Article
Multidisciplinary Sciences
Prajjval Pratap Singh, Sachin Kumar, Nagarjuna Pasupuleti, P. R. Weerasooriya, George van Driem, Kamani H. Tennekoon, Niraj Rai, Gyaneshwer Chaubey, R. Ranasinghe
Summary: The Sinhalese population in Sri Lanka has been genetically studied, revealing their homogeneity and a trace of North Indian affiliation.
Article
Biology
Karen L. Baab
Summary: Homo erectus, the first hominin species with a truly global distribution resembling recent humans, may have similar population structures to Homo sapiens due to microevolutionary events associated with dispersal and local adaptation. Homo erectus exhibits higher individual and group variation compared to Homo sapiens, likely reflecting different levels of genetic diversity and population history in these spatially disperse species. Additionally, distinct evolutionary histories for frontal and occipital bone shape in Homo erectus suggest a larger role for natural selection in the former, potentially driven by climate-induced facial adaptation.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Biochemical Research Methods
Xuecong Fu, Haoyun Lei, Yifeng Tao, Russell Schwartz
Summary: In this study, a tumor phylogeny method called TUSV-ext was developed, which integrates single-nucleotide variants (SNVs), copy number alterations (CNAs), and structural variations (SVs) into a single inference framework. The accuracy and usability of the method were demonstrated through simulations and application to real tumor data, revealing the evolutionary tree and clonal structure of the tumor.
Article
Astronomy & Astrophysics
Selim C. Hotinli, Matthew C. Johnson
Summary: In this paper, we demonstrate the effectiveness of kSZ tomography technique based on cross-correlation between CMB temperature and 21-cm surveys in improving constraints on models of inhomogeneous reionization and providing information about large-scale modes.
Article
Environmental Sciences
Yu-Sheng Lin, Viktor Morozov, Abdel-Razak Kadry, James L. Caffrey, Wei -Chun Chou
Summary: This study aimed to evaluate daily acrylamide exposure in US adults using blood and urinary biomarkers. The estimated exposure varied among the population, with cigarette smoking being the largest contributor. Other factors such as body mass index and race/ethnicity also played a role in determining estimated exposures.
Article
Multidisciplinary Sciences
Jeffrey A. Hostetler, Julien Martin, Michael Kosempa, Holly H. Edwards, Kari A. Rood, Sheri L. Barton, Michael C. Runge
Summary: The study utilized an integrated population model to reconstruct the population dynamics of Florida manatees over the past 20 years, revealing slow and fluctuating growth. Precise estimates of abundance could be derived from key parameter estimates, potentially reducing the need for frequent costly surveys. Retrospective analyses were shown to be useful for understanding age distribution dynamics, assessing conservation status, and predicting environmental effects on population dynamics.
SCIENTIFIC REPORTS
(2021)
Article
Evolutionary Biology
Mathieu Brevet, Nicolas Lartillot
Summary: The study introduces an integrative framework for reconstructing the phylogenetic history of Ne, allowing for testing the nearly neutral theory and estimating the evolution of genetic variation patterns. The results show that both Ne and u play important roles in modulating patterns of genetic variation, with opposing trends observed in their variations.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Ecology
Stephanie Sherpa, Daniele Salvi, Iolanda Silva-Rocha, Thibaut Capblancq, Josephine R. Paris, Miguel Angel Carretero, Gentile Francesco Ficetola
Summary: This study combines population genomics, demographic models, and paleogeographical reconstructions to investigate the colonization dynamics of wall lizards in Mediterranean archipelagos. The results reveal that many island populations were colonized long before human settlements, either through land bridges or over-sea rafting. However, islands further from the continent were often colonized more recently, coinciding with historical records of human arrival. Additionally, long-established island populations exhibit lower genetic diversity compared to recently colonized islands.
