Article
Engineering, Multidisciplinary
Panagiota D. Natsi, Petros G. Koutsoukos
Summary: This study investigated the growth of calcium carbonate on Acutodesmus obliquus microalgae and found that the presence of microalgae cultivation medium and illumination of supersaturated solutions accelerated the precipitation of CaCO3. The cell concentration of microalgae also affected the growth rate of calcite crystals.
Article
Materials Science, Multidisciplinary
Matteo Hirsch, Lorenzo Lucherini, Ran Zhao, Alexandra Clara Saracho, Esther Amstad
Summary: Nature can control the structure and composition of materials, resulting in organic/inorganic composites with superior mechanical properties. Inspired by this, researchers have developed a process that utilizes compartmentalization to fabricate high-strength porous CaCO3-based composites using nature-derived materials. This system has potential applications in art restoration, coral regeneration, and repair of natural mineral-based materials.
Article
Biotechnology & Applied Microbiology
Lyubov A. Ivanova, Vladimir V. Egorov, Yana A. Zabrodskaya, Aram A. Shaldzhyan, Alexander Ye. Baranchikov, Natalia V. Tsvigun, Anna N. Lykholay, Alexey D. Yapryntsev, Dmitry V. Lebedev, Anna A. Kulminskaya
Summary: In this study, the influence of medium components on CaCO3 precipitation and ECM composition induced by Bacillus cereus cells was analyzed. The accumulation of extracellular polysaccharides and amyloids was independent of calcium and urea, while the accumulation of eDNA and calcium carbonate precipitation required both ingredients. Removal of eDNA disrupted cell network formation and decreased the precipitate yield. The formation of CaCO3 minerals involved exopolysaccharides, negatively charged eDNA lattice, local Ca2+ supersaturation, and pH rise.
NPJ BIOFILMS AND MICROBIOMES
(2023)
Article
Chemistry, Physical
Yi-Ming Ju, Fang Huang, Xin Ding, Li-Bo Mao, Shu-Hong Yu
Summary: This study investigates the mechanism of Mg2+ ion-regulated mineralization of CaCO3 by tracing Mg isotope fractionation. The different mineralization pathways of CaCO3 under different Mg2+ ion concentrations are clarified, and the detailed regulatory role of Mg2+ ions at different stages of mineralization is proposed. These results provide important insights for finely controlling the phase of crystalline products.
Article
Chemistry, Physical
Yi-Ming Ju, Fang Huang, Xin Ding, Li-Bo Mao, Shu-Hong Yu
Summary: This study clarifies the different mineralization pathways of CaCO3 under different Mg2+ ion concentrations by tracing Mg isotope fractionation. The detailed regulatory role of Mg2+ ions at different stages of mineralization is proposed.
Article
Environmental Sciences
Xinwei Xiong, Yanfei Cao, Zhixin Li, Ronglian Huang, Yu Jiao, Liqiang Zhao, Xiaodong Du, Zhe Zheng
Summary: This study identified specific tyrosinases (NLSTyr) involved in nacre formation in pearl oysters, which inhibited calcium carbonate precipitation and affected crystal morphologies. These findings provide new insights into the evolution and function of tyrosinase in mollusks.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Engineering, Environmental
Zhong-Fei Xue, Wen-Chieh Cheng, Lin Wang, Wenle Hu
Summary: This study explored the potential of using MICP technology for lead remediation under the influence of urease activity and calcium source. Monitoring ureolytic bacterial activity and environmental parameters provided insights into urea hydrolysis.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Chemistry, Multidisciplinary
Meng Cai, Haoyue Song, Qihang Wang, Zhaoyong Zou, Zhengyi Fu
Summary: Researchers have successfully synthesized biomimetic fluorapatite nanorods using track-etched membranes and found that additives play an important role in controlling the crystallization process of the crystals. These findings provide valuable inspiration for the rapid synthesis of biomimetic materials with outstanding properties.
MATERIALS CHEMISTRY FRONTIERS
(2022)
Article
Biotechnology & Applied Microbiology
Zhong-Fei Xue, Wen-Chieh Cheng, Lin Wang, Shaojie Wen
Summary: This study investigated the effects of bacterial culture and calcium source addition on the remediation efficiency against lead and copper ions using test tube experiments and simulation software. The results showed that the degree of urea hydrolysis affected the remediation efficiency against lead ions, while higher degrees of urea hydrolysis caused the remediation efficiency against copper ions to reduce to zero. The findings highlight the importance of modifying pH surrounding conditions in capsulizing copper ions using the bioinspired calcium carbonate precipitation.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Chemistry, Inorganic & Nuclear
Huseyin Toktamis, Muhammed Hatib, H. Ibrahim Kilic, Hanifi Canakci
Summary: This study investigated the thermoluminescence (TL) properties of calcite formed by bacterial calcium carbonate precipitation (BCCP) in organic soils. The study found that calcite exhibits a clear TL glow curve with a wide linear dose response region and good reusability.
