Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetics of age-related maculopathy & Score statistics for X-linked quantitative trait loci

Age-related maculopathy (ARM) is a common cause of irreparable vision loss in industrialized countries. The disease is characterized by progressive loss of central vision making everyday tasks challenging. The etiology is complex and has both an environmental and a strong genetic components. The public health relevance of the work is to improve the understanding genetic causes in the disease etiology and ultimately to lead to better disease management and prevention. From my ARM work, I present four papers covering range of statistical approaches. The first paper presents fine-mapping efforts, using both linkage and association methods, under previously identified linkage peaks on chromosomes 1q31 and 10q26. We replicate the discovery of the complement factor H (CFH) gene on 1q31 and identify a novel locus, harboring three closely linked genes (PLEKHA1, LOC387715, and HTRA1), on 10q26. Both discoveries have been widely replicated. In the next paper I present meta-analysis of 11 CFH and 5 LOC387715 data sets. We also replicate these findings in two independent case-control cohorts, including one cohort, where ARM status was not a factor in the ascertainment. In the third paper we replicate discoveries of new complement related loci (C2 and CFB) on chromosome 19p13 as well as developing classification models based on SNPs from CFH, LOC387715, and C2. The last paper focuses on applying statistical techniques from the diagnostic medicine literature to ARM. We comment on the importance of understanding the difference and similarities between different goals of genetic studies: improving etiological understanding or finding variants that discriminate well between cases and controls. This work is particularly relevant today when there has been explosion in the availability of direct-to-consumer DNA tests.In addition to carrying out linkage and association analysis, I also have extended the statistical theory behind score-based linkage analyses for X chromosomal markers. This work has public health relevance because many complex common diseases have sex-specific differences, such as prevalence and age of onset. Modeling those appropriately with powerful and robust methods will bring an improved understanding of their genetic basis.
Temperature affects the limitation of Daphnia magna by eicosapentaenoic acid, and the fatty acid composition of body tissue and eggs

Summary 1. Poikilothermic animals incorporate more polyunsaturated fatty acids (PUFAs) into their cellular membranes as temperature declines, suggesting an increased sensitivity to PUFA limitation in cool conditions. To test this we raised Daphnia magna at different temperatures and investigated the effect of varying dietary PUFA on life history parameters (i.e. growth, reproduction) and the PUFA composition of body tissue and eggs. 2. Upon a PUFA-rich diet (Cryptomonas sp.) females showed higher concentrations of several ω3 PUFAs in their body tissue at 15 °C than at 20 °C and 25 °C, indicating a greater structural requirement for ω3 PUFAs at low temperature. Their eggs had an equal but higher concentration of ω3 PUFAs than their body tissue. 3. In a life history experiment at 15 and 20 °C we supplemented a diet of a PUFA-free cyanobacterium with the ω3 PUFA eicosapentaenoic acid (EPA). The growth of D. magna was more strongly EPA limited at low temperature. A greater requirement for structural EPA at 15 °C was indicated by a steeper increase in somatic EPA content with dietary EPA compared to 20 °C. 4. At 20 °C the development of eggs to successful hatching was high when EPA was supplied to the mothers. At 15 °C the hatching success was generally poor, despite of a higher maternal provision of EPA to eggs, compared to that at 20 °C, suggesting that EPA alone was insufficient for proper neonatal development at the low temperature. The growth of offspring from mothers raised at 20 °C without EPA supplementation was very low, indicating that the negative effects of EPA deficiency can be carried on to the next generation. 5. The fatty acid composition of Daphnia sp. in published field studies shows increasing proportions of saturated fatty acids with increasing environmental temperature, whereas ω3 PUFAs and EPA show no clear pattern, suggesting that variations in dietary PUFA may mask temperature-dependent adjustments in ω3 PUFA concentrations of cladocerans in nature.
Phylogenetic relationships in the genus Agathemera (Insecta: Phasmatodea) inferred from the genes 16S, COI and H3

We present a phylogenetic analysis that includes all known species of Agathemera, using as outgroup four species of the genera Heteronemia, Spinonemia, Monticomorpha, and Anisomorpha. Phylogenetic inference was based on three genes, 16S, COI (mitochondrial markers) and H3 (nuclear marker), based on the maximum-parsimony, maximum-likelihood and Bayesian inference methods. Our results show that the genus Agathemera is monophyletic; six of its eight species showed phylogenetic support, while the group A. claraziana + A. millepunctata was not resolved. The resulting topology shows two major clades, the first with A. maculafulgens, A. luteola, A. crassa, A. millepunctata, and A. claraziana, and the second including A. grylloidea, A. mesoauriculae, and A. elegans. Species of the first clade have large mesonotal processes and are found mainly east of the Andes, except for A. crassa. Members of the second clade have small or absent mesonotal processes and are distributed mainly to the west of the Andes. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165, 63–72.
Breeding Bird Community of a Primeval Temperate Forest (Białowieża National Park, Poland) at the Beginning of the 21st Century

