Article
Biochemical Research Methods
Hyun-Myung Woo, Byung-Jun Yoon
Summary: MONACO is a novel and versatile network alignment algorithm that achieves highly accurate pairwise and multiple network alignments through iterative optimal matching of 'local' neighborhoods around focal nodes. Extensive performance assessments on real and synthetic networks, where the ground truth is known, show that MONACO consistently outperforms all other state-of-the-art network alignment algorithms in terms of accuracy, coherence, and topological quality of the aligned network regions. Despite the significantly enhanced alignment accuracy, MONACO remains computationally efficient and scales well with increasing size and number of networks.
Article
Biology
Grzegorz Skoraczynski, Anna Gambin, Blazej Miasojedow
Summary: This article introduces an algorithm called Alignstein for LC-MS retention time alignment, which effectively overcomes the limitations of traditional algorithms in dealing with retention time drift. It does not require a reference sample or prior signal identification, and it can detect the information contained in chromatograms.
Article
Genetics & Heredity
Huiling Zhang, Ying Huang, Zhendong Bei, Zhen Ju, Jintao Meng, Min Hao, Jingjing Zhang, Haiping Zhang, Wenhui Xi
Summary: The study introduces a method based on duet feature sets and deep residual network for predicting protein inter-residue distances, showing superior performance in prediction accuracy, reliability, and robustness compared to peer methods.
FRONTIERS IN GENETICS
(2022)
Article
Chemistry, Multidisciplinary
Ashley D. Cardenal, Timothy R. Ramadhar
Summary: Single-crystal X-ray diffraction is a powerful technique for structural determination of organic molecules, but its applicability is limited by the requirement of suitable crystals. The use of preformed matrices that can absorb and stabilize organic compounds offers a way to overcome this limitation. The discussion focuses on the analysis of organic compounds in crystals and the absolute structure determination of chiral molecules using these preformed matrices.
ACS CENTRAL SCIENCE
(2021)
Review
Biochemistry & Molecular Biology
Weng Wan Chan, Fang Yu, Quang Bach Le, Sixun Chen, Marcus Yee, Deepak Choudhury
Summary: Cell-derived matrices (CDM) are decellularised extracellular matrices (ECM) obtained from tissue cultures, mimicking natural tissues for biomedical applications. However, the focus on scale-up production of CDM is limited, despite its significance for clinical trials and regulatory approval. Identifying and addressing gaps in technology early can accelerate product development and enhance progress in scale-up cell culture and ECM extraction processes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Joel Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gomez-Luna, Nika Mansouri Ghiasi, Onur Mutlu
Summary: This paper introduces a fast and memory-efficient genomic sequence aligner called Scrooge, which improves the alignment speed and efficiency through three algorithmic improvements. The experimental results show that Scrooge algorithm achieves better performance on multiple platforms and can be used as an improved version of the GenASM algorithm in the field of bioinformatics.
Article
Biochemistry & Molecular Biology
Ali Asli, Sabreen Higazy-Mreih, Meirav Avital-Shacham, Mickey Kosloff
Summary: The study compared RGS domains across the family and identified key interactions between RGS residues and G alpha switch regions. Modulatory and disruptor residues selectively modulated RGS activity.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Biochemical Research Methods
Xiaocong Yang, Yang Liu, Jianhong Gan, Zhi-Xiong Xiao, Yang Cao
Summary: Protein-ligand docking is crucial in drug design and bioinformatics. FitDock, a new method, has shown significant improvement in docking success rate and speed compared to popular methods, especially when template structures are available.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Giacomo Janson, Alessandro Paiardini
Summary: The PyMod project serves as an integrated interface between PyMOL and popular tools for structural bioinformatics. The latest release, PyMod 3, features a new graphical interface and expanded functionalities for users to perform homology modeling processes and other tasks in the PyMOL environment.
