Miracle-dz/UniFAR-FTUs huggingface dataset:
The Impact Of Recurrent Polyploidy On Photosynthesis In Glycine

The likelihood of duplicate gene retention following polyploidy varies by broadly defined functional properties (e.g., gene ontologies or PFAM domains), but little is known about the effects of whole genome duplication on gene networks related functionally by a common physiological process. Here, we examined the effects of both polyploid and non-polyploid duplications on genes encoding the major functional groups of photosynthesis (photosystem I, photosystem II, the light harvesting complex, and the Calvin cycle) in the cultivated soybean (Glycine max), which has experienced two rounds of whole genome duplication. Photosystem gene families exhibit retention patterns consistent with dosage sensitivity (preferential retention of polyploid duplicates and elimination of non-polyploid duplicates), whereas Calvin cycle and light harvesting complex gene families do not. We observed similar patterns in Medicago truncatula, which shared the older genome duplication with Glycine but has evolved independently for ca. 50 million years, and in Arabidopsis thaliana, which experienced two nested polyploidy events independent from the legume duplications. In both Glycine and Arabidopsis, Calvin cycle gene duplicates exhibit a greater capacity for functional differentiation than do duplicates within the photosystems, which likely explains the greater retention of very old duplicates and larger average gene family size for the Calvin cycle relative to the photosystems.
Anti-idiotype × Anti-LFA-1 Bispecific Antibodies Inhibit Metastasis of B Cell Lymphoma1

Abs to adhesion molecules can block tumor metastasis. However, they may also block the function of normal cells. To circumvent this adverse effect, we proposed the use of bispecific Abs that bind simultaneously to an adhesion receptor and to a tumor-specific Ag. Such Abs bind more avidly to tumor cells that coexpress both target Ags than to normal cells. The Id of the surface Ig of malignant B lymphocytes is a tumor-specific Ag. We therefore produced a bispecific Ab with specificity to the adhesion molecule LFA-1 and to the Id of the murine B cell lymphoma 38C-13. Here we demonstrate that this Ab blocked liver metastasis in mice carrying primary s.c. tumors and partially inhibited lymph node metastasis. Migration of 38C-13 cells to liver and lymph nodes was inhibited by the bispecific Ab, while migration to spleen was not affected. Hence, the bispecific Ab-mediated reduction in liver and lymph node metastasis resulted at least in part from reduced homing to these organs. In contrast to anti-LFA-1 monospecific Abs, the anti-Id × anti-LFA-1 bispecific Ab did not affect immune responses such as delayed-type hypersensitivity. Hence, bispecific Abs against adhesion molecules and against tumor-specific Ags may selectively block tumor metastasis in a way that may leave much of the immune system intact.
Genetic variability and inter-relationship among some ridgegourd (Luffa acutangula L.) accessions under foot hills of Arunachal Pradesh

Ten ridge-gourd accessions were evaluated during Kharif, 2011 to estimate the magnitude of genetic variability and the character association among some yield characters. The results revealed wide genetic variability among the accessions. The genotypic coefficient of variation and heritability estimates were high in days to 50% germination, vine length, fruit length and fruit yield per plant. However, genotypic coefficient of variation and heritability estimates were low in number of branches per plant and fruit weight. Vine length, fruit length, number of fruits per plant and fruit weight had a significant (P < 0.01) positive correlation with fruit yield per plant. Path analysis revealed that number of fruits per plant and fruit weight had the highest positive direct effect on fruit yield per plant. The results indicated that vine length, fruit length, number of fruits per plant and fruit weight can be used as selection criteria to increase fruit yield in ridge gourd.
DESENVOLVIMENTO INICIAL DE GRAMÍNEAS SUBMETIDAS AO ESTRESSE HÍDRICO

