Article
Biochemistry & Molecular Biology
Annabel C. Beichman, Pooneh Kalhori, Christopher C. Kyriazis, Amber A. DeVries, Sergio Nigenda-Morales, Gisela Heckel, Yolanda Schramm, Andres Moreno-Estrada, Douglas J. Kennett, Mark Hylkema, James Bodkin, Klaus-Peter Koepfli, Kirk E. Lohmueller, Robert K. Wayne
Summary: The genetic consequences of species-wide declines are seldom studied, but sea otters provide an exceptional case as their population decline occurred range-wide and simultaneously. By using genomic data and simulations, we found distinct population structure among sea otters and identified Californian sea otters as survivors of a divergent lineage isolated for thousands of years. The simulations also revealed that the extreme population decline could have long-lasting effects on the fitness of recovering populations, but historically low effective population sizes may have mitigated the impact of decline on genetic health.
Article
Genetics & Heredity
Sylvan C. Baca, Cassandra Singler, Soumya Zacharia, Ji-Heui Seo, Tunc Morova, Faraz Hach, Yi Ding, Tommer Schwarz, Chia-Chi Flora Huang, Jacob Anderson, Andre P. Fay, Cynthia Kalita, Stefan Groha, Mark M. Pomerantz, Victoria Wang, Simon Linder, Christopher J. Sweeney, Wilbert Zwart, Nathan A. Lack, Bogdan Pasaniuc, David Y. Takeda, Alexander Gusev, Matthew L. Freedman
Summary: Many genetic variants affect disease risk by altering context-dependent gene regulation. The cistrome-wide association study (CWAS) is a powerful framework for identifying variants that influence traits through effects on chromatin state.
Article
Plant Sciences
Rafael Gomes Barbosa-Silva, Caroline O. Andrino, Luisa Azevedo, Luisa Lucresia, Juliana Lovo, AliceL. Hiura, Pedro L. Viana, Tereza C. Giannini, Daniela Cristina Zappi
Summary: Inselbergs, non-zonal formations found in different biomes, have distinct and divergent flora in each biome. The inselberg flora is more related to the biome where it is located than to other factors, even when the microclimatic conditions in the outcrops differ strongly from those of the surrounding matrix. The Caatinga inselbergs have the highest level of species turnover and should be protected due to their unique plant lineages and vulnerability.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Quantum Science & Technology
Weichao Liang, Francesco Ticozzi, Giuseppe Vallone
Summary: This paper addresses the problem of evaluating the accuracy of quantum state preparation. The order of measurements is shown to be critical for quickly assessing accuracy. Different strategies are proposed to reduce the number of measurements needed for verification and an advantage is observed for the adaptive protocol, especially in assessing faulty preparations.
QUANTUM INFORMATION PROCESSING
(2023)
Article
Biology
Zefu Wang, Xiao Zhang, Weixiao Lei, Hui Zhu, Shengdan Wu, Bingbing Liu, Dafu Ru
Summary: Urban greening is important for providing ecosystem services and recreation spaces, and should be considered by municipal decision-makers. Robinia pseudoacacia, a tree species commonly planted in urban green spaces, has attractive flowers, fragrances, high trunks, wide adaptability, and essential ecosystem services. However, the genomic basis and consequences of its wide planting in urban green spaces are unknown.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Arjun K. Aditham, Craig J. Markin, Daniel A. Mokhtari, Nicole DelRosso, Polly M. Fordyce
Summary: This study utilized a high-throughput microfluidic platform to quantitatively characterize hundreds of TF variants, revealing that many mutations, while altering binding, preserved physiological binding. Additionally, biochemical double-mutant cycles across the TF-DNA interface elucidated molecular mechanisms driving recognition.
Article
Biodiversity Conservation
Martina Treurnicht, Frank M. Schurr, Jasper A. Slingsby, Karen J. Esler, Jorn Pagel
Summary: The study found considerable inter- and intraspecific variation in sensitivity to wildflower harvesting among Proteaceae shrubs with fire-driven life cycles in the Cape Floristic Region. Sensitivity to harvesting showed varying geographical patterns and was associated with environmental conditions, highlighting the importance of considering spatial demographic data and environmental variation when assessing harvesting effects. These findings emphasize the need for species-specific and spatially nuanced conservation guidelines to prevent overexploitation of harvested species.
