Miracle-dz/UniFAR-FTUs huggingface dataset:
Behavioral Ecology of American Pikas (Ochotona princeps) at Mono Craters, California: Living on the Edge

Abstract. The behavioral ecology of the American pika (Ochotona princeps) was investigated at a relatively hot south-facing, low-elevation site in the Mono Craters, California, a habitat quite different from the upper montane regions more typically inhabited by this species and where most prior investigations have been conducted. Mono Craters pikas exhibited a behavioral profile that contrasted significantly with that of pikas found in upper montane regions. Mono Craters pikas were less surface active than pikas in studies at high-elevation sites, although their rate of short-call vocalizations was similar. Mono Craters pikas did not exhibit typical foraging behavior: they fed and collected hay at significantly reduced rates, and did not construct large central-place hay piles. Social behaviors (conspecific aggression, social tolerance, avoidance) were infrequent compared with data from prior studies in upper montane environments. The Mono Craters site appears to be one of the warmest localities in which pikas have been observed. Recorded talus surface temperatures consistently exceeded 30 °C, and temperatures >40 °C were commonly recorded. In contrast, temperatures measured in the matrix of the talus were consistently cooler, and the apparent insulating effect of talus, as measured by the difference between surface and matrix temperatures, was typically most pronounced on the hottest days. Although pika activity was most frequent in early morning, late afternoon, and at night, pikas were also active during the hottest part of the day, presumably because of their ability to behaviorally thermoregulate by retreating into the cooler talus matrix. Data on populations of pikas which inhabit marginal sites can help us understand how pikas and other montane animals might respond in a world of climate change so that we may more effectively plan for their conservation.
Research data supporting "The ancestral ochrophyte plastid proteome"

This dataset contains all of the supporting information pertaining to the reconstruction of the plastid proteome of the last common ancestor of all extant ochrophytes, including: - Complete lists of plastid-targeted proteins identified in the study - Phylogenetic trees inferred using the single-gene, concatenated and multigene alignments - All supplementary datasets referenced in the linked publication A "readme" file in the main directory provides information regarding the location of each file
Predictions of marbled crayfish establishment in conurbations fulfilled: Evidences from the Czech Republic

Abstract The marbled craynsn (Procambarus fallax f. virginalis) has become one of the potentially most dangerous nonindigenous crayfish species spreading in European countries and elsewhere. This taxon reproduces parthenogenetically and recently has been verified as a vector of the crayfish plague pathogen. Here, we report on two established populations of marbled crayfish in the Czech Republic. The marbled crayfish was observed during autumn 2015 in an urban pond connected by sewer piping with the Rokytka brook near its mouth to the Vltava River in Prague. Subsequently, three adult females, two of them having well-developed glair glands and oocytes, were captured in this pond during spring 2016, suggesting successful overwintering of the local population. Furthermore, four adult females were captured in an artificial pond at the Radovesická lignite spoil heap in the vicinity to the industrial conurbation of Bílina in summer 2016; one of them carried eggs. We tested these for the presence of the crayfish plague pathogen Aphanomyces astaci, with negative results. The introduction pathway for both populations is most likely a release from private aquaria, as these sites are popular for recreation activities. Our findings substantiate previous predictions that conurbations are likely to be the primary areas for marbled crayfish introductions.
Advances in In Vivo Imaging Techniques for the Visualization and Quantification of DC-T Cell Interactions

Since the first application of two photon intravital microscopy (2PM) to the study of the immune system in 1997 [1], 2PM imaging has offered several major advantages over previous techniques for study immune interactions. Such as 2D plate based culture systems, as cells exhibit significantly different migratory behavior in 2D as compared to 3D. Whilst, 3D matrigel systems allow cells to migrate in a more natural manner, they fail to adequately replicate a physiological environment which is densely packed with other cell types and contains a myriad of environmental cues such as chemokines, adhesion molecules and lymphatic flow, these factors are largely overcome by the use of ex-vivo/explant organ imaging. However, this system also has significant limitations in that cells cannot be recruited to or exit the organ of interest and due to limitations in tissue oxygenation, imaging sessions can generally only be conducted for less than one hour [2]. Therefore, the use of intravital 2PM has opened up a new era of understanding in immunology. Especially in terms of how we view the importance of the migratory behavior and the interactions that occur between cells of the immune system under both homeostatic and inflammatory conditions.
Multi-objective optimization of cascade reservoirs using NSGA-II: A case study of the Three Gorges-Gezhouba cascade reservoirs in the middle Yangtze River, China

