Sanger Sequencing Method Research Articles

Cracking the code: Can forensic genetics distinguish identical twins? A technical perspective

DNA fingerprinting has revolutionized the field of forensic investigation in recent times. The utility of DNA fingerprinting technology in differentiating between monozygotic twins has always been an area of academic interest for researchers. While traditional chiral fingerprinting effectively differentiates monozygotic twins, situations may arise where the absence of conventional fingerprints at a crime scene necessitates DNA analysis for conclusive identification. Although Short Tandem Repeats (STR) profiling is of not much help in that case, monozygotic twins can still be differentiated using current advancements in the field of forensic genetics. The methods that can help discriminate between identical twins are mitochondrial genome (mtGenome) analysis, Single Nucleotide Polymorphism (SNP) profiling, Epigenetic profiling (DNA methylation profiling), Copy Number Variants (CNV) profiling, and studying Single Nucleotide Variants (SNV) in the genetic material by traditional sequencing methods like sanger sequencing or advanced methods like Whole Genome Sequencing (WGS). In conclusion, these alternative methods may be able to distinguish between monozygotic twins, but they also have drawbacks that must be considered when using them in real-world crime investigations. To establish their accuracy, dependability, and application in forensic situations, more study, validation, and standardization are required. A combination strategy will strengthen the case and lessen the fallacy of individual profiling methods.

Seeking the identity of an enigmatic moss by embracing phylogenomics

AbstractCurrently, a wide range of genomic techniques is available at a relatively affordable price. However, not all of them have been equally explored in bryophyte systematics. In the present study, we apply next‐generation sequencing to identify samples that cannot be assigned to a taxon by morphological analysis or by Sanger sequencing methods. These samples correspond to a moss with an enigmatic morphology that has been found throughout Western Europe over the last two decades. They exhibit several anomalies in the gametophyte and, on the rare occasions that they appear, also in the sporophyte. The most significant alterations are related to the shape of the leaves. Morphologically, all specimens correspond to mosses of the genus Lewinskya, and the least modified samples are potentially attributable to the Lewinskya affinis complex. Specimen identifications were first attempted using up to seven molecular markers with no satisfactory results. Thus, we employed data generated from targeted enrichment using the GoFlag 408 flagellate land plant probe set to elucidate their identity. Our results demonstrate that all the enigmatic samples correspond to a single species, L. affinis s.str. This approach provided the necessary resolution to confidently identify these challenging samples and may be a powerful tool for similar cases, especially in bryophytes.

Different effects of crizotinib treatment in two non-small cell lung cancer patients with SDC4::ROS1 fusion variants.

The possibility of stratifying patients according to differences in ROS proto-oncogene 1 (ROS1) fusion partners has been discussed. This study aimed to clarify the clinicopathological differences between two SDC4::ROS1 positive NSCLC cases who had different responses to crizotinib. Cytology and pathology samples from two NSCLC cases with SDC4::ROS1 who were diagnosed and treated with crizotinib at Nihon University Itabashi Hospital were obtained. Case 1 has been well-controlled with crizotinib for over 5 years, but case 2 was worse and overall survival was 19 months. Sequencing analysis of ROS1 fusion genes was performed by reverse-transcription-PCR and Sanger's sequencing methods. In addition, thyroid transcription factor (TTF)-1, ROS-1, Ki67, and phosphorylated extracellular signal-regulated kinase (pERK)1/2 expression were investigated using immunohistochemistry. Sequencing analysis showed SDC4 exon2::ROS1 exon 32 (exon33 deleted) in case 1, and coexistence of SDC4 exon2::ROS1 exon 34 and SDC4 exon2::ROS1 exon35 in case 2. The Ki67 index was not different, but ROS1 and pERK1/2 expression levels tended to be higher in the tumor cells of case 2 than in case 1. Therapeutic response to crizotinib and patients' prognosis in ROS1 rearranged NSCLC may be related to the activation of ROS1 signaling, depending on ROS1 and pERK1/2 overexpression status, even if the ROS1 fusion partner is the same.

