Miracle-dz/UniFAR-FTUs huggingface dataset:
Graph-guided assembly for novel HLA allele discovery

Accurate typing of human leukocyte antigen (HLA), a histocompatibility test, is important because HLA genes play various roles in immune responses, and have also been shown to be associated with many diseases such as cancer. The current gold standard for HLA typing uses DNA sequencing technology combined with sequence enrichment techniques using specially designed primers or probes, causing it to be slow and labor-intensive. Although there exist enrichment-free computational methods that use various types of sequencing data, hyper-polymorphism found in HLA region of the human genome makes it challenging to type HLA genes with high accuracy from whole genome sequencing data. Furthermore, these methods are database-matching approaches where their output is inherently limited by the completeness of already known types, forcing them to find the best matching known alleles from a database, thereby causing them to be unsuitable for discovery of rare or novel alleles. In order to ensure both high accuracy as well as the ability to type novel alleles, we have developed a graph-guided assembly technique for classical HLA genes, which is capable of assembling phased, full-length haplotype sequences of typing exons given high-coverage (>30-fold) whole genome sequencing data. Our method delivers highly accurate HLA typing, comparable to the current state-of-the-art database-matching methods. We also demonstrate that our method can type novel alleles by experimenting on various data including simulated, Illumina Platinum Genomes, and 1000 Genomes data.
Are free-floating planktonic hydroids (Cnidaria, Hydrozoa) common components of the pelagic fauna from the South Brazilian Bight?

We analysed 267 zooplankton samples collected in the South Brazilian Bight (SBB; 23–27°S) to determine whether hydroids, typically benthic, are common components of the pelagic SBB. Two species, Clytia arborescens, recorded for the first time in the Atlantic Ocean, and Clytia sp. were identified. While these planktonic hydroids were frequent or relatively so in shallow shelf waters (~23% of the samples <50 m isobaths, and 5% of the samples >100 m), abundances were low (up to 61 hydranths m−3) suggesting a low trophic impact. Such colonies are probably fragments of benthic colonies detached by storms and/or tides. Given the good condition of the coenosarc, existence of gastric content, and presence of reproductive structures, development of these species appears to be normal in the pelagic environment. Existence in the plankton may increase their capacity for dispersion.
First observations of living sea-ice diatom agglomeration to tintinnid loricae in East Antarctica

Tintinnid ciliates are an important link in marine food webs as they feed on phytoplankton and bacteria while providing nutrients to higher trophic levels. Tintinnids are known to agglutinate mineral particles or dead biogenic material such as diatom frustules to their shell-like housing (lorica), however, reasons for this agglutination remain questioned. We report on our observation of agglomeration of the living diatoms Fragilariopsis curta, F. cylindrus, F. pseudonana and F. rhombica to loricae of the Antarctic tintinnid ciliates Laackmanniella naviculaefera and Codonellopsis gaussi. These unusual associations between living diatoms and tintinnids were exclusively observed south of 63.59°S. We discuss the significance of our new finding and generate hypotheses to be tested by future research. It remains unclear where these living diatom–tintinnid associations are initially formed (in or near sea ice or also further north when abundances of L. naviculaefera, C. gaussi, F. curta, F. cylindrus, F. pseudonana and F. rhombica happen to be relatively high); who the beneficiary is in this association; what the exact benefits are; and how they might influence the Southern Ocean carbon cycle. Nevertheless, our observation provides a key step forward towards illuminating the largely unknown ecology of two Southern Ocean-endemic tintinnid species.
Crop production structure and stability under climate change in South America

1 Departamento Protección de Cultivos, Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (CSIC), Córdoba, Spain 2 Center of Applied Ecology & Sustainability (CAPES), Pontificia Universidad Católica de Chile, Santiago, Chile 3 Laboratorio Internacional de Cambio Global, LINCG (CSIC-PUC), Santiago, Chile 4 Departamento de Ecología, Pontificia Universidad Católica de Chile, Santiago, Chile
Effect of selected polymorphisms of genes lep, MTHFR and FTO to BMI level and gender-specificity

