Article
Multidisciplinary Sciences
Ozkan Aydemir, Benedicta Mensah, Patrick W. Marsh, Benjamin Abuaku, James Leslie Myers-Hansen, Jeffrey A. Bailey, Anita Ghansah
Summary: Antimalarial resistance surveillance in sub-Saharan Africa faces logistical and financial challenges, but a streamlined sample pooling process piloted in Ghana shows promise in providing accurate drug resistance mutation monitoring. This cost-efficient and highly-scalable approach could potentially be applied to other infectious diseases like tuberculosis.
Article
Chemistry, Multidisciplinary
Guodong Hu, Miao Zhong, Jintao Zhao, Hao Gao, Lu Gan, Hong Zhang, Shengxiang Zhang, Jianguo Fang
Summary: Cellular redox homeostasis is primarily regulated by the ratio of thiols and disulfides, with reversible thioldisulfide exchange reactions being crucial. Detecting protein disulfides (PDS) poses challenges due to dynamic exchanges of thiols and disulfides. Researchers have designed a probe that selectively recognizes PDS in live organisms, revealing an increase of PDS in mouse brains of a stroke model.
Article
Plant Sciences
Michael A. Hardigan, Mitchell J. Feldmann, Jason Carling, Anyu Zhu, Andrzej Kilian, Randi A. Famula, Glenn S. Cole, Steven J. Knapp
Summary: Genomic prediction in breeding populations containing hundreds to thousands of parents and seedlings is prohibitively expensive with current high-density genetic marker platforms designed for strawberry. We developed mid-density panels of molecular inversion probes (MIPs) to be deployed with the DArTag marker platform to provide a low-cost, high-throughput genotyping solution for strawberry genomic prediction. The 3K and 5K DArTag panels are able to target and amplify homologous alleles within subgenomic sequences with low-amplification bias between reference and alternate alleles, supporting accurate genotype calling while producing marker genotypes that can be treated as functionally diploid for quantitative genetic analysis.
Article
Multidisciplinary Sciences
Wei Zong, Tanbin Rahman, Li Zhu, Xiangrui Zeng, Yingjin Zhang, Jian Zou, Song Liu, Zhao Ren, Jingyi Jessica Li, Etienne Sibille, Adrian V. Lee, Steffi Oesterreich, Tianzhou Ma, George C. Tseng
Summary: Model organisms serve as substitutes for human studies and play an important role in accelerating research. However, the molecular congruence between model organisms and humans has been debated. This study proposes a framework called Congruence Analysis for Model Organisms (CAMO) to objectively quantify the resemblance of model organisms to humans in terms of molecular response.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biotechnology & Applied Microbiology
Ivan Hernandez-Neuta, Anastasia Magoulopoulou, Flor Pineiro, Jan Gorm Lisby, Mats Gulberg, Mats Nilsson
Summary: In this study, a cost-effective target enrichment method using molecular inversion probes (MIPs) was used to identify microbial infections from blood samples through short-read sequencing. The method showed high specificity, detecting pathogen DNA targets down to 1 in a 1000 within host DNA, and accurately surveyed pathogens and antimicrobial resistance genes in comparison to routine blood culture.
Article
Biochemistry & Molecular Biology
Teruaki Tozaki, Aoi Ohnuma, Masaki Takasu, Kotono Nakamura, Mio Kikuchi, Taichiro Ishige, Hironaga Kakoi, Kei-ichi Hirora, Norihisa Tamura, Kanichi Kusano, Shun-ichi Nagata
Summary: This study aimed to detect genetically engineered animals for gene-doping control using whole-genome resequencing techniques, successfully identifying transgenes as intron deletions. By conducting genome-wide screening, artificially introduced single-nucleotide polymorphisms and insertions/deletions in transgenes were identified.
Article
Cardiac & Cardiovascular Systems
Martin Ezeani, Asif Noor, Karen Alt, Sean Lal, Paul S. Donnelly, Christoph E. Hagemeyer, Be'eri Niego
Summary: This study demonstrated the feasibility and translation potential of molecular imaging with collagen-binding peptides for noninvasive imaging of diffuse cardiac fibrosis in both animal models and human hearts. Two collagen-targeted peptides were evaluated for their ability to detect collagen accumulation in the heart, showing promising results for noninvasive diagnosis and treatment of heart disease.
JOURNAL OF THE AMERICAN HEART ASSOCIATION
(2021)
Review
Chemistry, Multidisciplinary
Muhammad Kazim, Euna Yoo
Summary: In the past two decades, there has been a significant revolution in tumor immunology, with clinical progress in various immunotherapy strategies. These advancements have highlighted the potential of harnessing the immune system to fight against cancer. However, the complex and heterogeneous nature of tumors and immune responses result in varying patient responses, emphasizing the need for reliable biomarkers and therapeutic strategies to maximize the benefits of immunotherapy.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Chemistry, Analytical
Dongxu Zhao, Jian Cao, Lei Zhang, Shaohua Zhang, Song Wu
Summary: This article summarizes the importance of early diagnosis of hepatocellular carcinoma (HCC) and the limitations of current diagnostic methods. It introduces the applications of molecular imaging and MRI in HCC diagnosis, and discusses the prospects of developing molecular imaging probes.
