Common Molecular Markers Research Articles

Shared biological features between ovarian cancer and endometriosis based on co-expression networks analysis

Background: Endometriosis is a gynecologic disease common among younger females, impacts adversely the quality of life, and results in infertility. The evidence demonstrates that patients with endometriosis have a higher risk of developing ovarian cancer. Due to this similarity, we aimed to identify common molecular markers between ovarian cancer and endometriosis. Methods: We used publicly available microarray data (GSE9899) including ovarian tumor samples and alongside normal controls, common differentially expressed genes (DEGs) were identified in ovarian samples compared to controls. We constructed a co-expression network based on ovarian cancer and then extracted the hub genes. We validated the similarities between ovarian cancer and endometriosis by examining the expression of hub genes in endometriosis patients referred to Iranian Rasoul Akram Hospital. Results: In total 1000 DEGs were identified in grade 2 and grade 3 of ovarian cancer. We identified 34 co-expression modules in grade 3 ovarian cancer and 31 in grade 2. Modules were mostly enriched in inflammatory response and plasma membrane-bounded cell projection, mostly. To validate the comorbidity of ovarian cancer and endometriosis, we examined the expression of six significant hubs (resulting in an ovarian cancer co-expression network) in women with endometriosis. Conclusion: Our results suggest that patients with endometriosis have a higher risk of developing ovarian cancer. These findings will improve the diagnosis of ovarian cancer in endometriosis patients. More research is required to find the exact mechanism of hub genes affecting the development of ovarian cancer.

Screening of Genes Co-Associated with Sudden Infant Death Syndrome and Infectious Sudden Death in Infancy and Bioinformatics Analysis of Their Regulatory Networks.

The common differentially expressed mRNAs in brain, heart and liver tissues of deceased sudden infant death syndrome (SIDS) and infectious sudden death in infancy (ISDI) confirmed by autopsy was screened by bioinformatics to explore the common molecular markers and pathogenesis of SIDS and ISDI. The datasets of GSE70422 and GSE136992 were downloaded, the limma of R software was used to screen differentially expressed mRNA in different tissue samples of SIDS and ISDI decedents for overlapping analysis. The clusterProfiler of R software was used to conduct gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The protein-protein interaction (PPI) network was constructed by STRING database, while the hub gene was screened by cytoHubba plug-in. Compared with the control group, there were 19 significant differentially expressed genes in the tissue samples of SIDS and ISDI decedents, among which 16 in the heart tissue and 3 in the liver tissue, and the astrotactin 1 (ASTN1) gene expression difference in the heart tissue was most significant. The PPI network identified Ras homolog family member A (RHOA), integrin subunit alpha 1 (ITGA1), and H2B clustered histone 5 (H2BC5) were hub genes. The analysis of GO and KEGG showed that differentially expressed genes were enriched in the molecular pathways of actin cytoskeleton regulation, focal adhesion and response to mycophenolic acid. ASTN1, RHOA and ITGA1 may participate in the development of SIDS and ISDI. The enrichment of differentially expressed genes in immune and inflammatory pathways suggests a common molecular regulatory mechanism between SIDS and ISDI. These findings are expected to provide new biomarkers for molecular anatomy and forensic identification of SIDS and ISDI.

THU085 Can Genetic Mutations And Molecular Markers Predict Recurrence In Adamantinomatous Or Papillary Craniopharyngiomas? A Systemic Review.

