Review
Biochemistry & Molecular Biology
Andrew R. Ghazi, Philipp C. Munch, Di Chen, Jordan Jensen, Curtis Huttenhower
Summary: Microbiology has been studying the significant impacts of subtle genetic differences between closely related microbial strains on their phenotypes and the environments and communities around them. However, detecting and studying these strain-level differences remains challenging. This article provides an in-depth discussion of computational tools and statistical models available for strain-resolved shotgun metagenomic profiling of microbial communities, as well as the limitations and challenges in conducting such studies.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jin Wei, Mia Madel Alfajaro, Peter C. DeWeirdt, Ruth E. Hanna, William J. Lu-Culligan, Wesley L. Cai, Madison S. Strine, Shang-Min Zhang, Vincent R. Graziano, Cameron O. Schmitz, Jennifer S. Chen, Madeleine C. Mankowski, Renata B. Filler, Neal G. Ravindra, Victor Gasque, Fernando J. de Miguel, Ajinkya Patil, Huacui Chen, Kasopefoluwa Y. Oguntuyo, Laura Abriola, Yulia Surovtseva, Robert C. Orchard, Benhur Lee, Brett D. Lindenbach, Katerina Politi, David van Dijk, Cigall Kadoch, Matthew D. Simon, Qin Yan, John G. Doench, Craig B. Wilen
Summary: Identification of essential host genes for SARS-CoV-2 infection, including ACE2 and Cathepsin L, and the discovery of pro-viral genes and pathways specific to SARS lineage and pan-coronavirus provide potential therapeutic targets and insights into pathogenesis of COVID-19. Small-molecule antagonists of these gene products inhibited SARS-CoV-2 infection across species, highlighting their conserved role in susceptibility to highly pathogenic CoVs.
Article
Multidisciplinary Sciences
Kendall J. Condon, Jose M. Orozco, Charles H. Adelmann, Jessica B. Spinelli, Pim W. van der Helm, Justin M. Roberts, Tenzin Kunchok, David M. Sabatini
Summary: Our study identified a catalog of genes that impact the mTORC1 pathway and clarified the multifaceted ways in which mTORC1 senses mitochondria dysfunction.AMPK and HRI are two of the key kinases that signal mitochondria distress to mTORC1, and their loss renders mTORC1 signaling largely resistant to mitochondria dysfunction induced by various inhibitors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Mengfan Tang, Guangsheng Pei, Dan Su, Chao Wang, Xu Feng, Mrinal Srivastava, Zhen Chen, Zhongming Zhao, Junjie Chen
Summary: The study identified that CCNC is a critical survival target in cells with BRCA2 loss, potentially contributing to PARPi resistance.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Agriculture, Multidisciplinary
Haotian Deng, Bo Xue, Mingyue Wang, Yuqi Tong, Chang Tan, Meizhi Wan, Yanwen Kong, Xianjun Meng, Jinyan Zhu
Summary: In this study, the antibacterial mechanism of Aronia melanocarpa anthocyanins (AMAs) against Escherichia coli was explored at the protein level using a quantitative proteomics method. The results showed that AMAs can affect various protein pathways in E. coli, leading to morphological changes and cell death. These findings are important for understanding the molecular mechanism of plant-derived antimicrobial agents.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Entomology
Xiangzhao Yue, Yongkang Liang, Zhishuang Wei, Jun Lv, Yongjin Cai, Xiaobin Fan, Wenqing Zhang, Jie Chen
Summary: This study identified potential kkv transcriptional regulators through comprehensive RNA interference analyses and validated their roles in vivo using transgenic Drosophila lines. Fer3 was shown to be crucial for activating kkv transcription and regulating genes involved in chitin synthesis. The study also revealed a potential complex mechanism of kkv transcription regulation involving an interaction network with bithorax complex components.
