Miracle-dz/UniFAR-FTUs huggingface dataset:
Hallmarks of early sex-chromosome evolution in the dioecious plant Mercurialis annua revealed by de novo genome assembly, genetic mapping and transcriptome analysis

The evolution of sex chromosomes involves the suppression of recombination around a sex-determining locus, and the subsequent divergence in DNA sequence between the two homologous sex chromosomes. Dioecious plants offer the opportunity to study independent early stages of this process, because of multiple, recent transitions between hermaphroditism and dioecy. Here, we present data from de novo genome assembly and annotation, genetic mapping and transcriptome analysis of the diploid dioecious herb Mercurialis annua, revealing several of the typical hallmarks of early sex-chromosome evolution. Until now only a single sex-linked PCR marker has been published. Our analysis identified a single linkage group, LG10, as the likely sex chromosome, with a region containing 69 sex-linked transcripts with a clearly lower male than female recombination, high X/Y divergence and multiple incidences of premature stop codons on the Y allele. We found many genes with sex-biased expression. Female-biased genes were randomly distributed across the genome, but male-biased genes were slightly enriched on the Y chromosome. Interestingly, Y-linked genes had reduced expression compared with X-linked genes, a pattern consistent with Y chromosome degeneration. M. annua has been a powerful model for the study of rapid sexual-system transitions in plants; our results here establish it as a model for the study of the early stages of sex-chromosome evolution.
Effect of pre‐fermentation saignée treatment on phenolic compound profile in wine made of Cabernet Sauvignon

The saignee method was applied to Vitis vinifera L. Cabernet Sauvignon wine making to improve the phenolic component in fresh and 1-year aged wines. The physicochemical properties of the saignee-treated wine were similar to those of the control. A moderate enhancement of the total non-anthocyanin content was observed in the saignee-treated wine, but this was not significant (p > .05). After fermentation, the anthocyanin content was increased in the treated wine compared to the control (p ≤ .05). Anthocyanin content was reduced after aging (p ≤ .05), while the content of the treated wine was still higher than the control (p ≤ .05). After aging, the treated wine showed lower b* value (blue/yellow component) than the control. Principal component analysis (PCA) revealed that decreased anthocyanin was the major factor differentiating between aged and fresh wines. There were also significant differences in individual phenolic acid, flavonol, and anthocyanin contents between the treated and control wines from the PCA. Practical applications Saignee treatment could enhance extraction of phenolic compounds and improve wine color. This study could provide winemakers with an approach to compensate for poor color intensity and stability.
The impact of amur sleeper (Perccottus glenii Dybowsky, 1877) on the riverine ecosystem: food selectivity of amur sleeper in a recently colonized river

Abstract The presented study aimed at comprehensive assessment of the Perccottus glenii (Amur sleeper) impact on the aquatic ecosystem. Our objective was to analyze the diet, the characteristics of the prey and the feeding behavior of the Amur sleeper. Fish (349 individuals) were captured by electrofishing in autumn 2012. To estimate the dietary importance of each prey category, we calculated the percentage or proportion of each food item and its frequency of occurrence. The Costello graphical method was applied to describe the feeding strategy and prey importance. A total number of 55 taxa of benthic macroinvertebrates were identified, amounting to a total of 2448 individuals. The digestive tract was empty in 48 individuals of the Amur sleeper. The most frequent prey items of the Amur sleeper were Asellus aquaticus L, Baetis spp. , the Chironomidae family which was represented by 22 taxa identified to the genus and species levels, Corixa spp. and Physa acuta Drap. Depending on the frequency of prey items, two categories of size classes with specific diet compositions in the Amur sleeper populations were determined. Feeding strategy, cluster indicators of the size classes and traits of macroinvertebrates were the main aspects covered by our study of the Amur sleeper feeding behavior.
On a family of non-weight modules over Virasoro-type Lie (super)algebras.