Article
Endocrinology & Metabolism
Sebastian Alexis Vishnopolska, Maria Florencia Mercogliano, Maria Andrea Camilletti, Amanda Helen Mortensen, Debora Braslavsky, Ana Keselman, Ignacio Bergada, Federico Olivieri, Lucas Miranda, Roxana Marino, Pablo Ramirez, Natalia Perez Garrido, Helen Patino Mejia, Marta Ciaccio, Maria Isabel Di Palma, Alicia Belgorosky, Marcelo Adrian Marti, Jacob Otto Kitzman, Sally Ann Camper, Maria Ines Perez-Millan
Summary: This study in Argentina identified mutations in known and candidate genes for congenital hypopituitarism using genetic screening. The findings show that congenital hypopituitarism is a genetically heterogeneous disease with high phenotypic variation and incomplete penetrance, highlighting the importance of further gene discovery in the field. Identification of population-specific pathogenic variants can enhance the predictive value of genetic data for eventual clinical outcomes.
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2021)
Article
Multidisciplinary Sciences
Yu-Jia Wang, Lian Li, Jie Yu, Hong-Yu Hu, Zi-Xu Liu, Wen-Jie Jiang, Wei Xu, Xue-Ping Guo, Feng-Shan Wang, Ju-Zheng Sheng
Summary: Unnatural chemical moieties were incorporated into capsule polysaccharides through bacterial metabolism, resulting in metabolically labeled hyaluronan, heparin, and chondroitin sulfate precursors. Through bioorthogonal chemistry, the azido-labeled polysaccharides were reacted with dyes for detection and imaging. Additionally, the site-specific introduction of fluorophores onto cell surfaces allows for observing and quantifying bacteria both in vivo and in vitro.
Article
Chemistry, Medicinal
Rowan Swann, Samantha Slikboer, Afaf Genady, Luis Rafael Silva, Nancy Janzen, Amber Faraday, John F. Valliant, Saman Sadeghi
Summary: A near-infrared photoacoustic probe was developed for in vivo bone imaging using active and bioorthogonal pretargeting strategies. The probe showed comparable binding to hydroxyapatite in vitro compared to a nontargeted control. In vivo studies demonstrated retention and increased signal in bone when the probe was injected intrafemorally and intravenously using active and pretargeting strategies, respectively. The bone-targeted dye enables photoacoustic imaging, and the synthetic strategy provides a convenient platform for developing new targeted photoacoustic probes.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Yujia Zheng, Qianqian Li, Jing Wu, Ziyi Luo, Wenyi Zhou, Anguo Li, Yanling Chen, Tuerxunayi Rouzi, Tian Tian, Hui Zhou, Xiaodong Zeng, Yang Li, Xiaoding Cheng, Yongchang Wei, Zixin Deng, Fuling Zhou, Xuechuan Hong
Summary: Novel NIR-II small-molecule probe H4-PEG-Glu showed effective imaging and treatment targeting mitochondria in acute myeloid leukemia cells, inducing cell apoptosis and exhibiting moderate cytotoxicity without laser irradiation. Enhanced chemo- and photothermal therapy effects were observed with laser irradiation, presenting high synergistic effects in vivo and specific tumor imaging in AML patient-derived PDX mouse models.
Article
Chemistry, Analytical
Qiang Peng, Tao Xiong, Fangling Ji, Jun Ren, Lingyun Jia
Summary: Environment-sensitive fluorogenic antibodies have been developed for target-specific bioimaging, but their construction is challenging due to the design of fluorogenic probes and antibody labeling. In this study, a simple strategy to generate a fluorogenic nanobody, termed D-body, was reported by incorporating a reduction-responsive Nile blue foldamer. The D-body exhibited high fluorogenic activity upon lysosomal activation, allowing for wash-free cell imaging and fast in vivo imaging with high tumor-to-background ratio. The modular D-body is readily available and easy to handle, making it highly tunable for bioimaging applications.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Dana Al Kelabi, Avishek Dey, Lukman O. Alimi, Hubert Piwonski, Satoshi Habuchi, Niveen M. Khashab
Summary: Fluorescent microscopy is a powerful technique for studying cellular dynamics. The organic fluorophore OC1, with high cell permeability, photostability, and selectivity for mitochondria, has been identified. The keto-enol tautomerization of OC1 allows for consistent fluorescence in dilute solutions through supramolecular self-assembly.
