Honey bee as an alternative model invertebrate organism

Insects perfectly fit the flagship principle of animal research – 3R: to reduce (the number of animals), to replace (animals with alternative models) and to refine (methods). Bees have the most important advantages of a model organism: they cause minimal ethical controversy, they have a small and fully known genome, and they permit the use of many experimental techniques. Bees have a fully functional DNMT toolkit. Therefore, they are used as models in biomedical/genetic research, e.g. in research on the development of cancer or in the diagnostics of mental and neuroleptic diseases in humans. The reversion of aging processes in bees offers hope for progress in gerontology research. The cellular mechanisms of learning and memory coding, as well as the indicators of biochemical immunity parameters, are similar or analogous to those in humans, so bees may become useful in monitoring changes in behavior and metabolism. Bees are very well suited for studies on the dose of the substance applied to determine the lethal dose or the effect of a formula on life expectancy. Honeybees have proven to be an effective tool for studying the effects of a long-term consumption of stimulants, as well as for observing behavioral changes and developing addictions at the individual and social levels, as well as for investigating the effects of continuously delivering the same dose of a substance. The genomic and physiological flexibility of bees in dividing tasks among workers in a colony makes it possible to create a Single- Cohort Colony (SCC) in which peers compared perform different tasks. Moreover behavioral methods (e.g. Proboscis Extension Reflex – PER, Sting Extension Reflex – SER, free flying target discrimination tasks or the cap pushing response) make it possible to analyse changes occurring in honeybee brains during learning and remembering. Algorithms of actions are created based on the behavior of a colony or individual, e.g. Artificial Bee Colony Algorithm (ABCA). Honeybees are also model organisms for profiling the so-called intelligence of a swarm or collective intelligence. Additionally, they serve as models for guidance systems and aviation technologies. Bees have inspired important projects in robotics, such as B-droid, Robobee and The Green Brain Project. It has also been confirmed that the apian sense of smell can be used to detect explosive devices, such as TNT, or drugs (including heroin, cocaine, amphetamines and cannabis). This inconspicuous little insect can revolutionize the world of science and contribute to the solution of many scientific problems as a versatile model.

Genetic Diversity and Population Structure of Traditional Chinese Herb “Chai-Hu” Resources Using Genome-Wide SNPs Through Genotyping-By-Sequencing

Bupleurum (named “Chai-hu”) is an important traditional Chinese medicine resource in China. It has been widely used since ancient times and has antipyretic, analgesic and cholagogic functions, but there is little research on its genetic diversity. In this study, genotyping-by-sequencing (GBS) was used to detect SNP loci in 39 Bupleurum germplasm resources from different regions in China and analyse their genetic diversity. A total of 25.1 Gb of data was obtained by sequencing, with an average of 0.64 Gb per sample. After screening, 83898 high-quality SNPs were obtained. The results of genetic research were obtained by phylogenetic tree, principal component analysis and population structure analysis, and the 39 experimental materials were divided into three groups. The average observed heterozygosity and expected heterozygosity of Bupleurum populations were 0.24 and 0.17, respectively, indicating that Bupleurum populations from five different provinces had a low level of genetic diversity. Population nucleotide diversity analysis and analysis of molecular variance showed that the percentage of intrapopulation variation was 120.88%, while the percentage of interpopulation variation was only 2.46%. There was relative aggregation of Bupleurum samples with the same geographical origin, but the division of population structure was not completely correlated with sample origin. The results showed that the genetic diversity of the materials was low and that the genetic variation was narrow. This provides a good basis for the genetic breeding and protection of species diversity of Bupleurum.

Influence of preanalytical variables on the quality of cell-free DNA. Biobanking of cell-free DNA material

The search for early disease markers and the development of diagnostic systems has recently been expanding within genomics. Genomic deoxyribonucleic acid (DNA), cell-free DNA (cfDNA) and microbiome DNA obtained from different types of samples (tissues, blood and its derivatives, feces, etc.) are used as objects of genetic research. It has been shown that cfDNA that enters the bloodstream, in particular, as a result of apoptosis, necrosis, active tumor secretion and metastasis, is of great importance for studying molecular mechanisms of the pathological process and application in clinical practice. Circulating nucleic acid analysis can be used to monitor response to treatment, assess drug resistance, and quantify minimal residual disease. The review article reflects the following information about the biomaterial: source of cfDNA, methods of cfDNA isolation, storage and use for the diagnosis of certain diseases. Cell-free DNA can be present in biological fluids such as blood, urine, saliva, synovial and cerebrospinal fluid. In most cases, cfDNA is isolated from blood derivatives (serum and plasma), while it is most correct to use blood plasma for cfDNA isolation. Optimal and economically justifiable is the use of ethylenediaminetetra-acetic acid tubes for taking blood and obtaining plasma with subsequent cfDNA isolation. There is evidence that the optimal shelf life in an ethylenediaminetetra-acetic acid tube from the moment of blood sampling to subsequent isolation is a 2-hour interval. After centrifugation, cfDNA in plasma (or serum) can be stored for a long time at a temperature of -80O C. Storage at -20O C is undesirable, since DNA fragmentation increases.

