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Fig. 4 in The Role Of Different Mollusk Species In Maintaining The Transmission Of Polyhostal Trematode Species In Ukrainian Polissya Waters: The Specificity Of Trematode Parthenogenetic Generations To Mollusk Hosts

Fig. 4. The distribution of olygoxenic three-host trematode species in the parthenitae host species of mollusks: A — E. stantschinskii; B — P. ovata; C — C. cornutus; D — T. clavata.

Fig. 3 in The Role Of Different Mollusk Species In Maintaining The Transmission Of Polyhostal Trematode Species In Ukrainian Polissya Waters: The Specificity Of Trematode Parthenogenetic Generations To Mollusk Hosts

Fig. 3. The distribution of polyxenic trematode species in the parthenitae host species of mollusks: A — H. conoideum; B — E. recurvatum.

Fig. 6 in The Role Of Different Mollusk Species In Maintaining The Transmission Of Polyhostal Trematode Species In Ukrainian Polissya Waters: The Specificity Of Trematode Parthenogenetic Generations To Mollusk Hosts

Fig. 6. The distribution of olygoxenic two-host trematode species in the parthenitae host species of mollusks: A — P. ichikawai; B — D. subclavatus; C — F. hepatica; D — L. constantinovae; E — A. imitans.

Fig. 2 in The Role Of Different Mollusk Species In Maintaining The Transmission Of Polyhostal Trematode Species In Ukrainian Polissya Waters: The Specificity Of Trematode Parthenogenetic Generations To Mollusk Hosts

Fig. 2. The distribution of olygoxenic three-host trematode species in the parthenitae host species of mollusks: A — H. cylindracea; B — H. variegatus; C — E. aconiatum; D — E. revolutum.

Fig. 5 in The Role Of Different Mollusk Species In Maintaining The Transmission Of Polyhostal Trematode Species In Ukrainian Polissya Waters: The Specificity Of Trematode Parthenogenetic Generations To Mollusk Hosts

Fig. 5. The distribution of polyxenic trematode species in the parthenitae host species of mollusks: A — N. attentuatus; B — L. scotiae.

opencc-zeroApr 2022View details →

Food deprivation exposes sex-specific trade-offs between stress tolerance and lifespan in the copepod Tigriopus californicus

Long life is standardly assumed to be associated with high stress tolerance. Previous work shows that the copepod Tigriopus californicus breaks this rule, with longer lifespan under benign conditions found in males, the sex with lower stress tolerance. Here we extended this previous work, raising animals from the same families in food-replete conditions until adulthood and then transferring them to food-limited conditions until all animals perished. As in previous work, survivorship under food-replete conditions favored males. However, under food deprivation lifespan strongly favored females in all crosses. Compared to benign conditions, average lifespan under nutritional stress was reduced by 47% in males but only 32% in females. Further, the sex-specific mitonuclear effects previously found under benign conditions were erased under food limited conditions. Results thus demonstrate that sex-specific lifespan, including mitonuclear interactions, are highly dependent on nutritional environment.

opencc-zeroApr 2022View details →

Sex-specific body mass aging trajectories in adult Asian elephants

In species with marked sexual dimorphism, the classic prediction is that the sex which undergoes stronger intrasexual competition ages earlier or quicker. However, more recently, alternative hypotheses have been put forward, showing that this association can be disrupted. Here, we utilise a unique, longitudinal dataset of a semi-captive population of Asian elephants (Elephas maximus), a species with marked male-biased intrasexual competition, with males being larger and having shorter lifespans, and investigate whether males show earlier and/or faster body mass ageing than females. We found evidence of sex-specific body mass ageing trajectories: adult males gained weight up to the age of 48 years old, followed by a decrease in body mass until natural death. In contrast, adult females gained body mass with age until a body mass decline in the last year of life. Our study shows sex-specific ageing patterns, with an earlier onset of body mass declines in males than females, which is consistent with the predictions of the classical theory of ageing.

opencc-by-4.0Dec 2021View details →

SCADIE: simultaneous estimation of cell type proportions and cell type-specific gene expressions using SCAD-based iterative estimating procedure

This repository contains the source code and data used in the paper: SCADIE: simultaneous estimation of cell type proportions and cell type-specific gene expressions using SCAD-based iterative estimating procedure.1.

opencc-zeroMay 2022View details →

Conflict over the eukaryote root resides in strong outliers, mosaics and missing data sensitivity of site-specific (CAT) mixture models