HIV-1 Vif protein sequence variations in South African people living with HIV and their influence on Vif-APOBEC3G interaction

PurposeDespite extensive research, HIV-1 remains a global epidemic with variations in pathogenesis across regions and subtypes. The Viral Infectivity Factor (Vif) protein, which neutralizes the host protein APOBEC3G, has been implicated in differences in clinical outcomes among people living with HIV (PLHIV). Most studies on Vif sequence diversity have focused on subtype B, leaving gaps in understanding Vif variations in HIV-1C regions like South Africa. This study aimed to identify and compare Vif sequence diversity in a cohort of 51 South African PLHIV and other HIV-1C prevalent regions.MethodsSanger sequencing was used for Vif analysis in the cohort, and additional sequences were obtained from the Los Alamos database. Molecular modeling and docking techniques were employed to study the influence of subtype-specific variants on Vif-APOBEC3G binding affinity.ResultsThe findings showed distinct genetic variations between Vif sequences from India and Uganda, while South African sequences had wider distribution and closer relatedness to both. Specific amino acid substitutions in Vif were associated with geographic groups. Molecular modeling and docking analyses consistently identified specific residues (ARGR19, LYS26, TYR30, TYR44, and TRP79) as primary contributors to intermolecular contacts between Vif and APOBEC3G, essential for their interaction. The Indian Vif variant exhibited the highest predicted binding affinity to APOBEC3G among the studied groups.ConclusionsThese results provide insights into Vif sequence diversity in HIV-1C prevalent regions and shed light on differential pathogenesis observed in different geographical areas. The identified Vif amino acid residues warrant further investigation for their diagnostic, prognostic, and therapeutic potential.

Analysis of perrault syndrome caused by pathogenic variants in LARS2 and HARS2 genes

Objective: To investigate the molecular etiology of Perrault syndrome by analyzing the clinical phenotype and pathogenic gene variants of 2 male patients with bilateral severe sensorineural deafness. Methods: Two male patients with Perrault syndrome characterized by severe sensonrineual deafness adimitted to the First Affiliated Hospital of Zhengzhou University between February 2021 and March 2022 were selected, and the clinical phenotype and pathogenic gene variants of them and their family members were summarized. The whole exome sequencing technology was used to screen the pathogenic variants of the probands, and the candidate variants were determined by combining with clinical phenotype. The probands and their family members were verified by the Sanger sequencing method. Results: The whole exome sequencing results showed that the proband of family 1 had a compound heterozygous variants of the LARS2 (NM_015340.4) gene c.1565C>A (p.Thr522Asn) and c.1079T>C (p.Ile360Thr). The reported pathogenic variant c.1565C>A came from the mother, and the novel variant c.1079T>C came from the father. The second proband harbored compound heterozygous variants of HARS2 gene (NM_012208.4) c.1273C>T (p.Arg425Trp) and c.1403G>C (p.Gly468Ala), with the former from the proband's mother, the latter from the father. The c.1273C>T was novel and c.1403G>C was the reported pathogenic variant. All above variants were respectively classified as pathogenic, uncertain significance, uncertain significance and likely pathogenic based on the ACMG guidelines. Conclusion: This study expands the mutational spectrum of LARS2 and HARS2 genes, which highlights that genetic testing plays an important role in the early diagnosis of syndromic deafness.

Newborn Genetic Screening-Still a Role for Sanger Sequencing in the Era of NGS.

In the Norwegian newborn screening (NBS) program, genetic testing has been implemented as a second or third tier method for the majority of NBS disorders, significantly increasing positive predictive value (PPV). DNA is extracted from dried blood spot (DBS) filter cards. For monogenic disorders caused by variants in one single gene or a few genes only, Sanger sequencing has been shown to be the most time- and cost-efficient method to use. Here, we present the Sanger sequencing method, including primer sequences and the genetic test algorithms, currently used in the Norwegian newborn screening program.

