Article
Biology
Agneesh Barua, Ivan Koludarov, Alexander S. Mikheyev
Summary: Evolution can be predictably driven by ecological challenges, with oral venom serving as a tractable model of trait evolution. Studying the origins of kallikrein-like serine proteases in vertebrate venoms suggests that these toxins may have evolved from genes already present in saliva, blurring the line between venomous and non-venomous animals.
Article
Multidisciplinary Sciences
Nicoletta Commins, Mark R. Sullivan, Kerry McGowen, Evan M. Koch, Eric J. Rubin, Maha Farhat
Summary: The molecular clock rate of Mycobacterium abscessus (Mab) slows down coincident with the emergence of phylogenetic clusters, challenging the model of person-to-person transmission and providing insights into transmission inference in emerging pathogens.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Nhan Ly-Trong, Suha Naser-Khdour, Robert Lanfear, Bui Quang Minh
Summary: Sequence simulators are important in phylogenetics for evaluating methods, hypothesis testing, and generating data. AliSim is a new tool that efficiently simulates biologically realistic alignments, outperforming popular software in terms of speed and efficiency.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Cara Van Der Wal, Shane T. Ahyong, Maxim W. D. Adams, Kyle M. Ewart, Simon Y. W. Ho, Nathan Lo
Summary: Australia is a center of diversity for freshwater crayfish, particularly in the genus Euastacus. The genetic diversity and population structure of Euastacus spinifer were investigated, revealing a species complex with a close relative E. vesper. The results also suggest isolated and fragmented populations of a previously widespread ancestral species, raising the number of species within the E. spinifer complex to at least three. This study highlights the threats faced by freshwater crayfish due to their restricted and fragmented distributions, contributing to their endangered status globally.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Review
Biochemistry & Molecular Biology
Federico Scossa, Alisdair R. Fernie
Summary: Ancestral proteins were more promiscuous than modern ones, with specificity often evolving after gene duplication; some modern proteins are found to have evolved de novo from ancestors lacking those functions; new interactions evolved from just a few mutations, suggesting acquisition of new functions is not difficult but often lost to subsequent mutations.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Parasitology
Gabriel Jimenez-Avalos, Alina Soto-Obando, Maria Solis, Robert H. Gilman, Vitaliano Cama, Armando E. Gonzalez, Hector H. Garcia, Patricia Sheen, David Requena, Mirko Zimic, Cysticercosis Working Grp Peru
Summary: This study identified a novel set of 31 non-synonymous mutations that differentiate the main T. solium genotypes, distributed across the genomes of the African-American genotype. Furthermore, the analysis suggested a stratification of the African-American genotypes into an East African and a West African sublineage.
PARASITES & VECTORS
(2023)
Article
Biochemistry & Molecular Biology
Han Yan, Zhirui Hu, Gregg W. C. Thomas, Scott Edwards, Timothy B. Sackton, Jun S. Liu
Summary: The paper introduces PhyloAcc-GT, a method that extends PhyloAcc by modeling gene tree heterogeneity, to effectively identify lineage-specific accelerations in substitution rate while accounting for incomplete lineage sorting. The method outperforms other methods in detecting complex patterns of rate shifts and is robust to population size parameter specification.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Jose Cerca, Angel G. Rivera-Colon, Mafalda S. Ferreira, Mark Ravinet, Michael D. Nowak, Julian M. Catchen, Torsten H. Struck
Summary: Research on three morphologically similar Stygocapitella species suggests that shared genetic variance from incomplete lineage sorting and ancient admixture may explain their morphological similarity.
Article
Genetics & Heredity
Maria Satti, Monica Modesto, Akihito Endo, Takeshi Kawashima, Paola Mattarelli, Masanori Arita
Summary: The distribution of GH genes in bifidobacterial species is more closely related to the hosts' dietary pattern than to the phylogeny of the host animals or genomic features. Therefore, the hosts' dietary behavior plays a crucial role in determining the distribution and evolution of GH genes.
Article
Oncology
Joao M. Alves, Sonia Prado-Lopez, Laura Tomas, Monica Valecha, Nuria Estevez-Gomez, Pilar Alvarino, Dominik Geisel, Dominik Paul Modest, Igor M. Sauer, Johann Pratschke, Nathanael Raschzok, Christine Sers, Soulafa Mamlouk, David Posada
Summary: This study analyzed the evolutionary history of recurrent hepatic lesions in a patient with metastatic colorectal cancer (mCRC) using single-cell whole-genome sequencing data, revealing the impact of treatment on the genetic and evolutionary determinants.
