SNP and Structural Study of the Notch Superfamily Provides Insights and Novel Pharmacological Targets against the CADASIL Syndrome and Neurodegenerative Diseases

The evolutionary conserved Notch signaling pathway functions as a mediator of direct cell-cell communication between neighboring cells during development. Notch plays a crucial role in various fundamental biological processes in a wide range of tissues. Accordingly, the aberrant signaling of this pathway underlies multiple genetic pathologies such as developmental syndromes, congenital disorders, neurodegenerative diseases, and cancer. Over the last two decades, significant data have shown that the Notch signaling pathway displays a significant function in the mature brains of vertebrates and invertebrates beyond neuronal development and specification during embryonic development. Neuronal connection, synaptic plasticity, learning, and memory appear to be regulated by this pathway. Specific mutations in human Notch family proteins have been linked to several neurodegenerative diseases including Alzheimer's disease, CADASIL, and ischemic injury. Neurodegenerative diseases are incurable disorders of the central nervous system that cause the progressive degeneration and/or death of brain nerve cells, affecting both mental function and movement (ataxia). There is currently a lot of study being conducted to better understand the molecular mechanisms by which Notch plays an essential role in the mature brain. In this study, an in silico analysis of polymorphisms and mutations in human Notch family members that lead to neurodegenerative diseases was performed in order to investigate the correlations among Notch family proteins and neurodegenerative diseases. Particular emphasis was placed on the study of mutations in the Notch3 protein and the structure analysis of the mutant Notch3 protein that leads to the manifestation of the CADASIL syndrome in order to spot possible conserved mutations and interpret the effect of these mutations in the Notch3 protein structure. Conserved mutations of cysteine residues may be candidate pharmacological targets for the potential therapy of CADASIL syndrome.

Childhood and Adolescent Obesity with Somatic Indicators of Stress, Inflammation, and Dysmetabolism before and after Intervention: A Meta-Analysis

There have been numerous attempts to establish a correlation between obesity and stress, inflammatory, and dysmetabolism biomarkers in children and adolescents. Here, we performed a meta-analysis of existing studies to shed light on the elusive correlations of childhood and adolescent obesity with physiological indicators of stress, inflammation, and metabolism before and after lifestyle interventions. Observational studies, meta-analyses, narrative and systematic reviews were excluded. From a total of 53 articles, 11 were selected according to specific criteria. The biomarkers examined were circulating glucose, insulin, HDL, LDL, triglycerides, adiponectin, leptin, CRP, TNF-alpha, interleukin (IL)-6, systolic and diastolic blood pressure, and HOMA-IR. All analyses were performed using IBM SPSS Statistics Version 28.0.1.0 (142). The current meta-analysis provides evidence of a beneficial effect of a lifestyle intervention and/or drugs in children and adolescents living with obesity or overweight, consistent with a significant reduction in body fat-but not in BMI or waist circumference-an increase in circulating adiponectin and/or a reduction in serum insulin levels and diastolic blood pressure, and a trend towards a reduction of circulating leptin and glucose levels, as well as of the HOMA-IR. This meta-analysis indicates that lifestyle interventions could reduce overweight-/obesity-associated systemic inflammation and dysmetabolism even without an apparent decrease in BMI.

DRDs and Brain-Derived Neurotrophic Factor Share a Common Therapeutic Ground: A Novel Bioinformatic Approach Sheds New Light Toward Pharmacological Treatment of Cognitive and Behavioral Disorders

Cognitive and behavioral disorders are subgroups of mental health disorders. Both cognitive and behavioral disorders can occur in people of different ages, genders, and social backgrounds, and they can cause serious physical, mental, or social problems. The risk factors for these diseases are numerous, with a range from genetic and epigenetic factors to physical factors. In most cases, the appearance of such a disorder in an individual is a combination of his genetic profile and environmental stimuli. To date, researchers have not been able to identify the specific causes of these disorders, and as such, there is urgent need for innovative study approaches. The aim of the present study was to identify the genetic factors which seem to be more directly responsible for the occurrence of a cognitive and/or behavioral disorder. More specifically, through bioinformatics tools and software as well as analytical methods such as systemic data and text mining, semantic analysis, and scoring functions, we extracted the most relevant single nucleotide polymorphisms (SNPs) and genes connected to these disorders. All the extracted SNPs were filtered, annotated, classified, and evaluated in order to create the "genomic grammar" of these diseases. The identified SNPs guided the search for top suspected genetic factors, dopamine receptors D and neurotrophic factor BDNF, for which regulatory networks were built. The identification of the "genomic grammar" and underlying factors connected to cognitive and behavioral disorders can aid in the successful disease profiling and the establishment of novel pharmacological targets and provide the basis for personalized medicine, which takes into account the patient's genetic background as well as epigenetic factors.