Physiological and pathological 3R and 4R tau expression in marmoset brain

AbstractBackgroundCommon marmosets (Callithrix jacchus) have recently emerged as an important model for studying aging and neurodegenerative disorders, including Alzheimer’s disease (AD). Amyloid‐β deposits in the cerebral cortex of marmosets present naturally with aging, which has now been widely reported. However, the role of tau in the marmoset brain has been understudied. The purpose of the present studies was to comprehensively examine 3R and 4R tau isoform expression in the marmoset brain.MethodsThe mRNA expression in the marmoset brain was confirmed by RT‐PCR. The total mRNA was isolated from frozen tissue of various age groups and reverse transcribed to cDNA, which was used for RT‐PCR. The sequence of each fragment was confirmed by the Sanger sequencing method. The tau protein expression in Sarkosyl soluble and insoluble fractions was examined by western blot using tau‐specific antibodies, and expression levels of 3R/4R were quantified by Dot blot. Synaptic tau expression was analyzed from crude synaptosome extractions of the frontal cortex. Pathological tau aggregates in cryo‐slices of a 10‐year‐old marmoset brain were visualized by immunohistochemistry.Results3R and 4R tau were expressed in the marmoset brain, with 3R tau predominately expressed in neonatal brains and 4R tau in adult/aged brains. 3R and 4R tau were also localized in synaptic regions of the frontal cortex. The Sarkosyl soluble tau was phosphorylated on T181, T217, and T231 sites with evidence of oligomers. Insoluble tau was phosphorylated on S396/S404 and S202/S205 sites and contained high molecular weight aggregates comprising 3R and 4R tau. Moreover, a 10‐year‐old marmoset brain case study demonstrated a paired helical filament structure in the hippocampus and intracellular 3R and 4R tau accumulation.ConclusionsOur results reveal physiological and pathological 3R/4R tau distributions in the frontal and temporal cortex of the marmoset brain, confirming the presence of 3R tau and AD‐like pathological tau in aging marmosets. These data support the utility of common marmosets as appropriate models for studying AD and neurodegenerative disorders.

Complete Plastid Genomes of Nine Species of Ranunculeae (Ranunculaceae) and Their Phylogenetic Inferences.

The tribe Ranunculeae, Ranunculaceae, comprising 19 genera widely distributed all over the world. Although a large number of Sanger sequencing-based molecular phylogenetic studies have been published, very few studies have been performed on using genomic data to infer phylogenetic relationships within Ranunculeae. In this study, the complete plastid genomes of nine species (eleven samples) from Ceratocephala, Halerpestes, and Ranunculus were de novo assembled using a next-generation sequencing method. Previously published plastomes of Oxygraphis and other related genera of the family were downloaded from GenBank for comparative analysis. The complete plastome of each Ranunculeae species has 112 genes in total, including 78 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. The plastome structure of Ranunculeae samples is conserved in gene order and arrangement. There are no inverted repeat (IR) region expansions and only one IR contraction was found in the tested samples. This study also compared plastome sequences across all the samples in gene collinearity, codon usage, RNA editing sites, nucleotide variability, simple sequence repeats, and positive selection sites. Phylogeny of the available Ranunculeae species was inferred by the plastome data using maximum-likelihood and Bayesian inference methods, and data partitioning strategies were tested. The phylogenetic relationships were better resolved compared to previous studies based on Sanger sequencing methods, showing the potential value of the plastome data in inferring the phylogeny of the tribe.