JOURNAL OF BIOGEOGRAPHY
(2023)
Article
Evolutionary Biology
Catherine Beliveau, Patrick Gagne, Sandrine Picq, Oksana Vernygora, Christopher Keeling, Kristine Pinkney, Daniel Doucet, Fayuan Wen, J. Spencer Johnston, Halim Maaroufi, Brian Boyle, Jerome Laroche, Ken Dewar, Nikoleta Juretic, Gwylim Blackburn, Audrey Nisole, Bryan Brunet, Marcelo Brandao, Lisa Lumley, Jun Duan, Guoxing Quan, Christopher J. Lucarotti, Amanda D. Roe, Felix A. H. Sperling, Roger C. Levesque, Michel Cusson
Summary: Insects, such as the spruce budworm, have developed antifreeze proteins (AFPs) to survive harsh winter conditions. A study on the genome of the budworm found that the genes responsible for AFPs were present in other related species as well, suggesting a common origin. The study also identified a zonadhesin-like protein that may have served as a precursor to tortricid AFPs.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Astronomy & Astrophysics
Minsu Park, Marco Raveri, Bhuvnesh Jain
Summary: An effective-field-theory-based reconstruction of quintessence models of dark energy from cosmological data is presented, showing that current data has enough power to test various quintessence model properties without assuming the behavior of the scalar field potential. The standard cosmological model remains favored by data and deviations from its expansion history in quintessence models are bounded to be below 10% at 95% confidence level.
Article
Genetics & Heredity
Eden Avnat, Guy Shapira, Shelly Shoval, Ifat Israel-Elgali, Anna Alkelai, Alan R. Shuldiner, Claudia Gonzaga-Jauregui, Jamal Zidan, Taiseer Maray, Noam Shomron, Eitan Friedman
Summary: Through variant analysis of whole-genome sequencing of 40 Druze individuals (HGDP cohort) and whole exome sequencing of 118 Druze individuals (WES cohort), several pathogenic variants associated with autosomal recessive and autosomal dominant disorders were identified. These newly identified pathogenic variants should be considered for inclusion in prenatal screening options, but further validation in a larger study is required.
Article
Geography, Physical
Aikaterini Glykou, Lembi Lougas, Giedre Piliciauskiene, Ulrich Schmoelcke, Gunilla Eriksson, Kerstin Liden
Summary: The study revealed two phases of harp seal presence in the Baltic Sea, confirming that the first colonization and establishment of a local breeding population occurred during the Holocene Thermal Maximum. Human pressure, salinity fluctuations, and competition for food resources led to physiological stress and ultimately a population decline and local extinction.
QUATERNARY SCIENCE REVIEWS
(2021)
Article
Astronomy & Astrophysics
Bin Cheng, Yang Yu, Erik Asphaug, Patrick Michel, Derek C. Richardson, Masatoshi Hirabayashi, Makoto Yoshikawa, Hexi Baoyin
Summary: The distribution of boulders on the surface of top-shaped asteroids such as Bennu or Ryugu tells us about the processes driving their evolution. A model shows that the spin-up induced by the Yarkovsky-O'Keefe-Radzievskii-Paddack (YORP) effect can explain simultaneously both the latitudinal behavior of the boulders and the regolith migration.
Article
Astronomy & Astrophysics
Yanping Cong, Bin Yue, Yidong Xu, Yuan Shi, Xuelei Chen
Summary: The free-free absorption of low-frequency radio waves by thermal electrons in the warm ionized medium of our Galaxy becomes significant at ultralong wavelength. We propose that the 3D distribution of Galactic electrons can be reconstructed from ultralong-wavelength multifrequency maps, which will be a key science case of upcoming space missions.
ASTROPHYSICAL JOURNAL
(2022)
Editorial Material
Biology
Antonio Benitez-Burraco, Ljiljana Progovac
Summary: This theme issue delves into the study of prehistoric languages, outlining their structural and functional features and exploring the correlation between language features and changes in brain organization during prehistory. It provides a deeper and richer understanding of human prehistory and prehistoric languages.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Anatomy & Morphology
D. P. Aricatt, A. Prabhu, R. Avadhani, K. Subramanyam, A. S. Manzil, J. Ezhilan, R. Das
Summary: This study aimed to investigate the cardiac dominance percentages and its relationship with coronary artery stenosis. The results showed that left dominant and co-dominant hearts had a higher prevalence of coronary artery disease. This has important implications for interventional cardiologists.
FOLIA MORPHOLOGICA
(2023)
Article
Cell Biology
Yi Liu, Zhe Chen, Zong-Heng Wang, Katherine M. Delaney, Juanjie Tang, Mehdi Pirooznia, Duck-Yeon Lee, Ilker Tunc, Yuesheng Li, Hong Xu
Summary: This study reveals that the Drosophila mitochondrial RNA polymerase possesses inherent 3'-5' exoribonuclease activity, enabling it to generate short RNA primers for mitochondrial DNA replication. The exoribonuclease activity is crucial for the accuracy and efficiency of mtDNA replication and transcription.
