Miracle-dz/UniFAR-FTUs huggingface dataset:
Microsatellites in plants: a new class of molecular markers

The present status of research on microsatellites, also called simple sequence repeats (SSRs) or short tandem repeats (STRs) in higher plants has been reviewed. Results on the occurrence, distribution and the level of polymorphism of different microsatellites examined or searched from DNA sequence databases for different plant materials have been tabulated and briefly described. Information on number of loci for each SSR and the number of alleles at each locus, wherever available, has also been included. Methods used for developing microsatellite markers have been briefly discussed, Achievements made and the future possibilities for the use of microsatellites in areas like selection and diagnostics in segregating populations, genome selection during gene introgression (in backcross programmes), genome mapping, gene tagging, cultivar identification, germplasm characterization, estimation of genetic relatedness, etc, have also been reviewed and critically discussed, The addition of microsatellite markers to the repertoire of other available molecular markers should prove very useful in a variety of research areas involving plant systems.
Ensayo experimental para el trasplante de colonias de coral naranja (Astroides calycularis, Pallas 1766); especie insignia del litoral sur de la Península Ibérica.

En la actualidad, se han realizado muchos estudios acerca de metodologias a emplear para el trasplante de corales y otros organismos debido al deterioro o perdida de estos como consecuencia de la actividad humana. Sin embargo, estos estudios se han centrado en mares tropicales y subtropicales del planeta. Muy pocos estudios han sido realizados en el Mar Mediterraneo para testar la adherencia, supervivencia y crecimiento de corales u otros organismos vivos trasplantados, y menos aun cuando se tratan de organismos desprendidos del sustrato por causas antropogenicas y/o naturales. En el presente trabajo se prueban dos materiales de fijacion para el trasplante de colonias de coral naranja (Astroides calycularis, Pallas 1766) en el sur de la Peninsula Iberica, especie endemica del litoral sur-occidental del Mediterraneo. Los datos han mostrado una eficiencia del 100% en adherencia, supervivencia y crecimiento en las colonias del coral estudiado, lo que demuestra que los fondos marinos degradados o deteriorados por diferentes causas pueden ser restaurados con una metodologia adecuada.
The wood boring amphipod Chelura terebrans

Chelura terebrans is a widely distributed wood boring amphipod belonging to the little studied family Cheluridae. Previous studies have hinted that C. terebrans belongs to a small number of animals capable of degrading lignocellulose without the aid of symbiotic gut microorganisms. This study utilises a broad range of techniques to gain a better understanding of C. terebrans and their ability to digest wood. Molecular phylogenetic analyses of two Chelurid species largely agree with the current taxonomic organisation of this family. Examination of C. terebrans using scanning electron microscopy has offered a better understanding of their digestive system and revealed, with the exception of robust lateralia, few morphological adaptations to accommodate such an unusual diet. This examination also found no evidence of gut-resident microflora. Furthermore, quantitative real-time PCR confirmed the absence of any substantial resident symbiotic extra- or intracellular bacteria in the digestive tract by revealing very low levels of bacterial 16S gene sequences in comparison to the symbiont-containing isopod Porcellio scaber. Despite finding no evidence for resident symbiont gut-microflora, in-gel and in vitro enzymatic assays using extracts isolated from the hepatopancreas suggests that C. terebrans possesses a considerable repertoire of endogenous enzymatic capabilities useful for the digestion of wood, including mannosidase, β-glucosidase and β-xylosidase, endo-1, 4-β-glucanase and endo-1, 4-β-xylanase, with extracts also possessing mono- and diphenol oxidase activity. Furthermore, mass spectrometry analysis on gel regions presenting high mono- and diphenol oxidase activity detected several proteins belonging to the glycosyl hydrolase family and haemocyanins. Two transcriptomic libraries were obtained from the hepatopancreases of C. terebrans fed on a diet of either beech (Fagus sylvatica) or Scots pine (Pinus sylvestris). These data provided sequences and the relative abundances of genes thought to be involved in lignocellulose digestion. In both cases, a significant number of the total ESTs contributed towards contigs corresponding to genes for glycosyl hydrolases and haemocyanins. Furthermore, overall expression of each glycosyl hydrolase suggested variation according to the substrate on which C. terebrans were fed. Comparisons of the relative gene expression seen in the C. terebrans transcriptome with those found in both the wood boring isopod Limnoria quadripunctata and the non boring amphipod Echinogammarus marinus offer insight into the genes important for lignocellulose digestion. This study represents substantial progress in our understanding of how C. terebrans digests wood and has also opened up new avenues of investigation by revealing C. terebrans as a potential source of novel lignocellulolytic enzymes.
Effects of alendronate on kidney tissue of ovariectomized rats.

