The birth and development of the DNA theory of inheritance: sixty years since the discovery of the structure of DNA

3dRNA/DNA: 3D Structure Prediction from RNA to DNA

There is an increasing need for determining 3D structures of DNAs, e.g., for increasing the efficiency of DNA aptamer selection. Recently, we have proposed a computational method of 3D structure prediction of DNAs, called 3dDNA, which has been integrated into our original web server 3dRNA, now renamed 3dRNA/DNA (http://biophy.hust.edu.cn/new/3dRNA). Currently, 3dDNA can only output the predicted DNA 3D structures for users but cannot rank them as an energy function for assessing DNA 3D structures is still lacking. Here, we first provide a brief introduction to 3dDNA and then introduce a new energy function, 3dDNAscore, for the assessment of DNA 3D structures. 3dDNAscore is an all-atom knowledge-based potential by integrating 86 atomic types from nucleic acids. Benchmarks demonstrate that 3dDNAscore can effectively identify near-native structures from the decoys generated by 3dDNA, thus enhancing the completeness of 3dDNA.

Nucleic Acid Materials-Mediated Innate Immune Activation for Cancer Immunotherapy

Abnormally localized nucleic acids (NAs) are considered as pathogen associated molecular patterns (PAMPs) in innate immunity. They are recognized by NAs-specific pattern recognition receptors (PRRs), leading to the activation of associated signaling pathways and subsequent production of type I interferons (IFNs) and pro-inflammatory cytokines, which further trigger the adaptive immunity. Notably, NAs-mediated innate immune activation is highly dependent on the conformation changes, especially the aggregation of PRRs. Evidence indicates that the characteristics of NAs including their length, concentration and even spatial structure play essential roles in inducing the aggregation of PRRs. Therefore, nucleic acid materials (NAMs) with high valency of NAs and high-order structures hold great potential for activating innate and adaptive immunity, making them promising candidates for cancer immunotherapy. In recent years, a variety of NAMs have been developed and have demonstrated significant efficacy in achieving satisfactory anti-tumor immunity in multiple mouse models, exhibiting huge potential for clinical application in cancer treatment. This review aims to discuss the mechanisms of NAMs-mediated innate immune response, and summarize their applications in cancer immunotherapy.

A new wave of innovations within the DNA damage response

Genome instability has been identified as one of the enabling hallmarks in cancer. DNA damage response (DDR) network is responsible for maintenance of genome integrity in cells. As cancer cells frequently carry DDR gene deficiencies or suffer from replicative stress, targeting DDR processes could induce excessive DNA damages (or unrepaired DNA) that eventually lead to cell death. Poly (ADP-ribose) polymerase (PARP) inhibitors have brought impressive benefit to patients with breast cancer gene (BRCA) mutation or homologous recombination deficiency (HRD), which proves the concept of synthetic lethality in cancer treatment. Moreover, the other two scenarios of DDR inhibitor application, replication stress and combination with chemo- or radio- therapy, are under active clinical exploration. In this review, we revisited the progress of DDR targeting therapy beyond the launched first-generation PARP inhibitors. Next generation PARP1 selective inhibitors, which could maintain the efficacy while mitigating side effects, may diversify the application scenarios of PARP inhibitor in clinic. Albeit with unavoidable on-mechanism toxicities, several small molecules targeting DNA damage checkpoints (gatekeepers) have shown great promise in preliminary clinical results, which may warrant further evaluations. In addition, inhibitors for other DNA repair pathways (caretakers) are also under active preclinical or clinical development. With these progresses and efforts, we envision that a new wave of innovations within DDR has come of age.

Molecular elements: novel approaches for molecular building

Classically, a molecular element (ME) is a pure substance composed of two or more atoms of the same element. However, MEs, in the context of this review, can be any molecules as elements bonded together into the backbone of synthetic oligonucleotides (ONs) with designed sequences and functions, including natural A, T, C, G, U, and unnatural bases. The use of MEs can facilitate the synthesis of designer molecules and smart materials. In particular, we discuss the landmarks associated with DNA structure and related technologies, as well as the extensive application of ONs, the ideal type of molecules for intervention therapy aimed at correcting disease-causing genetic errors (indels). It is herein concluded that the discovery of ON therapeutics and the fabrication of designer molecules or nanostructures depend on the ME concept that we previously published. Accordingly, ME will be our focal point as we discuss related research directions and perspectives in making molecules and materials. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.

