Miracle-dz/UniFAR-FTUs huggingface dataset:
6 Circular DNA Plasmids of Yeasts

I. INTRODUCTION In addition to chromosomes and mitochondrial DNA, the genomes of most yeasts encompass a variety of stable extrachromosomal elements. These include double-stranded DNA plasmids, such as 2-micron circle and 2-micron-circle-like plasmids described in this chapter; double-stranded RNA viruses, described by Wickner (this volume); and a variety of retrotransposons, reviewed by Boeke and Sandmeyer (this volume). Because these elements appear neither to confer any selective advantages to the cells in which they are resident nor to inflict any particular harm, they most likely represent various forms of benign molecular parasitism. As such, each type of extrachromosomal element has evolved various strategies to subvert aspects of the host’s reproductive machinery to its own ends without placing undue stress on the host itself. Recent attempts to appreciate the molecular basis for the delicate tightrope act underlying the successful persistence of 2-micron circle have revealed novel and elegant processes of genome replication and segregation. Probing these processes has provided new and valuable perspectives on the analysis of DNA metabolism, cellular and nuclear architecture, and segregation of nuclear components during division. Not only have these studies uncovered unexpected mechanisms for selective amplification of specific DNA sequences and control of DNA replication, but they also have afforded the development of specialized vectors that have facilitated the use of yeast in the scientific and commercial application of genetic engineering. In this paper, we summarize our current understanding of the molecular biology of 2-micron circle, with special emphasis on those processes responsible for its successful persistence.
Tópicos sobre la biología de la almeja burra Spondylus calcifer (Carpenter, 1857)

Spondylus calcifer es la especie de mayor tamano dentro de la familia Spondylidae en los mares del Continente Americano. S distribuye desde el Golfo de California Mexico, hasta Ecuador. Las areas de captura en nuestro pais se localizan principalmente en la costa este de Baja California Sur, Mexico. Las espeies tipicas del genero se caracterizan por tener la cicatriz del musculo abductor grande y en el centro de la concha. El area cardinal de la valva derecha mas grande y el ligamento esta profundamente hundido. Debido a la importancia ecologica y economica de S. cacifer se realizo un estudio sobre su biologia y ecologia basicas. Se encontraron organismos con alturas entre 40 y 170mm. S. calcifer difiere de S. princeps y S. leucacanthus por su tamano y coloracion cafe clara del rinon, las cuales son caracteristicas utiles para diferenciarlas. Las partes blandas alcanzan 122g de peso. El musculo abductor de S. calcifer puede alcanzar en promedio hasta el 55% del peso de las partes blandas. La temporada de reproduccion ocurre en verano y la gonada alcanza en promedio el 8% del peso de las partes blandas, mientras que los ovocitos maduros miden 55 micras de diametro en promedio.
Error-rate Prediction for Mouse-based Rectangular-target Pointing with no Knowledge of Movement Angles

In rectangular-target pointing, movement angles towards targets are known to affect error rates. When designers determine target sizes, however, they would not know the frequencies of cursor-approaching directions for each target. Thus, assuming that there are unbiasedly various angles, we derived models to predict error rates depending only on the target width and height. We conducted two crowdsourced experiments: a cyclic pointing task with a predefined movement angle and a multi-directional pointing task. The shuffle-split cross-validation with 60% training data showed R^2>0.81, MAE<1.3%, and RMSE<2.1%, suggesting good prediction accuracy even for predicting untested target sizes when designers newly set UI elements.
First report and molecular characterization of an isolate of Papaya ringspot virus (PRSV-W) detected in pumpkin in Cuba

In this work, a virus isolate collected from squash plants ( Cucurbita pepo L.), showing severe symptoms of mosaic and leaf deformation, grown in Cuba, was analyzed using indicator plants, electron microscopy, and phylogenetic analysis. Plants of Squash, cv. Caserta, inoculated with this virus isolate showed mosaic, leaf distortion and blistering symptoms, whereas papaya plants were immune and did not show any symptoms. A transmission electron microscopic examination of leaf dip preparations made from infected squash leaves revealed the presence of elongated and flexuous particles, approximately 780-800 x 12 nm in size. Genomic fragments containing the coat protein (CP) and HC-Pro genes, amplified by specific primers for Papaya ringspot virus, W strain (PRSV-W), showed amino acid identities of both genes higher than 94% when compared to other PRSV-W isolates from America. In the phylogenetic tree, this virus isolate has grouped with other virus isolates from America, Australia, and India and was more distant from the Asian isolates. Taken together, the analyses allow the conclusion that this virus isolate is a W strain of PRSV, detected for the first time in Cuba.
Evolution after gene duplication

