Miracle-dz/UniFAR-FTUs huggingface dataset:
Cloning of JNK activation domain and Fas-binding domain of human apoptotic Daxx gene by homologous recombination in yeast

The death domain-associated protein (Daxx) was originally cloned as a Fas-interacting protein. It is ubiquitously expressed and highly conserved in mammals. Currently, the role of Daxx is controversy between apoptotic or anti-apoptotic molecules. To understand the precise function of human Daxx, yeast two hybrid screening will be used as a tool to identify interactions between human Daxx and other human proteins. The first step in a yeast two hybrid method is to express a bait plasmid in the recombinant form in yeast. We utilized the in vivo homologous recombination in yeast to insert a JNK activation domain and a Fas-binding domain of human Daxx, into the bait plasmid, pEG-NRT. Furthermore, the expression of a JNK activation domain and a Fas-binding domain of human Daxx was demonstrated by Western blot analysis. Yeast expressing a JNK activation domain and a Fas-binding domain of human Daxx will be used as bait strains to screen for human proteins interacting with Daxx, which may provide us the clue to uncover the mysterious function of human Daxx.
Life skills program for improving adolescent mental health in the af-termath Mount Merapi eruption, Yogyakarta-Indonesia

The ability of adolescents to cope with stressful life events has not been well developed. Facing stressful situations might trigger them to engage in many dangerous and self-destructive behaviors. Life skills program in improving mental health of adolescents has been proven in many countries, as it has in Indonesia. In postdisaster situation, there is rarely any community program which focuses on adolescent mental health. Life skills program is a psychological intervention to teach adolescents to improve their skill to cope with stress, develop self-esteem, deal with peer pressure, think critically, communicate appropriately and act assertively. Teachers and local health professionals who have already been trained about life skills program apply this program in adolescents experiencing a stressful event, a natural disaster from the eruption of Mount Merapi in YogyakartaIndonesia. This study attempts to apply and evaluate the effectiveness of the program for adolescents who had survived a natural disaster in Yogyakarta-Indonesia. Three-weeks life skills training was conducted in 2012 on 40 junior and senior high school students, post Mount Merapi eruption in Yogyakarta and Magelang. Subjects were assessed for their self-image using Rosenberg self-image questionnaire, and their emotional-behavioral problems and mental strength using Strength and Difficulties Questionnaire (SDQ), before and after the training. SPSS was used for the statistical analysis. The average age of the subjects was 14.48 + 1.21 years old. There were significant differences on the self-esteem and mental strength aspects of the subjects before and after intervention. Score on low self-esteem was improved (p=0.005), negative self perception also became better (p<0.001), and prosocial behavior was increased (p=0.001). There were also decreasing difficulties and emotional-behavioral problem score after intervention, and other aspects of self-esteem such as instability and selfconsciousness. Life skills training has several positive effects in improving mental strength and self-image and decreasing emotional and behavioral problems of adolescents post-disaster.
RHIZOSPHERE BACTERIA AS POTENTIAL BIOCONTROL AGENTS AGAINST SOFT ROT CAUSED BY VARIOUS PECTOBACTERIUM AND DICKEYA spp. STRAINS

In vitro screening was used to select potential biological control agents (BCAs) against soft rot caused by Pectobacterium and Dickeya spp. (including the newly characterised D. ‘solani’). Out of 1165 rhizobacteria screened, 18 potential BCAs were selected on the basis of their in vitro ability to inhibit the growth (antibiosis) of at least one pathogenic strain (group I) or to inactivate acyl-homoserine lactones (AHLs) involved in the quorum sensing of Pectobacterium spp. and Dickeya spp. (group II). The AHL-degrading Bacillus spp. were also screened by PCR for the presence of the aiiA gene, and this report is the first to document the presence of this gene in Bacillus simplex. The 18 antagonists, all identified as Pseudomonas or Bacillus, were further characterised for motility, production of siderophores, and biosurfactants. Although most group I isolates suppressed maceration of potato tuber slices by Pectobacterium spp. strains, the ability to cause antibiosis in vitro did not guarantee the ability to suppress disease in planta. Despite the poor efficacy against Dickeya spp. on potato slices, group I isolates were highly effective on chicory leaves, which indicates that the host plant is an important criterion in the selection of BCAs against Dickeya spp. The AHL-inactivating isolates of group II were active against a broad spectrum of both Dickeya spp. and Pectobacterium spp. strains. Significantly, the efficacy of some BCAs of both groups differed among pathogen species and pathogen strain within species. The selected rhizobacteria warrant additional study as potential BCAs for the control of soft rot.
Genome-Wide Identification and Analysis of Human Neuronal Activity-Dependent Enhancers in Evolution and Disease

