cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3823701
title: Table S2. Summary of proteins indentified in the secretome of WT and ∆pldA strains from The outer membrane phospholipase A is essential for membrane integrity and type III secretion in <i>Shigella flexneri</i>

description: Outer membrane phospholipase A (OMPLA) is an enzyme located in the outer membrane of Gram-negative bacteria. OMPLA exhibits broad substrate specificity, and some of its substrates are located in the cellular envelope. Generally, the enzymatic activity can only be induced by perturbation of the cell envelope integrity through diverse methods. Although OMPLA has been thoroughly studied as a membrane protein in <i>Escherichia coli</i> and is constitutively expressed in many other bacterial pathogens, little is known regarding the functions of OMPLA during the process of bacterial infection. In this study, the proteomic and transcriptomic data indicated that OMPLA in <i>Shigella flexneri</i>, termed PldA, both stabilizes the bacterial membrane and is involved in bacterial infection under ordinary culture conditions. A series of physiological assays substantiated the disorganization of the bacterial outer membrane and the periplasmic space in the <i>ΔpldA</i> mutant strain. Furthermore, the <i>ΔpldA</i> mutant strain showed decreased levels of type III secretion system expression, contributing to the reduced internalization efficiency in host cells. The results of this study support PldA, which is widespread across Gram-negative bacteria, as an important factor for the bacterial life cycle, particularly in human pathogens.
DOI: 10.7910/dvn/v1rjpf/zmy62f
title: iqa20161001_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823701.v1
title: Table S2. Summary of proteins indentified in the secretome of WT and ∆pldA strains from The outer membrane phospholipase A is essential for membrane integrity and type III secretion in <i>Shigella flexneri</i>

description: Outer membrane phospholipase A (OMPLA) is an enzyme located in the outer membrane of Gram-negative bacteria. OMPLA exhibits broad substrate specificity, and some of its substrates are located in the cellular envelope. Generally, the enzymatic activity can only be induced by perturbation of the cell envelope integrity through diverse methods. Although OMPLA has been thoroughly studied as a membrane protein in <i>Escherichia coli</i> and is constitutively expressed in many other bacterial pathogens, little is known regarding the functions of OMPLA during the process of bacterial infection. In this study, the proteomic and transcriptomic data indicated that OMPLA in <i>Shigella flexneri</i>, termed PldA, both stabilizes the bacterial membrane and is involved in bacterial infection under ordinary culture conditions. A series of physiological assays substantiated the disorganization of the bacterial outer membrane and the periplasmic space in the <i>ΔpldA</i> mutant strain. Furthermore, the <i>ΔpldA</i> mutant strain showed decreased levels of type III secretion system expression, contributing to the reduced internalization efficiency in host cells. The results of this study support PldA, which is widespread across Gram-negative bacteria, as an important factor for the bacterial life cycle, particularly in human pathogens.
DOI: 10.7910/dvn/v1rjpf/jjoiul
title: iqa20161129_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/n0r5wu
title: iqa20160813_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/tgrszk
title: iqa20151202_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823692
title: Table S4. Differential expression analysis of the transcriptome of WT and ΔpldA strains from The outer membrane phospholipase A is essential for membrane integrity and type III secretion in <i>Shigella flexneri</i>

description: Outer membrane phospholipase A (OMPLA) is an enzyme located in the outer membrane of Gram-negative bacteria. OMPLA exhibits broad substrate specificity, and some of its substrates are located in the cellular envelope. Generally, the enzymatic activity can only be induced by perturbation of the cell envelope integrity through diverse methods. Although OMPLA has been thoroughly studied as a membrane protein in <i>Escherichia coli</i> and is constitutively expressed in many other bacterial pathogens, little is known regarding the functions of OMPLA during the process of bacterial infection. In this study, the proteomic and transcriptomic data indicated that OMPLA in <i>Shigella flexneri</i>, termed PldA, both stabilizes the bacterial membrane and is involved in bacterial infection under ordinary culture conditions. A series of physiological assays substantiated the disorganization of the bacterial outer membrane and the periplasmic space in the <i>ΔpldA</i> mutant strain. Furthermore, the <i>ΔpldA</i> mutant strain showed decreased levels of type III secretion system expression, contributing to the reduced internalization efficiency in host cells. The results of this study support PldA, which is widespread across Gram-negative bacteria, as an important factor for the bacterial life cycle, particularly in human pathogens.
DOI: 10.6084/m9.figshare.3823692.v1
title: Table S4. Differential expression analysis of the transcriptome of WT and ΔpldA strains from The outer membrane phospholipase A is essential for membrane integrity and type III secretion in <i>Shigella flexneri</i>