Phylodynamic characteristics of the LMP-1 gene of the Epstein–Barr virus isolated in the Nizhny Novgorod region

Introduction. Epstein–Barr virus (EBV) is one of the most common herpesviruses and has a pronounced genetic polymorphism. The study of the phylodynamic characteristics of the virus is an important aspect of the study of evolutionary changes in the LMP-1 gene and their consequences.
 The aim of the work was a philodynamic analysis of EBV isolates from Nizhny Novgorod region based on the C-terminal fragment of the LMP-1 gene.
 Materials and methods. The study included 158 EBV isolates obtained from blood leukocytes and saliva of children aged 1–17 years with a diagnosis of infectious mononucleosis caused by EBV (n = 68) and apparently healthy children of comparable sex and age (n = 29). LMP-1 genovariants were obtained using the Sanger sequencing method. Comparative analysis of amino acid sequences was performed using the MEGA X program. Philodynamic analysis of the obtained nucleotide sequences and isolates deposited in GenBank was carried out using the BEAST v. 1.10.4 software package. Recombination analysis was performed using the Simplot program.
 Results. 158 nucleotide sequences of the C-terminal fragment of the LMP-1 gene from Nizhny Novgorod region EBV isolates were obtained and deposited in the GenBank database. The circulation time of the nearest common ancestor for the modified B95-8 genovariants with G212S + E328Q + S366T and NC mutations with the D250N substitution has been established dating back to 1994 and 1923. The rate of evolution of these genovariants was the highest and amounted to 1.298 × 10–4 and 7.868 × 10–4 nucleotide substitutions/site/year. Recombinations were detected in the Nizhny Novgorod region sequences Med-, B95-8, China 1 with mutations G212S, G212S, E214Q, respectively.
 Conclusion. For the first time, a phylodynamic characterization of Nizhny Novgorod region isolates and LMP-1 EBV genovariants isolated in various regions of the world is given. The data obtained expand the existing understanding of the circulation of EBV LMP-1 genovariants in the territory of the European part of Russia.

Genetic Screening of a New Transgenic Mouse Line Humanized for <i>HLA-A*02:01:01:01</i> and <i>hβ2m</i>

The development of new humanized transgenic mouse biomodels with the HLA-A*02:01:01:01 gene requires effective methods for target transgene verification in the animal genome. In the present study, we develop a system for genetic screening of animals based on real-time PCR and using highly specific primers to detect all functionally significant parts of the genetic construct. In addition, the Sanger sequencing method showed the absence of chimerism and complete correspondence between the primary nucleotide sequence of the HLA A*02:01:01:01 transgene and the developed engineered genetic construct and human gene HLA A*02:01:01:01. Based on the results of selection and genetic works with the resulting transgenic animals, three most promising sublines were identified. These lines are currently used for breeding a new line of humanized transgenic mice with the HLA-A*02:01:01:01 gene.

The complete mitochondrial genome of Semiothisa cinerearia Bremer & Grey 1853 (Lepidoptera: Geometridae: Ennominae) and its phylogenetic analysis

Semiothisa cinerearia Bremer & Grey, 1853 belongs to the lepidopteran family Geometridae, subfamily Ennominae. We sequenced the complete mitochondrial genome of S. cinerearia by PCR and Sanger sequencing method. The mitochondrial genome of S. cinerearia is 15,523 bp in length and contains a typical set of 37 genes with ‘MIQ’ type gene arrangement and a 394 bp AT-rich regions. Except for cox1 using CGA as initiation codon, all protein-coding genes (PCGs) start with ATN codons and except for nad2 and nad4l using TAG as termination codon, all PCGs terminated with TAA codon. A phylogenetic tree including 39 genus of subfamily Ennominae was first reconstructed based on the mitochondrial genome sequences with nucleotide substitution model GTR + G + I, which showed that the genera Amraica, Jankowskia, and Ectropis are not monophyletic and S. cinerearia and Macaria notata are classified together.

