Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative genomics of gene expression in eukaryotes

Advances made in genome sequencing in the past decade have produced a massive amount of genetic information. There is a need for developing quantitative methods aimed at exploiting this information, with the ultimate objective being to attain a better understanding of the biological processes taking place. Microarrays, which can characterize the transcriptional profiles of tens of thousands of genes simultaneously, have been widely used in comparative genomic studies. However, the analysis of microarray data is still challenging. To date, assessing cross-species conservation of gene expression using microarray data has been mainly based on comparison of expression patterns across corresponding tissues, or comparison of coexpression of a gene with a reference set of genes. We compared one corresponding tissue-based method and three coexpression-based methods for assessing conservation of gene expression, in terms of their pair-wise agreements, using a frequently used human-mouse tissue expression dataset. Gene expression patterns were then compared between human and mouse genomes using both corresponding tissue-based and coexpression-based methods. To detect and analyze synteny and collinearity, we have developed the MCScanX toolkit, which implements an adjusted MCScan algorithm and incorporates 14 utility programs. In Arabidopsis thaliana and Oryza sativa (rice), species that deeply sample botanical diversity and for which expression data are available from a wide range of tissues and physiological conditions, we have compared expression divergence between genes duplicated by six different mechanisms (whole-genome, tandem, proximal, DNAbased transposed, retrotransposed and dispersed duplications), and between positional orthologs. The findings imply that gene duplication modes differ in contribution to genetic novelty and redundancy, but show some parallels in taxa separated by hundreds of millions of years of evolution. INDEX WORDS: Microarray, gene expression, conservation, divergence, coexpression, synteny, collinearity, algorithm, software, gene family, gene duplication, genetic novelty, genetic redundancy, ortholog, phylogenetic analysis COMPARATIVE GENOMICS OF GENE EXPRESSION IN EUKARYOTES
Detection of Citrus Viruses by Graft Transmission: A Review

Plants are still the only "eyes" we have for the detection of most citrus viruses. This review will provide a brief history of the detection of citrus viruses by graft transmission. It will explore some of the factors affecting symptom expression, i.e., the importance of good plant growth and nutrition, temperature, light, inoculation techniques, and use of sensitive indicator plants. Also reviewed will be the importance of a virus bank and some problems of detecting mild virus isolates. An outline will be presented for an "ideal" indexing facility. This review is designed to lend impetus and direction for improving inoculation and detection procedures so that the mildest reacting isolates, or new and unknown agents, can readily be detected in the shortest possible time. There are other innovativk, rapid, and important means of virus dekection, e.g., mechanical transmission t o herbaceous hosts, chemical and histological techniques, culturing as with Spiroplasma citri, and observation of a virus in the electron microscope. Each method is important. However, there are many citrus diseases for which graft transmission to indicator plants is still the only means of detection. This review focuses on the most effective use of plants for citrus virus detection.
Understanding and Preventing Disease-Associated Anaerobic Choline Metabolism by the Human Gut Microbiota

The consortium of microorganisms inhabiting the human gastrointestinal tract, our gut microbiota, has an extensive set of metabolic capabilities that directly influence human health. Over the past decade, DNA sequencing has significantly improved our knowledge of this microbial community’s composition. However, the molecular details of how gut bacterial metabolism impacts human health and disease are largely unknown. We propose that by combining chemical knowledge with bioinformatics, we can uncover microbial metabolic pathways that contribute to human disease. By developing small molecule inhibitors specifically targeting these pathways, we can further elucidate the roles of bacterial metabolism in disease and create a new paradigm for therapeutics. To illustrate this strategy’s potential, we are investigating the catabolism of the essential nutrient choline by anaerobic gut microbes. Within the human gastrointestinal tract, bacteria can process choline in an entirely different manner than human cells, cleaving its C–N bond to produce trimethylamine (TMA), which is subsequently oxidized to trimethylamine N-oxide by hepatic enzymes. This microbialhuman co-metabolic pathway has been linked to several diseases, including non-alcoholic fatty liver disease and atherosclerosis. Even though anaerobic microbial choline conversion into TMA has been known for over a century, its genetic and biochemical bases had not been identified prior to our work. This thesis presents the discovery and validation of a gene cluster responsible for anaerobic choline utilization (cut gene cluster), as well as the characterization and inhibition of the key TMA-forming enzyme, choline TMA-lyase (CutC). Chapter 2 details the bioinformatic approach used to discover the cut gene cluster, and the genetic, spectroscopic and cultivation-based strategies to connect these genes to anaerobic choline metabolism. We also reveal the involvement of a C–N bond cleaving glycyl radical enzyme (CutC) in
Seed Germination and Seedling Recruitment Behavior of Winged Sea Lavender (Limonium lobatum) in Southern Australia