description: Outer membrane phospholipase A (OMPLA) is an enzyme located in the outer membrane of Gram-negative bacteria. OMPLA exhibits broad substrate specificity, and some of its substrates are located in the cellular envelope. Generally, the enzymatic activity can only be induced by perturbation of the cell envelope integrity through diverse methods. Although OMPLA has been thoroughly studied as a membrane protein in <i>Escherichia coli</i> and is constitutively expressed in many other bacterial pathogens, little is known regarding the functions of OMPLA during the process of bacterial infection. In this study, the proteomic and transcriptomic data indicated that OMPLA in <i>Shigella flexneri</i>, termed PldA, both stabilizes the bacterial membrane and is involved in bacterial infection under ordinary culture conditions. A series of physiological assays substantiated the disorganization of the bacterial outer membrane and the periplasmic space in the <i>ΔpldA</i> mutant strain. Furthermore, the <i>ΔpldA</i> mutant strain showed decreased levels of type III secretion system expression, contributing to the reduced internalization efficiency in host cells. The results of this study support PldA, which is widespread across Gram-negative bacteria, as an important factor for the bacterial life cycle, particularly in human pathogens.
DOI: 10.7910/dvn/v1rjpf/gts4rg
title: iqa20160822_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/byhtqj
title: iqa20150130_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823686
title: Bat Data from Using collision cones to assess biological deconfliction methods

description: Biological systems consistently outperform autonomous systems governed by engineered algorithms in their ability to reactively avoid collisions. To better understand this discrepancy, a collision avoidance algorithm was applied to frames of digitized video trajectory data from bats, swallows, and fish (<i>Myotis velifer</i>, <i>Petrochelidon pyrrhonota</i>, and <i>Danio aequipinnatus</i>). Information available from visual cues, specifically relative position and velocity, was provided to the algorithm which used this information to define collision cones that allowed the algorithm to find a safe velocity requiring minimal deviation from the original velocity. The subset of obstacles provided to the algorithm was determined by the animal's sensing range in terms of metric and topological distance. The algorithmic calculated velocities showed good agreement with observed biological velocities, indicating that the algorithm was an informative basis for comparison with the three species and could potentially be improved for engineered applications with further study.
DOI: 10.7910/dvn/v1rjpf/hegpri
title: iqa20150823_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823686.v1
title: Bat Data from Using collision cones to assess biological deconfliction methods

description: Biological systems consistently outperform autonomous systems governed by engineered algorithms in their ability to reactively avoid collisions. To better understand this discrepancy, a collision avoidance algorithm was applied to frames of digitized video trajectory data from bats, swallows, and fish (<i>Myotis velifer</i>, <i>Petrochelidon pyrrhonota</i>, and <i>Danio aequipinnatus</i>). Information available from visual cues, specifically relative position and velocity, was provided to the algorithm which used this information to define collision cones that allowed the algorithm to find a safe velocity requiring minimal deviation from the original velocity. The subset of obstacles provided to the algorithm was determined by the animal's sensing range in terms of metric and topological distance. The algorithmic calculated velocities showed good agreement with observed biological velocities, indicating that the algorithm was an informative basis for comparison with the three species and could potentially be improved for engineered applications with further study.
DOI: 10.7910/dvn/v1rjpf/khyceh
title: iqa20160803_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/r3bgq0
title: iqa20150731_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/l8dfjr
title: iqa20150325_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/yiowt1
title: iqa20161130_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/pjadgl
title: iqa20150803_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ylf2qe
title: iqa20160629_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/axhdgq
title: iqa20150318_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/3hbusb
title: iqa20150506_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823668
title: Bird Data from Using collision cones to assess biological deconfliction methods

description: Biological systems consistently outperform autonomous systems governed by engineered algorithms in their ability to reactively avoid collisions. To better understand this discrepancy, a collision avoidance algorithm was applied to frames of digitized video trajectory data from bats, swallows, and fish (<i>Myotis velifer</i>, <i>Petrochelidon pyrrhonota</i>, and <i>Danio aequipinnatus</i>). Information available from visual cues, specifically relative position and velocity, was provided to the algorithm which used this information to define collision cones that allowed the algorithm to find a safe velocity requiring minimal deviation from the original velocity. The subset of obstacles provided to the algorithm was determined by the animal's sensing range in terms of metric and topological distance. The algorithmic calculated velocities showed good agreement with observed biological velocities, indicating that the algorithm was an informative basis for comparison with the three species and could potentially be improved for engineered applications with further study.
DOI: 10.7910/dvn/v1rjpf/hiu0hh
title: iqa20150906_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823668.v1
title: Bird Data from Using collision cones to assess biological deconfliction methods

