Rasayana (anti-ageing) , Vrishya (aphrodisiac) , Shukrala (promotes semen) etc.
Alterações histopatológicas observadas no fígado do Lambarí Astyanax jacuhiensis (Cope, 1894) (Teleostei, Characidae) sob influência de efluentes petroquímicos

The Integrated System of Treatment of Liquid Waste (SITEL) is responsible for the treatment and final disposition of the waste generated by the Polo Petroquimico do Sul and it consists of eight lagoons of stabilization that are connected in series. Forty five specimens of Astyanax jacuihensis were collected at the Stabilization Tertiary lagoons 1 and 8 and thirty five in the arroio Bom Jardim in three period of samples (January and april of 1999 and October 2002). The material were embedded in paraffin and stained with Hematoxilin and Eosin (H&E) and PAS (Periodic Acid of Schiff reaction). The liver present histopatologic alterations in the specimens of the lagoon 1, being the anomalies considered of light and moderate intensity. The histological analysis also showed that the hystopatologic alterations in the individuals of the lagoon 1 liver were more intense than observed in the specimens of the lagoon 8 and of the arroio Bom Jardim, evidencing in this study a certain effectiveness of the system treatment of effluent. Key Words: Astyanax jacuhiensis, Histology, Liver
Cutaneous innervation of the hand

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Investigating How Ploidy and Stress-induced Ploidy Change Affects Fitness in Candida albicans

Candida albicans is a human pathogen that is lethal in 40-50% of systemic infections. Fluconazole (FLC) is the most commonly prescribed drug used to treat these infections. However, resistance to FLC is common and of the clinical isolates found to be FLC-resistant, 50% are aneuploid (having an abnormal number of chromosomes). To investigate differences between the adaptability of different ploidy states, isolates of two non-resistant diploid and two non-resistant tetraploid strains were grown up in 96-well plates with and without FLC. The resulting growth curves were similar between diploids and tetraploids in both approximate growth rate and final OD. After growing and passaging the plates for four consecutive growth cycles, the ploidy states of each of the isolates were measured using flow cytometry. A small number of diploid isolates changed ploidy, while a much larger number of tetraploid isolates changed ploidy and tetraploid isolates showed a much wider range of ploidies than diploids, with most changes being a decrease in ploidy. Tetraploids isolates usually decreased their growth rate when compared to their parents; few diploids showed this phenotype. Thus tetraploid strains exposed to FLC produced more variability in ploidy than diploids, and while YPAD growth rate decreases were observed a with ploidy change, they were not linearly associated with the degree of ploidy change.
Light intensity and fruiting effects on carbohydrate contents, spur development, and return bloom of 'Hartley' walnut.

Leaf number, area and chlorophyll content, and specific leaf wt were greater in light-exposed spurs of 'Hartley' walnut {Juglans regia L. ) than those grown in the shade. increased 4 early in the season in shaded spurs, but the accumulation ceased while the nuts stored dry matter. In exposed 1979.
Physical and chemical properties of protein seafood by-products

Publisher Summary It is a challenge to utilize more protein fractions from fish by-products as food ingredients. Many protein-rich marine by-products have a range of dynamic properties and can potentially be used in foods as binders, emulsifiers, and gelling agents. Fish proteins have unique functional properties such as capacity to bind water, lipids, rheological properties, etc. but, due to lack of a suitable purification process to preserve protein functionality, fish protein has been lacking in the rapidly growing protein ingredient and health markets. This chapter discusses the physical and chemical properties of protein seafood by-products. The functional properties of proteins are defined as physical and chemical properties that affect the behavior of proteins in food systems during processing, storage, preparation, and consumption. The sensory properties of foods result from interactions between several functional ingredients. The physical and chemical properties that determine protein functionality include the size and the shape of the proteins, the charge and the distribution of charge and the flexibility as well as the ratio between the hydrophobicity and the hydrophilicity. Handling, processing, and storage of raw materials will all affect the functional properties and it is therefore important to both characterize the functional properties of the raw material and find out how the different processing steps will affect these properties.
Complexities of conflict: the importance of considering social factors for effectively resolving human–wildlife conflict

