Miracle-dz/UniFAR-FTUs huggingface dataset:
New insight into bulb dynamics in the vacuolar lumen of Arabidopsis cells

Plant vacuoles are multifunctional organelles with dynamic and transient membranous structures, such as trans-vacuolar strands and bulbs. Bulbs are highly mobile structures that travel along trans-vacuolar strands. A candidate effector protein from Melampsora larici-populina (Mlp124357) fused with the enhanced green fluorescent protein (eGFP) was used to investigate the properties of central vacuoles and their bulbs. We discovered the coexistence of two bulb populations in Arabidopsis cells. In addition to previously-described bulbs, which present even marker protein distribution on the bulb surface, we discerned bulbs displaying irregular fusion protein distribution. Using fluorescence recovery after photobleaching (FRAP), we also demonstrated that bulbs do not exchange proteins with the tonoplast once they are formed. These results show that more than one type of bulb may co-exist in the same cell and provide evidence of micro-domains on the bulb surface. They also reveal that proteins do not flow freely from the tonoplast to the bulb membrane, giving new insight into the biology of tonoplast-derived substructures.
Mutations in the Drosophila splicing regulator Prp31 as a model for Retinitis pigmentosa 11

Retinitis pigmentosa is a clinically heterogeneous disease affecting 1.6 million people worldwide. A growing number of identified disease-causing genes are associated with the spliceosome, but the molecular consequences that link defects in splicing factor genes to the aetiology of the disease remain to be elucidated. In this paper, we present a Drosophila model for Retinitis pigmentosa 11, a human disease caused by mutations in the splicing factor PRPF31. Here, we induced mutations in the Drosophila orthologue Prp31. Mutant flies are viable and show a normal eye phenotype when kept under regular light conditions. However, when exposed to constant light, photoreceptors of mutant flies degenerate, thus resembling the human disease phenotype. Degeneration could be shown to be associated with increased oxidative stress. This increase was in agreement with severe dysregulation of genes involved in oxidation/reduction processes, as revealed by high throughput transcriptome sequencing. In fact, light induced photoreceptor cell degeneration could be attenuated by experimentally reducing oxidative stress. A comparable decrease in retinal degeneration was achieved by raising mutant larvae on a vitamin A-depleted medium, thereby reducing rhodopsin levels. Finally, transcriptome data further uncovered an overall retention of introns in mRNAs. Among those, mRNAs of genes involved in synapse assembly, growth and stability were most prominent. These results point to a multifactorial genesis of light induced degeneration in retinae of Prp31 mutant flies, including transcriptional and splicing dysregulation, oxidative stress and defects in vitamin A metabolism.
UJI EFEKTIFITAS FORMULA SPRAY DARI MINYAK ATSIRI HERBA KEMANGI (Ocimum Sanctum L ) SEBAGAI REPELLENT NYAMUK Aedes aegypti

Dengue fever is transmitted by the bite of Aedes aegypti mosquitoes infected with denguevirus. Preparations antinyamuk much use of harmful chemicals such as DEET (diethylmetatoluamide) and permethrin that can lead to pollution of the environment, leavingno residue and cause resistance to the drug. To determine the activity of essential oils from herbs basil (Ocimum Sanctum L) in the preparation of spray as a mosquito repellent and determine the effective concentrationof the spray.This type of research is True experiment with design Post Test Only Control Group Design. Repellent activity was observed by means of spray is sprayed on the back of the hand probandus, then tested on female mosquitoes with the introduction into the cage containing20 mosquitoes each treatment. Spray essential oils showed repellent activity of Aedes aegypti with a value of correlation r = 0.964 higher concentration of essential oils the fewer mosquitoes that land. Spray herbal essential oil of basil (Ocimum basilicum L) has a repellent activitycompared to the negative control. The effectiveness of the herb basil essential oil sprayobtainedat 74.131 ppm lC50 and lC90 of 775.711 ppm
Growth performance, nutrient digestibility, and selected fecal microbiota are improved by β-glucan supplementation in weaner pigs

