Miracle-dz/UniFAR-FTUs huggingface dataset:
Cytoskeletal reorganization in human blood platelets during spreading

Anucleate, human blood platelets play an important role in haemostasis to prevent excessive blood loss from a vascular damage. Their actin and microtubule (MT) cytoskeleton is especially responsible for bringing about dramatic morphological and biochemical changes in them, which enables the platelets to change their shape, secrete granular contents, aggregate, adhere, spread, and retract in a platelet haemostatic plug, to seal the vascular breach. The platelets are thus extremely important cells from a medical point of view and the study of their cytoskeletal changes is essential. Because platelets do not have a nucleus, they cannot be transfected, microinjected or manipulated in any way. This has restricted the study of their cytoskeleton with classic post chemical fixation approaches. Two novel, cytoskeletal, fluorogenic probes, SiR-actin and SiR-tubulin have been recently introduced, which bind to filamentous actin (F-actin) and MTs respectively. These probes have now made it possible to monitor the F-actin and MT cytoskeleton in real-time, in cells, which are otherwise difficult to transfect. In this dissertation, these SiR-actin and SiR-tubulin probes are used to directly visualize the F-actin and MT changes occurring during platelet spreading in real-time, and the temporal dynamics of these two cytoskeletal components during platelet spreading are explored. The real-time F-actin dynamics in platelets point towards the existence of multiple time-scales of F-actin reorganization during their spreading. The real-time MT dynamics in platelets point towards their role in platelet exocytosis and show that myosin plays a major role in this process. Overall, this technique of labeling human platelets with the SiR-actin and SiR-tubulin probes, to monitor any cytoskeletal changes occurring in real-time during their spreading, will improve our understanding of the role of the platelet cytoskeleton in aiding platelet functions, better. This may perhaps help lead to the development of novel agents that can alleviate platelet-related disorders in which the cytoskeleton is impaired.
Seasonal Variation in Small Mammal Granivory in Restored Tallgrass Prairie

This study answered the question of when seasonally rodents have the greatest impact on a restored tallgrass prairie plant community. Five complementary experimental methods were used spanning an entire year: cafeteria trials, plant identification using DNA analyses, trap lines, exclosures and enclosures. In combination my research suggests small mammals could potentially influence prairie plant diversity during a narrow seasonal window of late summer. Additionally, an unexpected appearance of a short-tail weasel population reduced rodent population size, possibly acting to mitigate rodent impacts on prairie plant communities.
ARABIDOPSIS MYOSIN IS INVOLVED IN THE DISTRIBUTION AND DYNAMIC BEHAVIOR OF THE CELLULOSE SYNTHASE COMPLEX

Cai, Chao. M.S., Purdue University, December 2015. Arabidopsis Myosin is Involved in the Distribution and Dynamic Behavior of the Cellulose Synthase Complex . Major Professor: Christopher Staiger. Plant cells are encased in cell walls which are important for the growth and development of the organism. Primary cell wall consists mainly of polysaccharides with cellulose as the most abundant component. In plant cells, cellulose is synthesized by a plasma membrane (PM) localized protein complex called the cellulose synthase complex (CSC). It was previously reported that disrupting normal actin organization resulted in a reduction of cellulose content in Arabidopsis dark-grown seedlings. Furthermore, actin was found to facilitate the delivery of CSC into the PM, and inferred to be involved in endocytosis. As a motor protein that translocates cargo along actin filaments, myosin plays an important role in organelle and vesicle trafficking. However, it is not known whether myosin is involved in regulating cellulose deposition or CSC behavior. Here, we used biochemical analysis to determine the cellulose content in Arabidopsis etiolated seedlings, and found a significantly decreased cellulose content in a myosin xi-1, xi-2, and xi-k triple knockout mutant (xi3KO), indicating that myosin is involved in cellulose deposition. To evaluate the molecular mechanism underlying the role of myosin in CSC trafficking, we characterized and employed a new plant myosin inhibitor,
Antimicrobial activity of fermented and non-fermented Oats ( Avena sativa ) against selected food borne pathogens

