Article
Geography, Physical
Samuel T. Turvey, Vijay Sathe, Jennifer J. Crees, Advait M. Jukar, Prateek Chakraborty, Adrian M. Lister
Summary: Understanding the dynamics of late Quaternary megafaunal extinctions in India is challenging due to taxonomic uncertainty and lack of reliable chronological data. Further research and exploration are needed to accurately reconstruct regional extinction patterns.
QUATERNARY SCIENCE REVIEWS
(2021)
Article
Anthropology
Allison L. Wolfe, Jack M. Broughton
Summary: The Associational Critique suggests that extinct megafauna are not as rare in North American late Pleistocene archaeological settings as previously believed due to the overkill hypothesis. An analysis focusing on the overlap period between humans and megafauna found no underrepresentation of extinct species in kill/scavenging sites. Contrary to previous assumptions, a positive correlation was actually found between paleontological and archaeological occurrences for all megafauna taxa, supporting the prey model of foraging theory.
JOURNAL OF ARCHAEOLOGICAL SCIENCE
(2021)
Article
Geography, Physical
Bruno David, Lee J. Arnold, Jean-Jacques Delannoy, Joanna Freslov, Chris Urwin, Fiona Petchey, Matthew C. McDowell, Russell Mullett, Jerome Mialanes, Rachel Wood, Joe Crouch, Johan Berthet, Vanessa N. L. Wong, Helen Green, John Hellstrom
Summary: The latest research on Cloggs Cave reveals that the youngest megafaunal specimens date back to 44,500-54,160 years ago, more than previously believed, aligning with the continental pattern of megafaunal extinctions. This suggests that the extinction of these megafauna could not have been caused by climate change leading into the Last Glacial Maximum.
QUATERNARY SCIENCE REVIEWS
(2021)
Article
Multidisciplinary Sciences
Peter M. Yaworsky, Shumon T. Hussain, Felix Riede
Summary: Changing climates in the past affected human and faunal populations, and this study finds that climate-driven animal habitat shifts had a greater impact on the natural abundances of prey species during the Late Upper Paleolithic than human-induced resource depression.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Mathew Stewart, W. Christopher Carleton, Huw S. Groucutt
Summary: Research suggests that the disappearance of North American megafauna may be more closely related to climate change than human overhunting. There is no evidence of a persistent relationship between human and megafauna population levels over time.
NATURE COMMUNICATIONS
(2021)
Article
Environmental Sciences
Liangju Zhao, Xiying Dong, Xiaohong Liu, Ninglian Wang, Christopher J. Eastoe, Na Wei, Cong Xie, Hang Liu, Chuntan Han, Ting Hua, Lixin Wang
Summary: Based on the analysis of 15 years' precipitation stable isotope composition in the Qilian Mountains, it was found that the summer monsoon has a significant impact on precipitation in this region, leading to heavy rainfall in August 2016 and 2018. This study has important implications for understanding past and future water resources in the Qilian Mountains.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Geography, Physical
Lidiane Asevedo, Alceu Ranzi, Risto Kalliola, Martti Parssinen, Kalle Ruokolainen, Mario Alberto Cozzuol, Ednair Rodrigues do Nascimento, Francisco Ricardo Negri, Jonas P. Souza-Filho, Alexander Cherkinsky, Mario Andre Trindade Dantas
Summary: This study utilized radiocarbon dating and stable isotope data to reconstruct the paleoecology of medium to large herbivorous mammals in the late Quaternary of southwestern Amazon, revealing their lifestyle in closed canopy forests to wooded savannas with varied feeding habits. Different feeding strategies helped avoid interspecific competition among the mammals.
QUATERNARY SCIENCE REVIEWS
(2021)
Article
Environmental Sciences
Yawen Chang, Xuequn Chen, Qinghua Guan, Chanjuan Tian, Dan Liu, Dandan Xu
Summary: The study of hydrochemistry and isotopes of the Quaternary aquifer on the southern coast of Laizhou Bay reveals the hydrodynamic and geochemical relationships between freshwater, seawater, and brine at different depths. The distribution of groundwater in the Holocene and Late Pleistocene sediments is controlled by sedimentary structure and saltwater formation background, and the origin of groundwater recharge mainly comes from atmospheric precipitation.