Next-Generation Sequencing Markup Language (NGSML): A Medium for the Representation and Exchange of NGS Data

With the increasing demand for low-cost high-throughput sequencing of large genomes, next-generation sequencing (NGS) technology has developed rapidly. NGS can not only be used in basic scientific research but also in clinical diagnostics and healthcare. Numerous software systems and tools have been developed to analyze NGS data, and various data formats have been produced to accommodate different sequencing equipment providers or analytical software. However, the data interoperability between these tools brings great challenges to researchers. A generic format that could be shared by most of the software and tools in the NGS field would make data interoperability and sharing easier. In this paper, we defined a general XML-based NGS markup language (NGSML) format for the representation and exchange of NGS data. We also developed a user-friendly GUI tool, NGSMLEditor, for presenting, creating, editing, and converting NGSML files. By using NGSML, various types of NGS data can be saved in one unified format. Compared with the unstructured plain text file, a structured data format based on XML technology solves the incompatibility of various NGS data formats. The NGSML specifications are freely available from http://www.sysbio.org.cn/NGSML. NGSMLEditor is open source under GNU GPL and can be downloaded from the website.

Supermolecules as a quality markers of herbal medicinal products

Herbal medicines have greatly contributed to human health worldwide for thousands of years. In particular, traditional Chinese medicine plays an essential role in the prevention and treatment of COVID-19. With the exponentially increasing use and global attention to herbal medicinal products (HMPs), efficacy and safety have become major public concerns in many countries. In general, the quantification and qualification of quality markers (Q-markers) is the most common way to solve this issue. In the last few decades, small molecules, including flavonoids, terpenes, phenylpropanoids, alkaloids, phenols, and glycosides have been extensively investigated as Q-markers for HMP quality control. With the development of biotechnology in the last decade, scientists have begun to explore HMPs macromolecules, including polysaccharides and DNA, for their establishment as Q-markers. In recent years, supermolecules with stronger biological activities have been found in HMPs. In this review, we summarize and discuss the current Q-markers for HMP quality control; in particular, the possibility of using supermolecules as Q-markers based on structure and activity was discussed.

Current Systemic Treatments for the Hereditary Cancer Syndromes: Drug Development in Light of Genomic Defects

Advances in the genetic basis of different tumors have led to identification of tumor vulnerabilities that can be turn into targeted therapies. In this regard, PARP inhibitors cause synthetic lethality with tumors harboring BRCA1 or BRCA2 genetic alterations. On the other hand, tumors with microsatellite instability, either due to germline or sporadic alterations, are candidates for immune checkpoint inhibitors. Finally, patients with von Hippel-Lindau disease who carry a germline alteration in the VHL gene may benefit form belzutifan, a hypoxia-inducible factor 2 alpha inhibitor. Overall, research on the underlying pathological mechanisms of these tumors has provided new therapeutic opportunities that might be expanded to other sporadic tumors with similar biology.

Ultrastructural changes of donor livers in liver transplantation indicate hepatocytes injury

The use of electron microscopy (EM) can provide details about cells and tissue down to the nanometer level. We aim to observe ultrastructural changes in the donor liver by EM and analyze the relationship with prognosis. Data from 89 liver transplant recipients were collected and analyzed for recovery of graft function. The results revealed significantly higher organelle injury scores in the primary liver graft nonfunction (PNF) group. High-score group had higher peak alanine aminotransferases, peak aspartate aminotransferases, and peak international normalized ratio (p = .041, .006 and .036, respectively). Warm ischemia time, score of rough endoplasmic reticulum and nucleus was larger in low-score group (p = .007, .006, and .025, respectively). Patients in high-score group had a significantly short survival time (60.0% vs. 92.9%, p = .0039). No significant difference was found in the analysis of 3-year survival rate (60% vs. 84.5%, p = .07). EM is one of feasible and effective strategy for evaluating the quality of donor liver and the patient's prognosis. Ultrastructural changes under EM indicate hepatocytes injury and a high score indicates a worse outcome in early period but does not affect long-term survival.

