Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi-locus phylogenetic analyses support the monophyly and the Miocene diversification of Iksookimia (Teleostei: Cypriniformes: Cobitidae)

The genus Iksookimia contains six species of primary freshwater fishes that are endemic to South Korea. Previous phylogenetic studies, based on DNA sequence data from three or fewer loci, have suggested non-monophyly of the genus, providing inconsistent resolutions of the relationships of Iksookimia. Our coalescent and concatenation-based phylogenetic analyses, utilizing seven unlinked nuclear-encoded genes, strongly supported Iksookimia as a monophyletic group, emphasizing the importance of multi-locus data in investigating complicated phylogenetic relationships. A relaxed molecular clock analysis using fossil calibrations, indicated that the origin of the major lineages of Iksookimia occurred between ∼12 to 5 Ma, which is consistent with the Miocene uplift of the Taebaek and Sobaek Mountains and the Miocene activation of the major south-eastern faults. These palaeogeographic events may have served as vicariant events in the diversification of Iksookimia.
Cytochrome c oxidase subunit I variability in Ruditapes decussatus (Veneridae) from the western Mediterranean

Abstract Ruditapes decussatus (Linnaeus, 1758) (Veneridae) is an Atlanto-Mediterranean bivalve whose populations have experienced reductions and, in some instances, hybridisation with allochthonous R. philippinarum. Acquisition of additional genetic knowledge concerning the present R. decussatus populations is essential to address adequate conservation plans for this species. For this purpose, we analysed a portion of the mtDNA cytochrome c oxidase subunit I (COI) region in populations from the western Mediterranean, where this species represents a harvested fishery resource. Our analyses revealed an overall lack of genetic structure within the western Mediterranean area, and the occurrence of mtDNA substructuring between the Aegean and Marmara seas and the remaining populations from the whole Mediterranean basin and the South European Atlantic coast. The results obtained for populations from Sardinia, where extensive restocking programmes have not been reported and where R. philippinarum is rare and localised, suggest that intensive harvesting and potential dispersal alone may have been able to shape the genetic variation identified in the local R. decussatus populations.
Genetic mapping of QTL for bolting time after winter in sugar beet (Beta vulgaris L.)

An approach for a distinct yield increase in sugar beet could be the cultivation of autumn sown winter beets. To realize this cropping system it is required that bolting of sugar beets after winter has to be controlled genetically. The aims of my study were the identification and genetic mapping of quantitative genetic factors affecting post-winter bolting delay and post-winter bolting resistance in beet. These aims were pursued by QTL mapping in segregating populations derived from crossing parents with noticeable bolting behavior. In such a segregating sugar beet population the bolting behavior was phenotyped in F3 families as days to bolt, as well as bolting rate. This data was used in combination with the genetic map based on F2 single plants to map QTL for both traits of interest. One QTL for each trait which explained about 65 % of the phenotypic variation was successfully mapped to the same region on chromosome 9. In a further mapping population the traits of interest were transferred from a leaf beet accession. While the F2 population was segregating for both traits, in the F3 families only post-winter bolting delay could be assessed in two different experiments under natural overwintering conditions as well as after artificial cold treatment. The phenotypic data was used in combination with the developed genetic map based on F2 single plants for QTL mapping. In total, two QTL for bolting delay after artificial cold treatment could be successfully mapped to chromosomes 3 and 5 as well as three QTL for bolting delay under natural overwintering conditions (chromosome 3, 5 and 9) explaining up to 54,6 % of the observed phenotypic variation. Confidence intervals and QTL positions indicate that the QTL mapped on chromosome 3 as well as the QTL mapped on chromosome 5 reflect the same underlying genetic factors.
Mechanisms of hormonal regulation of CAD gene expression and inhibition by Aryl hydrocarbon receptor agonist in human breast cancer cells