Neuronal activity-responsive gene expression plays a key role in the proper development, refinement, and plasticity of neural circuits, and the dysregulation of these gene responses have been implicated in developmental and cognitive disorders. Thus, identification and molecular characterization of the cis-regulatory DNA elements driving this response in neurons has the promise to profoundly advance our understanding of neurological disease mechanisms. The transcription factor cAMP/Ca2+-responsive element binding protein (CREB) is an important stimulus-responsive factor in many cell types of the body. CREB and its transcriptional co-activators are important for gene regulation in the brain and play a critical role in cognitive development, neuronal survival, and learning and memory. In the following studies we performed mechanistic analysis in human and mouse neurons to understand genome-wide binding of CREB and its neuronal co-activator, CREB Regulated Transcriptional Co-activator 1 (CRTC1, a.k.a. TORC1) at non-coding regulatory elements in response to neuronal depolarization. In addition, we investigated post-translational modifications of CRTC1 in response to BDNF treatment to better understand the biochemical basis of this co-factor’s activation in mouse neurons. iv! Using human induced pluripotent stem cell (iPSC)-derived neurons we hoped to explore CREB-associated regulatory element function that cannot be studied in rodent models. While transcriptional and epigenomic analysis of human post-mortem brain samples has allowed for recent advances in identifying neuronal cis-regulatory regions of the genome, these approaches cannot address the dynamic, experience-dependent nature of their function in neuronal gene expression programs. We have identified human and mouse neuronal activity-dependent regulatory elements using ChIP-seq for both histone modifications and transcription factors in human pluripotent stem cell derived neuronal cultures, and thus provide a resource map of neuronal activity responsive regulatory elements across the human and mouse genomes. We identified human neuronal stimulus-dependent binding sites for CREB and CRTC1, including those that contain SNPs associated with neurological disorders, such as the schizophrenia-associated locus of CACNB2. Other CREBassociated regulatory elements potentially control expression of primate-specific transcripts and could be important sites of genetic divergence. Further functional investigation of these sequences will allow us to understand their role in human disease and evolution.
How fast is a collective bacterial state established?

Bacteria in a biofilm colony have the capacity to monitor the size and growth conditions for the colony and modify their phenotypical behaviour to optimise attacks, defence, migration, etc. The quorum sensing systems controlling this involve production and sensing of diffusive signal molecules. Frequently, quorum sensing systems carry a positive feedback loop which produces a switch at a threshold size of the colony. This all-or-none switch can be beneficial to create a sudden attack, leaving a host little time to establish a defence. The reaction-diffusion system describing a basal quorum sensing loop involves production of signal molecules, diffusion of signal molecules, and detection of signal molecules. We study the ignition process in a numerical solution for a basal quorum sensor and demonstrate that even in a large colony the ignition travels through the whole colony in a less than a minute. The ignition of the positive feedback loop was examined in different approximations. As expected, in the exact calculation the ignition was found to be delayed compared to a calculation where the binding of signal molecules was quasistatic. The buffering of signal molecules is found to have little effect on the ignition process. Contrary to expectation, we find that the ignition does not start when the threshold is reached at the center—instead it allows for the threshold to be approached in the whole colony followed by an almost simultaneous ignition of the whole biofilm aggregate.
Enhanced species distribution models: a case study using essential population data from Actinotus helianthi (flannel flower)

Climate envelopes are generated by overlaying climate variables derived from temperature and rainfall data onto mapped geographic locations of occurrences. Typically the species data are amalgamated into a single climate envelope, missing the opportunity to account for the potential of different environments to independently shape the functional plant trait values within populations. Here we explore how climate envelopes vary among populations, and whether individuals with similar trait values are similarly matched to particular climate envelopes or to spatial layers of environmental classifications based on additional variables other than climate. We generated climate envelopes from 35 populations of the widely distributed plant species Actinotus helianthi Labill. (Apiaceae). Populations with at least 84% similarity in their local climate were grouped by hierarchical cluster analysis. We then tested whether the similar climate envelopes would co-vary with populations of plants with similar traits. The same method was used to examine whether populations with more individuals were better adapted to their local climate than populations with fewer individuals. We also compared whether the climate envelopes were representative of other environmental groupings, including the Interim Biogeographical Regionalisation of Australia (IBRA) and soil types. Plant trait values were significantly different among populations (P ≤ 0.001) and soil types (P ≤ 0.003). All traits, except diam and condist, were significantly different among bioregions. Seven climate envelopes were identified across sampled populations, and plant
Handbook of Microalgal Culture: Applied Phycology and Biotechnology

