Miracle-dz/UniFAR-FTUs huggingface dataset:
AN ANALYSIS OF BACTERIAL GROWTH KINETICS: THE TRADEOFF BETWEEN THE GROWTH RATE AND YIELD, AND THEIR EFFECTS IN THE ENVIRONMENT

OF THE THESIS An Analysis of Bacterial Growth Kinetics: The Tradeoff between the Growth Rate and Yield, and Their Effects in the Environment by Elinor W. Williams Master of Science in Biology San Diego State University, 2011 This thesis will be addressing the various relationships that can occur between the growth rate, μ and yield, Y, especially the inverse relationship, known as the rate yield tradeoff (RYTO), which can have significant effects on microbial communities as the understanding of this relationship at the community level is not well understood. The yield, Y is often excluded in the scientific literature. This thesis will review two definitions of the growth rate, μ, and one definition of yield, Y. The main body of this thesis will analyze the physiological conditions, where the inverse relationship between μ and Y is observed, and the effects of the tradeoff, resulting from this inverse relationship on microbial communities. Under stress conditions, the inverse relationship does not exist. A positive relationship can also occur between the two variables under other conditions. The conclusions are that the negative relationship between μ and Y can have many ecological and evolutionary implications and this concept needs to be scaled up to biochemicalgeosystems.
Environmental and geometric drivers of small mammal diversity along elevational gradients in Utah

The mechanisms shaping patterns of biodiversity along spatial gradients remain poorly known and controversial. Hypotheses have emphasized the importance of both environmental and spatial factors. Much of the uncertainty about the relative role of these processes can be attributed to the limited number of comparative studies that evaluate multiple potential mechanisms. This study examines the relative importance of six variables: temperature, precipitation, productivity, habitat heterogeneity, area, and the mid-domain effect on patterns of species richness for non-volant small mammals along four neighboring mountain ranges in central Utah. Along each of these elevational gradients, a hump-shaped relationship of richness with elevation is evident. This study evaluates whether the processes shaping this common pattern are also common to all gradients. Model selection indicates that no one factor or set of factors best explains patterns of species richness across all gradients, and drivers of diversity may vary seasonally. These findings suggest that commonality in the pattern of species richness, even among elevational gradients with a similar biogeographic history and fauna, cannot be attributed to a simple universal explanation.
Interactions of the Invasive PathogensSalmonella typhimurium, Listeria monocytogenes, and Shigella flexneri with M Cells and Murine Peyer’s Patches

ABSTRACT Invasive enteric bacteria must pass through the intestinal epithelium in order to establish infection. It is becoming clear that a common target for intestinal mucosa penetration is the specialized epithelial cell of Peyer’s patches, the M cell. In order to gain a better understanding of how bacteria interact with M cells, we have compared the interactions of Salmonella typhimurium,Listeria monocytogenes, and Shigella flexneriwith M cells by using a murine ligated-loop model. Our results indicate that S. typhimurium possesses a highly efficient mechanism for M cell entry that targets and destroys these cells, while L. monocytogenes and S. flexneri appear to be internalized into M cells in a less disruptive fashion. Early uptake ofListeria or Shigella into M cells appeared to lead to the death of some cells, as evidenced by the appearance of holes in the intestinal epithelium. At later time points, the follicle-associated epithelium of animals infected with these bacteria displayed extensive destruction. These data indicate that enteric pathogens use different strategies to interact with M cells and initiate infection of a host.
The Illness of Vincent van Gogh

Vincent van Gogh (1853–1890) was a wonderfully accomplished artist whose work is now widely appreciated. He created a great number of masterpiece paintings and drawings in just one decade devoted to art. His productivity is even more remarkable when considered in the context of his debilitating illness. He suffered from medical crises that were devastating, but in the intervening periods he was both lucid and creative. He left a profound, soul-searching description of his jagged life in his correspondence, which provides the basis for the present analysis. An inherited metabolic disease, acute intermittent porphyria, accounts for all of the signs and symptoms of van Gogh’s underlying illness. On this 150th anniversary of the birth of Vincent van Gogh it is appropriate to revisit the subject and to analyze the lack of organized skepticism in the popular media about other diagnoses.
GENETIC VARIATION IN YIELD PERFORMANCE FOR THREE YEARS IN NIGELLA SATIVA L. GERMPLASM AND ITS ASSOCIATION WITH MORPHO-PHYSIOLOGICAL TRAITS AND BIOCHEMICAL COMPOSITION

