Miracle-dz/UniFAR-FTUs huggingface dataset:
The Quest for a Key Gene Controlling Acquisition of Cell Competence During In Vitro Organogenesis in Tomato

THE QUEST FOR A KEY GENE CONTROLLING ACQUISITION OF CELL COMPETENCE DURING IN VITRO ORGANOGENESIS IN TOMATO Chanaka Roshan Abeyratne Plants show a remarkable capacity for vegetative propagation through de novo organogenesis. Unlike their wild relatives, most commercially important crop species lack this ability, which is largely attributed to their inability to acquire regeneration competence by dedifferentiation of somatic cells. In vitro micropropagation relies heavily on overcoming such regeneration recalcitrance for its success in biotechnology and clonal propagation in agriculture. Here, we investigate a key locus (Regeneration1) responsible for acquisition of competence that confers high rates of de novo shoot and root organogenesis in tomato. In vitro shoot regeneration assay was performed in several Solanum pennellii introgression lines into S. lycopersicum cv. Micro-Tom (MT) to help identify 29 candidate RG1 genes from a genomic region that originally occupied 6.16 Mbps with 293 genes. We used recalcitrant genotype MT as well as the highly regenerant S. pennellii and its introgression line MT-Rg3C in a subsequent in vitro shoot regeneration assay to characterize the expression of candidate genes using RT-qPCR. Two candidate genes were upregulated in both S. pennellii and MT-Rg3C in comparison to MT. Since the dominant recalcitrance trait may be conferred by mutations leading to lack of function in MT, sequence variations of the 29 candidates were compared between the S. pennellii and MT genomes. Ten genes were identified with mutations that may cause loss of function. Furthermore, 11 novel proteins with unknown functions were identified with polymorphisms for further investigation. Here we propose at least 10 candidate genes for functional characterization in other highly regenerant genotypes to ultimately end the quest for a key gene controlling organogenesis in tomato.
A comprehensive reanalysis of publicly available GWAS datasets reveals an X chromosome rare regulatory variant associated with high risk for type 2 diabetes

The reanalysis of publicly available GWAS data represents a powerful and cost-effective opportunity to gain insights into the genetics and pathophysiology of complex diseases. We demonstrate this by gathering and reanalyzing public type 2 diabetes (T2D) GWAS data for 70,127 subjects, using an innovative imputation and association strategy based on multiple reference panels (1000G and UK10K). This approach led us replicate and fine map 50 known T2D loci, and identify seven novel associated regions: five driven by common variants in or near LYPLAL1, NEUROG3, CAMKK2, ABO and GIP genes; one by a low frequency variant near EHMT2; and one driven by a rare variant in chromosome Xq23, associated with a 2.7-fold increased risk for T2D in males, and located within an active enhancer associated with the expression of Angiotensin II Receptor type 2 gene (AGTR2), a known modulator of insulin sensitivity. We further show that the risk T allele reduces binding of a nuclear protein, resulting in increased enhancer activity in muscle cells. Beyond providing novel insights into the genetics and pathophysiology of T2D, these results also underscore the value of reanalyzing publicly available data using novel analytical approaches.
Chemical composition and biological activities of peels and leaves essential oils of four cultivars of Citrus deliciosa var. tangarina

The hydrodistilled essential oils of peels and leaves of four cultivars of Citrus deliciosa var. tangarina (Fina Clementine, Nour Clementine, Spinosa Clementine and Thornless Clementine) belonging to family Rutaceae were analyzed by GC/MS. Limonene was the major constituent of all the oil samples under investigation except in case of Nour Clementine leaves, where sabinene was the major component. Generally, total hydrocarbons were of higher percentage than total oxygenated compounds, also total monoterpenes showed higher percentage than total sesquiterpenes. The studied essential oils showed a dose-dependent antioxidant activity. Thornless leaves oil showed the highest antioxidant potential, it recorded the same EC50 as ascorbic acid. The antimicrobial activity of Citrus peels and leaves oils was screened against Gram-positive and Gram-negative bacteria, yeast and fungi. Leaves oils showed higher antimicrobial activity than peels oils against all the tested microorganisms among them Thorny Clementine leaves oil was the most potent. Peels oils were tested for cytotoxic activity against liver, cervix, breast carcinoma and normal baby hamster kidney fibroblast cell lines. Peels oils showed potent cytotoxic activity against the tested carcinoma cell lines comparing to doxorubicin, while they exhibited no effect on normal baby hamster kidney fibroblast cell line which indicated their safety. The antiviral activity of the studied essential oils was tested by hemagglutination test of washed chicken erythrocytes. The allantoic amniotic fluid of embryonatic eggs inoculated with different Citrus essential oils under investigation, suspension of H5N1 virus and antibiotic gave a positive test, this indicates inactivated H5N1 virus.
In ovo Feeding – Technology of the Future – A Review