Algae are some of the fastest growing organisms in the world, with up to 90% of their weight made up from carbohydrate, protein and oil. As well as these macromolecules, microalgae are also rich in other high-value compounds, such as vitamins, pigments, and biologically active compounds, All these compounds can be extracted for use by the cosmetics, pharmaceutical, nutraceutical, and food industries, and the algae itself can be used for feeding of livestock, in particular fish, where on-going research is dedicated to increasing the percentage of fish and shellfish feed not derived from fish meal. Microalgae are also applied to wastewater bioremediation and carbon capture from industrial flue gases, and can be used as organic fertilizer.
Observations on cannibalism and feeding on dead arthropods in Scydmaenus tarsatus (Coleoptera: Staphylinidae: Scydmaeninae)

Scydmaenus tarsatus Müller & kunze, 1822, an ant-like stone beetle associated with decaying plant matter, is demonstrated to scavenge on dead arthropods (pseudoscorpions, immature isopods and adult flies). For the first time a conspecific aggression and cannibalism is reported to occur in Scydmaeninae under laboratory conditions.
Effectiveness of Selected Native Plants as Competitors with Non-indigenous and Invasive Knapweed and Thistle Species

Abstract : This work examined the response of native grass populations to long-term presence of non-indigenous invasive plant species (NIPS). Two native grass species common to arid and semi-arid rangelands were identified (alkalai sacaton [Sporobolus airoides] and needle and thread grass [Hesperostipa comata]) as remnants of native communities subjected to NIPS Russian knapweed [Rhaponticum repens]). Maternal grass individuals were collected to examine the influence of the invasions on population genetics and phenology of the two grass species. In controlled greenhouse settings and field plantings, this work examined the growth, seed production, and germination of seedlings of the two grasses in competition with Russian knapweed and NIPS Canada thistle [Cirsium arvense]; and genetic variability of the two grasses via amplified fragment length polymorphism and Inter-Simple Sequence Repeat analyses. Results showed that maternal lines of the grasses demonstrate evidence of natural selection via the presence of the invaders. Continued work was recommended to obtain superior seed sources for native species to target the tradeoffs between phenotypic plasticity and increased vegetative growth, to develop wild seed collection protocols and production techniques so that native plants may be used to restore degraded areas and to reduce the chances of future exotic invasion.
Skeletal muscle pericytes as signal mediators in the vessel wall

In this thesis a novel method to isolate and cultivate pericytes from hamster skeletal muscle is presented. By choosing a two-step approach with magnetic-bead cell sorting for the 3G5 antigen and culture in a selective growth medium a high percentage of pericytes could be reached and their nature could be verified in subsequent characterization steps. Morphologically the cells had a typical phenotype with flat and large cell bodies and long protruding processes. Immunocytochemistry and western blotting could confirm the expression of the previously reported pericyte markers NG2, PDGFR-β, and αSMA. However, in accordance with previous reports, even the cells isolated from the same muscle and tissue, were not a uniform population. A certain heterogeneity was also present in the functional studies investigating pericyte membrane channels by electrophysiology. In these experiments in a subset of the pericyte population the presence of the voltage sensitive potassium channel KV1.5 could be demonstrated. Upon pharmacological stimulation of these channels by FFA they were able to elicit a membrane hyperpolarization and conduct it to neighboring endothelial cells via gap junctions formed by connexin 43. The expression of the KV1.5 channel could also be demonstrated by immunohistochemistry in paraffin sections from hamster skeletal muscle. These findings are consistent with the hypothesis that pericytes could act as signal generators for hyperpolarization and vasodilatation in the vessel wall. The coupling with endothelial cells might relay an electric signal further along the vessel wall and lead to “EDHF mediated” dilations [48]. Interestingly in tissue sections KV1.5 positive pericytes were located predominantly at vascular branchings. We additionally studied whether gap junctions may also form a pathway for the exchange of miRNA between cells in a model co-culture system using HeLa. For the detection of the miRNA a detector system consisting of a luciferase reporter protein under control of a miR124 sensitive 3’ UTR was established. Our experiments could not conclusively confirm transfer of miRNA in this system. Similar results were obtained with human miR15b. Taken together these findings open up new possibilities for studying skeletal muscle pericyte physiology and to test novel concepts integrating the pericyte into the vascular signaling network under conditions of health and disease.
Ethanol production from potato flour by Saccharomyces cerevisiae

Flour prepared from potato tubers ( Solanum tuberosum ) after cooking and drying at 70°C was used for ethanol production. Homogenous slurry of potato flour was prepared in water at solid liquid ratio 1:4. Liquefaction of potato flour slurry with α-amylase (2.05 DUN U/g starch) at 80°C for 30 min followed by saccharification with glucoamylase (20.5 GA U/g starch) at 60°C for 2 h generated 15.2% total reducing sugars in the hydrolysate. Fermentation of hydrolysate with Saccharomyces cerevisiae HAU-1 at 30°C for 48 h resulted in production of 56.8 gl -1 ethanol. Supplementation of nitrogen sources to potato flour did not contribute significantly to ethanol yield. Simultaneous saccharification and fermentation of hydrolysate was as effective as separate hydrolysis and fermentation.
Genetic heterogeneity and gene diversity at ABO and Rh loci in the human population of Southern Punjab, Pakistan.