Abstract Winged sea lavender [Limonium lobatum (L.f. Chaz)] is emerging as a significant weed of field crops in southern Australia. Several environmental factors affecting germination and seedling recruitment were examined to provide a better understanding of the behavior of its seedbank. At maturity, weed seeds were dormant for a period of around 2 mo, but dormancy was easily broken with scarification or by pretreatment with 564mM NaOCL for 30 min, which confirms the role of the seed coat in regulating seed germination. Exposure to light significantly increased germination. Seeds were able to germinate over a broad range of temperatures (5 to 30 C), with maximum germination (∼92%) at temperatures between 10 and 30 C. At 20 to 25 C, 50% germination was reached within 1.3 to 2 d, and the predicted base temperature for germination of the two populations ranged from 1.4 to 3.9 C. The NaCl concentration required to inhibit germination by 50% was 230 mM, with some seeds capable of germination at salinity levels as high as 480 mM. These results indicated greater tolerance to salinity in L. lobatum than many other Australian agricultural weed species previously investigated. Seedling emergence was the highest (51% to 57%) for seeds present on the soil surface and was significantly reduced by burial at 1 cm (≤11%) and 2 cm (≤2%), with no emergence at 5 cm. Under field conditions, seedling recruitment varied considerably among the three experimental sites. The level of seedling recruitment was negatively associated with rainfall received at the site, organic carbon (OC) level, and microbial biomass of the soil. Rapid decay of weed seeds in high-OC soils appears to be an important determinant of seedling recruitment in this species and could explain greater occurrence of L. lobatum on soils with low OC and low microbial activity in low-rainfall areas of southern Australia. Furthermore, many such soils in southern Australia are affected by salinity, which would enable L. lobatum to be more competitive with crops and other weeds present at a site.
Spatiotemporal Gene Coexpression and Regulation in Mouse Cardiomyocytes of Early Cardiac Morphogenesis

Cardiac looping is an early morphogenic process critical for the formation of four-chambered mammalian hearts. To study the roles of signaling pathways, transcription factors (TFs) and genetic networks in the process, we constructed gene co-expression networks and identified gene modules highly activated in individual cardiomyocytes (CMs) at multiple anatomical regions and developmental stages. Function analyses of the module genes uncovered major pathways important for spatiotemporal CM differentiation. Interestingly, about half of the pathways were highly active in cardiomyocytes at outflow tract (OFT) and atrioventricular canal (AVC), including many well-known signaling pathways for cardiac development and several newly identified ones. Most of the OFT-AVC pathways were predicted to be regulated by 6 6 transcription factors (TFs) actively expressed at the OFT-AVC locations, with the prediction supported by motif enrichment analysis of the TF targets, including 10 TFs that have not been previously associated with cardiac development, e.g., Etv5, Rbpms, and Baz2b. Finally, our study showed that the OFT-AVC TF targets were significantly enriched with genes associated with mouse heart developmental abnormalities and human congenital heart defects.
Identification and Estimation of Endogenous Peer Effects Using Partial Network Data from Multiple Reference Groups