JOURNAL OF APPLIED ECOLOGY
(2021)
Article
Biology
Eloy Parra-Barrero, Kamran Diba, Sen Cheng
Summary: The study examines the relationships between theta phase, represented position, and true location in navigation through space in mammalian brains. Existing concepts of 'spatial' or 'temporal' theta sweeps are found to be inadequate in explaining how relevant variables change with running speed. A new concept of 'behavior-dependent' sweeps is introduced, where theta sweep length and place field properties vary based on running speed characteristics at different locations in the environment, providing essential structured heterogeneity for understanding the hippocampal code.
Article
Biology
Nicolas Dussex, Sara Kurland, Remi-Andre Olsen, Goeran Spong, Goeran Ericsson, Robert Ekblom, Nils Ryman, Love Dalen, Linda Laikre
Summary: The study examines the genome-wide diversity in moose populations in Sweden and finds limited impacts of the 1900s near-extinction event, but local variations in inbreeding, genetic load, and a risk of future reduction in genetic diversity and gene flow. The findings also indicate candidate genes for local adaptation and rapid temporal allele frequency shifts related to selective harvesting.
COMMUNICATIONS BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Danijela Popovic, Martyna Molak, Mariusz Ziolkowski, Alexei Vranich, Maciej Sobczyk, Delfor Ulloa Vidaurre, Guido Agresti, Magdalena Skrzypczak, Krzysztof Ginalski, Thiseas Christos Lamnidis, Nathan Nakatsuka, Swapan Mallick, Mateusz Baca
Summary: The Tiwanaku civilization flourished in the Lake Titicaca basin, and genetic analysis showed genetic continuity despite cultural and political changes. The ritual center of Tiwanaku exhibited high diversity, but most human offerings associated with it had pure Titicaca basin ancestry.
Article
Optics
Jie Liao, Lan Yang
Summary: Temperature measurement using optical barcodes from whispering-gallery sensors can be greatly improved by simultaneously monitoring different modes of optical signals. This technique overcomes limitations of existing single-mode sensors, providing high-precision and large-dynamic-range temperature measurements.
LIGHT-SCIENCE & APPLICATIONS
(2021)
Article
Plant Sciences
Hongyan Yin, Yu Yan, Wei Hu, Guoyin Liu, Hongqiu Zeng, Yunxie Wei, Haitao Shi
Summary: This study identified specific SNPs affecting ionomic variation in cassava through genome-wide association studies, with some SNPs associated with both calcium and magnesium. Many loci for different ionomic traits appear to be clustered on specific chromosome regions. The study also found peak SNPs in promoter regions of genes related to nitrogen and phosphorus accumulation, positively modulating nutrient levels in cassava.
Article
Chemistry, Analytical
Weinan Ye, Rong Cheng, Ming Zhang, Yu Zhu, Leijie Wang, Jinchun Hu, Xin Li
Summary: In this study, a novel interferometric reading head with a redundant design was proposed for wide-range displacement measurements. The reading head, using a one-dimensional grating splice module, was observed to be compatible with two orthogonal gratings, a compatibility that was verified experimentally with gratings possessing different grating line directions.
Article
Engineering, Electrical & Electronic
Wenbin Hu, Hongrui Ye, Shu Cheng, Jingjing Wang, Donglai Guo, Minghong Yang
Summary: Fiber interferometers are widely used in sensing various parameters. However, the conventional optical spectrum analyzer (OSA) fails to efficiently capture the interferometer spectrum change due to slow scanning speed. This article proposes a spectral processing strategy based on FFT frequency filtering and DTW spectral matching to achieve high-sensitivity and wide-range measurements.