Analysis of Multiple PCR Bands in Drimia Species Obtained by R-Gene Specific Degenerate Primers

Many studies confirmed that degenerate primers LM638 and LM637 amplify NBS-LRR Type R gene encoding sequences in both monocots and dicots. In addition, these primers also amplify nonspecific multiple bands along with specific amplification. The current study aims to explore the structure, role and reason for nonspecific bands in the amplification. The genomic DNA-degenerate PCR method was used to isolate the NBS-LRR type R-genes in Drimia species (synonym Urginea). Agarose gel electrophoresis was carried out for separation and visualization of amplified bands. The kit-based gel extraction method was followed to purify the PCR bands. Purified PCR bands were subjected to TA cloning. The plasmids which contain desired PCR bands were sequenced using the Sanger sequencing method. Multiple sequence alignment tool CLUSTALW was used to align sequences and MISA-Web tool was used to identify simple sequence repeats (SSR). The results of the study revealed that multiple sequence analysis of PCR bands of 600bp/500bp showed random deletions, presence of indels and frameshift mutations in the alignment. The sequence alignment also showed monomorphic sites between two sequences. Both 600 and 500bp were devoid of simple sequence repeats and the ORF finder confirmed the presence of irregular stop codons in the 600 bp sequences. The multiple sequence alignment tool was used in disclosing the structure and ancestor relationship between aligned Drimia sequences. The current study would help to explore pseudo genes in the genome of Drimia and to differentiate the orthologous and paralogous relationships in the sequences.

Human Papillomavirus genotypes distribution and associated risk factors among women living in Southern Morocco

PurposeThe aim of this work was to investigate potential risk factors associated with HPV infection and to determine the HPV genotype prevalence among women from the Southerns areas of Morocco. MethodsA total of n = 308 sexually active women provided their written consent to participate in this study. A detailed questionnaire was used to collect data, related to the age and life style of participants. HPV L1 gene detection was performed by a nested PCR method using consensus primers. HPV genotypes were determined using direct Sanger sequencing method. Statistical analysis of the results obtained was carried out using R software. ResultsWe detected HPV in 42.5 % of the total investigated samples. HPV infection was significantly associated with the following risk factors: age of the first intercourse (OR = 2.27, 95 % CI: 1.03–5.10, p = 0.044), and previous history of STIs (OR = 3.13, 95 % CI: 1.12–9.63, p = 0.034). High risk-HPV and Low risk-HPV genotypes were found in 26.6 % and 5.5 % of the participants, respectively. The most prevalent genotypes were HPV16 (22 %), HPV18 (2.6 %), HPV11 (1.6 %) and HPV83 (1.3 %). Multiple infections were found in 3.2 %. The genotypes covered by the bivalent, quadrivalent and nonavalent HPV vaccines account for 57.5 %, 62.8 % and 66.6 %, respectively. ConclusionHPV infection prevalence reported in this study among women from the Southerns areas of Morocco is one of the highest reported in the country so far. Our finding confirm that the current HPV vaccines directed against the most prevalent HPV16 genotype, recently introduced in the country, should offer a good protection to the most vulnerable population if implemented properly. These results highlight the importance of HPV screening and vaccination programs in this region.

Detection of Immune Escape and Basal Core Promoter/Precore Gene Mutations in Hepatitis B Virus Isolated from Asymptomatic Hospital Attendees in Two Southwestern States in Nigeria.