The aim of this study is to investigate the effect of selected polymorphisms LEP (G2548A), MTHFR (C677T) and FTO ( rs1121980 ) on body mass index in humans. In the study participated 79 people from Slovakia with some genetic relatedness. Genomic DNA was isolated from the buccal swabs using a commercial kit Qiagen DNA Mini Kit (Qiagen). The detection of SNP polymorphisms in human genes LEP, MTHFR and FTO was performed using molecular genetics methods such as PCR-RFLP and ARMS. The most common genotypes in all 3 polymorphism were found in heterozygous form (for LEP AG = 0.5190, for MTHFR CT = 0.519, for FTO CT =0.4051). The LEP gene had increased frequency of G allele (0.5506), the MTHFR gene T allele (0.6646) and FTO gene T allele (0.50635). The least frequent genotype in LEP was AA (0.1899), in MTHFR was TT (0.0759), in FTO it was CC (0.2911). According to the results we can assume that the genotypes AA (LEP G2548A), CC (FTO rs1121980 ) and TT (MTHFR C677T) in case of women have a protective effect on the prevalence of obesity, based on BMI, compared to the other genotypes and this polymorphism is gender-specific. Added anthropometric measurements, blood test and extension of the group in the future evaluation could increase the statistical relevance in relation to obesity and gender-specificity.
Pendugaan Komponen Ragam, Heritabilitas dan Korelasi untuk Menentukan Kriteria Seleksi Cabai (Capsicum annuum L.) Populasi F5

ABSTRACT Information on genetic variability and correlation between quantitative characters with yield are important for support the selection program. The objective of the research was to estimate the genetic variability, heritability, and path analysis on agronomic characters to determine the selection criteria in the chili. This research was conducted at Research Station of Leuwikopo, Darmaga, Bogor from November 2009 until May 2010. This research observed all populations i.e. F5 population: 320 plants, IPB C2 population: 20 plants, and IPB C5 population: 20 plants. The results showed that total fruit weight, thick and fruit diameter, middle fruit diameter, blossom end fruit diameter, fruit weight, and days to flowering have a high broad sense heritability . High coefficient of genetic variability values were obtained ini number of fruits per plant, fruit wei ght, stem diameter, fruit diameter, and fruit weight. Based on the heritability, genetic variability, correlations analysis and path analysis, characters that can be used as selection criteria in this study is the number of fruit per plant, fruit weight, and fruit diameter. Key words: genetic variability, heritability, path analysis, selection
Pengaruh sitokinin dan paklobutrazol terhadap pertumbuhan dan hasil benih kentang (Solanum tuberosum L.) G2 kultivar granola dengan sistem nutrient film technique

Percobaan ini dilakukan untuk mengetahui pengaruh sitokinin dan paklobutrazol terhadap pertumbuhan dan hasil benih kentang ( Solanum tuberosum L.) G 2 kultivar Granola dengan menggunakan sistem Nutrient Film Technique . Percobaan dilakukan di rumah plastik CV. Alam Pasundan, Cibiru, Bandung dari bulan April sampai dengan Agustus 2014 dengan ketinggian lokasi penelitian ± 700 m dpl. Rancangan perco-baan yang digunakan adalah Rancangan Acak Kelompok dengan enambelas perlakuan dan masing-masing terdiri dari tiga ulangan. Perlakuan yang digunakan adalah : A (kontrol), B (25 ppm sitokinin), C (50 ppm sitokinin), D (75 ppm sitokinin), E (50 ppm paklobutrazol), F (100 ppm paklobutrazol), G (150 ppm paklobutrazol), H (25 ppm sitokinin + 50 ppm paklobutrazol), I (25 ppm sitokinin + 100 ppm paklobutrazol), J (25 ppm sitokinin + 150 ppm paklobutrazol), K (50 ppm sitokinin + 50 ppm paklobutrazol), L (50 ppm sitokinin + 100 ppm paklobutrazol), M (50 ppm sitokinin + 150 ppm paklobutrazol), N (75 ppm sitokinin + 50 ppm paklobutrazol), O (75 ppm sitokinin + 100 ppm paklobutrazol), P (75 ppm sitokinin + 150 ppm paklobutrazol). Hasil perco-baan menunjukan bahwa terdapat pengaruh pemberian kombinasi konsentrasi sitokinin dan paklobutrazol terhadap tinggi tanaman, jumlah daun majemuk, bobot segartanaman, dan bobot kering tanaman, tetapi tidak terdapat pengaruh terhadap komponen hasil. Pemberian sitokinin dan paklobutrazol masih belum mampu meningkatkan hasil benih kentang. Kata kunci : Benih ∙ Kentang ∙ Sitokinin, paklobutrazol ∙ Nutrient film technique
Inducción in vitro de brotes de dos cultivares de aguacate raza Mexicana Persea americana var. drymifolia Schltdl. & Cham* In vitro induction seedlings to two cultivars Mexican race avocado Persea americana var. drymifolia Schltdl. & Cham

