Trioxidized cysteine in the aging proteome mimics the structural dynamics and interactome of phosphorylated serine

Aging is the primary risk factor for the development of numerous human chronic diseases. On a molecular level, it significantly impacts the regulation of protein modifications, leading to the accumulation of degenerative protein modifications (DPMs) such as aberrant serine phosphorylation (p-Ser) and trioxidized cysteine (t-Cys) within the proteome. The altered p-Ser is linked to abnormal cell signaling, while the accumulation of t-Cys is associated with chronic diseases induced by oxidative stress. Despite this, the potential cross-effects and functional interplay between these two critical molecular factors of aging remain undisclosed. This study analyzes the aging proteome of wild-type C57BL/6NTac mice over 2 years using advanced proteomics and bioinformatics. Our objective is to provide a comprehensive analysis of how t-Cys affects cell signaling and protein structure in the aging process. The results obtained indicate that t-Cys residues accumulate in the aging proteome, interact with p-Ser interacting enzymes, as validated in vitro, and alter their structures similarly to p-Ser. These findings have significant implications for understanding the interplay of oxidative stress and phosphorylation in the aging process. Additionally, they open new venues for further research on the role(s) of these protein modifications in various human chronic diseases and aging, wherein exacerbated oxidation and aberrant phosphorylation are implicated.     

Recent advances in the manipulation of murine gene expression and its utility for the study of human neurological disease

Transgenic mouse models have vastly contributed to our knowledge of the genetic and molecular pathways underlying the pathogenesis of neurological disorders that affect millions of people worldwide. Not only have they allowed the generation of disease models mimicking the human pathological state but they have also permitted the exploration of the pathological role of specific genes through the generation of knock-out and knock-in models. Classical constitutive transgenic mice have several limitations however, due to behavioral adaptation process occurring and conditional mouse models are time-consuming and often lack extensive spatial or temporal control of gene manipulation. These limitations could be overcome by means of innovative methods that are now available such as RNAi, viral vectors and large cloning DNA vectors. These tools have been extensively used for the generation of mouse models and are characterized by the superior control of transgene expression that has been proven invaluable in the assessment of novel treatments for neurological diseases and to further investigate the molecular processes underlying the etiopathology of neurological disorders. Furthermore, in association with classical transgenic mouse models, they have allowed the validation of innovative therapeutic strategies for the treatment of human neurological disorders. This review describes how these tools have overcome the limitations of classical transgenic mouse models and how they have been of value for the study of human neurological diseases.     

超声分子成像：机遇与挑战

随着分子生物学、蛋白组学、基因组学、计算机工程学等学科的不断进步,交叉融合,分子成像逐渐登上历史的舞台,成为研究热点。而超声分子成像随之迅猛发展,近年来超声微泡制备技术的成熟和超声造影检查技术的不断进步,超声造影不再局限获取组织的血流灌注信息,而是逐渐成为特异性的超声分子成像。目前使用超声对比剂研究分子成像和靶向治疗仍处于初级阶段。但是,各种分子成像技术的不断革新和发展,超声分子成像面临着重大的挑战,而在挑战背后同样面临着难逢的机遇。超声医学和分子生物学的迅猛发展,超声分子成像必将成为诊断和治疗疾病的新的手段和方法。超声造影剂仍有许多未能解决的问题,像如何延长微泡的半衰期、如何增强微泡的敏感性和特异性,如何增强目的基因的表达,如何处理组织损伤和高频超声之间的关系等问题,但是如果能解决这些问题,超声造影在现代医学的诊断和治疗中将起到重要的作用。现将超声分子成像综述如下。     

Cilia-related diseases

More and more attention is paid to diseases such as internal transfer and brain malformation which are caused by the abnormal morphogenesis of cilia. These cilia-related diseases are divided into two categories: ciliopathy resulting from defects of primary cilia and primary ciliary dyskinesia (PCD) caused by functional dysregulation of motile cilia. Cilia are widely distributed, and their related diseases can cover many human organs and tissues. Recent studies prove that primary cilia play a key role in maintaining homeostasis in the cardiovascular system. However, molecular mechanisms of cilia-related diseases remain elusive. Here, we reviewed recent research progresses on characteristics, molecular mechanisms and treatment methods of ciliopathy and PCD. Our review is beneficial to the further research on the pathogenesis and treatment strategies of cilia-related diseases.     

