Miracle-dz/UniFAR-FTUs huggingface dataset:
A Deep Learning Approach for Learning Intrinsic Protein-RNA Binding Preferences

Motivation The complexes formed by binding of proteins to RNAs play key roles in many biological processes, such as splicing, gene expression regulation, translation, and viral replication. Understanding protein-RNA binding may thus provide important insights to the functionality and dynamics of many cellular processes. This has sparked substantial interest in exploring protein-RNA binding experimentally, and predicting it computationally. The key computational challenge is to efficiently and accurately infer RNA-binding models that will enable prediction of novel protein-RNA interactions to additional transcripts of interest. Results We developed DLPRB, a new deep neural network (DNN) approach for learning protein-RNA binding preferences and predicting novel interactions. We present two different network architectures: a convolutional neural network (CNN), and a recurrent neural network (RNN). The novelty of our network hinges upon two key aspects: (i) the joint analysis of both RNA sequence and structure, which is represented as a probability vector of different RNA structural contexts; (ii) novel features in the architecture of the networks, such as the application of RNNs to RNA-binding prediction, and the combination of hundreds of variable-length filters in the CNN. Our results in inferring accurate RNA-binding models from high-throughput in vitro data exhibit substantial improvements, compared to all previous approaches for protein-RNA binding prediction (both DNN and non-DNN based). A highly significant improvement is achieved for in vitro binding prediction, and a more modest, yet statistically significant,improvement for in vivo binding prediction. When incorporating experimentally-measured RNA structure compared to predicted one, the improvement on in vivo data increases. By visualizing the binding specificities, we can gain novel biological insights underlying the mechanism of protein RNA-binding. Availability The source code is publicly available at https://github.com/ilanbb/dlprb. Contact yaronore@bgu.ac. il Supplementary information Supplementary data are available at Bioinformatics online.
Productivity and related soil properties mediate the population‐level consequences of rodent seed predation on Blanketflower, Gaillardia aristata

Plants are frequently attacked by consumers that reduce seed numbers. However, our ability to predict whether seed loss results in parallel changes in future recruitment or plant abundance remains poor. Progress in this area requires simultaneously understanding: (1) how spatial variation in environmental conditions influence recruitment and other demographic rates, and (2) how the magnitude of seed loss varies spatially and relative to seed limitation. We experimentally assessed how postdispersal seed predation by deer mice (Peromyscus maniculatus) influenced recruitment of the native perennial forb, Gaillardia aristata, in western Montana (USA) grasslands. To explore whether seed limitation and the population‐level consequences of seed predation varied predictably based on environmental conditions, we added seeds to plots where mice had access or were excluded at sites occurring over a strong gradient of soil characteristics and plant community productivity. We also quantified whether components of Gaillardia demography varied in ways that may compensate for or exacerbate the population‐level effects of seed predation across this environmental gradient. Across two replicate years, recruitment was highest at low productivity/soil nutrient sites and decreased towards the opposite end of the gradient. Postdispersal seed predation strongly reduced Gaillardia recruitment in both years, and the impacts of seed predation on recruitment were greater at sites with lower productivity and fewer soil nutrients and decreased towards the opposite end of the gradient. Growth and fecundity varied among populations in ways that could buffer Gaillardia populations from stronger effects of seed predation, whereas survival varied among populations in a way that may intensify these effects. Synthesis. Together, these results show that postdispersal seed predation can importantly limit plant recruitment and that the magnitude of these effects were predicted by variation in underlying environmental conditions that influence recruitment and other key demographic rates.
Influence of snail meat in the diet on mandibular bone loss in male rats: A densitometric, tomographic and morphometric study

