279 Works

Long non-coding RNA NEAT1 promotes steatosis via enhancement of estrogen receptor alpha-mediated AQP7 expression in HepG2 cells

Xiaohua Fu, Jing Zhu, Lin Zhang & Jing Shu
Hepatic steatosis is one of the most important features of the pathogenesis for non-alcoholic fatty liver disease. Fat deposition in liver cells can influence hepatic lipogenesis along with other metabolic pathways and further lead to the irreversible liver cirrhosis and injury. However, the underlying mechanism of steatosis remains largely unexplored. Our previous study revealed that AQP7 played an important role in liver steatosis. In this study, we determined that the transcriptional level of AQP7 was...

Nanitic scan sample data for division of labor in incipient Pogonomyrmex rugosus colonies

Peter Nonacs & Brittany Enzmann
Division of labor (DOL) is a principal characteristic of workers in mature colonies of many social insect species. In newly initiated ant colonies, however, the first workers (called nanitics) are few in number and much smaller in size than workers of mature colonies. This limited workforce must nevertheless perform most of the tasks of a mature colony, and it is unknown if they also exhibit DOL. In this study, we tracked several inside-nest and outside-nest...

DEPP: Deep learning enables extending species trees using single genes

Yueyu Jiang, Metin Balaban, Qiyun Zhu & Siavash Mirarab
Placing new sequences onto reference phylogenies is increasingly used for analyzing environmental samples, especially microbiomes. However, existing placement methods have a fundamental limitation: they assume that query sequences have evolved using specific models directly on the reference phylogeny. Thus, they can place single-gene data (e.g., 16S rRNA amplicons) onto their own gene tree. This practice is a proxy for a more ambitious goal: extending a (genome-wide) species tree given data from individual genes. No algorithm...

Moving in fast waters: the exaggerated claw gape of the new river crayfish (Cambarus chasmodactlyus) aids in locomotor performance

Zackary Graham
Humans are inherently fascinated by exaggerated and conspicuous morphological structures such as the elk antlers and the peacock trains. Because these traits are costly to develop and wield, the environment in which they are used can select for specific sizes or shapes to minimize such costs. In aquatic environments, selection to reduce drag can constrain the form of exaggerated structures; this is presumably why exaggerated morphologies are less common in aquatic environments compared to terrestrial...

Data from: Fat in the leg: function of the expanded hind leg in gasteruptiid wasps (Hymenoptera: Gasteruptiidae)

István Mikó, Sarthok Rasique Rahman, Salvatore S. Anzaldo, Thomas Van De Kamp, Ben A. Parslow, Nikolai J. Tatarnic, Maxwell T. Wetherington, Julie Anderson, Rudolf J. Schilder, Jonah M. Ulmer, Andrew R. Deans & Heather M. Hines
Among some of the most unusual traits of the gasteruptiid wasps is their unique hovering flight and the expansion of their hind tibiae. Tibial expansions in female parasitoid hymenopterans often involve an enlarged sensory structure for vibration detection, the subgenual organ, thus enabling refined substrate-borne detection of concealed hosts. In the present paper, we utilize a combination of microscopy, chemical analysis, gene expression, and behavior to explore the function of the expanded hind tibia of...

Map script with examples from: Taxonomic revision of the Temnothorax salvini clade (Hymenoptera: Formicidae), with a key to the clades of New World Temnothorax

Matthew Prebus
Temnothorax is a large myrmicine ant genus with a range spanning the northern hemisphere, including the northern half of the Neotropics. Many of the Neotropical species were originally placed in the now defunct genus Macromischa. Recent molecular work has revealed that distinct lineages of Neotropical Temnothorax have arrived by evolutionary convergence at a morphological syndrome with characteristics that were used to diagnose the former genus Macromischa. One such lineage is the salvini clade, which in...

Data from: Plastic collective endothermy in a complex animal society (army ant bivouacs: Eciton burchellii parvispinum)

Kaitlin M. Baudier, Catherine L. D'Amelio, Elisabeth Sulger, Michael P. O'Connor & Sean O'Donnell
Endothermic animals do not always have a single adaptive internal temperature; some species exhibit plastic homeostasis, adaptively allowing body temperature to drop when thermoregulatory costs are high. Like large-bodied endotherms, some animal societies exhibit collective thermal homeostasis. We tested for plasticity of thermoregulation in the self-assembled temporary nests (bivouacs) of army ants. We measured core bivouac temperatures under a range of environmental conditions and at different colony developmental (larval vs. pupal brood) stages. Contrary to...

