Miracle-dz/UniFAR-FTUs huggingface dataset:
Co-expression of lung alveolar epithelial type I and II cell-selective proteins in response to injury

The internal surface of the lung is covered by alveolar epithelial type I (ATI) and II (ATII) cells. In response to injury ATII cells proliferate and transdifferentiate to ATI cells. Currently, there are no simple methods to identify transdifferentiation in vivo. This study used a novel combination of ATI and ATII cell-selective antibodies to investigate the phenotype of the alveolar epithelium following Staphylococcus aureusinduced 'direct' lung injury. Imaging using confocal laser scanning microscopy with 2D and 3D image analysis allowed qualitative and quantitative investigation of the epithelial response to injury. Following distal airway instillation of S. aureus, the alveolar epithelium was covered with ATII cells (MMC4/RTII70-positive cells) and ATI cells (RTI40-positive cells) as seen in control lungs. However, the surface area covered by ATII cells was significantly increased, while the surface area covered by ATI cells was significantly decreased, in comparison with controls. Ultrastructural studies confirmed the decrease in ATI cell numbers following S. aMrews-inoculation. The alveolar wall of S. awrews-injured lungs also contained cells that co-stained with a unique combination of ATI and ATII cell proteins, RTI40 and MMC4. To determine whether RTI40/MMC4-positive cells were likely to be intermediates in the transition of ATII to ATI cells I examined ATII cells as they transformed to ATI-like cells in culture (day 0 to 5). Only cells on day 1 of culture were RTI^/MMX^l positive. I also examined the developing lung for RTI^/MMCd positive cells. Co-staining cells were not found in the developing alveolar epithelium, but they were present in small airways. I also developed a rat model of haemorrhagic shock induced 'indirect' alveolar epithelial injury as a platform for future work. Here I have developed a robust technique for imaging ATII cell transdifferentiation in vivo and in vitro. This work has identified a novel alveolar epithelial phenotype, RTI40/MMC4, in repairing lungs and in ATII cells as they transdifferentiate to ATI-like cells in vitro. These data suggest that RTI40/MMC4-positive cells can be used to both visualize alveolar epithelial intermediates in vivo and to investigate the regulation of ATII cell transdifferentiation following injury.
A biotechnological approach to directly assess the impact of elevated endogenous a-amylase on Asian white-salted noodle quality.

Flours from engineered wheat grain overexpressing a single β-amylase type 3 (TaAMY3) were compared to flour from germinated grains to study the impact of elevated levels of β-amylase on small scale noodle quality. Results showed that -amylase alone significantly reduced cooking time and increased cooking loss but had no detrimental effect on flour color, noodle color or firmness. Noodles produced from sprouted grains were significantly detrimentally affected for all the above quality characteristics, in particularly after 24 and 48 hours imbibition. A strong correlation was observed between decreases in unextractable polymeric protein (UPP) levels, and noodle firmness. These findings raise important questions as to the supposition that β-amylase is the source of the adverse effects of pre-harvest sprouting (PHS) and late maturity β-amylase (LMA) on Asian white salted noodles and highlights the usefulness of applying biotechnology in elucidating how flour components affect end product quality.
Sex specific molecular responses of Quick-To-Court in Indian malarial vector Anopheles culicifacies: conflict of mating and/or blood feeding?

