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Dataset for: "BACPHLIP: Predicting bacteriophage lifestyle from conserved protein domains"
<p>This is the dataset used in the manuscript titled "BACPHLIP: Predicting bacteriophage lifestyle from conserved protein domains". The dataset is necessary to run the code that can be found at <a href="https://github.com/adamhockenberry/dca-weighting">https://github.com/adamhockenberry/bacphlip-model-dev</a> and outside of the context of the code this data will likely not be super well-annotated or helpful. The code within that repository, however, should provide sufficient information about the structure and usage of this dataset. </p>
Nocturnal bees feed on diurnal leftovers and pay the price of day–night lifestyle transition
<p>Bees exemplify flights under bright sunlight. A few species across bee families have evolved nocturnality, displaying remarkable adaptations to overcome limitations of their daylight-suited apposition eyes. Phase inversion to nocturnality in a minority of bees that co-exist with diurnal bees provide a unique opportunity to study ecological benefits that mediate total temporal niche shifts. While floral traits and sensory modalities associated with the evolution of classical nocturnal pollination syndromes, e.g. by bats and moths, are well-studied, nocturnality in bees represent a poorly understood, recently invaded, extreme niche.To test the competitive release hypothesis, we examine how nocturnality shapes foraging by comparing pollen loads, nest pollen and flower visitation of sympatric nocturnal and diurnal carpenter bees. We predicted that nocturnal bees primarily use night-blooming flowers, show little/no resource overlap with diurnal species and competitive release favours night-time pollen collection for provisioning. Contrarily, we found substantial resource overlap between nocturnal and diurnal bees. Flower opening times, floral longevity and plant abundance did not define nocturnal flower use. Smaller pollen loads on nocturnal foragers suggests subsistence on resource leftovers largely from diurnal flowers. Greater pollen types/diversity on nocturnal foragers indicates lower floral constancy compared to diurnal congenerics. Reduced activity during new moon compared to full moon suggests constraints to nocturnal foraging.Invasion and sustenance within the nocturnal niche is characterised by: i) <i>opportunistic foraging</i> on residual resources as indicated by smaller pollen loads, extensive utilisation of day-blooming flowers and substantial overlap with diurnal bees, ii) <i>generalisation at two levels</i> – between and within foraging trips as indicated by lower floral constancy, iii)r<i>educed foraging on darker nights</i>, indicating visual constraints despite sensitive optics. This together with smaller populations and univoltine breeding in nocturnal compared to multivoltine diurnal counterparts, suggest that nocturnality imposes substantial fitness costs. In conclusion, the evolution of nocturnality in bees is accompanied by resource generalisation instead of specialisation. Reduced floral constancy suggests differences in foraging strategies of nocturnal and diurnal bees which merits further investigation. The relative roles of competition, floral rewards and predators should be examined to fully understand the evolution and maintenance of nocturnality in bees.</p>
Description of the final instar larva of Cephalaeschna risi Asahina, 1981 with notes on its semi-terrestrial lifestyle (Odonata: Aeshnidae)
<p>Video of hunting behavior of larva of Cephalaeschna risi Asahina, 1981.</p>
Symbiotic lifestyle triggers drastic changes in the gene expression of the algal endosymbiont Breviolum minutum (Symbiodiniaceae)
Coral-dinoflagellate symbiosis underpins the evolutionary success of corals reefs. Successful exchange of molecules between the cnidarian host and the Symbiodiniaceae algae enables the mutualistic partnership. The algae translocate photosynthate to their host in exchange for nutrients and shelter. The photosynthate must traverse multiple membranes, most likely facilitated by transporters. Here, we compared gene expression profiles of free-living cultured and freshly isolated <i>Breviolum minutum</i>, the homologous symbiont of the coral model, the sea anemone <i>Exaiptasia pallida</i>. Additionally, we assessed expression levels of a select a list of candidate host transporters-of-interest in anemones with and without symbionts. Our transcriptome analyses highlight the distinctive nature of the two algal life stages, with many gene expression level changes correlating to the different morphologies, cell cycles, and metabolisms adopted in hospite versus free-living. Morphogenesis-related genes that likely underpin the metamorphosis process observed when symbionts enter a host cell were up-regulated. Conversely, many down-regulated genes appear to be indicative of the protective and confined nature of the symbiosome. Our results emphasize the significance of transmembrane transport to the symbiosis, and in particular of ammonium and sugar transport. Further, we pinpoint and characterize candidate transporters—localized variously to the algal plasma membrane, the host plasma membrane, and the symbiosome membrane— that likely serve pivotal roles in the interchange of material during symbiosis. Our study provides new insights that expand our understanding of the molecular exchanges that enable symbiotic relationship.
