Molecular Genetic Techniques Research Articles

Single-cell multi-omics sequencing reveals chromosome copy number inconsistency between trophectoderm and inner cell mass in human reconstituted embryos after spindle transfer.

Is the chromosome copy number of the trophectoderm (TE) of a human reconstituted embryos after spindle transfer (ST) representative of the inner cell mass (ICM)? Single-cell multi-omics sequencing revealed that ST blastocysts have a higher proportion of cell lineages exhibiting intermediate mosaicism than conventional ICSI blastocysts, and that the TE of ST blastocysts does not represent the chromosome copy number of ICM. Preimplantation genetic testing for aneuploidy (PGT-A) assumes that TE biopsies are representative of the ICM, but the TE and ICM originate from different cell lineages, and concordance between TE and ICM is not well-studied, especially in ST embryos. We recruited 30 infertile women who received treatment at our clinic and obtained 45 usable blastocysts (22 from conventional ICSI and 23 reconstituted embryos after ST). We performed single-cell multi-omics sequencing on all blastocysts to predict and verify copy number variations (CNVs) in each cell. We determined the chromosome copy number of each embryo by analysing the proportion of abnormal cells in each blastocyst. We used the Bland-Altman concordance and the Kappa test to evaluate the concordance between TE and ICM in the both groups. The study was conducted at a public tertiary hospital in China, where all the embryo operations, including oocytes retrieval, ST, and ICSI, were performed in the embryo laboratory. We utilized single-cell multi-omics sequencing technology at the Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, to analyse the blastocysts. Transcriptome sequencing was used to predict the CNV of each cell through bioinformatics analysis, and the results were validated using the DNA methylation library of each cell to confirm chromosomal normalcy. We conducted statistical analysis and graphical plotting using R 4.2.1, SPSS 27, and GraphPad Prism 9.3. Mean age of the volunteers, the blastocyst morphology, and the developmental ratewere similar in ST and ICSI groups. The blastocysts in the ST group had some additional chromosomal types that were prone to variations beyond those enriched in the blastocysts of the ICSI group. Finally, both Bland-Altman concordance test and kappa concordancetest showed good chromosomal concordance between TE and ICM in the ICSI blastocysts (kappa = 0.659, P < 0.05), but not in ST blastocysts (P = 1.000), suggesting that the TE in reconstituted embryos is not representative of ICM. Gene functional annotation (GO and KEGG analyses) suggests that there may be new or additional pathways for CNV generation in ST embryos compared to ICSI embryos. This study was mainly limited by the small sample size and the limitations of single-cell multi-omics sequencing technology. To select eligible single cells, some cells of the embryos were eliminated or not labelled, resulting in a loss of information about them. The findings of this study are innovative and exploratory. A larger sample size of human embryos (especially ST embryos) and more accurate molecular genetics techniques for detecting CNV in single cells are needed to validate our results. Our study justifies the routine clinical use of PGT-A in ICSI blastocysts, as we found that the TE is a good substitute for ICM in predicting chromosomal abnormalities. While PGT-A is not entirely accurate, our data demonstrate good clinical feasibility. This trial was able to provide correct genetic counselling to patients regarding the reliability of PGT-A. Regarding ST blastocysts, the increased mosaicism rate and the inability of the TE to represent the chromosomal copy number of the ICM are both biological characteristics that differentiate them from ICSI blastocysts. Currently, ST is not used clinically on a large scale to produce blastocysts. However, if ST becomes more widely used in the future, our study will be the first to demonstrate that the use of PGT-A in ST blastocysts may not be as accurate as PGT-A for ICSI blastocysts. This study was supported by grants from the National Key R&D Program of China (2018YFA0107601) and the National Key R&D Program of China (2018YFC1003003). The authors declare no conflict of interest. N/A.

Probiotics as an alternative to antibiotics in modulating the intestinal microbiota and performance of broiler chickens.

Gut bacteria play an important role in poultry nutrition and the immune defense system. Changes in the intestinal microbiome affect the physiological state, metabolism and innate im-munity of poultry. The present study aimed to characterize age-related changes in the gastrointestinal tract microflora in broiler chickens, depending on supplementation of the diet with the in-feed antibiotic Stafac® 110 and a Bacillus subtilis strain-based probiotic. In this regard, a comprehensive analysis of the taxonomic structure of the microbial community in the gastrointestinal tract (GIT) of broiler chickens was carried out using a molecular genetic technique of the Terminal-Restriction Fragment Length Polymorphism analysis and taking into account age dynamics and feeding treatment. A beneficial effect on the microbiological composition and body weight of broilers was observed when using the antibiotic and probiotic in compound feeds. Different bacterial communities were revealed in the duodenum and cecum and their positive impact on broiler growth was established. The results obtained shed light on the formation of GIT microflora of broiler chickens during the growing period and its changes in response to the use of the antibiotic and the probiotic. We suggest that the implementation of the tested in-feed antibiotic and probiotic can be beneficial in regulating the intestinal microflora microbiological processes in the GIT and improving the feeding efficiency and productivity of broiler chickens.