Abstract Over the years, due to genetic selection, improvement of the characteristics of laying and meat poultry with less feed consumption per kilogram of body weight gain has been achieved (FCR). As the productivity of poultry increased, the demand of embryos for nutrients changed. However, the chemical composition of an egg has remained practically unchanged, and therefore, it began providing the embryos with suitable substances with the help of in ovo technology. Improvements in hatching were achieved through the administration of fructose, sucrose and grape seed extract (GSE), while the weight of a one-day-old chick is affected by the injection of amino acids with glucose and magnesium. In addition, amino acids and carbohydrates applied to an egg have contributed to an increase in the activity of digestive enzymes and maturation of the intestine. In connection with early stimulation of the intestinal tract of broiler chicks, they obtained higher weight gain. Supplementation with vitamins positively affects the increase of birds’ immunity and body weight at the end of breeding. On the other hand, the injection of an insulin-like growth factor (IGF-I) influenced the growth and development of muscle tissue during the first weeks of life.
The genus Apsiphortica from China with DNA barcoding information (Diptera: Drosophilidae)

Summary Two new species of the genus Apsiphortica are described from China: A. orthophallos n. sp. and A. sinuatipenis n. sp. Species delimitations are improved by integrating morphological and DNA barcoding information. The intra- and interspecific pairwise p-distances (proportional distance) are summarized for five Apsiphortica species from China. Furthermore, nucleotide sites with fixed status in the alignment of the COI sequences (639 nucleotide sites in length) are used as “pure” molecular diagnostic characters to delineate the five species. A key to all the Chinese species of the genus Apsiphortica is provided.
Can a QED Photon Propagate Out of the Black‐Hole Horizon?

We show at one‐loop approximation that the QED photon acquires a negative gauge‐invariant mass‐squared in the near‐horizon region of an evaporating Schwarzschild black hole. This result may imply that information about the inner structure of evaporating black holes is accessible, even without invoking the modification of the basic QFT and GR principles.
Enzymatic transesterification in a solvent-free system: synthesis of sn-2 docosahexaenoyl monoacylglycerol

Abstract The enzymatic transesterification of docosahexaenoic acid (DHA) ethyl ester with glycerol was carried out by using several immobilized lipases in a solvent-free system. This reaction involves the initial formation of sn-2 docosahexaenyl monoacylglycerol. This DHA derivative is highly relevant for improving the bioavailability of DHA and it has received increasing interest in the field of nutrition. Three commercial lipases, from Rhizomucor miehei (RML), Alcaligenes sp. (AQ) and Candida antarctica-fraction B (CALB) were immobilized by interfacial adsorption on a commercial hydrophobic support (a methacrylate resin containing octadecyl groups, Sepabeads C-18) and tested for glycerolysis of DHA ethyl ester. In certain cases (e.g. immobilized CALB), the transesterification reaction continues to the formation of triacylglycerol (80%) by using a very high excess of DHA ethyl ester ((115 mmols versus 1.24 mmols of glycerol and high temperatures (50 °C). However, the same biocatalyst working at lower temperatures, 37 °C, synthetizes a 90% of sn-2 monoacylglycerol even in the presence of that a high excess of DHA ethyl ester. Interestingly, immobilized RML derivative synthesizes a 98% of sn-2 monoacylglyceride (2-MG) in 15 min at 37 °C with a 4% of immobilized biocatalyst. These high activity and regioselectivity under very mild reaction conditions are very interesting for the thermal oxidative stability of the omega-3 fatty acid as well as for the thermal stability of the biocatalyst. Using Normal Phase HPLC-ELSD and accurate commercial markers, the formation of the 2-MG was confirmed.
Effect of Restricted Caloric Intake and Bariatric Surgery on PCSK9 Concentrations in Plasma