Article
Plant Sciences
Nianwu Tang, Annie Lebreton, Wenjun Xu, Yucheng Dai, Fuqiang Yu, Francis M. Martin
Summary: The study characterized the symbiotic transcriptomes of several milkcap species in association with different pine hosts, revealing the genetic basis of ectomycorrhizal development and the highly specific symbiotic gene repertoire of each Lactarius species. Up- or down-regulated genes are involved in signaling pathways, nutrient transport, cell wall modifications, and plant defenses during the symbiosis between Lactarius species and pine hosts.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Cristina Arias-Sarda, Sarah Quigley, Marta Farre
Summary: This study reconstructed ancestral karyotypes and identified chromosome rearrangements in ruminants using 26 genome assemblies. The results show that ruminant karyotype evolution is characterized by inversions, while interchromosomal rearrangements occurred preferentially in the oldest ancestor. Additionally, evolutionary breakpoints regions (EBRs) were found to be depleted of protein coding genes and not enriched in high GC regions.
Article
Biochemistry & Molecular Biology
Leeban H. Yusuf, Yolitzi Saldivar Lemus, Peter Thorpe, Constantino Macias Garcia, Michael G. Ritchie
Summary: The transition from oviparity to viviparity has occurred independently multiple times across vertebrates, presenting a case of phenotypic convergence. Although there is striking similarity among the genes and molecular pathways involved in the evolution of viviparity across different vertebrate groups, the extent of molecular convergence in genomic divergence remains unclear. Our study on a group of ray-finned freshwater fish suggests that independent transitions to viviparity are not strongly associated with an excess of molecular convergence, but a few genes show evidence of convergent evolution.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Sudhir Kumar
Summary: Molecular evolutionary analysis requires computationally intensive steps that have a significant environmental impact. However, innovative methods and heuristics can reduce the carbon footprint, lower environmental costs, and promote green evolutionary computing.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Yuqi Huang, Minghao Sun, Lenan Zhuang, Jin He
Summary: This study provides a comprehensive molecular phylogenetic analysis of vertebrate AIGs, revealing loss or gain of AIG members in different species during evolution. The findings can be used for future functional characterization of AIGs.
Article
Chemistry, Physical
M. Amin Mir, Mohammad Waqar Ashraf, Altaf Hussain, Bilal Ahmad Mir
Summary: In this study, three amylase-producing bacterial strains were isolated and identified from soil samples. Bacillus sp showed the highest amylase activity, followed by Shigella sp, and Proteus sp showed the lowest activity. Water extracts exhibited stronger inhibitory effects on bacterial growth compared to ethanol extracts. Among the bacterial strains, Shigella sp was the most affected by the plant extracts, followed by Proteus sp, while Bacillus sp showed the least inhibition.
CURRENT ORGANOCATALYSIS
(2022)
Article
Biophysics
Mohammed Tauseef Ali, Mohammad Saleem Mir, Sheikh Mehraj, Immad Ahmad Shah
Summary: Apple phenology is greatly affected by temperature, with higher temperatures in 2018 leading to earlier phenological stages and increased risk of spring frost, causing significant impact on growers and harvest.
INTERNATIONAL JOURNAL OF BIOMETEOROLOGY
(2022)
Editorial Material
Chemistry, Physical
Muhammad Waqar Ashraf, M. Amin Mir
Summary: Supported ionic liquid (SIL) membranes have great potential in separation science and catalysis. Membrane technology allows for the separation of complex mixtures and simultaneous chemical transformations. This editorial highlights the significant contribution of liquid membranes in catalysis and compares recent applications with conventional methods. SILs and their applications in catalysis, catalytic membranes, and membrane separation processes are also briefly described.
CURRENT ORGANOCATALYSIS
(2022)
Article
Chemistry, Physical
Mohd Amin Mir, Muhammad Waqar Ashraf
Summary: The study synthesized and analyzed azo-metal complexes of embelin and compared their antioxidant and antimicrobial properties. The results showed that complexation between metals and compounds significantly decreased the antioxidant potential, but had varying effects on antimicrobial activity depending on the type of metal.
CURRENT ORGANOCATALYSIS
(2022)
Article
Chemistry, Multidisciplinary
M. Waqar Ashraf, Michael P. Collins, M. Amin Mir, Abdus Salam, Anwar Ul-Hamid
Summary: This study explores the use of supported liquid membrane technology for the removal and recovery of crystal violet dye from wastewater, identifying optimal conditions and observing the gradual decrease in membrane stability after 24 hours.
JOURNAL OF CHEMISTRY
(2022)
Article
Chemistry, Physical
Mohd Amin Mir
Summary: The study synthesized oxadiazole, imidazole, benzimidazole, and cyclohexano analogues of 1,5-benzodiazepines. These derivatives have broad biochemical activities and may have positive impacts on the pharmaceutical industry.
