Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessing the performance of hybrids developed using iso-cytoplasmic restorers and identification of promising combiners in rice

Iso-cytoplasmic restorers (ICRs) are valuable source of fertility restoration for three linerice hybrids derived from wild- abortive cytosterile (WA-CMS) lines. They carry a full complement of fertility restorer (Rf) genes and sterile cytoplasm. We have test-crossed a set of 25 ICRs with four WA-CMS lines namely, IR 79156A, IR 58025A, Pusa 6A and RTN 12A following a line x tester mating design. Significant estimates of general and specific combining ability for agro-morphological traits revealed the involvement of both additive and non-additive gene effects. The combining ability estimates implied that some of the restorers were good general combiners for traits such as plant height, number of tillers per plant, panicle length,spikelet fertility, grain weight and yield per plant. Four promising ICRs namely, PRR317, PRR354, PRR381 and PRR390 with high general combining ability for yield across different environments were identified based on theirhybrid performance. Additionally, location-specific ICRs, namely PRR300 and PRR396 for timely sown conditions of New Delhi, PRR348 for Pusa and Karnal, and Pusa 307 for Karnal and late sown conditions of New Delhi environments were identified. The restorer turnover in the current study demonstrates ICRs as potential source for restorer development and can lead to the development of heterotic hybrids.
Improving Potato Vine Utilization by Sheep Using Biological Treatment

Twelve mature rams with an average body weight of 65.5±2.8kg were used at Regional Center for Food and Feed Station in four metabolism trials to study the effect of feeding a clover hay or potato vine hay or potato vine silage on nutritive values, rumen parameters, blood picture and economic efficiency. Determination of silage quality and anti - nutritional factors were also studied. Sheep were randomly distributed into 4 equalgroups and housed un seprated cages. The experimental diets were given according to NRC (1990). The feeding was 50% concentrate feed mixture (CFM) and 50% of one the three tested ingredients, clover hay , potato vine hay and potato vine silages. Clover hay was fed in the control group, while the other three tested rations included potato hay or potato vine silage. The results showed that: Solanine values of potato vines hay (PVH) , potato vines silage (PVS) and urea treated potato vines silage (UPVS) were 20.15,8.30 and 7.81 mg / 100g DM ,D respectively. The ensiling process sharply decreased solanine content. The two silages were of excellent quality, and had a normal pH 3.95-4.10 with tendency of superiority of ureated one. The overall means of TVFA's ranged between 7.75-8.15ml eq/100ml R. L. , being the higher was recorded for the unureated silage. Potato vines silage (PVS) recorded the least concentration of NH3 –N(1.72%). The digestibility of OM, NFE and CP of PVH was lower than that of UPVS group, while the highest significant (p<0.05) values of TDN (64%), CP(10.70%) and DE(2.98M cal/kg) were recorded with rations containing potato vine silages (PVS and UPVS) in comparison with feeding on clover hay. Also, rams given rations containing silages retained more nitrogen than other groups. Results explained that blood parameters for the group fed PVH were significantly (P<0.05) lower (RBC, total protein, albumin, globulin and cholesterol). However, hematocrit, AST, ALT, urea, creatinine and bilirubin values of PVH group were significantly (P<0.05) higher compared to PVS, UPVS and control groups. In conclusion, potato vine unureated silage could be used safely, successfully and economically as a good unconventional feed stuffs to raplace clover hay for ruminants, thus minimizing environmental pollution.
Polycomb Repressive Complex 2 antagonizes linker DNA methylation and chromatin compaction in Arabidopsis thaliana