Article
Microbiology
Nicole Pearcy, Yue Hu, Michelle Baker, Alexandre Maciel-Guerra, Ning Xue, Wei Wang, Jasmeet Kaler, Zixin Peng, Fengqin Li, Tania Dottorini
Summary: The study focuses on the identification of genetic determinants associated with antimicrobial resistance in E. coli using a computational approach that integrates machine learning with metabolic modeling. The findings reveal key genetic determinants linked to growth and metabolic adaptations, providing insights into the complex interplay between antibiotic resistance and metabolic rewiring in bacteria. This computational solution has the potential to be applied to other human and animal pathogens for further studies on antimicrobial resistance.
Article
Multidisciplinary Sciences
Pavlos Stephanos Bekiaris, Steffen Klamt
Summary: The study presents a computational framework to analyze the impact of redox cofactor swaps on the thermodynamic potential of a metabolic network. It suggests that the specificity of NAD(P)H reactions is influenced by the metabolic network structure, enabling thermodynamic driving forces close to the theoretical optimum.
NATURE COMMUNICATIONS
(2023)
Article
Infectious Diseases
Juan Li, Yuqin Song, Jianping Deng, Zhaoran Wang, Nai-Kei Wong, Chao Wang, Gang Zhang, Yang Wang, Shan Lu, Jie Che, Xiaofei Zhao, Zhengdong Zhang, Hong Wang, Ling Zhang, Yunfei Zhang, Xuemei Bai, Min Yuan, Xia Chen, Wen Zhang, Yanwen Xiong, Biao Kan, Jie Feng
Summary: This study explores the dynamics of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) transmission between food-producing animals and humans. The findings suggest that transmission primarily occurs through the high exposure group, which plays a crucial role as a medium, and the carriage rates of shared ARGs are higher in this group compared to the low exposure group.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2023)
Article
Multidisciplinary Sciences
Xu Feng, Mengfan Tang, Merve Dede, Dan Su, Guangsheng Pei, Dadi Jiang, Chao Wang, Zhen Chen, Mi Li, Litong Nie, Yun Xiong, Siting Li, Jeong-Min Park, Huimin Zhang, Min Huang, Klaudia Szymonowicz, Zhongming Zhao, Traver Hart, Junjie Chen
Summary: Exploiting cancer vulnerabilities is crucial for finding anticancer drugs. This study used CRISPR screens to uncover genetic interactions between tumor suppressor genes and protein-coding genes, leading to the discovery of high-confidence synthetic lethal interactions and essential paralog gene pairs. It also suggests that targeting certain tumor suppressors could suppress the proliferation of cells lacking other tumor suppressors, providing valuable information for targeted cancer therapy.
Article
Biology
Qingqing Fang, Yu Feng, Alan McNally, Zhiyong Zong
Summary: Fang et al. identified two previously unidentified phages that can inhibit the growth and decrease the virulence of carbapenem-resistant Klebsiella pneumoniae (CRKP). They also found that CRKP can develop phage resistance but can still be eliminated in a mouse intestinal colonization model, highlighting the potential of phage therapy as a treatment against drug-resistant pathogens.
COMMUNICATIONS BIOLOGY
(2022)
Review
Virology
Aditi Kanojia, Mansi Sharma, Rishad Shiraz, Shashank Tripathi
Summary: Genome-wide CRISPR screens are an effective tool for identifying and characterizing viral host dependency factors systematically, contributing to our understanding of Flavivirus-Host interactions.
Article
Agriculture, Dairy & Animal Science
Peng Zuo, Chaoxin Zhang, Yupeng Gao, Lijunyi Zhao, Jiaxu Guo, Yonglin Yang, Qian Yu, Yunna Li, Zhipeng Wang, Hua Yang
Summary: Epistatic effects, an important part of the genetic effect in livestock, were studied in synthetic ewes from China. Genome-wide single nucleotide polymorphisms (SNPs) were used to identify SNP-SNP interactions associated with birth weight and weaning weight. Significant interactions were found for weaning weight, but not for one-yearling weight. The interactions of sheep body weight were dynamic and time-dependent. Transcription factors were found to play a role in explaining epistatic effects, and the target genes of transcription factors were also identified. The study provides insights into the genetic mechanism of weight development.