Objetivou-se por este trabalho, avaliar o efeito da disponibilidade hidrica no desenvolvimento inicial de plantas de milho, sorgo e milheto. O experimento foi realizado na Universidade Federal de Mato Grosso, Campus de Rondonopolis, no periodo de maio a junho de 2010. O delineamento utilizado foi inteiramente casualizado, em esquema fatorial 3x3, com tres disponibilidades hidricas (30, 60% da capacidade de campo e alagado), tres gramineas (milho, sorgo e milheto) e tres repeticoes. A umidade do solo foi mantida por meio de manutencao de peso das parcelas experimentais. As variaveis avaliadas foram: altura de plantas, massa seca da parte aerea, numero de folhas e leitura SPAD. O milho, sorgo e milheto apresentam maior desenvolvimento inicial na disponibilidade hidrica de 60% da capacidade de campo, sendo essa a condicao que proporciona maior leitura SPAD. O sorgo apresenta tolerância ao alagamento e ao deficit hidrico, ao contrario do milho que e sensivel a essas duas condicoes e do milheto que e tolerante apenas ao deficit hidrico.
ROLE OF THE PHOSPHOENOLPYRUVATE: CARBOHYDRATE PHOSPHOTRANSFERASE SYSTEM IN THE VIRULENCE OF THE GROUP A STREPTOCOCCUS

Title of Dissertation: ROLE OF THE PHOSPHOENOLPYRUVATE: CARBOHYDRATE PHOSPHOTRANSFERASE SYSTEM IN THE VIRULENCE OF THE GROUP A STREPTOCOCCUS Kanika Gera, Doctor of Philosophy, 2014 Directed By: Dr. Kevin S. McIver, Associate Professor Department of Cell Biology and Molecular Genetics Group A Streptococcus (GAS) is a fastidious microorganism that has adapted to a variety of niches in the human body by sensing its surroundings and modifying its metabolism to elicit a wide array of diseases. The Phosphoenolpyruvate Phosphotransferase System (PTS) is a primary mechanism by which many bacteria transport sugars and sense the carbon state of the cell. The PTS uses the non-sugar specific ‘general’ proteins EI and Hpr, and sugar-specific membrane-spanning proteins (EIIs) for the PTS-mediated uptake of each sugar. The role of PTS in carbohydrate metabolism in GAS was investigated by generating a ∆ptsI mutant (EI deficient) in three different strains belonging to M1T1 and one of M4 GAS. All ∆ptsI mutant strains tested were unable to grow on multiple carbon sources (PTS and nonPTS). Complementation with ptsI expressed under its native promoter in single copy was able to rescue the growth defect of the mutant. Additional studies analyzing the role of PTS in pathogenesis of GAS, showed a ‘hypervirulent’ phenotype in the absence of ∆ptsI from M1T1 using soft tissue model of infection. The appearance of significantly larger and more severe ulcerative lesion observed in mice infected by ∆ptsI was correlated with increased transcript levels of sagA and early Streptolysin S (SLS) activity during exponential phase growth. The role of SLS in increased pathogenesis of ∆ptsI was investigated by the creation of a double mutant strain (∆ptsI sagB) that lacks the ability to secrete SLS. The infection of mice with a ∆ptsI sagB double mutant resulted in a lesion comparable to either a wild type or a sagB mutant alone. In addition to SLS, it was found that PTS influences the secretion of cysteine protease SpeB and the ability of GAS to produce capsule. This regulatory effect was found to be dependent on the status of sensor kinase (CovS) of the CovR/S two-component system. Moreover, PTS was shown to phosphorylate PTS regulatory domains (PRD) of a global virulence regulator, Mga, resulting in alteration of its regulon in both M1T1 and M4 background, suggesting the ability of GAS to alter expression of Mga regulon in response to carbohydrate availability. Overall, our studies indicate that a functional PTS is important for utilizing PTS and non-PTS sugars and influences virulence during GAS infection. ROLE OF THE PHOSPHOENOLPYRUVATE: CARBOHYDRATE PHOSPHOTRANSFERASE SYSTEM IN THE VIRULENCE OF THE GROUP A STREPTOCOCCUS
A Washing Technique for Collection of Honeybee Semen

