86 Works

Data from: The tree of life and a new classification of bony fishes

Ricardo Betancur-R., Adela Roa-Varon, Nancy I. Holcroft, W. Calvin Borden, Terry Grande, Kent Carpenter, Millicent Sanciangco, Chenhong Li, Dahiana Arcila, Jesus A Ballesteros, Guillermo Ortí, J. Andrés López, Matthew A. Campbell, Edward O. Wiley, Gloria Arratia, Guoqing Lu, Stuart Willis, Richard E. Broughton, , Feifei Zhang & Daniel J. Hough
The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny that includes all major groups. The situation is most critical for a large clade of spiny-finned fishes, traditionally referred to as percomorphs, whose uncertain relationships have plagued ichthyologists for over a century. Most of what we know about the higher-level relationships among fish lineages has been based on morphology, but rapid influx of molecular studies is...

Data from: The challenges of detecting subtle population structure and its importance for the conservation of emperor penguins

Jane L. Younger, Gemma V. Clucas, Damian Kao, Alex D. Rogers, Karim Gharbi, Tom Hart & Karen J. Miller
Understanding the boundaries of breeding populations is of great importance for conservation efforts and estimates of extinction risk for threatened species. However, determining these boundaries can be difficult when population structure is subtle. Emperor penguins are highly reliant on sea ice, and some populations may be in jeopardy as climate change alters sea-ice extent and quality. An understanding of emperor penguin population structure is therefore urgently needed. Two previous studies have differed in their conclusions,...

Variation in mouse pelvic morphology maps to locations enriched in Sox9 Class II and Pitx1 regulatory features

Charles Roseman, Terrence Capellini, Evelyn Jagoda, Scott Williams, Mark Grabowski, Christine O'Connor, John Polk & James Cheverud
Variation in pelvic morphology has a complex genetic basis and its patterning and specification is governed by conserved developmental pathways. Whether the mechanisms underlying the differentiation and specification of the pelvis also produce the morphological covariation on which natural selection may act is still an open question in evolutionary developmental biology. We use high-resolution Quantitative Trait Locus (QTL) mapping in the F34 generation of an advanced intercross experiment (LG,SM-G34) to characterize the genetic architecture of...

Abundance of Montane Salamanders over an elevational gradient

Joseph Milanovich, Daniel Hocking, William Peterman & John Crawford
Climate change is expected to systematically alter the distribution and population dynamics of species around the world. The effects are expected to be particularly strong at high latitudes and elevations, and for ectothermic species with small ranges and limited movement potential, such as salamanders in the southern Appalachian Mountains. In this study, we sought to establish baseline abundance estimates for plethodontid salamanders (family: Plethodontidae) over an elevational gradient in Great Smoky Mountains National Park. In...

Letter From the Editor

Georgianna L. Martin

Attempting genetic inference from directional asymmetry during convergent hindlimb reduction in squamates

Samantha Swank, Ethan Elazegui, Sophia Janidlo, Thomas Sanger, Michael Bell & Yoel Stuart
Loss and reduction of paired appendages is common in vertebrate evolution. How often does such convergent evolution depend on similar developmental and genetic pathways? For example, many populations of the Threespine Stickleback and Ninespine Stickleback (Gasterosteidae) have independently evolved pelvic reduction, usually based on independent mutations that caused reduced Pitx1 expression. Reduced Pitx1 expression has also been implicated in pelvic reduction in manatees. Thus, hind limb reduction stemming from reduced Pitx1 expression has arisen independently...

Additional file 4 of Metabolic engineering of Escherichia coli BW25113 for the production of 5-Aminolevulinic Acid based on CRISPR/Cas9 mediated gene knockout and metabolic pathway modification

Changchuan Ye, Yuting Yang, Xi Chen, Lijie Yang, Xia Hua, Mengjie Yang, Xiangfang Zeng & Shiyan Qiao
Additional file 4: Fig S4. Schematic illustration of DSB induction and homologous recombination. After preparing competent cells, the pTarget-gene and Donor DNA which harbored homology arms (HRR and HRL) that targeted a chromosomal locus spanning the middle of targeted gene and the DSB site were electroporated into cells.