Summary Alendronate is an aminophosphanate, selective inhibitory of bone resorbtion, used for treatment of osteoporosis in postmenopause. It is known that changes occurring in postmenopausal period effect the quality of life. In this study, effect of the alendronate treatment time on renal oxidative status was investigated in ovariectomized rats. Alendronate was intravenous administered at 0.3 mg/kg dosage on weeks 2, 4 and 8. Serum creatinine and uric acid levels and kidney malondialdehyde (MDA), glutathione (GSH), catalase (CAT), superoxide dismutase (SOD) and myeloperoxidase (MPO) level and activities were measured. Serum creatinine and uric acid levels increased in depending on the time of alendronate treatment on ovariectomized rats. Kidney MDA level and MPO activity increased in both ovariectomized and alendronate groups. Kidney GSH level and SOD and CAT activities decreased in the ovariectomized rats and these levels increased in depending on time of alendronate treatment. As a result, some oxidative changes occurred in the kidney tissue of ovariectomized rats with bone resorption and alendronate treatment increased the antioxidant capacity in depending on the time.
Evolution of colour discrimination in vertebrates and its implications for visual communication

The evolution of visual communication is explored in the context of recent findings of the potential for colour vision in the first vertebrates (the lampreys). Colour discrimination is important in visual communication in the aquatic realm, providing the basis for territorial, predatory and reproductive strategies among a large range of species. In order to perceive colour, a species must possess at least two cone photoreceptors with different spectral sensitivities and whose signals can be compared. The recent finding of five cone photoreceptors in a species of lamprey (Agnatha) suggests that the ancestral vertebrates had colour vision and that photoreception was based on photopic (cone-based) vision. This review explores the evolution of photoreception and spectral filters in vertebrates from a morphological, physiological and molecular perspective. Implications for the design of both visual signals and receptors and how these may be used in visual communication in early vertebrates is also discussed.
Molecular phylogenetic studies in nyctaginaceae: patterns of diversification in arid North America

MOLECULAR PHYLOGENETIC STUDIES IN NYCTAGINACEAE: PATTERNS OF DIVERSIFICATION IN ARID NORTH AMERICA by Norman Alan Douglas Department of Biology Duke University Date:_______________________ Approved: ___________________________ Paul Manos, Supervisor ___________________________ A. Jonathan Shaw ___________________________ John Willis ___________________________ Franҫois Lutzoni ___________________________ Richard Spellenberg An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Ph.D. in the Department of Biology in the Graduate School of Duke University
Significance of Protein Interactions in Mediating AF9 Function