The present study was carried out to study the antimicrobial activity of non-fermented oats and oats fermented with Lactobacillus acidophilus. Oats have a distinctive nutritional profile compared with other types of grain, including protein, fibre, essential fatty acids, vitamins, minerals and antioxidants. In the this study fermented oats was found to exhibit a potent antimicrobial activity when tested with a food borne pathogens such as E. coli, Salmonella typhi and Staphylococcus aureus, whereas the nonfermented oats did not exhibit any antimicrobial activity.
Total Phenolics, Antioxidant, Antibacterial and Cytotoxic Activity Studies of Ethanolic Extracts Arisarum vulgare O.Targ.Tozz. and Dracunculus vulgaris Schott.

The present study reports the antioxidant, total p henolics, antibacterial and cytotoxic activities of Arisarum vulgare and Dracunculus vulgaris of aerial and under ground ethanol extracts. The antioxidant activity was determined by DPPH radical scavenging activity and β-carotene linoleic acid assays. Folin-Ciocalteu assay was used to detect total phenolic contents in the extract. In vitro cytotoxic activity was determined by the Brine shrimp lethality test. Antibacterial activity was investigated with the microdilution method. As a result, under ground parts of the extract showed higher antioxidant activity than aerial parts of the extract. Total phenolics ranged from 14.5±2.02 to 53.4±2.01 mg GAE/g, and the antioxidant activity according to the β-carotene/linoleic acid assay ranged from 70.76±1.08 % to 85.43±1.05 and according to the DPPH assay IC 50 values ranged from 0.089±1.02 to 1.095±1.07 mg/ml. The A. vulgare under ground extract was tested against 2 and showed a good antibacterial activity at a concentration of <50 m g/mL Minimum inhibitory concentration (MIC) values for the bacteria S.aureus. The results of the cytotoxic activities showed a very high activity of the extracts, D.vulgaris under ground extract (LC 50 = 10.6 µg/mL).
The Relationship Between Plasmid Fingerprints and Chromosomal Fingerprints of Fish Pathogenic Vibrios

It is well known that many pathogenic vibrios of marine fish possess plasmids. When plasmid DNA fingerprints of Vibrio strains containing plasmids were compared their corresponding chromosomal DNA fingerprints, we found that some bands of the chromosomal fingerprints originated from plasmid DNA. The connection with plasmid DNA fingerprints and chromosomal fingerprints has to be considered to characterize Vibrio spp. properly.
Diets of Fishers (Pekania pennanti) and Evidence of Intraspecific Consumption in Pennsylvania

Abstract The fisher (Pekania pennanti) is a forest-dwelling mesocarnivore native to northern North America. The species had been extirpated from many southern parts of its historic range, but several states have implemented fisher re-introduction programs over the past 40 y. While many studies have previously examined fisher diet, most occurred in northern and western portions of the species' range where mixed and coniferous forests are the dominate cover types. We examined fisher diet, in a re-introduced population in the central Appalachian Mountains where deciduous forests were the dominate cover type. We collected 91 fisher carcasses from 2002–2014 and examined their stomach contents. We detected mammalian and avian prey in 82.6% and 10.9% of stomachs, respectively. Fishers we sampled consumed a variety of plant materials (n = 11) and prey items (n = 30 spp.). Diet composition of males and females overlapped considerably (O = 0.87). Our most noteworthy and novel finding was the presence of fisher remains in 11 (12%) stomachs. We suggest here that rapid population growth of Pennsylvania fishers may have resulted in aggressive behaviors underlying our observations of interspecific consumption. Future research that examines the cause for intraspecific consumption in this central Appalachian fisher population would be a worthy endeavor.
The complete chloroplast genome sequence of the threatened trident maple Acer buergerianum (Aceraceae)