ABSTRACT A multi-objective optimization model of cascade reservoirs was developed to maximize the power generation and minimizie the appropriate ecological flow shortage index (AEFSI) downstream from the reservoir. Additionally, the non-dominated sorting genetic algorithm (NSGA-II) was used to search for multi-objective Pareto optimal solutions. The paper took the Three Gorges-Gezhouba cascade reservoirs as a case study. After validating the model, data from three typical years were used in the optimization. The results indicated that maximizing power generation by adjusting the optimal rules increased power generation by 1.07%, 0.91%, and 1.03% in normal, wet, and dry hydrological years, respectively, while increasing the AEFSI by 22.12%, 11.78%, and 14.67% (compared to real operations). The AEFSI was improved (decreased) by 21.90%, 10.27%, and 18.52% when the optimal rules favored the downstream ecology, but power generation decreased by 1.61%, 1.06%, and 2.29%, respectively, in the different hydrological years. Moreover, the results provide a set of well-distributed optimal solutions along the Pareto front that allow decision-makers to easily determine the best compromised solutions based on the trade-offs between the economic and ecological benefits. The results of this study provide guidance for decision-makers to improve the comprehensive benefits of the Three Gorges-Gezhouba cascade reservoirs.
Benthic nitrogen fixation in oxygen minimum zones

The distribution and magnitude of benthic N2 fixation in OMZs, and its relevance for the community inhabiting these sediments was investigated. A possible coupling to sulfate reducers was determined by rate measurements of N2 fixation and sulfate reduction, as well as by molecular analysis in the respective environment. In sediments of the Peruvian OMZ, N2 fixation and sulfate reduction occurred throughout the sediment and depth profiles largely overlapped, suggesting a coupling of both processes. This coupling was further supported by the molecular analysis. In the Mauritanian OMZ N2 fixation activity often overlapped with sulfate reduction, as well as with ferrous iron concentrations. The molecular analysis confirmed the presence of sulfate- and iron-reducing bacteria. Burrowing organisms potentially create a biogeochemical zonation pattern in sediments that enhanced N2 fixation in deeper sediment layers. To examine the marine benthic diazotrophic diversity, samples from OMZs, methane seeps and brackish water sediments were used for high-throughput sequencing. Results showed a small diversity of diazotrophs among sites and a dominance of sulfate reducers. The redundancy analysis showed a positive correlation between diazotrophs and sulfate reduction. To conclude, the detection of benthic N2 fixation in OMZs, as well as the diversity study of benthic diazotrophs from different environments, shows that it is a ubiquitous process in the benthic environment. The global distribution of benthic diazotrophs, as revealed by the diversity study, highlights its previously underestimated role in the benthic N cycle, as well as in the marine N budgets. The controlling factors of diazotrophs in marine sediments are: abundance of sulfate reducers; organic matter content in the sediments; and sulfide concentration in the porewater, as a potential inhibitor.
AN IN SILICO STUDY OF NARINGENIN-MEDIATED NEUROPROTECTION IN PARKINSON’S DISEASE