One approach micropropagation avocado rootstock is the multiplication of commercial interest. In the present study aimed to identify the suitable culture medium for the stages of establishment and induction of buds of cultivars Huevo de Toro and butter, for which settled internodal segments with axillary buds (micropiles) in the media MS, DCR and Yasuda culture, added with 2 mg L -1 of 6-benzylaminopurine (BAP), 0.3 mg L -1 indolbutirico acid (AIB), 2 g L -1 of oxytetracycline and 2 g L -1 benomyl. The variables contamination, oxidation and viability of the explants were evaluated 14 days after sowing. The culture medium was Yasuda stage suitable for aseptic accommodation which induced the most viable explants (> 40%). These were subcultured in mass seedlings induction, MS, DCR and Yasuda supplemented with 20% coconut water (AC), 2 mg L -1 BAP, 0.5 mg L -1 of gibberellic acid (AG3) and 0.01 mg L -1 indoleacetic acid (AIA) (M1, M2 and M3); 2 g L -1 casein hydrolyzate (CH), 1 mg L -1 BAP and 0.3 mg L -1 AIB (M4, M5 and M6). The number of seedlings s per explants, seedlings length and number of leaves at 60 and 90 days subculture was evaluated. In the growing Huevo de Toro, M1 and M2 are satisfactory means for the proliferation of seedlings values 1.19-1.5, 1.07-1.09 cm
Alterations in yield, physicochemical components and mineral composition of onion following organic manure and inorganic nitrogen application

ABSTRACT Onion is the one of the most important vegetable crops grown extensively throughout the world; hence, understanding the response of the crop to the form and amount of N provided is of immense importance. In a field experiment, poultry and cattle manure (at 10 t/ha) were compared with four inorganic nitrogen (N) application levels (0, 60, 90 and 120 kg N/ha), and six combinations of manure and N applications were investigated. Plant growth and total yield (kg/ha) significantly increased, when N application increased from 0 to 120 kg/ha, with or without added poultry manure. Plant height, leaf number and neck thickness were significantly reduced at 0 kg/ha N plus cattle manure. The bulb ascorbic acid concentration significantly increased with the use of poultry manure (15.94 mg/100 g) and cattle manure (15.94 mg/100 g), compared with 120 kg/ha inorganic N (11.42 mg/100 g). No significant effects were observed on total phenolics and total soluble solids of onion bulbs following the different fertiliser treatments. Cattle manure increased P and K concentrations, whilst poultry manure significantly increased Zn and Fe concentrations in onion bulbs. Onion bulb Ca and Mg concentrations were lower when cattle manure (0.19% and 0.12%) was used than when other organic or inorganic fertilisers were used. Therefore, organic manure increases the concentrations of certain minerals in onions, compared with inorganic N application, without negatively affecting bulb size.
Non-viral induction of transient cell reprogramming in skeletal muscle to enhance tissue regeneration

Somatic cells can be reprogrammed to pluripotency in vivo by overexpression of defined transcription factors. While their sustained expression triggers tumorigenesis, transient reprogramming induces pluripotency-like features and proliferation only temporarily, without teratoma formation. We sought to achieve transient reprogramming within mouse skeletal muscle with a localized injection of plasmid DNA (pDNA) and hypothesized that this would enhance regeneration after severe injury. Intramuscular administration of reprogramming pDNA rapidly upregulated pluripotency (Nanog, Ecat1, Rex1) and early myogenesis genes (Pax3) in the healthy gastrocnemius of various mouse strains. Mononucleated cells expressing such markers appeared promptly in clusters among myofibers, but proliferated only transiently and did not lead to the generation of teratomas. Nanog was also upregulated in the gastrocnemius when reprogramming factors were administered 7 days after laceration of its medial head. Enhanced tissue regeneration after reprogramming was manifested by the accelerated appearance of centro-nucleated myofibers and reduced fibrosis. These results suggest that in vivo transient reprogramming may constitute a novel strategy towards the acceleration of regeneration following muscle injury, based on the induction of transiently-proliferative, pluripotent-like cells in situ. Further research to achieve clinically meaningful functional regeneration is warranted.
Status of cassava mosaic begomoviruses in farmers’ fields in Ghana