CURRENT ORGANOCATALYSIS
(2022)
Review
Biotechnology & Applied Microbiology
Shama Sehar, Tabassum Rasool, Hasnain M. Syed, M. Amin Mir, Iffat Naz, Abdul Rehman, Mir Sadiq Shah, Mohammad Salim Akhter, Qaisar Mahmood, Adnan Younis
Summary: Dyes are widely used in various industries, especially in the textile industry. The discharge of dye-containing wastewater poses threats to natural ecosystems. Microbial degradation has attracted attention as a sustainable, efficient, cost-effective, and eco-friendly method for dye removal.
Article
Biochemistry & Molecular Biology
Romain Launay, Elin Teppa, Carla Martins, Sophie S. Abby, Fabien Pierrel, Isabelle Andre, Jeremy Esque
Summary: This study focuses on the role of the UbiJ-UbiK(2) heterotrimer in UQ biosynthesis and membrane release. Molecular modeling reveals close interaction between UbiJ-UbiK(2) and the membrane, providing possible pathways for UQ release. The UbiJ-UbiK(2) complex is identified as the likely interface between the membrane and the enzymes of the Ubi metabolon.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Cell Biology
Ingrid Fliniaux, Guillaume Marchand, Caroline Molinaro, Mathieu Decloquement, Alain Martoriati, Matthieu Marin, Jean-Francois Bodart, Anne Harduin-Lepers, Katia Cailliau
Summary: Sialic acids are a group of monosaccharides with unique physicochemical properties that modulate the biological functions of molecules they are associated with. They play a role in various stages of the reproductive process, particularly in the formation and binding of gametes. Sialoglycoproteins form a specific coat on the surface of gametes, and marine species oocytes have specific polysialylated chains. Spermatozoa undergo crucial changes in sialic acid in the female reproductive tract, facilitating migration, survival, and binding with the oocyte.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
M. Amin Mir, Farah Manzer Manhas, Kim Andrews, Syed M. Hasnain, Abid Iqbal, Shama Sehar, Adnan Younis
Summary: The stability and biological importance of Pyrogallol were analyzed through computational and experimental studies. It was found to have potential interactions with various proteins and exhibited antibiotic properties similar to Ascorbic Acid, Gallic acid, and Ellagic acid.
RESULTS IN CHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Anne Harduin-Lepers
Summary: Every eukaryotic cell is covered with a thick layer of complex carbohydrates called glycans, which play essential roles in cellular interactions. Sialic acids, located at the outermost positions of these glycans, are known to be key players in various normal and pathological processes, such as host-pathogen interactions and cancer. The review provides a summary of current knowledge on sialyltransferases, enzymes responsible for adding sialic acids to glycoproteins and glycolipids, including their structure-function relationships, molecular evolution, and implications in human biology.
GLYCOCONJUGATE JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Virginie Cogez, Dorothee Vicogne, Celine Schulz, Lucie Portier, Giulia Venturi, Jerome de Ruyck, Mathieu Decloquement, Marc F. Lensink, Guillaume Brysbaert, Fabio Dall'Olio, Sophie Groux-Degroote, Anne Harduin-Lepers
Summary: The Sd(a) carbohydrate epitope and its biosynthetic B4GALNT2 enzyme are expressed in the healthy colon and down-regulated in colon cancer. The B4GALNT2 gene drives the expression of two protein isoforms (LF-B4GALNT2 and SF-B4GALNT2) sharing the same transmembrane and luminal domains. Mutations in the N-glycosylation sites of B4GALNT2 lead to decreased expression levels, impaired stability, reduced enzyme activity, and mislocalization of the protein isoforms. Furthermore, the formation of homodimers is affected by these mutations. N-glycosylation plays a crucial role in controlling the biological activity of B4GALNT2 isoforms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Sachin Kumar, Sandeep Kumar, M. Amin Mir, Vineet Kumar Vishnoi, Ashutosh Pandey, Akanksha Pandey
Summary: This study investigated the antibacterial activity of Sida cordifolia L. phytoextract and found that its ethanolic extract exhibited strong bactericidal effects against certain common foodborne bacteria. The study also optimized the extraction process parameters and confirmed the phenolic composition using ultra-performance liquid chromatography.
FUTURE MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
M. Amin Mir
Summary: The study utilizes computational, experimental, and analysis methods to investigate coumarin. The results confirm its stability and biological activity, as it can interact with different proteins.
ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING
(2023)
Article
Multidisciplinary Sciences
M. Amin Mir, Muhammad Waqar Ashraf
Summary: The study synthesized complexes of Co (II), Ni (II), Cu (II), and 5, 8-dihydroxy-1, 4-naphthoquinone in an efficient manner using simple inexpensive catalyst and base, and analyzed their crystal structures. The X-ray data revealed the cubic P lattices of all the polymetal chelates, with variations in interplaner spacing, unit cell dimensions, and density among the different metal chelates.
ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING
(2022)