IEEE TRANSACTIONS ON INSTRUMENTATION AND MEASUREMENT
(2023)
Article
Computer Science, Interdisciplinary Applications
Matteo Stefanini, Marta Lovino, Rita Cucchiara, Elisa Ficarra
Summary: This study proposes a new model called Perceiver for mRNA and protein level prediction, which utilizes a Transformer-based architecture with an attention module to capture long-range interactions in the sequences. The Perceiver models show effectiveness in predicting mRNA and protein levels.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2023)
Article
Biology
Aalok Patwa, Rikiya Yamashita, Jin Long, Tyler Risom, Michael Angelo, Leeat Keren, Daniel L. Rubin
Summary: The study utilizes high-dimensional tissue imaging technology to analyze the tumor-immune microenvironment in triple-negative breast cancer patients, revealing that profiling cell-to-cell interactions in the microenvironment can predict recurrence and overall survival, especially highlighting the importance of immunoregulatory proteins.
COMMUNICATIONS BIOLOGY
(2021)
Article
Infectious Diseases
Yuval Cohen, Nadav Bamberger, Orna Mor, Ronen Walfisch, Shay Fleishon, Itay Varkovitzky, Asaf Younger, Danit Oz Levi, Yishai Kohn, David M. Steinberg, Danny Zeevi, Oran Erster, Ella Mendelson, Zvi Livneh
Summary: This study introduces a bubble-based PCR testing approach that enables group testing using swab-pooling, offering advantages in time and cost efficiency. The method can be applied in school classes, airplanes, hospitals, military units, and workplaces, and may have potential applications in future pandemics.
CLINICAL MICROBIOLOGY AND INFECTION
(2022)
Editorial Material
Microbiology
Hagai Rossman, Eran Segal
NATURE MICROBIOLOGY
(2022)
Article
Oncology
Yogev Sela, Jinyang Li, Shivahamy Maheswaran, Robert Norgard, Salina Yuan, Maimon Hubbi, Miriam Doepner, Jimmy P. Xu, Elaine S. Ho, Clementina Mesaros, Colin Sheehan, Grace Croley, Alexander Muir, Ian A. Blair, Ophir Shalem, Chi V. Dang, Ben Z. Stanger
Summary: Solid tumors have heterogeneous metabolic microenvironments, with some regions being rich in oxygen and nutrients, while others are scarce. Cancer cells in the arid regions exhibit a slow-cycling state and are resistant to chemotherapy. Bcl-xL plays a central role in the adaptation of cancer cells to nutrient and oxygen deprivation. Combining traditional cancer therapies that target rapidly cycling cells with those that target quiescent, chemoresistant cells associated with nutrient and oxygen deprivation could improve treatment efficacy and patient survival.
Editorial Material
Biochemistry & Molecular Biology
Tal Keidar Haran, Leeat Keren
Summary: Twenty years ago, molecular biology shifted from studying genes in isolation to viewing them as part of complex modules, and now cell biology is undergoing a similar transition from studying individual cells to studying cellular modules.
MOLECULAR SYSTEMS BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Arno R. Bourgonje, Thomas Vogl, Eran Segal, Rinse K. Weersma
Summary: The adequate functioning of the intestinal barrier is crucial for protecting against pathogens and tolerating microbiota and self-antigens. Inflammatory bowel diseases (IBDs) are characterized by a disrupted intestinal barrier integrity, resulting in an abnormal immune response. Recent innovative antibody profiling technologies have the potential to provide a comprehensive understanding of humoral immunity and its applications in disease diagnosis, therapy, and prevention in IBD.
TRENDS IN MOLECULAR MEDICINE
(2022)
Article
Multidisciplinary Sciences
Sigal Leviatan, Saar Shoer, Daphna Rothschild, Maria Gorodetski, Eran Segal
Summary: This study produces a new human gut microbiome reference set of 3,594 species genomes, including 310 previously undescribed species, which serves as a valuable resource for further research.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Yochai Edlitz, Eran Segal
Summary: The study analyzed data from 44,709 UK Biobank participants to develop two different predictive models for T2D onset risk, one using non-laboratory data and one incorporating laboratory tests. These models accurately predict T2D risk, aiding medical decision-makers in assessing populations at elevated risk for T2D to improve medical strategies.