Article
Biology
Mateusz Baca, Danijela Popovic, Alexander K. Agadzhanyan, Katarzyna Baca, Nicholas J. Conard, Helen Fewlass, Thomas Filek, Michal Golubinski, Ivan Horacek, Monika V. Knul, Magdalena Krajcarz, Maria Krokhaleva, Loic Lebreton, Anna Lemanik, Lutz C. Maul, Doris Nagel, Pierre Noiret, Jerome Primault, Leonid Rekovets, Sara E. Rhodes, Aurelien Royer, Natalia V. Serdyuk, Marie Soressi, John R. Stewart, Tatiana Strukova, Sahra Talamo, Jaroslaw Wilczynski, Adam Nadachowski
Summary: By studying the ancient mitochondrial genomes of narrow-headed voles from Europe and Asia, the researchers found that the evolution of narrow-headed voles and collared lemings was influenced by climate fluctuations. They also identified time-structured mtDNA lineages in European narrow-headed voles during the Late Pleistocene, which helped explain the drivers of dynamics in steppe- and cold-adapted species.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Geography, Physical
Alba Rey-Iglesia, Adrian M. Lister, Anthony J. Stuart, Herve Bocherens, Paul Szpak, Eske Willerslev, Eline D. Lorenzen
Summary: The woolly rhinoceros was a cold-adapted herbivore widely distributed during the Late Pleistocene, with ecological flexibility and geographic variation in stable isotope compositions across time. In northeastern Siberia, stable nitrogen isotope values indicate long-term environmental stability, potentially enabling the species' survival. Isotopic similarities between the woolly rhinoceros and other contemporary herbivores suggest niche partitioning, while genetic data show three overlapping haplogroups expanding during the Last Glacial Maximum, reflecting environmental stability's influence on paleoecology.
QUATERNARY SCIENCE REVIEWS
(2021)
Review
Anthropology
Meghan S. McAllister, Mike W. Morley, Jonathan J. Tyler, Francesca A. McInerney, Alison J. Blyth
Summary: This article reviews the applications of stable isotope analysis in studying Late Pleistocene archaeological sites in Southeast Asia. Despite being in the early stages of development in the region and facing challenges related to diagenetic controls in hot and humid environments, stable isotope techniques have shown potential in providing insights into the environmental context of hominin dispersal. Limited research has already demonstrated the usefulness of stable isotope analysis in understanding the role of the environment in the timing and nature of human dispersals in Southeast Asia.
ARCHAEOLOGICAL AND ANTHROPOLOGICAL SCIENCES
(2022)
Article
Geography, Physical
Iuliana Vasiliev, Marcel T. J. van der Meer, Marius Stoica, Wout Krijgsman, Gert-Jan Reichart, Sergei Lazarev, Geanina A. Butiseaca, Eva M. Niedermeyer, Elmira Aliyeva, Christian G. C. van Baak, Andreas Mulch
Summary: Landlocked basins like the Caspian Sea are highly sensitive to hydrological changes, especially when disconnected from the global ocean. Using compound-specific hydrogen isotope data, palaeohydrological and palaeoenvironmental changes in the region were reconstructed, showing a connection with the Arctic domain and the Black Sea during different geological stages.
PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY
(2022)
Article
Geography, Physical
Matthew J. Kohn, Kathleen B. Springer, Jeffrey S. Pigati, Linda M. Reynard, Amanda E. Drewicz, Justin Crevier, Eric Scott
Summary: This study suggests that the relatively wet hydroclimate conditions in the southern Nevada's Las Vegas Valley during the late Pleistocene were likely driven by winter precipitation. The lower proportion of C4 grasses in the diet of herbivores during this time may be attributed to dietary competition among the diverse and abundant Pleistocene fauna.
QUATERNARY SCIENCE REVIEWS
(2022)
Article
Multidisciplinary Sciences
Margaux L. C. Depaermentier, Ben Krause-Kyora, Irka Hajdas, Michael Kempf, Thomas Kuhn, Norbert Spichtig, Peter-Andrew Schwarz, Claudia Gerling
Summary: The multi-isotope and aDNA analyses of the Basel-Waisenhaus burial community in Switzerland suggest that the burial ground was occupied by a local family around AD 400, contradicting previous assumptions of immigrant Alamans. This finding supports the idea of long-lasting occupation at the Roman periphery in the Upper and High Rhine region, rather than a replacement by immigrated populations.
Article
Ecology
Erik Alan Hobbie, Katriina Bendiksen, Nathan R. Thorp, Esteri Ohenoja, Andrew P. Ouimette
Summary: Ectomycorrhizal fungi can be divided into hydrophobic and hydrophilic types, with differences in proteolytic capabilities, nitrogen acquisition depth, and hyphal development. The study found that different taxa have varying responses to plant carbon fluxes and nitrogen dynamics.