Mechanisms of Hormonal Regulation of CAD Gene Expre ssion and Inhibition by Aryl Hydrocarbon Receptor Agonist in Human Breast Cancer Cells. (December 2005) Shaheen Munawar Ali Khan, B.Sc., St. Xaviers Colleg e; M.Sc., University of Mumbai Chair of Advisory Committee: Dr. Stephen H. Safe The CAD gene is trifunctional and expresses carbamo ylph sphate synthetase/aspartate carbamyltransferase/dihydrooro tase, which are required for pyrimidine biosynthesis. CAD gene activities are induced in MCF-7 human breast cancer cells, and treatment of MCF-7 or ZR-75 cells with 17 β-estradiol (E2) resulted in a 3-5 fold increase in CAD mRNA levels in both cell lines. E2 induced reporter gene activity in MCF-7 and ZR-75 cells transfected with a construct containing the growthresponsive –90/+115 (pCAD1) region of the CAD gene promoter, w hich contains three upstream GC-rich and two downstream E-box motifs. Deletion and mutat ion analysis of the CAD gene promoter demonstrated that only the GC boxes that bind Sp1 protein were required for E2-responsiveness. Results of gel shift and chromatin immunoprecipitation (CHIP) assays show that both Sp1 and estrogen receptor α (ERα) interact with the GC-rich region of the CAD gene promoter. Moreover, hormoneinduced transactivation of pCAD1 was inhibited by cotransfection with dominant-negative Sp1 expres sion plasmid and small inhibitory RNA for Sp1. These results dem onstrate that, in common with
Morphogenesis and plant regeneration from Anthurium andreanum cv Calypso leaf explant

Anthuriums are among the most attractive ornamental plants; however, the commercial production of these plants is limited by the slow propagation methods presently in use. This situation can be resolved with the application of in vitro culture techniques which allow massive plant propagation through morphogenic processes. Plant growth regulators (PGR) and the composition of the basal media comprising the culture medium are among the factors influencing the induction of morphogenesis. Optical and electron microscopy analysis suggested that the morphogenic routes induced were organogenesis and somatic embryogenesis. This report presents three protocols of morphogenesis, two for adventitious shoot organogenesis and one via somatic embryogenesis. The treatments which induced adventitious shoot organogenesis were Murashige and Skoog medium at half ionic strength supplemented with 0.2 μM of thidiazuron (TDZ) and 2.2 μM of 6-benzylaminopurine (BAP); 0.2 μM of TDZ and 6.6 μM of zeatin (ZEA); the treatment which induced somatic embryogenesis was 0.4 μM of TDZ and 0.5 μM of 2, 4-dichlorophenoxyacetic acid (2, 4-D). Key words: Anthuriums andreanum, morphogenesis, thidiazuron, 2, 4-dichlorophenoxyacetic acid (2, 4-D), organogenesis, somatic embryogenesis, electron microscopy.
THE GRASS GENERA ORCUTTIA AND NEOSTAPFIA: A STUDY IN HABITAT AND MORPHOLOGICAL SPECIALIZATION

Without a doubt, the endemic genera Orcuttia and Neostapfia are the most unusual and rarest of the California grasses. Orcuttia comprises five species and two varieties, while Neostapfia is monotypic. All are narrowly restricted annuals which develop in the summer beds of vernal pools and exhibit peculiar morphological features. Their relationship to other grasses is not apparent and quite likely they represent a relict group, the ancestors of which are unknown. Very few collections of them had been made up to the time Hoover (3) made known the degree of speciation and geographical range of the Orcuttia species. A relatively small number of these grasses has been collected since. In cooperation with the Department of Agronomy, University of California, Davis, and its grass research program, the author was privileged to spend part of the summer of 1958 observing the nature of the habitat and making extensive collections of these fascinating grasses. The results were very gratifying, and the success of this specialized exploration has prompted the author to present his findings and to provide additional information about the habit, habitat, and morphological development of these two unique genera in the California grass flora. The author is especially grateful for the helpful suggestions and criticisms by Dr. G. L. Stebbins, Department of Genetics, and Dr. Jack Major, Department of Botany, both of the Davis campus, University of California.
Effects of substituting alfalfa hay for concentrate on energy utilization and feeding cost of crossbred Simmental male calves in Gansu Province, China