A survey for cassava mosaic disease (CMD) was carried out in Ghana from 2007−2008 to determine the status of cassava mosaic begomoviruses in farmers’ fields. The survey covered cassava growing areas in five major cassava producing regions of Ghana. Out of 136 fields visited, the plants in 5% were not affected by CMD, 18% contained plants with mild symptoms, whereas 77% had cassava with moderately severe or severe symptoms. A total of 412 cassava leaf samples and a symptomatic Manihot glaziovii sample were analyzed using polymerase chain reaction. African cassava mosaic virus (ACMV) alone was detected in 42.0% of symptomatic cassava leaves with the remaining 58% being mixed infected by ACMV and Eas t African cassava mosaic virus (EACMV). Mixed ACMV and EACMV infections were detected in symptomatic M. glaziovii , two non-symptomatic cassava samples and in individual whitefly vectors. EACMV was not detected alone in any cassava or whitefly sample. South African cassava mosaic virus (SACMV), Indian cassava mosaic virus (ICMV), East African cassava mosaic Zanzibar virus (EACMZV) and the Uganda strain of EACMV were not detected in any cassava or whitefly sample. The occurrence of high proportion of mixed infections of cassava by cassava mosaic begomoviruses (CMBs), which could lead to emergence of new species or variants in the country, require concerted effort to mitigate the CMD problem.
Performance of the newly identified endoparasitoid Cotesia icipe Fernandez‐Triana & Fiaboe on Spodoptera littoralis (Boisduval)

Cotesia icipe Fernandez‐Triana & Fiaboe is a solitary koinobiont larval endoparasitoid, recently discovered in Kenya and new to science, that parasitizes select lepidopteran herbivores of amaranth. We investigated its host range on five commonly encountered amaranth lepidopteran defoliators. Cotesia icipe accepted, successfully and aggressively parasitized the amaranth noctuid defoliators Spodoptera littoralis (Boisduval) and Spodoptera exigua (Hübner), but failed to parasitize Herpetogramma bipunctalis (F.), Spoladea recurvalis (F.) and Udea ferrugalis (Hübner) all in Crambidae family. On S. littoralis, C. icipe was highly efficient, with 95% of females successfully ovipositing during 2 hr of exposure. Parasitism rate and larval and pupal non‐reproductive mortalities were significantly higher at higher parasitoid density. A single female of C. icipe parasitized 42.99 ± 2.66% of the 50 exposed larvae for oviposition in 24 hr, whereas a cohort of five females of C. icipe conferred 85.59 ± 1.46% parasitism rate. The efficiency ratio per female was much higher in single releases than in cohort releases while a balanced sex ratio was obtained in F1 offspring regardless of the density of female released. The potential use of C. icipe for conservation and augmentative biological control of S. littoralis in amaranth as well as its potential use against other Noctuid moths and in other commodities is discussed.
Remodeling Pathway Control of Oxidative Phosphorylation by Temperature in the Heart

The capacity of mitochondrial oxidative phosphorylation (OXPHOS) and fuel substrate supply are key determinants of cardiac muscle performance. Although temperature exerts a strong effect on energy metabolism, until recently numerous respiratory studies of mammalian mitochondria have been carried out below physiological temperature, with substrates supporting submaximal respiratory capacity. We measured mitochondrial respiration as a function of temperature in permeabilized fibers from the left ventricle of the mouse heart. At 37 °C, OXPHOS capacity with electron entry through either Complex I or Complex II into the Q-junction was about half of respiratory capacity with the corresponding physiological substrate combination reconstituting tricarboxylic acid cycle function with convergent electron flow through the NADH&succinate (NS) pathway. When separating the component core mitochondrial pathways, the relative contribution of the NADH pathway increased with a decrease of temperature from 37 to 25 ºC. The additive effect of convergent electron flow has profound consequences for optimization of mitochondrial respiratory control. The apparent excess capacity of cytochrome c oxidase (CIV) was 0.7 above convergent NS-pathway capacity, but would be overestimated nearly 2-fold with respect to respiration restricted by provision of NADH-linked substrates only. The apparent excess capacity of CIV increased sharply at 4 °C, caused by a strong temperature dependence of and OXPHOS limitation by NADH-linked dehydrogenases. This mechanism of mitochondrial respiratory control in the hypothermic mammalian heart is comparable to the pattern in ectotherm species, pointing towards NADH-linked mt-matrix dehydrogenases and the phosphorylation system rather than electron transfer complexes as the primary drivers of thermal sensitivity at low temperature and likely modulators of temperature adaptation and acclimatization. Delineating the link between stress and remodeling of OXPHOS is critically important for improving our understanding of metabolic perturbations in disease evolution and cardiac protection. Temperature is not a trivial experimental parameter to consider when addressing these questions.
Identification of Mutations, Expression Alterations and Fusion Transcriptsby Next Generation RNAseq in Castration-Resistant Prostate Cancer Celllines with Possible Clinical Relevance