Influence of snail meat in the diet on mandibular bone loss in male rats: A densitometric, tomographic and morphometric study The study was aimed at determining the effects of diets containing snail meat as the sole protein source, on mandible quality in male Wistar rats. In the experiment, three different snail-based diets were tested and compared with a casein-based control diet. These included snail meat from Helix pomatia, Cornu aspersum maxima and Cornu aspersum aspersum. In all diets, the protein content amounted to 10% (as calculated on a dry weight basis). Forty male Wistar rats with an initial body mass of 50 g ± 2 were randomly allocated to one control and three experimental groups. After 28 days of experimental feeding, the rats were sacrificed. Their mandibles were isolated and investigated by densitometric (DXA), tomographic (pQCT) and morphometric methods. Moreover, the mechanical parameters (ultimate strength and Young’s modulus) of the mandibles were measured. The results revealed that snail meat as the sole source of protein significantly decreased the bone mineral density (BMD) and content (BMC) of the mandibles. Moreover, the tomographic analysis demonstrated that each type of snail-based diet had a negative influence on the bone cortical and trabecular compartments (which was especially noticeable in the decreasing pQCT parameters). The investigation of mechanical resistance of the mandibles also revealed lower values of the ultimate strength and Young’s modulus in the snail-based diet groups, compared with the casein group.
Impairment of neuronal mitophagy by mutant huntingtin

Neuronal homeostasis depends on the proper functioning of different quality control systems. The accurate degradation of dysfunctional mitochondria by mitophagy is essential for maintaining mitochondrial quality and quantity in neurons. Huntingting protein (Htt) can interact with numerous other proteins and thereby perform multiple biological functions in the cell. We investigated the role of Htt during neuronal mitophagy in post-mitotic differentiated striatal neurons avoiding artificial overexpression of mitophagy-related proteins. Our study shows that Htt promotes the physical proximity of different protein complexes during initiation of the mitophagy process. Htt is needed to promote the ULK1 complex activation, the recruitment of the essential receptors of mitophagy –optineurin and NDP52- and the interaction of these receptors with LC3-II. Mutant Htt also causes a gain of toxic function avoiding the formation of the Beclin1-Vps34 initiation complex. We report that the presence of the expanded polyQ tract can affect the efficiency of neuronal mitophagy and consequently promote the accumulation of damaged mitochondria and increase oxidative stress, leading to mitochondrial dysfunction and contributing to neurodegeneration in Huntington’s disease.
The genetic background modulates the intensity of Rpv3‐dependent downy mildew resistance in grapevine

Communicated by: Thomas Debener Abstract Grape varieties with resistance to downy mildew (DM) carry alien chromosome segments in Vitis vinifera backgrounds. We previously showed that the largest descent group shares a non-vinifera haplotype at the locus Rpv3. Here, we performed a common garden experiment with 76 varieties to evaluate the level of field resistance across four years. All varieties exhibited effector-triggered immunity (ETI)-associated necrosis. On a scale of 1–9, the median OIV452 value for foliar resistance was 7.1 in the resistant lineage vs. 3.2 in vinifera controls. Genotype, year and their interaction significantly affected the level of resistance. Some resistant genotypes showed high mean values of OIV452 and low variance among years. Other resistant genotypes showed lower mean OIV452 and higher variance. They were capable of activating ETI, but the intensity was inadequate to restrict pathogen growth under highly conducive conditions. Rpv3-dependent responses were stronger in highly native genetic backgrounds and tended to attenuate in late backcross generations. Genetic backgrounds donated by European winegrapes of the convarietas occidentalis provided on average higher levels of Rpv3 resistance than backgrounds of orientalis table grapes.
Shaping species richness: ecological filtering in native and non- native plants along elevation gradients in the Swiss Alps

Ecological filtering, imposed by climatic constraints or competitive interactions, might shape distribution patterns of native and non-native plants differently along elevation gradients. However, patterns of species richness that might reflect these processes have rarely been compared between native and non-native plants. All angiosperms and gymnosperms were recorded along and away from three road-corridors that vertically extended >1100 m in a major valley of the Swiss Alps. Non-native species richness declined with elevation and distance from roadsides. Native richness was humped across the elevational range and varied little away from the road. Conversely, richness of native ruderals was distributed similarly as for the non-native plants whereas mountain species numbers strongly increased with elevation. Consistent with directional ecological filtering, non-native species either dropped out or exhibited progressively wider elevational tolerances if recorded at higher altitudes. A similar pattern was found for native ruderals and the opposite pattern for mountain specialist species, i.e. widening ranges in top-down direction. Furthermore, elevational limitations of species within these groups were mostly relaxed along the road-corridor compared to adjacent habitats. These results led to the following conclusions: (i) elevational richness patterns among the native plants strongly differ based upon ecological functional groups, (ii) richness patterns potentially reflect directional ecological filtering both in bottom-up (native ruderals, non-natives) and topdown (mountain plants) direction, (iii) species among groups with asymmetric richness distributions across elevation seem to be inhibited from laterally invading non-roadside habitats, especially towards their elevational range limits, (iv) understanding the processes of directional dispersal and biotic/abiotic components of ecological filters will help towards predictions of future distributions of plant groups, including the non-native group. D. Righetti / (2012) 3
Effect of exogenous application of indole-3-acetic acid (IAA) on cell maturity of Olea europaea L. and extractability of phenolic compounds in virgin olive oil -