Several mutations in the surface (S), basal core promoter (BCP), and precore (PC) genes of the hepatitis B virus have been linked to inaccurate diagnosis and the development of immune escape mutants (IEMs) of the infection, which can lead to chronic infection. Understanding the prevalence and spread of these mutations is critical in the global effort to eliminate HBV. Blood samples were collected from 410 people in Osun and Ekiti states, southwest Nigeria, between 2019 and 2021. Participants were drawn from a group of asymptomatic people who were either blood donors, outpatients, or antenatal patients with no record of HBV infection at the medical outpatients' unit of the hospital. DNA was extracted from plasma using a Qiagen DNEasy kit, followed by nested PCR targeting HBV S and BCP/PC genes. The Sanger sequencing method was used to sequence the positive PCR amplicons, which were further analyzed for IEMs, BCP, and PC mutations. HBV-DNA was detected in 12.4% (51/410) of individuals. After DNA amplification and purification, 47.1% (24) of the S gene and 76.5% (39) of the BCP/PC gene amplicons were successfully sequenced. Phylogenetic analysis showed that all the HBV sequences obtained in this study were classified as HBV genotype E. Mutational analysis of the major hydrophilic region (MHR) and a-determinant domain of S gene sequences revealed the presence of three immune escape mutations: two samples harbored a T116N substitution, six samples had heterogenous D144A/N/S/H substitution, and one sample had a G145E substitution, respectively. The BCP/PC region analysis revealed a preponderance of major BCP mutants, with the prevalence of BCP double substitutions ranging from 38.5% (A1762T) to 43.6% (G1764A). Previously reported classical PC mutant variants were observed in high proportion, including G1896A (33.3%) and G1899A (12.8%) mutations. This study confirms the strong presence of HBV genotype E in Nigeria, the ongoing circulation of HBV IEMs, and a high prevalence of BCP/PC mutants in the cohorts. This has implications for diagnosis and vaccine efficacy for efficient management and control of HBV in the country.

Determination of The GALT Gene in Galactosemic Cataract Patients in Azerbaijan

Galactosemia is one of the genetic diseases that can be treated thanks to early detection by genetic screening test. Galactosemia is a hereditary metabolic disease. This disease is heterogeneous and controlled by GALT, GALK, GALE and GALM genes. The presented article is dedicated to galactosemic disease among Azerbaijani patients as a result of GALT (galactose-1-phosphate uridyltransferase) gene mutations. This study reviews discusses the type of cataracts associated with galactosemia. The genetics of galactosemic patients are evaluated and details of galactose metabolism are described. This study describes the results of the GALT gene analysis of two Azerbaijanian patients with Galactosemic cataract. In one of the patients the heterzygous form of the same mutation, and the homozygous form in the other patient were found. In this study, control and experimental groups were determined, and DNA extracted from the peripheral blood of patients belonging to both groups was subjected to PCR amplification according to standard protocols and sequenced by Sanger sequence method. The symptoms of the disease were reviewed in these patients. Patients presented with jaundice, diarrhea, vomiting, malnutrition, seizures, allergies and more cataracts in the neonatal period. Commonly, Cataract disease is idiopathic origin. Also, patients with cataracts may have an underlying genetic abnormality of galactose metabolism. Elevated levels of galactose and galactose-1-phosphate and absence of GALT activity were diagnosed in the studied patients. Early biochemical and molecular-genetic diagnosis and genetic counseling of patients and their family members are extremely important in the treatment of galactosemia. We selected 25 cataract patients aged 0-45 years and 25 age and sex-matched controls for the study. Blood samples taken from the experimental and control groups, were biochemically and then molecular-genetically analyzed. Mutations Q188R, K285N and N314D were investigated in patients. Of these mutations, only the N314D mutation was detected in two patients. Both heterozygous and homozygous forms of N314D mutation were detected.

Mutational analysis of FOLR1 and FOLR2 genes in children with Myelomeningocele.

Myelomeningocele (MMC) is a congenital disease. For a long time, molecular mechanism of MMC, the role of folate receptor and transporter proteins remain unclear. Folate from maternal lumen to developing embryo is carried out with the help of folate transporters (SLC46A1, SLC19A1, FOLH1 and SLC25A32) and folate receptor (FOLR1, FOLR2 and FOLR3). Due to the loss of function of these important genes, complications can facilitate the risk of MMC. This study focused on the mutational analysis of FOLR1 and FOLR2 genes in children suffering from MMC. Myelomeningocele is a rare disorder so twenty blood samples from the children were collected. Primers of selected exons for FOLR1 and FOLR2 genes were designed with the help of PrimerFox software. Extracted DNA was amplified, and PCR based mutational analysis was done to check any type of mutation/SNPs in these genes. Sanger sequencing method was performed to confirm mutation in FOLR1 and FOLR2 genes. The results showed that certain environmental factors (smoking, low socio-economic status of mother bearing MMC fetus) were found to be significantly (P<0.05) associated with MMC but no mutation in the selected exons of FOLR1 and FOLR2 genes was detected. Thus, genetic variations in the folate transporter gene may have no role in the progression of MMC in the studied population.