Contributors. Preface 1 Understanding Gene Duplication through Biochemistry and Population Genetics (David A. Leberles, Grigory Kolesov, and Katharina Dittmar). 2 Functional Divergence of Duplicated Genes (Takashi Makino, David G. Knowles, and Aoife McLysaght). 3 Duplication Retention After Small- and Large-Scale Duplications (Steven Maere and Yves Van de Peer). 4 Gene Dosage and Duplication (Fyodor A. Kondrashov). 5 Myths and Realities of Gene Duplication (Austin L. Hughes and Robert Friedman). 6 Evolution After and Before Gene Duplication? (Tobias Sikosek and Erich Bornberg-Bauer). 7 Protein Products of Tandem Gene Duplication: A Structural View (William R. Taylor and Michael I. Sadowski). 8 Statistical Methods for Detecting Functional Divergence of Gene Familiies (Xun Gu). 9 Mapping Gene Gains and Losses Among Metazoan Full Genomes Using an Integrated Phylogenetic Framework (Athanasia C. Tzika, Raphael Helaers, and Michel C. Milinkovitch). 10 Reconciling Phylogenetic Trees (Oliver Eulenstein, Snehalata Huzurbazar, and David A. Liberles). 11 On the Energy and Material Cost of Gene Duplication (Andreas Wagner). 12 The Fate of a Duplication in a Network Context (Orkun S. Soyer). 13 Evolutionary and Functional Aspects of Genetic Redundancy (Ran Kafri and Tzachi Pilpel). 14 A Phylogenomic Approach to the Evolutionary Dynamics of Gene Duplication in Birds (Gene L. Organ, Matthew D. Rasmussen, Maude W. Baldwin, Manolis Kellis, and Scott V. Edwards). 15 Gene and Genome Duplications in Plants (Pamela S. Soltis, J. Gordon Burleigh, Andre S. Chanderbali, Mi-Jeong Yoo, and Douglas E. Soltis). 16 Whole Genome Duplications and the Radiation of Vertebrates (Shigehiro Kuraku and Axel Meyer). Index.
Function, phylogeny, and fossils : miocene hominoid evolution and adaptations

Function and Phylogeny in Miocene Hominoids C.V. Ward, et al. Comments on the Last Decades of Research on Miocene Hominoids and Hominid Origins D. Pilbeam. Inter-Relationships Between Functional Morphology and Paleoenvironments in Miocene Hominoids P. Andrews, et al. The Early Evolution of the Hominoid Face T.C. Rae. Functional and Phylogenetic Features of the Forelimb in Miocene M.D. Rose. Functional Anatomy and Phyletic Implications of the Hominoid Trunk and Hindlimb C.V. Ward. Dental Evidence for Diets in Some Miocene Catarrhines with Comments on the Effects of Phylogeny on the Interpretation of Adaptation R.F. Kay, P.S. Ungar. Miocene Hominoid Mandibles: Functional and Phylogenetic Perspectives B. Brown. Paleobiological and Phylogenetic Significance of Life History in Miocene Hominoids J. Kelley. Proconsul - Function and Phylogeny A. Walker. Afrophitecus - Function and Phylogeny M. Leakey, A. Walker. On the Relationships and Africa M.L. McCrossi, B.R. Benefit. The Taxonomy and Phylogeny of Sivapithecus Revisited S. Ward. Phyletic Affinities and Functional Convergence in Dryopithecus and Other Miocene and Living Hominids D. Begun, L. Kordo. 4 Additional Articles. Index.
Investigation of Multiple Concerted Mechanisms Underlying Stimulus-induced G1 Arrest in Yeast: A Dissertation