Myeloid/lymphoid neoplasms with eosinophilia and tyrosine kinase fusion genes: A workshop report with focus on novel entities and a literature review including paediatric cases.

Myeloid/lymphoid neoplasms with eosinophilia (M/LN-eo) and tyrosine kinase (TK) gene fusions are a rare group of haematopoietic neoplasms with a broad range of clinical and morphological presentations. Paediatric cases have increasingly been recognised. Importantly, not all appear as a chronic myeloid neoplasm and eosinophilia is not always present. In addition, standard cytogenetic and molecular methods may not be sufficient to diagnose M/LN-eo due tocytogenetically cryptic aberrations. Therefore, additional evaluation with fluorescence in-situ hybridisation and other molecular genetic techniques (array-based comparative genomic hybridisation, RNA sequencing) are recommended for the identification of specific TK gene fusions. M/LN-eo with JAK2 and FLT3-rearrangements and ETV6::ABL1 fusion were recently added as a formal member to this category in the International Consensus Classification (ICC) and the 5th edition of the WHO classification (WHO-HAEM5). In addition, other less common defined genetic alterations involving TK genes have been described. This study is an update on M/LN-eo with TK gene fusions with focus on novel entities, as illustrated by cases submitted to the Bone Marrow Workshop, organised by the European Bone Marrow Working Group (EBMWG) within the frame of the 21st European Association for Haematopathology congress (EAHP-SH) in Florence 2022. A literature review was performed including paediatric cases of M/LN-eo with TK gene fusions.

Prognostic value of CD4&lt;sup&gt;+&lt;/sup&gt; in patients with Т1–2N0M0 breast cancer

Aim. To evaluate the prognostic value of CD4+ in patients with T1–2N0M0 breast cancer.Materials and methods. We performed a quantitative assessment of CD4+ T-lymphocytes in tumor stromal cells and determined the prognostic parameter using the method developed by us (patent No. RU2697709C1 dated 19.08.2019) in 394 patients diagnosed with infiltrative breast cancer. Survival of patients in the analyzed group was assessed over a period of 10 years.Archival material from paraffin blocks of the «target group» was used in the work for molecular genetic profiling techniques (T1–2N0M0, 1118 patients, 2000–2009). A histological preparation stained with hematoxylin and eosin was scanned, and the central and peripheral zones of the tumor were isolated. To identify CD4+ T-lymphocytes, the immunohistochemical study of preparations obtained with rabbit anti-CD4 monoclonal antibodies was performed. After rescanning histological and immunohistochemical preparations, combining different immunohistochemical stains, the cell density in the tumor and stromal components was calculated in preparations stained with hematoxylin and eosin and CD4. For further calculations, we used the data obtained as a result of the number of stromal cells reduced to 1 mm2 (according to the preparation stained with hematoxylin and eosin), the so-called cell density per calculated number of CD4+-stained cells (cell area × proportion of CD4+ cells in percentages). The resulting ratio is used to predict the outcome of breast cancer: if its value is ≤ 50 %, the prognosis is assessed as favorable (in which the patient’s survival is 10 years or more).Results. In 296 (75 %) of 394 observed patients, the proportion of CD4+ T-lymphocytes in tumor stromal cells was ≤ 50 %. Over 10 years, the overall survival of patients in this group was 93 %, which is considered a statistically favorable group for breast cancer (stages T1–2, N0). In 98 (25 %) of 394 observed patients, the proportion of CD4+ T-lymphocytes in tumor stromal cells was ˃50 %. Over 10 years, the overall survival of patients in this group was 82 %, which is considered a statistically unfavorable group for breast cancer (stages T1–2, N0).Conclusion. Our findings suggest high accuracy of our method of breast cancer prognosis based on the quantitative assessment of CD4+ T-lymphocytes in tumor stromal cells. It can be used for breast cancer prognosis in early stages (T1–2, N0).