Objective: Naringenin is a dietary biomolecule with broad spectrum of activities which protects neurons from various neurotoxic insults and improves cognition and motor function in neurodegenerative diseases. DJ-1 has both, ubiquitin E3 ligase as well as chaperonic activity, and loss of ubiquitin E3 ligase activity of DJ-1 has been found to be associated with familial Parkinson’s disease (PD). Naringenin induced E3 ligase activity of DJ-1 which can have possible clinical relevance in PD. Methods: Various in silico parameters such as phylogenetic analysis, homology modeling, active site prediction, and molecular docking studies using AutoDock 4.2. 1 and LIGPLOT1.4. 5 were carried out. Results: Three-dimensional structure of DJ-1 was generated and Ramachandran plot was obtained for quality assessment. RAMPAGE displayed 99.5% of residues in the most favored regions. 0% residues in additionally allowed and 0.5% disallowed regions of DJ-1 protein. Further, initial screenings of the molecules were done based on Lipinski’s rule of five. CastP server used to predict the ligand binding site suggests that this protein can be utilized as a potential drug target. Finally, we have found naringenin to be most effective among four biomolecules in modulating DJ-1 based on minimum inhibition constant, Ki, and highest negative free energy of binding with maximum interacting surface area in the course of docking studies. Conclusion: Our study suggests that based on different in silico parameters and molecular docking studies, naringenin can provide a new avenue for PD therapeutics.
A Novel Method for Predicting Ribosomal RNA Genes in Prokaryotic Genomes

With the increased efficiency of sequencing methods, large quantities of genomic information are quickly becoming available. To make use of this, methods are needed that can discern useful information from these vast data quantities. Such information could be the presence and position of specified genes with known properties. Due to their highly conserved sequences and their prevalence across all genomes the ribosomal RNA (rRNA) genes have a wide range of application within bioinformatics. Previous methods for predicting rRNA genes include RNAmmer and barrnap which both use an approach based on Hided Markov Models (HMM). However these methods are problematic due to a number of reason. Here we present a new method for rRNA gene prediction that uses a new, k-mer based, approach. This method provides a large improvement in specificity for predicting 5S rRNA genes as well as higher precision in pinpointing the ends of the rRNA gene. At the same time it preserves the high sensitivity of earlier methods with a decrease in running time. We also demonstrate the ability of rRNA gene predictors to find potential errors in the RefSeq annotation database. (Less)
Axon Death Pathways Converge on Axed to Promote Axon Disassembly

Axons use a conserved program to actively drive their own destruction after injury. Axon degeneration is present in many neurological disorders and an axon death program could be a major pharmaceutical target to preserve neuronal function. This intrinsic signaling cascade activates pro-degenerative dSarm/Sarm1, rapidly depletes axonal stores of NAD+, and terminates in cytoskeletal breakdown. Conversely, loss of dSarm/Sarm1, maintenance of NAD+ levels or its biosynthetic enzyme Nmnat, result in long-term morphological perseveration of severed axons. Exactly how dSarm/Sarm1 and loss of NAD+ execute axon death remains poorly defined. We sought to uncover novel regulators of axon death and maintenance by performing a deficiency screen and a forward genetic mutagenesis screen in axotomized Drosophila wing sensory neurons. We identified a BTB domain protein enriched in neurons, we named Axundead (Axed), which is specifically required for axon death. Severed axons harboring loss of function mutations in axed, similar to dSarm mutants, remain preserved for 50 days post axotomy. Spontaneous neurodegeneration induced by activated dSarm or dNmnat depletion are both suppressed in axed mutants, but not in dSarm mutant alleles. Additionally, severed axed mutant axons also expressing activated dSarm or lacking Nmnat are preserved. These results indicate that dSarm acts upstream of dNmnat loss, and both events precede essential Axed function and axon destruction. Thus, the axon death pathway converges on Axed function.
Standardization of multivariate regression models for estimation of the gregariousness level of the main pest locust