NATURE CELL BIOLOGY
(2022)
Article
Neurosciences
Peter P. Zandi, Andrew E. Jaffe, Fernando S. Goes, Emily E. Burke, Leonardo Collado-Torres, Louise Huuki-Myers, Arta Seyedian, Yian Lin, Fayaz Seifuddin, Mehdi Pirooznia, Christopher A. Ross, Joel E. Kleinman, Daniel R. Weinberger, Thomas M. Hyde
Summary: This study analyzed transcriptome data from post-mortem brain samples of individuals with bipolar disorder and neurotypical controls, and identified specific genes and pathways associated with BD, as well as decreased gene expression in neuroimmune and synaptic pathways in BD patients.
NATURE NEUROSCIENCE
(2022)
Article
Hematology
Clare Sun, Chen Yun-Ching, Aina Martinez Zurita, Maria Joao Baptista, Stefania Pittaluga, Delong Liu, Daniel Rosebrock, Satyen Harish Gohil, Nakhle S. Saba, Theresa Davies-Hill, Sarah E. M. Herman, Gad Getz, Mehdi Pirooznia, Catherine J. Wu, Adrian Wiestner
Summary: In CLL, oncogenic processes are upregulated in the lymph nodes and in cases with unmutated IGHV region. Single-cell RNA sequencing reveals 3 major cell states in CLL: quiescent, activated, and proliferating. Activated tumor cells are associated with inferior treatment-free survival and the presence of activated CD4+ memory T cells and M2 macrophages in the lymph nodes. Clonal evolution occurs in approximately half of the patients, but is not associated with AICDA expression. However, a T-cell inflamed microenvironment in the lymph nodes is associated with clonal stability.
Article
Hematology
Xunde Wang, Kate Gardner, Mickias B. Tegegn, Clifton L. Dalgard, Camille Alba, Stephan Menzel, Hamel Patel, Mehdi Pirooznia, Yi-Ping Fu, Fayaz T. Seifuddin, Swee Lay Thein
Summary: This study identified 7 PKLR variants associated with hospitalization in 242 adult SCD-HbSS patients and 977 children with SCD-HbSS or SCD-HbSB0 thalassemia. The findings were consistent in both cohorts and significant in meta-analyses.
Article
Cardiac & Cardiovascular Systems
Samuel B. Brusca, Jason M. Elinoff, Yvette Zou, Moon Kyoo Jang, Hyesik Kong, Cumhur Y. Demirkale, Junfeng Sun, Fayaz Seifuddin, Mehdi Pirooznia, Hannah A. Valantine, Carl Tanba, Abhishek Chaturvedi, Grace M. Graninger, Bonnie Harper, Li-Yuan Chen, Justine Cole, Manreet Kanwar, Raymond L. Benza, Ioana R. Preston, Sean Agbor-Enoh, Michael A. Solomon
Summary: This study found that circulating cfDNA levels are elevated in patients with PAH, correlate with disease severity, and can predict patient survival.
Article
Biotechnology & Applied Microbiology
Richard H. Smith, Hanan Bloomer, Danielle Fink, Keyvan Keyvanfar, Md Nasimuzzaman, Fatima Sancheznieto, Roop Dutta, Kacey Guenther Bui, Luigi J. Alvarado, Thomas R. Bauer, Dennis D. Hickstein, David W. Russell, Punam Malik, Johannes C. M. van der Loo, Steven L. Highfill, Douglas B. Kuhns, Mehdi Pirooznia, Andre Larochelle
Summary: This study provides pre-clinical evidence of the therapeutic usefulness of a foamy virus vector (FVV) for correcting genetic defects in LAD-1. Results showed that transduced cells displayed improvements in cellular chemotactic defects associated with LAD-1, and transplantation of vector-transduced cells in mice resulted in long-term engraftment. Vector insertion site analysis revealed no genotoxicity. These findings support the development of FVVs for ex vivo gene therapy of LAD-1.