From August to September 2015 (trial 1 [T1]) and September to November 2015 (trial 2 [T2]), the effects of replacing concentrate feed (C) with alfalfa hay (AH) on the daily gain (DG), dietary energy utilization status and the economic advantage of AH feeding for growing beef cattle were studied in crossbred male Simmental calves (n = 18) in Gansu Province, China. The target DG was set as 1 kg for both trials. Animals in each trial were allocated to a conventional feeding group (CTRL), a low-level AH feeding group (LA), and a high-level AH feeding group (HA). In a one-way-layout design, they were fed iso-energetic experimental diets comprising harvested corn stover (CS) and C (T1-CTRL, T2-CTRL), diets replacing 22% (T1-LA) or 44% (T1-HA) of the quantity of C for T1-CTRL with AH, and diets replacing 13% (T2-LA) or 25% (T2-HA) of the quantity of C for T2-CTRL with AH. Measurements of feed intake and DG, respiration and metabolism trials were performed for 49 and 41 days in T1 and T2, respectively. Average DG did not reach the target value for HA in T1 and CTRL in T2. Energy metabolizability was slightly greater for CTRL than for LA and HA in T1 and significantly greater for CTRL than for the other groups in T2. There was no marked difference in energy metabolizability between LA and HA in both trials. Dietary substituting AH for C did not impair the feed intake of the animals, but it did not improve feed efficiency. In terms of economic feasibility, low-level AH inclusion in the diets of growing beef cattle appeared more profitable at the 1-kg DG level as compared with CTRL and high-level AH inclusion, and should be practiced in the drylands of Gansu Province, China.
Roles of Calcium and ABA in Alleviating Drought Stress Effects on Triticum aestivum L. Plants

Drought is one of the lethal environmental stress factors that diminish the crop production worldwide. In this study, we assessed the damaging effects of drought stress; imposed by 20% polyethylene glycol (6000) treatments on wheat seedlings, and investigated the possible roles of calcium and abscisic acid (ABA) in alleviating drought stress. The pretreatment of wheat seedlings with calcium and ABA has led to improvements in growth criteria, content of photosynthetic pigments and membrane integrity under drought stress treatment. As a defense mechanism, the activity of peroxidase, and content of proline have increased under drought stress, but deceased when the wheat seedlings have been pretreated with calcium. The application of the calcium channel blocker; lanthanum chloride (LaCl3) has confirmed the alleviating role of calcium to the drought stress damaging effects. In this study, amino acids content, total soluble proteins and carbohydrates have been analyzed to further assess the physiological effects of drought and the alleviating roles of calcium and ABA. The improvements in yield criteria including % of mature grains per spike and weight of grains per spike with calcium pretreatment have confirmed the prolonged effect of calcium in alleviating the damaging effects of drought stress on wheat plants. Taken together, data presented in this study showed that calcium treatment may represent a powerful agent to counterattack the lethal effects of drought stress on plants.
Overall development of a bioprocess for the outdoor production of Nannochloropsis gaditana for aquaculture

In this paper, a systematic methodology is shown for the scaling-up of Nannochloropsis gaditana production for aquaculture uses. First, an adequate culture medium was developed, prepared using fertilizers instead of pure chemicals. Subsequently, the performance of N. gaditana was modelled as a function of average irradiance; this model being validated in continuous culture experiments. The model was used to determine the optimal dilution rate as well as the expected biomass concentration and productivity at optimal conditions. Finally, outdoor experiments were performed to confirm the model's validity and to determine optimal conditions at real production step. Biomass productivity values of up to 0.08 g L−1 day−1 were obtained at an optimal dilution rate of 0.25 per day in 0.2 m wide flat-panel reactors using culture medium containing 0.4 g/L NO−3 and 0.034 g/L·PO4−3. Fish trials with Atlantic Salmon demonstrated that the inclusion of produced biomass into fed increase the final weight up to 5%, thus confirming the adequacy of the biomass produced for aquaculture uses. The growth model and the scaling-up strategy proposed here are necessary to develop real industrial-scale processes capable of supplying microalgal biomass to the aquaculture markets, which in turn require a guaranteed supply and quality of the raw materials provided.
Identification and characterisation of new models for age-related hearing loss