Additional file 4 of Metabolic engineering of Escherichia coli BW25113 for the production of 5-Aminolevulinic Acid based on CRISPR/Cas9 mediated gene knockout and metabolic pathway modification

Changchuan Ye, Yuting Yang, Xi Chen, Lijie Yang, Xia Hua, Mengjie Yang, Xiangfang Zeng & Shiyan Qiao
Additional file 4: Fig S4. Schematic illustration of DSB induction and homologous recombination. After preparing competent cells, the pTarget-gene and Donor DNA which harbored homology arms (HRR and HRL) that targeted a chromosomal locus spanning the middle of targeted gene and the DSB site were electroporated into cells.

Additional file 1 of NLRP3 inflammasome regulates astrocyte transformation in brain injury induced by chronic intermittent hypoxia

Ningning She, Yewen Shi, Yani Feng, Lina Ma, Yuqi Yuan, Yitong Zhang, Zine Cao, Xi Chen, Bingjie Zhao, Haiqin Liu & Xiaoyong Ren
Additional file 1: Figure S1. Research Supplementary Materials. a Process diagram of rat CIH model b Weight Trend Chart of Rat. ****P<0.0001.

Additional file 1 of Cardiovascular magnetic resonance images with susceptibility artifacts: artificial intelligence with spatial-attention for ventricular volumes and mass assessment

Marco Penso, Mario Babbaro, Sara Moccia, Marco Guglielmo, Maria Ludovica Carerj, Carlo Maria Giacari, Mattia Chiesa, Riccardo Maragna, Mark G. Rabbat, Andrea Barison, Nicola Martini, Mauro Pepi, Enrico G. Caiani & Gianluca Pontone
Additional file 1. Table S1. Correlations between CNN and manual gold standard on the artifacts-free images. Table S2. Internal validation: correlations on images with artifacts for the proposed CNN and the commercial software (Circle) in respect to the manual gold standard (GT). Also, the results relevant to interobserver variability between O1 and O2 reported for comparison. Table S3. External validation: correlations between CNN and manual gold standard on images with artifacts. Figure S1. Encoder module....

Cardiovascular magnetic resonance images with susceptibility artifacts: artificial intelligence with spatial-attention for ventricular volumes and mass assessment

Marco Penso, Mario Babbaro, Sara Moccia, Marco Guglielmo, Maria Ludovica Carerj, Carlo Maria Giacari, Mattia Chiesa, Riccardo Maragna, Mark G. Rabbat, Andrea Barison, Nicola Martini, Mauro Pepi, Enrico G. Caiani & Gianluca Pontone
Abstract Background Segmentation of cardiovascular magnetic resonance (CMR) images is an essential step for evaluating dimensional and functional ventricular parameters as ejection fraction (EF) but may be limited by artifacts, which represent the major challenge to automatically derive clinical information. The aim of this study is to investigate the accuracy of a deep learning (DL) approach for automatic segmentation of cardiac structures from CMR images characterized by magnetic susceptibility artifact in patient with cardiac implanted...

Additional file 3 of NLRP3 inflammasome regulates astrocyte transformation in brain injury induced by chronic intermittent hypoxia

Ningning She, Yewen Shi, Yani Feng, Lina Ma, Yuqi Yuan, Yitong Zhang, Zine Cao, Xi Chen, Bingjie Zhao, Haiqin Liu & Xiaoyong Ren
Additional file 3: Figure S3. Raw western bloats of NLRP3 (a), Capase-1 (b), ASC(c), IL-1β and β-actin (e) in Figure 5 The NLRP3, Capase-1, β-actin used 10% Gel; ASC, IL-1β used 12% Gel; all used 0.45 µm PVDF membrane.