Article
Genetics & Heredity
Ning Liu, Timothy Sadlon, Ying Y. Wong, Stephen Pederson, James Breen, Simon C. Barry
Summary: Using 3DFAACTS-SNP, we identified 36 SNPs with plausible Treg-specific mechanisms of action from a list of 1228 previously fine-mapped variants. Integration of cell type-specific chromosome conformation capture data in 3DFAACTS-SNP identified 266 regulatory regions and 47 candidate target genes that interact with these variant-containing regions in Treg cells. The workflow was further applied to three other SNP autoimmune datasets, identifying 16 Treg-centric candidate variants and 60 interacting genes.
EPIGENETICS & CHROMATIN
(2022)
Article
Genetics & Heredity
Melanie D. Smith, Shalem Y. Leemaqz, Tanja Jankovic-Karasoulos, Dale McAninch, Dylan McCullough, James Breen, Claire T. Roberts, Katherine A. Pillman
Summary: This study proposes a method for detecting haemolysis in miRNA high-throughput sequencing data and establishes a haemolysis signature. The results demonstrate that the abundance of miRNA in blood plasma is affected by haemolysis. The feasibility of this signature is further validated through validation experiments.
Article
Biology
Narges Rezaie, Masroor Bayati, Mehrab Hamidi, Maedeh Sadat Tahaei, Sadegh Khorasani, Nigel H. Lovell, James Breen, Hamid R. Rabiee, Hamid Alinejad-Rokny
Summary: In this study, the researchers analyzed the whole-genome sequencing data of 1,855 breast cancer samples and identified 1,030 candidate ncRNAs that were significantly and explicitly mutated in breast cancer samples. They found that these candidate ncRNAs were significantly enriched in various regulatory features and genomic elements associated with breast cancer. Furthermore, they demonstrated that these candidate ncRNAs interacted significantly with the promoter of protein-coding genes, suggesting their critical role in the activation of essential regulators of development and differentiation in breast cancer.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Stephen M. Richards, Leiting Li, James Breen, Nelli Hovhannisyan, Oscar Estrada, Boris Gasparyan, Matthew Gilliham, Alexia Smith, Alan Cooper, Heng Zhang
Summary: The study of well-preserved millet grains from the archaeological cave site Areni-1 in Southern Armenia reveals that DNA from these grains can be preserved for at least 1000 years, serving as a genetic resource for studying the domestication history of this cereal crop.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Jacqueline Rehn, Chelsea Mayoh, Susan L. Heatley, Barbara J. McClure, Laura N. Eadie, Caitlin Schutz, David T. Yeung, Mark J. Cowley, James Breen, Deborah L. White
Summary: RaScALL is a method for rapid detection of clinically relevant genomic alterations in acute lymphoblastic leukemia (ALL). It has high accuracy and short analysis time compared to other methods, making it an important tool for risk stratification and treatment selection in ALL.
Article
Genetics & Heredity
Laura N. Eadie, Jacqueline A. Rehn, James Breen, Michael P. Osborn, Sophie Jessop, Charlotte E. J. Downes, Susan L. Heatley, Barbara J. McClure, David T. Yeung, Tamas Revesz, Benjamin Saxon, Deborah L. White
Summary: Chromosomal rearrangements involving the KMT2A gene are common in acute lymphoblastic leukemia (ALL), particularly in infants less than 1 year old. KMT2A-rearranged ALL (KMT2Ar ALL) has a poor prognosis and often co-occurs with other chromosomal abnormalities, including disruption of the IKZF1 gene. This study reports a case of aggressive infant KMT2Ar ALL with rare IKZF1 gene fusions, and highlights the genomic complexity of this disease with the identification of novel gene fusions IKZF1::TUT1 and KDM2A::IKZF1.
Review
Genetics & Heredity
Leonard Taufik, Joao C. Teixeira, Bastien Llamas, Herawati Sudoyo, Raymond Tobler, Gludhug A. Purnomo
Summary: Genomic sequence data provides novel insights into human ancestry and migratory history. However, many Indigenous populations have been excluded from genomic surveys, hindering a comprehensive understanding of these fundamental questions. This review summarizes key findings from population genetic and phylogeographic studies in Wallacea and Sahul, highlighting their importance in addressing human evolutionary questions.
Article
Biochemistry & Molecular Biology
Doan T. Dinh, James Breen, Barbara Nicol, Natalie J. Foot, David C. Bersten, Alaknanda Emery, Kirsten M. Smith, Ying Y. Wong, Simon C. Barry, Humphrey H. C. Yao, Rebecca L. Robker, Darryl L. Russell
Summary: Progesterone receptor (PGR) plays diverse roles in reproductive tissues and coordinates mammalian fertility. The molecular mechanisms for PGR function in ovulation are poorly understood. Through genomic analysis, we identified a novel PGR transcriptional mechanism specific to ovulation and potential targets for infertility treatments or contraceptives.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Genetics & Heredity
Melanie D. Smith, Shalem Y. Leemaqz, Tanja Jankovic-Karasoulos, Dylan McCullough, Dale McAninch, Anya L. Arthurs, James Breen, Claire T. Roberts, Katherine A. Pillman
Summary: Researchers developed a tool called DraculR, which allows users to upload miRNA expression data and interactively calculate the degree of haemolysis contamination, providing an in silico approach to predict haemolysis when physical specimens are not available.