Age-related hearing loss (ARHL), or Presbycusis, is the most prevalent sensory impairment observed in the elderly. It is a progressive, symmetrical, age-related sensorineural hearing loss, most pronounced at higher frequencies. ARHL is a multifactorial disease, with contribution from both environmental and genetic factors. To date, little progress has been made in determining the genetic loci involved. The aim of my doctorate studies is to elaborate upon the genetics underlying ARHL through the identification and characterization of ENU-induced mouse models of ARHL. This approach has identified trombone, a recessive model of ARHL arising from the Harwell Ageing Screen. Recurrent auditory phenotyping at 2, 6, 9 and 12 months of age shows that affected animals display elevated ABR thresholds from 9 months of age, when compared to littermates, and these are further increased at 12 months of age. Genome mapping studies identified a 12.5Mb critical region on chromosome 2 and next generation sequencing identified a TGC mutation in the novel deafness gene Slc4a10, causing a leucine to proline substitution in the encoded protein. Immunohistochemical staining of cochlear sections demonstrates that Slc4a10 is expressed in the type II and V fibrocytes of the spiral ligament of wildtype mice, whereas no labelling is observed in Slc4a10trmb/trmb mice. In addition, ultrastructural studies show progressive sensory hair cell loss (inner and outer) in the Slc4a10trmb/trmb mice from G6 months of age. Furthermore, histological assessment of the lateral wall identified strial thinning in the Slc4a10trmb/trmb mice. Given the expression pattern and morphological changes observed, endocochlear potentials were measured in these mice. This identified that Slc4a10trmb/trmb mice have a chronically low endocochlear potential compared to their wildtype and heterozygous littermates. My findings establish the presence of Slc4a10 in the inner ear and suggest an important role for this sodium-coupled bicarbonate transporter in normal auditory function. I hypothesize that trombone is a novel model of strial presbycusis and further functional characterization of this model promises to increase our understanding of the pathobiology associated with age-related hearing loss.
Interpreting differentiation landscapes in the light of long-term linked selection

Identifying genomic regions underlying adaptation in extant lineages is key to understand the trajectories along which biodiversity evolves. However, this task is complicated by evolutionary processes that obscure and mimic footprints of positive selection. Particularly the long-term effects of linked selection remain underappreciated and difficult to account for. Based on patterns emerging from recent research on the evolution of differentiation across the speciation continuum, I illustrate how long-term linked selection affects the distribution of differentiation along genomes. I then argue that a comparative population genomics framework that exploits emergent features of long-term linked selection can help overcome shortcomings of traditional genome scans for adaptive evolution, but needs to account for the temporal dynamics of differentiation landscapes.
Mechanisms controlling mRNA processing and translation: decoding the regulatory layers defining gene expression through RNA sequencing

The work described in this thesis focuses on the mechanisms that give rise to alternative mRNAs and their alternative translation into proteins. Each of the described studies has been based on a specific set of high-throughput RNA sequencing technologies. An overview of the available RNA sequencing methods, together with an introduction to different regulatory layers which define the expression of a gene, are presented in Chapter 1. Our work in Chapter 2 and Chapter 3 investigates the process of alternative polyadenylation. Chapter 2 shows the role of alternative polyadenylation in the context of oculopharyngeal muscular dystrophy. Chapter 3 describes genetic variants associated with alternative polyadenylation. Chapter 4 focuses on mechanisms controlling protein synthesis (translation) during skeletal muscle differentiation, highlighting changes in the use of alternative translation initiation sites. In Chapter 5 we investigated the interdependence between alternative regulatory events in gene expression. In this study, based on single-molecule full-length RNA sequencing, we demonstrated coordination and interdependence between alternative transcription initiation, alternative splicing, and alternative polyadenylation. Finally, Chapter 6 connects fundamental research in the RNA field with clinical care, describing new diagnostic and therapeutic approaches.
Biological parameters and population development of Tetranychus urticae Koch, 1836 (Acari: Tetranychidae) on different pepper cultivars