ANIMAL BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Delia Tomoiaga, Jaclyn Bubnell, Liam Herndon, Paul Feinstein
Summary: Griffith proposed the concept of DNA transfer between bacteria in 1928. Researchers have demonstrated that E. coli can accept multiple plasmids simultaneously, resulting in widespread aclonality during colony development. Tracking clonally related bacteria allows for mosaic analysis of gene function. Additionally, it was discovered that clonally related bacterium rods self-organize fractally and can remain linked during colony growth, presenting a potential target for controlling microbiota growth.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Chien- Yang, Zikun Zhu, Jeffrey J. Jones, Brett Lomenick, Tsui-Fen Chou, Shu-Ou Shan
Summary: This study investigated the impact of PDF inhibition on bacterial physiology through the analyses of transcriptome and proteome in Escherichia coli. The results showed that loss of PDF activity rapidly induces cellular stress responses, especially those associated with protein misfolding and membrane defects, and leads to a global down-regulation of metabolic pathways. Furthermore, the study revealed that PDF inhibition causes rapid membrane hyperpolarization and impaired membrane integrity, indicating that formyl group retention on nascent proteins is the most immediate and primary consequence of plasma membrane disruption.
Article
Biochemistry & Molecular Biology
Thiago Seraphim, Nardin Nano, Yiu Wing Sunny Cheung, Siripat Aluksanasuwan, Carolina Colleti, Yu-Qian Mao, Vaibhav Bhandari, Gavin Young, Larissa Holl, Sadhna Phanse, Yuliya Gordiyenko, Daniel R. Southworth, Carol Robinson, Visith Thongboonkerd, Lisandra M. Gava, Julio C. Borges, Mohan Babu, Leandro R. S. Barbosa, Carlos H. Ramos, Philipp Kukura, Walid A. Houry
Summary: The R2TP complex, formed by RUVBL1 and RUVBL2 ATPases, associates with PIH1D1 and RPAP3 proteins and plays a role in promoting the formation of macromolecular complexes. RPAP3 is identified as the central subunit of R2TP, linking PIH1D1 and RUVBL1/2. The study provides insights into the structure and function of the R2TP complex.
Article
Hematology
Stephen Booth, Helen M. Curley, Csilla Varnai, Roland Arnold, Lennard Y. W. Lee, Naomi A. Campton, Gordon Cook, Karin Purshouse, James Aries, Andrew Innes, Lucy B. Cook, Oliver Tomkins, Helen S. Oram, Michael Tilby, Austin Kulasekararaj, David Wrench, Saoirse Dolly, Tom Newsom-Davies, Ruth Pettengell, Abigail Gault, Sam Moody, Sajjan Mittal, Mohammed Altohami, Tania Tillet, Jack Illingworth, Leena Mukherjee, Jane Apperly, John Ashcroft, Neil Rabin, Jonathan Carmichael, Jean-Baptiste Cazier, Rachel Kerr, Gary Middleton, Graham P. Collins, Claire Palles
Summary: Patients with active haematological cancer infected with SARS-CoV-2 have a higher risk of mortality, especially patients with acute leukemia and myeloma. Factors such as poor disease control and receiving second or beyond line of treatment are associated with increased mortality risk.
BRITISH JOURNAL OF HAEMATOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sang Hyun Lim, Jamie Snider, Liron Birimberg-Schwartz, Wan Ip, Joana C. Serralha, Hugo M. Botelho, Miqueias Lopes-Pacheco, Madalena C. Pinto, Mohamed Taha Moutaoufik, Mara Zilocchi, Onofrio Laselva, Mohsen Esmaeili, Max Kotlyar, Anna Lyakisheva, Priscilla Tang, Lucia Lopez Vazquez, Indira Akula, Farzaneh Aboualizadeh, Victoria Wong, Ingrid Grozavu, Teuta Opacak-Bernardi, Zhong Yao, Meg Mendoza, Mohan Babu, Igor Jurisica, Tanja Gonska, Christine E. Bear, Margarida D. Amaral, Igor Stagljar
Summary: Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) is a chloride and bicarbonate channel that plays a critical role in maintaining fluid homeostasis. Mutations in CFTR are associated with Cystic Fibrosis (CF), the most common lethal autosomal recessive disorder in Caucasians. This study used a high-throughput screening technique to map the protein-protein interactions of CFTR and identify potential drug targets for CF treatment. They discovered candidate proteins, such as FGL2, that may have significant effects on CFTR function in CF pathophysiology.