Abstract This study was conducted to evaluate the effects of dietary β-glucan supplementation on growth performance, nutrient digestibility, blood profiles, and fecal characteristics in weaner pigs. A total of 140 weaner pigs [(Yorkshire × Landrace) × Duroc] with an average body weight of 6.37±1.14 kg were allotted to one of the following dietary treatments: 1) negative control (NC, basal diet); 2) positive control (PC, basal diet supplemented with 39 ppm Tiamulin); 3) basal diet supplemented with 0.1% β-glucan (G1); 4) basal diet supplemented with 0.2% β-glucan (G2). During days 22 to 42 and 1 to 42, pigs offered PC and G2 diets grew faster than those offered NC diet (P<0.05). Additionally, during the same periods, pigs fed G2 and PC diets exhibited improved gain:feed ratio compared to pigs receiving NC and G1 diets (P<0.05). Pigs fed G2 diet exhibited higher coefficient of total tract apparent digestibility of dry matter than those fed NC diet (P<0.05). There were no differences on blood profiles, fecal scores, fecal moisture, and fecal pH (P>0.05). Fecal lactic acid bacteria counts in G2 treatment were higher compared with PC and NC treatments (P<0.05). Coliform bacteria concentrations were decreased in pigs fed PC and G2 diets compared with those fed NC diet (P<0.05). In conclusion, the results of the current study indicate that dietary supplementation of 0.2% β-glucan can improve growth performance and dry matter digestibility, increase fecal lactic acid bacteria concentration but decrease fecal coliform bacteria concentration in weaner pigs.
Interscapular brown adipose tissue recruitment is hindered by a temperature environment of 33°C: uncoupling protein-1 underexpression is not associated with obesity development in rats

Paper description: In rat’s brown adipose tissue (BAT), cold environment recruits adipocytes, stimulates Uncoupling protein-1 (UCP-1) expression and development of specific, uncoupled mitochondria (UC-mitochondria). The authors showed that at thermoneutral environment of 33°C, rat pups failed to recruit BAT. The tissue remains atrophic, composed of preadipocytes and adipocytes that are smaller but packed with lipids and UC-mitochondria, having 9-fold less of UCP-1 and newly described intramitochondrial inclusions. In BAT of pups raised at 33°C, underexpression of UCP-1 does not lead to obesity; lack of UCP-1 does not affect proliferation of UC-mitochondria but may contribute to development of intramitochondrial inclusions. Abstract: Brown adipose tissue (BAT) generates heat due to unique thermogenic UC-mitochondria, an event known as nonshivering thermogenesis. Cold, adrenergic agents, hormones, etc., activate nonshivering thermogenesis, resulting in lipid mobilization, an increase in the mitochondria and mitochondrial cristae, and increased uncoupling protein-1 (UCP1) expression and its incorporation into mitochondrial cristae. BAT precursor cells mature and contribute to BAT growth in a process known as BAT recruitment. For the first time, we herein report the effect of a thermoneutral environment of 33°C on interscapular BAT (IBAT) in rats delivered and raised at 33°C. The control animals were housed at 20°C. Thermoneutral IBAT was atrophic (73 mg vs. 191 mg) but with more adipocyte precursor cells; euthermia (37.6°C) was maintained without nonshivering thermogenesis. Although IBAT was inactive, the thermoneutral animals did not develop obesity, and on the contrary, the thermoneutral environment of 33°C hindered the rats’ growth, weight (65 gm vs. 139 gm), volume (67 gm vs.136 gm) and length (12 cm vs. 16 cm). The thermoneutral brown adipocytes were smaller (7234 µm 3 vs. 9198 µm 3 ) with more lipids (4919 µm 3 vs. 4507 µm 3 ) and a smaller mitochondrial cristae area (52504 µm 2 vs. 61288 µm 2 /adipocyte). Lipoprotein lipase mRNA expression was 11% (vs. 58% in control) and UCP1 mRNA expression was 34% (vs. 93% control). UCP1 immunoelectron microscopic study detected 160 UCP1-gold particles (vs. 700 in control) per UC-mitochondrion; thermoneutral brown adipocytes had 9-fold fewer UCP1-gold particles (0.34x10 6 vs. 2.99x10 6 UCP1-gold particles), and thermoneutral UC-mitochondria developed specific intramitochondrial tubular inclusions. https://doi.org/10.2298/ABS171215018J Received: December 15, 2017; Revised: March 7, 2018; Accepted: April 18, 2018; Published online: May14, 2018 How to cite this article: Juric-Lekic G, Bedrica Lj, Loncar D. Interscapular brown adipose tissue recruitment is hindered by a temperature environment of 33°C: Uncoupling protein-1 underexpression is not associated with obesity development in rats. Arch Biol Sci. 2018;70(3):…
De nouveaux systèmes hôtes-virus associés aux sources hydrothermales océaniques profondes