Data from: Juvenile social experience generates differences in behavioral variation but not averages

Nicholas DiRienzo, J. Chadwick Johnson & Anna Dornhaus
Developmental plasticity is known to influence the mean behavioral phenotype of a population. Yet, studies on how developmental plasticity shapes patterns of variation within populations are comparatively rare and often focus on a subset of developmental cues (e.g. nutrition). One potentially important but understudied developmental experience is social experience, as it is explicitly hypothesized to increase variation among individuals as a way to promote ‘social niches.’ To test this we exposed juvenile black widow spiders...

Data from: Machine learning to classify animal species in camera trap images: applications in ecology

Micheal A. Tabak, Mohammad Sadegh Norouzzadeh, Michael A. Tabak, David W. Wolfson, Steven J. Sweeney, Paul A. Di Salvo, Ryan S. Miller, Jesse S. Lewis, Jeff Clune, Ryan K. Brook, Elizabeth G. Mandeville, Paul M. Lukacs, Anna K. Moeller, Raoul K. Boughton, Bethany Wight, James C. Beasley & Peter E. Schlichting
Motion‐activated cameras (“camera traps”) are increasingly used in ecological and management studies for remotely observing wildlife and are amongst the most powerful tools for wildlife research. However, studies involving camera traps result in millions of images that need to be analysed, typically by visually observing each image, in order to extract data that can be used in ecological analyses. We trained machine learning models using convolutional neural networks with the ResNet‐18 architecture and 3,367,383 images...

Data from: To grunt or not to grunt: factors governing call production in female olive baboons, Papio anubis

Joan B. Silk, Eila R. Roberts, Veronika Staedele, Shirley C. Strum & Veronika Städele
Vocal signals often play an important role in synchronizing the activities of group members, coordinating decisions about when and where to travel, and facilitating social interactions in which there are potential conflicts of interest. In chacma baboons, Papio ursinus, low amplitude grunts facilitate nonaggressive social interactions and reconcile conflicts. Grunts seem to function as signals of benign intent and reduce uncertainty about the signaler's subsequent behavior. Here, we replicate and extend these findings in another...

Aminoacyl-tRNA synthetase gene alignments from multiple Sileneae species generated from full-length transcripts using Iso-Seq and raw microscopy image files

Jessica Warren
Trimmed and untrimmed alignments for the final aminoacyl-tRNA synthetases in Sileneae species and Arabidopsis thaliana. We investigated the evolution of subcellular localization of aaRS enzymes in five different species from the plant lineage Sileneae that has experienced extensive and rapid mitochondrial tRNA loss. By analyzing full-length mRNA transcripts with single-molecule sequencing technology (PacBio Iso-Seq) and searching genome sequences, we found instances of predicted retargeting of an ancestrally cytosolic aaRS to the mitochondrion as well as...

Survey data from: Can community laboratory facilities increase access and inclusivity in geoscience?

Lee Corbett, Paul Bierman, Steven Semken & Joseph Whittaker
Geochronology and geochemistry are critical tools in geoscience research and research training, but students and faculty at many institutions have little or no access to the specialized and expensive facilities needed for sample preparation and analysis. Here, we assess whether community laboratories, dedicated to hosting visitors, can help address these inequities by increasing access to cutting-edge methods and the resulting data. We report the first three years of outcomes from such a community laboratory, the...

Data and code from: Correlates of individual participation in boundary patrols by male chimpanzees

Anthony Massaro, Ian Gilby, Nisarg Desai, Alexander Weiss, Joseph Feldblum, Anne Pusey & Michael Wilson
Group territory defense poses a collective action problem: individuals can free-ride, benefiting without paying the costs. Individual heterogeneity has been proposed to solve such problems, as individuals high in reproductive success, rank, fighting ability, or motivation may benefit from defending territories even if others free-ride. To test this hypothesis, we analyzed 30 years of data from chimpanzees (Pan troglodytes) in the Kasekela community, Gombe National Park, Tanzania (1978-2007). We examined the extent to which individual...

Identification of differentially expressed miRNAs and their target genes in response to brassinolide treatment on flowering of tree peony (Paeonia ostii)

Lin Zhang, Chengwei Song, Dalong Guo, Lili Guo, Xiaogai Hou & Huafang Wang
Tree peony is a famous flower plant in China, but the short and concentrated flowering period limits its ornamental value and economic value. Brassinolide (BR) plays an important role in plant growth and development including flowering. There have been a large number of reports on the molecular aspects of the flowering process, but the genetic mechanism that was responsible for miRNA-guided regulation of tree peony is almost unclear. In this study, the leaves of tree...

Generational variation in nutrient regulation for an outbreaking herbivore

Marion Le Gall
Multivoltine insects can produce multiple generations in one year. Favorable conditions support more generations, leading to serious outbreaks. For herbivores, plant nutrient availability is a major environmental factor affecting fitness and it can shift substantially throughout seasons. In a stochastic environment, organisms can adopt several strategies to regulate their nutrient intake and maximize performance. However, data regarding nutrient regulation of wild herbivores are scarce, and even more so regarding potential intergenerational plasticity. To bridge this...