In plants and mammals, DNA methylation is a hallmark of transposable element (TE) sequences that contributes to their epigenetic silencing. In contrast, histone H3 lysine 27 trimethylation (H3K27me3), which is deposited by the Polycomb Repressive Complex 2 (PRC2), is a hallmark of repressed genes. Nevertheless, there is a growing body of evidence for a functional interplay between these pathways. In particular, many TE sequences acquire H3K27me3 when they lose DNA methylation and it has been proposed that PRC2 can serve as a back-up silencing system for hypomethylated TEs. Here, we show in the flowering plant Arabidopsis thaliana that hundreds of TEs gain H3K27m3 in the mutant ddm1, which is defective in the maintenance of DNA methylation specifically over TE and other repeat sequences. Moreover, this gain depends solely on CURLY LEAF (CLF), which is one of two otherwise partially redundant H3K27 methyltransferases active in vegetative tissues. Finally, our results challenge the notion that PRC2 can be a compensatory silencing system for hypomethylated TEs, as the complete loss of H3K27me3 in ddm1 clf double mutant plants was not associated with further reactivation of TE expression nor with a burst of transposition. Instead, ddm1 clf plants exhibited a partial suppression of ddm1 molecular phenotypes with with TE silencing, chromatin recompaction and hypermethylation of linker DNA compared to ddm1. Thus, we have uncovered a novel role for PcG in antagonizing both chromatin compaction and linker DNA methylation at pericentromeric TEs, which could be particularly important during the reproductive stage, when TE become hypomethylated in the pollen and the endosperm.
Ultrasonographic, Morphometric and Histological Study of Testicular Parameters in Egyptian Water Buffalo Bulls (Bubalus Bubalis)

This study was carried out to identify testicular biometric data of native Egyptian buffalo-bulls through the determination of testicular parameters by using ultrasound examination of the testis and scrotum and determination of scrotal circumference of the life animal and morphometric data of the testis after slaughter of the bulls and their correlations with body weight at the different ages that will provide data base for the reproductive anatomy of the local Egyptian buffalo bull. The animals were divided into three groups (G1, G2 and G3) according to the age and the weight of the animals. All animals were examined with ultrasonography to determine the different parameters of the testis, epididymis and pampiniform plexus. After slaughter of the animals, the left and right testes were taken for morphometric and histological analysis. The results revealed significant (p˂0.05) variations between body weight and testicular parameters that included (Testicular Weight, Testicular Width, Testicular Circumference, Testicular Thickness and Testicular Length) as there was an increase in all parameters with the advancement in age and body weight. Histological analysis of G1 declared that only sertoli cells rested on basal lamina of seminiferous tubules and Gonocyt cells are predominant but there was no spermatogenic cells, no spermatocyte and no spermatid in the lumen of seminiferous tubules. In G2 group, there was replacement of Gonocyt cells with differentiated spermatogenic cell and spermatocyte in the lumen of seminiferous tubule but there was no spermatid. In G3 group, there were different stages of developmental spermatogenic cell clusters within the epithelium of seminiferous tubules (sertoli cells spermatogenia cells, different cells type of spermatocyte, and round spermatid as well as several threads like sperms were in the lumen of seminiferous tubules) that indicate the early maturity of Egyptian buffalo bull noticed at this age Statistical analysis revealed significant (p <0.05) changes in the testicular parameters with the advancement in the age and weight of the animals concluding that ultrasonographic imaging of the testis and epididymis of buffalo-bulls was given appreciable benefits in studying the developmental changes of the testes and epididymis of buffalo-bulls, so that ultrasound examination of testicular parameters is a good tool for prediction of the future fertility of buffalo-bulls.
Insect diversity and population dynamics of natural enemies under sorghum–legume intercrops

The effect of intercropping sorghum with legumes on insect diversity and population dynamics of natural enemies was evaluated in the 2015/2016 cropping season at Botswana University of Agriculture and Natural Resources in Sebele, Gaborone. Sorghum monocrop, Sorghum bicolar (L) Moench, was intercropped with four commonly grown legumes, namely cowpea, Vigna unguiculata (L) Walp. ; groundnut, Arachis hypogea L. ; Bambara groundnut, Vigna subterranean (L.) Verdc; and chickpea, Cicer arietinum L. The study showed that intercropping significantly increased insect abundance, from 176.50 individuals on the monocrop to 438 individuals when sorghum was intercropped with cowpea being the highest among the intercrops. Similarly, species diversity significantly increased from 0.24 on monocrop to 0.54 when sorghum was intercropped with cowpea. There were more herbivores than predators, and the predominant insect herbivore found infesting sorghum was Melanaphis sacchari (Zehntner) (n = 2495), followed by Chilo partellus (Swinhoe) (n = 650). There was a significant difference in the level of parasitism between monocrop and intercrop systems. There were significantly more stemborer parasitoids found in the intercrops, ranging from 1 to 5%, compared to sorghum monocrop where no parasitism was observed. Predatory coccinellid density was not significantly influenced by intercropping but was by time of sampling. The results add to the body of knowledge indicating that intercropping significantly increases insect diversity and reduces the pressure of herbivores on crops in agroecosystems. Intercropping sorghum with legumes increased the number of biological control agents and reduced herbivore populations, and therefore can be recommended as a component of integrated pest management.
THE PHENOTYPIC PERFORMANCE OF KAMBRO CROSSBREEDS OF FEMALE BROILER COBB 500 AND MALE PELUNG BLIRIK HITAM