III ACKNOWLEDGEMENT I would first like to express my deepest gratitude to my committee chair and mentor, Dr. Charles S. Hemenway for being an extraordinary mentor. This dissertation would not have been possible without his continuous support and guidance both personally and professionally. His enthusiasm and optimism always helped me to move forward towards my goal. I would also like to thank my committee members, Drs. and Clodia Osipo for their invaluable time and suggestions. Their critical thinking and vast knowledge always helped me to move in the right direction of my dissertation. I will always look forward for their guidance throughout my scientific career. A special thanks to Dr. Chris Wiethoff for being so patient in teaching me how to use FPLC in his lab. The milieu of lab is made by the lab mates and I feel so fortunate to have met wonderful and helping peoples in my laboratory. I would like to thank Amanda Winters, and especially Nisha Barretto for all their wonderful scientific discussions. It has been really great working with Nisha in the lab, which has great sense of scientific literature. I would also like to thank my other colleagues, Alyson Lokken, Yousaf Mian, Noah Birch, Laurie Risner and Nick for all their wonderful suggestions IV during lab meetings. Special thanks to my friend and senior, Deepali Bhandari for helping me in every way possible with my dissertation work. Finally, I wish to thank my family, without their support nothing would have been possible. Even words could not do the justice of thanking my father, Rajinder Lumba, and my mother, Sarvish Lumba for the support and help that they have provided. Their continuous belief and encouragement always helped me to pass through all the hard times. My brothers, Bharat and Sharad, who are pillars of my strength, always motivated me with their optimism. Continuous blessings from my grandmother, Satya Vati Lumba get me going through all these times. I would also like to thank my in-laws, Pitam Singh and Rita Malik for being so helpful and supportive through all these years. Their willingness to help whenever needed has been very much appreciated. Last but not the least; I would like to thank my loving husband, Rohit Malik and our adorable son, Armaan Singh Malik for making my PhD journey a memorable one. I believe I owe my husband the deepest gratitude for being so supportive, …
A Histopathological Spectrum of Gastrointestinal Tract Lesions in a Tertiary Care Centre in South Western Part of India: An Epidemiological Study

Background: Diseases of Gastro-intestinal Tract (GIT) are more common than any other systems in human body. Adenocarcinomas are more common in intestine. Aim and Objectives: To study the age, sex, and site wise distribution of various types of benign and malignant GI lesions. Material and Methods: The prospective study of 159 patients having gastrointestinal lesion were included in this study over a period of one year from October 2016 to September 2017. The materials were collected in the form of biopsy and resected specimens of gastrointestinal tract with relevant clinical history and sent in 10% Formalin and processed in automatic tissue processor. Routine Hematoxylin and Eosin stain and special stains were done wherever needed. Results: Out of total 5000 specimens 159 cases (3.18%) were GIT lesions, both benign and malignant. Appendicitis was the most common benign lesion comprising of 52.14% of cases. Adenocarcinoma being the most common type of gastrointestinal tract malignancy (48.57%). The second most common malignancy was squamous cell carcinoma (37.14%). Most common lesion of the oesophagus was squamous cell carcinoma whereas adenocarcinomas were the most common lesion of stomach and large intestine followed. Conclusion: Histopathological evaluation is the gold standard for the early detection of GI tract lesions especially malignant one hence it helps in their early management.
Reconstructing Biological Systems Incorporating Multi-Source Biological Data via Data Assimilation Techniques

More than twenty thousands genes are coded on human’s 3 billion base pairs of deoxyribonucleic acid (DNA) sequences. The functions of these genes are mutually regulated by their products, e.g., proteins and ribonucleic acid (RNA), and other factors, and the elucidation of the entire structure of these biological systems has broad utility in applications of drug development, medical treatment and preventive medicine. Therefore, this has been one of the major challenges in the field of systems biology. Especially, in recent technological advances in biotechnology, microarray technologies have been greatly contributed to systems biology researches since we can infer the regulatory relationships and biological processes by comparing the expression levels of RNAs and proteins in several conditions. In the field of systems biology, there exist two types of data obtained by microarrays; thus, time-course data and static (non time-course) data. The time-course data is a set of expression data measured at designed time points after drug stimulations, heat shocks and so on. The static data is measured at the steady state condition in knock-down cells, drug stimulated cells and so on. In this thesis, we handle the time-course microarray data for the elucidation of biological systems. In using such time-course observation data, there are two major approaches, i.e., simulationbased and statistical approaches. The simulation-based approach uses biologically validated mathematical equations, e.g., ordinary differential equation (ODE) and stochastic differential equation (SDE), to represent the complex dynamics of biological systems and has constructed several biological simulation models including gene regulatory networks and metabolic pathways by combining the accumulated knowledge of biomolecular reactions. Here, the purposes of these constructions are to understand the dynamic behavior of biological systems, to infer the relationships among genes and to predict the changes of their dynamics when adding or removing some biomolecules. However, we have two major problems in this approach; (i) we cannot apply this approach when most part of target systems are unknown due to computational difficulties in evaluating a lot of candidate models and (ii) we cannot handle systems consisting of ten or more genes due to a computational problem known as the curse of dimensionality. In contrast, the statistical approach uses highly abstract models with assumptions such as linearity and simply describes biological systems to infer relationships among several hundreds of genes from the data. In this approach, many computational methods, e.g., dynamic Bayesian networks, state space models (SSM) and vector auto-regressive (VAR) models, have been proposed. Recently, these approaches have further incorporated several biological findings, e.g., transcription factor (TF)
Analyse bioinformatique du transcriptome des champignons mycorhiziens Tuber melanosporum et Glomus intraradices