The evolution of epistemological methodologies in anatomy: From antiquity to modern times

Present day scenario regarding epistemological methods in anatomy is in sharp contrast to the situation during ancient period. This study aimed to explore the evolution of epistemological methodologies in anatomy across centuries. In ancient times Egyptian embalmers acquired anatomical knowledge from handling human bodies and likewise anatomical studies in India involved human dissection. Ancient Greeks used theological principles-based methods, animal dissection and human dissection in practice of anatomy. Human dissection was also practiced in ancient China for gaining anatomical knowledge. Prohibition of human dissection led to use of animal dissection in ancient Rome and the trend continued in Europe through Middle Ages. Epistemological methods used by Muslim scholars during Middle Ages are not clearly chronicled. Human dissection returned as primary epistemological method in Renaissance Europe and empirical methods were reinstated after ancient period in human dissection during 16th century. The situation further improved with introduction of pragmatic experiment based approach during 17th century and autopsy-based methods during 18th century. Advances in anatomical knowledge continued with advent of microscope-based methods and emergence of anatomical sections in practice of human dissection in 19th century. Introduction of human observational studies, medical imaging, and molecular methods presented more options in terms of epistemological methods for investigating the human body during 20th century. Onset of 21st century has witnessed dominance of technology-based methods in anatomy. Limited emphasis on ethics in epistemological methodologies since antiquity is a dark aspect of otherwise an eventful evolutionary journey but recent developments are in positive direction.

DNA damage repair: historical perspectives, mechanistic pathways and clinical translation for targeted cancer therapy

Genomic instability is the hallmark of various cancers with the increasing accumulation of DNA damage. The application of radiotherapy and chemotherapy in cancer treatment is typically based on this property of cancers. However, the adverse effects including normal tissues injury are also accompanied by the radiotherapy and chemotherapy. Targeted cancer therapy has the potential to suppress cancer cells' DNA damage response through tailoring therapy to cancer patients lacking specific DNA damage response functions. Obviously, understanding the broader role of DNA damage repair in cancers has became a basic and attractive strategy for targeted cancer therapy, in particular, raising novel hypothesis or theory in this field on the basis of previous scientists' findings would be important for future promising druggable emerging targets. In this review, we first illustrate the timeline steps for the understanding the roles of DNA damage repair in the promotion of cancer and cancer therapy developed, then we summarize the mechanisms regarding DNA damage repair associated with targeted cancer therapy, highlighting the specific proteins behind targeting DNA damage repair that initiate functioning abnormally duo to extrinsic harm by environmental DNA damage factors, also, the DNA damage baseline drift leads to the harmful intrinsic targeted cancer therapy. In addition, clinical therapeutic drugs for DNA damage and repair including therapeutic effects, as well as the strategy and scheme of relative clinical trials were intensive discussed. Based on this background, we suggest two hypotheses, namely "environmental gear selection" to describe DNA damage repair pathway evolution, and "DNA damage baseline drift", which may play a magnified role in mediating repair during cancer treatment. This two new hypothesis would shed new light on targeted cancer therapy, provide a much better or more comprehensive holistic view and also promote the development of new research direction and new overcoming strategies for patients.

The cell theory and cellular pathology: Discovery, refinements and applications fundamental to advances in biology and medicine

This review explores the developments leading up to the establishment of the cell theory and cellular pathology and their subsequent refinements and applications while focusing on the individuals who have made seminal advances in the field. The links between cell biology, cell pathology and cell injury research are emphasized. Recognition also is given to the importance of technological advances in microscopy, histology, biochemical and molecular methods for discovery in cell biology and cell pathology. Particular attention is focused on the work of Rudolph Virchow and his former students in the formulation of the cell theory in biology and pathology and John F. R. Kerr and colleagues who identified and developed a comprehensive characterization of apoptosis, thereby giving impetus to the contemporary field of cell injury research. Cell injury research remains an important and fruitful field of ongoing inquiry and discovery.

The Texas Society of Pathologists: molded by the legacy of pathology and focused on excellence in medicine for 100 years and beyond

In 1921, 16 Texas pathologists gathered in Dallas, Texas, to found the Texas Society of Pathologists (TSP). The TSP is now the oldest state pathology society in the USA with continuity traced back to its founding 100 years ago. This article aims to both commemorate the TSP centennial and to provide context for the remarkable success of the society. The article takes a look back and a look forward from 1921. The look back focuses on the development of the field of pathology and the maturation of medicine and pathology in the USA and Texas. The look forward encompasses developments in science, technology, American health care policy, and medicine that have impacted Texas pathologists and influenced proactive initiatives of the TSP. The review of the life and times of the TSP highlights the importance of leaders and leadership in shaping outcomes. Complexities and uncertainties of the contemporary health care scene point to the need for continued strong leadership. The successful past century and hopeful future of the TSP are inextricably linked to the guiding principle of the TSP, which is a focus on continual striving for excellence in medicine.

Gene editing technology for improving life quality: A dream coming true?

