Miracle-dz/UniFAR-FTUs huggingface dataset:
Cinnamon oil downregulates virulence genes of poultry respiratory bacterial agents and revealed significant bacterial inhibition: An in vitro perspective

Background and Aim: Respiratory bacterial agents represent one of the most harmful factors that ordinarily threaten the poultry industry and usually lead to great economic losses. Meanwhile, there is a global demand to avoid the highly emerging antibiotic resistance and antibiotic residues in edible meat. Whereas, the use of alternatives became of great priority, especially for those substances extracted from natural plant origin. The study aimed to evaluate the antibacterial effect of cinnamon oil as a herbal extract on different respiratory bacterial agents. Materials and Methods: One hundred and fifty biological samples were collected through targeted surveillance for respiratory diseased poultry farms representing three governorates, from which bacterial isolation and identification, DNA sequencing of representative strains were performed. Furtherly, phenotypic and genotypic evaluation of the antibacterial effect of cinnamon oil was performed by minimum inhibitory concentration, agar disk diffusion, and virulence genes expression real-time polymerase chain reaction. Results: Cinnamon oil gave rise to acceptable degrees of virulence genes downregulation of 0.15, 0.19, 0.37, 0.41, 0.77, and 0.85 for Staphylococcus aureus sed gene, Escherichia coli stx1 gene, Avibacterium paragallinarum HPG-2 gene, Pasteurella multocida ptfA gene, Mycoplasma gallisepticum Mgc2 gene, and Ornithobacterium rhinotracheale adk gene, respectively. Phenotypically, using agar disk diffusion assay and broth microdilution susceptibility, cinnamon oil showed also tolerable results as it stopped the growth of S. aureus, E. coli, P. multocida, and A. paragallinarum with varying zones of inhibition. Conclusion: The encountered results declared the successful in vitro effect of cinnamon oil that recommends its application for living birds for future use as a safe antibacterial in the poultry industry.
THE GENETICS OF MORPHOLOGICAL EVOLUTION IN SILKWORMS (BOMBYCIDAE: BOMBYX)

16 Introduction 17 Materials and Methods 20 Results 26 Discussion 38 References 43 Supporting Information 52 Chapter Two: Non-competitive Allele Specific Expression (ncASE) method for reducing mapping bias Abstract 74 Introduction 75 Materials and Methods 78 Results and Discussion 82 References 89 Supporting Information 94
Differential complex formation via paralogs in the human Sin3 protein interaction network

Despite the continued analysis of HDAC inhibitor efficacy in clinical trials, the heterogeneous nature of the protein complexes they target limits our understanding of the beneficial and off-target effects associated with their application. Among the many HDAC protein complexes found within the cell, Sin3 complexes are conserved from yeast to humans and likely play important roles as regulators of transcriptional activity. The functional attributes of these protein complexes remain poorly characterized in humans. Contributing to the poor definition of Sin3 complex attributes in higher eukaryotes is the presence of two Sin3 scaffolding proteins, SIN3A and SIN3B. Here we show that paralog switching influences the interaction networks of the Sin3 complexes. While SIN3A and SIN3B do have unique interaction network components, we find that SIN3A and SIN3B interact with a common set of proteins. Additionally, our results suggest that SIN3A and SIN3B may possess the capacity to form hetero-oligomeric complexes. While one principal form of SIN3B exists in humans, the analysis of rare SIN3B proteoforms provides insight into the domain organization of SIN3B. Together, these findings shed light on the shared and divergent properties of human Sin3 proteins and highlight the heterogeneous nature of the complexes they organize.
Predictive whisker kinematics reveal context-dependent sensorimotor strategies

