cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b8gtht7f7
title: Drought timing and species growth phenology determine intra-annual recovery of tree height and diameter growth

description: These are the data reported in van Kampen et al. (2022) "Drought
 timing and species growth phenology determine intra-annual recovery of
 tree height and diameter growth" published in AoB Plants. They
 describe patterns of height and diameter growth for saplings of six tree
 species undergoing experimental drought conditions at different times of
 year. 
description: A full description can be found in the published manuscript.
 Briefly, weekly measurements of soil moisture, height, and diameter growth
 were conducted for 288 potted tree saplings of six tree
 species (<em>Acer rubrum</em>, <em>Betula
 papyrifera</em>, <em>Prunus serotina</em>,
 <em>Juniperus virginiana</em>, <em>Pinus
 strobus</em>, and <em>Thuja occidentalis</em>). Droughts
 were applied in spring, summer, or fall for a subset of these trees. The
 data reported here are the processed data used to generate the plots and
 statistics reported in the publication.
DOI: 10.5061/dryad.9s4mw6mjd
title: Composition and functional potential of the mammary microbiota prior to and following breast tumor diagnosis

description: These data were generated to analyze the human breast tissue microbiome
 composition and functional potential. We analyzed and compared the
 resident bacterial taxa of histologically normal breast tissue (healthy,
 H) with those of tissues donated prior to (pre-diagnostic, PD, ) and after
 (adjacent normal, AN, and tumor, T) breast cancer diagnosis to determine
 the role of the breast tissue microbiome in breast cancer. DNA was
 isolated from 165 tissue samples, 9 negative controls, and 1 positive
 control and submitted for Illumina Miseq paired-end sequencing of the V3 -
 V4 region of the 16S gene. 16S amplicons were pre-processed into amplicon
 sequence variants (ASVs) using DADA2. To infer bacterial function in
 breast cancer, we predicted the functional bacteriome from these ASVs
 using PICRUSt2 and the Kyoto Encyclopedia of Genes and Genomes (KEGG)
 database. 
description: This data was collected via 16S ribosomal RNA gene sequencing of
 breast tissue from four different groups of women. Healthy (H) tissue is
 tissue donated to the Susan G. Komen Tissue Bank (KTB) by healthy women,
 Pre-diagnostic (PD) tissue is tissue donated to the KTB by healthy women
 who later were diagnosed with breast cancer. Adjacent normal (AN) tissue
 is tissue next to a malignant tumor donated by women with cancer. Tumor
 (T) tissue is breast tumor tissue. The AN and T tissues were selected from
 the Indiana University Simon Comprehensive Cancer Center Tissue Bank
 (IUSCCC). Specifically, the V3 - V4 region of the 16S gene was amplified
 and library prepped for Illumina MiSeq paired-end sequencing. Following
 sequencing, data was pre-processed into amplicon sequence variants (ASVs),
 which are represented in this file. These ASVs were further analyzed
 according to the methods outlined in the associated publication: DOI:
 10.1128/msystems.01489-21. Additionally, we predicted the functional
 potential of the microbiota using PICRUSt2 and the Kyoto Encyclopedia of
 Genes and Genomes (KEGG) Database. This functional metagenome was
 predicted from the ASVs in this file and is represented in this file.
 Please reference the manuscript, DOI: 10.1128/msystems.01489-21, for
 additional analyses performed on these data.
DOI: 10.5061/dryad.m905qfv35
title: Long-term Spartina alterniflora invasion simplified soil seed bank and regenerated community in a coastal marsh wetland