SummaryA simple and fast method for collecting honeybee semen in large quantity is described. Semen and mucus of many drones, everted and ejaculated by hand, were scraped into Kiev diluent in a semen-washing funnel and a collecting tube. The semen-mucus-diluent mixture was centrifuged at 2500 rpm for 10 min to separate semen from mucus and the diluent. The collecting tube containing semen was incorporated into a special large-capacity syringe, and the semen was used to inseminate queen honeybees.No significant differences were found in the amount of brood produced between 31 queens instrumentally inseminated with semen collected by this method, queens inseminated with semen collected by the conventional Mackensen technique, and open-mated queens (P > 0·05 in all cases). However, significant differences were observed in the onset of oviposition (P < 0·05 in all cases). There was a delay before oviposition by all the instrumentally inseminated queens, which was greatest for queens inseminated with semen col.
Dades sobre la biologia de l'àliga cuabarrada ("Hieraaetus fasciatus" [Vieill.]) a la Serralada Pre-Litoral Catalana

This paper is based on the study of biology and ethology of the Bonelli's Eagle, namely of a couple from the Catalan Prelittoral range, with additional remarks on several other couples belonging to the same range. Bearing in mind that this species has already been studied by other authors, the aims of this study are, on the one hand, to gather data on aspects not studied so far, and on the other, to compare the obtained results with those of other authors from France, Castile, Navarra, Andalusia, while making available some of the first data on this species in Catalonia, where the eagle reaches one of the greatest densities in all Europe. The study is divided into two parts, of different length: out of breeding period and during the breeding period. The most important part is the breeding period, which begins when the eagles start preparing their nests, ending when the young ones become definitively independent. Therefore, we shall begin with prenuptial behaviour as restoring of nests and copulation until the laying of two eggs. The first egg was laid between the 26th II and 1st III, and the incubation lasted from 37 to 41 days for the first egg and 37 to 40 for the second. During the incubation period, done almost entirely by the female, green branches are brought in by the male and sometimes also by the female; we have also described behaviours already referred to by other authors, such as the turning of eggs, accommodation movement during the incubation and nest keeping. The first chick hatched between the 7th and 8th IV, while the second did it between the 9th and the 10th IV. During the breeding, behaviours such as covering, waste disposal, etc. were observed. In what feeding is concerned, we may emphasize that a 22 % of Oryctolagus cuniculus has been observed, a low percentage if compared to what has been observed by other authors, while Sciurus vulgaris, Columba palumbus and Lacerta lepida make up the 60 % of its diet. We also comment upon some observations of hunting, vocal activity and specific behaviour of the chicks, from allopreening to flight exercises, ending with their leaving the nest on 10th-11th VI (least feathered young, male) and 13th-14th VI (most feathered young, female); until the 30th VIII they were regularly observed in the breeding area.
Markers of immunosenescence and oxidative stress in healthy adults

This thesis investigated markers of oxidative stress and immunosenescence in healthy adults. The results presented represent several novel findings which support the notion that oxidative stress and infection with micro-organisms shape our biology and can accelerate aspects of ageing. Acute exercise of high intensity was shown to cause alterations in the cellular composition of blood, which was most pronounced in lymphocyte sub-populations important for immunosurveillance. This exercise also resulted in increased markers of oxidative stress in lymphocytes, and resulted in a whole body oxidative stress, which was more pronounced and prolonged, following ultra-endurance exercise. Studies also showed that infection with a highly prevalent and asymptomatic herpes virus, Cytomegalovirus (CMV), shapes our immune biology in two significant ways. First, CMV amplified the magnitude and kinetics of lymphocyte responses to exercise, which could potentially facilitate immune surveillance, or aggravate inflammatory processes. Second, CMV was seen to drive the development of an ‘Immune Risk Profile’ in young adults, characterised by increased inflammatory activity and smaller responses to vaccination. These outcomes are associated with frailty, cognitive decline, and mortality in the elderly.
RNA and DNA Sequence analysis of the human transcriptome