Abstract Trident maple Acer buergerianum Miq. , belonging to the family of Aceraceae, is an important ornamental tree. Here, we report the complete chloroplast genome sequence of A. buergerianum. The circular genome was 156,477 bp in size, and comprised a pair of inverted repeat (IR) regions of 26,090 bp, a large single-copy (LSC) region of 86,246 bp and a small single-copy (SSC) region of 18,062 bp. It contained 134 genes, including 89 protein-coding genes, 40 transfer RNA genes, and 8 ribosomal genes. Maximum likelihood phylogenomic analysis shows that A. buergerianum is closely related to other Acer species, including A. miaotaiense, A. morrisonense, and A. davidii.
Screening and Identification of Potential Bacillus Spp. for the Management of Bacterial Wilt of Brinjal

Among 100 isolates of Bacillus spp. screened in vitro against Ralstonia solanacearum that causes bacterial wilt of brinjal, ten were found inhibitory to R. solanacearum . Bacillus megaterium isolate NBAII 63 was highly inhibitory with 29.20 mm of inhibition zone against R. solanacearum as compared to the other nine strains of Bacillus . Six of them were identified by 16S rDNA analysis. The bioefficacy of talc formulation of B. megaterium was evaluated under greenhouse for plant growth promotion and suppression of bacterial wilt in brinjal. The bacterial wilt was effectively managed by B. megaterium through different methods of applications. A combination of four methods (seed treatment + soil application + seedling root dip + foliar spray) was the most effective. Maximum root length (23.42 cm), shoot length (65.21 cm), fresh weight (40.39 g), dry weight (10.33 g) and highest wilt reduction (50.54%) was recorded in the combination method. Among single application methods, seed treatment was effective exhibiting 41% reduction of bacterial wilt followed by soil application which gave 36% wilt reduction. The bacterial wilt reduction in chemical control (streptomycin sulphate) was 71%. Good growth of the brinjal plants was recorded due to application of B. megaterium . Highest rhizosphere population of 67.0 × 10 6 cfu/g was recorded in brinjal at 40 days after transplanting when the antagonist was applied by combining the different application methods.
Usefulness of a Locus LE21085 in the Genetic Differentiation of Tomato Varieties

The microsatellites are specific for each individual genome or species. In order to evaluate the genetic diversity and the relationships within the genus Lycopersicon , microsatellites markers were used. The main objective of this study was to determine the usefulness of the locus LE21085 in the genetic differentiation among six morphologically different tomato varieties of Lycopersicon esculentum Mill. (var. grandifolium subsp. cultum ; var. cerasiforme - red and yellow, var. pruniforme, var. pyriforme subsp. subspontaneum and var. racemigerum subsp. spontaneum ). For the microsatellites locus LE21085 were detected two alleles in all estimated tomato varieties, that differed by one base pair (122 and 123 bp). The biggest allele frequency was found for the allelic variant of 122 bp, and its values were: 0.8462 for L. esculentum subsp. subspontaneum var. cerasiforme (red), 0.6923 for L. esculentum subsp. subspontaneum var. cerasiforme (yellow), 0.5769 for L. esculentum subsp. cultum var. grandifolium , 0.6923 for L. esculentum subsp. subspontaneum var. pruniforme , 0.6154 for L. esculentum subsp. subspontaneum var. pyriforme and 0.8077 for L. esculentum subsp. spontaneum var. racemigerum . The average of observed heterozygosity for the locus LE21085 (Ho = 0.5641) was higher than average expected heterozygosity (He = 0.4158). The average PIC value for the locus LE21085 was 0.3294 and it was classified as a modest informative markers. From the obtained results it can be concluded that locus LE21085 could be used in genetic differentiation of tomato varieties, but in combination with other polymorphic microsatellite loci.
In vitro salt stress induced enhancement of ascorbic acid in Emblica officinalis