description: The coastal wetland is easily invaded by alien species due to its location
 in the land and sea transitional area. As a potential driving regeneration
 force, the soil seed bank is vital to community restoration and species
 diversity protection. To reveal the long-term S. alterniflora invasion
 impact on the soil seed banks and regenerated communities, we investigated
 the seed banks under the different vegetation types (S. alterniflora,
 Phragmites australis, Scirpus mariquete, ruderal and unvegetated site) and
 soil depths (0–5 cm and 5–10 cm) in the Chongming island coastal salt
 marsh wetland. The results showed that the soil seed bank richness and
 species density under different vegetation types were higher than
 aboveground vegetation, and those of 0–5 cm seed banks were higher than
 5–10 cm, except for the unvegetated site. The species richness and the S.
 alterniflora seed proportion in the seed banks under the S. alterniflora
 communities (S.AS) were lower and larger, respectively, than other sites.
 The species composition between S.AS and the aboveground communities
 showed high similarity with aggregation phylogenetic structures in two
 soil depths. The seed bank variations at 0–5 cm and 5–10 cm depths were
 interpreted 3.03% and 2.25% by aboveground communities, while 4.92% and
 5.55% were interpreted by soil microbial biomass. The SEM model explained
 98.1% and 91.8% of the seed banks' richness at the 0–5 cm depth and
 5–10 cm depth, respectively, and explained 98.8% and 46.1% of the seed
 banks' species density at the 0–5 cm depth and 5–10 cm depth,
 respectively. The aboveground vegetation biomass and abundance directly
 affected the 0–5 cm seed banks' richness and species density, while
 its height and biomass only affected the 5–10 cm seed banks' species
 density. The microbial biomass of the 0–10 cm soil depth indirectly
 affected the richness and species density of the 0-5 cm seed bank, and
 only affected the richness of the 5–10 cm seed bank. Soil physical and
 chemical properties only indirectly affected the 0–5 cm seed banks'
 species density. The results provided a reference for the ecological
 evaluation of the impacts of S. alterniflora invasion into the coastal
 salt marsh wetland of eastern China and guidance for the protection and
 restoration of the native plant communities.
DOI: 10.5061/dryad.mgqnk991r
title: Increased precipitation and nitrogen addition accelerate the temporal increase of soil respiration during eight-year old-field grassland succession

description: Ecological succession after disturbance plays a vital role in influencing
 ecosystem structure and functioning. However, how global change factors
 regulate ecosystem carbon (C) cycling in successional plant communities
 remains largely elusive. As part of an eight-year (2012-2019) manipulative
 experiment, this study was designed to examine the responses of soil
 respiration and its heterotrophic component to simulated increases in
 precipitation and atmospheric nitrogen (N) deposition in an old-field
 grassland undergoing secondary succession. Over the eight-year
 experimental period, increased precipitation stimulated soil respiration
 by 11.6%, but did not affect soil heterotrophic respiration. Nitrogen
 addition increased both soil respiration (5.1%) and heterotrophic
 respiration (6.2%). Soil respiration and heterotrophic respiration
 linearly increased with time in the control plots, resulting from changes
 in soil moisture and shifts of plant community composition from grass-forb
 codominance to grass dominance in this old-field grassland. Compared to
 the control, increased precipitation significantly strengthened the
 temporal increase of soil respiration through stimulating belowground net
 primary productivity. By contrast, N addition accelerated temporal
 increases of both soil respiration and its heterotrophic component by
 driving plant community shifts and thus stimulating soil organic C. Our
 findings indicate that increases in water and N availabilities may
 accelerate soil C release during old-field grassland succession and reduce
 their potential positive impacts on soil C accumulation under future
 climate change scenarios.
DOI: 10.5061/dryad.41ns1rng6
title: Tyrosine phosphorylation tunes chemical and thermal sensitivity of TRPV2 ion channel