In the present study, thirty two genotypes of Nigella sativa L. , germplasm were evaluated for various agriculturally important traits for 3 consecutive years along with biochemical composition. Low variance was recorded in four genotypes viz., Pk-020545, Pk-020561, Pk-020576 and Pk-020646 that indicated stability. Performance of the most of the genotypes was affected by environmental fluctuations that might be attributed to cultural practices or genetic inference. High genetic variability and heritability provide an estimate and opportunity for breeders to select the promising genotypes for specific traits. The association of oil content and fatty acid methyl esters profile (oil extracted with n-hexane) revealed that linoleic acid was significant with yield during first year. Oil content, oleic acid, linoleic acid, monounsaturated fatty acids (MUFA), and polyunsaturated fatty acids (PUFA) (with n-hexane) were significant during second year. Zn was significantly associated with yield obtained in the third year traits with high significance could be exploited for further hybridization and breeding program is suggested. By employing biotechnological tools in preparation of effective and safe products can be obtained, additionally they could play important role in medicinal plants cultivation, new sources of production of bioactive secondary metabolites and other aspects of medicinal plant biochemistry.
A new species of sea anemone from the Chilean fjord region, Paraisanthus fabiani (Actiniaria: Isanthidae), with a discussion of the family Isanthidae Carlgren, 1938

A new species of Paraisanthus, P. fabiani, is described from Chile, the eighth species of this small family of mesomyarian anemones. Specimens of this species are characterized by six pairs of macrocnemes and 18 pairs of microcnemes in the middle and lower column and a fourth incomplete cycle of extremely small mesenteries in the uppermost column, between 66 and 110 tentacles, and a smooth column without holotrichs or heterotrichs. Specimens occur from the shallow subtidal to at least 30 m around exposed islands and in less protected channels of the fjord region between Chiloe Island (41°7’04.8’’S; 73°53’02.4’’W) and the Madre de Dios Archipelago (50°20’23.1’’S; 75°22’39.2’’W). They often protrude from small rocky crevices or between polychaete tubes, so that in situ only the oral disc is visible. The description is based on examination of 27 specimens collected between 1997 and 2007 and on documentation of live specimens in both their natural environment and aquaria. Paraisanthus fabiani was found at only 15 of over 150 study sites along the Chilean coast. If it was present at a site, generally more than 10 specimens were found. For the first time, in situ photographs are provided for a member of the family Isanthidae. In addition, live photographs are provided for the type species of the family Isanthidae, Isanthus capensis from South Africa. Family Isanthidae constitutes five genera, which are distinguished mainly by number of macrocnemes, texture and division of the column, and direction of growth of mesenteries.
Role of reduced glutathione in improving post-thaw seminal parameters in poor freezable Jersey crossbred bull semen

The role of reduced glutathione in improving the post thaw seminal characters in good and poor freezable Jersey crossbred bull semen was studied and compared with the control group. Two test groups, the test group each contains 18 ejaculates in both good and poor freezable bull. The reduced glutathione was added (5mM) to the conventional Tris extender, fast freezing and followed by thawing and measured the post thaw seminal parameters. Out these parameters the total motility has showed significant (p < 0.05) different between the two groups in both freezable bull semen, where as the other parameters such as livability, total sperm abnormality, loss of acrosomal integrity, percentage of hypo osmotic swelling positive sperm and vanguard distance traveled by sperm (mm/hour) in cervical mucus were highly significant (p < 0.01) between the reduced glutathione treated and control group. However, the lipid peroxide formation is none-significant between the two groups, but the glutathione had reduced the production of more ROS as compared to the control group. The addition of reduced glutathione had maintained the functional parameters of good and enhances the poor freezable semen. Thus the reduced glutathione improves post thaw sperm functional parameters such as motility, viability, functional membrane integrity and acrosomal integrity in poor freezable semen suggesting that addition of glutathione in semen extender may improve fertility in these bulls.
Effect of time of planting and spacing on flower production behaviour of statice (Limonium sinuatum) cultivars