PCSK9 is a major modulator of LDLc through internalization and endosomal degradation of LDL receptor. It has been shown that PCSK9 plasma levels predict CVD risk. Bariatric surgery is known to reduce both LDLc and CVD. However, its exact effect on circulating PCSK9 levels has not been fully investigated. We have now investigated the effect of strict caloric restriction and Roux-en-Y bariatric surgery (RYGB) in 15 morbidly obese patients on plasma PCSK-9 levels. Subjects were instructed to follow a regimen of 4 liquid shakes (up to 16g carbohydrate, 0g fat, and 33g of protein, total daily intake was 550-785 calories) during the 2-weeks strict caloric restriction period prior to surgery and the usual dietary regime after surgery. Blood samples were obtained at 2 weeks before, at the time of surgery and 6 months after RYGB. There was a significant weight loss of 7.8±2.4 Kg during the 2 weeks prior to surgery and of additional 26.6±5.3 Kg 6 months after surgery. At completion of strict caloric restriction, subjects had a significant reductions in glucose, insulin and HOMA-IR (7.1±1.1 to 4.5± 1.0) which continued following surgery (HOMA-IR (4.5±1.0 to 2.1± 0.3). LDL(c) fell significantly by 11±7% (from 120±6 to 109±7mg/dl) following the strict caloric restriction and by 15±8% (from 109±7 to 95±6mg/dl) following surgery. There was a reduction of 38±11% (from 227±25 to 139±15 ng/ml) in plasma PCSK9 concentration in the 2 weeks of caloric restriction. Thereafter, PCSK9 levels increased to 166±22ng/ml over the next 6 months. Our data show that there is an impressive and concurrent fall in PCSK9, LDL(c) concentrations and insulin resistance following strict caloric restriction. The marked weight loss over 6 months has only a marginal effect on PCSK9 concentrations while metabolic improvements persisted. This reduction in PCSK9 may contribute to the known benefit in cardiovascular outcomes following bariatric surgery. Disclosure H. Ghanim: None. S. Abuaysheh: None. S. Monte: Stock/Shareholder; Self; Mobile Pharmacy Solutions (Community Pharmacy). Employee; Self; Synergy Bariatrics, a Department of ECMC. P. Dandona: Advisory Panel; Self; AstraZeneca. Consultant; Self; AstraZeneca. Research Support; Self; AstraZeneca.
Molecular characterization and partial purification of lipase from lipolytic bacteria isolated from oil mills

Enzymes are considered as natures Bio-Catalyst, today they are produced by fermentation of bio-based materials. Lipolytic enzymes play important role in the mobilization of Lipids within cell or individual organisms as well as in the transfer of Lipids from one organism to another. The majority of lipolytic enzyme in industrial use is currently attracting an enormous attention because of their bio-technological applications. The high level production of microbial lipase requires not only efficient, but also detail understanding of its molecular mechanism. The industrially relevant lipase can be achieved for the synthesis of Biopolymers, Bio-diesel, Agro chemicals and flavor compounds. In the present study an attempt was made to screen the strains of lipase producing bacteria. Samples collected from oil, mills were allowed to grow on kings-A and kings-B medium and sub cultured on Cetramide agar. Lipase activity was checked on Tributryin agar. Later the isolates are confirmed based on their standard Microscopic, Colony characteristics, Bio-chemical and physiological features.
Molecular Analysis of Hotspot Regions of ARX and MECP2 Genes in Intellectual Disability and Cornelia De Lange Syndrome

ABSTRACT Intellectual disability is a generalized developmental disorder. The present paper is focused on mutational screening of ARX and MECP2 genes in syndromic (Cornelia De Lange Syndrome cases (CdLS)) and non-syndromic intellectual disability. Mutational analysis was carried out by PCR followed by conformation sensitive gel electrophoresis and sequencing. In CdLS cases two polymorphisms were obtained in ARX gene where one of these was probably deleterious polymorphism. In NSID cases total five polymorphisms were obta ined in ARX gene, wher e one was pr oba bly deleterious polymorphism. The MECP2 gene showed presence of one polymorphism which was known deleterious variant. Except one all sequence variants found in this pap er were novel.
Descrição de transmissão horizontal e vertical de Porcine circovirus 2b (PCV2b) em camundongos (CH3/Rockfeller) inoculados experimentalmente