description: Transient receptor potential vanilloid 2 (TRPV2) is a multimodal ion
 channel implicated in diverse physiopathological processes. Its important
 involvement in immune responses has been suggested such as in the
 macrophages’ phagocytosis process. However, the endogenous signaling
 cascades controlling the gating of TRPV2 remain to be understood. Here, we
 report that enhancing tyrosine phosphorylation remarkably alters the
 chemical and thermal sensitivities of TRPV2 endogenously expressed in rat
 bone marrow-derived macrophages. We identify that the protein tyrosine
 kinase JAK1 mediates TRPV2 phosphorylation at the molecular sites
 Tyr(335), Tyr(471), and Tyr(525). JAK1 phosphorylation is required for
 maintaining TRPV2 activity and the phagocytic ability of macrophages. We
 further show that TRPV2 phosphorylation is dynamically balanced by protein
 tyrosine phosphatase non-receptor type 1 (PTPN1). PTPN1 inhibition
 increases TRPV2 phosphorylation, further reducing the activation
 temperature threshold. Our data thus unveil an intrinsic mechanism where
 the phosphorylation/dephosphorylation dynamic balance sets the basal
 chemical and thermal sensitivity of TRPV2. Targeting this pathway will aid
 therapeutic interventions in physiopathological contexts.
description: Electrophysiological data were mainly collected
 from traditional patch-clamp recordings.
description: This
 dataset contains 2 excel sheets including all the data used to analyze
 “Tyrosine phosphorylation tunes chemical and thermal sensitivity of TRPV2
 ion channel". Each statistical result in the figures can be found in
 the excel sheet. Dataset for
 Figures Data used for Figure 1-6. It contains
 electrophysiological data.  Dataset for Supplemental
 Information Electrophysiological data used for supplement
 figures.
DOI: 10.5061/dryad.5dv41ns7k
title: miR-1285-3p targets TPI1 to regulate the glycolysis metabolism signaling pathway of Tibetan sheep Sertoli cells

description: Glycolysis in sertoli cells (SCs) can provide energy substrates for the
 development of spermatogenic cells. Triose phosphate isomerase 1 (TPI1) is
 one of the key catalytic enzymes involved in glycolysis. However, the
 biological function of TPI1 in SCs and its role in glycolytic metabolic
 pathways are poorly understood. On the basis of previous research, we
 isolated primary SCs from Tibetan sheep and overexpressed TPI1 gene to
 determine its effect on the proliferation, glycolysis, and apoptosis of
 SCs. Secondly, we investigated the relationship between TPI1 and
 miR-1285-3p, and whether miR-1285-3p regulates the proliferation and
 apoptosis of SCs, and participates in glycolysis by targeting TPI1.
 Results showed that overexpression of TPI1 increased the proliferation
 rate and decreased apoptosis of SCs. In addition, overexpression of TPI1
 altered glycolysis and metabolism signaling pathways and significantly
 increased the amount of the final product lactic acid. Further analysis
 showed that miR-1285-3p inhibited TPI1 by directly targeting its
 3'untranslated region. Overexpression of miR-1285-3p suppressed the
 proliferation of SCs, and this effect was partially reversed by
 restoration of TPI1 expression. In summary, this study shows that the
 miR-1285-3p/TPI1 axis regulates glycolysis in SCs. These findings add to
 our understanding of the regulation of spermatogenesis in sheep and other
 mammals.
DOI: 10.5061/dryad.12jm63z0s
title: Dataset: Co-administration of adjuvanted recombinant Ov-103 and Ov-RAL2 vaccines confer protection against natural challenge in a bovine O. ochengi infection model of human onchocerciasis

description: [Abstract from accompanying manuscript] Onchocerciasis (river blindness),
 caused by the filarial nematode Onchocerca volvulus, is a neglected
 tropical disease endemic to sub-Saharan Africa. Worldwide, an estimated
 20.9 million individuals live with infected and a further 205 million are
 at risk of disease. Current control methods rely on mass drug
 administration of ivermectin to suppress microfilarial development.
 Presently, there are no viable treatment options effective against the
 long-lived adult worms. The identification and development of efficacious
 vaccine candidates as complementary tools to support ongoing elimination
 efforts are therefore a major objective of onchocerciasis research. We
 evaluated the immunogenicity and protective effects of co-administering
 two leading O. volvulus-derived recombinant vaccine candidates (Ov-103 and
 Ov-RAL2) in cattle with subsequent natural exposure to Onchocerca ochengi,
 a close phylogenetic relative of O. volvulus. Immunisation induced strong
 IgG responses against both vaccine candidates. Following natural exposure
 to O. ochengi, vaccination status and resulting serum antibody response
 was associated with delayed nodule development and onset of
 microfilaridermia. Peptide arrays identified several Ov-103 and
 Ov-RAL2-specific epitopes recognised by IgG from immunised cattle which
 warrant further investigation. Our data provide supporting evidence for
 ongoing development of a recombinant vaccine for control of human
 onchocerciasis.
description: Samples collected and analysed from a longitudinal vaccine trial
 using a bovine <em>Onchocerca ochengi </em>natural infection
 model for human onchocerciasis. See accompanying
 ReadMe.txt file for detailed descriptions of datasets. 
description: Six separate .csv files upon which manuscript analysis was
 based. ReadMe.txt file included in upload for detailed
 explanation of datasets.
DOI: 10.5061/dryad.g79cnp5rh
title: Compositionally constrained sites drive long branch attraction