Collaborative Platforms and Matchmaking Algorithms for Research and Education, Establishment, and Optimization of Consortia

Matchmaking has a great position in the rational allocation of resources in several fields, ranging from market operation to people's daily lives. Matchmakers have evolved through artificial intelligence technologies and are being introduced in numerous aspects of industry, research, and academia in solving decision issues, research innovation design, and building robust and efficient networks. The goal of this report is to describe the collaborative platforms and matchmaking algorithms for research and education, as well as the establishment and optimization of consortia.

An Updated Evolutionary and Structural Study of TBK1 Reveals Highly Conserved Motifs as Potential Pharmacological Targets in Neurodegenerative Diseases

TANK-binding kinase 1 protein (TBK1) is a kinase that belongs to the IκB (IKK) family. TBK1, also known as T2K, FTDALS4, NAK, IIAE8, and NF-κB, is responsible for the phosphorylation of the amino acid residues, serine and threonine. This enzyme is involved in various key biological processes, including interferon activation and production, homeostasis, cell growth, autophagy, insulin production, and the regulation of TNF-α, IFN-β, and IL-6. Mutations in the TBK1 gene alter the protein's normal function and may lead to an array of pathological conditions, including disorders of the central nervous system. The present study sought to elucidate the role of the TBK1 protein in amyotrophic lateral sclerosis (ALS), a human neurodegenerative disorder. A broad evolutionary and phylogenetic analysis of TBK1 was performed across numerous organisms to distinguish conserved regions important for the protein's function. Subsequently, mutations and SNPs were explored, and their potential effect on the enzyme's function was investigated. These analytical steps, in combination with the study of the secondary, tertiary, and quaternary structure of TBK1, enabled the identification of conserved motifs, which can function as novel pharmacological targets and inform therapeutic strategies for amyotrophic lateral sclerosis.

A Genomic Study of the Japanese Population Focusing on the Glucocorticoid Receptor Interactome Highlights Distinct Genetic Characteristics Associated with Stress Response

All living organisms have been programmed to maintain a complex inner equilibrium called homeostasis, despite numerous adversities during their lifespan. Any threatening or perceived as such stimuli for homeostasis is termed a stressor, and a highly conserved response system called the stress response system has been developed to cope with these stimuli and maintain or reinstate homeostasis. The glucocorticoid receptor, a transcription factor belonging to the nuclear receptors protein superfamily, has a major role in the stress response system, and research on its interactome may provide novel information regarding the mechanisms underlying homeostasis maintenance. A list of 149 autosomal genes that have an essential role in GR function or are prime examples of GRE-containing genes was composed in order to gain a comprehensive view of the GR interactome. A search for SNPs on those particular genes was conducted on a dataset of 3554 Japanese individuals, with mentioned polymorphisms being annotated with relevant information from the ClinVar, LitVar, and dbSNP databases. Forty-two SNPs of interest and their genomic locations were identified. These SNPs have been associated with drug metabolism and neuropsychiatric, metabolic, and immune system disorders, while most of them were located in intronic regions. The frequencies of those SNPs were later compared with a dataset consisting of 1465 Korean individuals in order to find population-specific characteristics based on some of the identified SNPs of interest. The results highlighted.that rs1043618 frequencies were different in the two populations, with mentioned polymorphism having a potential role in chronic obstructive pulmonary disease in response to environmental stressors. This SNP is located in the HSPA1A gene, which codes for an essential GR co-chaperone, and such information showcases that similar gene may be novel genomic targets for managing or combatting stress-related pathologies.