Progression through the cell cycle is tightly controlled, and the decision whether or not to enter a new cell cycle can be influenced by both internal and external cues. For budding yeast one such external cue is pheromone treatment, which can induce G1 arrest. Two distinct mechanisms are known to be involved in this arrest, one dependent on the arrest protein Far1 and one independent of Far1, but the exact mechanisms have remained enigmatic. The studies presented here further elucidate both of these mechanisms. We looked at two distinct aspects of the Far1-independent arrest mechanism. First, we studied the role of the G1/S regulatory system in G1 arrest. We found that deletion of the G1/S transcriptional repressors Whi5 and Stb1 compromises Far1-independent arrest, but only partially, and that this partial arrest failure correlates to partial de-repression of G1/S transcripts. Deletion of the CKI Sic1, however, is more strongly required for arrest in the absence of Far1, though not when Far1 is present. Together, this demonstrates that functionally overlapping regulatory circuits controlling the G1/S transition collectively provide robustness to the G1 arrest response. We also sought to reexamine the phenomenon of pheromone-induced loss of G1/S cyclin proteins, which we suspected could be another Far1-independent arrest mechanism. We confirmed that pheromone treatment has an effect on G1 cyclin protein levels independent of transcriptional control. Our findings suggest that this phenomenon is dependent on SCF but is at least partly independent of Cdc28
Snails can survive passage through a bird’s digestive system

Aim Predation is generally viewed as a factor that limits the distribution of animal prey species. However, in certain instances, such as seed dispersal, predation may enhance the dispersal capability of prey species. In a prior study, we found that land snails are preyed upon by the Japanese white‐eye (Zosterops japonicus) and the brown‐eared bulbul (Hypsipetes amaurotis) in the Ogasawara Islands. In this paper we provide experimental and field evidence indicating that land snails could potentially be dispersed through bird predation.
New gall midges (Diptera: Cecidomyiidae) from Papua New Guinea

Two new species of gall midges that feed on trees in Papua New Guinea are described. The larvae of Schizomyia novoguineensis Kolesik sp. nov. transform the flowers of Macaranga aleuritoides (Euphorbiaceae) into spherical galls preventing sexual reproduction of the host tree. The larvae of Rhopalomyia psychotriae Kolesik sp. nov. induce pustulate leaf galls on Psychotria ramuensis (Rubiaceae). Descriptions of adults and immature stages, and DNA sequences of the cytochrome oxidase unit I mitochondrial gene segment, are given for each of the new species.
In Vivo implantation Murine Modeling

xiv! Abbreviations . xvi! 1! Introduction . 1! 1.1! Rationale . 1! 1.2! Objectives . 2! 1.3! Outline of thesis . 3! 2! Literature review . 5! 2.1! Background to murine implantation . 5! 2.2! In vivo implantation murine modelling . 15! 3! Materials and methodology . 49! 3.1! Materials . 49! 3.2! Methodology . 70! 4! Results – Optimal and suboptimal in vivo implantation murine models . 91! 4.1! Natural mouse pregnancy . 91! 4.2! ET into superovulated recipient mice . 97! 4.3! Administration of progesterone antagonist following ET . 109! 4.4! Synchronous and asynchronous ET . 118! 4.5! Ability of Optimal Model to detect negative consequences of manipulated embryos . 149! 4.6! Ability of Suboptimal Model to detect positive consequences of manipulated embryos . 176! 5! Results Refinement of in vivo implantation murine models . 192! 5.1! Exploring the beginning of endometrial receptivity in natural mouse pregnancy . 192!
Genetic markers for beer-spoilage by lactobacilli and pediococci