Article
Chemistry, Applied
Chow-Feng Chiang, Po-Lin Liao, Kuo-Chiang Hsu, Jung-Yu Shen, Jau-Tien Lin, Deng-Jye Yang
Summary: The optimal conditions for extracting HAs were established and applied to popular food products in the Taiwan market. Coffee and braised products contained high levels of HAs, resulting in relatively high intake. The dietary intake of HAs in plant-based protein food products should also be of concern.
Article
Chemistry, Applied
Jiahui Chen, Qianni Gao, Xing Zhang, Anthony Pius Bassey, Xianming Zeng, Guanghong Zhou, Xinglian Xu
Summary: This study investigated the changes in protein digestibility in different food matrices and proposed a structural description of proteins responding to nanocrystalline cellulose (NCC) treatment. The conformational alterations of various samples were verified using variable-temperature X-ray diffraction (VT-XRD) and multi-spectroscopic methods. The results showed that NCC induced moderate unfolding and aggregation of distinct protein samples. The findings also highlighted the importance of matrix structures and composition in protein digestibility.
FOOD HYDROCOLLOIDS
(2023)
Article
Biochemistry & Molecular Biology
Anh T. Q. Cong, Taylor L. Witter, Matthew J. Schellenberg
Summary: This article introduces a series of anti-GFP and anti-mCherry nanobody affinity matrices and analyzes their application in purifying GFP/YFP or mCherry fusion proteins, while determining the molecular basis of their binding to target proteins through X-ray crystallography. Ultimately, the utility of the mCherry-tag system in purifying recombinant human topoisomerase 2 alpha protein was experimentally validated.
Review
Biochemical Research Methods
Qiaozhen Meng, Fei Guo, Jijun Tang
Summary: Protein structure problems are a hotspot for understanding protein folding and function mechanisms, and they heavily rely on co-evolutionary information obtained by multiple sequence alignments (MSA). However, for orphan proteins without homologous sequences, the performance of MSA-based methods like AlphaFold2 is unsatisfactory. This paper constructs two datasets and proposes MSA-enhanced and MSA-free methods to effectively solve the issue of insufficient MSAs.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Rajinder Gupta, Yannick Schrooders, Marcha Verheijen, Adrian Roth, Jos Kleinjans, Florian Caiment
Summary: Researchers propose to improve RNA-Seq analyses by grouping transcripts with similar functions and using FuSe to predict functional similarities of proteins. By calculating confidence scores for protein pairs, FuSe identifies overlapping pairs of proteins with high confidence, leading to the discovery of genes related to cell adhesion and glycogen regulation that were overlooked by traditional analysis methods.
Article
Genetics & Heredity
Victor Raggio, Martin Grana, Erik Winiarski, Santiago Mansilla, Camila Simoes, Soledad Rodriguez, Mariana Brandes, Alejandra Tapie, Laura Rodriguez, Lucia Cibils, Martina Alonso, Jennyfer Martinez, Tamara Fernandez-Calero, Fernanda Dominguez, Melania Rosas Mezquida, Laura Castro, Alfredo Cerisola, Hugo Naya, Adriana Cassina, Celia Quijano, Lucia Spangenberg
Summary: The SPATA5 gene is involved in maintaining mitochondrial function and integrity during spermatogenesis, and has also been associated with neuronal development. The use of blood cells for diagnosing and monitoring mitochondrial diseases has been validated, and in this study, a patient with epileptogenic encephalopathy was diagnosed using next generation sequencing. Compound heterozygous variants in the SPATA5 gene were identified as likely causative, and impaired mitochondrial function was observed in the patient's cells compared to a healthy control. These findings suggest a pathogenic effect of the SPATA5 mutations on mitochondrial function, particularly in energy production and biogenesis.