Animals actively move their sensory organs in order to acquire sensory information. Some rodents, such as mice and rats, employ cyclic scanning motions of their facial whiskers to explore their proximal surrounding, a behavior known as whisking. Here we investigated the contingency of whisking kinematics on the animal’s behavioral context that arises from both internal processes (attention and expectations) and external constraints (available sensory and motor degrees of freedom). We recorded rat whisking at high temporal resolution in two experimental contexts - freely moving or head-fixed – and two spatial sensory configurations – a single row or three caudal whiskers on each side of the snout. We found that rapid sensorimotor twitches, called pumps, occurring during free-air whisking carry information about the rat’s upcoming exploratory direction, as demonstrated by the ability of these pumps to predict consequent head and body locomotion. Specifically, pump behavior during both voluntary motionlessness and imposed head-fixation exposed a backward redistribution of sensorimotor exploratory resources. Further, head-fixed rats employed a wide range of whisking profiles to compensate for the loss of head- and body-motor degrees of freedom. Finally, changing the number of intact vibrissae available to a rat resulted in an alteration of whisking strategy consistent with the rat actively reallocating its remaining resources. In sum, this work shows that rats adapt their active exploratory behavior in a “homeostatic” attempt to preserve sensorimotor coverage under changing environmental conditions and changing sensory capacities, including those imposed by various laboratory conditions.
Fitness decline in hatchery-enhanced salmon populations is manifested by global warming

Despite historical maximum hatchery releases and biomass of chum salmon in the North Pacific, chum salmon returning to Japan, where the world largest chum salmon hatchery programme runs, have declined substantially for two decades. However, the causal mechanisms are unknown. We analysed catch/release data of chum salmon and SST in Japanese coastal waters, and synthesized LDH (lactate dehydrogenase) and PEPB (tripeptide aminopeptidase) gene frequencies of 21,911 adult chum salmon collected from 166 rivers and areas in the North Pacific Rim. We also evaluated athletic performance of Japanese chum salmon in comparison with foreign salmon populations on social network videos. We found significant negative correlation between the average SST for spring and summer and total catch of Japanese chum salmon (r=-0.77), and 59% of the variation in the decreasing catch was explained by the increasing SST. Frequencies of the thermal adaptation genes LDH-A1 and LDH-B2 were altered disregarding with directions of natural selection which eventually lead hatchery fish to adapt to colder environments, while those of the digestive gene PEPB-1 were positively correlated with latitude. Because LDH-A and LDH-B are found in skeletal and cardiac muscles, this change may have lowered the survival rates particularly for juveniles and growth of Japanese chum salmon. We argue that the long-term hatchery releases have reduced the athletic ability of hatchery fish, resulting in a continuous decline in fitness of whole populations. A genetic mechanism of fitness decline in hatchery-enhanced salmon populations is first manifested by global warming at the southern margin of the species.
In Vitro Phytochemistry and Antiplasmodial Activity of Leaf Extract and Fractions of Nauclea diderrichii

The current investigation deals with phytochemical screening and in vitro antiplasmodial activity of crude ethanol leaf extract and three fractions of crude ethanol leaf-extract of Nauclea diderrichii. Phytochemical test to screen bioactive compounds was carried out via standard protocols which uncovered the presence of alkaloids, saponins, steroids, phenols, tannins, flavonoids, glycosides and carbohydrates, extraction was done using absolute ethanol to afford the crude extract (Nd-ET) while maceration was done using solvents of different polarity gradient (petroleum ether, chloroform and ethyl acetate) to afford the remaining fractions (Nd-F1, Nd-F2 and Nd-F3). The antiplasmodial activity of the crude-extract and those of crude-extract-fractions against plasmodium falciparum unveil promising percentage elimination at all concentrations, with ethanol crude extract (Nd-ET) and ethyl acetate fraction (Nd-F3) having the highest, with 75.50% and 72.65% at 625µg/ml, and 87.83% and 86.33% at 5000µg/ml, respectively. These results clearly indicated that the active compounds present in the crude leaf extract/fractions of Nauclea diderrichii are highly potent eliminators of plasmodium falciparum and validate their popular usage in folk medicine in Gusau Local Government, Zamfara State, Nigeria, for the treatment of malaria.
The Effect of Mackerel Meat on the Number of Purkinje Cell in the Cerebellum of Congenital Hypothyroid Rat (Rattus norvegicus)