Understanding the molecular basis of mosquito behavioral complexity is central to the design of novel molecular tool to fight against their vector borne diseases. Although, olfactory system play important role to guide and manage many behavioral co-ordinates including feeding, mating, breeding etc., but the sex specific regulation of olfactory responses remains unanswered. From our ongoing transcriptomic data annotation of blood fed adult female olfactory tissue of A. culicifacies mosquito, we identified a 383 bp long unique transcript encoding Drosophila homolog of Quick-To-Court protein, previously shown to regulate the courtship behavior in adult male Drosophila. A comprehensive in silico analysis predicts Ac-qtc is 1536 bp long single copy gene encoding 511 AA long protein, having high degree of conservation with other insect homolog. Age dependent increased expression of putative Ac-qtc in the naïve mosquitoes correlates the maturation of olfactory system, necessary to meet sex specific conflicting demand of mating (mate finding) vs. host-seeking behavioral responses. Though, 16-18 hour of starvation did not altered Ac-qtc expression in both the sexes, however blood feeding significantly modulated its response in the adult female mosquitoes, confirming that it may not be involved in sugar feeding associated behavioural regulation. Finally, a behavioural-cum-molecular assay indicated that natural dysregulation of Ac-qtc in late evening may promotes key mating event of successful insemination process. We hypothesize that Ac-qtc may play unique role to meet and manage the sex specific conflicting demand of mosquito courtship behaviour and/or blood feeding behaviour in the adult female mosquitoes. A molecular mechanism elucidation may provide new knowledge to consider Ac-qtc as a key molecular target for mosquito borne disease management.
Identification of Somatic Mutations in LGL Leukemia through Whole Genome Sequencing and Correlation of STAT3 Y640F Mutation with Treatment Response to Methotrexate.

The rare disorder, large granular lymphocyte (LGL) leukemia is characterized by a clonal expansion of cytotoxic cells. Normal LGL are critical to the removal of virally-infected or tumor cells from the body. These cells normally expand when there is an immune challenge and then rapidly undergo apoptosis when the antigen is cleared, but leukemic LGLs are resistant to apoptosis. Serological evidence indicates that LGL leukemia may be driven by chronic infection of an unknown retrovirus. Patients with LGL leukemia frequently experience autoimmune conditions such as rheumatoid arthritis and also experience cytopenias requiring medical intervention. The study of LGL leukemia is therefore important both from a patient standpoint and as a model of normal LGL. We have recently discovered and characterized multiple somatic mutations in exon 20 and 21 of STAT3 from exome sequencing of an LGL leukemia patient and confirmed this mutation to be present in both Natural Killer and T cell leukemias. A small percentage was also found to have mutations in STAT5B, with some associated with an aggressive phenotype. Concurrently, we have undertaken whole genome sequencing to determine what other mutations may contribute to LGL leukemia and to expand our knowledge of STAT3 activation. Given the antigen driven nature of LGL leukemia, it is unclear what mutations are necessary for their lack of apoptosis and whether these will resemble those seen in other leukemias. The current treatment of choice for LGL leukemia is immunosuppressive methotrexate. Firstly, we present the first large prospective trial of immunosuppressive therapy in LGL leukemia. In this trial we identify a correlation between a particular Y640F mutation in STAT3 and a favorable response to first line treatment with methotrexate. We measure and report 27 serum cytokines collected for this trial, none of which were a priori predictive of treatment response. Through microarray analysis we identified a gene expression signature indicative of response. Interestingly, this gene signature does not appear to be driven by STAT3 mutation in
A Novel Role For Repetitive Sequences In Recognition Of The Drosophila Melanogaster X Chromosome

A NOVEL ROLE FOR REPETITIVE SEQUENCES IN RECOGNITION OF THE DROSOPHILA MELANOGASTER X CHROMOSOME by SONAL SURESH JOSHI August 2016 Advisor: Dr. Victoria H. Meller Major: Biological Sciences Degree: Doctor of Philosophy In humans and fruit flies, males have one X chromosome while females have two. This imbalance in gene dosage is potentially lethal, and the process of dosage compensation corrects it. The MSL (Male Specific Lethal) complex, which is composed of five proteins and one of two functionally redundant long non-coding roX (RNA on the X) RNAs, brings about dosage compensation in Drosophila melanogaster. In fruit fly dosage compensation, all the genes on the single male X chromosome are upregulated approximately twofold, via chromatin modifications, to equalize gene dosage with the two X chromosomes of females. This process calls for highly selective identification of the X chromosome in the nucleus. The current model for X-recognition does not explain how specific binding to the X-chromatin is achieved. It is known however, that the X chromosome assumes a distinct three-dimensional conformation in the male nucleus, and that the siRNA pathway aids in X-recognition. We hypothesized that repetitive sequences found exclusively on the X chromosome, called the 1.688 repeats, could be a possible source of siRNAs
Canopy height and competition explain species segregation in wet heathlands