Semantic and Population Analysis of the Genetic Targets Related to COVID-19 and Its Association with Genes and Diseases

SARS-CoV-2 is a coronavirus responsible for one of the most serious, modern worldwide pandemics, with lasting and multifaceted effects. By late 2021, SARS-CoV-2 has infected more than 180 million people and has killed more than 3 million. The virus gains entrance to human cells through binding to ACE2 via its surface spike protein and causes a complex disease of the respiratory system, termed COVID-19. Vaccination efforts are being made to hinder the viral spread, and therapeutics are currently under development. Toward this goal, scientific attention is shifting toward variants and SNPs that affect factors of the disease such as susceptibility and severity. This genomic grammar, tightly related to the dark part of our genome, can be explored through the use of modern methods such as natural language processing. We present a semantic analysis of SARS-CoV-2-related publications, which yielded a repertoire of SNPs, genes, and disease ontologies. Population data from the 1000 Genomes Project were subsequently integrated into the pipeline. Data mining approaches of this scale have the potential to elucidate the complex interaction between COVID-19 pathogenesis and host genetic variation; the resulting knowledge can facilitate the management of high-risk groups and aid the efforts toward precision medicine.

ADRA2B and HTR1A: An Updated Study of the Biogenic Amine Receptors Reveals Novel Conserved Motifs Which Play Key Role in Mental Disorders

Mental disorders are strongly connected with several psychiatric conditions including depression, bipolar disorder, schizophrenia, eating disorder, and suicides. There are many biological conditions and pathways that define these complicated illnesses. For example, eating disorders are complex mental health conditions that require the intervention of geneticists, psychiatrists, and medical experts in order to alleviate their symptoms. A patient with suicidal ideation should first be identified and consequently monitored by a similar team of specialists. Both genetics and epigenetics can shed light on eating disorders and suicides as they are found in the main core of such investigations. In the present study, an analysis has been performed on two specific members of the GPCR family toward drawing conclusions regarding their functionality and implementation in mental disorders. Specifically, evolutionary and structural studies on the adrenoceptor alpha 2b (ADRA2B) and the 5-hydroxytryptamine receptor 1A (HTR1A) have been carried out. Both receptors are classified in the biogenic amine receptors sub-cluster of the GPCRs and have been connected in many studies with mental diseases and malnutrition conditions. The major goal of this study is the investigation of conserved motifs among biogenic amine receptors that play an important role in this family signaling pathway, through an updated evolutionary analysis and the correlation of this information with the structural features of the HTR1A and ADRA2B. Furthermore, the structural comparison of ADRA2B, HTR1A, and other members of GPCRs related to mental disorders is performed.

Dark DNA and stress (Review)

Over the past few decades, research at the molecular level has focused on the part of the genome that does not encode protein sequences. Since the discovery of transcriptional evidence from the hitherto considered 'junk' DNA, this region of the genome, which is currently termed dark DNA, is constantly gaining interest. The term borrows an analogy from the corresponding eminent fields of dark matter and dark energy in physics and cosmology. In fact, an increasing number of attempts are being made to enhance the current understanding of the non‑coding RNA (ncRNA) transcripts produced by such regions. Although the base‑pair length and gene number appear to be very diverse between species, it appears that the amount of the non‑coding regions of the genome of an organism is a sign of evolutional superiority. ncRNA molecules are able to orchestrate the expression of genetic information in the most complex, rapid and reversible manner, participating in almost every major biological process. A prime example of such a process is the maintenance of homeostasis, the internal physiological balance, despite internal and external stressful stimuli. These molecules have been shown to be excellent regulators of gene expression, with marked spatiotemporal specificity, rendering them ideal tools for regulating stress responses. Herein, an attempt is made to extract and fuse information from a repertoire of studies, which have demonstrated that the expression of a number of these molecules was modified following exposure to acute and chronic stress, as well as in patients with anxiety disorders and their respective animal models. All in all, ncRNAs have the potential to be used either as biomarkers or as therapeutic targets for disorders resulting from the loss of equilibrium, the disruption of homeostasis and the destabilization of the hypothalamic‑pituitary‑adrenal axis.

Endosymbiosis in Nature and the Gut-Brain Axis

Exploring the origin of plastids is an interesting theme for study because it enhances our knowledge of the basis of photosynthesis in flora. Plastids, which are organelles, are actually the major sites of photosynthesis in eukaryotic cells. Plastids are also every chloroplast which contains cytoplasmic organelles, enabling the harvesting and conversion of light and carbon dioxide into food and energy. Plastids can be found in eukaryotic cells, and according to their structure in their membrane, they can be separated in primary (which can be found in most algae and plants) and secondary plastids (which can be found in plankton).