Early detection through screening of congenital hypothyroid is not a regular program of the government. so that cases of congenital hypothyroid can not be managed appropriately. Therefore, it needs to be done the research . about the benefits of the granting of a bloated fish containing omega3 on congenital hypothyroid as a food supplement to stimulate nerve growth especially brain development. The sample of this research is the droppings of a white rat (Rattus norvegicus). The 30 rats are divided into 6 groups consisting of 5 rats. Four groups was induced with hypothyroid on the day 5 of gestation until nenonatus of the day 15, . and two other groups . stayed normally.Thyroxine and mackerel meat were given on the 21st day after the birth until the 8th week. Histology and preparations werw made of cells Purkinje after being observed in the cerebellum. The number of Purkinje cells was analized with One-way Anova continued with multiple comparison test. The result is that the number of Purkinje cells in the normal group, normal + mackerel, hypothyroid, hypothyroid + mackerel, hypothyroid treatment with thyroxine, and thyroxine treatment with hypothyroid + mackerel are as follows: 60±12, 71±16, 40±6, 64±7, 70±5, and 65±20. The average number of Purkinje cells in the group that got mackerel significantly (p<0,05) increases compared to hypothyroid. The conclusion is that the supplementation of mackerel fish increases the number of Purkinje cells in the cerebellum of the rat with congenital hypothyroid.
Mixed Responses to Woody Encroachment in Icelandic Herbaceous Plant Morphology and Phenology

Climate change and afforestation efforts are promoting tree growth into traditionally treeless locations in Iceland. This study examined this woody encroachment’s effect on the phenology and morophology of eight plants (Agrostis aequivalvis, Equisetum pratense, Equisetum arvense, Alchemilla alpina, Ranunculus acris, Lupinus nootkatensis, Anthriscus sylvestris, and Taraxacum sp.) in Kjarnaskógur forest, Akureyri, Iceland. An initial transplantation experiment testing trees’ effect on A. aequivalvis, E. pratense, R. acris, and A. sylvestris failed due to plant death. A subsequent observational study examined trees’ effect on E. pratense, A. alpina, R. acris, L. nootkatensis, A. sylvestris, and Taraxacum by observing morphological characteristics (leaf size, plant height, leaf number) in individuals (between 56 and 200 per species) within and outside of wooded environments. Some species grew larger leaves and experienced growth delays in a wooded environment, suggesting adaptation to competition. Other species grew smaller leaves in a wooded environment, suggesting outcompetition by trees. This suggests that the expansion of trees in Iceland will create morphological and phenological changes in herbaceous plants, possibly having ramifications throughout Icelandic ecosystems.
Molecular Characterization of Soybean Genotypes in Response to Charcoal Rot Disease by using SSR Markers

Charcoal rot disease caused by Macrophomina phaseolina is one of the most damaging diseases of soybean resulting to 70% losses and till date no immune genotype is known for the same.Charcoal rot (CR) disease caused by Macrophomina phaseolina is responsible for signiﬁcant yield losses in soybean production. The present study helped to evaluate soybean genotypes for identifying promising genotypes which proved to be resistant to charcoal rot. The present study was carried out at Department of Agricultural Botany, Dr. Deshmukh Krishi Vidyapeeth, Akola during the year 2018-19 to evaluate various genotypes of soybean for charcoal rot resistance. Among the methods available for controlling this disease, breeding for resistance is the most promising. Molecular characterization of these genotypes was done by using RGA markers. Molecular profiles revealed remarkable polymorphism and observations showed that in total 38 amplicons were tested with an average of 5.42 alleles per locus. Out of the total screened alleles 13 were monomorphic alleles with an average of 1.85 and 25 were polymorphic alleles with an average of 3.57. Results showed an average of 65.03 polymorphism percent. The PIC (Polymorphic information content) value ranged from 0.43 to 0.83 with an average value of 0.62, these studies will help in mapping studies and breeding program for development of charcoal rot resistance in soybean genotypes which will be of utmost importance.
TEMPORAL AND SPATIAL CHARACTERISTICS OF EXTREME TEMPERATURE IN THE MIDDLE REACH OF THE YELLOW RIVER, CHINA