One of the main issues in plant community ecology is the role of interspecific interactions in shaping the species assemblage of a community. Geographic constraints, environmental filtering and stochastic events such as longdistance dispersal explain differences between communities at large scales, but species interactions play a major role at local scales (Boulangeat, Gravel, & Thuiller, 2012; Kneitel & Chase, 2004; Meier et al., 2010). Departure from neutral coexistence in plant community assemblages can be negative, driven by competition, or positive, explained by facilitation (Callaway & Walker, 1997). In plants, competition results from limited availability of water and soil nutrients, and limited exposure to sunlight in the vicinity of other plants. In turn, facilitation takes Received: 12 January 2018 | Revised: 2 June 2018 | Accepted: 5 June 2018 DOI: 10.1111/jvs.12661
FUCCI tracking shows that Neurog3 levels vary with cell-cycle phase in endocrine-biased pancreatic progenitors

Neurog3HI endocrine-committing cells are generated from a population of Sox9+ mitotic progenitors with only a low level of Neurog3 transcriptional activity (Neurog3TA.LO). Low-level Neurog3 protein, in Neurog3TA.LO cells, is required to maintain their mitotic endocrine-lineage-primed status. Herein, we describe a Neurog3-driven FUCCI cell-cycle reporter (Neurog3P2A.FUCCI) derived from a Neurog3 BAC transgenic reporter that functions as a loxed cassette acceptor (LCA). In cycling Sox9+ Neurog3TA.LO progenitors, the majority of cells in S-G2-M phases have undetectable levels of Neurog3 with increased expression of endocrine progenitor markers, while those in G1 have low Neurog3 levels with increased expression of endocrine differentiation markers. These findings support a model in which variations in Neurog3 protein levels are coordinated with cell-cycle phase progression in Neurog3TA.LO progenitors with entrance into G1 triggering a concerted effort, beyond increasing Neurog3 levels, to maintain an endocrine-lineage-primed state by initiating expression of the downstream endocrine differentiation program prior to endocrine-commitment.
The Antibacterial and Antioxidant Effect of Salvadora persica on Antibiotic Resistant Strains

Many efforts have been devoted to studying the inhibitory effect of Salvadora persica (Miswak) on oral microorganisms. However, information regarding its antibacterial activity against other human pathogens is rare. Particularly, against Pseudomonas aeruginosa, Acinetobacter baumannii and Enterobacter cloacae. The purpose of this piece of work was to evaluate the antioxidant power and in vitro antibacterial activities of Salvadora persica extract against the three bacterial clinical isolates mentioned above. Therefore, the action of Salvadora persica extract on the three germs, studied via the aromatograms method, has given an inhibition zone 20, 18 and 14 respectively on Pseudomonas aeruginosa, Acinetobacter baumannii and Enterobacter cloacae. The methanol extract of Salvadora persica using Soxhlet has given an output of 19%. The antioxidant evaluation, which was performed using the DPPH (1,1-diphenyl-2-picryl-hydrazyl), free radical scavenging method, indicated that the methanol extract showed good antioxidant efficiency (IC50 = 15.47 mg/ml) compared to ascorbic acid with (IC50 = 0.097 mg/ml).
Aroma profiling of jasmine (Jasminum sambac Ait.) flowers using electronic nose technology

The Jasmine (Jasminum sambac Ait.) flowers are highly fragrant and used for extraction of essential oil, preparation of perfumes and scented water. Since there is a growing demand for the fresh flowers, there arises a need to develop a technique to identify the flower quality in non-destructive and quickest possible manner. A study was undertaken using hand held electronic nose technology (HEN) at the Department of Floriculture and Landscaping, Tamil Nadu Agricultural University, Coimbatore during the year 2013-2015. The result showed that, the HEN device generated Aroma Index (AI) score increased over the flower development stages and varied from 0.41 in immature bud (stage I) to 4.26 in matured bud (stage V). The comprehensive study on quantum of fragrance releasing pattern at different flower opening stages (physiologically matured bud to fully opened flower) over period of time interval showed that, minimum of 5.41 was recorded in an unopened closed bud stage which gradually increased upto 41.26 in the fully opened flowers. The biochemical constituents responsible for the unique jasmine flower fragrance were identified using Gas Chromatography –Mass Spectrometry (GC-MS).
The evolution of developmental strategy in Cretaceous spatangoid sea urchins