Design and use of a new primer pair for the characterization of the cyanobacteria Synechococcus and Prochlorococcus communities targeting petB gene through metabarcoding approaches

During the last years, the application of next-generation sequencing (NGS) technologies to search for specific genetic markers has become a crucial method for the characterization of microbial communities. Illumina MiSeq, likely the most widespread NGS platform for metabarcoding experiments and taxonomic classification, allows processing shorter reads than the classical SANGER sequencing method and therefore requires specific primer pairs that produce shorter amplicons. Specifically, for the analysis of the commonly studied Prochlorococcus and Synechococcus communities, the petB marker gene has recently stood out as able to provide deep coverage to determine the microdiversity of the community. However, current petB primer set produce a 597 bp amplicon that is not suitable for MiSeq chemistry.Here, we designed and tested a petB primer pair that targets both Prochlorococcus and Synechococcus communities producing an appropriate amplicon to be used with state-of-the-art Illumina MiSeq. This new primer set allows the classification of both groups to a low taxonomic level and is therefore suitable for high throughput experiments using MiSeq technologies, therefore constituting a useful, novel tool to facilitate further studies on Prochlorococcus and Synechococcus communities.•This work describes the de novo design of a Prochlorococcus and Synechococcus-specific petB primer pair, allowing the characterization of both populations to a low taxonomic level.•This primer pair is suitable for widespread Illumina MiSeq sequencing technologies.•petB was confirmed as an adequate target for the characterization of both picocyanobacteria.

NGS study in a sicilian case series with a genetic diagnosis for Gerstmann-Sträussler-Scheinker syndrome (PRNP, p.P102L).

Gerstmann Sträussler Scheinker (GSS) is an inherited, invariably fatal prion disease. Like other human prion diseases, GSS is caused by missense mutations in the prion protein (PrP) gene (PRNP), and by the formation and overtime accumulation of the misfolded, pathogenic scrapie PrP (PrPSc). The first mutation identified in the PRNP gene, and the one blamed as the main cause of the disease, is c.C305T:p.P102L. The Sanger sequencing method was performed on the PRNP gene for the detection of c.C305T:p.P102L mutations in a cohort of 10 subjects; moreover, a study was carried out, using Next Generation Sequencing (NGS), by sequencing a group of genes related to amyotrophic lateral sclerosis (ALS), Alzheimer's disease (AD), movement disorders and dementia which show a phenotypic profile similar to that of GSS. The results obtained from the study using NGS indicate the potential role of other genetic variants which could contribute to the various GSS phenotypes. In conclusion, we highlight the large clinical variability in subjects presenting with GSS and p.P102L, as well as the hypothesis that the mutation in PrP codon 102 alone is not sufficient to trigger the cardinal clinical signs of the disease; furthermore, we do not exclude the possibility that further genetic variants play a decisive role in the aspects of the various phenotypes with which GSS manifests itself.