Article
Endocrinology & Metabolism
Ishant Khurana, Natasha J. Howard, Scott Maxwell, Anelle Du Preez, Harikrishnan Kaipananickal, James Breen, Sam Buckberry, Jun Okabe, Keith Al-Hasani, Soontaree Nakasatien, Thep Himathongkam, Mark E. Cooper, Louise Maple-Brown, Yotsapon Thewjitcharoen, Alex Brown, Assam El-Osta
Summary: This study investigated epigenomic indices of diabetic kidney disease (DKD) susceptibility among high-risk populations. The results demonstrated that reduced methylation and elevated gene expression were associated with increased DKD risk, and these findings were validated in different populations. These findings suggest that epigenomic scores can serve as diagnostic criteria for DKD and outperform traditional clinical modeling.
DIABETES RESEARCH AND CLINICAL PRACTICE
(2023)
Article
Biochemistry & Molecular Biology
Dawn A. Lewis, Rebecca Simpson, Azure Hermes, Alex Brown, Bastien Llamas
Summary: The rise of sedimentary ancient DNA studies has provided new possibilities for studying past environments by using sediments to identify organisms. However, managing this substrate in Indigenous Australian contexts requires special considerations due to the cultural significance of the genetic information obtained. Benefit sharing, particularly the integration of Traditional Knowledges, is crucial in ensuring research outcomes are shared equitably with Indigenous communities and that the research is conducted ethically.
MOLECULAR ECOLOGY RESOURCES
(2023)
Editorial Material
Geology
James S. Crampton, Richard Jongens, Alan Cooper
NEW ZEALAND JOURNAL OF GEOLOGY AND GEOPHYSICS
(2023)
Article
Cell Biology
Neerjah Skantharajah, Shakuntala Baichoo, Tiffany F. Boughtwood, Esmeralda Casas-Silva, Subhashini Chandrasekharan, Sanjay M. Dave, Khalid A. Fakhro, Aida B. Falcon de Vargas, Sylvia S. Gayle, Vivek K. Gupta, Rachele Hendricks-Sturrup, Ashley E. Hobb, Stephanie Li, Bastien Llamas, Catalina Lopez-Correa, Mavis Machirori, Jorge Melendez-Zajgla, Mareike A. Millner, Angela J. H. Page, Laura D. Pagilone, Maili C. Raven-Adams, Lindsa Smith, Ericka M. Thomas, Judi Kumthini, Manuel Corpas
Summary: The lack of diversity hinders equitable leadership and access to precision medicine in the field of genomics for health. To address this issue, the Global Alliance for Genomics and Health has implemented measures to promote diversity and inclusion in its standards and membership.
Article
Immunology
Anya L. Arthurs, Melanie D. Smith, Mhyles D. Hintural, James Breen, Dylan McCullough, Francesca I. Thornton, Shalem Y. Leemaqz, Gustaaf A. Dekker, Tanja Jankovic-Karasoulos, Claire T. Roberts
Summary: Parturition signals the end of immune tolerance in pregnancy. The activation of placental inflammasome differs in terms of mode of delivery and neonatal sex. Assessing placental inflammasome activation may identify babies who have been exposed to aberrant inflammation at birth.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Ophthalmology
Sean Mullany, Henry Marshall, Tiger Zhou, Daniel Thomson, Joshua M. Schmidt, Ayub Qassim, Lachlan S. W. Knight, Georgina Hollitt, Ella C. Berry, Thi Nguyen, Minh-Son To, David Dimasi, Abraham Kuot, Joshua Dubowsky, Rhys Fogarty, Michelle Sun, Luke Chehade, Shilpa Kuruvilla, Devaraj Supramaniam, James Breen, Shiwani Sharma, John Landers, Stewart Lake, Richard A. Mills, Mark M. Hassall, Weng O. Chan, Sonja Klebe, Emmanuelle Souzeau, Owen M. Siggs, Jamie E. Craig
Summary: The study identified significant gene expression differences in patients with PEX, with upregulation of genes associated with viral gene expression pathways and downregulation of cell adhesion protein transcripts. This comprehensive transcriptomic resource sheds light on novel and previously recognized pathogenic pathways in PEX.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2022)