Current Data and New Insights into the Genetic Factors of Atherogenic Dyslipidemia Associated with Metabolic Syndrome.

Atherogenic dyslipidemia plays a critical role in the development of metabolic syndrome (MetS), being one of its major components, along with central obesity, insulin resistance, and hypertension. In recent years, the development of molecular genetics techniques and extended analysis at the genome or exome level has led to important progress in the identification of genetic factors (heritability) involved in lipid metabolism disorders associated with MetS. In this review, we have proposed to present the current knowledge related to the genetic etiology of atherogenic dyslipidemia, but also possible challenges for future studies. Data from the literature provided by candidate gene-based association studies or extended studies, such as genome-wide association studies (GWAS) and whole exome sequencing (WES,) have revealed that atherogenic dyslipidemia presents a marked genetic heterogeneity (monogenic or complex, multifactorial). Despite sustained efforts, many of the genetic factors still remain unidentified (missing heritability). In the future, the identification of new genes and the molecular mechanisms by which they intervene in lipid disorders will allow the development of innovative therapies that act on specific targets. In addition, the use of polygenic risk scores (PRS) or specific biomarkers to identify individuals at increased risk of atherogenic dyslipidemia and/or other components of MetS will allow effective preventive measures and personalized therapy.

Evaluating the virulence factors of Salmonella typhi isolated from children suffering from severe diarrhea using molecular genetic techniques

Abstract. Jaber AS. 2023. Evaluating the virulence factors of Salmonella typhi isolated from children suffering from severe diarrhea using molecular genetic techniques. Biodiversitas 24: 3543-3549. Salmonella enterica subsp. serotype Typhi is the bacteria that causes typhoid fever. Although its prevalence has significantly decreased in affluent nations, it continues to be a leading cause of illness and mortality in emerging nations. Because of changes in ecology, eating habits, and agricultural and food production techniques, Salmonella infections have increased in frequency in industrialized countries. This study aimed to use qualitative RT-PCR (based on the ttr gene) and conventional PCR to measure the frequency of Salmonella typhi in Iraqi children with chronic diarrhea (based on PagN and TolC genes). This study included 100 stool samples collected from children suffering from continuous diarrhea. Those samples were inoculated on CHROM-agar and incubated 37°C for 18-24 hours, then Salmonella was identified using a Vitek 2 compact system. DNA has been extracted, and qRT-PCR has been done to detect Salmonella sp. by the amplification of the ttr gene. Then PCR also done to amplify TolC and PagN genes. The amplified products then sequenced to reveal mutations within the amplified regions. The results of PagN gene showed 41 samples were positive, and 40 samples were positive for TolC. Results of qRT-PCR according to the ttr gene amplification showed 38 samples positive. The blood group O+ showed a higher number of positive samples (13), and males showed higher positive samples than females (23 and 15, respectively). Sequencing revealed various number of mutations within the amplified regions of both PagN and TolC in the samples which isolated from children with the longest period of illness.

Immunocytochemistry as an Ancillary Technique in the Cytologic Diagnosis of Synovial Sarcoma: Lock With Cell Block

Introduction: Synovial sarcomas are rare tumors accounting for approximately 5-10% of soft tissue sarcomas. For synovial sarcomas that arise at unusual locations, cytologic diagnosis is challenging despite characteristic cytomorphologic features.&#x0D; Material and Methods: The use of ancillary diagnostic procedures such as immunocytochemistry (ICC) using cell blocks and molecular genetic techniques using aspirated material help in the confirmation of diagnosis. During the period of 18 months from Nov 16 to Feb 18 we reported three cases of SS that occurred in rare locations with the help of ICC on cell blocks in 2 cases and IHC in the third case.&#x0D; Results: Cells arranged in bundles, perivascular arrangement, tight clusters, acini &amp; singly. Cells are elongated, oval to spindle, presence of uni or bipolar cytoplasmic processes with mildly pleomorphic , hyperchromatic nuclei &amp; fine granular chromatin. TLE1 was positive in all 3 cases.&#x0D; Conclusion: TLE1 marker is an extremely useful marker that distinguishes SS from other cytological &amp; histological mimics.&#x0D; The objective of the present study was to call attention and also highlight the variable cytology of synovial sarcoma arising at rare locations. Furthermore, we discuss use of adjunctive ICC on cell blocks that help to lock the diagnosis.