description: Biological systems consistently outperform autonomous systems governed by engineered algorithms in their ability to reactively avoid collisions. To better understand this discrepancy, a collision avoidance algorithm was applied to frames of digitized video trajectory data from bats, swallows, and fish (<i>Myotis velifer</i>, <i>Petrochelidon pyrrhonota</i>, and <i>Danio aequipinnatus</i>). Information available from visual cues, specifically relative position and velocity, was provided to the algorithm which used this information to define collision cones that allowed the algorithm to find a safe velocity requiring minimal deviation from the original velocity. The subset of obstacles provided to the algorithm was determined by the animal's sensing range in terms of metric and topological distance. The algorithmic calculated velocities showed good agreement with observed biological velocities, indicating that the algorithm was an informative basis for comparison with the three species and could potentially be improved for engineered applications with further study.
DOI: 10.7910/dvn/v1rjpf/a0kvtm
title: iqa20150625_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/z62kba
title: iqa20151225_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/z5ribb
title: iqa20150716_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/vcm82u
title: iqa20150326_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823659
title: Supporting Dataset S4 from Onychophoran-like musculature in a phosphatized Cambrian lobopodian

description: The restricted, exclusively terrestrial distribution of modern Onychophora contrasts strikingly with the rich diversity of onychophoran-like fossils preserved in marine Cambrian <i>Lagerstätten</i>. The transition from these early forebears to the modern onychophoran body plan is poorly constrained, in part, owing to the absence of fossils preserving details of the soft anatomy. Here, we report muscle tissue in a new Early Cambrian (stage 3) lobopodian, <i>Tritonychus phanerosarkus</i> gen. et sp. nov., preserved in the Orsten fashion by three-dimensional replication in phosphate. This first report of Palaeozoic onychophoran musculature establishes peripheral musculature as a characteristic of the ancestral panarthropod, but documents an unexpected muscular configuration. Phylogenetic analysis reconstructs <i>T. phanerosarkus</i> as one of a few members of the main onychophoran lineage—which was as rare and as cryptic in the Cambrian period as it is today.
DOI: 10.6084/m9.figshare.3823659.v1
title: Supporting Dataset S4 from Onychophoran-like musculature in a phosphatized Cambrian lobopodian

description: The restricted, exclusively terrestrial distribution of modern Onychophora contrasts strikingly with the rich diversity of onychophoran-like fossils preserved in marine Cambrian <i>Lagerstätten</i>. The transition from these early forebears to the modern onychophoran body plan is poorly constrained, in part, owing to the absence of fossils preserving details of the soft anatomy. Here, we report muscle tissue in a new Early Cambrian (stage 3) lobopodian, <i>Tritonychus phanerosarkus</i> gen. et sp. nov., preserved in the Orsten fashion by three-dimensional replication in phosphate. This first report of Palaeozoic onychophoran musculature establishes peripheral musculature as a characteristic of the ancestral panarthropod, but documents an unexpected muscular configuration. Phylogenetic analysis reconstructs <i>T. phanerosarkus</i> as one of a few members of the main onychophoran lineage—which was as rare and as cryptic in the Cambrian period as it is today.
DOI: 10.7910/dvn/v1rjpf/p5djpw
title: iqa20160828_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/dn2gkx
title: iqa20160711_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/yewldw
title: iqa20150707_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/eetnpk
title: iqa20161220_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/wcgveh
title: iqa20150601_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/uegoq0
title: iqa20161214_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/evvzox
title: iqa20150112_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/vnv5ro
title: iqa20150225_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/twq4bg
title: iqa20160109_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/abyjkr
title: iqa20160602_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/jjt5im
title: iqa20150724_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/bnzngp
title: iqa20150322_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/dhuvqm
title: iqa20150909_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/sn25qe
title: iqa20150128_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/dvrbzg
title: iqa20150212_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/gqiaab
title: iqa20160818_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/uqxurn
title: iqa20161221_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/4aktju
title: iqa20160929_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/6nbadl
title: iqa20161016_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/z5xqvj
title: iqa20150422_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/qcfh9f
title: iqa20160831_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/xvjile
title: iqa20160907_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/5xpdym
title: iqa20151217_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/mwejyl
title: iqa20151117_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ypstkv
title: iqa20151210_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/oygtc6
title: iqa20160805_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/zx2vxo
title: iqa20150219_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823602
title: Freshwater vertebrate and invertebrate diversity patterns in an Andean-Amazon basin: implications for conservation efforts