MOLECULAR SYSTEMS BIOLOGY
(2022)
Article
Virology
Subha Dahal, Ran Cheng, Peter K. Cheung, Terek Been, Ramy Malty, Melissa Geng, Sarah Manianis, Lulzim Shkreta, Shahrazad Jahanshahi, Johanne Toutant, Rose Chan, Sean Park, Mark A. Brockman, Mohan Babu, Samira Mubareka, Karen Mossman, Arinjay Banerjee, Scott Gray-Owen, Martha Brown, Walid A. Houry, Benoit Chabot, David Grierson, Alan Cochrane
Summary: In this study, the medicinal chemistry optimization of a known HIV-1 inhibitor led to the discovery of a new derivative, GPS491, which showed potent anti-HIV-1 activity with reduced toxicity. The study demonstrated that GPS491 not only blocked HIV-1 replication, but also inhibited the replication of adenovirus and multiple coronaviruses. Furthermore, GPS491 induced changes in viral RNA processing and altered the accumulation/phosphorylation/function of splicing regulatory SR proteins. This study highlights the potential of targeting cellular factors involved in RNA processing for the development of broad-spectrum antiviral agents.
Article
Neurosciences
Elisabet Jakova, Mohamed Taha Moutaoufik, Jeremy S. Lee, Mohan Babu, Francisco S. Cayabyab
Summary: This study found that adenosine and A1R receptor ligands interact with alpha-syn to modulate its aggregation and neurodegeneration. A1R agonists and drugs promoting a knot conformation of alpha-syn can cause alpha-synucleinopathy and increase neuronal degeneration, whereas A1R antagonists and drugs promoting a loop conformation of alpha-syn can be harnessed for possible neuroprotective therapies.
TRANSLATIONAL NEURODEGENERATION
(2022)
Article
Biochemistry & Molecular Biology
Karla N. Valenzuela-Valderas, Gabriel Moreno-Hagelsieb, John R. Rohde, Rafael A. Garduno
Summary: Research has shown that the bacterial pathogen Legionella pneumophila's chaperonin protein HtpB has a unique function in interaction with the eukaryotic protein ECM29, which can be mapped to specific amino acid positions.
Article
Genetics & Heredity
Anshita Goel, Douglas G. Ward, Boris Noyvert, Minghao Yu, Naheema S. Gordon, Ben Abbotts, John K. Colbourne, Stephen Kissane, Nicholas D. James, Maurice P. Zeegers, Kar Keung Cheng, Jean-Baptiste Cazier, Celina M. Whalley, Andrew D. Beggs, Claire Palles, Roland Arnold, Richard T. Bryan
Summary: Through whole-exome and transcriptome sequencing, it was found that NMIBC can be classified into different expression subtypes, with amplifications of ARNT and ERBB2 being significant indicators of worse PFS across all NMIBCs, and high APOBEC mutagenesis and high tumor mutation burden potentially indicating better PFS in G3pT1 NMIBCs; in G3pT1 NMIBCs, downregulated interferon-alpha and gamma response pathways were significantly associated with worse PFS.
Article
Genetics & Heredity
Victor H. Tierrafria, Claire Rioualen, Heladia Salgado, Paloma Lara, Socorro Gama-Castro, Patrick Lally, Laura Gomez-Romero, Pablo Pena-Loredo, Andres G. Lopez-Almazo, Gabriel Alarcon-Carranza, Felipe Betancourt-Figueroa, Shirley Alquicira-Hernandez, J. Enrique Polanco-Morelos, Jair Garcia-Sotelo, Estefani Gaytan-Nunez, Carlos-Francisco Mendez-Cruz, Luis J. Muniz, Cesar Bonavides-Martinez, Gabriel Moreno-Hagelsieb, James E. Galagan, Joseph T. Wade, Julio Collado-Vides
Summary: This paper presents a radical upgrade of RegulonDB, offering more than 2000 high-throughput datasets on transcriptional regulation. The datasets have been processed for comparison and include information on transcription termination sites, transcription units, transcription factor binding interactions, and expression profiles. The browsing and visualization tools have also been expanded, allowing comparisons against previous knowledge, genome viewing, and metadata querying.