Supplementary materials: Return of the pika: American pikas re-occupy long-extirpated, warm locations

Constance Millar & Andrew Smith
To accompany: Return of the pika: American pikas re-occupy long-extirpated, warm locations by Constance I. Millar and Andrew T. Smith, Nature Notes. American pika re-colonization sites identified in this study Bodie State Historic Park – Noonday Mine 38.004 N; -119.1005 W; 2,615 m Site also clearly identified in maps in Smith (1974a), Smith & Gilpin (1997), Smith & Nagy (2015). North Mono Craters Site 37.9116 N; -118.9985 W; 2,145-2,250 m

Additional file 2 of Housekeeping gene gyrA, a potential molecular marker for Bacillus ecology study

Yan Liu, Polonca Štefanič, Youzhi Miao, Yansheng Xue, Weibing Xun, Nan Zhang, Qirong Shen, Ruifu Zhang, Zhihui Xu & Ines Mandic-Mulec
Additional file 2: TableS1 The information of 127 strains for colony PCR. TableS2 The genomes information for nucleotide variability analysis of gyrA gene and 16S rRNA gene in inter- and intraspecies Bacillus. TableS3 The gyrA gene database information of Bacillus for computer simulation. TableS4 The general primers converted from degenerate primer pair gyrA3. TableS5 The genomes information for SNP analysis of gyrA gene and 16S rRNA gene in four Bacillus species. TableS6 The information of...

Additional file 10 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 10. Differential expression analysis details. For conciseness, the labels of pairwise comparisons were coded in two letters: the first one represents the phenotype (M: mothers, F: fathers, P: paternal males, A: attackers), whereas the second one represents the structure (M: MPOA, N: NAc, L: LS). For instance, PLvAL refers to the comparison between the Paternal and Attackers phenotypes in the LS. DE: differentially expressed.

Additional file 10 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 10. Differential expression analysis details. For conciseness, the labels of pairwise comparisons were coded in two letters: the first one represents the phenotype (M: mothers, F: fathers, P: paternal males, A: attackers), whereas the second one represents the structure (M: MPOA, N: NAc, L: LS). For instance, PLvAL refers to the comparison between the Paternal and Attackers phenotypes in the LS. DE: differentially expressed.

Additional file 14 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 14. Functional enrichment of genes differentially expressed in the medial preoptic area (MPOA), the nucleus accumbens (NAc), or the lateral septum (LS). For each pairwise comparison, the functional enrichments in gene ontologies of the biological processes (BP), cellular components (CC), and molecular functions (MF) categories as well as in pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG) were tested for the differentially expressed genes up- or down-regulated (UP, and DOWN, respectively)....

Gapless genome assembly of East Asian finless porpoise, Neophocaena asiaeorientalis sunameri

Denghua Yin, Chunhai Chen, Danqing Lin, Jialun Zhang, Congping Ying, Yan Liu, Wang Liu, Zhichen Cao, Chenxi Zhao, Chenhe Wang, Liping Liang, Pao Xu, Jianbo Jian & Kai Liu
There are the genome sequence, gene set, coding sequence and protein sequence of Neophocaena asiaeorientalis sunameri.

Additional file 7 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 7. Detailed results from the linear regressions between all behaviors scored during the parental behaviors test, testing for an interaction of Group (Mothers/Fathers/Paternal).

Additional file 9 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 9. Functional enrichment across structures and phenotypes. For each pairwise comparison, the functional enrichments in gene ontologies of the biological processes (BP), cellular components (CC), and molecular functions (MF) categories as well as in pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG) were tested for the differentially expressed genes up- or down-regulated (UP, and DOWN, respectively). The labels of pairwise comparisons were coded in two letters: the first one represents the...

Systemic racial disparities in funding rates at the National Science Foundation

Christine Chen, Sara Kahanamoku, Aradhna Tripati, Rosanna Alegado, Vernon Morris, Karen Andrade & Justin Hosbey
Concerns about systemic racism at academic and research institutions have increased over the past decade. Here, we investigate data from the National Science Foundation (NSF), a major funder of research in the United States, and find evidence for pervasive racial disparities. In particular, white principal investigators (PIs) are consistently funded at higher rates than most non-white PIs. Funding rates for white PIs have also been increasing relative to annual overall rates with time. Moreover, disparities...

Additional file 21 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 21. Number of immediate early genes (IEG) in the genes differentially expressed in the medial preoptic area (MPOA), nucleus accumbens (NAc), and lateral septum (LS).

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