Gender Determination by PCR Assay for The Sex-Determining Region Y(SRY) Gene Amplification in Linnaeus’s Two-Toed Sloth (Choloepus Didactylus)

In Linnaeus’s two-toed sloths (Choloepus didactylus), there is no distinct sexual dimorphism. It is an obstacle for gender determination from the external genitalia, especially in newborns or young sloths. Hence, easy, rapid, and reliable genetics-based methods for gender identification of the sloths are needed to continue captive breeding more successfully. In this study, a PCR-based technique that allows gender determination of two-toed sloths by using a sex-determining region Y (SRY) gene marker was described. The hair samples from young (suspect gender) and adult sloths (known gender) were used in genetic analysis. Initially, genomic DNA was isolated from hair root samples using Roche high pure PCR template preparation kit. The SRY primers were specifically designed based on the NCBI and Ensembl databases, and they were verified with the BLAST program concerning the two-toed sloth genome. PCR amplification with the SRY-specific primers was carried out by a programmable thermal cycler device using FastStart High Fidelity PCR System, Roche dNTPack. The samples were then electrophoresed on 2% agarose gels and were visualized by a gel documentation and analysis system. A specific band in the electrophoresis pattern is diagnostic for a male individual with a partial SRY region. Hence, the analysis demonstrated that the samples belonged to a male two-toed sloth. Two-toed sloth species are commonly preferred animals in zoos. Gender determination is inevitable for these animals in captivity to be raised successfully and healthily. Molecular genetic techniques allow high efficiency in taxonomic evaluations and gender identification in species that do not display sexual dimorphism. The PCR assay described here may be helpful for a rapid genetic analysis that can be widely used in gender determination for two-toed sloths.

P-736 Balanced cryptic chromosomal rearrangement carriers detection by optical genome mapping (OGM)

Abstract Study question To evaluate diagnosis value of optical genome mapping (OGM) for potential preimplantation genetic testing in chromosomal structural rearrangement (PGT-SR) patients with cryptic chromosomal rearrangement. Summary answer OGM is an efficient method for cryptic chromosomal rearrangement detection. However, SVs near telomere and centromere regions could hardly be reported with this method. What is known already About 5∼10% infertility or sterility people carry balanced chromosomal structural variations (SVs) with high risks of miscarriage and birth defects resulting from imbalanced gametes when producing fetus. However, some balanced cryptic SVs with specific location or small fragments cannot be detected by traditional cytogenetic techniques like G-banding testing or CNV-seq. Currently, several optimized techniques are able to detect typically cryptic structural abnormality. OGM, the molecular genetic detection technique relying on new principle in recent years, have overcome the shortcomings of former techniques and are potentially capable to detect both routine and cryptic SVs well. Study design, size, duration From 2019 to 2022, 12 couples in The First Affiliated Hospital of Sun Yat-sen University and The First People’s Hospital of Yunnan Province with history of offspring birth defect, recurrent unexplained recurrent miscarriage or unexpected copy number variation in embryos from previous PGT cycles were included for diagnosis or re-analysis. Participants/materials, setting, methods Peripheral blood lymphocytes from these patients were collected and detected by OGM or traditional karyotype analysis(G-400 banding), FISH, CNV-seq, third generation sequencing(Nanopore). The results of traditional genetic test and OGM were compared to evaluate the accuracy of OGM detection of chromosomal structure vatiation. Main results and the role of chance In the 11 couples bearing adverse pregnancy or childbirth defect with normal karyotype by G-banding, OGM discovered novel chromosome translocations or inversion in 9 couples (81.81%). In 1 couple with t(4:17)(q12;p13) diagnosed by G-banding, OGM detect an additional chromosomal translocation of t(17;19)(q12;p13), which produced the repeated CNVs in chromosome19 observed in embryos from two previous PGT cycles. For small fragment translocation, terminal translocation and inversion, OGM is able to detected balanced structure abnormal of 500kbs. The OGM diagnosis were confirmed by FISH or third generation sequencing (Nanopore) or embryo mutation. The breaking position reported by OGM and Nanopore were comparable. In sum, OGM reported further information of balanced SVs in 83.33% (10/12) potential patients with duplication and depletion in embryos or abortus. Limitations, reasons for caution Due to the limitation of principle, the structural abnormalities of some special locations (centromere, secondary constriction, etc.) cannot be detected. OGM has high sensitivity and many mutations, which requires examiners to have strong ability to analyze results and genetic counseling. The price of OGM also limits the promotion and application. Wider implications of the findings OGM can provide more precious result for SVs, and PGT-SR can definitely improve the outcome of certain population with cryptic chromosomal rearrangements. The shortcoming of OGM has not been overcame yet, so it is suggested as auxiliary method beside conventional G-binding in certain circumstances in ART population. Trial registration number Not applicable