The brewing industry has considerable economic impact worldwide; therefore, demand exists for a better understanding of the organisms that cause beer-spoilage. Low nutrient levels, depleted oxygen levels, high alcohol levels, and the presence of antimicrobial hop compounds all play a role in making beer an inhospitable environment for most microorganisms. Nonetheless, there are bacteria that are resistant to all of these selective pressures. The most common beer-spoilage bacteria are the Gram-positive lactic acid bacteria Lactobacillus and Pediococcus. It is currently believed that hop-resistance is the key factor(s) permitting Lactobacillus and Pediococcus bacteria to grow in beer. However, it is likely that in addition, ethanol-tolerance and the ability to acquire nutrients also play roles in the beer-spoilage ability of Lactobacillus and Pediococcus isolates. The ability of Lactobacillus and Pediococcus to grow in beer was assessed and correlated to the presence of previously described beer-spoilage related genes, as well as with the presence of novel genes identified in this study. Molecular and culture-based techniques for detection and differentiation between Lactobacillus and Pediococcus isolates that can and cannot grow in beer were established and described in detail. Interestingly, beer-spoilage related proteins were often found to share homology with multi-drug transporters. As such, the presence of these beer-spoilage associated genes was also compared to the ability of isolates to grow in the presence of a variety of antibiotics and, unexpectedly, beer-spoiling bacteria were found to be more susceptible to antibiotics than were non beer-spoiling isolates of the same genus. Additionally, it was found that isolates of Lactobacillus and Pediococcus that can grow in beer do not group phylogenetically. In order to fully appreciate the relationship of speciation with beer-spoilage, phylogenetic and whole genome/proteome studies were conducted to clarify the taxonomy of the Lactobacillus and Pediococcus genera. Through the research in this thesis, a greater understanding of the mechanism(s) enabling bacteria to grow in beer has been gained and taxonomy of the genera Lactobacillus and Pediococcus has been clarified.
Study of Small Area Estimation on Overdispersion Data with the Zero-Inflated Poisson Regression

Small area estimation method is a method that is widely used to estimate the parameters of sub populations based on available survey data with very small sample sizes. Infant mortality data is a rare occurrence in a certain period of time so that small area estimation model is used with Poisson distribution. However, infant mortality data has a large number of zero value in each survey unit, so that the data indicating the existence of overdispersion that will certainly have an effect on the estimation process, then the proposed model is small area estimation with zero-inflated Poisson. This study compares the small area estimation with Poisson regression and small area estimation with zero-inflated Poisson regression. The goodness of the model is tested through simulation and revealed that small area estimation with zero-inflated Poisson regression is better than small area estimation with Poisson regression. Implementation on infant mortality data in West Java also shows that small area estimation with zero-inflated Poisson regression is better than small area estimate with Poisson regression. It is indicated by smaller standard error of small area estimation with zero-inflated Poisson regression than small area estimation with Poisson regression model.
A new method for estimating animal abundance with two sources of data in capture–recapture studies

1. Mark–recapture studies are often used to estimate population size based on a single source of individual identification data such as natural markings or artificial tags. However, with the development of molecular ecology, multiple sources of identification can be obtained for some species and combining them to obtain population size estimates would certainly provide better information about abundance than each survey can provide alone.
The effects of in vitro culture on the leaf anatomy of Jatropha curcas L. (Euphorbiaceae) = Efeitos da cultura in vitro na anatomia foliar de Jatropha curcas L. (Euphorbiaceae)

Jatropha curcas (Euphorbiaceae) is an evergreen tree traditionally used in popular medicine, and also as a promising source for bio-fuel production. The in vitro propagation of this species has been studied as an alternative to conventional methods such as cutting and seedling. In vitro culture environment consists on closed flasks, with high relative humidity, reduced gas exchanges and artificial temperature and luminosity conditions. These conditions may induce physiological and anatomical alterations in cultivated plants. The occurrence of anatomical alterations on the leaves of J. curcas was examined in plants cultivated both in vitro and ex vitro , under greenhouse conditions. The stomatal index was higher on the leaves from greenhouse plants. Mesophyll thickness did not differ, but the greenhouse leaves presented an additional palisade layer, which reflects the environmental influence on cell division. The cells of the chlorophyllous parenchyma of young plants grown in greenhouse conditions have larger chloroplasts than those of the plants grown in vitro. The chloroplasts of mature leaves are similar in height, but the mitochondria are smaller. Current results indicate that the leaves of J. curcas respond distinctly to both environments. It is necessary to adjust the abiotic conditions in vitro to avoid precocious senescence, diagnosed by chloroplasts and mesophyll degradation.
Parallel cDNA synthesis from thousands of individually encapsulated cancer cells : Towards large scale single cell gene expression analysis