Are lifestyle pattern changes associated to poor subjective sleep quality?: a cross-sectional study by gender among the general Japanese population underwent specified medical checkups in 2014 and 2015.
<p>Objectives: Subjective sleep quality (SSQ) is defined by the satisfaction of one's overall sleep experience, and is composed of sleep depth and restfulness. It has not been clarified how poor SSQ is associated to changes in lifestyles. The purpose is to reveal the association of lifestyle pattern changes and poor SSQ.</p> <p>Design: A cross-sectional study.</p> <p>Setting: The data on basic attributes, SSQ, and lifestyle such as presence/absence of smoking, exercise, physical activity, supper time close to bedtime, drinking habits, and alcohol intake amount per day were obtained from database and questionnaire of specified medical checkups in FY 2014 and 2015 in Japan. The analysis was conducted in 2019.</p> <p>Participants: The subjects comprised 49,483 residents (26,087 males and 23,396 females), aged 40 to 74 years who had undergone an annual specified medical checkup from 2014 to 2015 in Fukushima Prefecture, Japan.</p> <p>Outcome measure: Status of SSQ in 2015 was assessed using a question asking whether or not the subjects usually got enough sleep. Poor SSQ in 2015 and lifestyle pattern changes in 2014-2015 were compared between those who were in healthy status both in 2014 and 2015 (referent) and non-referent, using binary logistic regression analysis.</p> <p>Results: Unhealthy lifestyle pattern for 2014-2015 was significantly associated to poor SSQ in 2015: "absent to absent" in exercise for males (Odds ratio [OR] = 1.472; 95% confidence interval [CI] = 1.316, 1.647) and females (OR = 1.428; 95%CI = 1.285, 1.587), physical activity for males (OR = 1.420; 95%CI = 1.270, 1.588) and females (OR = 1.471; 95%CI = 1.322, 1.638), and "present to present" in supper time for males (OR = 1.149; 95%CI = 1.020, 1.294) and females (OR = 1.288; 95%CI = 1.102, 1.505).</p> <p>Conclusions: Health care workers may be able to contribute to the improvement of SSQ, focusing on changeable lifestyles.</p>
Data from: EdAl-2 (Educació en Alimentació) programme: reproducibility of a cluster randomised, interventional, primary-school-based study to induce healthier lifestyle activities in children
Objectives: To assess the reproducibility of an educational intervention EdAl-2 (Educació en Alimentació) programme in 'Terres de l'Ebre' (Spain), over 22 months, to improve lifestyles, including diet and physical activity (PA). Design: Reproduction of a cluster randomised controlled trial. Setting: Two semi-rural town-group primary-school clusters were randomly assigned to the intervention or control group. Participants: Pupils (n=690) of whom 320 constituted the intervention group (1 cluster) and 370 constituted the control group (1 cluster). Ethnicity was 78% Western European. The mean age (±SD) was 8.04±0.6 years (47.7% females) at baseline. Inclusion criteria for clusters were towns from the southern part of Catalonia having a minimum of 500 children aged 7–8 year; complete data for participants, including name, gender, date and place of birth, and written informed consent from parents or guardians. Intervention: The intervention focused on eight lifestyle topics covered in 12 activities (1 h/activity/session) implemented by health promoting agents in the primary school over three academic years. Primary and secondary outcomes: The primary outcome was obesity (OB) prevalence and the secondary outcomes were body mass index (BMI) collected every year and dietary habits and lifestyles collected by questionnaires filled in by parents at baseline and end-of-study. Results: At 22 months, the OB prevalence and BMI values were similar in intervention and control groups. Relative to children in control schools, the percentage of boys in the intervention group who performed ≥4 after-school PA h/week was 15% higher (p=0.027), whereas the percentage of girls in both groups remained similar. Also, 16.6% more boys in the intervention group watched ≤2 television (TV) h/day (p=0.009), compared to controls; and no changes were observed in girls in both groups. Conclusions: Our school-based intervention is feasible and reproducible by increasing after-school PA (to ≥4 h/week) in boys. Despite this improvement, there was no change in BMI and prevalence of OB.