#5124 GENETIC GLOMERULAR DISEASES IN THE ADULT PATIENT: A WORK IN PROGRESS – SINGLE CENTRE COHORT

Abstract Background and Aims Recent advances in genetic molecular techniques have allowed the expansion of knowledge in glomerular diseases of genetic cause, including the identification of genes involved in focal and segmental glomerular sclerosis (FSGS). The prevalence of adult-onset genetic FSGS varies widely depending on the population studied. In central Europe, NPHS2 and COL4A3, COL4A4 e COL4A5 genes are postulated to be the most frequent genes implicated in genetic causes of adult FSGS. This study aims to characterize patients submitted to genetic study of glomerular diseases in the Nephrogenetics Clinic of our centre. Method We conducted a single-centre retrospective analysis of the patients submitted to genetic study of glomerular diseases in the Nephrogenetics Clinic of our centre from 2016 to 2022. Adult patients with a glomerular disease phenotype suggestive of a genetic cause were studied, using a predetermined phenotype-targeted panel of genes, through massive parallel sequencing. The number of genes included in this panel has increased (from 21 genes in 2016 to 49 genes since 2018); given this change, patients with a negative result on the first approach repeated screening with the broader panel. Additionally, patients presenting with advanced chronic kidney disease (CKD) without an identifiable phenotype, studied with a larger panel for CKD causing genes, are reported. In patients with a negative result but highly suggestive presentation, whole exome sequencing (WES) was considered, after multidisciplinary discussion with a Geneticist's evaluation. Patients with variants of unknown significance (VUS) were referred to a Genetics’ consultation for genetic counselling and segregation studies. Results Of the 80 patients studied (comprising 74 families), 52.5% were female (n=42) and 79% (n=63) of Caucasian ascent. Mean age was 45.4 ± 16.0 years. Nine patients were studied with the larger gene panel for CKD. 85% (n=68) had CKD (all stages) at presentation, with proteinuria (ranging from sub-nephrotic to nephrotic range) and 15% had asymptomatic urinary changes. 50% (n=40) of patients had positive family history, and 31% (n=25) had a syndromic presentation and/or extra renal manifestations. 27.5% (n=22) had a renal biopsy, and the most prevalent result was FSGS (11%; n=9). Genetic variants were identified in 70% (n=56) of the patients; but pathogenicity is not fully established in all: genotype-phenotype correlations, including inheritance pattern and histological correlation, and segregation studies (when indicated and possible) are ongoing. In 5 patients results are pending. Pathogenic / likely pathogenic variants were identified in at least 47.5% (n=38) patients. The most frequently implicated genes were: COL4A3, COL4A4 e COL4A5 (n=21), high risk APOL1 (n=8); NPSH2 (n=5), IFN2 (n=6, 3 pathogenic, 1 variant of unknown significance (VUS), 2 under segregation studies) and MYH9 (n=3). COL4A3, COL4A4 e COL4A5 mutations occur with Alport syndrome, but also with histologically documented FSGS, sub-nephrotic and nephrotic proteinuria, nephrotic syndrome and asymptomatic urinary changes. In our cohort, NPHS2 p.R229Q was identified in 5 patients (6%), but only with pathogenic significance in 3 patients, and APOL1 high risk haplotype was co-identified with COL4 variants in 3 patients. Conclusion The genetic study of a cohort of patients suspected of genetic FSGS allowed the identification of genetic variants in the genes of interest in a high percentage of cases. The most frequently implicated genes were COL4A3, COL4A4 e COL4A5, NPHS2, INF2 and APOL1 high risk haplotype. The high percentage of gene variants identified in our cohort is probably due to the selection of a population with a high likelihood of genetic FSGS. Further studies will clarify the causal and/or modifier effect of some genes, namely COL4A3, COL4A4 e COL4A5. The future use of WES in cases of high likelihood of genetic cause will probably allow the identification on novel candidate genes and increase the clinical benefits of a genetic diagnosis of FSGS.