Human–wildlife conflict is one of the most critical threats facing many wildlife species today, and the topic is receiving increasing attention from conservation biologists. Direct wildlife damage is commonly cited as the main driver of conflict, and many tools exist for reducing such damage. However, significant conflict often remains even after damage has been reduced, suggesting that conflict requires novel, comprehensive approaches for long‐term resolution. Although most mitigation studies investigate only the technical aspects of conflict reduction, peoples' attitudes towards wildlife are complex, with social factors as diverse as religious affiliation, ethnicity and cultural beliefs all shaping conflict intensity. Moreover, human–wildlife conflicts are often manifestations of underlying human–human conflicts, such as between authorities and local people, or between people of different cultural backgrounds. Despite evidence that social factors can be more important in driving conflict than wildlife damage incurred, they are often ignored in conflict studies. Developing a broader awareness of conflict drivers will advance understanding of the patterns and underlying processes behind this critical conservation issue. In this paper, I review a wide variety of case studies to show how social factors strongly influence perceptions of human–wildlife conflict, and highlight how mitigation approaches should become increasingly innovative and interdisciplinary in order to enable people to move from conflict towards coexistence.
Aflatoxin B1 induced pathomorphological changes in lymphoid organs of broilers.

The present study reports the pathomorphological changes in lymphoid organs induced by aflatoxicosis in broiler chicken. One hundred and eighty day-old broiler chicks were obtained and divided into six groups of thirty birds each (Group I, II, III, IV, V and VI) and they were given 0, 20, 40, 60, 80 and 100 ppb of AFB1 respectively. Severe lymphoid depletion along with decreased bursa weight were recorded in Group IV, V and VI. Spleenic atrophy and lymphoid depletion was noticed in all the groups except in Group V and VI on 45th day. Thymus revealed lymphoid depletion in all the groups throughout the experimental period.
Antifungal activity of plant extracts against Embellisia astragali, the fungal causal agent of yellow dwarf and root-rot disease of standing milkvetch

Abstract. In an attempt to find biological fungicides, we screened 18 medicinal plants used in Chinese traditional medicine for their activity against Embellisia astragali, the causative fungus of yellow dwarf and root-rot disease in standing milkvetch (Astragalus adsurgens Pall.). The antifungal eﬃcacy of ethanolic extracts of these plants was tested in vitro. Our results show that among the 18 plants tested, the ethanolic extracts of Saposhnikovia divaricata, Allium sativum and Juglans regia totally inhibited mycelial growth of E. astragali. These three extracts also significantly inhibited spore germination of E. astragali, with inhibition rates ranging from 86% to 88%. In addition, the same extract from the same plant part indicated the strongest antifungal activity against E. astragali, with a minimal inhibitory concentration value of 50 mg mL–1. These results demonstrate that plant-derived products have a high potential to control yellow dwarf and root-rot disease in standing milkvetch.
HPV-16 E6、E7基因慢病毒真核表达载体的构建及鉴定

日的构建人乳头瘤病毒（HPV）E6、E7基因慢病毒真核表达载体。 方法以Si Ha宫颈癌细胞总RNA为模板,利用RT-PCR技术扩增出E6、E7日的片段;选用病毒载体p Lenti6/V5 Directional TOPO Cloning Kit系统构建E6、E7基因慢病毒真核表达载体;分别使用构建好的E6、E7载体转染病毒包装细胞,获得含病毒的上清液,并测定上清液中慢病毒的滴度。 结果质粒测序所得序列与人乳头瘤病毒E6、E7基因序列完全吻合,载体构建成功;慢病毒滴度测定结果显示E6样品的慢病毒滴度为1. 5×108TU/m L,E7样品的慢病毒滴度为2×108TU/m L,该滴度能够满足后续研究所需。 结论 HPV-16 E6、E7基因慢病毒真核表达载体构建成功,可以为进一步研究人乳头瘤病毒E6、E7基因致病机理奠定物质基础。
A Novel Family of Major Histocompatibility Complex Class I Genes in Marsupials and Monotremes

The Major Histocompatibility Complex (MHC) class I family of genes encode for molecules that have well-conserved structures, but have evolved to perform a diverse functions. The availability of an opossum genome from the grey, short-tailed opossum, Monodelphis domestica, has allowed for analysis of MHC class I genes in a marsupial. Traditional methods for gene discovery uncovered 13 MHC class I genes in the opossum. Utilization of a novel method to search for MHC domain structures discovered a family of 17 novel MHC class I genes. These genes, named ModoUT1-17, were located in a cluster on chromosome 1, unlinked to the MHC. UT homologues are only found in marsupial and monotreme genomes, consistent with being ancient in mammals yet lost in eutherians. Twelve of the ModoUT loci are transcribed in the opossum thymus. The majority of UT transcription is in the thymus or skin, with limited expression in other tissues. Full-
Desarrollo testicular y pubertad de la raza guzerat desde el destete hasta los 36 meses de edad bajo condiciones de manejo extensivo en la sierra minera