In this thesis we classify modules over a Witt-type Lie algebra and superalgebra such that when considered as modules of $\mathcal{U}(\mathfrak{h})$ they are free of rank 1. We provide sufficient conditions for simplicity, and compute the action of an automorphism on the module. Lastly, we apply the weighting functor and show that the resulting modules are intermediate series modules.
Evidence that dispersal barriers influence blaberoid cockroach assemblages in a neotropical savanna–forest matrix

The forest refuge hypothesis to explain Amazonian diversity places an importance on dry savanna as a landscape feature isolating populations of humid forest‐dwelling animals. Leaf‐litter cockroaches are a useful group to study this as they are terrestrial and occupy a high‐humidity microclimate. We examine the role of savanna, forests and flood zones in affecting blaberoid cockroach assemblage composition in the north Rupununi of Guyana, an expansive savanna–forest matrix. We test whether stretches of dry savanna and flood zones are barriers to dispersal for leaf‐litter cockroaches. Our study area is the ˜10 000 hectares of Karanambu Eco‐Lodge. We collected 1061 individuals of 17 species from 28 sites. Using a landscape classification based on satellite imagery, we generated models of relative isolation of the 28 sites using a cost of travel algorithm. We also used non‐metric multi‐dimensional scaling and Mantel tests to determine whether the similarity of cockroach assemblages could be explained by different landscape categories (savanna, forests and flood zones) or by geographic distance. We identified a single model that best predict observed variation in cockroach abundance and species richness. Differences in assemblage similarity were largely due to differences in the savanna–forest habitat axis. Geographic distance was also found to effect assemblage similarity. Our data suggest that savannas are barriers to dispersal, whereas flood zones are not. Future investigation of savanna driving speciation in some species is warranted, and this is a key feature of the forest refuge hypothesis.
Coupled exuviae of the Ordovician Ovalocephalus (Pliomeridae, Trilobita) in South China and its behavioral implications

Ecdysis was a vital process during the lives of trilobites. In addition to preserving the morphological changes in trilobite ontogeny, the preservation of its action often captured interesting behavioral information. Abundant exuviae of Ovalocephalus tetrasulcatus are preserved in the Ordovician strata in central Hubei, China, and some of them are arranged with two or three together end to end or superimposed. The preserved patterns and burial conditions indicate that these specimens were caused by the active behavior of trilobites. It is speculated that these exuvial clusters were formed by two or three trilobites in line to molt; that is, after one trilobite finished molting, other trilobites molted in front of, behind, or overlying the previously molted shells. This ecdysis strategy is interpreted as related to the postulated herding behavior of some trilobites, representing a behavioral response of the trilobites to choose a nearby safe zone during some risky life activities.
Humoral Immune Memory to Hepatitis B Vaccine after Primary Vaccination of Children and Adolescents in Assiut, Egypt

Objectives We sought to assess the prevalence of hepatitis B virus (HBV) seroprotection among vaccinated children in the Assiut governorate, Egypt, and assess a booster dose immune memory response among non-seroprotected children. Methods Using a multistage cluster sample, 566 children were recruited from three clusters: one urban and two rural. Children were aged from nine months to 16 years old. All participants received the full three doses of the compulsory HBV vaccine during infancy. Serum hepatitis B surface antigen (HBsAg), total anti-hepatitis B core (anti-HBc) antibodies, and quantitative detection of anti-HBs were measured using enzyme-linked immunosorbent assay. Repeatedly positive samples for HBsAg/anti-HBc were submitted for quantitative HBV DNA detection using real-time polymerase chain reaction. Non-seroprotective participants (anti-HBs < 10 IU/L) were given a booster dose of HBV vaccine. Two weeks later, a blood sample was taken from each child to assess an anamnestic response. Results The seroprotection rate was 53.2%, and only two children had HBV breakthrough infection (0.4%) with positive serum anti-HBc and HBV DNA. Age was the only significant predictor for non-seroprotection with an adjusted odds ratio (OR) of 3.2, 9.4, and 9.9 among children aged 5–10, 11–15, and > 15 years, respectively, compared to younger children (p < 0.001). About 85% of non-seroprotected children developed an anamnestic response after receiving the booster dose, and 84.3% of responders had a good response (3 100 IU/L). Undetectable pre-booster titer was found to be the only risk factor for non-response to booster with OR = 3.2 (p < 0.010). About 95.7% of children who were not responding to booster dose developed immune response after receiving the three doses of HBV vaccine. Conclusions Older age of children was the only significant predictor for HBV non-seroprotection. High anamnestic response rate signifies the presence of immune memory with long-term protection despite the waning of anti-HBs over time. However, some children with pre-booster undetectable anti-HBs titers may be unable to develop anamnestic response, and a second vaccination series might be necessary for HBV protection for these children.
Mechanisms of rod photoreceptor motility in development and following transplantation