Southern Punjab in Pakistan is a heterogeneous assemblage of human populations which have diverse origins. Various waves of pre- and post-partition (1947) migrations, urbanization and high inbreeding coefficient have profoundly influenced the diversity and substructuring of this multiethnic and multilinguistic population. In order to get an insight into the genetic structure of Southern Punjab population, we have employed classical immuno-genetic markers of ABO and Rh loci. Five administrative districts, i.e., Dera Ghazi Khan, Muzaffargarh, Multan, Bahawalpur, and Liaquatpur, were included in this study and the phenotypic and genotypic data of approximately 60,000 subjects was assembled. Various genetic parameters including maximum likelihood estimates of allelic frequencies, Hardy-Weinberg Equilibrium, locus specific and combined heterozygosities, and phenotypic and allelic variances, were investigated to understand population dynamics. Affinities between recruited populations were measured through tests of homogeneity, and gene diversity and coefficient of gene differentiation was computed in sub- and total-population. These analyses established that Southern Punjab population is markedly distinct from the upper Punjab/Punjab populations for the genetic systems studied. Additionally, population stratification and substructuring were significantly higher in Southern Punjab compared to upper Punjab/Punjab, depicting the likely role of micro-evolutionary forces shaping the dynamics of this interesting population. This pilot study would help understand the genetic structure of Southern Punjab population and to find its affinities with other Pakistani populations.
Eliciting Beliefs as Distributions in Online Surveys

Abstract Citizens’ beliefs about uncertain events are fundamental variables in many areas of political science. While beliefs are often conceptualized in the form of distributions, obtaining reliable measures in terms of full probability densities is a difficult task. In this letter, we ask if there is an effective way of eliciting beliefs as distributions in the context of online surveys. Relying on experimental evidence, we evaluate the performance of five different elicitation methods designed to capture citizens’ uncertain expectations. Our results suggest that an elicitation method originally proposed by Manski (2009) performs well. It measures average citizens’ subjective belief distributions reliably and is easily implemented in the context of regular (online) surveys. We expect that a wider use of this method will lead to considerable improvements in the study of citizens’ expectations and beliefs.
Studies on Wheat Scab in Alabama

Wheat scab is one of the more destructive diseases of wheat in the US. In Alabama, scab was not considered a problem in the past; however, during recent years it has been reported in north Alabama. The overall goal of this study was to address the prevailing status and management of wheat scab in Alabama. The specific objectives were: 1) to evaluate the efficacy of fungicides in control of wheat scab and foliar diseases of wheat in Alabama; 2) to evaluate perithecial development by Gibberella zeae on wheat straw; and 3) to determine the distribution of wheat scab incidence across Alabama and collect and characterize Fusarium species associated with the disease. For the first objective, fungicide trials were conducted for two years at each of three locations. Fungicides were evaluated for controlling scab as well as foliar diseases of wheat, which were effective in reducing foliar diseases in the areas with relatively high disease pressure, and had a consistently positive effect in improving yield components. Concentration of the mycotoxin, deoxynivalenol (DON), was assayed for wheat samples in 2012, where only a few samples had detectable levels of DON. To address the second objective, wheat straw were incubated in different soils with varying levels of moisture and temperature. Incubated straw were later inoculated with G. zeae and observed for perithecial development. Results showed greater perithecial development on straw incubated in finer textured soils from Tennessee Valley (Decatur silt loam) or Plant Breeding Unit (Independence loamy fine sand) compared to a coarse soil from Headland
Role of Zonula Occludens (ZO) proteins in regulating kidney collecting duct principal cell proliferation and adhesion

The role of tight junctions (TJs) in regulating epithelial cell proliferation in conjuction with scaffolding zonula occludens (ZO) proteins has come to light recently. We examined the influence of each ZO protein (ZO-1, -2 and -3) on kidney collection duct (CD) cell proliferation. All tree ZO proteins are expressed in native CD and are present at both intercellular junctions and nuclei of cultures CD principal cells MCCDc11). Suppression of either ZO-1 or ZO-2 resulted in increased G0/G1 retention. ZO-2 suppression decreased cyclin D1 abundance whilw ZO-1 suppression increased nuclear p21 localization, the depletion of which restores cell density and relied on the presence of ZO-1. ZO-3 depletion increased cell detachment with increased cyclin D1 abundance, altered s1 –integrin subcellular distribution and decrased occludin expression. These data reveal diverging, but interconnected, roles for each ZO protein in mCCDc11 proliferation.