There has been a considerable amount of interest in the empirical investigation of social influence in the marketing and economics literature in the last decade or so. Among the many different empirical models applied for such investigations, the most common class of model is the linear-in-means model. These models can be used to examine whether social influence is truly a result of agents affecting each other through their choices simultaneously (endogenous effect) or of having similar taste and characteristics (homophily). However, the two effects are not separately identified in general in the standard linear-in-means model unless data on all members of an individual’s network are available. With data on a sample of individuals from a network, these effects are not identified. In this research, we leverage a very natural aspect of social settings, namely that consumers are usually part of multiple—as opposed to single—networks. We discuss the sufficient conditions for identification when the standard linear-in-means model is extended to allow for multiple sources of social influence. We also show how the additional variation generated by more than one source of social influence actually allows estimation of endogenous effects with sample data. We demonstrate the feasibility of our approach via simulation and on the National Longitudinal Study on Adolescent Health data, which has been used in a number of studies examining social influence. Our approach is, therefore, likely to be useful in typical marketing settings. This paper was accepted by Matthew Shum, marketing.
Bacterium-triggered remodeling of chromatin identifies BasR, a novel regulator of fungal natural product biosynthesis

Fungi produce numerous secondary metabolites (SMs), which possess various functions e.g. as communication signals during coexistence with other microorganisms. Many SM biosynthesis gene clusters are silent under standard laboratory conditions because their environmental or developmental triggers are unknown. Previously, we discovered that the silent orsellinic acid (ors) gene cluster in the filamentous fungus Aspergillus nidulans is activated upon interaction with the bacterium Streptomyces rapamycinicus and that this induction is dependent on the GcnE lysine-acetyltransferase catalyzing histone H3 acetylation. Here, we report a genome-wide analysis of chromatin acetylation changes during this interaction and relate these to changes in the fungal transcriptome. Our results reveal that only a functional interaction with S. rapamycinicus changes the chromatin landscape and activates amino acid cross-pathway control in the fungus. We identified the Myb-like transcription factor BasR as novel regulator required for bacteria-triggered SM production and show that its function is conserved in other Aspergillus species.
The Rufous‐thighed KiteHarpagus diodonis not an endemic breeder of the Atlantic Forest: lessons to assess Wallacean shortfalls

The migratory Rufous-thighed Kite Harpagus diodon is widely distributed in South America, and a recent spatiotemporal analysis of its distribution that was largely based on citizen science data concluded that it breeds (almost) exclusively in the Atlantic Forest, constituting a ‘hidden endemism’, and that it is a complete migrant, overwintering in the eastern Amazonian lowlands. However, that study missed key data from large areas that would have resulted in a different biogeographical pattern. Here, we reject the ‘hidden endemism’ hypothesis and show that the Rufous-thighed Kite is a more widespread breeder. We propose that to uncover Wallacean shortfalls of migratory birds correctly, (1) citizen science data must be integrated with thorough bibliographical searches and specimen examination and (2) life-cycle categories should be critically determined: failing to recognize the importance of these two key issues can undermine the ability of researchers to uncover the true extent of breeding ranges and timing of migration, resulting in erroneous ecogeographical patterns. By proposing and following a set of recommendations, and using previously unpublished and published documented records mostly from the southwestern portion of the distribution of Rufous-thighed Kite, we here show that this species breeds in the Cerrado of eastern Bolivia and is present during the austral spring and summer in the Austral Yungas but largely absent during the austral autumn and winter, mirroring the seasonality of the species in the Atlantic Forest.
Feeds and fodder dynamics in selected river basins of Bangladesh