description: The Napo Basin in Ecuador is an important drainage of the Amazon Basin, the most biodiverse ecosystem for freshwater species. At the same time, this basin has conspicuous information gaps on its biodiversity patterns and human threats. Here, we estimated the diversity distribution patterns of freshwater vertebrates and invertebrates in the Napo Basin, as a tool for present and future management and conservation efforts. Also, we assessed the spatial congruence of the diversity patterns observed between aquatic vertebrates and invertebrates. For this, we compiled occurrence records for 481 freshwater vertebrate species (amphibians, birds, mammals, reptiles, and fish), and 54 invertebrate families obtained across an altitudinal gradient of the basin (200–4500 m). Using these occurrence records and environmental variables, we modeled the distribution of each vertebrate species and invertebrate family. Then, we stacked these distributions to build species richness maps for vertebrates, and a family richness map for invertebrates. We found that the most diverse areas for vertebrate species are the lowlands (&lt;600 m), whereas richness of invertebrate families peaks at higher elevations (lower montane forests). Congruence among species richness patterns of the five vertebrate groups was high (<i>r</i> = 0.66), with fish being the best predictor for vertebrates (<i>r</i> = 0.78). However, congruence decreased at higher elevations (<i>r</i> = 0.14), suggesting that specific species or habitat-based approaches should be used in the highlands. Also, we found a high correlation between species and family richness of freshwater invertebrates (<i>r</i> = 0.66), suggesting that family richness of invertebrates could be used as a surrogate of species richness in this basin. We highlight this correlation because, at the watershed scale, it allows working with family groups where species-level taxonomy is challenging. Our results provide the first comprehensive representation of freshwater biodiversity patterns at high resolution in an Andean-Amazon basin, and calls attention to the need for incorporating different taxonomic groups when assessing diversity patterns. Given these different diversity patterns, conservation programs for this basin should incorporate both vertebrate and invertebrate groups as biodiversity indicators. Finally, our study provides a practical methodological guidance in the estimation of freshwater diversity in regions of scarce information with high conservation priority, such as the Andean-Amazon basins.
DOI: 10.6084/m9.figshare.3823602.v1
title: Freshwater vertebrate and invertebrate diversity patterns in an Andean-Amazon basin: implications for conservation efforts

description: The Napo Basin in Ecuador is an important drainage of the Amazon Basin, the most biodiverse ecosystem for freshwater species. At the same time, this basin has conspicuous information gaps on its biodiversity patterns and human threats. Here, we estimated the diversity distribution patterns of freshwater vertebrates and invertebrates in the Napo Basin, as a tool for present and future management and conservation efforts. Also, we assessed the spatial congruence of the diversity patterns observed between aquatic vertebrates and invertebrates. For this, we compiled occurrence records for 481 freshwater vertebrate species (amphibians, birds, mammals, reptiles, and fish), and 54 invertebrate families obtained across an altitudinal gradient of the basin (200–4500 m). Using these occurrence records and environmental variables, we modeled the distribution of each vertebrate species and invertebrate family. Then, we stacked these distributions to build species richness maps for vertebrates, and a family richness map for invertebrates. We found that the most diverse areas for vertebrate species are the lowlands (&lt;600 m), whereas richness of invertebrate families peaks at higher elevations (lower montane forests). Congruence among species richness patterns of the five vertebrate groups was high (<i>r</i> = 0.66), with fish being the best predictor for vertebrates (<i>r</i> = 0.78). However, congruence decreased at higher elevations (<i>r</i> = 0.14), suggesting that specific species or habitat-based approaches should be used in the highlands. Also, we found a high correlation between species and family richness of freshwater invertebrates (<i>r</i> = 0.66), suggesting that family richness of invertebrates could be used as a surrogate of species richness in this basin. We highlight this correlation because, at the watershed scale, it allows working with family groups where species-level taxonomy is challenging. Our results provide the first comprehensive representation of freshwater biodiversity patterns at high resolution in an Andean-Amazon basin, and calls attention to the need for incorporating different taxonomic groups when assessing diversity patterns. Given these different diversity patterns, conservation programs for this basin should incorporate both vertebrate and invertebrate groups as biodiversity indicators. Finally, our study provides a practical methodological guidance in the estimation of freshwater diversity in regions of scarce information with high conservation priority, such as the Andean-Amazon basins.
DOI: 10.7910/dvn/v1rjpf/agwexf
title: iqa20150421_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/mp5xl3
title: iqa20161027_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ehjatp
title: iqa20150412_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/bznnaj
title: iqa20160825_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/yrt6zy
title: iqa20151203_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/xaqmil
title: iqa20160719_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/gl20v9
title: iqa20150117_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/gbzkrh
title: iqa20150218_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/vs2rrv
title: iqa20161209_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/xkmkzv
title: iqa20150411_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/fmhdxs
title: iqa20161021_03.txt.gz

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DOI: 10.7910/dvn/v1rjpf/kzlvhh
title: iqa20150404_03.txt.gz

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DOI: 10.7910/dvn/v1rjpf/ozdg8i
title: iqa20150323_03.txt.gz

description: :unav