Metabolically Active Microbial Communities in Oilfields: A Systematic Review and Synthesis of RNA Preservation, Extraction, and Sequencing Methods

Characterizing metabolically active microorganisms using RNA-based methods is a crucial tool for monitoring and mitigating operational issues, such as oil biodegradation and biocorrosion of pipelines in the oil and gas industry. Our review, a pioneering study, addresses the main methods used to preserve, isolate, and sequence RNA from oilfield samples and describes the most abundant metabolically active genera studied. Using the MEDLINE/PubMed, PubMed Central, Scopus, and Web of Science databases, 2.561 potentially eligible records were identified. After screening, 20 studies were included in our review, underscoring the scarcity of studies related to the subject. Data were extracted and reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA). These studies evaluated different samples, including produced water (PW), injection water (IW), solid deposits (SD), oil (OIL), and oily sludge (OS) collected from oilfields located in Australia, China, India, Mexico, and the United Arab Emirates. Environmental samples accounted for 55% of the studies, while enriched cultures and microbial consortia represented 35% and 15% of studies, respectively. PW was the most frequently studied sample, comprising 72% of all samples. Filtration and centrifugation were the only processes employed to concentrate the biomass present in samples. For RNA preservation, the most used method was a solution composed of 95:5 v/v ethanol/TRIzol, while for RNA isolation, the TRIzol reagent was the most cited. The Sanger sequencing method was used in all studies evaluating functional genes (alkB, dsrA, aprA, assA, and mcrA), and the Next-Generation Sequencing (NGS) method was employed in studies for sequencing transcripts of the 16S rRNA gene and metatranscriptomes. Pseudomonas (16S rRNA = PW: 2%; IW: 8%; metatranscriptome = PW: 20%) and Acinetobacter (16S rRNA = PW: 1%; IW: 4%; metatranscriptome = PW: 17%) were the most abundant genera. This study outlined the primary methods employed in researching metabolically active microorganisms. These data provide a foundation for future research. However, it is essential to note that we cannot yet determine the most effective method. We hope that this study will inspire further research related to the standardization of RNA preservation, extraction, and sequencing methods and significantly contribute to our understanding of active microbial communities in oilfields.

CRISPR/Cas9-Induced Fam83h Knock-out Leads to Impaired Wnt/β-Catenin Pathway and Altered Expression of Tooth Mineralization Genes in Mice.

Dental enamel formation is a complex process that is regulated by various genes. One such gene, Family With Sequence Similarity 83 Member H (Fam83h), has been identified as an essential factor for dental enamel formation. Additionally, Fam83h has been found to be potentially linked to the Wnt/β-catenin pathway. This study aimed to investigate the effects of the Fam83h knockout gene on mineralization and formation of teeth, along with mediators of the Wnt/β-catenin pathway as a development aspect in mice. To confirm the Fam83h-KnockOut mice, both Sanger sequencing and Western blot methods were used. then used qPCR to measure the expression levels of genes related to tooth mineralization and formation of dental root, including Fam20a, Dspp, Dmp1, Enam, Ambn, Sppl2a, Mmp20, and Wnt/β-catenin pathway mediators, in both the Fam83h-Knockout and wild-type mice at 5, 11 and 18 days of age. also the expression level of Fgf10 and mediators of the Wnt/β-catenin pathway was measured in the skin of both Knockout and wild-type mice using qPCR. A histological assessment was then performed to further investigate the results. A significant reduction in the expression levels of Ambn, Mmp20, Dspp, and Fgf10 in the dental root of Fam83h-Knockout mice compared to their wild-type counterparts was demonstrated by our results, indicating potential disruptions in tooth development. Significant down-regulation of CK1a, CK1e, and β-catenin in the dental root of Fam83h-Knockout mice was associated with a reduction in mineralization and formation-related gene. Additionally, the skin analysis of Fam83h-Knockout mice revealed reduced levels of Fgf10, CK1a, CK1e, and β-catenin. Further histological assessment confirmed that the concurrent reduction of Fgf10 expression level and Wnt/β-catenin genes were associated with alterations in hair follicle maturation. The concurrent reduction in the expression level of both Wnt/β-catenin mediators and mineralization-related genes, resulting in the disruption of dental mineralization and formation, was caused by the deficiency of Fam83h. Our findings suggest a cumulative effect and multi-factorial interplay between Fam83h, Wnt/Β-Catenin signaling, and dental mineralization-related genes subsequently, during the dental formation process.