description: Accurate phylogenies are fundamental to our understanding of the pattern
 and process of evolution. Yet, phylogenies at deep evolutionary
 timescales, with correspondingly long branches, have been fraught with
 controversy resulting from conflicting estimates from models with varying
 complexity and goodness of fit. Analyses of historical as well as current
 empirical datasets, such as alignments including Microsporidia, Nematoda
 or Platyhelminthes, have demonstrated that inadequate modeling of
 across-site compositional heterogeneity, which is the result of
 biochemical constraints that lead to varying patterns of accepted amino
 acids along sequences, can lead to erroneous topologies that are strongly
 supported. Unfortunately, models that adequately account for across-site
 compositional heterogeneity remain computationally challenging or
 intractable for an increasing fraction of contemporary datasets. Here, we
 introduce "compositional constraint analysis", a method to
 investigate the effect of site-specific amino acid diversity on
 phylogenetic inference, and show that more constrained sites with lower
 diversity and less constrained sites with higher diversity exhibit
 ostensibly conflicting signal under models ignoring across-site
 compositional heterogeneity and thus contribute to topological bias and
 long branch attraction artifacts. We demonstrate that  more
 complex models accounting for across-site compositional heterogeneity can
 ameliorate this bias. We present CAT-PMSF, a pipeline for diagnosing and
 resolving phylogenetic bias resulting from inadequate modeling of
 across-site compositional heterogeneity based on the CAT model. CAT-PMSF
 is robust against long branch attraction in all alignments we have
 examined. We suggest using CAT-PMSF when convergence of the CAT model
 cannot be assured. We find evidence that compositionally constrained sites
 are driving long branch attraction in two metazoan datasets and recover
 evidence for Porifera as the sister group to all other animals.
description: Please see the README document ("README.md") and the
 accompanying published article: Lénárd L. Szánthó, Nicolas Lartillot,
 Gergely J. Szöllősi and Dominik<br>Schrempf 2023. Compositionally
 constrained sites drive long branch attraction. Systematic Biology.
 Accepted. DOI: 10.1093/sysbio/syad013
description: Please see the README document ("README.md") and the
 accompanying published article: Lénárd L. Szánthó, Nicolas Lartillot,
 Gergely J. Szöllősi and Dominik<br>Schrempf 2023. Compositionally
 constrained sites drive long branch attraction. Systematic Biology.
 Accepted. DOI: 10.1093/sysbio/syad013
DOI: 10.5061/dryad.rbnzs7hcz
title: Direct and legacy-mediated drought effects on plant performance are species-specific and depend on soil community composition