A baseline survey was conducted with the objectives to determine seasonal availability, utilization of feeds and fodder resources and livestock production systems in different river basin areas and to identify the constraints of fodder production in selected river basins of Bangladesh. Based on cattle population, 2 upazilas from each of 10 districts were selected for household survey (HHS). A randomly selected 50 farmers from each upazila were considered for collecting information. After screening a total of 963 HHs were considered for statistical analyses. Results show that about 51%HHs were landless. Having an average population size of 3.3, about 99% HHs in the surveyed areas was keeping cattle, whereas, buffalo was not found in all regions which were found only in1.7% HHs with an average population size of 2.31 per buffalo keeper HH. Sheep was found only in about 1% HHs with an overall number of 3.22 per sheep keeper HH. About 16% HHs were keeping goats with an average size of 2.9 per sheep keeper HH. Significant differences on performance potentials were found both in native and crossbred cows among different regions. It was observed that all types of farm categories HHs reared cattle and most of them reared by tethering (around 23%) and free grazing (around 22%) management systems but semi-grazing was followed by around 14% HHs. Rest of the farmers followed different combinations of methods. Rice straw and naturally grown green grasses were the main roughages for feeding their cattle. About 95% HHs fed rice straw and about 81% HHs fed cut and carry green grass to their cattle. There were no seasonal variations on feeding rice straw but variations occurred for supplying cut and carry green grasses. Concentrates provided to animals in the surveyed areas were mainly rice polish, wheat bran, broken rice, pulse bran and mustard oil cake, among which rice polish and wheat bran were supplied by more HHs (about 93% and 75%, respectively). The variations of supplying concentrates among seasons were very negligible. Although, there were about 1.14% HHs who cultivated some fodder crops, they harvest grains for human consumption and residues for their cattle. However, high yielding varieties of fodders are very rarely cultivated by the farmers for feeding cattle in the riverside regions. The reason not to cultivate fodder and main constraint behind it was not accurately mentioned by the farmers. In the survey among different riverside regions, about48 different native green fodders were obtained in different agro-ecological zones, among which most available native green fodders were Durba, Badla, Kawn, Shama, Khesari, Gamma, Ura, Gobra, Shama and Maskalai . Most of the native grasses are grown more in summer and some others like Kawn, Khesari and Maskalai are grown in winter. Finally, it may be concluded that extensive fodder cultivation program by motivating farmers through training and demonstrating high yielding fodder crops are essential in the riverside regions for increasing productivity of livestock in the respective areas. Bang. J. Anim. Sci. 2017. 46 (3): 206-214
Two-dimensional penalized splines via Gibbs sampling to account for spatial variability in forest genetic trials with small amount of information available

Abstract Spatial environmental heterogeneity are well known characteristics of field forest genetic trials, even in small experiments (<1ha) established under seemingly uniform conditions and intensive site management. In such trials, it is commonly assumed that any simple type of experimental field design based on randomization theory, as a completely randomized design (CRD), should account for any of the minor site variability. However, most published results indicate that in these types of trials harbor a large component of the spatial variation which commonly resides in the error term. Here we applied a two-dimensional smoothed surface in an individual-tree mixed model, using tensor product of linear, quadratic and cubic B-spline bases with different and equal number of knots for rows and columns, to account for the environmental spatial variability in two relatively small (i.e., 576 m2 and 5,705 m2) forest genetic trials, with large multiple-tree contiguous plot configurations. In general, models accounting for site variability with a two-dimensional surface displayed a lower value of the deviance information criterion than the classical RCD. Linear B-spline bases may yield a reasonable description of the environmental variability, when a relatively small amount of information available. The mixed models fitting a smoothed surface resulted in a reduction in the posterior means of the error variance (σ2e), an increase in the posterior means of the additive genetic variance (σ2a) and heritability (h2HT), and an increase of 16.05% and 46.03% (for parents) or 11.86% and 44.68% (for offspring) in the accuracy of breeding values, respectively in the two experiments.
Insecticide Seed Treatments as Safeners to Drift Rates of Herbicides in Soybean and Grain Sorghum