MICROBIAL GENOMICS
(2022)
Article
Multidisciplinary Sciences
Alla Gagarinova, Ali Hosseinnia, Matineh Rahmatbakhsh, Zoe Istace, Sadhna Phanse, Mohamed Taha Moutaoufik, Mara Zilocchi, Qingzhou Zhang, Hiroyuki Aoki, Matthew Jessulat, Sunyoung Kim, Khaled A. Aly, Mohan Babu
Summary: By studying genetic interactions among all transcription factor genes in E. coli, this research reveals condition-dependent interactions and uncovers the roles of uncharacterized transcription factors.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Juan M. Escorcia-Rodriguez, Mario Esposito, Julio A. Freyre-Gonzalez, Gabriel Moreno-Hagelsieb
Summary: Orthologs and paralogs exhibit differences in functional stability and divergence based on gene mutation rates and protein similarity. Choosing orthologs as functionally coherent genes remains the right approach in comparative genomics.
Review
Biochemistry & Molecular Biology
Khaled A. Aly, Mohamed Taha Moutaoufik, Mara Zilocchi, Sadhna Phanse, Mohan Babu
Summary: Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is a rare early-onset neurodegenerative disease caused by mutations in the SACS gene. Understanding the function of Sacsin and using ARSACS disease models can improve our knowledge of this disease. Gene correction strategies and delivery methods provide hope for the development of therapeutics for ARSACS.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Xin Wei, Gabriel Moreno-Hagelsieb, Bernard R. Glick, Andrew C. Doxey
Summary: Cytokinin, the plant hormone used in agriculture, is synthesized by the enzyme Isopentenyl transferase (IPT). Comparisons of IPT genes between plant pathogens and plant growth-promoting bacteria (PGPB) show differences in gene structure, regulation, and activity levels, which may determine their effects on host plants.
Article
Multidisciplinary Sciences
Julie E. Hernandez-Salmeron, Tanya Irani, Gabriel Moreno-Hagelsieb
Summary: Average Nucleotide Identity (ANI) is a standard measure for bacterial species delimitation, but its calculation time is often longer than similarity estimates based on short nucleotide sampling. In this study, two sketching programs, mash and dashing, were compared to ANI in delimiting species among Esterobacterales genomes. The results showed that fast estimates of genome similarity were as accurate as ANI for species delimitation, indicating their potential use in efficient bacterial identification and clustering.
Article
Biochemical Research Methods
Mara Zilocchi, Matineh Rahmatbakhsh, Mohamed Taha Moutaoufik, Kirsten Broderick, Alla Gagarinova, Matthew Jessulat, Sadhna Phanse, Hiroyuki Aoki, Khaled A. Aly, Mohan Babu
Summary: Mitochondrial protein assemblies are crucial for neuronal and brain function. This study presents a co-fractionation-mass spectrometry platform to study native mitochondrial assemblies in brain and cultured nerve cells. The results show that co-fractionation-mass spectrometry can identify complexes and predict protein-protein interactions.
Article
Chemistry, Analytical
Premkumari Kumarathasan, Nazila Nazemof, Dalibor Breznan, Erica Blais, Hiroyuki Aoki, James Gomes, Renaud Vincent, Sadhna Phanse, Mohan Babu
Summary: This study evaluated the internalization and mitochondrial effects of silica nanoparticles (SiNPs) with different sizes and surface modifications. The findings suggest that physicochemical properties are determinants of SiNP exposure-related mitochondrial effects. Mitochondrial exposures combined with proteomic analysis can serve as a new approach in risk assessment, providing insights into related toxicity mechanisms.