Differential diagnosis of Crohn’s disease and intestinal tuberculosis: development and assessment of a nomogram prediction model

Shaoxiong Zeng, Ying Lin, Jiaxiang Guo, Xi Chen, Qiong Liang, Xiaoming Zhai & Jin Tao
Abstract Background China is a region with a high incidence of tuberculosis, and the incidence of IBD has also been rising rapidly in recent years. Differentiating Crohn’s disease(CD) from intestinal tuberculosis (ITB) has become a very challenging issue. We aimed to develop and assess a diagnostic nomogram to differentiate between CD and ITB to improve the accuracy and practicability of the model. Methods A total of 133 patients (CD 90 and ITB 43) were analyzed...

Data from: Comparative population genomics reveals key barriers to dispersal in Southern Ocean penguins

Gemma V. Clucas, Jane L. Younger, Damian Kao, Louise Emmerson, Colin Southwell, Barbara Wienecke, Alex D. Rogers, Charles-Andre Bost, Gary D. Miller, Michael J. Polito, Patrick Lelliot, Jonathan Handley, Sarah Crofts, Richard A. Phillips, Michael J. Dunn, Karen J. Miller, Tom Hart & Patrick Lelliott
The mechanisms that determine patterns of species dispersal are important factors in the production and maintenance of biodiversity. Understanding these mechanisms helps to forecast the responses of species to environmental change. Here we used a comparative framework and genome-wide data obtained through RAD-seq to compare the patterns of connectivity among breeding colonies for five penguin species with shared ancestry, overlapping distributions, and differing ecological niches, allowing an examination of the intrinsic and extrinsic barriers governing...

Microhabitat contributes to microgeographic divergence in threespine stickleback

Meghan Maciejewski, Cynthia Jiang, Yoel Stuart & Daniel Bolnick
Since the New Synthesis, most migration-selection balance theory predicted that there should be negligible differentiation over small spatial scales (relative to dispersal), because gene flow should erode any effect of divergent selection. Nevertheless, there are classic examples of microgeographic divergence, which theory suggests can arise under specific conditions: exceptionally strong selection, phenotypic plasticity in philopatric individuals, or non-random dispersal. Here, we present evidence of microgeographic morphological variation within lake and stream populations of threespine stickleback...

Exploring Relationships Between Fraternity and Sorority Membership and Socially Responsible Leadership

John P. Dugan

Data for morphometric analysis and DNA barcode sequence for the new fish species Polymixia hollisterae

Mark Wilson & Terry Grande
Two datasets are provided to support the journal article (https://doi.org/10.1643/i2020112) by T. C. Grande and M. V. H. Wilson naming the new Bermuda fish species Polymixia hollisterae. The first dataset is for 2-D multivariate morphometric comparisons of selected specimens and species of the fish genus Polymixia. The file is in TPS format, as a plain text file, for use in the application MorphoJ. The data are for 27 specimens with pixel coordinates for 34 landmarks...

A genome-wide test for paternal indirect genetic effects on lifespan in Drosophila melanogaster

Vinesh N Shenoi, Martin I Brengdahl, Jaime L Grace, Björn Eriksson, Patrik Rydén & Urban Friberg
Exposing sires to various environmental manipulations has demonstrated that paternal effects can be non-trivial also in species where male investment in offspring is almost exclusively limited to sperm. Whether paternal effects also have a genetic component (i.e. paternal indirect genetic effects - PIGEs) in such species is however largely unknown, primarily because of methodological difficulties separating indirect from direct effects of genes. PIGEs may nevertheless be important, since they have the capacity to contribute to...

Additional file 3 of Metabolic engineering of Escherichia coli BW25113 for the production of 5-Aminolevulinic Acid based on CRISPR/Cas9 mediated gene knockout and metabolic pathway modification

Changchuan Ye, Yuting Yang, Xi Chen, Lijie Yang, Xia Hua, Mengjie Yang, Xiangfang Zeng & Shiyan Qiao
Additional file 3: Fig S3. Gene map for targeted Cas9-mediated gene Knock-In. (A) The knock-out site of hemF in BW25113-T7. (B) map of hemF knock-out in ideal condition and the location of PCR product (899 bp) for sequencing.