A field trial was conducted to study the effect of time of planting and spacing on flower production behaviour of 6 cultivars of statice (Limonium sinuatum). The cultivars were Forever White, Forever Yellow, Forever Pink, Forever Blue and Forever Purple using 3 spacings 60cm × 30cm, 60cm×45cm and 60cm × 60cm and 2 plantings, i.e. November and December during 1994–95. Forever White produced maximum flowering stems (30.88) which were significantly better than those of Forever Pink (23.11) and Forever Purple (18.44) when planted in November. Plant spacing of 60cm × 45cm produced maximum stems (23.05) in December planting. Forever White took more time (104.66) days, whereas Forever Purple lesser time (87.44 days) in November and (88.33 days) in December to bolt.
Controle estratégico do carrapato Amblyomma cajennense em eqüinos

Infestations by Amblyomma cajennense on horses grazing in a pasture (pasture 1) under natural conditions were evaluated quantitatively before and after acaricide treatments performed at seven day-intervals on the horses during the period of A. cajennense larvae and nymphs predomination on the horses (April to October). Horses grazing in another area (pasture 2) were subjected to acaricide treatments every seven days however, only during the larval predominating period (April to July). Acaricide treatments were performed using a commercial alfametrin (Pyrethroid) composition. The reduction of A. cajennense adult tick loads on horses after the acaricide treatments was 89.7 and 58.6% for horses from pastures 1 and 2, respectively. The reduction values of adult female ticks were even greater (95.4 and 69.0% for horses from pastures 1 and 2, respectively). The results comprove the efficacy of a strategic control protocol of A. cajennense on horses which is based in acaricide treatments every seven days during the periods when infestations by A. cajennense larvae and nymphs predominate on the horses.
Novel Genus of Phages Infecting Streptococcus thermophilus: Genomic and Morphological Characterization

Despite decades of research and adapted antiphage strategies such as CRISPR-Cas systems, virulent phages are still a persistent risk for the milk fermentation industry worldwide, as they can cause manufacturing failures and alter product quality. Phages P738 and D4446 are novel virulent phages that infect the food-grade Gram-positive bacterial species Streptococcus thermophilus. These two related viruses represent a fifth group of S. thermophilus phages, as they are significantly distinct from other known S. thermophilus phages. Both phages share similarities with phages infecting nondairy streptococci, suggesting their recent emergence and probable coexistence in dairy environments. These findings highlight the necessity of phage surveillance programs as the phage population evolves in response to the application of antiphage strategies. ABSTRACT Streptococcus thermophilus is a lactic acid bacterium commonly used for the manufacture of yogurt and specialty cheeses. Virulent phages represent a major risk for milk fermentation processes worldwide, as they can inactivate the added starter bacterial cells, leading to low-quality fermented dairy products. To date, four genetically distinct groups of phages infecting S. thermophilus have been described. Here, we describe a fifth group. Phages P738 and D4446 are virulent siphophages that infect a few industrial strains of S. thermophilus. The genomes of phages P738 and D4446 were sequenced and found to contain 34,037 and 33,656 bp as well as 48 and 46 open reading frames, respectively. Comparative genomic analyses revealed that the two phages are closely related to each other but display very limited similarities to other S. thermophilus phages. In fact, these two novel S. thermophilus phages share similarities with streptococcal phages of nondairy origin, suggesting that they emerged recently in the dairy environment. IMPORTANCE Despite decades of research and adapted antiphage strategies such as CRISPR-Cas systems, virulent phages are still a persistent risk for the milk fermentation industry worldwide, as they can cause manufacturing failures and alter product quality. Phages P738 and D4446 are novel virulent phages that infect the food-grade Gram-positive bacterial species Streptococcus thermophilus. These two related viruses represent a fifth group of S. thermophilus phages, as they are significantly distinct from other known S. thermophilus phages. Both phages share similarities with phages infecting nondairy streptococci, suggesting their recent emergence and probable coexistence in dairy environments. These findings highlight the necessity of phage surveillance programs as the phage population evolves in response to the application of antiphage strategies.
Molecular detection of Mycobacterium tuberculosis from bovine milk samples