CRISPR/Cas9 Mediated Genome Editing in Crop Plants

Recently, most genomic research has focused on genome editing methods to develop new technologies that could be easy, reliable, and feasible to edit plant genomes for highly productive agriculture. Genome editing is based on alternating a specific target DNA sequence by adding, replacing, and removing DNA bases. This newest technology called CRISPR/Cas9 seems to be less time-consuming, more effective and used in many research areas of plant genetic research. CRISPR/Cas9 systems have many advantages in comparison with ZFNs and TALENs and has been extensively used for genome editing to many crop plant species. Around 20 crop species are successfully worked out for trait improvements, for example, yield improvement, disease resistance, herbicide tolerance, and biotic and abiotic stress management. This review paper will overview recent advances in CRISPR/Cas genome editing research in detail. The main focus will be on the use of CRISPR/Cas9 technology in plant genome research.

Pertussis in Children: Clinical and Epidemiological Features, the Possibilities of Vaccine Preventio

Relevance. Despite the specific immunization carried out, pertussis still has great medical and social significance for pediatricians, since it continues to remain a common bacterial infection, involving children of different age groups in the epidemic process. The lack of persistent immunity to whooping cough, combined with a high susceptibility index, contributes to an increase in the incidence among schoolchildren and adolescents, who are diagnosed only during epidemiological and laboratory examinations, and who, in most cases, serve as sources of infection for young children. Aim. To study the clinical and epidemiological features of whooping cough in children aged 0 to 14 years hospitalized in an infectious diseases hospital under conditions of mass vaccine prevention, as well as to identify the features of the disease in vaccinated people using the example of an outbreak of the disease in an organized group. Materials and methods. A retrospective analysis of 164 case histories of children diagnosed with Pertussis hospitalized in the infectious hospital of the Regional Interdistrict Children’s Clinical Hospital № 1 in Krasnoyarsk in 2015–2019, as well as 25 outpatient records of patients identified during the epidemiological investigation of the focus of infection in December 2019 was carried out. For the etiological interpretation of the diagnosis of whooping cough, a comprehensive laboratory examination was carried out using bacteriological, serological and molecular genetic research methods. Results. According to official statistics, in the Krasnoyarsk territory in 2019, among children with pertussis, patients aged 7 to 17 prevailed (38,7%). At the same time, in the age structure of patients hospitalized in a hospital, the primary importance was occupied by children of the first year of life, unvaccinated against this disease. Most of them were diagnosed with a moderate form of the disease with frequent development of complications from the respiratory and nervous systems. At the same time, among schoolchildren and adolescents, as a rule, who have received a completed course of vaccination, there is an atypical, erased course of the disease, while the difficulties of its diagnosis lead to a high incidence of pertussis in children of the first year of life who have not yet been protected by vaccination. Conclusions. Despite the high coverage of decreed groups with preventive vaccinations against whooping cough in the Krasnoyarsk territory, an assessment of the state of specific immunity based on the results of a serological survey conducted in 2019 revealed 50.6% of seronegative individuals already at the age of 3–4 years, which confirms the need to improve the schemes immunization against this disease; and inclusion of pertussis vaccination in the regional immunization schedule.

A High-Density Genetic Map Enables Genome Synteny and QTL Mapping of Vegetative Growth and Leaf Traits in Gardenia

The gardenia is a traditional medicinal horticultural plant in China, but its molecular genetic research has been largely hysteretic. Here, we constructed an F1 population with 200 true hybrid individuals. Using the genotyping-by-sequencing method, a high-density sex-average genetic map was generated that contained 4,249 SNPs with a total length of 1956.28 cM and an average genetic distance of 0.46 cM. We developed 17 SNP-based Kompetitive Allele-Specific PCR markers and found that 15 SNPs were successfully genotyped, of which 13 single-nucleotide polymorphism genotypings of 96 F1 individuals showed genotypes consistent with GBS-mined genotypes. A genomic collinearity analysis between gardenia and the Rubiaceae species Coffea arabica, Coffea canephora and Ophiorrhiza pumila showed the relativity strong conservation of LG11 with NC_039,919.1, HG974438.1 and Bliw01000011.1, respectively. Lastly, a quantitative trait loci analysis at three phenotyping time points (2019, 2020, and 2021) yielded 18 QTLs for growth-related traits and 31 QTLs for leaf-related traits, of which qBSBN7-1, qCD8 and qLNP2-1 could be repeatably detected. Five QTL regions (qCD8 and qSBD8, qBSBN7 and qSI7, qCD4-1 and qLLLS4, qLNP10 and qSLWS10-2, qSBD10 and qLLLS10) with potential pleiotropic effects were also observed. This study provides novel insight into molecular genetic research and could be helpful for further gene cloning and marker-assisted selection for early growth and development traits in the gardenia.