Additional file 5 of Metabolic engineering of Escherichia coli BW25113 for the production of 5-Aminolevulinic Acid based on CRISPR/Cas9 mediated gene knockout and metabolic pathway modification

Changchuan Ye, Yuting Yang, Xi Chen, Lijie Yang, Xia Hua, Mengjie Yang, Xiangfang Zeng & Shiyan Qiao
Additional file 5: Fig S5. Detection of successful gene knock-outs of BW25113-T7.

Additional file 6 of Metabolic engineering of Escherichia coli BW25113 for the production of 5-Aminolevulinic Acid based on CRISPR/Cas9 mediated gene knockout and metabolic pathway modification

Changchuan Ye, Yuting Yang, Xi Chen, Lijie Yang, Xia Hua, Mengjie Yang, Xiangfang Zeng & Shiyan Qiao
Additional file 6: Fig S6. Standard Plot for ALA measurement. x: the absorbance at 554 nm; y: ALA concentration of sample after diluted (mg/L).

Additional file 7 of Metabolic engineering of Escherichia coli BW25113 for the production of 5-Aminolevulinic Acid based on CRISPR/Cas9 mediated gene knockout and metabolic pathway modification

Changchuan Ye, Yuting Yang, Xi Chen, Lijie Yang, Xia Hua, Mengjie Yang, Xiangfang Zeng & Shiyan Qiao
Additional file 7: Table S1. Growth rate of strain expressing various related genes in different medium.

Data from: Genome-wide association studies across environmental and genetic contexts reveal complex genetic architecture of symbiotic extended phenotypes

Rebecca Batstone, Hanna Lindgren, Cassandra Allsup, Laura Goralka, Alex Riley, Michael Grillo, Amy Marshall-Colon & Katy Heath
A goal of modern biology is to develop the genotype-phenotype (G→P) map, a predictive understanding of how genomic information generates trait variation that forms the basis of both natural and managed communities. As microbiome research advances, however, it has become clear that many of these traits are symbiotic extended phenotypes, being governed by genetic variation encoded not only by the host’s own genome, but also by the genomes of myriad cryptic symbionts. Building a reliable...

Phosphodiesterase 10A (PDE10A) as a novel target to suppress β-catenin and RAS signaling in epithelial ovarian cancer

Rebecca M. Borneman, Elaine Gavin, Alla Musiyenko, Wito Richter, Kevin J. Lee, David K. Crossman, Joel F. Andrews, Annelise M. Wilhite, Steven McClellan, Ileana Aragon, Antonio B. Ward, Xi Chen, Adam B. Keeton, Kristy Berry, Gary A. Piazza, Jennifer M. Scalici & Luciana Madeira da Silva
Abstract A leading theory for ovarian carcinogenesis proposes that inflammation associated with incessant ovulation is a driver of oncogenesis. Consistent with this theory, nonsteroidal anti-inflammatory drugs (NSAIDs) exert promising chemopreventive activity for ovarian cancer. Unfortunately, toxicity is associated with long-term use of NSAIDs due to their cyclooxygenase (COX) inhibitory activity. Previous studies suggest the antineoplastic activity of NSAIDs is COX independent, and rather may be exerted through phosphodiesterase (PDE) inhibition. PDEs represent a unique chemopreventive...

Additional file 1 of Differential diagnosis of Crohn’s disease and intestinal tuberculosis: development and assessment of a nomogram prediction model

Shaoxiong Zeng, Ying Lin, Jiaxiang Guo, Xi Chen, Qiong Liang, Xiaoming Zhai & Jin Tao
Supplementary Material 1. Supplementary Figure 1. The flow chart of this study. Supplementary Figure 2 Typical endoscopic features in Crohn?s disease and and intestinal tuberculosis. Supplementary Figure 3 Typical findings of computed tomographic enterography (CTE) in Crohn?s disease. Supplementary Figure 4. Pathological features in Crohn’s disease and intestinal tuberculosis. Supplementary Table 1. Comparison of general conditions of patients with CD and ITB. Supplementary Table 2. Comparison of clinical manifestations and laboratory examination in patients with...

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Affiliations

  • Loyola University Chicago
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  • Baylor College of Medicine
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  • Affiliated Hospital of Southwest Medical University
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  • Third Affiliated Hospital of Guangzhou Medical University
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