The effect of exogenous application of indole-3-acetic acid (IAA) at fruit set and at veraison on the cell maturity of the olive and on extractability of phenolic compounds (PC) in virgin olive oil was studied. The IAA was sprayed on the olive trees at fruit set and on other olive trees at veraison at a concentration of 10-3 mg / l. The effect of these treatments was evaluated by fruit yield and the period of growth and maturation of olives. The extractability of olive oil and diffusion of PC in this latest as well as the embrittlement of the parietal structures are also tracked. The IAA applied at fruit set leads to inhibition of fruit drop but without changing the period of growth and maturation. At full maturity, a significant increase in total lipids was observed and the quantity of oil extracted but without changing their phenolic quality. The treatment at veraison leads to precocity of maturation estimated a month and a gain of 11% fruit. At this stage, a significant increase in the accumulation of fat and the amounts of extracted oils and a significant improvement in the extractability of PC diffusible in these oils at maturity.
Complete mitochondrial genome and the phylogenetic position of the Caroun croaker Johnius carouna (perciformes: Sciaenidae)

Abstract In this study, the complete mitogenome of the Caroun croaker Johnius carouna was obtained. Its mitogenome is 18,752 bp in length, consisting of 37 genes with the typical gene order and direction of transcription in vertebrates. Gene rearrangement was found in J. carouna, same as another two Johnius species available in GenBank, J. distinctus (MF083699) and J. grypotus (KC491206). The overall nucleotide composition is: 24.2% A; 18.0% C; 21.4% G, and 36.4% T. Sizes of the 23 tRNA genes range from 67 to 75 bp. One start codons (ATG) and three stop codons (TAG, AGG, and TAA/TA/T) were detected in 13 protein-coding genes. In the Bayesian tree based on the complete mitogenomes of 21 species (including J. carouna) from the family Sciaenidae, all nodes were strongly supported. The result shows that J. carouna was placed as sister to the silver croaker J. grypotus of the same genus. The mechanism of gene rearrangement in the genus Johnius merits further investigation.
Gene editing can generate fragile bivalents in mouse oocytes

Mouse female meiotic spindles assemble from acentriolar MTOCs (aMTOCs) that fragment into discrete foci. These are further sorted and clustered to form spindle poles, thus providing balanced forces for faithful chromosome segregation. To assess the impact of aMTOCs biogenesis on spindle assembly, we genetically induced their precocious fragmentation in mouse oocytes using conditional overexpression of Plk4, a master MTOC regulator. Excessive microtubule nucleation from these fragmented aMTOCs accelerated spindle assembly dynamics. Prematurely formed spindles promoted the breakage of three different fragilized bivalents, generated by the presence of recombined Lox P sites. Reducing the density of microtubules diminished the extent of chromosome breakage. Thus, improper spindle forces can lead to widely described yet unexplained chromosomal structural anomalies with disruptive consequences on the ability of the gamete to transmit an uncorrupted genome.
The ecology of tree reproduction in an African medium altitude rain forest

