Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome Editing—Principles and Applications for Functional Genomics Research and Crop Improvement

ABSTRACT Genome editing technologies are powerful tools for studying gene function and for crop improvement. The technologies rely on engineered endonucleases to generate double stranded breaks (DSBs) at target loci. The DSBs are repaired through the error-prone non-homologous end joining (NHEJ) and homology-directed repair (HDR) pathways in cells, resulting in mutations and sequence replacement, respectively. In the widely used CRISPR/Cas9 system, the endonuclease Cas9 is targeted by a CRISPR small RNA to DNA sequence of interest. In this review, we describe the four available types of genome editing tools, ZFN, TALEN, CRISPR/Cas9 and CRISPR/Cpf1, and show their applications in functional genomics research and precision molecular breeding of crops.
Genomic characterisation and conservation genetics of the indigenous Irish Kerry cattle breed

Kerry cattle are an endangered landrace heritage breed of cultural importance to Ireland. In the present study we have used genome-wide SNP data (Illumina® BovineSNP50 array) to evaluate genomic diversity within the Kerry cattle population and between Kerry cattle and other European cattle breeds. Visualisation of patterns of genetic differentiation and gene flow among cattle breeds using phylogenetic trees with ancestry graphs highlighted, in particular, historical gene flow from the British Shorthorn breed into the ancestral population of modern Kerry cattle. Principal component analysis (PCA) and genetic clustering emphasised the genetic distinctiveness of Kerry cattle relative to comparator British and European cattle breeds. Modelling of genetic effective population size (Ne) revealed a demographic trend of diminishing Ne over time and that recent estimated Ne values for the Kerry breed may be less than the threshold for sustainable genetic conservation. In addition, analysis of genome-wide autozygosity (FROH) showed that genomic inbreeding has increased significantly during the 20 years between 1992 and 2012. Finally, signatures of selection revealed genomic regions subject to natural and artificial selection as Kerry cattle adapted to the climate, physical geography and agro-ecology of southwest Ireland. Note 1: This is an Associate Editor (D.E.M) Inaugural Article submission to Frontiers in Genetics: Livestock Genomics Note 2: British English language style preferred for publication of this article.
Three new species of Hydnophlebia (Polyporales, Basidiomycota) from the Macaronesian Islands

The genus Hydnophlebia includes two species of wood-inhabiting fungi, Hydnophlebia chrysorhizon and Hydnophlebia omnivora. Both are characterized by cream to reddish-orange, resupinate basidiome, with hydnoid hymenophore, margin with strands, a monomitic hyphal system, tubular to ventricose cystidia and elliptical spores. In this paper, a taxonomic study of Hydnophlebia, using morphology and molecular analyses of large subunit nuclear ribosomal DNA (LSU) and the internal transcribed spacer nrDNA operon (ITS), is reported. Three new species, Hydnophlebia canariensis, H. gorgonea and H. meloi, from the Macaronesia bioregion (Canary Islands and Cape Verde Archipelago), are described.
A plant growth promoting rhizospheric Pseudomonas aeruginosa strain inhibits seed germination in Triticum aestivum (L) and Zea mays (L)

Various rhizobacteria strains are isolated and tested worldwide for their plant growth promoting activities. A strain is said to be a plant growth promoter if it has the ability to influence plant growth directly or indirectly. Though the main focus has always been to realize the plant growth promoting traits of rhizobacteria and use them as biofertilizers, but the disadvantages or deleterious effects of such plant growth promoting rhizobacteria (PGPR) if any have also been ignored to a greater extent. The present study deals with the characterization of both promoting as well as deleterious activities of an isolated strain of Pseudomonas aeruginosa on plants. The bacterium was isolated from the soil of the college campus of Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh and was characterized as P. aeruginosa by various positive biochemical tests such as oxidase, catalase, citrate tests and confirmed by MALDI-TOF-MS. Its growth as well as IAA producing ability at different salt (NaCl) concentrations was tested. Tests examining HCN, Ammonia and siderophore production, flocculation ability, phosphate and zinc solubilization by the strain were carried out. Its anti-microbial property was tested against three phytopathogenic fungi: Fusarium solani, Aspergillus niger and Curvularia lunata and two bacterial strains - Klebsiella pneumoniae and E. coli . Its effect over seed germination of Triticum aestivum and Zea mays was inspected in plates as well as in pots. The strain showed a great potential as a plant growth promoter growing up to 10% NaCl concentration and producing considerable amount of IAA upto 8% NaCl concentration. It showed antagonistic nature against the three phytopathogenic fungi, solubilized phosphate and produced siderophore and NH3. Though supernatant of the bacterial culture did not show any deleterious effect over seed (of the test plants T. aestivum and Z. mays ) germination but the seeds inoculated with the strain itself, failed to germinate. The seed turned dormant and grew a pale brown color showing bacterial growth over it. Thus it maybe concluded that the isolated strain of P. aeruginosa has abilities to both promote and at the same time inhibit plant growth (by inhibiting seed germination).
Bovine immune responses to Fasciola hepatica during the early stages of infection