Should Bacteriophages Be Classified As Parasites Or Predators?

Bacteriophages are viruses infecting bacteria and propagating in bacterial cells. They were discovered over 100 years ago, and for decades they played crucial roles as models in genetics and molecular biology and as tools in genetic engineering and biotechnology. Now we also recognize their huge role in natural environment and their importance in human health and disease. Despite our understanding of bacteriophage mechanisms of development, these viruses are described as parasites or predators in the literature. From the biological point of view, there are fundamental differences between parasites and predators. Therefore, in this article, I asked whether bacteriophages should be classified as former or latter biological entities. Analysis of the literature and biological definitions led me to conclude that bacteriophages are parasites rather than predators and should be classified and described as such. If even more precise ecological classification is needed, bacteriophages can perhaps be included in the group of parasitoids. It might be the most appropriate formal classification of these viruses, especially if strictly virulent phages are considered, contrary to phages which lysogenize host cells and those which develop according to the permanent infection mode (or chronic cycle, like filamentous phages) revealing features of classical parasites.     

Animal models of human genetic diseases: do they need to be faithful to be useful?

With the advances in molecular genetics, animal models of human diseases are becoming more numerous and more refined every year. Despite this, one must recognize that they generally do not faithfully and comprehensively mimic the homologous human disease. Faced with these imperfections, some geneticists believe that these models are of little value, while for others, on the contrary, they are important tools. We agree with this second statement, and in this review, we examine the reasons that may explain the observed differences and suggest means to circumvent or even exploit them. Our opinion is that animal models should be regarded more as tools capable of answering specific questions rather than mere replicas, at a smaller scale, of a given human disease. Far from disappointing they are probably called for a promising future.     

Basement membranes and human disease

In 1990, the role of basement membranes in human disease was established by the identification of COL4A5 mutations in Alport’s syndrome. Since then, the number of diseases caused by mutations in basement membrane components has steadily increased as has our understanding of the roles of basement membranes in organ development and function. However, many questions remain as to the molecular and cellular consequences of these mutations and the way in which they lead to the observed disease phenotypes. Despite this, exciting progress has recently been made with potential treatment options for some of these so far incurable diseases.     

Origins of highly mosaic mycobacteriophage genomes

Bacteriophages are the most abundant organisms in the biosphere and play major roles in the ecological balance of microbial life. The genomic sequences of ten newly isolated mycobacteriophages suggest that the bacteriophage population as a whole is amazingly diverse and may represent the largest unexplored reservoir of sequence information in the biosphere. Genomic comparison of these mycobacteriophages contributes to our understanding of the mechanisms of viral evolution and provides compelling evidence for the role of illegitimate recombination in horizontal genetic exchange. The promiscuity of these recombination events results in the inclusion of many unexpected genes including those implicated in mycobacterial latency, the cellular and immune responses to mycobacterial infections, and autoimmune diseases such as human lupus. While the role of phages as vehicles of toxin genes is well established, these observations suggest a much broader involvement of phages in bacterial virulence and the host response to bacterial infections.     

Modelling the stability of Stx lysogens

Shiga-toxin-converting bacteriophages (Stx phages) are temperate phages of Escherichia coli, and can cause severe human disease. The spread of shiga toxins by Stx phages is directly linked to lysogen stability because toxins are only synthesized and released once the lytic cycle is initiated. Lysogens of Stx phages are known to be less stable than those of the related lambda phage; this is often described in terms of a 'hair-trigger' molecular switch from lysogeny to lysis. We have developed a mathematical model to examine whether known differences in operator regions and binding affinities between Stx phages and lambda phage can account for the lower stability of Stx lysogens. The Stx phage 933W has only two binding sites in its left operator region (compared to three in phage lambda), but this has a minimal effect on 933W lysogen stability. However, the relatively weak binding affinity between repressor molecules and the second binding site in the right operator is found to significantly reduce the stability of its lysogens, and may account for the hair-trigger nature of the switch. Reduced lysogen stability can lead to increased frequency of genetic recombination in bacterial genomes. The development of the mathematical model has considerable utility in understanding the behaviour and evolution of the molecular switch, with implications for phage-related diseases.     

Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs

The recent discovery that the human and other mammalian genomes produce thousands of long non-coding RNAs (lncRNAs) raises many fascinating questions. These mRNA-like molecules, which lack significant protein-coding capacity, have been implicated in a wide range of biological functions through diverse and as yet poorly understood molecular mechanisms. Despite some recent insights into how lncRNAs function in such diverse cellular processes as regulation of gene expression and assembly of cellular structures, by and large, the key questions regarding lncRNA mechanisms remain to be answered. In this review, we discuss recent advances in understanding the biology of lncRNAs and propose avenues of investigation that may lead to fundamental new insights into their functions and mechanisms of action. Finally, as numerous lncRNAs are dysregulated in human diseases and disorders, we also discuss potential roles for these molecules in human health.     

Understanding risk perceptions to enhance communication about human-wildlife interactions and the impacts of zoonotic disease

Inclusion of wildlife in the concept of One Health is important for two primary reasons: (1) the physical health of humans, domesticated animals, and wildlife is linked inextricably through shared diseases, and (2) humans' emotional well-being can be affected by their perceptions of animal health. Although an explicit premise of the One Health Initiative is that healthy wildlife contribute to human health, and vice versa, the initiative also suggests implicitly that wildlife may pose threats to human health through zoonotic disease transmission. As people learn more about One Health, an important question surfaces: How will they react to communications carrying the message that human health and wildlife health are linked? In the absence of adequate relevant research data, we recommend caution in the production and dissemination of One Health messages because of possible unintended or collateral effects. Understanding how and why individuals perceive risks related to wildlife diseases is essential for determining message content that promotes public support for healthy wildlife populations, on the one hand, and, on the other, for identifying messages that might inadvertently increase concern about human health effects of diseased wildlife. To that end, we review risk perception research and summarize the few empirical studies that exist on perceived risk associated with zoonoses. We conclude with some research questions that need answering to help One Health practitioners better understand how the public will interpret their messages and thus how to communicate positively and without negative collateral consequences for wildlife conservation.     

The genomic stability regulator PTIP is required for proper chromosome segregation in mitosis

The centrosome is a multifunctional organelle that is known primarily for its microtubule organising function. Centrosomal defects caused by changes in centrosomal structure or number have been associated with human diseases ranging from congenital defects to cancer. We are only beginning to appreciate how the non-microtubule organising roles of the centrosome are related to these clinical conditions. In this review, we will discuss the historical evidence that led to the proposal that the centrosome participates in cell cycle regulation. We then summarize the body of work that describes the involvement of the mammalian centrosome in triggering cell cycle progression and checkpoint signalling. Then we will highlight work from the fission yeast model organism, revealing the molecular details that explain how the spindle pole body (SPB, the yeast functional equivalent of the centrosome), participates in these cell cycle transitions. Importantly, we will discuss some of the emerging questions from recent discoveries related to the role of the centrosome as a cell cycle regulator.

     

Introduction to Thematic Series: Protein Interactions,Structures, and Networks

Protein interactions are fundamental to the proper functioning of cells, and aberrant formation or regulation of protein interactions is at the heart of many diseases, including cancer. The advancement of methods to study the identity, function, and regulation of protein complexes makes possible the understanding of how those complexes malfunction in human diseases. New methodologies in mass spectrometry, microscopy, and protein structural analysis are rapidly advancing the amount and quality of the data, as well as the level of detail that can be obtained from experiments. With this progress, the questions that can be addressed and the biological landscape are changing. This series of minireviews highlights methodological advances and how they have been applied in novel ways to explore the function and regulation of pathways and dynamic networks in cells.     

Phage therapy of coral disease

At present there are no known procedures for preventing or treating infectious diseases of corals. Toward this end, the use of phage therapy has been investigated. Lytic bacteriophages (phages) were isolated for two bacterial pathogens that are responsible for coral diseases, Vibrio coralliilyticus, which is the causative agent of bleaching and tissue lysis of Pocillopora damicornis, and Thalosomonas loyaeana, which causes the white plague-like disease of Favia favus. By using these phages in controlled aquaria experiments, it was demonstrated that each of these diseases could be controlled by the pathogen-specific phage. The data indicate that initially the phages bind to the pathogen in seawater and are then brought to the coral surface where they multiply and lyse the pathogen. The phages remained associated with the coral and could prevent subsequent infections. These data suggest that phage therapy has the potential to control the spread of infectious coral diseases.     