Data from: Genetic and lifestyle risk factors for MRI-defined brain infarcts in a population-based setting
Objective: We explored genetic and lifestyle risk factors of MRI-defined brain infarcts (BI) in large population-based cohorts. Methods: We performed meta-analyses of genome-wide association studies (GWAS) and examined associations of vascular risk factors and their genetic risk scores (GRS) with MRI-defined BI and a subset of BI, namely small sub-cortical BI (SSBI), in eighteen population-based cohorts (N=20,949) from five ethnicities (3,726 with BI, 2,021 with SSBI). Top loci were followed up in seven population-based cohorts (N=6,862, 1,483 with BI, 630 with SBBI), and tested associations with related phenotypes including ischemic stroke and pathologically-defined BI. Results: The mean prevalence was 17.7% for BI and 10.5% for SSBI, steeply rising after age 65. Two loci showed genome-wide significant association with BI: FBN2, P=1.77×10-8 and LINC00539/ZDHHC20, P=5.82×10-9. Both have been associated with blood pressure (BP) related phenotypes, but did not replicate in the smaller follow-up sample nor show associations with related phenotypes. Age and sex-adjusted associations with BI and SSBI were observed for BP traits (P-value for BI, P[BI]=9.38×10-25; P[SSBI]=5.23×10-14 for hypertension), smoking (P[BI]=4.4×10-10; P[SSBI]=1.2×10-4), diabetes (P[BI]=1.7×10-8; P[SSBI]=2.8×10-3), previous cardiovascular disease (P[BI]=1.0×10-18; P[SSBI]=2.3×10-7), stroke (P[BI]=3.9×10-69; P[SSBI]=3.2×10-24), and MRI-defined white matter hyperintensity burden (P[BI]=1.43×10-157; P[SSBI]=3.16×10-106), but not with body-mass-index or cholesterol. GRS of BP traits were associated with BI and SSBI (P≤0.0022), without indication of directional pleiotropy. Conclusions: In this multi-ethnic GWAS meta-analysis, including over 20,000 population-based participants, we identified genetic risk loci for BI requiring validation once additional large datasets become available. High BP, including genetically determined, was the most significant modifiable, causal risk factor for BI.
Data from: Phylogenetic analyses reveal molecular signatures associated with functional divergence among Subtilisin like Serine Proteases are linked to lifestyle transitions in Hypocreales
Background: Subtilisin-like serine proteases or Subtilases in fungi are important for penetration and colonization of host. In Hypocreales, these proteins share several properties with other fungal, bacterial, plant and mammalian homologs. However, adoption of specific roles in entomopathogenesis may be governed by attainment of unique biochemical and structural features during the evolutionary course. Due to such functional shifts Subtilases coded by different family members of Hypocreales acquire distinct features according to respective hosts and lifestyle. We conducted phylogenetic and DIVERGE analyses and identified important protein residues that putatively assign functional specificity to Subtilases in fungal families/species under the order Hypocreales. Results: A total of 161 Subtilases coded by 10 species from five different families under the fungal order Hypocreales was included in the analysis. Based on the presence of conserved domains, the Subtilase genes were divided into three subfamilies, Subtilisin (S08.005), Proteinase K (S08.054) and Serine-carboxyl peptidases (S53.001). These subfamilies were investigated for phylogenetic associations, protein residues under positive selection and functional divergence among paralogous clades. The observations were co-related with the life-styles of the fungal families/species. Phylogenetic and Divergence analyses of Subtilisin (S08.005) and Proteinase K (S08.054) families of proteins revealed that the paralogous clades were clear-cut representation of familial origin of the protein sequences. We observed divergence between the paralogous clades of plant-pathogenic fungi (Nectriaceae), insect-pathogenic fungi (Cordycipitaceae/Clavicipitaceae) and nematophagous fungi (Ophiocordycipitaceae). In addition, Subtilase genes from the nematode-parasitic fungus Purpureocillium lilacinum made a unique cluster which putatively indicated that the fungus might have developed distinctive mechanisms for nematode-pathogenesis. Our evolutionary genetics analysis revealed evidence of positive selection on the Subtilisin (S08.005) and Proteinase K (S08.054) protein sequences of the entomopathogenic and nematophagous species belonging to Cordycipitaceae, Clavicipitaceae and Ophiocordycipitaceae families of Hypocreales. Conclusions: Our study provided new insights into the evolution of Subtilisin like serine proteases in Hypocreales, a fungal order largely consisting of biological control species. Subtilisin (S08.005) and Proteinase K (S08.054) proteins seemed to play important roles during life style modifications among different families and species of Hypocreales. Protein residues found significant in functional divergence analysis in the present study may provide support for protein engineering in future.
