Article
Multidisciplinary Sciences
Philippe J. Batut, Xin Yang Bing, Zachary Sisco, Joao Raimundo, Michal Levo, Michael S. Levine
Summary: Past studies have provided contradictory claims about the role of genome organization in gene activity regulation. This study demonstrates that the Drosophila genome is organized by two independent classes of regulatory sequences, tethering elements and insulators. These two levels of genome organization operate independently to ensure precise transcriptional dynamics and reliable complex patterning processes.
Article
Ecology
Megan C. Milligan, Aaron N. Johnston, Jeffrey L. Beck, Kaitlyn L. Taylor, Embere Hall, Lee Knox, Teal Cufaude, Cody Wallace, Geneva Chong, Matthew J. Kauffman
Summary: Migration is crucial for population persistence and ecosystem functioning, but human activities, including wind energy development, disrupt migration routes. We studied the effects of wind energy development on pronghorn migration in Wyoming, USA. Pronghorn made behavioral adjustments during migration to avoid turbines, select areas farther from turbines, and reduce fidelity to migration routes near construction sites. These adjustments could reduce the functional benefits of pronghorn migration over time.
ECOLOGY AND EVOLUTION
(2023)
Article
Geography
Andrew Flachs
Summary: Crises present opportunities for social and environmental reorganization, with charismatic actors playing a key role. Alternative agrarian development models help restructure political, social, and ecological relationships, with charisma tied to political relationships that have the potential for collective action and violent Othering. Case studies from Indian agriculture demonstrate how charismatic entities capitalize on crises to form new alliances outside of state and local programs.
JOURNAL OF RURAL STUDIES
(2021)
Article
Polymer Science
Yue Shao, Yilan Ye, Dayin Sun, Zhenzhong Yang
Summary: Polymer-derived Janus particles, with their unique morphologies and functionalities, show great promise as key elements in future applications. This Perspective describes recent progress in the synthesis and generation of polymer-derived Janus particles at different length scales, and emphasizes the control of compartmentalization and large-scale synthesis. The challenges and opportunities associated with polymer-derived Janus particles are also outlined to inspire the development of new strategies for their large-scale synthesis with integrated functionalities.
Article
Engineering, Manufacturing
Brian Snider-Simon, George Frantziskonis
Summary: As metal additive manufacturing moves towards producing in-service parts, there is a need for methodologies to predict material response and reliability. Physics-based approaches and data-driven models have their pros and cons, with physics-based methods requiring high computational costs and data-driven models struggling with interpretation and potential bias. This paper introduces a novel workflow that combines process parameters, build strategy, and standard material science tests data to develop finite element models for predicting material reliability without explicitly modeling the physics behind the manufacturing process.
ADDITIVE MANUFACTURING
(2022)
Article
Engineering, Civil
Georgia Papacharalampous, Hristos Tyralis, Yannis Markonis, Martin Hanel
Summary: In this study, a new methodological framework is proposed for exploring and comparing multi-scale analyses in a hydroclimatic context, in order to comprehensively understand the behaviors of geophysical processes and evaluate time series simulation models. By computing the feature values at different temporal resolutions and three hydroclimatic time series types, similarities and differences in the evolution patterns are identified. The computed features are also used for meaningful clustering of hydroclimatic time series, which allows for interpretation of hydroclimatic similarity at various temporal resolutions.
JOURNAL OF HYDROLOGY
(2023)
Article
Materials Science, Multidisciplinary
Brett Henderson, Archita N. S. Adluri, Jeffrey T. Paci, Irina Paci
Summary: Nanocomposites with metallic inclusions have vast potential as tunable functional materials for applications requiring high permittivities. However, existing computational approaches face challenges in dealing with these materials due to the quantum and interfacial effects dominating in composites with small inclusions. In this study, we propose an adjustable finite element approach that incorporates interfacial layers to accurately calculate the permittivities of nanocomposites consisting of metal-oxide matrices with nanometer-scale silver inclusions. This continuum model, informed by quantum mechanical results, successfully captures relevant polarization effects with significantly reduced computational costs compared to full quantum mechanics simulations.
MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING
(2023)
Review
Plant Sciences
Kate Harline, Jesus Martinez-Gomez, Chelsea D. Specht, Adrienne H. K. Roeder
Summary: Modeling has become a popular tool in biological disciplines, but the literacy among biologists has not kept pace. The lack of understanding inhibits communication and progress in data analysis. A blueprint has been proposed to empower biologists to apply models in their field.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Cell Biology
Hao Deng, Bomyi Lim
Summary: The study explores the impact of interallelic interactions on gene regulation. It found that allelic competition exists in homozygotes, but can be eliminated by changing the position of the reporter construct. The transcriptional machinery, such as RNA Pol II, may be responsible for this competition. The study provides new insights into the role of interallelic interactions in gene regulation.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biodiversity Conservation
Greta M. Schmidt, Megan K. Jennings, Julia G. Smith, Erin E. Boydston, Lisa M. Lyren, Rebecca L. Lewison
Summary: Urban areas have a significant impact on wildlife populations due to habitat fragmentation and degradation. Bobcats in San Diego County demonstrate how individual and population levels of space use are influenced by development, providing insight into the mechanisms behind wildlife response to urbanization.
BIOLOGICAL CONSERVATION
(2023)
Article
Cell Biology
Matthew A. Reyer, Shriram Chennakesavalu, Emily M. Heideman, Xiangqian Ma, Magda Bujnowska, Lu Hong, Aaron R. Dinner, Carin K. Vanderpool, Jingyi Fei
Summary: Small RNAs (sRNAs) are important gene regulators in bacteria, acting post-transcriptionally by affecting translation and degradation of target mRNAs. Some sRNAs can regulate targets co-transcriptionally early in an mRNA's lifetime, potentially mediated by Rho-dependent termination. Data also reveals that certain kinetic steps and sRNA binding to target mRNA may dictate the regulation hierarchy within sRNA regulons.
Article
Biochemical Research Methods
Andres F. Lopez-Lopera, Nicolas Durrande, Mauricio A. Alvarez
Summary: The regulatory process of Drosophila is studied using physically-inspired stochastic models, focusing on post-transcriptional events. Two different Gaussian processes models are investigated based on reaction-diffusion equations, with performance assessments on high-resolution datasets.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2021)
Article
Environmental Sciences
Velio Coviello, Gianluca Vignoli, Silvia Simoni, Walter Bertoldi, Michael Engel, Anuschka Buter, Giulia Marchetti, Andrea Andreoli, Sara Savi, Francesco Comiti
Summary: This study analyzes the bedload flux in a glacier-fed river in Italy using 7 years of continuous data. The findings highlight the variability of bedload rates, the influence of flood events and sediment supply on bedload rates, and the impact of climatic factors on bedload transport. The results suggest that climate change in the Alps will likely lead to increased peak bedload rates in the future.
WATER RESOURCES RESEARCH
(2022)
Article
Ecology
Joshua I. Brian, David C. Aldridge
Summary: Understanding how ecological communities are assembled is crucial for ecosystem ecology. This study focused on parasites as a natural system to explore the idea of factors acting at multiple scales in community structure. The researchers used a Markov Random Fields model to assess the contribution of different factors and found that patterns at one level can mask those at another, highlighting the importance of considering variation at higher scales.
JOURNAL OF ANIMAL ECOLOGY
(2023)
Article
Computer Science, Artificial Intelligence
Cigdem Beyan, Sukumar Karumuri, Gualtiero Volpe, Antonio Camurri, Radoslaw Niewiadomski
Summary: This article proposes a novel Convolutional Neural Network-based architecture for classifying emotions from full-body movements. The architecture consists of two shallow networks that process 8-bit RGB images obtained from time intervals of 3D-positional data. By combining different temporal scales, the classification results of a dataset composed of professional dancers' performances interpreting affective states were improved. The article also investigates the effects of data chunk duration, overlapping, input image size, and data augmentation strategies on the proposed method's performance.