Article
Multidisciplinary Sciences
Matthias Munz, Mohammad Khodaygani, Zouhair Aherrahrou, Hauke Busch, Inken Wohlers
Summary: Mice have been extensively used as animal models to study genotype to phenotype relationships, with inbred mice being particularly useful due to genetic homogeneity. A method for in silico fine-mapping using genotypic data of 37 inbred mouse strains and user-provided phenotypic data is presented in this study. This method efficiently queries public genome-wide genotype data to propose candidate variants and genes for the phenotype under study.
Article
Clinical Neurology
Dmitry Prokopenko, Sarah L. Morgan, Kristina Mullin, Oliver Hofmann, Brad Chapman, Rory Kirchner, Sandeep Amberkar, Inken Wohlers, Christoph Lange, Winston Hide, Lars Bertram, Rudolph E. Tanzi
Summary: Thirteen new candidate loci for AD were identified through rare variant analysis, highlighting synaptic function as a potential novel pathway for the disease.
ALZHEIMERS & DEMENTIA
(2021)
Article
Immunology
Mareike Ohms, Carolina Ferreira, Hauke Busch, Inken Wohlers, Ana Cristina Guerra de Souza, Ricardo Silvestre, Tamas Laskay
Summary: Visceral leishmaniasis (VL) is a fatal parasitic disease with limited treatment options due to drug resistance. Studying the immunometabolic profile of neutrophils during Leishmania infection could provide new targets for host-directed therapies against VL. Glycolysis serves as a major energy source for antimicrobial effector functions against Leishmania.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemical Research Methods
Sven Schrinner, Manish Goel, Michael Wulfert, Philipp Spohr, Korbinian Schneeberger, Gunnar W. Klau
Summary: Genome assembly is a crucial issue in computational genomics, and this paper introduces a new approach to tackle homology-based scaffolding, demonstrating its effectiveness in solving realistic instances resulting from partial Arabidopsis thaliana assemblies.
ALGORITHMS FOR MOLECULAR BIOLOGY
(2021)
Article
Biology
Julia Hesse, Christoph Owenier, Tobias Lautwein, Ria Zalfen, Jonas F. Weber, Zhaoping Ding, Christina Alter, Alexander Lang, Maria Grandoch, Norbert Gerdes, Jens W. Fischer, Gunnar W. Klau, Christoph Dieterich, Karl Koehrer, Juergen Schrader
Summary: In this study, the cellular composition, location, and hierarchy of epicardial stromal cells (EpiSC) were analyzed in comparison to activated myocardial fibroblasts/stromal cells in infarcted mouse hearts. The findings identified 11 transcriptionally distinct EpiSC populations, including cells with cardiomyogenic potential and enriched in hypoxia-inducible factor (HIF) in response to epicardial hypoxic niche. Additionally, the expression of paracrine factors was found to be a general feature of activated cardiac stromal cells.
Article
Genetics & Heredity
Theresa Lueth, Joshua Lab, Susen Schaake, Inken Wohlers, Jelena Pozojevic, Roland Dominic G. Jamora, Raymond L. Rosales, Norbert Brueggemann, Gerard Saranza, Cid Czarina E. Diesta, Kathleen Schlueter, Ronnie Tse, Charles Jourdan Reyes, Max Brand, Hauke Busch, Christine Klein, Ana Westenberger, Joanne Trinh
Summary: This study used Nanopore sequencing to investigate SVA genetic variability and methylation in XDP patients. The results showed that Nanopore sequencing can reliably detect SVA repeat numbers and methylation frequency, and there were only subtle differences in predicted enhancer sites between XDP patients and controls at the SVA locus.
Article
Multidisciplinary Sciences
Sven Schrinner, Rebecca Serra Mari, Richard Finkers, Paul Arens, Bjoern Usadel, Tobias Marschall, Gunnar W. Klau
Summary: This article presents a genetic phasing method for plant breeding that can phase the haplotype sequences of parental samples using a large number of low-depth progeny samples. By integrating weak Mendelian progeny signals with a Bayesian log-likelihood model and utilizing an interval scheduling approach, the method can compute high-quality sparse phasings.