the middle reach of Yellow River is a production area for main grain crops in China and is also an emerging industrial cluster. this study adopts meteorological data from 1951 to 2014 provided by 73 national ordinary stations in the study area, combines Kendall-tau non-parametric test method, Sen’s slope estimation method and Savitzky-Golay smoothing filtering method based on sub-regions divided by fuzzy clustering method and analyzes the variation trend of extreme temperature indexes. The results show that: (1) in the middle reach of Yellow River, the variation trend of extreme temperature events is basically similar, but the intensity is different, and the spatial distribution is inconsistent. (2) On time scale, an upward trend has been found in extreme temperature events in the past 60 years. (3) On spatial scale, the change rate of multiple indexes in the arid sub-region is greater than that of those in the humid sub-region; the proportion of meteorological stations with significant index changes in the arid region is higher than that in the humid sub-region. Some indexes have different trends in small areas, which may be caused by local microclimates in urban heat islands and hilly areas, but further analysis and verification is also required.
Estimating IUCN Red List population reduction: JARA—A decision‐support tool applied to pelagic sharks

The International Union for Conservation of Nature's (IUCN) Red List is the global standard for quantifying extinction risk but assessing population reduction (criterion A) of wide‐ranging, long‐lived marine taxa remains difficult and controversial. We show how Bayesian state–space models (BSSM), coupled with expert knowledge at IUCN Red List workshops, can combine regional abundance data into indices of global population change. To illustrate our approach, we provide examples of the process to assess four circumglobal sharks with differing temporal and spatial data‐deficiency: Blue Shark (Prionace glauca), Shortfin Mako (Isurus oxyrinchus), Dusky Shark (Carcharhinus obscurus), and Great Hammerhead (Sphyrna mokarran). For each species, the BSSM provided global population change estimates over three generation lengths bounded by uncertainty levels in intuitive outputs, enabling informed decisions on the status of each species. Integrating similar analyses into future workshops would help conservation practitioners ensure robust, consistent, and transparent Red List assessments for other long‐lived, wide‐ranging species.
A relative density measure for mixed-species stands: tree-area ratios are more accurate than stocking charts

elative density is an index of crowding for forest stands. It is expressed as the ratio of absolute density (number of trees or basal area per acre) to the density of a stand the same size and species composition at maximum density (for example, an undisturbed stand). The ratio is useful for prescribing silvicultural treatments in many forest types where absolute densities vary because of species composition, average stand size, and stand structure.
Phytoremediation of some heavy metals using Prosopis juli flora and Conocarpus lancifolius– Soil analysis

Environmental pollution is causing damage to the flora and fauna, resulting in a number of negative impacts on the environment. The present study aims towards evaluation of soil heavy metals (chromium, lead, and nickel) from different locations of Jeddah using leaves of two plant species. Two naturally grown plant species, Prosopis juli flora and Conocarpus lancifolius were collected from four different sites. The soil samples were collected near the factories, main roads, and branch roads in Jeddah. The soil samples were dried and sieved through a 2mm plastic sieve to remove large gravel-sized materials. Soil texture, pH, and EC evaluation were conducted. The amount of Cr, Pb, and Ni was determined using Atomic Absorption Spectrophotometer Model Inductivity coupled plasma emission spectrometer ICP (PARKIN ELEMER). SPSS, ANOVA, and Post-Hoc Test were used to analyze the data. The results showed that the amount of heavy metal in the soil of Prosopis juli flora were between 0.74-54. 0μg/g D.wt. for Cr, 0.31-4.64 μg/g D.wt. for Pb and 1.22-24.5 μg/g D.wt. for Ni. The range of Cr, Pb and Ni in the leaves were between 0.04-13.3. 0μg/g D.wt. for Cr, 0.06-20.0 μg/g D.wt. for Pb and 0.16-9. 0μg/g D.wt. for Ni. For the soil of Prosopis juli flora, the EC ranged between 0.27- 1.05 mS/cm; whereas, pH ranged from 7.29-7.55 and 78.5-96.5% for sand, 1.0-16.5% for silt, and 1.0-6.0 for clay. There was a significant correlation between the soil textures, clay, and silt at selected sites. Phytoremediation is an effective strategy to overcome the effects of heavy metals including Cr, Pb, and Ni that are being absorbed in plants.
Human–elephant interactions in areas surrounding the Rungwa, Kizigo, and Muhesi Game Reserves, central Tanzania