土壤噬菌体及其介导的抗生素抗性基因水平转移研究进展

土壤中抗生素耐药性的扩散对全球的公共卫生和食品安全造成威胁,严重挑战人类感染类疾病的预防与治疗.噬菌体介导的抗生素抗性基因(ARGs)的水平转移是环境中抗性基因扩散的重要机制.但是,噬菌体对土壤环境中抗性基因传播的贡献尚未见报道.本文综述了土壤环境中噬菌体的分布特征与影响因子,总结了纯化和富集土壤噬菌体的主要研究方法;...     

Advancing ecological understandings through technological transformations in noninvasive genetics

Noninvasive genetic approaches continue to improve studies in molecular ecology, conservation genetics and related disciplines such as forensics and epidemiology. Noninvasive sampling allows genetic studies without disturbing or even seeing the target individuals. Although noninvasive genetic sampling has been used for wildlife studies since the 1990s, technological advances continue to make noninvasive approaches among the most used and rapidly advancing areas in genetics. Here, we review recent advances in noninvasive genetics and how they allow us to address important research and management questions thanks to improved techniques for DNA extraction, preservation, amplification and data analysis. We show that many advances come from the fields of forensics, human health and domestic animal health science, and suggest that molecular ecologists explore literature from these fields. Finally, we discuss how the combination of advances in each step of a noninvasive genetics study, along with fruitful areas for future research, will continually increase the power and role of noninvasive genetics in molecular ecology and conservation genetics.     

The variability of autophagy and cell death susceptibility

Impaired autophagic machinery is implicated in a number of diseases such as heart disease, neurodegeneration and cancer. A common denominator in these pathologies is a dysregulation of autophagy that has been linked to a change in susceptibility to cell death. Although we have progressed in understanding the molecular machinery and regulation of the autophagic pathway, many unanswered questions remain. How does the metabolic contribution of autophagy connect with the cell’s history and how does its current autophagic flux affect metabolic status and susceptibility to undergo cell death? How does autophagic flux operate to switch metabolic direction and what are the underlying mechanisms in metabolite and energetic sensing, metabolite substrate provision and metabolic integration during the cellular stress response? In this article we focus on unresolved questions that address issues around the role of autophagy in sensing the energetic environment and its role in actively generating metabolite substrates. We attempt to provide answers by explaining how and when a change in autophagic pathway activity such as primary stress response is able to affect cell viability and when not. By addressing the dynamic metabolic relationship between autophagy, apoptosis and necrosis we provide a new perspective on the parameters that connect autophagic activity, severity of injury and cellular history in a logical manner. Last, by evaluating the cell’s condition and autophagic activity in a clear context of regulatory parameters in the intra- and extracellular environment, this review provides new concepts that set autophagy into an energetic feedback loop, that may assist in our understanding of autophagy in maintaining healthy cells or when it controls the threshold between cell death and cell survival.     

Mitochondrial matters of the brain: amyloid formation and Alzheimer’s disease introduction

In recent years mitochondria, as the most abundant organelles in animal and human cells, have come to the forefront of biomedical research as they are now recognized not only as the major producers of ATP needed to drive cellular functions critical for life, but they are also the instruments of cell death. Not surprisingly, therefore, mitochondria are now known to be involved in many different diseases ranging from those that affect millions worldwide to those that affect only a few, i.e., rare diseases. These diseases include in addition to cardio-myopathies and cancer also diseases that affect many other organs/tissues including the brain/nervous system, the latter diseases now commonly referred to as “neurodegenerative diseases”. Specifically, the subject of this mini-review series focuses on the role of mitochondria in Alzheimer’s disease, a major age related neurodegenerative disease that results in loss or decline of memory and other cognitive abilities. This devastating disease affects millions of Americans, and globally multi-millions with very grim predictions for the future. Although the molecular and gene-related details that underlie Alzheimer’s disease remain to be clearly elucidated, mitochondria appear to be very intimately involved. The purpose of this mini-review series is to summarize how various investigators working on this subject envision the role(s) of mitochondria in Alzheimer’s disease. The development of future therapies for this disease is likely to rely heavily on the new knowledge gained.