This research was conducted to measure the phenotypic performance of Kambro crossbreeds of Pelung Blirik Hitam and Broiler Cobb 500. Based on Body Weight (BT) measurement, Kambro population (n = 17) has an average BT of 1,244.14 ± 453.82 grams significant (p <0.01) to F1 Pelung (n = 7) with an average BT of 602.88 ± 79.93 grams in 8 weeks period with ad libitum diet of standard feed. Phenotypic performance of Kambro significant to F1 Pelung based on the measurement of linear bodyweight parameter, vitality parameter, PPa-PBe parameter and phenotype parameter. Kambro has the phenotype combination of parental generation based on phenotype parameter. PPa parameter was suitable BT estimation model based on non-linear quadratic regression (r = 0.956) with formula 1.84E3 ±3.54E2*x+31.73*x2. Difference between chicken group (p<0.014) was significant to BT and interaction between group and linear bodyweight parameter was not significant based on Analysis of Covariance. The mortality rate of Kambro was lower than F1 Pelung with the absent of vaccination in semi-intensive rearing system. As the size of hybrids population was limited, research findings must be validated with larger population size of hybrids.
RNA-Seq analysis reveals pluripotency-associated genes and their interaction networks in human embryonic stem cells

Insight into the key genes of pluripotency in human and their interrelationships is necessary for understanding the underlying mechanism of pluripotency and hence their successful application in regenerative medicine. The recent advances in transcriptomics technologies have created new opportunities to decipher the genes involved in pluripotency, genetic network that governs the unique properties of embryonic stem cells and lineage differentiation mechanisms in a deeper scale. There are a large number of experimental studies on human embryonic stem cells (hESCs) being routinely conducted for unfolding the underlying biology of embryogenesis and their clinical prospects. However, the outcome of these studies often lacks consensus due to differences in samples, experimental techniques and/or analysis protocols. A universal stemness gene list is still lacking. In this quest, we compared transcriptomic profiles of pluripotent and non-pluripotent samples from diverse cell lines/types generated through RNA-sequencing (RNA-seq). We used a uniform pipeline for the analysis of raw RNA-seq data in order to reduce the amount of variation. Our analysis revealed a consensus set of 498 pluripotency-associated genes and 432 genes as potential pluripotent cell differentiation markers. Furthermore, we predicted 32 genes as “pluripotency critical genes”. Reconstruction and analysis of co-expression networks further highlighted the importance of these genes. Gene ontology (GO) and pathway enrichment analysis, StemChecker and literature survey confirmed the involvement of the genes in the induction and maintenance of pluripotency, though more experimental studies are required for understanding their molecular mechanisms in human.
The changes in growth performance and lipid metabolism of pigs with yellow fat induced by high dietary fish oil

Abstract: The aim of this study was to investigate the alteration in growth performance and lipid metabolism during the development of yellow fat in pigs. A total of 30 pigs (9.23 ± 0.21 kg) were assigned to three treatments: (1) low fish oil (LFO), basal diet + 2% fresh fish oil; (2) high fish oil (HFO), basal diet + 8% fresh fish oil; and (3) oxidized fish oil (OFO), basal diet + 8% OFO (peroxide value = 250 meqO2 kg-1). Pigs fed HFO and OFO diets showed yellow staining of fat and decreased growth performance, including average daily gain, average daily feed intake, and final body weight (P < 0.01). The oxidized lipid markers malondialdehyde, yellowness b* of backfat, perirenal fat, and abdominal fat were markedly increased in the pigs fed with HFO and OFO (P < 0.05). Furthermore, following HFO feeding, pigs showed significant decreases in n-6 polyunsaturated fatty acid, n-6/n-3 polyunsaturated fatty acid ratio and mRNA expression levels of CCAAT-/enhancer-binding protein alpha, fatty acid synthase, lipoprotein lipase, and hormone-sensitive lipase in backfat (P < 0.01). Overall, pigs with yellow-fat trait showed decreased growth performance and altered lipid metabolism by the high fish oil feeding.
Diffusely Adherent E. coli Burden in Low Socio-Economic Pediatric Population