Fasciola hepatica (liver fluke), is a trematode parasite, particularly of ruminants, that is found throughout the world. Sheep show no resistance to the parasite, cattle may develop partial resistance and rats show complete resistance, which is immune-mediated, to challenge infections. In rats, resistance occurs early during infection, at the level of the gut and/or peritoneum. Little is known regarding the natural immune responses in cattle that occur during this period. This study was designed to investigate the effect that pre-exposure of cattle to 1-2 and 5-6 day old flukes had upon subsequent challenge infections, when compared to naive and chronically infected animals. Infection parameters, together with peripheral and local cellular and antibody responses to various F. hepatica protein preparations were investigated. A primary exposure to 5-6 day old flukes, terminated by triclabendazole treatment, was found to reduce the degree of liver damage and eosinophilia experienced after a challenge infection. Lower levels of the enzymes gammaglutamyl transferase and glutamate dehydrogenase were detected in sera, compared to those in naive animals (P < 0.05). Eosinophilia was also reduced (P < 0.01), as was egg output in the faeces during the early patent period (P < 0.05). Calves that were pre-exposed to 1-2 day old flukes showed no significant differences in the levels of these parameters, when compared to their nai've counterparts. Sera taken prior to the secondary challenge from pre-exposed animals and those receiving an unterminated primary infection recognised a variety of proteins in Western blots of whole adult fluke somatic antigen (WFA) and excretory-secretory (ES) preparations. The IgGl antibody response to protein bands of 96-82, 76-68 and 60-52 kDa predominated. After secondary challenge the response of the chronically infected animals to these protein species was reduced and extremely strong recognition of bands in the region 30-28 kDa was observed. Pre-exposed animals maintained the response to the higher weight bands, showing a similar, but initially stronger recognition pattern, to that of naive challenged animals. The lower weight protein bands were not detected in these groups until much later. The IgGl/IgG2 isotype antibody response to purified cathepsin and haemcontaining high molecular weight fractions were also examined by ELISA. A
Rice bran real-time stabilisation technology with flowing microwave radiation: its impact on rancidity and some bioactive compounds

A pilot-scale real-time flowing microwave drum (PRFM) heating system was designed and adopted to stabilise rice bran (RB) for retarding rancidity. Meanwhile, the influence of PRFM radiation on fat-soluble bioactive compounds of RB were evaluated. Results revealed that PRFM processing could effectively inactivate lipase (LA) and lipoxygenase (LOX) of RB in minutes. The RB sample irradiated at 4 kW for 10 min with PRFM acquired the optimal stabilisation effect, and its residual LA activity was 7.94% and LOX was completely destroyed. The free fatty acids content and peroxide value of RB sample treated at optimal condition only increased by 1.06% and 5.32 meq O2/kg rice bran oil at 35 °C for 60 days, respectively. No significant decrease in fatty acid, tocopherols and γ-oryzanol content were noticed in bran sample treated at optimal condition. Therefore, PRFM radiation would be used as a practical and real-time technology for stabilising RB on-line.
Total Phenolic and Flavonoid Content and Antioxidant Activities of Ten Malaysian Wild Mushrooms