Prenatal diagnosis and genetic analysis of a fetus with partial deletion of Yq and mosaicism of 45,X

To carry out prenatal diagnosis and genetic analysis for a fetus with disorders of sex development (DSDs). A fetus with DSDs who was identified at the Shenzhen People's Hospital in September 2021 was selected as the study subject. Combined molecular genetic techniques including quantitative fluorescence PCR (QF-PCR), multiplex ligation-dependent probe amplification (MLPA), chromosomal microarray analysis (CMA), quantitative real-time PCR (qPCR), as well as cytogenetic techniques such as karyotyping analysis and fluorescence in situ hybridization (FISH) were applied. Ultrasonography was used to observe the phenotype of sex development. Molecular genetic testing suggested that the fetus had mosaicism of Yq11.222qter deletion and X monosomy. Combined with the result of cytogenetic testing, its karyotype was determined as mos 45,X[34]/46,X,del(Y)(q11.222)[61]/47,X,del(Y)(q11.222),del(Y)(q11.222)[5]. Ultrasound examination suggested hypospadia, which was confirmed after elective abortion. Combined the results of genetic testing and phenotypic analysis, the fetus was ultimately diagnosed with DSDs. This study has applied a variety of genetic techniques and ultrasonography to diagnose a fetus with DSDs with a complex karyotype.

ИЗМЕНЕНИЯ МИКРОФЛОРЫ ПОЛОСТИ РТА И РАЗВИТИЕ ОРАЛЬНОГО МУКОЗИТА ПРИ ПРОВЕДЕНИИ СИСТЕМНОЙ ПРОТИВООПУХОЛЕВОЙ ТЕРАПИИ У БОЛЬНЫХ СО ЗЛОКАЧЕСТВЕННЫМИ НОВООБРАЗОВАНИЯМИ

This paper is devoted to the problem of the relationship between the oral microflora and oral mucositis (OM) induced by systemic anti-tumour therapy in patients with malignant neoplasms (MN). The paper covers current views on the composition of the normal oral microbiota and its changes during chemotherapeutic treatment. It is shown that normal oral microbiota includes representatives of such genera as Actinomyces, Corynebacterium, Fusobacterium, Leptotrichia, Neisseria, Prevotella, Streptococcus, Veillonella and others. It is emphasized that even despite the existence of modern molecular genetic techniques and the formation of a database of oral microbiota, it is still difficult to determine the role of individual taxonomic units in oral homeostasis. Existing studies of changes in the qualitative and quantitative composition of oral microflora against the background of anticancer therapy have demonstrated that treatment is associated with significant changes in the oral microbiological landscape, namely increasing the number of Gram-negative anaerobic opportunistic pathogenic flora and decreasing representation of protective commensal flora. It is demonstrated that bacterial cell components can modulate local macroorganism reaction through the system of Toll-like receptors, thus acting multidirectionally. A number of unresolved fundamental questions relating to the place of the oral microbiota in the pathogenesis of OM have also been highlighted.

Plants and Small Molecules: An Up-and-Coming Synergy.

The emergence of Arabidopsis thaliana as a model system has led to a rapid and wide improvement in molecular genetics techniques for studying gene function and regulation. However, there are still several drawbacks that cannot be easily solved with molecular genetic approaches, such as the study of unfriendly species, which are of increasing agronomic interest but are not easily transformed, thus are not prone to many molecular techniques. Chemical genetics represents a methodology able to fill this gap. Chemical genetics lies between chemistry and biology and relies on small molecules to phenocopy genetic mutations addressing specific targets. Advances in recent decades have greatly improved both target specificity and activity, expanding the application of this approach to any biological process. As for classical genetics, chemical genetics also proceeds with a forward or reverse approach depending on the nature of the study. In this review, we addressed this topic in the study of plant photomorphogenesis, stress responses and epigenetic processes. We have dealt with some cases of repurposing compounds whose activity has been previously proven in human cells and, conversely, studies where plants have been a tool for the characterization of small molecules. In addition, we delved into the chemical synthesis and improvement of some of the compounds described.