Abstract. The 2000–2004 results of the mapping technique censuses carried out in permanent plots situated in three types of old-growth primeval BNP stands (ash-alder riverine, oak-hornbeam, mixed coniferous) are presented and compared with data gathered in the same plots in the late 1990s. These data supplement earlier observations in the BNP and extend the long-term set of data on the breeding bird numbers there to a 30-year uninterrupted series (1975–2004). Most community parameters, such as the composition of breeding avifauna, the species richness, and the make-up and cumulative share of dominants, have remained basically unchanged. The overall bird density has increased by 8–20% in different plots; in 2001 it reached the highest level within the 30-year study period. The increase was due to parallel increases in numbers of several species, widely differing in their nesting sites, food requirements and migratory habits — during this period 14 of the 26 most numerous species attained their highest numbers in the 30-year study period. Since numbers increased simultaneously in all the plots, the density differences across habitats remained the same, from the highest densities in riverine stands at the forest edge (up to 149 p/10 ha), through oak-hornbeam stands, to the lowest densities in the coniferous stands (54–56 p/10 ha). In most cases the numerical increases could not be attributed to changes in local environmental factors, such as food resources, or to detectable changes in habitat structure. The apparent lack of a relationship between the changes in bird numbers and the local situation suggests that factors acting on a larger scale (beyond the study area) could have been involved. Despite the directional changes in bird abundance observed in the Białowieża Forest, its breeding bird assemblage, when compared with the amplitude of changes recorded over the same period in other areas and habitats, stands out as an example of remarkable stability.
Effect of Application Timing on Rhizome Johnsongrass (Sorghum halepense) Control with DPX-V9360

Field, greenhouse, and laboratory studies were conducted to examine the effect of application timing on the activity of DPX-V9360 on rhizome johnsongrass. Field and greenhouse studies indicated that johnsongrass treated with postemergence applications of DPX-V9360 at late growth stages (>5 leaves) was controlled more effectively than when treated in early growth stages (<5 leaves). Johnsongrass control was optimized with split-postemergence applications (treatments applied at early and late growth stages) in field studies compared to a single postemergence application at either early or late growth stages. The pattern of translocation of 2-14C (pyrimidine)-labeled DPX-V9360 applied to a fully expanded johnsongrass leaf did not differ significantly between three different growth stages of 10-, 30-, and 60-cm height. Over 60% of the absorbed 14C remained in the treated leaf. Most of the translocated 14C moved out of the treated leaf within 3 days after application and distributed to the shoot in greater quantities than to the rhizomes. About 40% of 14C-DPX-V9360 applied to the leaf surfaces of a tolerant species (corn) or susceptible species (johnsongrass) was absorbed into the leaf. Corn metabolized over 90% of absorbed DPX-V9360 within 20 h, while there was no perceptible metabolism of DPX-V9360 in johnsongrass leaves after 24 h. Late growth stage and split-postemergence applications appear to provide more effective control than early growth stage applications because of better control of regrowth (new shoot emergence from rhizomes after application) and because tillering and plant emergence are more nearly complete at application time.
Molecular and Neuronal Analysis of Circadian Photoresponses in Drosophila : A Dissertation

Most organisms, from cyanobacteria to humans are equipped with circadian clocks. These endogenous and self-sustained pacemakers allow organisms to adapt their physiology and behavior to daily environmental variations, and to anticipate them. The circadian clock is synchronized by environmental cues (i.e. light and temperature fluctuations). The fruit fly, Drosophila melanogaster , is well established as a model for the study of circadian rhythms. Molecular mechanisms of the Drosophila circadian clock are conserved in mammals. Using genetic screens, several essential clock proteins (PER, TIM, CLK, CYC, DBT, SGG and CK-II) were identified in flies. Homologs of most of these proteins are also involved in generating mammalian circadian rhythms. In addition, there are only six neuronal groups in the adult fly brain (comprising about 75 pairs of cells) that express high levels of clock genes. The simplicity of this system is ideal for the study of the neural circuitry underlying behavior. The first half of this dissertation focuses on a genetic screen designed to identify novel genes involved in the circadian light input pathway. The screen was based on previous observations that a mutation in the circadian photoreceptor CRYPTOCHROME (CRY) allows flies to remain rhythmic in constant light (LL), while wild type flies are usually arrhythmic under this condition. 2000 genes were overexpressed and those that showed a rhythmic behavior in LL (like cry mutants) were isolated. The candidate genes isolated in the screen present a wide variety of biological functions. These include genes involved in protein degradation, signaling pathways, regulation of transcription, and even a pacemaker gene. In this dissertation, I describe work done in order to validate and characterize such candidates. The second part of this dissertation focuses on identifying the pacemaker neurons that drive circadian rhythms in constant light (LL) when the pacemaker gene period is overexpressed. We found that a subset of pacemaker neurons, the DN1s, is responsible for driving rhythms in constant light. This attractive finding reveals a novel role for the DN1s in driving behavioral rhythms under constant conditions and suggests a mechanism for seasonal adaptation in Drosophila .
Biodegradation of selected insecticides by Bacillus and Pseudomonas sps in ground nut fields