Recurrent locust population outbreaks have a tremendous impact on ecosystems and economies around the globe. These population outbreaks are associated with a shift from the usual solitary locust phase to a gregarious one. Most molecular research on locusts is focused on uncovering the basis underlying the change to gregariousness. With the increasing availability of ‘omics’ data, the research on this subject is entering a functional testing era. In order to successfully test functionality of a gene or molecule, quantitative measurements of the level of gregariousness are needed. Currently no valid molecular marker is available, thus the assessment of the degree of locust gregariousness is based on mathematical modeling. However, the absence of one single model means heterogeneity and implies that researchers have to spend time and effort building one for their specific experiments. Here, we offer a script to simplify extraction of the data from locust behavioral video tracks. We also suggest two mathematical equations for assessing the levels of gregariousness of one of the most notorious pest locusts – Schistocerca gregaria (Forskål) (Orthoptera: Acrididae). One model uses morphometric variables and is valid for the comparison of nymphs, whereas the other has no morphometric variables and is for testing the adults and the same specimens of non‐molted nymphs. The sensitivity of these models was optimized and the effects of sex, developmental stage, and locust size were considered. The models were tested with independent samples and were found to work both for solitary and gregarious locusts. They were also found to be quantitative and could be used to distinguish populations of different densities and states. We therefore offer accessible, reliable, time, and effort‐saving tools for researchers to use. The use of these models by multiple laboratories would standardize and homogenize methodologies to the benefit of reliable results and interpretations.
Distance, environmental and substrate factors impacting recovery of bryophyte communities after harvesting

Aims: Bryophyte re-colonization after disturbance is largely governed by environmental conditions within disturbed forests. In particular, distance to a forest edge is an important predictor of bryophyte community re-colonization, through either direct constraints, such as dispersal limitation, or indirectly by altering environmental conditions. This study examines a range of factors – environmental, distance to an edge, substrate specific environment or local-level environment – to determine which are important in the re-colonization of bryophyte communities after forest harvesting. As bryophyte communities vary with the particular substrate inhabited, responses were examined across four substrates (rock, exposed roots, ground and CWD). Location: Tasmanian southern forests, Australia. Methods: Bryophyte composition was examined on four substrates (ground, coarse wood debris, exposed roots, rocks) within three ages (~7, ~27 and ~45 yr post-disturbance) of harvested wet eucalypt forest. Re-colonization success of bryophyte communities was determined by comparing communities in regeneration forest to mature forest communities using axis scores from one-dimensional constrained ordination. The importance of various environmental conditions for re-colonization success was then modelled. Finally, path analysis was used to determine whether the impact of distance to a forest edge was meditated through its effects on key environmental variables. Results: Multiple environmental factors impacted re-colonization of mature bryophyte communities. Local-level conditions such as microclimate (temperature, humidity and VPD) and LAI were the most important in determining re-colonization across substrates. Path analysis showed that distance to a forest edge had a significant impact on re-colonization success, but only a relatively small part of this was mediated through its impact on environmental factors. Conclusions: Bryophyte re-colonization is driven by a combination of microclimate conditions and factors related to distance from a forest edge (most likely dispersal distance). While some substrate-specific factors impact bryophyte re-colonization success, the consistent impact of local environmental factors across substrates suggests that harvesting management strategies that develop more ‘mature’ microclimate conditions and increase proximity to nearby mature forest patches will be beneficial for all bryophytes communities. As bryophyte re-colonization was correlated with temporally dynamic environmental conditions, we suggest that forest age needs to be considered in future work.
Short communication: First data on the prevalence and distribution of pathogens in bumblebees (Bombus terrestris and Bombus pascuorum) from Spain

Bumblebees provide pollination services not only to wildflowers but also to economically important crops. In the context of the global decline of pollinators, there is an increasing interest in determining the pathogen diversity of bumblebee species. In this work, wild bumblebees of the species Bombus terrestris and Bombus pascuorum from northern and southern Spain were molecularly screened to detect and estimate prevalence of pathogens. One third of bumblebees were infected: while viruses only infected B. pascuorum , B. terrestris was infected by Apicystis bombi , Crithidia bombi and Nosema bombi . Ecological differences between host species might affect the success of the pathogens biological cycle and consequently infection prevalence. Furthermore, sex of the bumblebees (workers or males), sampling area (north or south) and altitude were important predictors of pathogen prevalence. Understanding how these factors affect pathogens distribution is essential for future conservation of bumblebee wild populations.
THE OLIVE TREE, A SOURCE OF ANTIOXIDANT COMPOUNDS