Role of FTL_0445 in Francisella tularensis Susceptibility to Resazurin

Tularemia is a potentially fatal disease caused by the Category A bioterrorism agent Francisella tularensis. Aminoglycosides, fluoroquinolones, and tetracyclines can be used to treat tularemia; however, there is a high incidence of relapse and treatment failures when using these drugs. Furthermore, there is no tularemia vaccine licensed for use in the United States. Therefore, new antibiotics that target F. tularensis are being investigated. A novel family of resazurin-based antibiotics called resazomycins exhibit antimicrobial activity against F. tularensis and other Gram-negative pathogens including Neisseria gonorrhoeae. The mode of action of resazomycins has yet to be determined. To elucidate potential targets of resazurin (Rz), we screened for spontaneous Rz-resistant (Rzr) F. tularensis LVS mutants. Through the screen, 93% of all Rzr mutants sequenced contained mutations within the coding regions of FTL_0421, FTL_0895, and FTL_1504. In addition, 100% of all Rzr mutants sequenced contained a mutation approximately 50bp upstream of the gene FTL_0445. To understand the effect the mutation has on transcription of FTL_0445, RNA was isolated from wild-type LVS and an Rzr mutant (Rzr1). Quantitative reverse transcription PCR revealed FTL_0445 was upregulated in Rzr1 compared to wild-type LVS. To determine the role of FTL_0445 in Rz resistance, a FTL_0445 null deletion mutant is being generated in Rzr1 using standard molecular genetic techniques. Upon completion, the Rz sensitivity of the deletion mutant will be assessed using agar dilution assays. Understanding the role of FTL_0445 in Rz susceptibility would facilitate further development of these compounds as potential treatments for tularemia and gonorrhea.

Molecular genetic surveillance based on the identification of borrelia in ixodid ticks

Aim. To improve emergency diagnostic measures and preventive antimicrobial therapy in patients with ixodid tick bites using molecular genetic techniques for identification of Вorrelia spp.Materials and Methods. Borrelia strains were isolated by inoculation of tick suspension on the BSK-H medium. Molecular genetic screening of Вorrelia spp. was performed by real-time polymerase chain reaction (PCR) and sequencing. In total, we examined 4,276 patients including 272 bitten by Ixodes persulcatus and 3,108 bitten by Dermacentor reticulatus. In addition, we investigated blood of 896 patients for molecular signatures of Borrelia spp.Results. Borrelia spp. was detected by PCR in 30.1% of Ixodes persulcatus and 3.2% of Dermacentor reticulatus suspensions. However, detection of Borrelia spp. in blood was rare, reaching only 1.1% in those bitten by Ixodes persulcatus and two cases of Dermacentor reticulatus bites. Genotyping of Borrelia spp. in 8 tick suspensions showed the presence of Borrelia garinii in 1 sample, Borrelia afzelii in 5 samples, Borrelia bavariensis in 1 sample, and Borrelia miyamotoi in 1 sample.Conclusion. Molecular genetic screening showed the significant proportion of Ixodid ticks bearing Borrelia spp., indicating the need in specific antimicrobial therapy.

Ethics in pre-ART genetics: a missed X-linked Menkes disease case

Assisted reproductive technology (ART) has experienced dramatic progress over the last 30 years, and gamete donation is routine in fertility clinics. Major advances in genetic diagnostics are part of this development due to the ability to analyze multiple genes or whole genomes fast and to an affordable prize. This requires knowledge and capability to evaluate genetic variants correctly in a clinical setting. Here we report a Menkes disease case, born after ART, where genetic screening and variant scoring failed to identify an egg donor as carrier of this fatal X-linked disorder. The gene variant is a deletion of a single base pair leading to a frameshift and premature termination of the protein, predicted to result in no or severely diminished function. The variant would be classified as likely pathogenic (class 4) and should be readily detectable by molecular genetic screening techniques. We wish to highlight this case to prevent future similar cases. IVI Igenomix has developed and embarked on an ambitious screening program to detect and prevent a large number of inherited severe childhood disorders in ART pregnancies. The company has recently achieved ISO 15189 certification with competence to evaluate and deliver timely, accurate, and reliable results. Failure to identify a pathogenic variant in the ATP7A gene leading to birth of two boys with Menkes disease invokes the required procedures to screen and detect disease-causing gene variants. This calls for ethical and legal considerations in ART diagnostics to prevent fatal errors like the present.

The Recent Advances in Molecular Diagnosis of Soft Tissue Tumors

Soft tissue tumors are rare mesenchymal tumors with divergent differentiation. The diagnosis of soft tissue tumors is challenging for pathologists owing to the diversity of tumor types and histological overlap among the tumor entities. Present-day understanding of the molecular pathogenesis of soft tissue tumors has rapidly increased with the development of molecular genetic techniques (e.g., next-generation sequencing). Additionally, immunohistochemical markers that serve as surrogate markers for recurrent translocations in soft tissue tumors have been developed. This review aims to provide an update on recently described molecular findings and relevant novel immunohistochemical markers in selected soft tissue tumors.

Natural selection differences detected in key protein domains between non-pathogenic and pathogenic feline coronavirus phenotypes.