Bacterial cultures isolated by selective enrichment technique were identified as species of Bacillus and Pseudomonas. These isolates were tested for their ability to degrade the respective insecticides in mineral salts medium. Within 7 days of incubation, nearly 75% of chlorpyrifos and phorate and 50% of dichlorvos, methyl parathion and methomyl were degraded by cultures of soil bacteria. Qualitative analysis of chlorpyrifos and methyl parathion residues by gas chromatography revealed the formation of one unidentified metabolite in inoculated samples. Whereas no metabolite formation was detected in case of other insecticides inoculated samples. Moreover, dichlorvos and phorate were completely degraded by soil isolates at the end of 14 days. Order of microbial degradation of selected insecticides in the present experiment is as follows: phorate > dichlorvos > methyl parathion > chlorpyrifos> methomyl.
Anaerobe Laboratory manual

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Food and feeding habits of Cynoglossu arel (Family: Cynoglossidae) from Karachi Coast, Pakistan

The pattern of food and feeding habits Cynoglossus arel was studied during the period from June 2012 to June 2013, using point’s methods. The composition of food of different size groups and seasons was calculated. Analysis of fullness of stomach revealed gorged – full constituted 0.67%, 3/4full 0.90%, 1/2 full 7.18%, 1/4full 13.68%, barely full 70.85% and empty 6.73% in a year. Analysis of stomach contents showed the occurrence (in percentage) of polychaetes 8.12%, crustaceans 17.56%, molluscs 9.31%, fish 0.84%, sand-mud 10.39% and miscellaneous items 53.76%. Total points of fish were determined to be 4.45% for polychaetes, 21.52% for crustaceans, 7.93% for molluscs, 0.73% for fish, 7.88% for sand-mud and 57.50% for miscellaneous items.
The Preservation of species : the value of biological diversity

For all persons seriously concerned about the destruction of natural environments in the contemporary world, this book presents a comprehensive rationale for preserving wild species and ecosystems. Bryan G. Norton appeals most centrally to "transformative value," the power of human contacts with wild species to transform and uplift the human spirit. Until now species preservationists have found a theoretical basis for their policies in the "demand" value of wild species for fulfilling certain narrowly defined human needs or in controversial and badly understood proposals about the "intrinsic" values of species. This work examines such rationales and diverges from them by pointing to new sources of value for wild species: they have worth because they can transform human values.Because of the central role of biological diversity in environmental concerns, the book also provides a fresh perspective on environmental ethics more generally. Why Preserve Natural Variety? is sponsored by the Center for Philosophy and Public Policy at the University of Maryland, as was "The Preservation of Species: The Value of Biological Diversity," which was edited by Professor Norton.Originally published in 1986.The Princeton Legacy Library uses the latest print-on-demand technology to again make available previously out-of-print books from the distinguished backlist of Princeton University Press. These paperback editions preserve the original texts of these important books while presenting them in durable paperback editions. The goal of the Princeton Legacy Library is to vastly increase access to the rich scholarly heritage found in the thousands of books published by Princeton University Press since its founding in 1905.
Inducible protein dimerization: New tools and applications to understanding the mitotic checkpoint

Cellular processes such as growth, migration, signaling and cell division require choreographed interactions between dozens or hundreds of proteins carefully organized in time and space. In order to test hypotheses about complex cellular functions, it is desirable to experimentally perturb the interactions of individual proteins that perform these functions with a level of spatial and temporal control commensurate with the time and space scales over which the system is naturally organized. Inducible protein dimerization offers the ability to experimentally control protein-protein interactions. Inducible dimerization can be used to test the immediate effects of dimerizing two proteins, or it can be engineered to create or destroy a protein or change a protein's localization. Several different techniques for inducible dimerization using small molecules or light have been developed, each with its own strengths and weaknesses. Ultimately, only light-inducible dimerization offers the potential for both temporal and spatial experimental control. In this thesis, I describe the application of inducible dimerization to further our understanding of a complex signaling network, the Mitotic Checkpoint, which monitors chromosome segregation and is regulated by the localization of its constituent checkpoint proteins. I discovered that relocalizing a single key checkpoint protein, Mad1, to kinetochores at metaphase is sufficient to reactivate the checkpoint. I also describe the development of a novel photochemical technique which has allowed us to achieve light-induced dimerization at centromeres, a cellular compartment which has not been successfully targeted by previously reported light-inducible dimerization systems. This technology enables us to perform experimental biology on living cells with a new level of spatial and temporal control. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Biochemistry & Molecular Biophysics First Advisor Michael A. Lampson
IN VITRO EVALUATION OF WHEAT STRAW VARIETIES FOR CHEMICAL COMPOSITION, GAS PRODUCTION AND DIGESTIBILITY