To establish the mature neuroepithelial tissue architecture, newborn neurons often migrate from their place of birth, usually at the apical neuroepithelial limit, towards their target destination. Even before neurons are born, the nucleus of the mitotic neuronal progenitor cell migrates within the apico-basal cellular extent in synchrony with the cell cycle (interkinetic nuclear migration or IKNM) – a migratory pattern so far only observed in mitotic epithelial progenitor cells. Rod photoreceptors, too, are born at the apical limit of the retinal neuroepithelium. They then populate a layer directly adjacent (outer nuclear layer or ONL), but not the more basal retinal layers. How rod photoreceptors become enriched specifically within the ONL is presently ill-defined. Here, it was identified that rod photoreceptor somata of the developing mouse retina are constantly pushed basally (presumably caused by proximal progenitor IKNM events). To become enriched apically within the (presumptive) ONL despite this, the post-mitotic rod photoreceptors utilised an IKNM-like migratory behaviour more typically associated with dividing cells: rod somata actively migrated apically, driven by microtubule-associated dynein I motors. Another microtubule-associated motor protein, KIF1A, acts as a molecular brake during basal displacement, preventing ectopic basal positions. Rod somata oscillate between apical and basal motions at least from P1 up until ~P10. Whether this involves a component of glial-guided migration could not be established beyond reasonable doubt. Nonetheless, this is the first report of an oscillatory, IKNM-like migration behaviour occurring within a post-mitotic neuronal cell population. Rod photoreceptors have also been assumed to migrate into the adult neural retina following sub-retinal transplantation for cell-replacement therapeutic purposes, although this has not been directly observed. Here, time-lapse footage for the first time showed rod photoreceptors migrating from the sub-retinal space into the host retina. This supports the notion that photoreceptor cell replacement therapy could become a clinically viable treatment option.
Circulating tumor DNA (ctDNA) and correlations with clinical prognostic factors in patients with metastatic castration-resistant prostate cancer (mCRPC).

186Background: Sequencing of ctDNA is a minimally invasive method to study somatic DNA alterations. Quantitation and characterization of ctDNA may correlate with tumor burden and poor risk clinical features, but this is unproven in mCRPC. Methods: We performed deep targeted sequencing of 73 mCRPC-related genes in plasma ctDNA from 136 treatment naive mCRPC patients. Fraction of ctDNA was determined by quantifying somatic mutant allele frequency and the deviation from heterozygosity for germline single nucleotide polymorphisms at regions of somatic copy number alterations. Baseline clinical factors were correlated with ctDNA fraction and genomic aberrations. Results: ctDNA could be quantified in 86/136 (63%) patients. Increasing fraction correlated with elevated ALP (chi2, p < 0.001), LDH (p < 0.001) and presence of liver metastasis (p = 0.01). Patients with any one of these factors were more likely to have a ctDNA fraction ≥ 40% (67% vs 36% of patients with neither factor, p = 0.001) and less likely to ha.
Nuclear genome size variation in the allopolyploid Onosma arenaria – O. pseudoarenaria species group: methodological issues and revised data

We used flow cytometry (FCM) to investigate genome size variation in two polymorphic allopolyploids, Onosma arenaria Waldst. and Kit. and O. pseudoarenaria Schur, in Central Europe and the Balkan Peninsula. An intercalating DNA stain, propidium iodide (PI), and internal standardization were used. Our data showed that cytosolic compounds may be present in FCM samples and could inhibit, or more frequently promote, PI intercalation. In the absence of PI intercalation interference, leaf-based genome size estimates were observed to be lower than seed-based ones in O. pseudoarenaria, whereas no difference was recorded in O. arenaria. In incubation tests, genome size values frequently increase after a longer staining period. For final genome size measurements, we applied the FCM protocol based on seed material using a ∼150 min incubation period, and provide evidence of mean genome size variation among populations of both species. Two and four natural genome size groups were revealed in O. arenaria and O. pseudoarenaria respectively. Group mean genome sizes varied considerably in both O. arenaria (5.36–5.76 pg) and O. pseudoarenaria (5.98–6.58 pg). This extensive genome size variation is attributed to unexplored taxonomic heterogenity in both taxa. Future taxonomic revision of the group may be supported with genome size measurements obtained using an appropriately standardized methodology.
Habitat use of Raccoon dogs, Nyctereutes procyonoides^ in southern Finland