La symbiose mycorhizienne est une interaction mutualiste formee entre les racines des plantes terrestres et des champignons du sol. Les changements morphoanatomiques associes au developpement de cette symbiose sont accompagnes de modifications dans la regulation de l'expression genique. L'etude des profils transcriptomiques est donc fondamentale afin de caracteriser les mecanismes moleculaires gouvernant la symbiose mycorhizienne. Le developpement recent des approches de transcriptomique a haut debit offre de nouvelles perspectives pour la comprehension de ces mecanismes. Le travail entrepris dans le cadre de ce projet de these visait a caracteriser in silico le transcriptome symbiotique du champignon ectomycorhizien Tuber melanosporum et du champignon endomycorhizien Glomus intraradices. Il s'agissait de mettre en place les outils et les protocoles bioinformatiques permettant l'exploitation des donnees transcriptomiques issues des nouvelles technologies de sequencage, afin de caracteriser les transcrits exprimes par les symbiotes et d'identifier les genes regules au cours de la symbiose. Ce travail original a permis de souligner l'existence de traits communs aux profils d'expression des champignons mycorhiziens. De plus, la caracterisation du transcriptome de G. intraradices a permis d'etablir le premier repertoire de genes a l'echelle du genome pour un champignon endomycorhizien. Cette etude de genomique contribue a l'amelioration des connaissances sur les processus moleculaires qui sous-tendent la symbiose mycorhizienne et constitue une ressource unique pour de futures recherches sur les reseaux de genes controlant la symbiose
Helminths of small mammals (Erinaceomorpha, Soricomorpha, Chiroptera, Rodentia, and Lagomorpha) of Mongolia /

Ninety-eight species of small mammal, excluding carnivores and ungulates, are currently recognized in the fauna of Mongolia. a list of species of helminths known to infect these species, both within Mongolia and across their range, is presented in an effort to aid in their study. a detailed bibliography of pertinent survey and related publications is provided.
EPIDEMIOLOŠKO ISTRAŽIVANJE BOLESTI ŽIVOTINJA UZROKOVANIH SOJEVIMA CLOSTRIDIUM PERFRINGENS IZOLIRANIH IZ HRANE

C. perfringens is the primary cause of clostridial enteric diseases in domestic animals. Diagnostic difficulties result from common occurrence of these microorganisms in the intestinal tract of healthy vertebrates and laboratory serotyping methods cannot discriminate isolates reliably. C. perfringens caused disease may be confirmed by presence of these bacteria in feed and a, high number of these anaerobes in animal intestinal tract by typing methods of comparably high differentiation power.
Performance of selected strains of Lactobacillus bulgaricus, Streptococcus lactis and Saccharomyces cerevisiae alone and in different combinations in broilers

Dietary supplementation of the selected strains of Lactobacillus bulgaricus (L4), Streptococcus laetis (S 1) and Saccrharomyces cerevisae (Y3) alone and in different combinations on 'IBL-80' broilers revealed significantly higher growth rates (+14.05% and 10.15%) and feed efficiency ratio (+7.80 and 2.29%) coupled with zero mortality by the combination of the 3 microbes (L. bulgaricus + S. lactis + S. cerevisiae) and L4 of L. bulgaricus as compared to control during the starter phase. Contrary to this, none of the treatments showed significantly better performance than control during the finisher phase. The overall (1 to 6 weeks) growth performance and feed efficiency ratios were significantly (P<0.05) better under the treatments involving the combination of the 3 microbes (+7.22 and +2.55%) as well as L. bulgaricus (+6.86 and 2.55%) than that of control, and their performance may be correlated to significantly (P<0.05) higher digestibilities of dry matter and crude fibre. The differences tor the dressing percentage, gut pH and duodenal thickness under different treatments were statistically non-significant. On the basis of overall picture with respect to growth rate, feed efficiency ratio, mortality per cent, the combination of the 3 microbes (L. bulgaricus + S. lactis + S. cerevisiae) and L4 strain of L. bulgaricus was the most promising probiotics.
Comparaison de la production de complexes enzymatiques par fermentation en milieu solide et par fermentation en milieu liquide