Straws of five wheat varieties viz, Raj3077, PBW373, PBW154, Raj3765 and LOK1 were evaluated for their chemical composition, in vitro digestibility and gas production. It was found that IVDMD and IVOMD content were higher in varieties PBW154 and Raj 3077 as compared to other varieties. The gas production/gm DM and gas production/gm digestible DM were significantly (P< 0.05) higher in variety PBW 154. The gas production at 6th and 12th hrs of incubation did not vary significantly among the varieties where as, the gas production at 24th and 48th hrs were significantly (P< 0.05) different. It was found to be highest for variety PBW 154 (21.75 and 37.33 ml at 24th and 48th hours respectively). For the wheat straw variety PBW 154, their exists a positive relation between the gas production and digestibility.
Crustaceans of extreme environments

Crustaceans are a remarkably diverse group of organisms, which have colonized and occupied a broad variety of niches. Many crustacean species are found in extreme environments, inhospitable to the majority of animal taxa, including Antarctic lakes, subterranean waters, hydrothermal vents, dry deserts, hypersaline lakes, and highly acidic habitats. Particular adaptations have evolved in response to the environmental conditions in these extreme habitats, shaping the lifestyle of crustaceans. In this chapter, some of the morphological, physiological, and life history adaptations that enabled crustaceans to colonize these habitats are reviewed. An overview of the main crustacean taxa in these extreme environments is given and their evolutionary adaptations are briefly compared to those of other organisms co-occurring in the same habitats. Although not exhaustive, this review highlights how successful crustaceans have been in adapting to extreme conditions. Nowadays, anthropogenic activities risk irreversibly altering the delicate equilibrium these crustaceans have achieved in extreme environments.
Sewall Wright and evolutionary biology

"Provine's thorough and thoroughly admirable examination of Wright's life and influence, which is accompanied by a very useful collection of Wright's papers on evolution, is the best we have for any recent figure in evolutionary biology. "--Joe Felsenstein, "Nature" "In "Sewall Wright and Evolutionary Biology" . Provine has produced an intellectual biography which serves to chart in considerable detail both the life and work of one man and the history of evolutionary theory in the middle half of this century. Provine is admirably suited to his task. The resulting book is clearly a labour of love which will be of great interest to those who have a mature interest in the history of evolutionary theory. "-John Durant,; ITimes Higher Education Supplement; X
Workers often predominate in dusk ‘drone flights’ of the giant honey bee Apis dorsata

Mating flights of queen and drone honey bees are performed at a particular, species-specific time of day. Mating flights of Apis dorsata drones take place in mass flights at dusk (Koeniger & Wijayagunasekara, 1976; Koeniger et al., 1988; Rinderer et al., 1993; Koeniger et al., 1994; Woyke et al., 2001). Queens of A. dorsata fly at the same time (Tan et al., 1999). Although only drones and queens have been reported as taking part in these mass flights at dusk, we have observed workers flying together with drones (unpublished observation). The research we report here documents flight activity of worker A. dorsata during dusk mass flights (DMFs).
In-vitro anticancer activity of standard extracts used in ayurveda

The hydro-alcoholic extracts of five Ayurvedic medicinal plants, pericarp of Terminalia chebula, rhizome of Acorus calamus, stem bark of Bauhinia variegate, whole plant of Phyllanthus amarus, root of Glycyrrhiza glabra were evaluated for their antiproliferative activity on fourteen cancer cell lines. These plant extracts were tested by sulforhodamine-B (SRB) assay for its anti proliferative activity and four extracts except Glycyrrhiza glabra were found active against prostrate cancer cell line (DU145. In addition to this Terminalia chebula exhibited activity against leukemia cancer cell line (K562).
Two new species of Anthurium section Xialophyllium (Araceae) from Panama

Two new species of Anthurium section Xialophyllium from Panama are described here. Both species have close affinities with Anthurium microspadix , A. davidsoniae and A. myosuroides . Anthurium monteazulense sp. nov. , known only from Chiriqui Province, is characterized by its epiphytic habit, internodes somewhat longer than broad, loosely intact cataphylls, leaf blades subcordate, bullate, ovate with two pairs of basal veins and short-stipitate green to greenish yellow cylindroid spadix. The other species, Anthurium batistae sp. nov. , known only from Veraguas Province, is characterized by its terrestrial habit, elongate internodes, deciduous cataphylls, leaf blades rounded at base, ovate with one pair of basal veins and prominently stipitate purplish red cylindroid spadix.