Abstract Previous research has shown that some insecticide seed treatments provide safening effects in rice following exposure to low rates of the herbicides glyphosate and imazethapyr. However, no research has been conducted to determine whether a similar effect may be seen in soybean or grain sorghum, two important rotational crops across the Midsouth. To evaluate the potential safening effects of insecticide seed treatments in these two crops, field trials were conducted in Marianna, AR, in 2015 and 2016, and near Colt, AR, in 2016. In soybean, glyphosate, glufosinate, 2,4-D, dicamba, halosulfuron, mesotrione, tembotrione, and propanil were applied at low rates to simulate drift events, in combination with the insecticide seed treatments thiamethoxam and clothianidin at labeled rates. In grain sorghum, glyphosate, imazethapyr, and quizalofop were applied at low rates in combination with the insecticide seed treatments thiamethoxam, clothianidin, and imidacloprid at labeled rates. Injury reduction was seen at 1 site-year for glyphosate, glufosinate, 2,4-D, dicamba, mesotrione, and tembotrione, and at 2 of 3 site-years for halosulfuron. At 1 site-year, the safening in halosulfuron resulted in increases in both crop height and yield. In grain sorghum, reducing injury via seed treatments was generally more successful. All three herbicides applied in sorghum displayed instances of injury reduction when seed treatments were used at 1 or more site-years, including reducing injury upward of 40% in the case of quizalofop + clothianidin at Marianna in 2016. For 2 site-years, injury reduction through the use of insecticides resulted in increases in crop height and grain yield in grain sorghum compared with no insecticide use. Although the degree of safening seen varied depending on site-year in both crops, growers who use insecticide seed treatments on an annual basis may expect to see a safening effect from drift events of most herbicides evaluated in both soybean and grain sorghum. Nomenclature: 2,4-D; clothianidin; dicamba; glyphosate; glufosinate; halosulfuron; imazethapyr; imidacloprid; mesotrione; propanil; quizalofop; tembotrione; thiamethoxam; rice, Oryza sativa L. ; soybean, Glycine max (L.) Merr; grain sorghum, Sorghum bicolor (L.) Moench
Oak Kernels—Volatile Constituents and Coffee-Like Beverages

Modern consumers are much aware of potential health benefits of food and food ingredients. The food industry has been constrained to develop new products with improved sensory, nutritive and functional characteristics. In this work a potential use of English (Quercus robur) and Turkish oak (Quercus cerris) kernels as functional food components was estimated. Volatiles from native and roasted kernels were isolated using continuous hydro distillation with CH2Cl2 and analyzed with GC/MS. Coffee-like beverages were prepared from roasted kernels of both species and a sensory assessment was conducted. In the native samples the main compounds were beta-eudesmol and palmitic acid (39.9 and 24.9%, respectively) in Q. robur, and palmitic acid (53.8%) in Q. cerris. In the roasted samples the main compounds were furans: furfural (51.7 and 60.6%) and 5-methyl-furfural (8.6 and 9.4%, respectively). Coffee-like beverages from roasted oak samples were evaluated for sensory properties gaining high scores for appearance, with satisfying taste and fullness. The presented results, along with previous findings on substantial antioxidant and antiradical activities of English and Turkish Oak kernels, draw attention to these easy available, cheap, but neglected native raw materials as valuable functional food components. Further investigations on this matter are warranted.
Effect of organic seed pelleting on seedling quality, gas exchange, growth, yield and resultant seed quality parameters of black gram

Seed pelleting with leaf powders of two botanicals viz., pungam (Pongamia glabra) and prosopis (Prosopis juliflora) was done to study the effect of botanical seed pelleting on seedling quality, gas exchange, growth, yield and resultant seed quality parameters of black gram in the laboratory and field. From the results, it was found that, seeds pelleted with pungam leaf powder @ 150 g kg-1 recorded higher germination percentage (93.00), root length (18.35 cm), shoot length (19.34 cm), dry matter production (0.48 mg seedling-10) and vigour index (3505.10). The yield parameters such as pod length, number of pods plant-1, pod yield plant-1, number of seeds pod-1 and 100 seed weight were also found higher in pungam leaf powder pelleting treatment @ 150 g kg-1. The control recorded the least values in all these growth and yield parameters of black gram.