In this article, I critically analyze the impact of the new biology and the biological revolution. I argue that indiscriminate use of the words such as 'interdisciplinary,' 'integrative,' and 'revolution' has caused only confusion when applied to biology. The recent debate, especially after the exploding field of systems biology, has brought back the controversy whether molecular biology is reductionist or holistic. I look at the issues involved critically. I discuss the problem of defining the word 'gene' and argue that recent attempts to redefine the central dogma of molecular biology about the information flow from DNA to RNA to protein are not justified. I support my view with comments from the scientist who discovered RNA splicing. Several aspects of evo-devo, a new branch of biology, are discussed. I give examples from this evolution-developmental biology to show how some of Darwin's inspired guesses have had resounding victory when it was found that specific genes during embryonic development of the Galapagos finches decided the size and shape of their beaks. I discuss the recent publications which show that the conditions in the island, such as wet to dry to wet season, can bring about evolutionary changes from year to year. Thus it is essential to monitor both short and long-term evolutionary changes to get the full picture of evolution.
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J Am Chem Soc
January 2025
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China.
Effective delivery and controlled release of metallo-prodrugs with sustained activation and rapid response feed the needs of precise medicine in metal chemotherapeutics. However, gold-based anticancer drugs often suffer from detoxification binding and extracellular transfer by sulfur-containing peptides. To address this challenge, we integrate a thiol-activated prodrug strategy of newly prepared hypercoordinated carbon-centered gold(I) clusters (HCGCs) with their photosensitization character to augment the mitochondrial release of Au(I) in tumors.
View Article and Find Full Text PDFOrg Lett
January 2025
Key Laboratory of Chemical Biology and Traditional Chinese Medicine (Ministry of Educational of China), Key Laboratory of the Assembly and Application of Organic Functional Molecules of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China.
We disclose herein a chiral phosphoric-acid-catalyzed enantioselective addition reaction of alcohols to fluoroalkylated biaryl 1,3-oxoazepines, which furnished a wide range of bridged biaryls bearing a fluoroalkylated quaternary carbon stereocenter on the seven-membered ring in high yields (up to 99%) with excellent enantioselectivities (up to 98% ee). Our method can be used for the modification of several natural products and bioactive molecules. Preliminary studies revealed that the products obtained in this reaction exhibit good in vitro bioactivities against two plant pathogens.
View Article and Find Full Text PDFBrief Bioinform
November 2024
School of Engineering, Westlake University, No. 600 Dunyu Road, 310030 Zhejiang, P.R. China.
Single-cell RNA sequencing (scRNA-seq) offers remarkable insights into cellular development and differentiation by capturing the gene expression profiles of individual cells. The role of dimensionality reduction and visualization in the interpretation of scRNA-seq data has gained widely acceptance. However, current methods face several challenges, including incomplete structure-preserving strategies and high distortion in embeddings, which fail to effectively model complex cell trajectories with multiple branches.
View Article and Find Full Text PDFBrief Bioinform
November 2024
Biotherapeutics Molecule Discovery, Boehringer Ingelheim Pharmaceutical Inc., 900 Ridgebury Road, Ridgefield, CT 06877, United States.
Antibody generation requires the use of one or more time-consuming methods, namely animal immunization, and in vitro display technologies. However, the recent availability of large amounts of antibody sequence and structural data in the public domain along with the advent of generative deep learning algorithms raises the possibility of computationally generating novel antibody sequences with desirable developability attributes. Here, we describe a deep learning model for computationally generating libraries of highly human antibody variable regions whose intrinsic physicochemical properties resemble those of the variable regions of the marketed antibody-based biotherapeutics (medicine-likeness).
View Article and Find Full Text PDFBrief Bioinform
November 2024
Guangdong Provincial Key Laboratory of Mathematical and Neural Dynamical Systems, Great Bay University, No. 16 Daxue Rd, Songshanhu District, Dongguan, Guangdong, 523000, China.
Multimodal omics provide deeper insight into the biological processes and cellular functions, especially transcriptomics and proteomics. Computational methods have been proposed for the integration of single-cell multimodal omics of transcriptomics and proteomics. However, existing methods primarily concentrate on the alignment of different omics, overlooking the unique information inherent in each omics type.
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