HUMAN GENE THERAPY
(2022)
Article
Hematology
Jack Chovanec, Ilker Tunc, Jason Hughes, Joseph Halstead, Allyson Mateja, Yihui Liu, Michael P. O'Connell, Jiwon Kim, Young Hwan Park, Qinlu Wang, Quang Le, Mehdi Pirooznia, Neil N. Trivedi, Yun Bai, Yuzhi Yin, Amy P. Hsu, Joshua McElwee, Sheryce Lassiter, Celeste Nelson, Judy Bandoh, Thomas DiMaggio, Julij Selb, Matija Rijavec, Melody C. Carter, Hirsh D. Komarow, Vito Sabato, Joshua Steinberg, Kurt M. Hafer, Elizabeth Feuille, Christopher S. Hourigan, Justin Lack, Paneez Khoury, Irina Maric, Roberta Zanotti, Patrizia Bonadonna, Lawrence B. Schwartz, Joshua D. Milner, Sarah C. Glover, Didier G. Ebo, Peter Korosec, George H. Caughey, Erica H. Brittain, Ben Busby, Dean D. Metcalfe, Jonathan J. Lyons
Summary: Basal serum tryptase (BST) levels >20 ng/mL are a minor criterion for the diagnosis of systemic mastocytosis. Genetic trait H alpha T leads to elevated BST levels due to overexpression of TPSAB1 gene. The study provides personalized clinical reference values and demonstrates the clinical utility of tryptase genotyping.
Article
Hematology
Jianqiong Zhu, Hongzhen Li, Wulin Aerbajinai, Chutima Kumkhaek, Mehdi Pirooznia, Ankit Saxena, Pradeep Dagur, Kyung Chin, Griffin P. Rodgers
Summary: This study investigated the role of KLF1-GATA1 fusion proteins in hemoglobin expression and phenotypic correction of SCD. The results showed that KLF1-GATA1 fusion proteins enhanced the expression of δ-globin and HbA2, reducing hypoxia-related sickling in erythroid cells. Furthermore, transplantation of SCD mouse hematopoietic stem cells expressing KLF1-GATA1 fusion proteins improved anemia severity, reduced sickling of red blood cells, and restored organ function in SCD mice, suggesting the potential of KLF1-GATA1 fusion constructs as a new gene therapy approach for hemoglobinopathies.
Article
Cell Biology
Helen Eachus, Lara Oberski, Jack Paveley, Irina Bacila, John-Paul Ashton, Umberto Esposito, Fayaz Seifuddin, Mehdi Pirooznia, Eran Elhaik, Marysia Placzek, Nils P. Krone, Vincent T. Cunliffe
Summary: This article investigates glucocorticoid resistance commonly observed in depression, which has been linked to reduced expression and/or function of the glucocorticoid receptor (GR). By comparing the brain methylomes and transcriptomes of wild-type and GR-mutant zebrafish, the authors identify 249 differentially methylated regions (DMRs) regulated by GR. They also find GR-regulated genes associated with chaperone-mediated protein folding, circadian rhythm regulation, metabolism regulation, and behavior, which are known to be related to unipolar depression and anxiety. The findings provide insights into the molecular mechanisms through which GR mediates stress responses in the adult zebrafish brain and support the use of the zebrafish GR mutant as a model for studying affective disorders.
DISEASE MODELS & MECHANISMS
(2023)
Article
Biochemical Research Methods
Sara Behnamian, Umberto Esposito, Grace Holland, Ghadeer Alshehab, Ann M. Dobre, Mehdi Pirooznia, Conrad S. Brimacombe, Eran Elhaik
Summary: Radiocarbon dating is commonly used in archaeology to estimate the age of skeletons, but it has limitations in providing reliable dates. Researchers developed a new DNA-based dating method called TPS and applied it to ancient and modern Eurasian samples, resolving conflicting reports and improving the study of phenotypic traits over time.
CELL REPORTS METHODS
(2022)
Meeting Abstract
Critical Care Medicine
B. P. Matthew, A. Lebron, Y. Chen, M. Pirooznia, S. Rollison, T. A. Worthy, A. M. Jones, P. Julien-Williams, M. Y. Chen, J. Moss, H. Wen
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2022)
Meeting Abstract
Cardiac & Cardiovascular Systems
T. E. Andargie, I. Tunc, K. Singh, F. Seifuddin, H. Kong, M. Pirooznia, M. Jang, S. Agbor-Enoh
JOURNAL OF HEART AND LUNG TRANSPLANTATION
(2022)