APPLIED RADIATION AND ISOTOPES
(2022)
Article
Construction & Building Technology
I. Rohini, R. Padmapriya
Summary: Copper ore processing generates a large amount of copper slag, which can be a substitute for fine aggregate in the construction industry. Microbiologically induced calcium carbonate precipitation can improve the performance of copper slag concrete. By replacing varying amounts of fine aggregate with copper slag and adding bacteria during the casting procedure, concrete with superior mechanical properties and a greater density can be produced. The load-deflection patterns of bacterial copper slag concrete were used to investigate beam flexural behaviour.
Article
Biotechnology & Applied Microbiology
Peng Liu, Yu Zhang, Qiang Tang, Shenjie Shi
Summary: The bioremediation using S. pasteurii was effective in reducing heavy metal leaching concentrations in contaminated soils, with a significant reduction in soluble-exchangeable Pb, Zn, and Cd levels. Additionally, the urease hydrolyzing bacteria helped accelerate metal precipitation by increasing pH. The primary goal of metal stabilization was achieved through immobilizing Pb, Zn, and Cd in carbonate precipitates driven by urease, leading to reduced metal toxicity in the treated soil.
BIOCHEMICAL ENGINEERING JOURNAL
(2021)
Article
Multidisciplinary Sciences
Nattapong Yamasamit, Panisa Sangkeaw, Wittaya Jitchaijaroen, Chanachai Thongchom, Suraparb Keawsawasvong, Viroon Kamchoom
Summary: This research investigates the effectiveness of Bacillus subtilis (B. subtilis) in self-healing cracks in concrete and enhancing concrete strength through microbial induced calcium carbonate precipitation (MICP). The study evaluates the ability of the mortar to cover cracks within 28 days, taking into account the width of the crack, and observes the recovery of strength after self-healing. The use of microencapsulated endospores of B. subtilis is also examined for its impact on the strength of concrete. Compressive, splitting tensile, and flexural strengths are compared between normal mortar and biological mortar, and it is found that biological mortar has a higher strength capacity. Microstructure analysis using SEM and EDS shows that bacterial growth increases calcium production, contributing to the improved mechanical properties of the bio-mortar.
SCIENTIFIC REPORTS
(2023)
Article
Construction & Building Technology
Jirapa Intarasoontron, Wiboonluk Pungrasmi, Peem Nuaklong, Pitcha Jongvivatsakul, Suched Likitlersuang
Summary: The study compared the crack healing performances of self-healing concretes using cell/nutrient dropping and immobilization methods. Results showed that the cell dropping method was more effective in closing cracks and recovering ultimate load after repair, while specimens mixed with microencapsulated bacterial spores exhibited lower ultimate loads than control specimens.
CONSTRUCTION AND BUILDING MATERIALS
(2021)
Article
Energy & Fuels
Ping Zhang, Yuan Liu, Nan Zhang, Amy T. Kan, Mason B. Tomson
Summary: This study evaluated the feasibility of using an attach-and-release strategy for controlling mineral scale deposition in aqueous fluid transporting pipelines. The research found that the inhibitor release behavior is significantly impacted by brine chemistry and flow rate. Efforts were also made to calculate the effluent inhibitor concentrations from pipe surfaces and predict inhibition effectiveness, promoting the potential application of this strategy in the field.