The manifestation of phenotype at the cellular and organismal level is determined in large part by gene expression, or the transcription of DNA into RNA. As such, the study of the transcriptome, or the characterization and quantification of all RNA produced in the cell, is important. Recent advances in sequencing technology have allowed for unprecedented interrogation of the transcriptome at singlenucleotide resolution. In the first part of this thesis, we use RNA-Sequencing (RNA-Seq) to study the human B-cell transcriptome and determine the experimental parameters necessary for sequencing-based studies of gene expression. We discover that deep sequencing is necessary to detect fully and quantify accurately the complexity of human transcriptomes. Furthermore, we find that at high sequencing depths, the vast majority of transcribed elements in human B-cells are detected. In the second part of this thesis, we utilize the sequence information provided by RNA-Seq to analyze systematic differences between DNA and RNA sequence. The transmission of information from DNA to RNA is a critical process and is expected to occur in a one-to-one fashion. By comparing the DNA sequence to RNA sequence of the same individuals, we found all 12 types of RNA-DNA sequence differences (RDDs), the majority of which cannot be explained by known mechanisms such as RNA editing or transcriptional infidelity. We developed computational methods to robustly identify RDDs and control for false positives resulting from genotyping, sequencing, and alignment error. Finally, we explore the genetic basis of RDD levels, or the proportion of reads at a site bearing the sequence difference allele. In particular, we analyzed the levels of RNA editing in unrelated and related individuals and found that a significant portion of individual variation in A-to-G editing levels contains a genetic component. In summary, our results demonstrate that RNA-Seq is a powerful technique for comprehensive and quantitative analysis of gene expression. In addition, the resolution offered by RNA-Seq enables a detailed view of sequence differences between RNA and DNA. Future work will focus on understanding the mechanisms and factors influencing RDDs. Our results suggest that RDD levels may be considered a quantitative and heritable phenotype; as such, a genetic approach may be a sensible method for finding the determinants and mechanism of RDDs. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Genomics & Computational Biology First Advisor Frederic Bushman This dissertation is available at ScholarlyCommons: http://repository.upenn. edu/edissertations/709 Second Advisor Nancy Zhang
Evaluation of alternative genotypes and production systems for natural and organic poultry markets in the U.S.

Interest is growing in the U.S. in natural and organic poultry production. An experiment was conducted to assess the impact of genotype and production system of performance and meat quality. Specifically, a slow-growing genotype (SLOW) (SG each genotype was also assigned to 4 floor pens in a small portable facility with outdoor access. The diet was formulated to be low in energy and protein for a slower rate of production. Birds were commercially processed and deboned at 4h postmortem. Data were analyzed by ANOVA. The FAST birds gained more weight than the SLOW birds despite difference in age. The Outdoor birds had a higher feed intake and a poorer feed efficiency than Indoor birds. The FAST birds had a higher breast yield, while SLOW birds had a higher wing and leg yield as a percent of body weight. The SLOW birds had lower mortality than FAST. The Indoor birds had a higher wing yield than birds with Outdoor access. An interaction was evident in which the meat and skin of the SLOW birds became more yellow (higher b*) when the birds had outdoor access; however, this did not occur when FAST birds had outdoor access. The breast meat of the SLOW birds had more protein and less fat than the FAST birds. The SLOW birds were higher in α-tocopherol (per unit of fat) than FAST birds. The SLOW birds were more tender than the FAST birds. The SLOW birds had a higher drip loss than FAST but a lower cook loss and a higher total moisture loss. A descriptive analysis of breast and thigh meat was conducted by a trained panel and data indicated that the breast meat from the Outdoor birds was more cohesive than the meat from the Indoor birds in the first bite stage. In terms of flavor, there were no significant differences for most basic tastes; however, both the breast and thigh meat of the FAST birds tasted more salty than the SLOW birds. The SLOW birds had more dark meat fat flavor than the FAST birds. Results from the consumer panel showed no significant differences between SLOW-Out and FAST-In treatments in overall liking, appearance, texture, and flavor of the breast meat or thigh meat. Overall, the production system had less of an impact than genotype.
Organosulfates in atmospheric aerosol: synthesis and quantitative analysis of PM2.5 from Xi'an, northwestern China