Nos connaissances sur la diversite virale associee aux micro-organismes presents dans les sources hydrothermales oceaniques profondes restent encore limitees. Seules quelques etudes concernant l’abondance virale et l’impact de ceux-ci sur la mortalite microbienne dans ces ecosystemes sont disponibles. En effet, seuls 6 bacteriovirus et 2 archeovirus provenant de ces ecosystemes ont ete caracterises a l’heure actuelle. Les deux archeovirus infectent des archees anaerobies hyperthermophiles appartenant a l’ordre des Thermococcales et ont ete decrits au laboratoire.Afin d’etendre nos connaissances sur la diversite virale associee aux micro-organismes colonisant ces environnements, il a ete decide d’elargir les recherches a l’ordre bacterien des Thermotogales. Cet ordre bacterien est compose de bacteries chimio-organotrophes anaerobies en majorite thermophiles ou hyperthermophiles. De nombreux transferts lateraux de genes ont contribue a l’histoire evolutive des Thermotogales supposant une forte implication des virus dans celle-ci. Ces travaux de these ont permis la caracterisation fonctionnelle et genomique de deux nouveaux siphovirus, MCV1 et MCV2, infectant deux souches de Marinitoga camini. Ces souches ont ete isolees de deux sites hydrothermaux profonds (Menez Gwen et Lucky Strike) au niveau de la dorsale medio-atlantique. Ces virus mettent en oeuvre un cycle lysogenique avec une production basale sans induction relativement haute (>107 virions/ml). Une comparaison de ces deux genomes viraux a celui de MPV1, virus precedemment isole de Marinitoga piezophila, a ete realisee, revelant la presence de nombreuses similarites. Un core genome de 35 ORFs partage par ces trois genomes a ete identifie, incluant des proteines impliquees dans le metabolisme de l’ADN, l’assemblage des virions et le cycle lysogenique. Des proteines hypothetiques ont aussi ete identifiees parmi ces genes communs, elles portent donc probablement des fonctions importantes pour ces bacteriovirus. Par ailleurs, 60% des genes de ces virus ayant une correspondance dans les bases de donnees, apres exclusion des Thermotogales, partagent des similarites avec lesFirmicutes et les bacteriovirus qui leurs sont associes. Le genome d’une autre Thermotogales, Thermosipho sp. AT1244-VC14 a ete etudie ainsi que son systeme CRISPR-cas. Ces resultats indiquent que cette souche, qui porte un systeme CRISPR-cas qui semble complet et fonctionnel, a probablement deja ete infectee par MCV1, MCV2 ou un virus similaire. Ces travaux permettent d’etendre nos connaissances sur les virus portes par les bacteries du phylum Thermotogae, encore peu decrits a ce jour. Les elements genetiques mobiles associes a ce phylum sont particulierement interessants car ils ont probablement eu un impact important dans l’evolution de ces communautes microbiennes ainsi que dans leur adaptation aux conditions physico-chimiques extremes et fluctuantes presentes dans les ecosystemes qu’elles colonisent.
Ontogenetic changes in diet, feeding behaviour and activity of the western blue groper, Achoerodus gouldii