Feline coronaviruses (FCoVs) commonly cause mild enteric infections in felines worldwide (termed feline enteric coronavirus [FECV]), with around 12 per cent developing into deadly feline infectious peritonitis (FIP; feline infectious peritonitis virus [FIPV]). Genomic differences between FECV and FIPV have been reported, yet the putative genotypic basis of the highly pathogenic phenotype remains unclear. Here, we used state-of-the-art molecular evolutionary genetic statistical techniques to identify and compare differences in natural selection pressure between FECV and FIPV sequences, as well as to identify FIPV- and FECV-specific signals of positive selection. We analyzed full-length FCoV protein coding genes thought to contain mutations associated with FIPV (Spike, ORF3abc, and ORF7ab). We identified two sites exhibiting differences in natural selection pressure between FECV and FIPV: one within the S1/S2 furin cleavage site (FCS) and the other within the fusion domain of Spike. We also found fifteen sites subject to positive selection associated with FIPV within Spike, eleven of which have not previously been suggested as possibly relevant to FIP development. These sites fall within Spike protein subdomains that participate in host cell receptor interaction, immune evasion, tropism shifts, host cellular entry, and viral escape. There were fourteen sites (twelve novel sites) within Spike under positive selection associated with the FECV phenotype, almost exclusively within the S1/S2 FCS and adjacent to C domain, along with a signal of relaxed selection in FIPV relative to FECV, suggesting that furin cleavage functionality may not be needed for FIPV. Positive selection inferred in ORF7b was associated with the FECV phenotype and included twenty-four positively selected sites, while ORF7b had signals of relaxed selection in FIPV. We found evidence of positive selection in ORF3c in FCoV-wide analyses, but no specific association with the FIPV or FECV phenotype. We hypothesize that some combination of mutations in FECV may contribute to FIP development, and that it is unlikely to be one singular 'switch' mutational event. This work expands our understanding of the complexities of FIP development and provides insights into how evolutionary forces may alter pathogenesis in coronavirus genomes.

DEGUM Recommendations on Diagnostic Puncture in Prenatal Medicine.

Diagnostic puncture (amniocentesis, chorionic villus sampling, and fetal blood sampling) is an essential part of prenatal diagnostics and the only established and sufficiently scientifically evaluated possibility of diagnosing genetic diseases from pregnancy-specific cells. The number of diagnostic punctures in Germany, as in other countries, has fallen significantly. This is largely due to the introduction of first-trimester screening with further detailed ultrasound examination of the fetus and the analysis of cf-DNA (cell-free DNA) from maternal blood (noninvasive prenatal test - NIPT). On the other hand, knowledge about the incidence and appearance of genetic diseases has increased. The development of modern molecular genetic techniques (microarray and exome analysis) makes a differentiated investigation of these diseases increasingly possible. The requirements for education and counseling regarding these complex correlations have thus increased. The studies performed in recent years make it clear that diagnostic puncture performed in expert centers is associated with a low risk of complications. In particular, the procedure-related miscarriage risk hardly differs from the background risk for spontaneous abortion. In 2013, the Section of Gynecology and Obstetrics of the German Society for Ultrasound in Medicine (DEGUM) published recommendations on diagnostic puncture in prenatal medicine 1. The developments described above and new findings in recent years make it necessary to revise and reformulate these recommendations. The aim of this review is to compile important and current facts regarding prenatal medical puncture (including technique, complications, genetic examinations). It is intended to provide basic, comprehensive, and up-to-date information on diagnostic puncture in prenatal medicine. It replaces the publication from 2013 1.

Quality analysis of genomic DNA and authentication of fisheries products based on distinct methods of DNA extraction.

Molecular genetic techniques are an effective monitoring tool, but high-quality DNA samples are usually required. In this study, we compared three different protocols of DNA extraction: NaCl (saline); phenol-chloroform and commercial kit (Promega)-from three biological tissues of five individuals of Lutjanus purpureus under two methods of storage. The evaluated items included DNA concentration and purity, processing time and cost, as well as the obtaining of functional sequences. The highest average values of DNA concentration were obtained using the saline procedure and the commercial kit. Pure DNA was only obtained using the saline protocol, evaluated by the ratio of 260/280. The saline and phenol-chloroform protocols were the least expensive methods. The commercial kit costs are counterbalanced by the short time required. The procedure based on phenol-chloroform presented the worst results regarding DNA yield and the time required to perform all steps. The saline and commercial kit protocols showed similar results concerning the amount and quality of extracted DNA. Therefore, the final choice should be based on the available financial resources and the available time for carrying out each procedure of DNA extraction.