Data from: A new phylogenetic hypothesis of turtles with implications for the timing and number of evolutionary transitions to marine lifestyles in the group
Evolutionary transitions to marine habitats occurred frequently among Mesozoic reptiles. Only one such clade survives to the present: sea turtles (Chelonioidea). Other marine turtles originated during the Mesozoic, but uncertain affinities of key fossils have obscured the number of transitions to marine life, and the timing of the origin of marine adaptation in chelonioids. Phylogenetic studies support either a highly‐inclusive chelonioid total‐group including fossil marine clades from the Jurassic and Cretaceous (e.g. protostegids, thalassochelydians, sandownids) or a less inclusive chelonioid total‐group excluding those clades. Under this paradigm, these clades belong outside Cryptodira, and represent at least one additional evolutionary transition to marine life in turtles. We present a new phylogenetic hypothesis informed by high resolution computed tomographic data of living and fossil taxa. Besides a well‐supported Chelonioidea, which includes protostegids, we recover a previously unknown clade of stem‐group turtles, Angolachelonia, which includes the Late Jurassic thalassochelydians, and the Cretaceous–Palaeogene sandownids. Accounting for the Triassic Odontochelys, our results indicate three independent evolutionary transitions to marine life in non‐pleurodiran turtles (plus an additional two‐three in pleurodires). Among all independent origins of marine habits, a pelagic ecology only evolved once, among chelonioids. All turtle groups that independently invaded marine habitats in the Jurassic–Cretaceous (chelonioids, angolachelonians, bothremydid pleurodires) survived the Cretaceous–Palaeogene mass extinction event. This highlights extensive survival of marine turtles compared to other marine reptiles. Furthermore, deeply‐nested clades such as chelonioids are found by the middle Early Cretaceous, suggesting a rapid diversification of crown‐group turtles during the Early Cretaceous.
Effect of Structured Diet with Exercise Education on Anthropometry and Lifestyle Modification in Patients with Type 2 Diabetes: A 12-Month Randomized Clinical Trial
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lifestyle_dataset
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Figure 3 from: Santos-Silva C, Louro R, Natário B, Nobre T (2021) Lack of knowledge on ecological determinants and cryptic lifestyles hinder our understanding of Terfezia diversity. MycoKeys 84: 1-14. https://doi.org/10.3897/mycokeys.84.71372
Figure 3 Terfezia species collected in the present work AT. arenariaBT. fanfaniCT. cistophilaDT. griseaET. dunensisFT. extremadurensisGT. lusitanicaHT. piniIT. solaris-libera.
Figure 1 from: Santos-Silva C, Louro R, Natário B, Nobre T (2021) Lack of knowledge on ecological determinants and cryptic lifestyles hinder our understanding of Terfezia diversity. MycoKeys 84: 1-14. https://doi.org/10.3897/mycokeys.84.71372
Figure 1 a Phylogenetic relationship between Terfezia species. The reconstructed phylogeny corresponds to the majority rule consensus tree higher than 0.50 of trees sampled in a Bayesian analysis, and the posterior probability values are shown for main nodes b clades with new sequenced specimens collected within the present study.
Figure 2 from: Santos-Silva C, Louro R, Natário B, Nobre T (2021) Lack of knowledge on ecological determinants and cryptic lifestyles hinder our understanding of Terfezia diversity. MycoKeys 84: 1-14. https://doi.org/10.3897/mycokeys.84.71372
Figure 2 Phylogenetic reconstruction of intra-species diversity (Fig. 1) linking to soil properties and putative host plant aT. arenariabT. fanfanicT. grisea [specimens in the circle represent deviations from the ecological grouping, see text for details] dT. lusitanica. The other species are identified and their relation to soil and host plant are presented in the main text.