Molecular Mechanisms and Risk Factors for the Pathogenesis of Hydrocephalus

Hydrocephalus is a neurological condition due to the aberrant circulation and/or obstruction of cerebrospinal fluid (CSF) flow with consequent enlargement of cerebral ventricular cavities. However, it is noticed that a lot of patients may still go through symptomatic progression despite standard shunting procedures, suggesting that hydrocephalus is far more complicated than a simple CSF circulative/obstructive disorder. Growing evidence indicates that genetic factors play a fundamental role in the pathogenesis of some hydrocephalus. Although the genetic research of hydrocephalus in humans is limited, many genetic loci of hydrocephalus have been defined in animal models. In general, the molecular abnormalities involved in the pathogenesis of hydrocephalus include brain development and ependymal cell dysfunction, apoptosis, inflammation, free radical generation, blood flow, and cerebral metabolism. Moreover, recent studies have indicated that the molecular abnormalities relevant to aberrant cerebral glymphatic drainage turn into an attractive subject in the CSF circulation disorder. Furthermore, the prevalent risk factors could facilitate the development of hydrocephalus. In this review, we elicited some possible fundamental molecular mechanisms and facilitating risk factors involved in the pathogenesis of hydrocephalus, and aimed to widen the diagnosis and therapeutic strategies for hydrocephalus management. Such knowledge could be used to improve patient care in different ways, such as early precise diagnosis and effective therapeutic regimens.

Guideline for feedback of individual genetic research findings for genomics research in Africa

As human genomics research in Africa continues to generate large amounts of data, ethical issues arise regarding how actionable genetic information is shared with research participants. The Human Heredity and Health in Africa Consortium (H3Africa) Ethics and Community Engagement Working group acknowledged the need for such guidance, identified key issues and principles relevant to genomics research in Africa and developed a practical guideline for consideration of feeding back individual genetic results of health importance in African research projects. This included a decision flowchart, providing a logical framework to assist in decision-making and planning for human genomics research projects. Although presented in the context of the H3Africa Consortium, we believe the principles described, and the decision flowchart presented here is applicable more broadly in African genomics research.

Clinical, hormonal and molecular-genetic characteristics of monogenic diabetes mellitus associated with the mutations in the INS gene

Background: Currently more than 50 mutations of the INS gene are known to affect the various stages of insulin biosynthesis in the beta cells of the pancreas. However only individual cases of diabetes mellitus (DM) associated with heterozygous mutations in the coding region of the INS gene were reported in Russian Federation. We report a group of patients with a clinical manifestation of DM caused by mutations in both coding and non-coding regions of the INS gene. The patients with a mutation in the intron of the INS gene are reported for the first time in Russian FederationMaterials and methods: 60 patients with an isolated course of neonatal DM (NDM), 52 patients with a manifestation of DM at the age of 7–12 months and the absence of the main autoimmune markers of type 1 DM, 650 patients with the MODY phenotype were included in the study. NGS technology was used for molecular genetic research. Author’s panel of primers (Custom DNA Panel) was used for multiplex PCR and sequencing using Ion Ampliseq™ technology. The author’s panel “­Diabetes Mellitus” included 28 genes (13 candidate genes of MODY and other genes associated with DM).Results: 13 heterozygous mutations were identified in 16 probands and 9 relatives. The majority of mutations were detected in patients with PNDM (18.75%) and in patients with an onset of DM at the age of 7–12 months (9.6%). Mutations in the INS gene were detected in 2 patients (0.3%) in the group with the MODY phenotype. Mutations in the INS gene were not detected in patients with transient NDM (TNDM). Analysis of clinical data in patients with PND and onset of diabetes at the age of 7–12 months did not show significant differences in the course of the disease. The clinical characteristics of the cases of MODY10 and diabetes caused by a mutation in the intron of the INS gene are reported in details.Conclusion: The role of INS gene mutations in NDM, MODY, and DM with an onset at the age of 7–12 months was analyzed in a large group of patients. The clinical characteristics of DM due to a mutation in the intron of the INS gene are reported for the first time in the Russian Federation.