Article
Genetics & Heredity
Ang Li, Shouye Liu, Andrew Bakshi, Longda Jiang, Wenhan Chen, Zhili Zheng, Patrick F. Sullivan, Peter M. Visscher, Naomi R. Wray, Jian Yang, Jian Zeng
Summary: Gene-based association tests are widely used in post-GWAS analysis to aggregate multiple SNP-trait associations into sets defined by gene boundaries. However, the common approach of combining SNP associations by summing c2 statistics ignores the directions of SNP effects, leading to a loss of power for SNPs with masking effects. In this study, we introduce a new set-based test called "mBAT-combo" that has better power to detect multi-SNP associations in the context of masking effects. We validate the method through simulations and real data applications, and find evidence for masking effects in a majority of gene-trait pairs.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)
Review
Genetics & Heredity
Abdel Abdellaoui, Loic Yengo, Karin J. H. Verweij, Peter M. Visscher
Summary: The GWAS era has led to significant discoveries in various fields, including population genetics, complex trait genetics, epidemiology, social science, and medicine. The emergence of large-scale biobanks and whole-genome sequencing will further enhance our understanding of human genetic variation and its implications for complex traits and diseases.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Multidisciplinary Sciences
Zhen Qiao, Julia Sidorenko, Joana A. Revez, Angli Xue, Xueling Lu, Katri Parna, Harold Snieder, Peter R. Visscher, Naomi Wray, Loic Yengo
Summary: This study characterizes the genetic regulation of post-prandial glucose levels and identifies the heritability of non-fasting glucose levels over time. The genetic control of glucose is largely constant across fasting durations and accounting for heritability differences improves the discovery of genetic variants associated with glucose. The study also identifies genetic loci controlling the variation of glucose levels in non-fasting individuals, which can be used to predict fasting glucose levels.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
V. Kartik Chundru, Riccardo E. Marioni, James G. D. Prendergast, Tian Lin, Allan J. Beveridge, Nicholas G. Martin, Grant W. Montgomery, David A. Hume, Ian J. Deary, Peter M. Visscher, Naomi R. Wray, Allan F. McRae
Summary: Testing the effect of rare variants on phenotypic variation is challenging due to the need for large cohorts. This study investigates the effect of rare genetic variants on DNA methylation (DNAm) and demonstrates their role in phenotypic variation. The study also shows that extreme levels of DNAm have functional consequences on gene expression.
HUMAN MOLECULAR GENETICS
(2023)
Article
Multidisciplinary Sciences
Carolina Makowski, Hao Wang, Anjali Srinivasan, Anna Qi, Yuqi Qiu, Dennis van der Meer, Oleksandr Frei, Jingjing Zou, Peter M. Visscher, Jian Yang, Chi-Hua Chen
Summary: Human cortical expansion has not occurred uniformly across the brain. By comparing two sets of genome-wide association studies, we assessed the genetic architecture of cortical global expansion and regionalization in 32,488 adults. The genetic factors contributing to total surface area of the cortex expand anterior/frontal regions, while those contributing to thicker cortex increase dorsal/frontal-parietal thickness. The consideration of global measures is important for understanding the genetic variants underlying cortical morphology.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Qile Dai, Geyu Zhou, Hongyu Zhao, Urmo Vosa, Lude Franke, Alexis Battle, Alexander Teumer, Terho Lehtimaki, Olli T. Raitakari, Tonu Esko, Michael P. Epstein, Jingjing Yang
Summary: Most TWAS tools require individual-level eQTL reference data, making them not suitable for summary-level reference eQTL datasets. Hence, the development of TWAS methods that can utilize summary-level reference data is valuable. In this study, a TWAS framework called OTTERS is introduced, which adapts multiple polygenic risk score methods to estimate eQTL weights from summary-level data and performs omnibus TWAS. Both simulations and application studies demonstrate the practicality and power of OTTERS as a TWAS tool.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Yu-Han Hsu, Greta Pintacuda, Ruize Liu, Eugeniu Nacu, Apri Kim, Kalliopi Tsafou, Natalie Petrossian, William Crotty, Jung Min Suh, Jackson Riseman, Jacqueline M. Martin, Julia C. Biagini, Daya Mena, Joshua K. T. Ching, Edyta Malolepsza, Taibo Li, Tarjinder Singh, Tian Ge, Shawn B. Egri, Benjamin Tanenbaum, Caroline R. Stanclift, Annie M. Apffel, Steven A. Carr, Monica Schenone, Jake Jaffe, Nadine Fornelos, Hailiang Huang, Kevin C. Eggan, Kasper Lage
Summary: Genetics have identified many schizophrenia risk genes and found common signals between schizophrenia and neurodevelopmental disorders. However, there is often a lack of functional interpretation of these genes in relevant brain cell types. In this study, the researchers investigated the protein network of six schizophrenia risk genes in induced cortical neurons, finding that it is enriched for common variant risk of schizophrenia and down-regulated in affected individuals. They also identified a sub-network centered on HCN1 that is enriched for common variant risk and contains proteins associated with rare protein-truncating mutations in schizophrenia and bipolar disorder. This study highlights the importance of brain cell-type-specific interactomes in interpreting genetic and transcriptomic data in schizophrenia and related disorders.