The diet and feeding behaviour of the western blue groper, Achoerodus gouldii, were examined at seven sites in southern Australia: small fish ( 60 cm) at Pearson, Ward and St Francis Is, S.A. The diet of small fish is mainly small epifaunal crustacea and small bivalves and gastropods. The diet of medium-sized to large fish also includes small crustacea, but an increasing proportion of larger decapod, molluscan, and echinoid species are taken with increasing size of fish, as they adopt a wider range of feeding modes. Preference experiments with large fish showed that large prey were preferred to small epifaunal prey in algal mats; of the large prey, crabs were preferred to abalone, which were preferred to sea-urchins. Daily time allocation to various activities changed with increasing size: the total daily period of emergence increased, but the proportion of emergent time spent foraging decreased, while swimming time increased. Overall the absolute proportion of time spent foraging changed little with size. Bite rates also declined with increasing size, and, diurnally, bite rates of adults peaked toward and during high tide. Generally, large fish exploited habitats according to their availability, with a substantial bias for feeding in Caulerpa mats. The foraging range of fish, and the pattern of foraging changed with increasing size. The smallest fish exploited a foraging range up to 20 m 2 and the largest a range of ~78,000 m 2 , while swimming changed from employing convoluted movement patterns in a
Quantitative genomic analysis of agroclimatic traits in sorghum

Climate change has been anticipated to affect agriculture, with most profound effects in regions where low input agriculture is being practiced. Understanding of how plants evolved in adaptation to diverse climatic conditions in the presence of local stressors (biotic and abiotic) can be beneficial for improved crop adaptation and yield to ensure food security. Great genetic diversity exists for agroclimatic adaptation in sorghum (Sorghum bicolor L. Moench) but much of it has not been characterized. Thus, limiting its utilization in crop improvement. The application of next-generation sequencing has opened the plant genome for analysis to identify patterns of genome-wide nucleotide variations underlying agroclimatic adaptation. To understand the genetic basis of adaptive traits in sorghum, the genetic architecture of sorghum inflorescence traits was characterized in the first study. Phenotypic data were obtained from multi-environment experiments and used to perform joint linkage and genome-wide association mapping. Mapping results identified previously mapped and novel genetic loci underlying inflorescence morphology in sorghum. Inflorescence traits were found to be under the control of a few large and many moderate and minor effect loci. To demonstrate how our understanding of the genetic basis of adaptive traits can facilitate genomic enabled breeding, genomic prediction analysis was performed with results showing high prediction accuracies for inflorescence traits. In the second study, the sorghum-nested association mapping (NAM) population was used to characterize the genetic architecture of leaf erectness, leaf width, and stem diameter. About 2200 recombinant inbred lines were phenotyped in multiple environments. The obtained phenotypic data was used to perform joint linkage mapping using ~93,000 markers. The proportion of phenotypic variation explained by QTL and their allele frequencies were estimated. Common and moderate effects QTL were found to underlie marker-trait associations. Furthermore, identified QTL co-localized with genes involved in both vegetative and inflorescence development. Our results provide insights into the genetic basis of leaf erectness and stem diameter in sorghum. The identified QTL will also facilitate the development of genomic-enable breeding tools for crop improvement and molecular characterization of the underlying genes Finally, in a third study, 607 Nigerian accessions were genotyped and the resulting genomic data [about 190,000 single nucleotide polymorphisms (SNPs)] was used for downstream analysis. Genome-wide scans of selection and genome-wide association studies (GWAS) were performed and alongside estimates of levels of genetic differentiation and genetic diversity. Results showed that phenotypic variation in the diverse germplasm had been shaped by local adaptation across climatic gradient and can provide plant genetic resources for crop improvement. Quantitative genomic analysis of agroclimatic traits in sorghum
Intragenic differential expression in archaea transcriptomes revealed by computational analysis of tiling microarrays