Abstract Phylogenetic reconstruction using concatenated loci ("phylogenomics" or "supermatrix phylogeny") is a powerful tool for solving evolutionary splits that are poorly resolved in single gene/protein trees (SGTs). However, recent phylogenomic attempts to resolve the eukaryote root have yielded conflicting results, along with claims of various artefacts hidden in the data. We have investigated these conflicts using two new methods for assessing phylogenetic conflict. ConJak uses whole marker (gene or protein) jackknifing to assess deviation from a central mean for each individual sequence, while ConWin uses a sliding window to screen for incongruent protein fragments (mosaics). Both methods allow selective masking of individual sequences or sequence fragments in order to minimize missing data, an important consideration for resolving deep splits with limited data. Analyses focused on a set of 76 eukaryotic proteins of bacterial-ancestry previously used in various combinations to assess the branching order among the three major divisions of eukaryotes: Amorphea (mainly animals, fungi and Amoebozoa), Diaphoretickes (most other well-known eukaryotes and nearly all algae) and Excavata, represented here by Discoba (Jakobida, Heterolobosea, and Euglenozoa). ConJak analyses found strong outliers to be concentrated in under-sampled lineages, while ConWin analyses of Discoba, the most under-sampled of the major lineages, detected potentially incongruent fragments scattered throughout. Phylogenetic analyses of the full data using an LG-gamma model support a Discoba sister scenario (neozoan-excavate root), which rises to 99-100% bootstrap support with data masked according to either protocol. However, analyses with two site-specific (CAT) mixture models yielded widely inconsistent results and a striking sensitivity to missing data. The neozoan-excavate root places Amorphea and Diaphoretickes as more closely related to each other than either is to Discoba, a fundamental relationship that should remain unaffected by additional taxa.

opencc-by-4.0May 2022View details →

JPG images from the publication "Corncob structures in dental plaque reveal microhabitat taxon specificity"

Images of bacteria in human dental plaque after fluorescence in situ hybridization, hyperspectral imaging with a Zeiss LSM 780 or LSM 880 laser-scanning confocal microscope, and spectral unmixing.  Each image is presented as a color JPG. Cells hybridizing with the probe for Streptococcus cristatus are shown in cyan; cells hybridizing with the probe for Streptococcus mitis, S. oralis, and S. infantis are shown in red; cells of genus Corynebacterium are shown in magenta; cells of genera Haemophilus and Aggregatibacter are shown in yellow; and cells of genus Porphyromonas are shown in blue. Images labeled as "set 1" (probe set 1) include all probes; "set 2" (probe set 2) and "set 3" (probe set 3) include only probes for S. cristatus, the S. mitis group, the Streptococcus genus, Corynebacterium genus, and Porphyromonas genus.

opencc-by-4.0May 2022View details →

TIFF images from the publication "Corncob structures in dental plaque reveal microhabitat taxon specificity"

Images of bacteria in human dental plaque after fluorescence in situ hybridization, hyperspectral imaging with a Zeiss LSM 780 or LSM 880 laser-scanning confocal microscope, and spectral unmixing.  Each image is presented as a TIFF file. Cells hybridizing with the probe for Streptococcus cristatus are shown in cyan; cells hybridizing with the probe for Streptococcus mitis, S. oralis, and S. infantis are shown in red; cells of genus Corynebacterium are shown in magenta; cells of genera Haemophilus and Aggregatibacter are shown in yellow; and cells of genus Porphyromonas are shown in blue. Images labeled as "set 1" (probe set 1) include all probes; "set 2" (probe set 2) and "set 3" (probe set 3) include only probes for S. cristatus, the S. mitis group, the Streptococcus genus, Corynebacterium genus, and Porphyromonas genus.

opencc-by-4.0May 2022View details →

Unmixed images from the publication "Corncob structures in dental plaque reveal microhabitat taxon specificity"

Images of bacteria in human dental plaque after fluorescence in situ hybridization, hyperspectral imaging with a Zeiss LSM 780 or LSM 880 laser-scanning confocal microscope, and spectral unmixing.  Each image is presented as a stack of the individual unmixed fluorophore channels readable using FIJI (ImageJ) with the Image5D plugin. Channels are shown for Streptococcus cristatus; the Streptococcus mitis group including S. oralis and S. infantis; Streptococcus gordonii; Streptococcus genus; Corynebacterium genus; Corynebacterium matruchotii; Porphyromonas genus; and family Pasteurellaceae including genera Haemophilus and Aggregatibacter.  A channel for the residual signal after linear unmixing is also included, as well as a transmitted light image (transmitted PMT).  Images labeled as "set 1" (probe set 1) include all probes; "set 2" (probe set 2) and "set 3" (probe set 3) include only probes for S. cristatus, the S. mitis group, the Streptococcus genus, Corynebacterium genus, and Porphyromonas genus.