Habitat use of raccoon dogs {Nyctereutes procyonoides) was studied in southern Finland during the snow-free seasons of 1990-1992 using radio tracking. Habitat selection within the study area and habitat use within the home ränge were examined. Raccoon dogs favoured shore areas especially during early Summer. Shore areas with dense undergrowth provide food (e.g. frogs) and shelter, and raccoon dogs often escape into water when attacked. During autumn, raccoon dogs favoured moist heaths with abundant berries, which serve as an important food source before entering winter dormancy. The habitat use of raccoon dogs is thus affected by the availabihty of food, shelter and suitable den sites. Two features are common to dogs in all areas: 1) the are very often found near water and 2) during autumn they are more or less dependent on fruits and berries, which affects their habitat selection.
Towards structure determination of the hepatitis C virus p7 protein

The hepatitis C virus (HCV) affects 3% of the world's population and is a major cause of liver cirrhosis and cancer. The p7 protein of HCV has recently gained much attention due, in part, to its essential role in viral infectivity. This small integral membrane protein containing two transmembrane helices is thought to perform this function by forming a heptameric cation-specific ion channel. In order to gain insight into its channel function I have initiated nuclear magnetic resonance (NMR) experiments that can start to reveal the structure of this protein. For this purpose a C-terminally His6tagged p7 was expressed in E. coli as a C-terminal fusion protein to glutathione-Stransferase (GST). This fusion protein was purified under denaturing conditions using nickel affinity chromatography and cleaved using thrombin to separate p7 from GST. Greater than 90% pure His-tagged p7 was obtained using reversed-phase highperformance liquid chromatography. N, C-labeled samples were reconstituted in detergent solutions to allow analysis by solution NMR. A limited series of sample optimization experiments were performed to identify conditions that would give rise to folded p7 in a detergent-micelle complex that would be amenable for chemical shift assignment. Of the conditions tested, p7 solubilized in the lysophospholipid LMPG at 40°C was found to give rise to the most favorable spectrum with a chemical shift dispersion indicative of a helical protein. A suite of three-dimensional triple resonance experiments were then performed and assignment of backbone chemical shifts was initiated. Based on these experiments it was possible to make preliminary chemical shift assignments for over half of the observed resonances. Secondary chemical shift calculations performed with these chemical shifts are consistent with expectations for a-
Interactive effects of marine heatwaves and eutrophication on the ecophysiology of a widespread and ecologically important macroalga

Extreme temperature events are becoming more recurrent and are more frequent with major impacts on coastal ecosystems, which are additionally impacted by increasing urbanization, resulting in high nutrient load. So far little is known about cumulative and/or interactive effects of global and local stressors on species' performance. Here, we evaluated the single and combined effects of simulated heatwaves and eutrophication on the ecophysiology of Laurencia catarinensis in a bi‐factorial mesocosm experiment. The algae were exposed for 30 d to three different temperatures (20°C, 24°C, 28°C) and nutrient concentrations (low, intermediate, high) and their nutrient uptake rates, photosynthetic performance, growth rates, pigment and phenolic compound concentrations, as well as antioxidant capacity was determined and compared between treatments. Under low nutrient concentration, physiological performance and growth decreased with increasing temperatures. In contrast, they increased with higher nutrient availability and moderate temperature increase close to the summer average temperature, but largely declined upon exposure to higher temperature (28°C). This decline seemed to be related to oxidative stress, as indicated by an increase of compounds with antioxidant properties (lutein, zeaxanthin, phenols). Our data show that all measured parameters were affected by temperature and nutrient availability, with an interactive effect between these two factors, indicating that increasing temperature will influence macroalgal performance, and even more dramatically in coastal systems that are highly impacted by urbanization. However, the direction of the response will be determined by nutrient availability and will also depend on the magnitude of the temperature increase, that is, whether it surpasses the thermal threshold of the species.
Genetic relatedness of sweet cherry (Prunus avium L.) cultivars from Ukraine determined by microsatellite markers