Article
Genetics & Heredity
Xiaotong Wang, Alicia Walker, Joana A. Revez, Guiyan Ni, Mark J. Adams, Andrew M. McIntosh, Peter M. Psychiatric Genomics Consortium, Peter M. Visscher, Naomi R. Wray
Summary: In polygenic score (PGS) analysis, the coefficient of determination (R-2) is used to evaluate efficacy. However, in real data analyses, R-2 has been found to exceed the theoretical upper limit of the out-of-sample prediction calculated by SNP-based heritability (h(SNP)(2)). This is likely due to heterogeneities in cohort-specific h(SNP)(2) and genetic correlations between cohorts. We provide simulated and real data evidence to support these observations and emphasize the need for a better approach to address between-cohort heterogeneity.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Genetics & Heredity
Adrian I. Campos, Shinichi Namba, Shu-Chin Lin, Kisung Nam, Julia Sidorenko, Huanwei Wang, Yoichiro Kamatani, Ling-Hua Wang, Seunggeun Lee, Yen-Feng Lin, Yen-Chen Anne Feng, Yukinori Okada, Peter M. Visscher, Loic Yengo
Summary: Simulations and applications to real data show that adjustment of genome-wide association analyses for polygenic scores increases the statistical power for discovery across all ancestries, suggesting an analytical strategy for future studies in underrepresented populations.
Article
Multidisciplinary Sciences
Erik D. Enbody, Ashley T. Sendell-Price, C. Grace Sprehn, Carl-Johan Rubin, Peter M. Visscher, B. Rosemary Grant, Peter R. Grant, Leif Andersson
Summary: This study used whole-genome data of Darwin's finches to identify six loci associated with beak size variation in Geospiza fortis. The major locus is a supergene composed of four genes. Changes in allele frequencies at these loci accompanied a significant change in beak size caused by natural selection during a drought, while introgressive hybridization with another species resulted in gradual changes in beak size in another population.
Article
Cell Biology
Hao Wang, Carolina Makowski, Yanxiao Zhang, Anna Qi, Tobias Kaufmann, Olav B. Smeland, Mark Fiecas, Jian Yang, Peter M. Visscher, Chi-Hua Chen
Summary: The study investigates the impact of chromosomal inversions on human brain morphology by analyzing genotypes of adults with European ancestry. Several common inversions, including 2p22.3, 16p11.2, and 17q21.31, show significant associations with cortical and subcortical morphology. The inverted orientations of these regions have a noticeable effect on brain size and motor cortex. These findings contribute to understanding the role of inversions in shaping human brain phenotypes.
Article
Genetics & Heredity
Xiaotong Wang, Valentin Hivert, Shiane Groot, Ying Wang, Loic Yengo, John J. McGrath, Kathryn E. Kemper, Peter M. Visscher, Naomi R. Wray, Joana A. Revez
Summary: The study investigates the complex relationship between vitamin D levels, skin colour, and ancestral background, and identifies new genetic determinants of vitamin D levels. The findings suggest shared genetic mechanisms underlying the synthesis and metabolism of vitamin D across diverse ancestry groups. Additionally, the study reveals genetic variants that influence both skin colour and vitamin D levels, with variants showing different effects in individuals with different complexions.
Article
Cell Biology
Yang Wu, Ting Qi, Naomi R. Wray, Peter M. Visscher, Jian Zeng, Jian Yang
Summary: This study introduces OPERA, a method that enhances the identification of molecular phenotypes associated with complex traits by analyzing GWAS and multi-omics xQTL summary statistics together. The study finds that 50% of GWAS signals are shared with at least one molecular phenotype, and GWAS signals shared with multiple molecular phenotypes are particularly informative for understanding the genetic regulatory mechanisms of complex traits. Future research with more molecular phenotypes and larger sample sizes is needed to obtain a more saturated map linking molecular intermediates to GWAS signals.
Article
Cell Biology
Yeda Wu, Slavina B. Goleva, Lindsay B. Breidenbach, Minsoo Kim, Stuart Macgregor, Michael J. Gandal, Lea K. Davis, Naomi R. Wray
Summary: The study conducted a genome-wide association analysis to explore the genetic factors related to diverticular disease (DivD) of the intestine. The results indicated significant associations between DivD development and specific cell types and genes. The study also proposed a polygenic score that can effectively predict the risk of DivD and identified potential mechanisms involved in DivD development through statistical and bioinformatic analyses.
Article
Cell Biology
Eduardo A. Maury, Maxwell A. Sherman, Giulio Genovese, Thomas G. Gilgenast, Tushar Kamath, S. J. Burris, Prashanth Rajarajan, Erin Flaherty, Schahram Akbarian, Andrew Chess, Steven A. McCarroll, Po-Ru Loh, Jennifer E. Phillips-Cremins, Kristen J. Brennand, Evan Z. Macosko, James T. R. Walters, Michael O'Donovan, Patrick Sullivan, Jonathan Sebat, Eunjung A. Lee, Christopher A. Walsh
Summary: This study suggests that somatic copy-number variants (sCNVs) may play a potential role in the risk of schizophrenia (SCZ). Early-developmental sCNVs were more common in SCZ cases, including recurrent somatic deletions in the NRXN1 gene. Additionally, recurrent intragenic deletions of the ABCB11 gene were observed in treatment-resistant SCZ cases.