La fermentation en milieu solide est un bioprocede pouvant eventuellement etre utilise comme technologie de rupture pour diminuer le cout des biocatalyseurs utilises dans la conversion de biomasse lignocellulosique comme le son de ble. La premiere partie de ces travaux de recherche a donc etudie le potentiel de cette technologie par rapport a celle de fermentation en milieu submerge lors d'une comparaison en application. Plusieurs tests de saccharification ont ainsi ete realises sur differentes matieres premieres (cellulose, son de ble) et ont permis de montrer l'avantage differentiateur des biocatalyseurs produits par fermentation en milieu solide. Ensuite, la deuxieme partie de ces travaux de recherche a porte sur l'etude des facteurs de la recalcitrance du son de ble a l'hydrolyse enzymatique. Deux principaux facteurs ont ainsi pu etre demontres : un facteur physique, lie a l'accessibilite des biocatalyseurs aux polysaccharides, et un facteur biochimique, lie a l'absence ou a la faible presence de certaines activites enzymatiques (feruloyl esterase,…) dans le complexe enzymatique de Trichoderma reesei Rut-C30. Cette etude a egalement permis d'identifier l'origine des differentes fractions glucidiques hydrolysees et de determiner le potentiel glucidique actuellement hydrolysable a partir de cette biomasse. Enfin, la derniere partie de ces travaux de recherche a ete consacree a l'etude pratique d'un concept innovant de procede permettant de favoriser la conversion des polysaccharides contenus dans le son de ble. Une levee de la barriere physique au transfert de masse et par consequent une validation de ce concept a finalement pu etre realisee.
Effect of vitamin D levels on radiographic knee osteoarthritis and functional status.

Objectives This study aims to investigate the effect of serum levels of 25 hydroxyvitamin D (25(OH)D) in patients with primary knee osteoarthritis (OA) and to assess its relationship with the radiographic grading and functional status. Patients and methods Serum 25(OH)D levels were measured in 107 patients (90 females, 17 males; mean age 63.0±9.6 years; range, 40 to 86 years) with primary knee OA. Radiographic grading was based on the Kellgren-Lawrence Grading Scale and the Osteoarthritis Research Society International (OARSI) Atlas Grading Scale, while the functional status was assessed using the Lequesne indices and Turkish version of the Knee Injury and Osteoarthritis Outcome Score-Physical Function Short-Form (KOOS-PS). Pain was evaluated using the Visual Analog Scale for Pain (VAS-Pain). Data including age, sex, disease duration, body mass index (BMI), and pain severity were recorded. Results The mean 25(OH)D level was 13.4±10.6 ng/mL, and 90 patients (84.1%) had vitamin D deficiency. The presence of severe osteophytes was observed in 67 patients (62.6%) and 85 patients (79.4%) had Grade 2-3 joint space narrowing (JSN). The mean KOOS-PS and Lequesne scores were 40.1±12.3 and 12.9±3.6, respectively. There was no correlation between serum 25(OH)D levels and functional status. Conclusion Our study results show that serum 25(OH)D level is not related to the severity of the radiographic knee OA grading or to the functional assessment. Age and BMI are the factors affecting the radiological knee OA severity, while age, sex, BMI, and pain severity are the main determinants of the functional status.
Quality of life in painful bone metastases : results from the Dutch bone metastasis study

This thesis focuses on several aspects of quality of life in patients with painful bone metastases, treated with palliative radiotherapy within the randomized Dutch Bone Metastasis Study.The detailed course of quality of life after treatment was studied, as was the relation between a pain response and quality of life. Also prognostic factors predicting a pain response, psychological distress, side-effects and survival were studied.