Abstract. The sources, formation mechanism and amount of organosulfates (OS) in atmospheric aerosol are not yet well understood, partly due to the lack of authentic standards for quantification. In this study, we report an improved robust procedure for the synthesis of organosulfates with different functional groups. Nine authentic organosulfate standards were synthesized and four standards (benzyl sulfate, phenyl sulfate, glycolic acid sulfate, and hydroxyacetone sulfate) were used to quantify their ambient concentrations. The authentic standards and ambient aerosol samples were analyzed using an optimized ultra performance liquid chromatography–electrospray ionization-tandem mass spectrometric method (UPLC–ESI–MS/MS). The recovery ranged from 80.4 to 93.2 %, the limits of detection and limits of quantification obtained were 1.1–16.7 and 3.4–55.6 pg m−3, respectively. Measurements of ambient aerosol particle samples collected in winter 2013/2014 in urban Xi'an, northwestern China, show that glycolic acid sulfate (77.3 ± 49.2 ng m−3) is the most abundant species of the identified organosulfates followed by hydroxyacetone sulfate (1.3 ± 0.5 ng m−3), phenyl sulfate (0.14 ± 0.09 ng m−3), and benzyl sulfate (0.04 ± 0.01 ng m−3). Except for hydroxyacetone sulfate, which seems to form mainly from biogenic emissions in this region, the organosulfates quantified during winter in Xi'an show an increasing trend with an increase in the mass concentrations of organic carbon indicating their anthropogenic origin.
Genetic and pathogenic diversity within Ascochyta rabiei (Pass.) Lab. populations in Pakistan causing blight of chickpea (Cicer arietinum L.)

Abstract Pathogenic and genetic diversity in Ascochyta rabiei populations in Pakistan were evaluated. Biological pathotyping of 130 A. rabiei isolates (obtained from hierarchically collected samples) was conducted on a set of three chickpea differentials, i.e. ILC 1929 (susceptible), ILC 482 (tolerant) and ILC 3279 (resistant), under controlled conditions. Disease severity data were recorded 12 days after inoculation. Statistical analysis grouped the isolates into three pathotype classes. Four isolates belonged to pathotype I (least aggressive), 79 isolates to pathotype II (medium aggressive) and 47 isolates to pathotype-III (highly aggressive). Genetic analysis was performed using RAPDs and oligonucleotide fingerprinting, where Hinf I-digested DNA was hybridized to the 32 P-endlabeled oligonucleotide probes (CAA) 5 , (GAA) 5 , (GA) 8 , (CA) 8 and (GATA) 4 . Dendrograms produced by cluster analysis discriminated 46 genotypes in the A. rabiei population of Pakistan. Genetic distances and relatedness between isolates were calculated. At a genetic distance of 0.3, genotypes were divided into six distinct genotype groups A, B, C, D, E and F containing 16, 11, 2, 5, 5 and 7 isolates, respectively. Most of the genotypes were area specific or predominated in certain areas but did not belong to a distinct pathotype, while most of the aggressive isolates (pathotype III) occurred in Northern Punjab and in the North Western Frontier Province.
The white cell pheromone response pathway in Candida albicans provides insights into the evolution of new signal transduction pathways

Candida albicans is the most common fungal pathogen that infects humans. The research described in this thesis focuses on an in-depth characterization of the regulatory pathways controlling white-opaque switching, mating and biofilm formation, and the relationships among these programs in this pathogen. It was demonstrated in 2006 that minority opaque cells of C. albicans release pheromone to signal majority white cells of the opposite mating type to form enhanced biofilms. The white cell biofilms in turn facilitate opaque cell chemotropism, an essential step in mating. The white cell pheromone response is a general characteristic of C. albicans, occuring in all tested strains and in all common lab media. By generation of deletion mutants of select genes in the opaque cell mating pathway, it was demonstrated that the pathway regulating the white cell response shares all of the components of the opaque mating pathway, from the pheromone receptor through the MAP kinase cascade with the exception of the downstream transcription factor. In addition, it was demonstrated that a C. albicansspecific region in the first intracellular loop, IC1, of the α-pheromone receptor is required for the white, but not the opaque, pheromone response. Furthermore, the cis-acting element in the promoters of genes induced by pheromone in white cells was identified. The white-specific pheromone response element, WPRE, is important for the regulation of the white pheromone response and induction of white-specific genes by pheromone. Finally, based on a misexpression library screening of transcription factors previously implicated in adhesion, cell wall biogenesis, filamentation or biofilm formation, the transcription factor Tec1 was identified to be the key regulator in the white pheromone response pathway. Tec1 binds to the WPRE in the promoters of genes induced by pheromone in white cells to mediate the white cell response. The white pheromone response pathway appears to be a relatively young pathway that borrowed the upstream components from the opaque mating pathway, the transcription factor from the ancestral