Products from Olea europaea L. i.e. leaves, olive oil and pomace are promising sources of bioactive compounds. In leaves, antioxidant compounds show a concentration dependence on the vegetative cycle of the trees, higher antioxidant concentration coinciding with seasonal vegetative changes. Olive oil, but particularly pomances are a rich source of health-giving effect compounds more specifically polyphenolic antioxidants. Many of these compounds may be of interest for pharmaceutical, cosmetic and food industry, especially because both pomance and leaves are currently considered waste of the olive oil production.
Epigenetic DNA modification monitored by a new fluorescence based tool

DNA methylation patterns are key epigenetic marks which control tissue specific gene expression. These patterns are faithfully replicated by the DNMT1 enzyme which is directed by the UHRF1 protein to hemi-methylated (HM) CpG sites. The high specificity of UHRF1 to HM CpG sites is related to the ability of its SRA domain to selectively flip methylcytosine (mC) residues. Therefore, the understanding of how UHRF1 reads DNA sequences and flips mC residues is an important question in molecular epigenetics. In the present work, we apply environment-sensitive nucleobase analogues to study the SRA-induced base flipping. We found that only labelling by 2-thienyl-3-hydroxychromone (3HCnt) outside but close to the target methylated CpG allows monitoring the SRA-induced mC-flipping and its dynamics. Fluorescence steady-state spectroscopy and stopped flow measurements showed significant differences in the recognition and binding kinetics of SRA for HM and non-methylated (NM) DNA. Indeed, SRA was found to bind and slide with fast kinetics on NM duplexes, in line with the reader role of UHRF1. In contrast, the kinetics of mC flipping was found to be much slower, substantially increasing the lifetime of UHRF1 bound to a CpG site in HM duplexes and thus, the probability of recruiting DNMT1 in order to faithfully duplicate the DNA methylation profile. Therefore, we proposed for the first time an assay able to sensitively monitor the UHRF1-induced base flipping, which helped us to provide a possible mechanism for the UHRF1 directing function on DNMT1.
An Electrochemical DNA-Hybridization Assay for Acinetobacter baumannii Detection

The present paper reported the analysis of the Acinetobacter baumannii using an electrochemical biosensor fabricated based on a gold electrode (AuE) with the electroactive label of β-cyclodextrin (βCD). Due to the formation of an Au–S bond, a thiol decorated single-stranded DNA probe was covalently immobilized onto the electrode surface. For the working mechanism of differential pulse voltammetry (DPV) on the DNA hybridization, the electrochemical signals of the β-CD binding reduction to the double-stranded DNA (ds-DNA) were recorded. Moreover, the as-prepared biosensor has the potential of being used for the analysis of Acinetobacter baumannii in excrement specimens.
Development of RNA-Seq SSR Markers and Application to Genetic Relationship Analysis among Sea Buckthorn Germplasm

A BSTRACT . Sea buckthorn ( Hippophae rhamnoides ) is an ecologically and economically valuable species that has been widely cultivated as a new berry crop rich in nutritional and medicinal compounds. RNA Sequencing (RNA-Seq) simple sequence repeat (SSR) markers were developed to evaluate the genetic relationships among 91 plants of 31 cultivars from two subspecies, mongolica and sinensis , as well as intraspeciﬁc hybrids between them. A total of 7540 RNA-Seq SSRs were identiﬁed as potential molecular markers, in which AG/CT (27.57%) was the most abundant unit type. AT/AT (9.93%), and AAG/CTT (11.95%) are the other main repeat motifs. A total of 110 primer pairs were randomly selected for validation of ampliﬁcation. Seventeen SSR loci, located in genes encoding metabolic processes and cellulose synthases, were identiﬁed to be polymorphic among different sea buckthorn cultivars. These SSR loci generated 48 alleles, ranging from 2 to 5 per locus. Cluster analysis based on the proportion of shared alleles and unweighted pair group method with arithmetic average (UPGMA) algorithm divided all the genotypes into two main groups, with all of the ssp. sinensis cultivars (native to China) and hybrids in one group and ssp. mongolica cultivars (introduced from Russia) in the other group, which was in good agreement with their taxonomic classiﬁcation. The RNA-Seq SSRs developed in this study have a potential use in the conservation of sea buckthorn germplasm and marker-assisted breeding (MAB).