opencc-zeroMay 2022View details →

β-cell-specific deletion of Zfp148 improves nutrient-stimulated β-cell Ca2+ responses

Insulin secretion from pancreatic β-cells is essential for glucose homeostasis. An insufficient response to the demand for insulin results in diabetes. We previously showed that β-cell-specific deletion of Zfp148 (β-Zfp148KO) improves glucose tolerance and insulin secretion in mice. Here, we performed Ca2+ imaging of islets from β‑Zfp148KO and control mice on both a chow and a Western-style diet. β-Zfp148KO islets demonstrate improved sensitivity and sustained Ca2+ oscillations in response to elevated glucose. β-Zfp148KO islets also exhibit elevated sensitivity to amino acid-induced Ca2+ influx under low glucose conditions, suggesting enhanced mitochondrial phosphoenolpyruvate (PEP)-dependent KATP channel closure, independent of glycolysis. RNA sequencing and proteomics of β-Zfp148KO islets revealed altered levels of enzymes involved in amino acid metabolism (SLC3A2, SLC7A8, GLS, GLS2, PSPH, PHGDH, PSAT1) and intermediary metabolism (GOT1, PCK2), consistent with altered PEP cycling. In agreement with this, β-Zfp148KO islets displayed enhanced insulin secretion in response to L-glutamine and activation of glutamate dehydrogenase. Understanding pathways controlled by ZFP148 may provide promising strategies for improving β-cell function that are robust to the metabolic challenge imposed by a Western diet.

opencc-zeroMay 2022View details →

Meta-analysis suggests variable, but pCO2-specific, effects of ocean acidification on crustacean biomaterials

Crustaceans comprise an ecologically and morphologically diverse taxonomic group. They are typically considered resilient to many environmental perturbations found in marine and coastal environments, due to effective physiological regulation of ions and hemolymph pH, and a robust exoskeleton. Ocean acidification can affect the ability of marine calcifying organisms to build and maintain mineralized tissue and poses a threat for all marine calcifying taxa. Currently, there is no consensus on how ocean acidification will alter the ecologically-relevant exoskeletal properties of crustaceans. Here, we present a systematic review and meta-analysis on the effects of ocean acidification on the crustacean exoskeleton, assessing both exoskeletal ion content (calcium and magnesium) and functional properties (biomechanical resistance and cuticle thickness). Our results suggest that the effect of ocean acidification on crustacean exoskeletal properties varies based upon seawater pCO2 and species identity, with significant levels of heterogeneity for all analyses. Calcium and magnesium content were significantly lower in animals held at pCO2 levels of 1500-1999 μatm as compared to those under ambient pCO2. At lower pCO2 levels, however, statistically significant relationships between changes in calcium and magnesium content within the same experiment were observed: a negative relationship between calcium and magnesium content at pCO2 of 500-999 μatm and a positive relationship at 1000-1499 μatm. Exoskeleton biomechanics, such as resistance to deformation (microhardness) and shell strength, also significantly decreased under pCO2 regimes of 500-999 μatm and 1500-1999 μatm, indicating functional exoskeletal change coincident with decreases in calcification. Overall, these results suggest that the crustacean exoskeleton can be susceptible to ocean acidification at the biomechanical level, potentially predicated on changes in ion content, when exposed to high influxes of CO2. Future studies will need to accommodate the high variability of crustacean responses to ocean acidification, as well as ecologically-relevant ranges of pCO2 conditions, when designing experiments with conservation-level endpoints. --

opencc-by-4.0Jun 2022View details →

In-depth characterization revealed polymer type and chemical content specific effects of microplastic on Dreissena bugensis

The files contain datasets that were generated during laboratory-based real-time valvometry, and laser doppler anemometry measurements. The article was published in Journal of Hazardous Materials (accepted June 8, 2022).

opencc-zeroJun 2022View details →

Data from: Sex-specific life history affected by stocking in juvenile brown trout

Salmonids are a socioeconomically and ecologically important group of fish that are often managed by stocking. Little is known about potential sex-specific effects of stocking, but recent studies found that the sexes differ in their stress tolerances already at late embryonic stage, i.e., before hatchery-born larvae are released into the wild and long before morphological gonad formation. It has also been speculated that sex-specific life histories can affect juvenile growth and mortality, and that a resulting sex-biassed demography can reduce population growth. Here we test whether juvenile brown trout (Salmo trutta) show sex-specific life histories and whether such sex effects differ in hatchery- and wild-born fish. We modified a genetic sexing protocol to reduce false assignment rates and used it to study the timing of sex differentiation in a laboratory setting, and in a large-scale field experiment to study growth and mortality of hatchery and wild-born fish in different environments. We found no sex-specific mortality in any of the environments we studied. However, females started sex differentiation earlier than males, and while growth rates were similar in the laboratory, they differed significantly in the field depending on location and origin of fish. Overall, hatchery-born males grew larger than hatchery-born females while wild-born fish showed the reverse pattern. Whether males or females grew larger was location-specific. We conclude that juvenile brown trout show sex-specific growth that is affected by stocking and by other environmental factors that remain to be identified.