Abstract This study assesses the patterns of crop damage by elephants Loxodonta africana in areas adjacent to the Rungwa, Kizigo and Muhesi Game Reserves in Tanzania. We used a questionnaire survey to collect data from a total of 210 household heads from seven villages, with 30 household heads in each village, during June–August 2015. Proximity was a significant factor influencing losses, with crop farms within < 1 km from the reserves having higher losses, followed by those 1–5 km and > 5 km distant. Most households (81.0%) < 1 km from a reserve reported crop damage whereas those within 1–5 km (65.9%) and > 5 km (20.0%) reported less damage. Most of the losses (79.8%) occurred in the first half of the year (the wet season). Immigrants reported higher average losses to crops than Indigenous respondents. Noise making, flashlights, setting fire around fields and disturbance by shooting were the methods used to deter elephants from entering crop fields. We recommend that communities around these game reserves avoid areas that are < 1 km from the reserve boundary, plant crops such as chilli, use honeybee Apis mellifera fences to deter elephants from their crops, and receive education on available mitigation methods, to help minimize crop losses to elephants.
CRISPR screening of porcine sgRNA library identified host factors essential for Japanese encephalitis virus replication

Japanese encephalitis virus (JEV) is a mosquito-borne zoonotic flavivirus that causes encephalitis and reproductive disorders in mammalian species. However, key host genes involved in the JEV life cycle and cell death are poorly understood. Here, we designed 85,674 single guide RNAs (sgRNAs) targeting 17,743 protein-coding genes, 11,053 long ncRNAs (lncRNAs), and 551 microRNAs (miRNAs) in the porcine genome, and subsequently developed a porcine sgRNA library and genome-scale CRISPR/Cas9 knockout (PigGeCKO) system. These sgRNAs were delivered into porcine kidney-15 (PK-15) cells that constitutively express Cas9, positive selection screening of the resulting PigGeCKO cell collection for resistance to JEV-induced cell death led to the identification of several previously unreported genes required for JEV infection. We conducted follow-up studies to verify the dependency of JEV on these genes, and identified functional contributions for six of the many candidate JEV-related host genes, including an endoplasmic reticulum membrane protein complex subunit 3 (EMC3) and calreticulin (CALR). Additionally, we identified that four genes associated with heparan sulfate proteoglycans (HSPGs) metabolism, specifically those responsible for HSPG sulfurylation, facilitated JEV entry into PK-15 cells. Thus, beyond our development of the largest CRISPR-based functional genomic screening platform for pig research to date, this work deepens our basic understanding of flavivirus infection and identifies multiple potentially vulnerable targets for the development of medical and breeding technologies to prevent and treat diseases caused by Japanese encephalitis virus.
The Role of Soil pH in Plant Nutrition and Soil Remediation

In the natural environment, soil pH has an enormous influence on soil biogeochemical processes. Soil pH is, therefore, described as the “master soil variable” that influences myriads of soil biological, chemical, and physical properties and processes that affect plant growth and biomass yield. This paper discusses how soil pH affects processes that are interlinked with the biological, geological, and chemical aspects of the soil environment as well as how these processes, through anthropogenic interventions, induce changes in soil pH. Unlike traditional discussions on the various causes of soil pH, particularly soil acidification, this paper focuses on relationships and effects as far as soil biogeochemistry is concerned. Firstly, the effects of soil pH on substance availability, mobility, and soil biological processes are discussed followed by the biogenic regulation of soil pH. It is concluded that soil pH can broadly be applied in two broad areas, i.e., nutrient cycling and plant nutrition and soil remediation (bioremediation and physicochemical remediation).