Review
Immunology
Rochi Saurabh, Cesaire J. K. Fouodo, Inke R. R. Konig, Hauke Busch, Inken Wohlers
Summary: This paper reviews current publicly available GWAS and PGS data on autoimmune diseases, summarizes the diseases investigated and the respective studies conducted, and provides an overview of the genetic data and autoimmune disease patients in the UK Biobank. The study finds that only the more prevalent autoimmune diseases are covered by both GWAS and PGS catalogs in the UK Biobank.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Immunology
Heba R. Gouda, Iman M. Talaat, Amal Bouzid, Hoda El-Assi, Amira Nabil, Thenmozhi Venkatachalam, Poorna Manasa Bhamidimarri, Inken Wohlers, Amena Mahdami, Saba El-Gendi, Ahmed ElKoraie, Hauke Busch, Maha Saber-Ayad, Rifat Hamoudi, Nahed Baddour
Summary: The study identified potential mutations in complement regulating genes in patients with glomerulonephritis, suggesting their possible role in disease pathogenesis. A novel variant was found in the Egyptian population for the first time. Further research is needed to understand the impact of these gene variants on protein function, disease progression, and prognosis.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biology
Kenneth N. McGuinness, Gunnar W. Klau, Shaunna M. Morrison, Elisha K. Moore, Jan Seipp, Paul G. Falkowski, Vikas Nanda
Summary: Protein-coordinated iron-sulfur clusters play a crucial role in electron flow in metabolic pathways across different organisms. The incorporation of iron-sulfur clusters into proteins remains unknown. Through analyzing large protein and mineral crystallographic structure data sets, we found limited similarity between ancient iron-sulfur protein clusters and iron-sulfur mineral lattices, suggesting a weaker evolutionary connection between them than previously thought.
ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES
(2022)
Editorial Material
Genetics & Heredity
Inken Wohlers, Shilpa Garg, Jayne Y. Hehir-Kwa
FRONTIERS IN GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Nick D. Bergkamp, Jeffrey R. van Senten, Hendrik J. Brink, Maarten P. Bebelman, Jelle van den Bor, Tugce S. Cobanoglu, Kasper Dinkla, Johannes Koester, Gunnar Klau, Marco Siderius, Martine J. Smit
Summary: The G-protein coupled receptor US28 encoded by human cytomegalovirus (HCMV) is associated with accelerated progression of glioblastomas. In this study, it was found that US28 enhances signaling mediated by sphingosine-1-phosphate (S1P), promoting glioblastoma cell proliferation and survival. The study also uncovers the roles of S1P and CIP2A in US28-mediated exacerbation of glioblastoma.
Article
Microbiology
Mirja Thomsen, Axel Kuenstner, Inken Wohlers, Michael Olbrich, Tim Lenfers, Takafumi Osumi, Yotaro Shimazaki, Koji Nishifuji, Saleh M. Ibrahim, Adrian Watson, Hauke Busch, Misa Hirose
Summary: Dysbiosis of both the skin and the gut was observed in cAD in Shiba Inu dogs. Our findings provide a basis for the potential treatment of cAD by manipulating the gut microbiota as well as the skin microbiota.
Meeting Abstract
Developmental Biology
Veronica Calonga Solis, Helena Fabbri-Scallet, Axel Kuenstner, Inken Wohlers, Fabian Ott, Gil Guerra-Junior, Hauke Busch, Olaf Hiort, Ralf Werner
SEXUAL DEVELOPMENT
(2022)
Article
Psychology, Multidisciplinary
Martin Papenberg, Gunnar W. Klau
Summary: Numerous applications in psychological research require partitioning a pool of elements into multiple parts, with an emphasis on similarity between the parts. Traditional methods include manual assignment, random assignment, and matching, but anticlust is an easy-to-use, free software package that efficiently partitions elements into groups that are as similar as possible.
PSYCHOLOGICAL METHODS
(2021)