Article type: Research Article Background: DAEC seems to be a neglected pathogen among diarrheagenic E. coli since its association with pediatric diarrhea is rarely reported. But, the emergence and spread of MDR diarrhea causing bacterial pathogens have become a global burden. This study investigated the prevalence of MDR DAEC among the Mizo pediatric diarrheal patients aged less than 5 years. Methods: A total of 334 E. coli isolates isolated from the fecal samples were subjected to multiplex PCR assays to categorize the pathotypes of diarrheagenic E. coli and subjected to antimicrobial sensitivity assay, phenotypic and genotypic ESBL assays (blaCTX-M-9, blaCTX-M-15, blaOXA and CMY-2). Results: Of 334 E. coli isolates, only 0.9% of the isolates were detected as DAEC, when compared with 0.9% and 1.2% of the isolates categorized as ETEC and EAEC from diarrheic samples and 0.6% of the EAEC also detected from the non-diarrheic samples. Among the isolates, 25%, 50% and 8.3% of the isolates were carrying the blaCTX-M-9, blaCTX-M-15 and CMY-2 respectively and 8.3% isolates from non-diarrheic samples also carried CMY-2. Conclusion: Though a low frequency of DAEC was observed in comparison to other pathotypes of DEC, majority of them being resistant to commonly used antibiotics and having a high MDR rate, which is a matter of concern to the public health. This pathotype could possibly a natural source for MDR spread among the other diarrheal pathogens of pediatric population. Article history: Received: 08 Jun 2019 Revised: 14 Jul 2019 Accepted: 19 Aug 2019 Published: 20 Sep 2019
Line×tester analysis in lilium×formolongi: identification of superior parents for growth and flowering traits

An experiment was carried out using eight double cross F1s (DCF1s) as lines and two testers to obtain sixteen Line ×Tester hybrids for the evaluation of major growth and flowering traits thereby to understand the breeding potentiality of the parental lines. The performance of growth and flowering traits of all twenty-six genotypes were evaluated in a randomized complete block design (RCBD) with three replications. The analysis of variance (ANOVA) showed all the genotypes were significantly different for all agro-morphological traits under study. The estimated general combining ability (GCA) effects showed that parent 5(P5), were superior for plant height, stem diameter, number of leaves, leaf length, days to flowering and attitude of floral axis followed by parent 2(P2) for leaf length, leaf width, days to flowering and attitude of floral axis and parent7 (P7) for number of flower, flower diameter, bud length and attitude for floral axis. Likewise; tester 1 found to be best combiner with significant GCA effect for almost all growth and flowering traits (except number of leaves). The plant height, leaf width, number of flower and attitude of floral axis showed prevailing additive gene action while stem diameter, number of leaves, leaf length, days to flowering, flower diameter and bud length indicated predominance of dominance gene action. We can conclude that parent P5, parent P2 and parent P7 can be used as good mother lines and the tester 1, as good donor for the seed production. SAARC J. Agri. , 17(1): 175-187 (2019)
CK2-Dependent Phosphorylation of the Brg1 Chromatin Remodeling Enzyme Occurs during Mitosis