Novel computational pipelines in antiviral structure‑based drug design (Review)

Viral infections constitute a fundamental and continuous challenge for the global scientific and medical community, as highlighted by the ongoing COVID-19 pandemic. In combination with prophylactic vaccines, the development of safe and effective antiviral drugs remains a pressing need for the effective management of rare and common pathogenic viruses. The design of potent antivirals can be informed by the study of the three-dimensional structure of viral protein targets. Structure-based design of antivirals in silico provides a solution to the arduous and costly process of conventional drug development pipelines. Furthermore, rapid advances in high-throughput computing, along with the growth of available biomolecular and biochemical data, enable the development of novel computational pipelines in the hunt of antivirals. The incorporation of modern methods, such as deep-learning and artificial intelligence, has the potential to revolutionize the structure-based design and repurposing of antiviral compounds, with minimal side effects and high efficacy. The present review aims to provide an outline of both traditional computational drug design and emerging, high-level computing strategies.

Multiple sclerosis and computational biology (Review)

Multiple sclerosis (MS) is an autoimmune neurodegenerative disease whose prevalence has increased worldwide. The resultant symptoms may be debilitating and can substantially reduce the of patients. Computational biology, which involves the use of computational tools to answer biomedical questions, may provide the basis for novel healthcare approaches in the context of MS. The rapid accumulation of health data, and the ever-increasing computational power and evolving technology have helped to modernize and refine MS research. From the discovery of novel biomarkers to the optimization of treatment and a number of quality-of-life enhancements for patients, computational biology methods and tools are shaping the field of MS diagnosis, management and treatment. The final goal in such a complex disease would be personalized medicine, i.e., providing healthcare services that are tailored to the individual patient, in accordance to the particular biology of their disease and the environmental factors to which they are subjected. The present review article summarizes the current knowledge on MS, modern computational biology and the impact of modern computational approaches of MS.

Recent approaches on Huntington's disease (Review)

Huntington's disease (HD) is a neurodegenerative disorder characterized by severe motor, cognitive and psychiatric symptoms. Patients of all ages can present with a dysfunction of the nervous system, which leads to the progressive loss of movement control and disabilities in speech, swallowing, communications, etc. The molecular basis of the disease is well-known, as HD is related to a mutated gene, a trinucleotide expansion, which encodes to the huntingtin protein. This protein is linked to neurogenesis and the loss of its function leads to neurodegenerative disorders. Although the genetic cause of the disorder has been known for decades, no effective treatment is yet available to prevent onset or to eliminate the progression of symptoms. Thus, the present review focused on the development of novel methods for the timely and accurate diagnosis of HD in an aim to aid the development of therapies which may reduce the severity of the symptoms and control their progression. The majority of the therapies include gene-silencing mechanisms of the mutated huntingtin gene aiming to suppress its expression, and the use of various substances as drugs with highly promising results. In the present review, the latest approaches on the diagnosis of HD are discussed along with the need for genetic counseling and an up-to-date presentation of the applied treatments.

The medical cyborg concept

Medical technology has made significant advances in the 21^st century and, at present, medicine makes use of information technology, telecommunications, and state-of-the-art engineering to provide the best possible healthcare services. Electronic sensors provide health practitioners with the ability to constantly monitor their patients’ health, to streamlines a number of medical processes, and to increase patients’ access to health services. Mobile phones also empower patients and play a major role in their health’s monitoring. The use of cybernetics technology can now help patients overcome even serious disabilities, enabling many disabled patients to live their lives similarly to their non-disabled fellow men through the use of artificial organs and implants. All these advances have paved the way for a more personalized type of healthcare that provides individualized solutions to each patient. Once a number of hurdles are overcome, medical technology will bring forth a new era of more precise and enabling medicine.

Molecular fusion events in carcinogenic organisms: a bioinformatics study for the detection of fused proteins between viruses, bacteria and eukaryotes

Molecular fusion events have a prominent role in the initial steps of carcinogenesis. In this study, a bioinformatics analysis was performed between four organisms that are known to induce cancer development in humans: two viruses, Human Herpesvirus 4, and Human T-cell leukaemia virus, one bacterium, Helicobacter Pylori, and one trematode, Schistosoma mansoni. The annotated proteomes from these organisms were analysed using the SAFE software to identify protein fusion events, which may provide insight into protein function similarities and possible merging events during the course of evolution. Based on the results, five fused proteins with very similar functions were detected, whereas proteins with different functions that might act in the same molecular complex or biochemical pathway were not found. Thus, this study analysed the above four well-known cancer-related organisms with de novo bioinformatics programs and provided useful information on protein fusion events, hopefully leading to deeper understanding of carcinogenenesis.