Mushrooms have been studied and found to accumulate a variety of secondary metabolites with antioxidant activities such as phenolic compounds. Besides phenolics, other bioactive components such as flavanoids from mushrooms are also generally associated with antioxidant activities. Previous studies have reported the association of mushrooms with their antioxidant potentials. However, very few studies are related to unexplored Malaysian wild mushrooms as a new potential source of antioxidant for which to best of our knowledge, no records are available. In this study, ten Malaysian wild mushrooms were collected from the forests around Selangor and Sabah and their potential antioxidant activity were evaluated. The total phenolic content and total flavonoid content were quantified. Antioxidant activities of the mushroom extracts were analyzed by Ferric Reducing Antioxidant Power (FRAP) and 2,2-diphenylpicrylhydrazyl (DPPH) assays for their iron-reducing capacity and free-radical scavenging capacity. The total phenolic content of all ten mushrooms ranged from 0.015-0.075 mg GAE/g dried extract and the total flavonoid content ranged from 0.025-0.131 mg QE/g dried extract. The FRAP values lies between 0.859-2.929 μM TE/g dried extract and the percentage of inhibition observed from DPPH assay ranged from 2%-57% respectively. There is a positive correlation between total phenolic content and antioxidant activities of these mushroom extracts.
Taxonomic survey of benthic diatoms in Neum Bay, southeastern Adriatic

The objective of this work was to contribute to the knowledge of microphytobenthos in the Adriatic Sea, by studying for the first time the benthic diatom communities in the Neum Bay in Bosnia and Herzegovina. For this purpose, the benthic diatoms naturally growing on stones and macroalgae were identified at one station in the small semi-enclosed oligotrophic Neum Bay during 2010 and 2011. A total of 24 samples were collected at two different depths, 0.5 m and 8 m, and analysed with light and scanning electron microscopy. Altogether, 425 pennate and 58 centric taxa (species and infraspecific taxa) belonging to 60 families and 115 genera were noted. Genera with the greatest number of taxa were: Mastogloia (46 taxa), Navicula (36), Diploneis (35), Nitzschia (34), Amphora (31), Cocconeis (27), Achnanthes (14), Halamphora (12), Lyrella (11), and Surirella and Licmophora (10 each). Amphora bigibba var. interrupta and Cocconeis scutellum were the most frequent taxa, being present in 87.5% of the samples. In total, 142 taxa were found only once (sporadic taxa). Although benthic diatom richness is high in the bay, taxa are apparently not distributed evenly temporally. Consistent quantitative and qualitative data are still needed to better determine the seasonal and spatial changes of the epilithic assemblages in the region.
Potential for quality protein maize for reducing proteinenergy undernutrition in maize dependent Sub-Saharan African countries: A review

Most cereal crops, including maize ( Zea mays L .), are deficient in essential amino acids, such as lysine and tryptophan; hence they are poor in protein quality. A mutant maize with elevated levels of lysine and tryptophan was developed by the International Maize and Wheat Improvement Centre (CIMMYT) and was called quality protein maize (QPM). Nonetheless, people in sub-Saharan Africa (SSA) continue to use normal endosperm maize (non-QPM) instead of QPM. The objective of this article was to examine the existing information on institutional arrangements, infrastructure and social systems hampering adoption of QPM and to identify opportunities for promoting the campaign for its utilisation in SSA, through innovative research for development initiatives. It is clear that QPM has superior nutritional value, both to humans and to monogastric animals compared to non-QPM. Lack of sound policies and awareness among farmers about the existence and advantages of QPM are some of major drawbacks to QPM adoption and realisation of its benefits. Most farmers hardly believe information regarding nutritional composition of varieties, without convincing visual evidence such as grain yield from demonstration plots. Many African governments have mounted campaigns geared to promote adoption of QPM varieties. Varying levels of QPM adoption have been recorded in South Africa, Burkina Faso, Uganda and Ghana with high QPM production under areas ranging from 12 500 to 71 250 ha. In order to reduce protein-energy undernutrition (PEU), SSA countries should implement policies that promote QPM adoption such as providing farmers with a premium price for the QPM grain. Results from meta-analysis community based studies revealed that QPM based diets resulted in a 12% improvement on weight and 9% increase in height in infant and young children compared to non-QPM based diets. Therefore, quality protein maize bears great potential for reducing PEU and its adoption could be high given that most SSA countries depend on maize as the major source of calories and protein. Key Words : Bio-fortification, lysine, malnutrition, tryptophan, Zea mays L.
Effect of 50% ethanolic extract of roots of Cissampelos pareira on some bio-chemical parameters to investigate the hepato-protective study in animal model (Rats)