Bu calismada Tetranychus urtic ae Koch, 1836 (Acari: Tetranychidae)’nin farkli biber cesitleri arasindaki konukcu tercihi Bursa (Turkiye)’da 2015-2016 yillari arasinda kontrollu laboratuvar kosullarinda (16:8 aydinlik: karanlik, 27±1oC sicaklik, %65 ±5 orantili nem) elde edilen zararlinin gelisim, canlilik, ovipozisyon, hayat tablosu parametreleri ve populasyon gelisim verileri karsilastirilarak belirlenmistir. Alti farkli biber cesidi (BT-Ince Sivri, BT-Burdem, BT-Burkalem, AHCRI-Carliston, AHCRI-Yaglik ve AHCRI-Kandil Dolma) yapraklariyla yapilan testler sonucunda akarin yumurta acilimi, ergin oncesi donemlerinin gelisme suresi, kalitsal ureme yetenegi (r m ), net ureme gucu (R o ) ve toplam ureme orani (GRR) acisindan istatistiki anlamda onemli farkliliklar bulunmustur. Bu calismada, T. urticae farkli biber cesitleri uzerinde beslendigi zaman hayat tablosu parametre degerlerinin r m (0.16-0.24), R o (10.99-35.19) ve T (14.22-16.39) degisiklik gosterdigi belirlenmistir. Tetranychus urticae ’de onemli duzeyde daha dusuk biyodemografik parametre degerleri (r m , R o ve T) sirasiyla BT-Ince Sivri, BT-Burdem ve BT-Burkalem cesitlerinde saptanmistir. Buna ek olarak, bu uc cesidin biber fideleri uzerindeki populasyon yogunlugu da diger uc ceside (AHCRI-Carliston, AHCRI-Yaglik ve AHCRI-Kandil Dolma) gore onemli duzeyde daha dusuk bulunmustur. Ayrica, gelisme doneminde en dusuk akar canliligi BT-Ince Sivri cesidinde gozlemlenmistir. Sivri biber cesitleri arasinda ise istatistiki anlamda en dusuk hayat tablosu parametreleri BT-Ince Sivri cesidinde belirlenmistir. Sonucta, bulgular AHCRI-Carliston, AHCRI-Yaglik ve AHCRI-Kandil Dolma cesitlerinin diger uc ceside kiyasla T. urticae’ ye daha hassas oldugunu ortaya koymustur.
Induction of Malformation of the External Eye with Adhesive Parts and Other External Malformations Caused by a Single Dose of Hypervitaminosis A in Swiss Mouse Embryo

The result of this study shows a new type of eye malformations, when the pregnant mice were injected intraperitoneally in the 7 day of gestation, with a single dose of 15,000 IU of VA. We suggest to call this malformation as the external eye with adhesive and hard components. The external eye appeared in all living embryos and the histological studies showed five different forms of it. A description of other external malformations were discussed in details. ــــــ ـ ــــــــــــــ ـــ ـــــــــــــــــــــــــــ حاتفلا دبع بيسح نانج و ةعمج يرادنج دمح 17
In-vitro susceptibility to colistin and tigecycline in New Delhi metallo-beta- lactamase-1 producing Enterobacteriaceae

sample was faint positive by both the ICTs before and after administration of antimalarial therapy. It was found negative by both microscopy and molecular methods. Moreover, the QBC is found to be negative for all the parasitic forms as well as the pigment containing mononuclear cell, which persists for few days after clearance of parasites. This suggests that the faint band might be appeared falsely because of some nonspecifi c antibodies in the blood sample. [5] We know that, during pregnancy, there may be presence of certain nonspecifi c antibody such as rheumatoid factor etc., that can cross react with the immunoglobulin of ICT strip giving false positive result. The risk of false positivity increases with a less intense band. Hence, we suggest, during pregnancy, blood sample with weak positive band by ICT strip should be confi rmed by another method (i.e., microscopy or molecular method) before a malaria diagnosis is made. References