Review
Genetics & Heredity
Jacek Radwan, Wieslaw Babik, Jim Kaufman, Tobias L. Lenz, Jamie Winternitz
TRENDS IN GENETICS
(2020)
Article
Zoology
Marta E. Niedzicka, Bartosz M. Glowacki, Piotr Zielinski, Wieslaw Babik
Review
Ecology
Krystyna Nadachowska-Brzyska, Mateusz Konczal, Wieslaw Babik
Summary: Effective population size (Ne) is a key evolutionary parameter that determines genetic variation levels and selection efficacy. Ne estimation and interpretation are essential in evolutionary and conservation biology, with diverse applications and methods available. Recent advancements in estimating temporal Ne trends provide a comprehensive understanding of the evolutionary continuum.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Bernardo Antunes, Clara Figueiredo-Vazquez, Katarzyna Dudek, Marcin Liana, Maciej Pabijan, Piotr Zielinski, Wieslaw Babik
Summary: This study investigates the connectivity patterns of two closely related newt species using genomic data and tools from landscape genetics. The results show that forest habitat is important for connectivity in both species, but they differ in their use of forested habitat. Anthropogenic landscapes increase resistance in both species, but have a stronger effect on the range-restricted species.
Article
Ecology
Jonathan M. Parrett, Sebastian Chmielewski, Eylem Aydogdu, Aleksandra Lukasiewicz, Stephane Rombauts, Agnieszka Szubert-Kruszynska, Wieslaw Babik, Mateusz Konczal, Jacek Radwan
Summary: Populations of a bulb mite experimentally selected for a male weapon showed reduced diversity across the genome, indicating increased purifying selection due to strong sexual selection. The populations selected for the weapon exhibited lower genome-wide diversity, particularly in terms of non-synonymous positions, suggesting enhanced purifying selection.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Tomasz S. S. Gaczorek, Marzena Marszalek, Katarzyna Dudek, Jan W. W. Arntzen, Ben Wielstra, Wieslaw Babik
Summary: This study provides evidence for the prevalence of MHC gene introgression across multiple Triturus hybrid zones, indicating that MHC introgression between divergent hybridizing species may be widespread and adaptive.
Article
Evolutionary Biology
Ke He, Wieslaw Babik, Mateusz Majda, Piotr Minias
Summary: We used genomic data to reconstruct the macroevolution of the MHC region in amphibians and found that the ancestral MHC region was relatively simple and compact, with a close physical linkage between MHC-I and MHC-II regions. This structure was conserved in anurans, but there was evidence for dynamic evolutionary trajectories in the duplication and expansion of gene copy number in the class I subregion. We also found that intronic regions of amphibian classical MHC genes were longer compared to other tetrapod lineages, possibly due to genome size expansion.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Tomasz Sebastian Gaczorek, Mateusz Chechetkin, Katarzyna Dudek, Guilherme Caeiro-Dias, Pierre-Andre Crochet, Philippe Geniez, Catarina Pinho, Wieslaw Babik
Summary: Major histocompatibility complex (MHC) genes are crucial for the adaptive immune response of jawed vertebrates. This study found widespread MHC introgression in the Podarcis lizards inhabiting the Iberian Peninsula, suggesting its adaptiveness. The study supports the emerging view of adaptive introgression as a key mechanism shaping MHC diversity and raises questions about the effect of elevated MHC variation and factors leading to the asymmetry of adaptive introgression.
Article
Evolutionary Biology
W. Babik, K. Dudek, M. Marszalek, G. Palomar, B. Antunes, S. Sniegula
Summary: The process of urbanization presents significant challenges to organisms, and this study aims to understand the genetic adaptations of damselflies to urban environments. Using genome scanning methods, the researchers identified candidate genetic markers related to urbanization in different geographical regions. Interestingly, genes involved in synapse organization were found to be associated with the adaptive response in the nervous system. This finding highlights the polygenic nature of adaptation to urbanization and mirrors previous studies in different species.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Ecology
Maciej J. Ejsmond, Jacek Radwan, Anna Ejsmond, Tomasz Gaczorek, Wieslaw Babik
Summary: The coevolution between host and pathogen can influence the evolution of host life histories, including age at maturation and body size. The MHC-pathogen coevolution and its impact on host mortality rates can lead to postponed maturation and increased body size.
FUNCTIONAL ECOLOGY
(2023)
Article
Ecology
David Herczeg, Gemma Palomar, Piotr Zielinski, Isolde van Riemsdijk, Wieslaw Babik, Robert Dankovics, Balint Halpern, Milena Cvijanovic, Judit Voros
Summary: This study examined the population genomic structure of smooth newt lineages in the Carpathian Basin and found high genetic diversity, especially in the North Hungarian Mountains and at the interfluves of the main rivers in the South. The study also revealed that the river Tisza acts as a geographical barrier limiting gene flow between different lineages of smooth newts.
ECOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Ismael Reyes-Moya, Gregorio Sanchez-Montes, Wieslaw Babik, Katarzyna Dudek, Inigo Martinez-Solano
Summary: Preserving functional connectivity is crucial for maintaining genetic diversity and the viability of biotic communities. This study investigated the relationships between genetic connectivity and demographic parameters in five pond-breeding amphibians. The results showed that local population sizes had a significant effect on genetic differentiation at small spatial scales. Movement records and cluster-derived kernels provided reliable inferences on likely dispersal paths.