In phytotherapeutic approach, the emphasis is on the development of a new drug whose extraction and fractionation have emanated on the basis of therapeutic activity. Cissampelos pareira Linn. (C. microcarpa, De Candolle) is a very variable, lofty, slender, dioecious, perennial, climber commonly distributed throughout topical and sub topical India, ascending up to an altitude of c 2,000m. The plant is very common in orchards, hedges, parks and gardens on moist soils, either creeping or twining around other plants. The roots of Cissampelos pareira (L.) Hirsuta (Menispermaceae) were collected and extracted with 50% ethanol solution. The selected plant extract was subjected for the preliminary acute toxicity studies in mice at different dose levels up to 2000 mg/kg. The results showed no abnormal symptoms either p.o or i.p and cause no mortality. Before the actual LD50 determination, a pilot study was made on a small group of mice mainly to select the dose ranges for the subsequent study. The 50% ethanolic extract of Cissampelos pareira were taken at various dose levels (200, 500, 1000, 1500, 2000 mg/kg b.wt.) dissolved in 1 % carboxymethyl cellulose administered orally to pairs of mice per dose level. The value of probability less than 5% (P < 0.05) was considered statically significant. Histological architecture of the C. pariera treated liver samples showed the ability of the C. papeira to prevent hepatocellular necrosis. In conclusion, the antitubercular drugs (isoniazid and rifampicin)-induced alterations on protein metabolism and hepatic antioxidant defense system were normalized by Cissampelos pareira co-administration, indicating a possible cytoprotective role of Cissampelos pareira against drug induced hepatotoxicity. Thus our studies give scientific evidences to support this plant’s traditional uses as claimed in folklore medicine. It was concluded from the results that the alcoholic extract of Cissampelos pareira (L.) possesses hepato-protective effect in experimental animals Key words: Cissampelos pareira Linn, C. pariera,dioecious
Comparative study of rapid urease test and histopathological examination for detection of H. pylori infection

Helicobacter pylori (H. pylori) infection is very common throughout the world, occurring in 40-50% of the population in developed countries and 80-90 % of population in developing regions. Since the discovery of H. pylori by Marshall and Warren in 1983, overwhelming evidence has accumulated to confirm that H. pylori infection plays a significant role in the development of chronic active gastritis and peptic ulcer. H. pylori is the etiologic agent of acute and chronic gastritis, peptic ulcer disease and two forms of gastric cancer. ABSTRACT
Comparative Transcriptomic and Metabolomic Analyses in Response to Cold in Tartary Buckwheat (Fagopyrum tataricum)

Plants recognize multiple environmental signals that lead to substantial changes in the regulation of primary and secondary metabolism in order to adapt to environmental stresses. In this study, we investigate the effects of cold on the metabolome and transcriptome of tartary buckwheat, focusing on the phenylpropanoid biosynthetic pathway. Using RNA-sequencing analysis of the cold-regulated transcriptome of buckwheat, we identified several phenylpropanoid biosynthetic transcripts that accumulated in response to cold. To confirm the transcriptome data, we analyzed the expression of the phenylpropanoid biosynthetic transcripts in cold-treated buckwheat and showed that all the phenylpropanoid biosynthetic transcripts were upregulated in coldtreated buckwheat seedlings with the exception of FtDFR. From the metabolic profiling based on the GC-TOF-MS analysis, we show that most of the sugars and their derivatives significantly increase in response to cold, while some of amino acids and their derivatives decrease in cold-treated plants. Some organic acids derived from the tricarboxylic acid (TCA) cycle increased in the cold-treated plants compared with in the plants grown at 25°C. In particular, the contents of anthocyanins and proanthocyanidins were significantly increased by cold treatment. In summary, these results indicate that the metabolome and transcriptome of tartary buckwheat are extensively affected by cold stresses. Highlight Using the RNA-sequencing data and the metabolic profiling analysis, we identified the changes that occur in the transcriptome and metabolome of tartary buckwheat in response to cold, focusing on the flavonoid biosynthetic pathway. Abbreviations ANR anthocyanidin reductase ANS Anthocyanin synthase C4H cinnamate 4-hydroxylase CHI chalcone isomerase CHS chalcone synthase 4CL 4-coumarate:CoA ligase DFR dihydroflavonol reductase DPPH 2,2-diphenyl-1-picrylhydrazyl F3H flavanone 3-hydroxylase F3’H flavonoid 3’-hydroxylase FLS flavonol synthase GC-TOFMS gas chromatography-time of flight mass spectrometry 3GT flavonoid 3-O-glucosyltransferase HPLC high-performance l iquid chromatography LAR leucoanthocyanidin PA proanthocyanidin PAL phenylalanine ammonia-lyase RT 3-O-rhamnosyltransferase TCA tricarboxylic acid.
Role of anterograde motor Kif5b in clathrin-coated vesicle uncoating and clathrin-mediated endocytosis