Sea urchins, like many marine invertebrates, have two major strategies for larval development. Some species have planktotrophic (feeding) larvae, which feed in the water column for a period of weeks to months prior to metamorphosis into a juvenile sea urchin. Other species have nonplanktotrophic (non-feeding) larvae, which are produced in much smaller numbers and do not feed but are instead supplied with nourishment in the form of an egg for the much shorter period they spend prior to metamorphosis. This thesis aims to understand the evolution of these larval modes by focusing on the Cretaceous spatangoid echinoids, where larval mode can be inferred from adult tests, which have an abundant fossil record. The taxonomy of the group was revised in order to ensure that species used in the subsequent analyses are biologically meaningful. Phylogenetic analyses of the species considered valid were then undertaken to provide hypotheses of evolutionary relationships that form the basis of analyses of the evolution of larval strategy. Larval modes were determined for a large number of species. When these data were mapped onto spatangoid phylogeny, non-planktotrophy was shown to have evolved independently on five occasions. The first occurrence of each of the five non-planktotrophic clades is in either the Campanian or Maastrichtian (the final two Cretaceous stages) with no instances of non-planktotrophy prior to the Campanian. There is no support for the hypothesis that non-planktotrophic groups originate preferentially at high latitudes, despite the fact that nonplanktotrophic species are unusually abundant at these latitudes today. Analysis of raw data showed that there is a significant association between non-planktotrophic larval development and both increased speciation rates and reduced species longevity. However, when phylogeny was considered, it was not possible to discount the possibility that significant associations result simply from shared ancestry. No significant associations were identified between larval mode and geographical range, latitude or depth.
Interactions Among Multiple Plastic Traits in Caterpillar Thermoregulation

8 INTRODUCTION . 10 PRESENT STUDY . 15 REFERENCES . 20 APPENDIX A. Proximate and ultimate interactions among adaptively plastic traits . 24 APPENDIX B. Why have multiple plastic responses? Interactions between color change and heat avoidance behavior in Battus philenor larvae . 59 APPENDIX C. Color alters thermoregulatory behavior in Battus philenor caterpillars by modifying the cue received . 94 APPENDIX D. Effects of developmental change in body size on ectotherm body temperature and behavioral thermoregulation: caterpillars in a heat-stressed environment . 119 APPENDIX E. Thermoregulatory color plasticity and behavior are maintained unaltered across the range of Battus philenor . 150
The Role of N1-Src in Neuronal Development

Protein phosphorylation by tyrosine kinases evolved in multicellular organisms to regulate intracellular signalling pathways associated with proliferation, differentiation and migration. In most tissues, basal protein tyrosine phosphorylation is maintained at low levels, but in the brain, basal tyrosine kinase activity is high and regulates key processes in the developing and mature brain and is dysregulated in neurological disorders. N1-Src is a neuronal splice variant of the ubiquitous proto-oncogene C-Src tyrosine kinase, which differs by a six amino acid insert in its SH3 domain. Since the SH3 domain confers substrate specificity, it is anticipated that both C- and N1-Src will have different substrates and functions. Specifically, N1-Src is highly active in the developing brain and has been implicated in neuronal differentiation. Studies also suggest a role for N1-Src in ion channel regulation, however, the mode of action of N1-Src remains poorly understood. The primary aim of this study was to further clarify the role of N1-Src in both the developing and adult brain. To achieve this, a multidisciplinary approach was adopted, which sought to 1) identify novel N1-Src substrates 2) determine the function of N1-Src in developing neurons and 3) dissect the signalling pathways downstream of N1-Src. Recombinant, active Src kinases were generated to undertake in vitro kinase assays with putative N1-Src substrates. Src-dependent phosphorylation of HCN1, a pacemaker channel identified as an N1-Src interactor in a yeast 2-hybird screen, could not be detected. This result was not conclusive as surprisingly, the assay did not detect Src or PKC phosphorylation of NR2A, an NMDA receptor subunit, previously characterised as a robust Src and PKC substrate. However, a screen of several putative N1-Src SH3 binding peptides revealed some encouraging candidates to pursue as substrates. To address the function of N1-Src in neuronal development, N1-Src was overexpressed or knocked down in cultured hippocampal neurons. Both manipulations were detrimental to neurite outgrowth and neuronal polarization, suggesting that N1-Src activates cytoskeletal remodelling pathways and precise levels of N1-Src are required for normal cellular development in vitro. The molecular mechanism of this phenomenon was investigated in a fibroblast cell line, in which N1-Src overexpression induces neurite-like processes. Using this model, an investigation into the role of N1-Src in RhoA signalling implied that N1-Src does not drive process outgrowth via the inhibition of RhoA, however constitutive activation of RhoA, prevented N1-Src mediated process extension. Preliminary results suggested that N1-Src overexpression enhances RhoA activation, which could form part of a negative feedback loop. Taken together, I have implicated N1-Src in neurite outgrowth, which provides a starting point for understanding the mechanistic role of N1-Src in pathways that dictate neuronal morphology.
EliteTree™: an advanced biomass tree crop technology that features greater wood density and accelerated stem growth