Mycobacterium tuberculosis and Mycobacterium bovis are the major causes of tuberculosis. These may infect many animal species, and are likely to be the main source of infection in humans. A total of 181 bovine raw milk samples and 123 pre-scapular lymph node biopsy samples were collected and subjected to acid fast staining, fluorescent staining, isolation and identification. Genus specific PCR to identify the Mycobacterium tuberculosis complex (MTBC) organism, and multiplex PCR (mPCR) were done to differentiate M. tuberculosis and M. bovis. Among the milk samples tested, only one sample was culture-positive for M. tuberculosis. Four samples were positive by MTBC-PCR and mPCR; all these four were proved to be M. tuberculosis. It is quite likely that animals can be infected with human-originated M. tuberculosis, which in turn may act as a source of infection in humans, becoming a reverse zoonosis. Hence, control strategies for human tuberculosis caused by M. tuberculosis should necessarily include the control strategies in animals too.
Taxonomy and Distribution of Narrow-Mouth Frogs of the Genus Microhyla Tschudi, 1838 (Anura: Microhylidae) from Vietnam with Descriptions of Five New Species

We review the taxonomy and distribution of Microhyla Tschudi, 1838 (Anura: Microhylidae) species from Vietnam, with a special regional focus on the southern parts of the Annamite mountain range (Kon Tum and Langbian Plateaus, Tay Nguyen highlands) and its foothills. Recent field work in this area revealed specimens of five yet undescribed species, which are differentiated from all congeners by a combination of morphological traits: Microhyla pineticola sp. nov. from Lam Dong and Dak Lak provinces; Microhyla pulchella sp. nov. from Lam Dong Province; Microhyla minuta sp. nov. from Dong Nai Province; Microhyla darevskii sp. nov. from Kon Tum Province; and Microhyla arboricola sp. nov. from Dak Lak and Khanh Hoa provinces. Microhyla annamensis Smith, 1923 is redescribed based on recently collected material. The intrageneric systematic relationships of the new species are discussed. We provide first larval descriptions for four of the new species as well as for Microhyla annamensis Smith 1923. Notes on the breeding ecology and natural history of all above mentioned species are compiled for the first time. With Microhyla minuta sp. nov. and Microhyla arboricola sp. nov. we describe the probably smallest tetrapods currently known from mainland Southeast Asia. The latter species also represents the second record of a phytotelm breeder within the genus Microhyla . A key to the currently known Vietnamese species of Microhyla is provided.
Regression model for predicting the air resistance of fabric made from doubled yarns and with different weave structures

The purpose of the investigation is to model the effect of doubled yarns produced from conventional and compact yarns in three different combinations and weave structures on the air resistance of fabrics. A series of woven fabrics differing only in weave structures and having the common count and fabric sett was produced from three types of doubled yarns, namely compact/compact, conventional/conventional and compact/conventional. The hybrid combination was produced principally to reduce the cost of manufacturing doubled yarns. Essential data for the fabrics such as CFF (crossing over firmness factor), FYF (floating yarn factor), FFF (fabric firmness factor), mass per unit area, thickness and porosity were determined. Air resistance was determined by performing the standard test KES-F8 API. Analysis of the results in respect of fabrics produced from the compact/compact, conventional/conventional and conventional/compact yarns shows a strong correlation between the air resistance, porosity, CFF, FYF, FFF, mass per unit area and thickness (R = conventional/conventional 0.97, compact/compact 0.861, conventional/compact 0.974) and the generated statistical models have given the satisfactory prediction of air resistance. Among the parameters, thickness exerts a strong influence on the air resistance. It is concluded that in order to predict air resistance, a number of parameters are needed and any conclusion which has been drawn using only CFF and FYF should be treated with caution. Also the possibility of cost saving as a result of using hybrid doubled yarn has been pointed out.
Influence of stress history on the response of the dioecious plant Urtica dioica L. to abiotic stress