Kif5b-driven anterograde transport and clathrin-mediated endocytosis (CME) are responsible for opposite intracellular trafficking, contributing to plasma membrane homeostasis. However, whether and how the two trafficking processes coordinate remain unclear. Here, we show that Kif5b directly interacts with clathrin heavy chain (CHC) at a region close to that for uncoating catalyst (Hsc70) and preferentially localizes on large clathrin-coated vesicles (CCVs). Uncoating in vitro is decreased for CCVs from the cortex of kif5b conditional knockout (mutant) mouse and facilitated by adding CHC-binding Kif5b fragments, while cell peripheral distribution of CHC or Hsc70 keeps unaffected by Kif5b depletion. Furthermore, cellular entry of vesicular stomatitis virus that internalized into large CCV is inhibited in cells by Kif5b depletion or introducing a dominant-negative Kif5b fragment. These findings showed a new role of Kif5b in CCV uncoating and CME, indicating Kif5b as a molecular knot connecting anterograde transport to CME.
Influence of lipid supplementation on milk components and fatty acid profile

ABSTRACT The objective of this study was to evaluate the effects of different lipid sources in diets for lactating cows on milk yield and composition, conjugated linoleic acid (CLA) content, and fatty acid profile in the milk fat. Five primiparous Holstein cows were distributed in a 5 × 5 Latin square design. Treatments were: control (no lipid addition) and four other diets containing different lipids sources – ground raw soybean, cottonseed, soybean oil, and calcium salts of soybean fatty acids [. ]
Flexible sensor concept and an integrated collision sensing for efficient human-robot collaboration using 3D local global sensors

Human-robot collaboration with traditional industrial robots is a cardinal step towards agile manufacturing and re-manufacturing processes. These processes require constant human presence, which results in lower operational efficiency based on current industrial collision avoidance systems. The work proposes a novel local and global sensing framework, which discusses a flexible sensor concept comprising a single 2D or 3D LiDAR while formulating occlusion due to the robot body. Moreover, this work extends the previous local global sensing methodology to incorporate local (co-moving) 3D sensors on the robot body. The local 3D camera faces toward the robot occlusion area, resulted from the robot body in front of a single global 3D LiDAR. Apart from the sensor concept, this work also proposes an efficient method to estimate sensitivity and reactivity of sensing and control sub-systems The proposed methodologies are tested with a heavy-duty industrial robot along with a 3D LiDAR and camera. The integrated local global sensing methods allow high robot speeds resulting in process efficiency while ensuring human safety and sensor flexibility.
Molecular Cooperativity Leads to Monoallelic Olfactory Receptor Expression

expresses only one out of thousands of olfactory receptor alleles and the molecular mechanism remains as one of the biggest puzzles in neurobiology. We constructed a mathematical model and identified a three-layer regulation mechanism that robustly generates single-allele expression: zonal separation, epigenetic activation and subsequent allele competition for a limited number of enhancers. Model analyses conclude that the regulatory system has been evolutionarily optimized to minimize multiple allele activation and alleles trapped in incomplete epigenetic activation states. The identified design principles demonstrate the importance of molecular cooperativity in selecting and maintaining monoallelic olfactory receptor expression.