Brg1 (Brahma related gene 1) is one of two mutually exclusive ATPases that can act as the catalytic subunit of mammalian SWI/SNF chromatin remodeling enzymes that facilitate utilization of the DNA in eukaryotic cells. Brg1 is a phospho-protein and its activity is regulated by specific kinases and phosphatases. Previously, we showed that Brg1 interacts with and is phosphorylated by casein kinase 2 (CK2) in a manner that regulates myoblast proliferation. Here we demonstrate that the Brg1-CK2 interaction occurred during mitosis in embryonic somites and in primary myoblasts derived from satellite cells isolated from muscle tissue. The interaction of CK2 activity with Brg1 and the incorporation of a number of other subunits into the mSWI/SNF enzyme complex were independent of CK2 enzymatic activity. CK2-mediated hyperphosphorylation of Brg1 was observed in mitotic cells derived from multiple cell types and organisms, suggesting functional conservation across tissues and species. The mitotically hyperphosphorylated form of Brg1 was localized with soluble chromatin, demonstrating that CK2-mediated phosphorylation of Brg1 is associated with specific partitioning of Brg1 within sub-cellular compartments. Thus CK2 acts a mitotic kinase that regulates Brg1 phosphorylation and sub-cellular localization.
Quasi-Phase-Matching Efficiency Optimization for Coupled Second-Order Nonlinear Processes

It is well known how to tailor the conversion efficiency grid of a single quasi-phase-matching (QPM) grating when the involved processes are uncoupled. However, it becomes much more sophisticated in the presence of coupling between multiple processes. In this case, different processes compete for the same QPM “resources” throughout the grating, and one process can outweigh the others over a certain range of interaction. Here we propose the generalized iterative domino (GID) algorithm to meet these challenges for the first time (to our best knowledge). Instead of tailoring the strength of each “global” Fourier coefficient, GID algorithm can properly adjust the spatially varying “local” Fourier coefficients in favor of the final yield. Three methods, including cascaded single-period (C1P) structure, quasi-periodic optical superlattice (QPOS), and hyperfine aperiodic optical superlattice (HAOS) optimized by GID, are numerically and experimentally investigated under the platform of third-harmonic generation (THG). It shows that the THG efficiency of HAOS + GID can exceed the record achieved by C1P structure by 33%. This method is applicable to general wavelength converters involving with multiple coupled nonlinear processes.
PI 3‐kinase delta enhances axonal PIP 3 to support axon regeneration in the adult CNS

Peripheral nervous system (PNS) neurons support axon regeneration into adulthood, whereas central nervous system (CNS) neurons lose regenerative ability after development. To better understand this decline whilst aiming to improve regeneration, we focused on phosphoinositide 3-kinase (PI3K) and its product phosphatidylinositol(3,4,5)-trisphosphate (PIP3). We demonstrate that adult PNS neurons utilise two catalytic subunits of PI3K for axon regeneration: p110α and p110δ. However in the CNS, axonal PIP3 decreases with development at the time when axon transport declines and regenerative competence is lost. Overexpressing p110α in CNS neurons had no effect, however expression of p110δ restored axonal PIP3 and increased regenerative axon transport. p110δ expression enhanced CNS regeneration in both rat and human neurons and in transgenic mice, functioning in the same way as the hyperactivating H1047R mutation of p110α. Furthermore, viral delivery of p110δ promoted robust regeneration after optic nerve injury, demonstrating potential for translational development. These findings establish a deficit of axonal PIP3 as a key reason for intrinsic regeneration failure and demonstrate that native p110δ facilitates axon regeneration by functioning in a hyperactive fashion.
Remote sensing of ploidy level in quaking aspen (Populus tremuloides Michx.)

Ploidy level in plants may influence ecological functioning, demography and response to climate change. However, measuring ploidy level typically requires intensive cell or molecular methods. We map ploidy level variation in quaking aspen, a dominant North American tree species that can be diploid or triploid and that grows in spatially extensive clones. We identify the predictors and spatial scale of ploidy level variation using a combination of genetic and ground‐based and airborne remote sensing methods. We show that ground‐based leaf spectra and airborne canopy spectra can both classify aspen by ploidy level with a precision‐recall harmonic mean of 0.75–0.95 and Cohen's kappa of c. 0.6–0.9. Ground‐based bark spectra cannot classify ploidy level better than chance. We also found that diploids are more common on higher elevation and steeper sites in a network of forest plots in Colorado, and that ploidy level distribution varies at subkilometer spatial scales. Synthesis. Our proof‐of‐concept study shows that remote sensing of ploidy level could become feasible in this tree species. Mapping ploidy level across landscapes could provide insights into the genetic basis of species' responses to climate change.