El presente estudio caracterizo el desarrollo testicular, evaluo la asociacion existente entre el perimetro escrotal (PE) y el volumen testicular (VOL) e identifico los parametros testiculares en la pubertad en machos de la raza guzerat. Se evaluaron 330 machos que totalizaron 1757 observaciones realizadas cada tres meses, desde el destete hasta los 36 meses. Se realizaron mediciones del PE, longitud y ancho testiculares. Se calculo el VOL siguiendo el metodo descrito por Fields et al. Los animales que presentaron PE ≥ 20 cm fueron sometidos a la recoleccion de semen utilizando estimulo electroeyaculatorio. Se consideraron puberes los animales que presentaron por lo menos un espermatozoide movil en el eyaculado. La curva de desarrollo testicular se describio utilizando la funcion logistica, siendo el punto de inflexion maximo del perimetro escrotal y del volumen testicular a los 13,2 meses de edad (18,1 cm) y 23,3 meses de edad (389,4 cm3), respectivamente. La tasa de crecimiento promedio del perimetro escrotal y volumen testicular antes y despues del punto de inflexion fueron respectivamente 0,58 cm/m; 16,3 cm3/m; 0,29 cm/m; 7,7 cm3/meses de edad. La edad promedio en la pubertad fue de 19,6 meses, con 250,6 kg de peso, 22,8 cm de perimetro escrotal y 284,7 cm3 de volumen testicular. La proporcion de machos puberes en la franja de 12-16 meses fue de 7,4 %; de 16-20 meses, 41,23 %; de 20-24, 68 %; de 24-28 fue de 91,96 %. A los 24 meses de edad 91,96 % de los animales se encontraban puberes. Se verifico una alta correlacion positiva entre PE y VOL (r = 0,91; P < 0,001). Estos resultados indican que en la raza guzerat el perimetro escrotal predice de forma eficiente el volumen escrotal, pudiendo ser usado como una medida segura para la seleccion de jovenes reproductores.
Characterization of Interleukin 10 gene variations and serum levels as predictive factors for the clinical outcome of Non-Hodgkin Lymphoma patients and Analysis of molecular mechanisms of Interleukin 10 gene regulation in B cells

Aggressive Non-Hodgkin lymphoma (aNHL) comprises a heterogeneous group of lymphatic malignancies. Although current treatment regiments can achieve high response rates, many patients do not achieve complete remission. Reliable and clinically applicable prognostic markers are needed to improve treatment strategies. Previous studies suggested a role for the cytokine interleukin 10 (IL10) for the initiation and progression of lymphomas. Conflicting data about associations of IL10 gene variations or elevated IL10 serum levels with the clinical outcome of aNHL exists. Therefore, this study aimed at elucidating whether these two factors could be of prognostic relevance for aNHL outcome in independent larger clinical cohorts and to investigate molecular mechanisms contributing to this. Overall 1724 aNHL patients from three different clinical trials (NHL-B, RICOVER-60 and MInT) have been included into this study. 604 patients were from RICOVER-60 trial, of which sera were available from 523 patients. Survival analyses revealed that patients with low IL10 serum levels had a better treatment outcome compared to patients with elevated IL10 serum levels. This is also true for patients, treated with Rituximab in addition to chemotherapy, which is the current standard therapy. Therefore, circulating levels of IL10 could be of prognostic relevance for aNHL outcome. In addition, in vitro studies showed that IL10 treatment of target cells seems to reduce Rituximab-mediated antibody dependent cellular cytotoxicity (ADCC) but not complement dependent cytotoxicity (CDC). Furthermore, it was found that homozygous carriers the of IL10-11.668AA far distal IL10 gene variation, located within an evolutionary conserved sequence, showed a better treatment outcome compared to carriers of the other two genotypes in the RICOVER-60 cohort (OS: HR=0.6; CI= 0.38-0.95; EFS: HR=0.6; CI= 0.41-0.87). Chromatin immunoprecipitation (ChIP) of modified histones revealed enhancer specific histone modifications around IL10-11.668G/A and other conserved sequences in transformed B cells. Therefore, they seem to be involved in IL10 gene regulation. Moreover, a very long non-coding RNA has been found to be transcribed from the IL10 gene locus. The results of this study confirm an important role for IL10 in the clinical course of aNHL and provide new insight into the structure and regulation of the IL10 gene.