opencc-by-4.0Aug 2021View details →

Sex-specific tuning of modular muscle activation patterns for locomotion in young and older adults

There is increasing evidence that including sex as a biological variable is of crucial importance to promote rigorous, repeatable and reproducible science. In spite of this, the body of literature that accounts for the sex of participants in human locomotion studies is small and often produces controversial results. Here, we investigated the modular organization of muscle activation patterns for human locomotion using the concept of muscle synergies with a double purpose: i) uncover possible sex-specific characteristics of motor control and ii) assess whether these are maintained in older age. We recorded electromyographic activities from 13 ipsilateral muscles of the lower limb in young and older adults of both sexes walking (young and old) and running (young) on a treadmill. The data set obtained from the 215 participants was elaborated through non-negative matrix factorization to extract the time-independent (i.e., motor modules) and time-dependent (i.e., motor primitives) coefficients of muscle synergies. We found sparse sex-specific modulations of motor control. Motor modules showed a different contribution of hip extensors, knee extensors and foot dorsiflexors in various synergies. Motor primitives were wider (i.e., lasted longer) in males in the propulsion synergy for walking (but only in young and not in older adults) and in the weight acceptance synergy for running. Moreover, the complexity of motor primitives was similar in younger adults of both sexes, but lower in older females as compared to older males. In essence, our results revealed the existence of small but defined sex-specific differences in the way humans control locomotion and that these strategies are not entirely maintained in older age. In this supplementary data set we made available: a) the metadata with anonymized participant information; b) the raw EMG, already concatenated for the overground trials; c) the touchdown and lift-off timings of the recorded limb, d) the code to process the data. In total, 520 trials from 215 participants are included in the supplementary data set. The file “metadata.dat” is available in ASCII format and contains: <ul> <li>Code: the participant’s code</li> <li>Group: the participant's group (G1=young adults, walking; G2=old adults, walking; G3=young adults, running)</li> <li>Sex: the participant’s sex (M or F)</li> <li>Locomotion: the type of locomotion (walking or running)</li> <li>Speed: the speed at which the recordings were conducted in [m/s]</li> <li>Speed_type: the distinction between fixed (decided by the researchers) or preferred (selected by the participant) speed</li> <li>Age: the participant’s age in years</li> <li>Height: the participant’s height in [cm]</li> <li>Mass: the participant’s body mass in [kg].</li> </ul> The "RAW_DATA.RData" R list consists of elements of S3 class "EMG", each of which is a human locomotion trial containing cycle segmentation timings and raw electromyographic (EMG) data from 13 muscles of the right-side leg. Cycle times are structured as data frames containing two columns that correspond to touchdown (first column) and lift-off (second column). Raw EMG data sets are also structured as data frames with one row for each recorded data point and 14 columns. The first column contains the incremental time in seconds. The remaining 13 columns contain the raw EMG data, named with the following muscle abbreviations: ME = gluteus medius, MA = gluteus maximus, FL = tensor fasciæ latæ, RF = rectus femoris, VM = vastus medialis, VL = vastus lateralis, ST = semitendinosus, BF = biceps femoris, TA = tibialis anterior, PL = peroneus longus, GM = gastrocnemius medialis, GL = gastrocnemius lateralis, SO = soleus. Trials are named like “ID0020_M_YOUNG_TW_01,” where the characters “ID0020” indicate the participant number (in this example the 20th), the character “M” indicates the sex, the characters “YOUNG” indicate the age group, the characters “TW” indicate the locomotion type and environment (T=treadmill, W=walking, R=running), and the numbers “01” indicate the trial number. Old versions not compatible with the R package <a href="https://CRAN.R-project.org/package=musclesyneRgies">musclesyneRgies</a> The files containing the gait cycle breakdown are available in RData format, in the file named “CYCLE_TIMES.RData”. The files are structured as data frames with one row for each gait cycle and two columns. The first column contains the touchdown incremental times in seconds. The second column contains the duration of each stance phase in seconds. Each trial is saved as an element of a single R list. Trials are named like “CYCLE_TIMES_ID0020_M_YOUNG_TW_01,” where the characters “CYCLE_TIMES” indicate that the trial contains the gait cycle breakdown times, the characters “ID0020” indicate the participant number (in this example the 20th), the character “M” indicates the sex, the characters “YOUNG” indicate the age group, the characters “TW” indicate the locomotion type and environment (T=treadmill, W=walking, R=running), and the numbers “01” indicate the trial number. The files containing the raw, filtered, and the normalized EMG data are available in RData format, in the files named “RAW_EMG.RData” and “FILT_EMG.RData”. The raw EMG files are structured as data frames with one row for each recorded data point and 14 columns. The first column contains the incremental time in seconds. The remaining 13 columns contain the raw EMG data, named with the following muscle abbreviations: ME = gluteus medius, MA = gluteus maximus, FL = tensor fasciæ latæ, RF = rectus femoris, VM = vastus medialis, VL = vastus lateralis, ST = semitendinosus, BF = biceps femoris, TA = tibialis anterior, PL = peroneus longus, GM = gastrocnemius medialis, GL = gastrocnemius lateralis, SO = soleus. Each trial is saved as an element of a single R list. Trials are named like “RAW_EMG_ID0003_F_OLD_TW_01”, where the characters “RAW_EMG” indicate that the trial contains raw emg data, the characters “ID0003” indicate the participant number (in this example the 3rd), the character “F” indicates the sex, the characters “OLD” indicate the age group, the characters “TW” indicate the locomotion type and environment (see above), and the numbers “01” indicate the trial number. All the code used for the pre-processing of EMG data and the extraction of muscle synergies is available in R format. Explanatory comments are profusely present throughout the script “muscle_synergies.R”. The latest version of this code can be found at https://github.com/alesantuz/musclesyneRgies.