The studies of mice susceptibility to PCV2 infection are still controversial, despite the importance of PCV2 infection in pigs. Therefore, the aim of this study is to verify the occurrence of horizontal and vertical transmission of PCV2b in mice experimentally infected. Two experiments were performed. In experiment 1 an infected male mice covered a female to verify vertical infection. The pups were tested to detected viral DNA. In experiment 2 the 21 days of age mice were inoculated with PCV2 and allocated with uninfected, i.e. contactantes, to evaluate the horizontal infection. Subsequently, the contactants and inoculated mice were tested for PCV2 DNA. The samples collected from both experiments had their DNA extracted and were further submitted to polymerase chain reaction (PCR). In experiment 1, after the gestation period, the female farrowed 10 mices of which 60% (6/10) were positive for the agent. In experiment 2, both the inoculated and the contacts animals showed no clinical changes and gross lesions of PCV2 infection, but viral DNA was recovered in four of the five animals of the contactant group. The detection of viral DNA in the offspring of the primo-infected females and in the mice that had contact with inoculated mice demonstrated that PCV2 can be transmitted vertically and horizontally.
Testing for co-adaptation of plants and arbuscular mycorrhizal fungi in a biodiversity experiment

Co-evolution between plants and arbuscular mycorrhizal fungi (AMF) may occur over short time spans. However, whether plants and AMF co-adapt and how this may be influenced by plant diversity has never been addressed. We carried out a plant–AMF experiment using five plant species and AMF selected over 11 years in plant monocultures or mixtures. Single plants were grown in sterile soil or soil inoculated with monoculture or mixture AMF or with a positive control (Rhizoglomus irregulare). We measured plant biomass, plant functional traits and AMF colonization. Mixture AMF were more beneficial than monoculture AMF for two plant species. Of the other three species, Veronica chamaedrys showed reduced performance with all tested AMF. Mixture-type plants generally grew better than monoculture-type plants, which suffered less leaf damage by pathogens. This suggests that plant mixtures were selected for increased growth at the expense of reduced defence and the opposite happened in plant monocultures. Cases of co-adaptation between AMF and plants from mixtures or AMF and plants form monocultures were rare and mostly in the direction of increased parasitism of the AMF, suggesting an arms-race leading to reduced performance of plant partners.
Gaps in kelp cover may threaten the recovery of California sea otters

Despite more than a century of federal protection, the California sea otter Enhydra lutris nereis remains threatened under the U.S. Endangered Species Act (ESA), and the population has not appreciably expanded its range in two decades. Here, we examine a novel dataset of 725 sea otter live strandings from 1984–2015 to gain insights into demographic and environmental factors underlying threats to sea otter recovery. Using multinomial logistic regression to evaluate spatiotemporal patterns of stranding causes, we demonstrate that increases in stranding rates, particularly outside the range center, are related to a substantial increase in shark bites. By contrast, trauma linked to human activities has declined dramatically, and now accounts for less than 5% of stranding cases. Within the range core, where the sea otter population seems regulated by prey availability, symptoms of energetic stress represent more than 63% of all strandings and are strongly associated with high sea otter density. Conversely, in range peripheries, the majority of strandings are caused by shark bite and neurological disease. Notably, these threats are virtually absent where nearshore habitat is characterized by at least 10% kelp canopy cover. Our analyses reveal that declining kelp cover may therefore constrain the population’s spatial expansion and recovery in two key ways. Absence of kelp intensifies density-independent threats in the range peripheries, and likely limits dispersal of reproductive females, which depend on kelp canopy for nursery habitat. These results highlight the significance of both top-down and bottomup processes in population dynamics, and inform an ecosystem-based approach to conservation planning.
Evaluation of Chemical Termination Options for Cover Crops