Emblica officinalis is highly nutritious and important dietary source of vitamin C, minerals and amino acids. It also contains phenolic compounds, tannins, phyllembelic acid, phyllemblin, rutin, curcuminoides and emblicol callus was raised from cotyledonary explant on Murashige and Skoog (M S) medium supplemented with different concentrations of auxin and cytokinin. Callus initiation and Best callus growth was observed on 1.0 mg/l 2, 4-Diphenoxy acetic acid (2, 4-D). Callus was transferred from 1.0 mg/l 2, 4-D to different concentrations of Sodium Chloride (NaCl) i.e. 50, 100, 150, 200 mM NaCl. The effect of NaCl on proline, protein, phenolics and ascorbic acid were observed after four weeks. Addition of salt (50 mM) led to decrease in protein and proline but increase in phenolics and ascorbic acid content. Further increase in NaCl (100,150 and 200 mM) led to increase in protein, proline, phenolics and ascorbic acid content. Interestingly, ascorbic acid content in the salt (200 mM) treated calli was approximately as much as reported in fruits in vivo .
Mathematical modeling of pathways involved in cell cycle regulation and differentiation

Cellular processes critical to sustaining physiology, including growth, division and differentiation, are carefully governed by intricate control systems. Deregulations in these systems often result in complex diseases such as cancer. Hence, it is crucial to understand the interactions between molecular players of these control systems, their emergent network dynamics, and, ultimately, the overall contribution to cellular physiology. In this dissertation, we have developed a mathematical framework to understand two such cellular systems: an early checkpoint (START) in the budding yeast cell cycle (Chapter 1), and the canonical Wnt signaling pathway involved in cell proliferation and differentiation (Chapter 2). START transition is an important decision point where the cell commits to one round DNA replication followed by cell division. Several years of experimental research have gone into uncovering molecular details of this process, but a unified understanding is yet to emerge. In chapter one, we have developed a comprehensive mathematical model of START transition that incorporates several findings including information about the phosphorylation state of key START proteins and their subcellular localization. In the second chapter, we focus on modeling the canonical Wnt signaling pathway, a cellular circuit that plays a key role in cell proliferation and differentiation. The Wnt pathway is often deregulated in colon cancers. Based on some evidence of bistability in the Wnt signaling pathway, we proposed the existence of a positive feedback loop underlying the activation and inactivation of the core protein complex of the pathway. Bistability is a common feature of biological systems that toggle between ON and OFF states because it ensures robust switching back and forth between the two states. To study and explain the behavior of this dynamical system, we developed a mathematical model. Based on experimentally determined interactions, our simple model recapitulates the observed phenomena of bimodality (bistability) and hysteresis under the effects of the physiological signal (Wnt), a Wnt-mimic (LiCl), and a stabilizer of one of the key members of core complex (IWR-1). Overall, we believe that cell biologists and molecular geneticists can benefit from our work by using our model to make novel quantitative predictions for experimental verification.
Genetic structure and variation of five Shorea leprosula natural populations based on microsatellite marker

MAHARDIKA PUTRA PURBA. Genetic structure and variation of five Shorea leprosula natural populations based on microsatellite marker. Supervised by ISKANDAR Z. SIREGAR and SRI WILARSO BUDI Shorea leprosula is an economically and ecologically important timber species and one of the most common tropical lowland rain forest tree species in Southeastern Asia. Eleven microsatellites DNA loci were used to investigate the genetic structure and diversity among five natural populations from Sumatera (CS and NS), Peninsular Malaysia (SM) and Borneo (WKa and WKb). Results indicated that expected mean heterozygosity (He) was high (0.721) with values ranging from 0.542 to 0.788, with the highest values found in the populations from west Kalimantan (WKb). Most of the populations showed high and positive fixation indices indicating excess of homozygotes. This implies a high level of inbreeding which may be caused by selfing or/and mating among relatives. A gene diversity analysis showed that 89.9% of the variation was harbored within populations and 11.1% (FST= 0.111) was due to differences among populations. STRUCTURE analysis showed that five natural populations were clustered into two main groups namely: i) Sumatera-Peninsular Malaysia, and ii) Borneo. Mean gene flow (Nm) was high (2.00) indicating extensive gene flow in the past among the natural populations. Three populations (WKb, NS and SM) were identified to be genetically unique and we recommended for further consideration in formulation of genetic conservation strategies.
Circadian Clocks and Photoperiodic Diapause in the Northern House Mosquito, Culex pipiens : Search for the Missing Link