The fact that monogenic diseases are related to mutations in one specific gene, make gene correction one of the promising strategies in the future to treat genetic diseases or alleviate their symptoms. From this perspective, and along with recent advances in technology, genome editing tools have gained momentum and developed fast. In fact, clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR/Cas9), transcription activator-like effector nucleases (TALENs), and zinc-finger nucleases (ZFNs) are regarded as novel technologies which are able to correct a number of genetic aberrations in vitro and in vivo. The number of ongoing clinical trials employing these tools has been increased showing the encouraging outcomes of these tools. However, there are still some major challenges with respect to the safety profile and directed delivery of them. In this paper, we provided updated information regarding the history, nature, methods of delivery, and application of the above-mentioned gene editing tools along with the meganucleases (an older similar tool) based on published in vitro and in vivo studies and introduced clinical trials which employed these technologies.

Heredity determined by the environment: Lamarckian ideas in modern molecular biology

Inheritance of acquired characteristics (IAC) is a well-documented phenomenon occurring both in eukaryotes and prokaryotes. However, it is not included in current biological theories, and the risks of IAC induction are not assessed by genetic toxicology. Furthermore, different kinds of IAC (transgenerational and intergenerational inheritance, genotrophic changes, dauermodifications, vernalization, and some others) are traditionally considered in isolation, thus impeding the development of a comprehensive view on IAC as a whole. Herein, we discuss all currently known kinds of IAC as well as their mechanisms, if unraveled. We demonstrate that IAC is a special case of genotype × environment interactions requiring certain genotypes and, as a rule, prolonged exposure to the inducing influence. Most mechanisms of IAC are epigenetic; these include but not limited to DNA methylation, histone modifications, competition of transcription factors, induction of non-coding RNAs, inhibition of plastid translation, and curing of amyloid and non-amyloid prions. In some cases, changes in DNA sequences or host-microbe interactions are involved as well. The only principal difference between IAC and other environmentally inducible hereditary changes such as the effects of radiation is the origin of the changes: in case of IAC they are definite (determined by the environment), while the others are indefinite (arise from environmentally provoked molecular stochasticity). At least some kinds of IAC are adaptive and could be regarded as the elements of natural selection, though non-canonical in their origin and molecular nature. This is a probable way towards synthesis of the Lamarckian and Darwinian evolutionary conceptions. Applied issues of IAC are also discussed.

The mechanisms of epigenetic inheritance: how diverse are they?

Although epigenetic inheritance (EI) is a rapidly growing field of modern biology, it still has no clear place in fundamental genetic concepts which are traditionally based on the hereditary role of DNA. Moreover, not all mechanisms of EI attract the same attention, with most studies focused on DNA methylation, histone modification, RNA interference and amyloid prionization, but relatively few considering other mechanisms such as stable inhibition of plastid translation. Herein, we discuss all known and some hypothetical mechanisms that can underlie the stable inheritance of phenotypically distinct hereditary factors that lack differences in DNA sequence. These mechanisms include (i) regulation of transcription by DNA methylation, histone modifications, and transcription factors, (ii) RNA splicing, (iii) RNA-mediated post-transcriptional silencing, (iv) organellar translation, (v) protein processing by truncation, (vi) post-translational chemical modifications, (vii) protein folding, and (viii) homologous and non-homologous protein interactions. The breadth of this list suggests that any or almost any regulatory mechanism that participates in gene expression or gene-product functioning, under certain circumstances, may produce EI. Although the modes of EI are highly variable, in many epigenetic systems, stable allelic variants can be distinguished. Irrespective of their nature, all such alleles have an underlying similarity: each is a bimodular hereditary unit, whose features depend on (i) a certain epigenetic mark (epigenetic determinant) in the DNA sequence or its product, and (ii) the DNA sequence itself (DNA determinant; if this is absent, the epigenetic allele fails to perpetuate). Thus, stable allelic epigenetic inheritance (SAEI) does not contradict the hereditary role of DNA, but involves additional molecular mechanisms with no or almost no limitations to their variety.

Bacterial Small Regulatory RNAs and Hfq Protein

Small regulatory RNA (sRNA) is a unique noncoding RNA involved in regulation of gene expression in both eukaryotic and bacterial cells. This short review discusses examples of positive and negative translation regulation by sRNAs in bacteria and participation of Hfq in these processes. The importance of structure investigation of nucleotide-protein and RNA-protein complexes for designing a model of Hfq interaction with both mRNA and sRNA simultaneously is demonstrated.