Abstract Cover crop acreage has substantially increased over the last few years due to the intent of growers to capitalize on federal conservation payments and incorporate sustainable practices into agricultural systems. Despite all the known benefits, widespread adoption of cover crops still remains limited due to potential cost and management requirements. Cover crop termination is crucial, because a poorly controlled cover crop can become a weed and lessen the yield potential of the current cash crop. A field study was conducted in fall 2015 and 2016 at the Arkansas Agricultural Research and Extension Center in Fayetteville to evaluate preplant herbicide options for terminating cover crops. Glyphosate-containing treatments controlled 97% to 100% of cereal rye and wheat, but glyphosate alone controlled less than 57% of legume cover crops. The most effective way to control hairy vetch, Austrian winterpea, and crimson clover with glyphosate resulted from mixtures of glyphosate with glufosinate, 2,4-D, and dicamba. Higher rates of auxin herbicides improved control in these mixtures. Glufosinate alone or in mixture controlled legume cover crops 81% or more. Paraquat plus metribuzin was effective in terminating both cereal and legume cover crops, with control of cereal cover crops ranging from 87% to 97% and control of legumes ranging from 90% to 96%. None of these herbicides or mixtures adequately controlled rapeseed. Nomenclature: 2,4-D; dicamba; glufosinate; glyphosate; metribuzin; paraquat; Austrian winterpea, Lathryrus hirsutus L. ; cereal rye, Secale cereale L. ; crimson clover, Trifolium incarnatum L. ; hairy vetch, Vicia villosa Roth; rapeseed, Brassica napus L. ; wheat, Triticum aestivum L.
Growth performance, carcase characteristics and meat quality of crossbred bulls and heifers from double-muscled Belgian Blue sires and Brown Swiss, Simmental and Rendena dams

Abstract Growth, conformation, carcase and meat quality traits of crossbred calves obtained in the Alps from selected Belgian Blue sires (BB) and Brown Swiss (BS), Simmental (Si) and Rendena (Re) dams were studied, emphasising differences on dairy and dual purpose maternal breed. Six pens with five heifers (3 BB × BS, 1 BB × Si, 1 BB × Re) and six pens with four young bulls (2 BB × BS, 1 BB × Si, 1 BB × Re) were used. In total 53 crossbred calves were tested: 30 from BS dams and 23 from dual purpose (12 from Si and 11 from Re dams). Growth performances were measured, carcases were scored for muscle conformation and fatness, the fifth rib was dissected, and the Longissimus thoracis (LT) was analysed. The maternal breed had significant effects when the calves from dairy cows (BB × BS) were compared to those of the dual purpose breeds (BB × Si and BB × Re), as at slaughter the former were 1.2% taller, 6.0% less in vivo muscle score, 5.0% less carcase muscle score, with a 13% greater proportion of bone in the rib, and their LT had 12.5% less drip losses, but 3% greater cooking losses and 25% greater shear force. It was concluded that when using a BB as a sire, the dam breed has influence on the growth performance traits of the derived crossbreds, but the major influence would regard the carcase and meat quality traits. In the Alps, these differences are reflected in different sold prices of the crossbred calves from dairy and dual purpose breeds at local auctions.
End-To-End Time-Lapse Video Synthesis From a Single Outdoor Image

Time-lapse videos usually contain visually appealing content but are often difficult and costly to create. In this paper, we present an end-to-end solution to synthesize a time-lapse video from a single outdoor image using deep neural networks. Our key idea is to train a conditional generative adversarial network based on existing datasets of time-lapse videos and image sequences. We propose a multi-frame joint conditional generation framework to effectively learn the correlation between the illumination change of an outdoor scene and the time of the day. We further present a multi-domain training scheme for robust training of our generative models from two datasets with different distributions and missing timestamp labels. Compared to alternative time-lapse video synthesis algorithms, our method uses the timestamp as the control variable and does not require a reference video to guide the synthesis of the final output. We conduct ablation studies to validate our algorithm and compare with state-of-the-art techniques both qualitatively and quantitatively.
Spliceosomal Introns: New Insights into Their Evolution Dispatch

A new genome-wide analysis of spliceosomal introns indicates massive loss and gain of introns has taken place in many eukaryotic lineages. Only a small subset of the analyzed introns was present in the common ancestor of plants, fungi, animals and Plasmodium. Since introns were discovered in 1977 [1], a continuing debate has raged over their origin, evolution, potential role in the evolution of genes and possible benefit for the host organism. Currently, all known introns can be divided into three groups based on their splicing mechanism. Group I and group II introns are self-splicing; group II introns are abundant in Bacteria and were recently found in the Archaeal genus Methanosarcina [2]. The third group of introns, the so-called spliceosomal introns, require a sophisticated complex consisting of small nuclear RNAs (snRNAs) and proteins — the spliceosome — to splice out of heterogeneous nuclear (hn)RNA to form messenger (m)RNA. Spliceosomal introns are found only among the Eukaryotes; they are widely distributed throughout the Eukaryotic domain, including the presumably deep-branching eukaryotes Giardia lamblia and Carpediemonas membranifera where a few spliceosomal introns were recently discovered [3,4].