Epitranscriptomics of cardiovascular diseases (Review)

RNA modifications have recently become the focus of attention due to their extensive regulatory effects in a vast array of cellular networks and signaling pathways. Just as epigenetics is responsible for the imprinting of environmental conditions on a genetic level, epitranscriptomics follows the same principle at the RNA level, but in a more dynamic and sensitive manner. Nevertheless, its impact in the field of cardiovascular disease (CVD) remains largely unexplored. CVD and its associated pathologies remain the leading cause of death in Western populations due to the limited regenerative capacity of the heart. As such, maintenance of cardiac homeostasis is paramount for its physiological function and its capacity to respond to environmental stimuli. In this context, epitranscriptomic modifications offer a novel and promising therapeutic avenue, based on the fine‑tuning of regulatory cascades, necessary for cardiac function. This review aimed to provide an overview of the most recent findings of key epitranscriptomic modifications in both coding and non‑coding RNAs. Additionally, the methods used for their detection and important associations with genetic variations in the context of CVD were summarized. Current knowledge on cardiac epitranscriptomics, albeit limited still, indicates that the impact of epitranscriptomic editing in the heart, in both physiological and pathological conditions, holds untapped potential for the development of novel targeted therapeutic approaches in a dynamic manner.

Haematological malignancies implications during the times of the COVID-19 pandemic

The COVID-19 pandemic has complicated current healthcare services for cancer patients. Patients with haematological malignancies specifically seem vulnerable to SARS-CoV-2 infection due to their immunosuppressed status. The COVID-19 pandemic influences every step of the assessment and treatment of a haematological malignancy. Clinicians must adhere to strict policies to not spread the virus to their patients while they must also adjust their workflow for maximum productivity. These difficulties accentuate the ever-present need to improve the healthcare services for cancer patients. This improvement is needed not only to combat the problems that arose from the COVID-19 pandemic but also to establish a framework for the management of patients with haematological malignancies in potential future pandemics.

Human Emotions on the Onset of Cardiovascular and Small Vessel Related Diseases

BACKGROUND/AIM

The aim of the present study was to examine the relation between understanding of emotions and cardiovascular related diseases, namely coronary heart disease, diabetes mellitus and obesity. The uniqueness of this study lies in the fact that it examined the relationship between the cardiovascular related diseases named above and the understanding of emotions in the context of Emotional Intelligence (EI).

PATIENTS AND METHODS

The study was conducted in 300 participants during a 3 year period. All participants completed a self-report questionnaire, assessing various aspects of EI, such as self-emotion appraisal, other emotion appraisal, emotion regulation and use of emotions. As hypothesized, coronary heart disease is a prognostic factor of regulation of emotions.

RESULTS

The present study is an attempt to examine the relation between emotional understanding and cardiovascular related diseases, namely coronary heart disease, diabetes mellitus and obesity. Establishing which diseases are independent risk factors for the understanding of emotions, could have a significant impact on emotional health, through the treatment of these cardiovascular related diseases. Emotions were studied within the theoretical context of Emotional Intelligence (EI), which affects people's physical and mental health.

CONCLUSION

The results of this study emphasize on the relationship of cardiovascular related diseases and psychological characteristics, such as anxiety and anger, being aspects of EI. Additionally, this work fills a gap in the relevant Greek literature, as a first attempt to examine the correlation of EI with cardiovascular related diseases.

HCV genetics and genotypes dictate future antiviral strategies

At the end of the 1980s, the hepatitis C virus (HCV) was cloned and formally identified as the cause of the majority of non-A and non-B hepatitis cases. Today, around 170 million people worldwide are infected with HCV, making it five times more common than infection with the human immunodeficiency virus (HIV). Several methods exist which mediate the spread of infection. One of the most common and efficient is sharing or re-using injecting equipment; studies have indicated that 80-90% of individuals in some populations of intravenous drug users test positive in serum HCV assays. Contracting HCV from infected blood transfusions was also a major cause of infection before screening tests were introduced in the early 1990s. Other possible, but less common, methods of infection transmission include mother-to-child during pregnancy, sexual contact and nosocomial acquisition (for example between surgical or dialysis patients). It appears that concurrent HIV-1 infection increases the risk of HCV transmission via the mother-to-child or sexual routes.