Supplementary material 1 from: Santos-Silva C, Louro R, Natário B, Nobre T (2021) Lack of knowledge on ecological determinants and cryptic lifestyles hinder our understanding of Terfezia diversity. MycoKeys 84: 1-14. https://doi.org/10.3897/mycokeys.84.71372
Table S1
Figure 13 in Amphibioplanidae: a new branch and family on the phylogenetic tree of the triclad flatworms (Platyhelminthes: Tricladida), represented by a species from Sardinian caves with a remarkable lifestyle
Figure 13. Amphibioplana onnisi. Schematic horizontal reconstruction of the copulatory apparatus.
Figure 3 in Underestimated diversity and range size of diving beetles in tank bromeliads-Coleoptera of 'hygrofloric' lifestyle (Dytiscidae)
Figure 3. Distributional map of bromeliadicolous Copelatus species.
Fig. 8 in Gill dimensions in near-term embryos of Amazonian freshwater stingrays (Elasmobranchii: Potamotrygonidae) and their relationship to the lifestyle and habitat of neonatal pups
Fig. 8. Dendrogram showing the association of freshwater stingrays based on the gill morphometry of the embryos.
◂Fig. 1 Live photos and dissection of parasitized Aphrodita longipalpa and Veneriserva pygoclava. A Ventral view of A. longipalpa. B Dorsal view of A. longipalpa with removed feltage chaetae, revealing the parasite visible through the body wall. C Ventrally dissected A. longipalpa, exposing the sizable female parasite. Veneriserva pygoclava individuals within the host are indicated by arrowheads. D Juvenile female V. pygoclava, with developing oocytes visible through the body wall along the mid-dorsal orange line. E Female V. pygoclava showing the mid-dorsal orange pigmentation and the white mark at the base of the prostomium. F Male V. pygoclava. G A large female and smaller male V. pygoclava, extracted from the same host. The pygidium is club-shaped in both males and females and juveniles. H Juvenile V. pygoclava shown from multiple angles, characterized by a complete white coloration; black jaws are magnified in panel in Hardly Venus's servant-morphological adaptations of Veneriserva to an endoparasitic lifestyle and its phylogenetic position within Dorvilleidae (Annelida)
◂Fig. 1 Live photos and dissection of parasitized Aphrodita longipalpa and Veneriserva pygoclava. A Ventral view of A. longipalpa. B Dorsal view of A. longipalpa with removed feltage chaetae, revealing the parasite visible through the body wall. C Ventrally dissected A. longipalpa, exposing the sizable female parasite. Veneriserva pygoclava individuals within the host are indicated by arrowheads. D Juvenile female V. pygoclava, with developing oocytes visible through the body wall along the mid-dorsal orange line. E Female V. pygoclava showing the mid-dorsal orange pigmentation and the white mark at the base of the prostomium. F Male V. pygoclava. G A large female and smaller male V. pygoclava, extracted from the same host. The pygidium is club-shaped in both males and females and juveniles. H Juvenile V. pygoclava shown from multiple angles, characterized by a complete white coloration; black jaws are magnified in panel
Data from: Mechanistic model of evolutionary rate variation en route to a nonphotosynthetic lifestyle in plants
Because novel environmental conditions alter the selection pressure on genes or entire subgenomes, adaptive and nonadaptive changes will leave a measurable signature in the genomes, shaping their molecular evolution. We present herein a model of the trajectory of plastid genome evolution under progressively relaxed functional constraints during the transition from autotrophy to a nonphotosynthetic parasitic lifestyle. We show that relaxed purifying selection in all plastid genes is linked to obligate parasitism, characterized by the parasite's dependence on a host to fulfill its life cycle, rather than the loss of photosynthesis. Evolutionary rates and selection pressure coevolve with macrostructural and microstructural changes, the extent of functional reduction, and the establishment of the obligate parasitic lifestyle. Inferred bursts of gene losses coincide with periods of relaxed selection, which are followed by phases of intensified selection and rate deceleration in the retained functional complexes. Our findings suggest that the transition to obligate parasitism relaxes functional constraints on plastid genes in a stepwise manner. During the functional reduction process, the elevation of evolutionary rates reaches several new rate equilibria, possibly relating to the modified protein turnover rates in heterotrophic plastids.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.