The occurrence of flowering and fruiting in tropical trees will be affected by a variety of factors, linked to availability of resources and suitable climatic triggers, that may be affected by increasing global temperatures. Community‐wide flowering and fruiting of 2526 trees in 206 plots were monitored over 24 years in the Budongo Forest Reserve (BFR), Uganda. Factors that were assessed included the size of the tree, access to light, the impacts of liana load, effects of tree growth, and variation between guilds of trees. Most flowering occurs at the end of the long dry season from February to April. Trees that had access to more light flowered and fruited more frequently. Pioneer and non‐pioneer light‐demanding species tended to reproduce more frequently than shade‐bearing species. Trees that grew faster between 1993 and 2011 also fruited more frequently. When examining all factors, growth rate, tree size, and crown position were all important for fruiting, while liana load but not growth rate was important in reducing flowering. Trees in BFR show a large decline in fruiting over 24 years, particularly in non‐pioneer light demanders, shade‐bearers, and species that produce fleshy fruits eaten by primates. The decline in fruit production is of concern and is having impacts on primate diets and potential recruitment of mahogany trees. Whether climate change is responsible is unclear, but flowering of the guilds/dispersal types which show declines is correlated with months with the coolest maximum temperatures and we show temperature has been increasing in BFR since the early 1990s.
DNA damaged protective activity of the crude metabolites of endophytic fungi isolated from two ethno-pharmacologically important medicinal plants of the khasi hills of Meghalaya, India

Traditional medical practitioners of the Khasi Hills of Meghalaya, India, rely on herbs and plants for treating various ailments. These medicinal plants are found to be protected from human interferences in the sacred groves by the tribal population. Endophytic microorganisms residing in the plant tissues without causing any apparent harm to the host have been proven to produce metabolites with anti-cancerous and anti-oxidant properties. It is hypothesized that the metabolites produced by these endophytes may also protect DNA damage. The present study clearly indicates that the endophytic fungal metabolites were able to prevent UV and hydrogen peroxide induced DNA damage in the laboratory conditions.
Biphonal calls in Atlantic spotted dolphins (Stenella frontalis): bitonal and burst-pulse whistles

Abstract Biphonation, the simultaneous production of two sounds by a single animal, is found in the vocalizations of a range of mammalian species. Its prevalence suggests it plays an important role in acoustic communication. Concurrent vocal and behavioural recordings were made of Atlantic spotted dolphins (Stenella frontalis) off Bimini, The Bahamas. The occurrence of two types of biphonal signals is reported: burst-pulse whistles with combined tonal and burst-pulse elements, and bitonal whistles. Biphonal whistles are rarely described in reports of dolphin acoustic repertoires, but were common in these dolphins: of all whistles analysed (n = 1211), 26.84% were burst-pulse whistles and 4.71% were bitonal whistles. A subset of whistles (n = 397) were attributed to dolphins of specific age classes, and used to compare prevalence of biphonation across age. Biphonation occurred in 61.54% of sexually mature and 48.32% of sexually immature dolphins’ whistles. Sexually immature dolphins emitted more burst-pulse whistles than older dolphins: 44.13% of sexually immature dolphins’ whistles were burst-pulse whistles, while 15.38% of adult whistles were burst-pulse whistles. Bitonal whistle production was more prevalent in sexually mature dolphins: 41.03% of adult whistles were bitonal, while only 4.19% of sexually immature dolphins’ whistles were bitonal. The prevalence of a biphonal component in specific repeated, stereotyped whistle contours suggests that these acoustic features could be important components of contact calls, or signature whistles. The biphonal components of spotted dolphin whistles may serve to convey additional information as to identity, age or other factors to conspecifics.
Karyological reports for some Salvia taxa from Turkey

Abstract The aim of this study is to determine of the some karyological properties and chromosome numbers of eight Salvia taxa (S. euphratica var. euphratica, S. euphratica var. leicalycina, S. hypargeia, S. candidissima subsp. candidissima, S. frigida, S. virgata, S. suffruticosa, and S. verticillata subsp. verticillata) from Turkey. The ploidy levels, karyotype formula, chromosome length range, total karyotype length, several karyotype asymmetry values, Stebbins classification and the A1 and A2 were a determined in this study. Also, Pearson correlations between the karyotype asymmetries of the Salvia taxa were calculated and dispersion diagram was formed. It was determined that the Salvia taxa had 2n = 14, 18, 22 and 32. The basic chromosome number of x = 7 may be regarded as primary, the others (x = 9, 11, 16) are estimated to be secondary basis. Based on Stebbins classification, it was found that S. euphratica subsp. euphratica was 1A, S. hypergeia and S. suffruticosa were 3A and the other taxa were 2A. The taxa had median point (M), median (m), submedian (sm), subterminal (st) chromosomes. There were no observed satellites and B chromosomes in the studied taxa.
Chemo-enzymatic synthesis of 3-O- (β-d-glycopyranosyl)-sn-glycerols and their evaluation as preservative in cosmetics