Background: Reaching maturity is thought to affect plant responses to stress, but few studies have examined thus far how stress periods during the juvenile phase can alter the response of plants in a mature stage, particularly in dioecious plants. Aims: This study tested the hypothesis that sex and stress history can alter the response of Urtica dioica plants to abiotic stress. Methods: Stress indicators (water content, chlorophylls, the F v/F m ratio and the extent of lipid peroxidation) were measured in leaves of juvenile and mature plants exposed to a combination of water and nutrient deficit, with an emphasis on evaluating the effects of stress during the juvenile phase on the stress response of mature plants. Results: Stress treatment during the juvenile phase affected plant response to stress during the mature phase. Leaves of reproductive shoots were the most sensitive to stress history, as shown by increases in lipid peroxidation in leaves of reproductive shoots relative to non-reproductive ones. Leaves of both shoot types responded similarly in males and females, which showed no significant differences in any of the parameters measured. Conclusions: Stress history appears to determine the response of mature U. dioica plants to abiotic stress, plants with a stress history showing acclimation to subsequent stress, leaves of non-reproductive shoots of both males and females being more stress tolerant and allowing plant survival under severe stress.
Physical and Functional Interaction between DNA Ligase IIIα and Poly(ADP-Ribose) Polymerase 1 in DNA Single-Strand Break Repair

ABSTRACT The repair of DNA single-strand breaks in mammalian cells is mediated by poly(ADP-ribose) polymerase 1 (PARP-1), DNA ligase IIIα, and XRCC1. Since these proteins are not found in lower eukaryotes, this DNA repair pathway plays a unique role in maintaining genome stability in more complex organisms. XRCC1 not only forms a stable complex with DNA ligase IIIα but also interacts with several other DNA repair factors. Here we have used affinity chromatography to identify proteins that associate with DNA ligase III. PARP-1 binds directly to an N-terminal region of DNA ligase III immediately adjacent to its zinc finger. In further studies, we have shown that DNA ligase III also binds directly to poly(ADP-ribose) and preferentially associates with poly(ADP-ribosyl)ated PARP-1 in vitro and in vivo. Our biochemical studies have revealed that the zinc finger of DNA ligase III increases DNA joining in the presence of either poly(ADP-ribosyl)ated PARP-1 or poly(ADP-ribose). This provides a mechanism for the recruitment of the DNA ligase IIIα-XRCC1 complex to in vivo DNA single-strand breaks and suggests that the zinc finger of DNA ligase III enables this complex and associated repair factors to locate the strand break in the presence of the negatively charged poly(ADP-ribose) polymer.
Palaeobiology and evolution of the late Cenozoic freshwater molluscs of the Turkana Basin: Unionidae Rafinesque, 1820, partim Coelatura (Bivalvia: Unionoidea)

The Plio-Pleistocene freshwater molluscs of the Omo-Turkana Basin were long considered to be a prima facie example of punctuated equilibrium evolution. However, the absence of a study on their taxonomy has significantly hampered the debate on assumed evolutionary patterns. This paper addresses the systematics and palaeobiology of the bivalve genus Coelatura Conrad, 1853 in the basin. It reveals that a Coelatura species was assigned to the extinct genus Pseudobovaria Adam, 1957 in earlier studies, while another species formerly assigned to Coelatura is not discussed here because it belongs to the extinct Pseudodiplon Adam, 1957. Six Coelatura species are recognized in the Plio-Pleistocene Omo-Turkana Basin, two of which are new to science: C. rhomboidalis sp. nov. and C. magna sp. nov. These two species are considered lacustrine adapted species, both with a strongly dorsally protruded umbo. This adaptation apparently evolved twice independently in the basin within a ∼1 Ma period, but it is not observed in any other fossil or extant Coelatura species. Three of the other Coelatura forms can be identified as belonging to the extant C. aegyptiaca, C. bakeri and C. alluaudi. Disentangling the genealogical relationships of these extant species with neontological techniques will provide a test of the palaeontological systematics here proposed. General evaluation of the Turkana Basin coelaturids, and particularly their apparent absence from the first so-called punctuative Suregei Isolate period, corroborates the hypothesis of biological invasions in the basin, but indicates that in situ evolutionary events occurred occasionally.