Recent advances, in high-throughput technologies allows whole transcriptome analysis, providing a complete and panoramic view of intragenic differential expression in eukaryotes. However, intragenic differential expression in prokaryotes still mystery and incompletely understood. In this study, we investigated and collected the evidence for intragenic differential expression in several archaeal transcriptomes such as, Halobacterium salinarum NRC-1, Pyrococcus furiosus, Methanococcus maripaludis, and Sulfolobus solfataricus, based on computational methods; specifically, by well-known self-organizing map (SOM) for cluster analysis, which transforms high dimensional data into low dimensional. We found 104 (3.86%) of genes in Halobacterium salinarum NRC-1, 59 (2.56%) of genes in Pyrococcus furiosus, 43 (2.41%) of genes Methanococcus maripaludis and 13 (0.42%) of genes in Sulfolobus solfataricus have two or more clusters, i.e., showed the intragenic differential expression at different conditions.
The effect size of aphid‐tending ants in an agricultural tri‐trophic system

Most studies regarding ant–aphid interactions focus only on the direct effects of ants on tended aphids and aphidophagous predators, or the indirect effects on the host plant. Studies evaluating the effects of aphid‐tending ants on more than one trophic level are rare and evaluate only the presence or absence of such effects. Here we assessed the effect sizes of ants in a tri‐trophic system (common bean plants, aphids and lacewing larvae). We tested if the presence of aphid‐tending ants has positive effects on aphid abundance and host‐plant production and negative effects on aphid predator abundance. We also hypothesized that aphid‐tending ants affect more intensely trophic levels that are more directly related to them (i.e., first aphids, then aphid predators and then host plants). We tested these hypotheses in field mesocosms experiments using the presence and absence of ants. We found that aphid‐tending ants have great positive effects on final aphid abundance. Ants also positively affected the number of seeds; however, it was not possible to measure the effect size for this trophic level. Furthermore, ants had negative effects on lacewing larvae only at first release. The effect size of ants was greater for aphids, followed by lacewing larvae, and with no effects on the number of seeds produced. Ants positively affect aphids and host‐plant production, probably by way of honeydew collection preventing the development of entomophagous/saprophytic fungi. On the other hand, ants negatively affect lacewing larvae by excluding them from the host plant. In natural systems, several ant species may attend aphids, differently affecting the organisms of the various trophic levels within the ant–aphid interaction, thereby obscuring the real effect size of ants. Assessing the effect size of aphid‐tending ants on the organisms involved in ant–aphid interactions provides more realistic information about the effects of this interaction on natural systems.
Continuous traits and speciation rates: Alternatives to state‐dependent diversification models

Many quantitative traits, for example body size, have been hypothesized to influence the diversification dynamics of lineages over macroevolutionary time‐scales. The Quantitative State Speciation‐Extinction (QuaSSE) model and related methods provide an elegant framework for jointly modelling the relationship between change in continuous traits and diversification. However, model misspecification and phylogenetic pseudoreplication can result in elevated false discovery rates in this and other state‐dependent speciation‐extinction models. Here, we evaluate alternative trait‐dependent diversification methods that do not formally model the relationship between traits and diversification, but instead test for correlations between summary statistics of phylogenetic branching patterns and trait variation at the tips of a phylogenetic tree (hereafter tip‐rate correlations or TRCs). We compare alternative branching pattern statistics and significance tests, and we evaluate their performance relative to QuaSSE under a range of evolutionary scenarios. We found that a simple statistic derived from branch lengths (inverse equal splits) can detect trait‐associated rate variation, and that a simulation‐based method performs better than phylogenetic generalized least squares for testing the significance of trait‐rate correlations. This test (ES‐sim) had better power to detect trait‐dependent diversification than other TRCs. By testing the approach across a diverse set of simulation scenarios, we found that ES‐sim is similar to QuaSSE in statistical power. However, the approach rarely led to false inferences of trait‐dependent diversification, even under conditions that are problematic for formal state‐dependent models. We illustrate the application of ES‐sim to real data by re‐assessing the relationship between dispersal ability and diversification in Furnariid birds. We conclude that simple, semi‐parametric tests like ES‐sim represent a promising approach for trait‐dependent diversification analyses in groups with heterogeneous diversification histories and provide a useful alternative or complement to formal state‐dependent speciation‐extinction models.