Androgen Deprivation Therapy (ADT) would benefit prostate cancer patients initially but cancer cells can eventually develop castration resistance. In this study, we compared androgen-dependent and androgenindependent cell lines to find potential genes associated with acquired resistance to ADT. Using RNAseq, we found 4397 mutations distributed in 2579 genes, out of which, 1574 mutated genes could also be found in prostate cancer tumor samples collected in Cosmic database (http://cancer.sanger.ac.uk/cosmic). We also discovered 157 and 549 genes which were down and up-regulated respectively in both PC3 and DU145 compared to LNCaP. Network analysis resulted in 3 dominant connection notes: GCR/MCR (NR3C1) and PKA-cat kinase (PRKACB) and PKC family (PRKD1). By ChimeraScan analysis, 48, 117 and 60 chimeric transcripts were discovered in DU145, LNCaP and PC3 respectively. Among them, six predicted fusions expressed specifically in androgen-independent cell lines (DU145 and PC3). Some of these gene mutations and transcription alterations have been reported in tumor samples from prostate cancer patients and may have certain associations with acquired resistance to anti-hormone therapy in prostate cancer. A proportion of mutations are enriched in genes involved in immune response pathways, suggesting new targets to develop effective treatments to overcome castration resistance.
Neural Control and Precision of Spike Phasing in Flight Muscles

Rhythmic locomotor behavior in animals requires exact timing of muscle activation within the locomotor cycle. Neural strategies for timing control that employ higher brain function, however, suffer from synaptic and neural transmission delays, making them inefficient for control of fast-frequent locomotor systems. Evolutionary pressure on muscle timing control is particularly pronounced in flying insects with wing flapping periods of few milliseconds. In these animals, sensory integration is often achieved at the level of the peripheral nervous system, circumventing the central brain and controlling spike activation phases with little delay, rather than muscle spike frequency. This review is engaged in the precision with which flies adjust power output of their flight muscles and highlights the significance of visual and proprioceptive feedback loops for muscle spike control. Recent results suggest that in flies peripheral feedback loops are keys enabling precise heading control and body stability in flight, and potentially similar to the function of local circuits for locomotor control found in the spinal chord of vertebrates.
Microarray Analysis of Gene Expression in Triploid Black Poplar

Abstract Triploidy is a widespread phenomenon in cultivated and natural breeding plants and it can confer some growth advantages. Here, we analyzed genome-wide gene expression in triploid Populus euramericana (black poplar) using the Affymetrix poplar microarray to detect any possible correlation between triploid vigor and a unique gene expression profile. Among the 38,400 transcripts that were detected in triploid poplar, 1,564 and 2,015 genes were up- or downregulated, respectively, compared with the diploid. The majority of the upregulated genes in the triploid were associated with carbon and nitrogen metabolism, especially lignin and secondary metabolism. Other genes upregulated in the triploid included genes involved in sugar transport, and brassinosteroid (BR) and auxin metabolism. Downregulated genes were mostly related to the assembly and biosynthesis of ribosomes and the nucleosome macromolecular complex. The results suggested that BR and auxin levels were crucial in controlling sugar transport, photosynthesis and cell wall biosynthesis. Downregulated genes were associated with chromatin regulation in the triploid. The information from this analysis could provide an insight into the vigor of triploid poplar.
New Taxa for Marine Fungi from Western Coast of Libya

Background: Marine fungi can be found in every marine habitat and are important organisms from ecological and biotechnological perspectives. However, there is little information on marine fungi in Libya. Objective: To report on marine fungi species from Libya. Method: Organisms were isolated from drift wood and phanerogamic plant remains from six different locations along the western coast of Libya. The collected specimens were examined under light microscope and standard identification keys were used. Result and Conclusion: Thirteen marine fungal species have been identified from driftwood and phanerogamic plant remains. These species belong to the classes Ascomycetes (eleven species) and Hyphomycetes (two species). The identified organisms were not reported previously from Libya. More studies are needed in the future to address the importance of marine fungi ecologically and biotechnologically in Libya.