Article
Biology
Yan Yang, Guoyu Liu, Feng Li, Lucas B. Carey, Changjin Sun, Kaiping Ling, Hiroyuki Tachikawa, Morihisa Fujita, Xiao-Dong Gao, Hideki Nakanishi
Summary: The multiligand receptor RAGE plays a crucial role in mediating phagocytosis by non-professional phagocytes (NPPs) through the use of RNA fragments as ligands for internalization. This study reveals a new mechanism of phagocytosis by NPPs, showing that spores of Saccharomyces cerevisiae are efficiently internalized by NPPs due to the attachment of RNA fragments derived from cytosolic RNA species to the spore wall. Furthermore, the researchers demonstrate that RAGE is involved in phagocytosis by NPPs, not only in response to spores but also to other macromolecules containing RAGE ligands.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Thomas Vogl, Iris N. Kalka, Shelley Klompus, Sigal Leviatan, Adina Weinberger, Eran Segal
Summary: This study reveals distinct antibody responses against gut microbiota in patients with severe ME/CFS compared to healthy controls. Machine learning algorithms utilizing these differences provide improved molecular diagnostics for ME/CFS, indicating the involvement of the microbiota-immune axis in its pathogenesis.
Review
Oncology
Ofer Elhanani, Raz Ben-Uri, Leeat Keren
Summary: The tumor microenvironment (TME) is composed of various components that contribute to tumor growth, invasion, metastasis, and therapy response. Recent technological advancements in spatial profiling provide a comprehensive view of TME components. This review highlights major spatial profiling technologies, their applications, findings, and challenges in cancer research, as well as the potential of integrating spatial profiling into cancer research for improved diagnosis, prognosis, treatment stratification, and therapeutics development.
Article
Cell Biology
Ayya Keshet, Smadar Shilo, Anastasia Godneva, Yeela Talmor-Barkan, Yaron Aviv, Eran Segal, Hagai Rossman
Summary: Despite the increasing prevalence of diabetes, its diagnosis still relies on blood tests. Continuous glucose monitoring (CGM) devices provide a potential tool to better understand glucose control and variability in individuals with and without diabetes. This study presents CGMap, the characterization of CGM data collected from over 7,000 non-diabetic individuals, aged 40-70 years, between 2019 and 2022. The study provides reference values for key CGM-derived clinical measures and explores the relationship between CGM-derived measures and diabetes-related clinical parameters, revealing novel research directions for understanding the influence of glucose levels on various aspects of human health.
Article
Endocrinology & Metabolism
Ayya Keshet, Lee Reicher, Noam Bar, Eran Segal
Summary: The authors review the current and emerging wearable and digital devices that can provide information about specific metabolic outcomes, and discuss their potential for tailoring preventive and therapeutic strategies against cardiometabolic disease.
Article
Biochemistry & Molecular Biology
Liron Zahavi, Amit Lavon, Lee Reicher, Saar Shoer, Anastasia Godneva, Sigal Leviatan, Michal Rein, Omer Weissbrod, Adina Weinberger, Eran Segal
Summary: This study developed a framework for metagenome-wide association studies (MWAS) to systematically detect bacterial SNPs and associate them with host phenotypes. The researchers discovered 1,358 statistically significant associations between a bacterial SNP and host body mass index (BMI), most of which were independent of diet, medications or physical exercise. Seventeen associations replicated in a geographically independent cohort. The study highlights the importance of considering nucleotide-level diversity in microbiome studies and reveals bacterial SNPs associated with BMI.
Article
Multidisciplinary Sciences
Yael Amitay, Yuval Bussi, Ben Feinstein, Shai Bagon, Idan Milo, Leeat Keren
Summary: CellSighter is a deep-learning based pipeline that accelerates cell classification in multiplexed images. It achieves over 80% accuracy for major cell types and can be trained with only thousands or even hundreds of labeled examples. CellSighter's design reduces overfitting and provides prediction confidence for downstream experts.
NATURE COMMUNICATIONS
(2023)