IEEE TRANSACTIONS ON AFFECTIVE COMPUTING
(2023)
Article
Biochemistry & Molecular Biology
Xiaofei Wang, Tianyin Zhou, Zeba Wunderlich, Matthew T. Maurano, Angela H. DePace, Sergey V. Nuzhdin, Remo Rohs
MOLECULAR BIOLOGY AND EVOLUTION
(2018)
Article
Genetics & Heredity
Ben J. Vincent, Max V. Staller, Francheska Lopez-Rivera, Meghan D. J. Bragdon, Edward C. G. Pym, Kelly M. Biette, Zeba Wunderlich, Timothy T. Harden, Javier Estrada, Angela H. DePace
Article
Genetics & Heredity
Zeba Wunderlich, Charless C. Fowlkes, Kelly B. Eckenrode, Meghan D. J. Bragdon, Arash Abiri, Angela H. DePace
G3-GENES GENOMES GENETICS
(2019)
Article
Biology
Jeehae Park, Javier Estrada, Gemma Johnson, Ben J. Vincent, Chiara Ricci-Tam, Meghan D. J. Bragdon, Yekaterina Shulgina, Anna Cha, Zeba Wunderlich, Jeremy Gunawardena, Angela H. DePace
Article
Genetics & Heredity
Francheska Lopez-Rivera, Olivia K. Foster Rhoades, Ben J. Vincent, Edward C. G. Pym, Meghan D. J. Bragdon, Javier Estrada, Angela H. DePace, Zeba Wunderlich
G3-GENES GENOMES GENETICS
(2020)
Article
Biology
Rachel Waymack, Alvaro Fletcher, German Enciso, Zeba Wunderlich
Review
Genetics & Heredity
Evgeny Z. Kvon, Rachel Waymack, Mario G. Elabd, Zeba Wunderlich
Summary: Shadow enhancers are redundant cis-regulatory elements that regulate the same gene and drive overlapping expression patterns. They play a crucial role in animal development, protecting gene expression from mutations and contributing to phenotypic robustness. Despite their apparent redundancy, shadow enhancers are evolutionarily conserved and key players in emerging gene regulatory networks in metazoans.
NATURE REVIEWS GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Bryan A. Ramirez-Corona, Stephanie Fruth, Oluchi Ofoegbu, Zeba Wunderlich
Summary: The study found that the mode of expression divergence varies between conditions within the Drosophila fat body. Trans-acting effects dominate in response to Gram-negative infection, while cis-acting effects dominate in Gram-positive and preinfection conditions. Before infection, compensatory effects in the fat body due to metabolic activity lead to changes in cis and trans that counteract each other.
Correction
Genetics & Heredity
Evgeny Z. Kvon, Rachel Waymack, Mario Gad, Zeba Wunderlich
NATURE REVIEWS GENETICS
(2021)
Article
Genetics & Heredity
Lily Li, Rachel Waymack, Mario Gad, Zeba Wunderlich
Summary: The study reveals that the expression of developmental genes is regulated by multiple enhancers and core promoters, which provide both redundancy and specificity. Specific burst properties during transcription, such as burst size and frequency, are most strongly tuned by the combination of promoters and enhancers. The presence of multiple promoters in a locus is due to enhancer preference and a need for redundancy, with broad promoters being common among developmental genes.
Article
Multidisciplinary Sciences
Rachel Waymack, Mario Gad, Zeba Wunderlich
Summary: Transgenic reporters are valuable tools for studying enhancers, but they may inhibit the expression of other genes. Competition for transcription factors is thought to be partially responsible for this inhibition of gene expression.
Article
Biology
Jungmin Han, Sudheesha Perera, Zeba Wunderlich, Vipul Periwal
Summary: Advances in single-cell techniques have made measuring gene dynamics at cellular resolution practical, but the increased complexity of data has made it computationally challenging to unravel underlying biological mechanisms. This study presents an iterative regression algorithm for inferring gene networks, showing that the predictive power of the inferred model is higher than other methods.
MATHEMATICAL BIOSCIENCES
(2021)
Article
Multidisciplinary Sciences
Bryan A. Ramirez-Corona, Anna C. Love, Srikiran Chandrasekaran, Jennifer A. Prescher, Zeba Wunderlich
Summary: This article introduces a non-invasive bioluminescent imaging strategy that allows real-time observation of pathogen load changes in individual fruit flies. By using luminescent bacteria for monitoring, stochastic responses to infection can be studied over time in individuals, and the dynamics of microbial clearance can be visualized with high temporal resolution.
Article
Biochemical Research Methods
Alvaro Fletcher, Zeba Wunderlich, German Enciso
Summary: Enhancers are regulatory DNA sequences that bind transcription factors and control the expression of a target gene. Shadow enhancers are multiple enhancers that regulate the same target gene and are associated with most animal developmental genes. Studies show that shadow enhancers can provide more consistent transcription than single enhancers. However, it is still unknown why shadow enhancer TF binding sites are distributed across multiple enhancers instead of within a single large enhancer.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Correction
Genetics & Heredity
Evgeny Z. Kvon, Rachel Waymack, Mario Gad, Zeba Wunderlich
NATURE REVIEWS GENETICS
(2021)