In this review we explore links between circadian clocks and the clock involved in photoperiodic regulation of diapause in insects. Classical resonance (Nanda-Hamner) and night interruption (Bünsow) experiments suggest a circadian basis for the diapause response in nearly all insects that have been studied. Neuroanatomical studies reveal physical connections between circadian clock cells and centers controlling the photoperiodic diapause response, and both mutations and knockdown of clock genes with RNAi point to a connection between the clock genes and photoperiodic induction of diapause. We discuss the challenges of determining whether the clock, as a functioning module, or individual clock genes acting pleiotropically, are responsible for the photoperiodic regulation of diapause, and how a stable, central circadian clock could be linked to plastic photoperiodic responses without compromising the clock’s essential functions. Although we still lack an understanding of the exact mechanisms whereby
Analysis of Dystrophin Gene Deletions Indicates that the Hinge III Region of the Protein Correlates with Disease Severity

We have investigated the frequency of deletions in the dystrophin gene in 108 unrelated Duchenne and Becker muscular dystrophy (DMD/BMD) patients from southern Italy (DMD, n. 47; BMD, n. 61) and identified 89 deletions. The de novo mutation rate (about 30%), and the preferentially maternal origin of deletional mutations, analysed in families in which the maternal grandparents were available or their haplotypes could be unequivocally reconstructed, are in agreement with data reported for other populations. The correlation between BMD phenotype and type of deletion suggests that, in the distal rod domain region, the deletion size may not be as crucial as the particular combination of missing exons. In fact, we provide immunohistochemical and clinical evidence that in‐frame deletion of the hinge III region in the distal rod domain results in a milder phenotype as compared with shorter deletions that do not include the hinge III region. Our data obtained in BMD patients, by confirming inferences arising from minigene transfection experiments in mdx mice, represent an important contribution to gene therapy approaches.
Wood density and anatomy of three Eucalyptus species: implications for hydraulic conductivity

Aim of the study : To characterize wood anatomical traits of three Eucalyptus species that differ in wood density and ecological requirements, and to examine the relationships between some anatomical features, wood density, and theoretical xylem hydraulic conductivity ( Ks ). Area of study : We analyzed 86 trees from three sites of Argentina (Entre Rios and Buenos Aires Provinces). Methods: The sampled trees were Eucalyptus globulus , E. grandis and E. viminalis ranging from 11 to 15 years old. One stem disc was cut from each tree to determine wood density and identify quantitative anatomical features of vessels and fibers. Vessel composition (S, size - to-number ratio, a measure of vessel size distribution) and lumen fraction (F, the total sapwood area available for water transport) were estimated. Results: E. grandis, the species with the highest growth rates, presented the highest theoretical Ks. This was associated with anatomical features such as a high density of wide vessels resulting in high F. On the other hand, E. viminalis, the species with the lowest growth rates and highest resistance to environmental stress, showed lower Ks as a result of a low density of wide vessels. These two species differed not only greatly in wood density but also in fiber characteristics. In the case of E. globulus , vessels were relatively narrow, which resulted in the lowest theoretical Ks , fibers were small, and wood density intermediate. Research highlights: F had greater influence on Ks than S. The anatomical characteristics and wood density could only partly explain the differential growth or resistance to stress of the studied species.
DIVERSITY OF STONY CORALS IN BANGGAI WATER

Banggai waters, located in Central Sulawesi Province, is part of the worldâ€™s coral triangle area which is wellâ€“known to have the highest diversity on stony corals (Scleractinia). A research on stony corals has been carried out at 9 study sites between Juneâ€“July 2011, practicing line transect methods and free collection in order to determine the recent condition and diversity of the given coral group. The average of live corals coverage was recorded at 46% (ranging between 24â€“77%), and categorized as fair condition. The number of coral species found was 194, distributed in 54 genera. The Banggai waters condition was considered good and potential to sustain the coralsâ€™growth. Even though so, in several particular areas, there were still threats on coral reefs.