description: Droughts affect plant communities, but their impacts may be mediated by
 soil biota. Soil communities may ameliorate drought stress, and droughts
 may leave legacies of altered soil communities that may affect future
 plant growth. However, it is not yet understood which groups of soil biota
 in particular affect plant performance under drought, nor which groups
 contribute to drought-legacy effects on future plant growth. We
 hypothesized that increasing soil-community complexity ameliorates drought
 stress and that drought-legacy effects are species-specific and
 soil-community-dependent. To test these hypotheses, we performed a
 two-phase experiment with six grassland species. In the first phase, we
 examined plant performance under drought and ambient conditions, in soils
 inoculated with a sterilized inoculum, or increasingly complex soil
 communities created by wet-sieving through 20-, 40-, and 200-µm mesh
 sieves. In the second phase, we examined drought-legacy effects on
 conspecific plant performance. We separately analysed plant performance in
 both phases, and integrated data from both phases using structural
 equation models. Drought effects on first-phase root biomass depended on
 soil inoculum, and this interaction differed among plant species, while
 effects on shoot biomass differed among species, but did not depend on
 inoculum. Only one species experienced drought-stress-ameliorating effects
 of soil biota. Drought-legacy effects on plant performance were positive,
 but depended on soil inoculum in case of root biomass, and on soil
 inoculum and species identity in case of shoot biomass. Drought-legacy
 effects were often mediated by first-phase biomass. In some species this
 effect was independent of inoculum, suggesting an abiotic legacy effect.
 In others, low first-phase biomass corresponded with high second-phase
 performance in presence of the most complex soil community. We conclude
 that drought-legacy effects on plant performance were
 soil-community-dependent but positive, suggesting that plants establishing
 after drought may benefit from increased nutrient availability and more
 positive impacts of soil biota.
description: Plant performance data from a two-phase experiment. In the first
 phase, 6 grassland plant species were exposed to a drought treatment and
 different soil communities, created using wet-sieving with different mesh
 sizes. In the second phase, the same plant species were grown in soil
 conditioned by conspecifics, and the legacy effects of first-phase
 treatments (drought and inoculum) were examined. In both phases, root,
 shoot and total biomass were determined.
DOI: 10.5061/dryad.qfttdz0k1
title: Ant body size mediates functional performance and species interactions in carrion decomposer communities

description: Growing concern over rapid species declines and extinctions has led to
 considerable interest in the role of biodiversity for maintaining
 ecological processes. However, the loss of particular species has more
 pronounced effects on ecosystem services than others, highlighting the
 importance of key functional species traits and their relationships to
 ecosystem functioning. Human induced disturbances, such as species
 invasions, land use changes or abiotic changes, appear to
 disproportionally impact larger species rather than smaller ones. The loss
 of large-bodied species in the community diminishes key ecosystem services
 like seed dispersal, pest control, pollination and decomposition. Here we
 use carrion, a nutrient-rich ephemeral resource, to test the hypotheses
 that ants positively affect decomposition rates and that their role in the
 necrophilous community – as predator or decomposer – is mediated by body
 size. We further investigate the relative contribution of maggots vs. ants
 to biomass decomposition. Our results show that ants contributed
 positively to the decomposition process. Moreover, decomposition was
 shaped by an intricate interplay between competition and predation among
 the guild of decomposer insects. As predicted, larger ants show a double
 action in increasing decomposition rate and predating on maggots, while
 small ants are rather inefficient decomposers and did not act as predators
 on other decomposer species. Our study shows that differentiating key
 taxonomic groups in function of their body size is key to untangle the
 diversity and directions of the various roles they play within complex
 ecological processes.
DOI: 10.5061/dryad.jwstqjqbk
title: Genetic compensations for letm1 deficiency

description: Mitochondria are fundamental for life and require balanced ion exchange to
 maintain proper functioning. The mitochondrial cation exchanger LETM1
 sparks interest because of its pathophysiological role in seizures in the
 Wolf Hirschhorn Syndrome (WHS). Despite observation of sleep
 disorganization in epileptic WHS patients, and growing studies linking
 mitochondria and epilepsy to circadian rhythms, LETM1 has not been studied
 from the chronobiological perspective. Here we established a viable letm1
 knock-out, using the diurnal vertebrate Danio rerio to study the metabolic
 and chronobiological consequences of letm1 deficiency. We report diurnal
 rhythms of Letm1 protein levels in wild-type fish. We show that
 mitochondrial nucleotide metabolism is deregulated in letm1-/- mutant
 fish, the rate limiting enzyme of NAD+ production is up-regulated, while
 NAD+ and NADH pools are reduced. These changes were associated with
 increased expression amplitude of circadian core clock genes in letm1-/-
 compared to wild-type under light/dark conditions, suggesting decreased
 NAD(H) levels as a possible mechanism for circadian system perturbation in
 Letm1 deficiency. Replenishing NAD pool may ameliorate WHS-associated
 sleep and neurological disorders.