We present microfluidic droplet-based cDNA synthesis of 65 000 individually isolated lung cancer cells in parallel. Cells are encapsulated, individually lysed and the RNA from each cell is reverse transcribed in droplets at a massively parallel scale resulting in thousands of droplets each containing the cells gene expression profile encoded in stable DNA for downstream analysis (figure 1). This could be used for distinguishing between different cell types and study heterogeneity within a cell sample at high throughput scale.
A STUDY ON THE BIOCHEMICAL AND CELLULAR EFFECTS OF ENVIORMENTAL TOBACCO SMOKE ON ADULT AND DEVELOPING RAT BRAIN BIOCHEMISTRY

xi Motivation . xiii Research Objectives . xv Chapter 1 EFFECTS OF ENVIRONMENTAL TOBACCO SMOKE IN ADULT BRAIN . 1 1.1. Epidemiology of Environmental Tobacco Smoke in Adult Brian . 1 1.2. Molecular Effects of Environmental Tobacco Smoke Exposure . 3 2 EFFECTS OF ENVIRONMENTAL TOBACCO SMOKE ON ADULT RAT BRAIN BIOCHEMISTRY . 8 2.1. Abstract . 8 2.2. Introduction . 9 2.3. Experimental Procedures . 11 2.4. Results . 14 2.5. Discussion . 17
Comparative behaviour analysis of some colubrids with reference to suitability of captive bred snakes for reintroduction to natural habitat.

Comparative behaviour analysis of some colubrids with reference to suitability of captive bred snakes for reintroduction to natural habitat. A sample of newly hatched American colubrids, divided according to their level of domestication, understood herewith as the generation history in captivity, was tested in an open eld test (OFT) for degree of activity and con dence in open terrain and in confrontation with individuals of such species as Pantherophis guttatus and Lampropeltis getula splendida as well as L. g. californiae, in order to compare their antagonistic and feeding behaviour reactions. The cluster comparison of defence reactions revealed no effect of domestication (many generation in captivity) in the face of potential danger. Even albino phase Kingsnakes, considered to be the form of this species most affected by captivity (altered genome), maintained their natural feeding response. The degree of activity in OFT conditions was seen to decrease with the snakes’ age. Thus it was demonstrated that captive specimens bred in terrariums may be considered a gene bank for ex situ conservation strategy. However it is recommended that specimens as young as possible should be used in reintroduction to natural habitat, as these will respond most faithfully to the pressure of natural selection, based on their behavioural variation not supressed by apathy caused by captivity.
A Comparative Study on Limno-biological Aspects of the Dammed Lakes in the Youngsan River in Korea - Centering on Fish Fauna -

Some aspects of limno-biology of the five dammed lakes such as Tamyang, Changsong, Kwangju, Naju, and Youngsan Lake along the Yongsan River were investigated from June 1986 to July 1988 for the comparison on the lentic ecosystems in relation to the fish fauna. Sixty four fish species representing 48 genera and 21 families of fishes were collected in these dammed areas, which included 29 species of the family Cyprinidea and 40 speaies of the primary fresh-water fishes. Among, these, 12 species such as Rhodeus Acheilognothus yamatsutae, A canathorhodeus gracilis, Sarcocheilichthys nigripinis morii, S. variegatus wakiyae, Gnathopogon strigatus, Squalidus gracilis majimae, Microphysogobio yaluensis, Cobitis longicorpus sp, Liobagrus mediadiposalis and Odontobutis platycephala are enddmic to Korea. Leiocassis nitidus and Gasterosteus aculeatus which occur in these water areas take note of the zooge rographic study of Korea. The fish species in each of the dammed lakes is in proportion of the scale of the lakes such as 32 species in Thamyang, 40 species in Changsong, 24 species in Kwangju, 35 species in Jaju, and 52 species in Yongsan Lake. The dominant fish species of the 4 upper dammed lakes of Thamyang, Changsong, Kwangju and Naju Lake are Zacco platypus and Rhodeus uyekii, while those of Youngsan Lake are Hemiculter eigenmanni and Carassius auratus. This difference of fish species of those areas suggests that the upper damed lake differ from the lower dammed lakes in the habitable condition of fishes. The migratory fish species have significantly declined and will continue to decline in both population size and number of species in the dammed lakes in near future as a result of the dam construction barriers in the river estuary. The major migratory fishes of this water area are as follows; Anguilla japonica, Plecoglossus altivelis, Hypomesus olidus, Gasterosteus aculeatus, Konosirus Punctatus, Coilia ectens, Hemirhampus sajori, Mugil cephalus. Acanthogobius flavimanus, and Takifugu ocellatus.