Due to wood's potential for large‐scale commercial production of biofuels, a rapid increase in the use of wood as a source of energy is expected as policies promoting greater use of renewable energy are adopted globally. However, the economics of purpose‐grown tree feedstocks for energy show that these production systems are not financially viable without improvement in the base growth rate. Conventional breeding programs have produced willow and poplar clones that show potential for rapid growth, but current top‐performing clones do not grow fast enough for profitable biofuel production. Genetic manipulation of secondary wall biosynthesis is the most direct path to resolving this growth barrier. To that end, we developed an innovative biomass tree crop technology, EliteTree™, that results in greater wood density and accelerated growth of stems. This technology is built on overexpression of Gibberellin 20‐oxidase to increase plant stem growth in both height and diameter and increase lignocellulosic biomass accumulation through overexpression of the transcription factor MYB46, which is a master regulator for secondary wall biosynthesis. EliteTree™ technology uses 2A‐mediated bicistronic gene expression, with our proprietary utility promoter DX15, such that the genetic manipulation is limited to wood tissue, yielding transgenic poplars with xylem‐specific co‐expression of MYB46 and PdGA20ox1. The development of faster growing elite tree genotypes with increased wood density and growth rates will pave the way for truly sustainable and economically viable bioenergy/biofuel production using short rotation tree plantations, and ultimately will lessen carbon emissions and has the potential to revitalize rural economies. © 2017 Society of Chemical Industry and John Wiley & Sons, Ltd
Serum Transferrin Receptors of Iron Deficiency Anemic Rats That Feeding Tempe Fortification Combination Iron and Vitamin A

Abstract. This research investigated tempe fortified with iron and vitamin A on serum transferrin receptors. Experimental research Randomized Pre Test-Post Test Control Group Design was conducted on 30 Sprague-Dawley rats with iron deficiency anemia. The rats divided into 6 groups randomly, was treated for 6 weeks with a standard feed supplemented by soybean tempe fortified with iron and vitamin A. Group 1 control group was given standard feed AIN93G (SF), group 2 SF+T0, group 3 SF+T1, group 4 SF+T2, group 5 SF+T2+V15, (6) SF+T2+V50. T0 was tempe without fortification. T1 and T2 was tempe that was fortified with 230 ppm and 271 ppm of iron (FeSO47H20, respectively. V15 and V50 was tempe that was fortified with 15 ppm and 50 ppm of vitamin A (retinyl acetate, respectively. Statistical test was used Kruskal Wallis test. The result showed that before intervention, there was no significantly different on mean of serum transferrin receptors (sTfR) (p=0,280). After intervention, sTfR became 13,0±4,0; 8,7±2,8; 8,5±2,6; 7,4±3,4; 7,2±1,7 and 1,9±0,4 µg/mL, respectively. Tempe fortification with iron and vitamin A significantly decreased sTfR (p=0,004). Average of sTfR lowest in the treatment of SF+T2+V50 (standard feed+tempe was fortified with 271 ppm of iron + 50 ppm vitamin A).