ABSTRACT Microsatellite (SSR) markers were used to characterise 23 sweet cherry cultivars of Ukrainian, and four cultivars of non-Ukrainian, origin. To assess their genetic diversity and relatedness, 11 pairs of primers were applied to microsatellite loci, resulting in amplification of 66 SSR alleles. The mean value of the number of different alleles, and the polymorphic index content, amount to 7.333 and 0.700, respectively, demonstrating a significant genetic diversity of the investigated sweet cherry cultivars. Four highly polymorphic SSR loci (EMPAS02, EMPAS06, PceGA34, UDP98-412), which belong to the list recommended by the European Cooperative Program for Plant Genetic Resources, can be used as a minimum genetic marker set for identification of the majority of the studied cultivars; however, for successful discrimination of the most similar cultivars, more markers, located on all chromosomes of sweet cherry, appear to be necessary. Application of unweighted variable-group method using averages clustering allowed elucidation of the relatedness among the sweet cherry varieties, and showed that the Ukrainian cultivars combine genetic material of local, western European, and probably Caucasian origin; however, the origin of several cultivars still remains unclear, and should be studied additionally.
Integrative taxonomy of the Rhinolophus macrotis complex (Chiroptera, Rhinolophidae) in Vietnam and nearby regions

The taxonomic status of Rhinolophus macrotis sensu lato (s.l.) in Vietnam and adjacent territories remains problematic. To address this issue, we performed an integrated study of morphological, acoustic, and genetic characters of R. macrotis s.l. specimens and compared these with sympatric species within the philippinensis group (R. marshalli, R. paradoxolophus, and R. rex). Our results reveal that in addition to a cryptic species of R. macrotis previously found in Jiangxi and Jingmen, China, R. macrotis s.l. in continental Asia includes three further species, namely R. cf. siamensis, R. cf. macrotis, and R. cf. macrotis “Phia Oac. ” These four taxa are distinguished from genuine R. macrotis in Nepal and R. siamensis in Thailand by their morphological and/or genetic features. Further taxonomic evaluation of the subspecies of R. macrotis s.l. is needed to determine their affinities with recently recognized cryptic species and to possibly describe new taxa. Our results also show that interspecific divergences in mitochondrial DNA sequences (Cytb and COI genes) among taxa within the philippinensis group (particularly between R. cf. siamensis/R. cf. macrotis and R. rex/R. paradoxolophus) are significantly lower than those of other morphological groups in the genus. These phylogenetic patterns might be explained by recent allopatric speciation or ancient introgression events among ancestors of the taxa during the Pleistocene. However, further investigations including genetic analyses of nuclear genes are needed to test the latter hypothesis.
De novo assembly and identification of antennal transcriptome reveals an olfactory system in Heortia vitessoides (Lepidoptera: Crambidae)

Olfactory systems in insects are used to detect volatile chemical odors, and play crucial roles in survival, reproduction, and mediating key behaviors. Here, RNA sequencing technology was used to sequence and assemble the antennal transcriptome of Heortia vitessoites, a defoliating pest in Aquilaria sinensis (Loureiro) Sprenger forests and a non-model species with no genomic resources. Analysis of the transcriptome of female and male antennae generated 22.16 gigabases of genomic data, from which 52,383 unigenes were assembled. We identified 80 candidate olfactory genes: eight for odorant binding proteins (OBPs), 14 for chemosensory proteins (CSPs), 35 odorant receptors (ORs), 18 ionotropic receptors (IRs), three gustatory receptors (GRs), and two for sensory neuron membrane proteins (SNMPs). Furthermore, phylogenetic trees and fragments per kilobase of transcript per million fragments mapped (FPKM) were used to analyze these olfactory genes. This study is the first comprehensive antennal transcriptome analysis for H. vitessoites, and these novel olfactory genes will increase understanding of the molecular mechanism of chemoreception and further contribute to exploring strategies to manage this insect.