opencc-zeroJun 2022View details →

Raw data from: Inter- and intra-specific variation in mycotoxin tolerance: A study of four Drosophila species

Many mycophagous Drosophila species have adapted to tolerate high concentrations of mycotoxins, an ability not reported in any other eukaryotes. Although an association between mycophagy and mycotoxin tolerance has been established in many Drosophila species, the genetic mechanisms of the tolerance are unknown. This study presents the inter- and intraspecific variation in the mycotoxin tolerance trait. We studied the mycotoxin tolerance in four Drosophila species from four separate clades within the immigrans-tripunctata radiation from two distinct locations. The effect of mycotoxin treatment on 20 isofemale lines per species was studied using seven gross phenotypes: survival to pupation, survival to eclosion, development time to pupation and eclosion, thorax length, fecundity, and longevity. We observed interspecific variation among four species, with D. falleni being the most tolerant, followed by D. recens, D. neotestacea, and D. tripunctata, in that order. The results also revealed geographical variation and intraspecific genetic variation in mycotoxin tolerance. This report provides the foundation for further delineating the genetic mechanisms of the mycotoxin tolerance trait.

opencc-by-4.0Jul 2022View details →

Transcriptomic analysis of deceptively pollinated Arum maculatum (Araceae) reveals association between terpene synthase expression in floral trap chamber and species-specific pollinator attraction

A compressed folder containing the R script and input files required to replicate the results in our manuscript entitled "Transcriptomic analysis of deceptively pollinated Arum maculatum (Araceae) reveals association between terpene synthase expression in floral trap chamber and species-specific pollinator attraction". Note: Raw Illumina sequencing files associated with this study have been uploaded to NCBI SRA, under the BioProject accession PRJNA856436. ABSTRACT Deceptive pollination often involves volatile organic compound (VOC) emissions that mislead insects into performing non-rewarding pollination. Among deceptively pollinated plants, Arum maculatum is particularly well-known for its potent dung-like VOC emissions and specialized floral chamber, which traps pollinators – mainly Psychoda phalaenoidesand P. grisescens – overnight. However, little is known about the genes underlying the production of many A. maculatumVOCs, and their influence on variation in pollinator attraction rates. Therefore, we performed de novo transcriptome sequencing of A. maculatum appendix and male floret tissue collected during- and post-anthesis, from ten natural populations across Europe. These RNA-seq data were paired with GC-MS analyses of floral scent composition and pollinator data collected from the same inflorescences. Differential expression analyses revealed candidate transcripts in appendix tissue linked to malodourous VOCs including indole, p-cresol, and 2-heptanone. Additionally, we found that terpene synthase expression in male floret tissue during anthesis significantly covaried with sex- and species-specific attraction of Psychoda phalaenoides and P. grisescens. Taken together, our results provide the first insights into molecular mechanisms underlying pollinator attraction patterns in A. maculatum, and highlight floral chamber sesquiterpene (e.g.bicyclogermacrene) synthases as interesting candidate genes for further study.