Abstract d-Glycopyranosyl glycerols are common natural products and exhibit strong biological properties, notably as moisturizing agents in cosmetics. Their chemical synthesis remains tedious thus decreasing their potential industrial and economic development, as well as the study of their structure-function relationships. In this work, the chemo-enzymatic synthesis of three enantiopure 3-O-(β-d-glycopyranosyl)-sn-glycerols was efficiently performed using an original glycosidase from Dictyoglomus thermophilum and their preservatives properties were assessed using a challenge test method. Amongst them, the 3-O-(β-d-glucopyranosyl)-sn-glycerol exhibited a specific anti-fungus activity.
Revision of the genus Penthoscapha Heller (Coleoptera, Curculionoidea, Entiminae, Eupholini) with notes on the genera of Eupholini from New Guinea

A preliminary key to the genera of Papuan Eupholini is given. The hitherto monotypic subgenus Niphetoscapha Heller 1914 is transferred from Rhinoscapha Montrouzier 1855 to Gymnopholus Heller 1901: Gymnopholus (Niphetoscapha) wichmanni (Heller), comb. n. It is closely related to G. audax Gressitt 1966 and G. nitidus Gressitt & Sedlacek 1967 which are moved from the subgenus Symbiopholus Gressitt 1966 to Niphetoscapha. The record of the genus Celebia Thomson 1857 for New Guinea is reported as erroneous. The genus Penthoscapha Heller from montane and subalpine habitats of the central mountains of West New Guinea is revised. A lectotype is designated for the type-species, P. lorentzi Heller, 1914. Penthoscapha toxopei (Gressitt & Sedlacek 1967), comb. n. is transferred from Gymnopholus. Four new species of Penthoscapha are proposed: P. doormanensis sp. n. , P. gerhardschereri sp. n. , P. pulverea sp. n. , P. similis sp. n. All species of Penthoscapha are described, a key is provided, and their distribution is mapped. Reduction of hind wings in Penthoscapha and fusion of elytra in P. gerhardschereri are interpreted as consequences of flightlessness. Extracuticular pigments are described and illustrated for P. doormanensis, P. gerhardschereri, and P. pulverea. The phylogenetic placement of Penthoscapha among Eupholini is briefly discussed.
Effects of dietary supplementation with increasing doses of lactose on faecal bacterial populations and metabolites and apparent total tract digestibility in adult dogs

Abstract The effect of increasing dietary doses of lactose on canine faecal microbiota and apparent digestibility was evaluated. Fourteen adult healthy dogs [1–5 years of age, mean body weight (BW) of 19.0 kg] were fed with an extruded diet containing silica (5 g/kg) as a digestion marker. After a 20 d adaptation period, increasing doses of lactose were added to the dogs’ diet (0.5, 1 and 2 g/kg BW0.75/d) during three consecutive 20-d supplementation periods. Faeces were collected at the end of each period for analyses. Four dogs refused the diet added with lactose at 0.5 g/kg BW0.75/d and were excluded from the trial, as well as two dogs, which developed acute diarrhoea when lactose was fed at 1 g/kg BW0.75/d. Conversely, eight dogs remained healthy throughout the study. Faecal moisture was influenced by lactose (quadratic, p = .001), while faecal pH and ammonia were not affected by treatments. Lactose supplementations tended to linearly decrease isovalerate (p = .051) and quadratically influence n-valerate (p = .056) in canine faeces. No changes in faecal microbial populations were observed. Apparent digestibility of dry matter, Ca, K, Mn and Fe was influenced by lactose supplementation (quadratic, p < .05). Increasing doses of lactose linearly decreased Mg digestibility (p < .05). Furthermore, coefficients of crude protein, crude ash, P, Mg and Zn digestibility were tendentially affected (quadratic, p = .055, .089, .091, .065 and .065, respectively). In conclusion, 8 of 14 dogs displayed a good tolerance (absence of gastrointestinal signs) up to the highest dose of lactose (2 g/kg BW0.75/d). An evident prebiotic effect was not observed.