Abstract Disclosure: M. Nicholas: None. U. Mahfuza: None. A. De Ieva: None. M. Rodriguez: None. V.A. Preda: None. Craniopharyngiomas are rare, but clinically significant intracranial tumors. According to the WHO criteria, two clinicopathological subtypes, adamantinomatous (aCP) and papillary (pCP) (WHO 2021) are distinct entities[1]. They may have a poor prognosis due to their high recurrence rate and anatomical location. The association between surgical procedures and recurrence is well reported, however, a definitive predictive factor for recurrence based on tumor molecular markers has yet to be elucidated. The genetic mutations BRAF V600E and CTNNB1 are mutually exclusive to aCP and pCP respectively and their presence has been well documented (WHO). The expression of molecular markers ki67, p53, VEGF, PD-L1, pATM, RARγ, RARβ, CD166, CD133, E-Cadherins, FABP5, CRAPBII, Vimentins, CXCL12, CXCR4, MCM6 and DNA Topo II alpha have also all been found in populations of craniopharyngiomas, but the level of their expression and proliferation indices have not previously been clearly summarized in the literature as markers of recurrence. Aim: To perform a systematic review of the common genetic and molecular markers found in either adamantinomatous or papillary craniopharyngiomas and assessment of their impact on recurrence rate. Methods: MEDLINE, Embase, PubMed, Cochrane Library and Scopus electronic were searched in December 2022 using a search string with key words “craniopharyngioma”, “adamantinomatous”, “papillary”, “genetic mutation”, “molecular markers” and “recurrence”. The initial search resulted in 1105 studies. These studies were assessed against inclusion and exclusion criteria. Results: The final review included 26 studies that included 905 patients. Ki67, p53, PD-L1, CXCL12, CXCR4, RARγ FABP5, CRABPII, MCM6 and DNA Topo II alpha molecular markers and CTNNB1 and PTTG-1 gene mutations were found to have an association with an increase in recurrence of adamantinomatous craniopharyngiomas, while VEGF, TERTp, pATM, RARβ, CD166, CD133, E-Cadherins and Vimentins were not. Ki67, p53, PD-L1, FABP5, CRABPII, MCM6 and DNA Topo II alpha molecular markers and BRAF and PTTG-1 gene mutations were found to have an association with an increase in recurrence of papillary craniopharyngiomas, while TERTp, pATM were not. The association of other molecular markers and tumour recurrence, despite large scale studies, gave conflicting results. Conclusion: Our systematic review demonstrates that a multitude of molecular markers and genetic mutations are markers of recurrence or worsening clinicopathology. The identification of genetic mutations and expression of molecular markers and their role in the likelihood of recurrence in either adamantinomatous or papillary craniopharyngiomas provides insight into the potential for novel targets in future therapies.

Contribution of viral and bacterial infections to senescence and immunosenescence.

Cellular senescence is a key biological process characterized by irreversible cell cycle arrest. The accumulation of senescent cells creates a pro-inflammatory environment that can negatively affect tissue functions and may promote the development of aging-related diseases. Typical biomarkers related to senescence include senescence-associated β-galactosidase activity, histone H2A.X phosphorylation at serine139 (γH2A.X), and senescence-associated heterochromatin foci (SAHF) with heterochromatin protein 1γ (HP-1γ protein) Moreover, immune cells undergoing senescence, which is known as immunosenescence, can affect innate and adaptative immune functions and may elicit detrimental effects over the host's susceptibility to infectious diseases. Although associations between senescence and pathogens have been reported, clear links between both, and the related molecular mechanisms involved remain to be determined. Furthermore, it remains to be determined whether infections effectively induce senescence, the impact of senescence and immunosenescence over infections, or if both events coincidently share common molecular markers, such as γH2A.X and p53. Here, we review and discuss the most recent reports that describe cellular hallmarks and biomarkers related to senescence in immune and non-immune cells in the context of infections, seeking to better understand their relationships. Related literature was searched in Pubmed and Google Scholar databases with search terms related to the sections and subsections of this review.

Aprobation of common wheat molecular markers for the determination of the allelic composition of gliadins of Triticum spelta L.

Aim. The purpose of this work was to test and compare the methods of storage proteins electrophoresis in acid PAGE and PCR with wheat primers for spelt samples and to evaluate their using for the identification of allelic variants of gliadins. Methods. Research was conducted on samples of eight varieties of Tr. spelta using electrophoresis of storage proteins in acid PAAG and PCR with allele-specific primers designed to the Gli-B1 locus of common wheat. PCR products were separated by 7 % PAAG, gels were stained with argentum (II) nitrate. Results. The possibility of using molecular markers to identify allelic variants of spelt gliadins was shown. Using PCR using allele-specific primers for the Gli-B1 locus, five alleles were detected, two of which were also described for Tr. aestivum species. According to the results of electrophoresis and based on PCR results, six allelic variants of gliadins, divided into two groups, were identified. Conclusions. Approbation of the PCR for the species Tr. spelta using allele-specific primers developed for common wheat, showed the polymorphism and the possibility of using primers to identify allelic variants of gliadins for spelt wheat. Compared to the method of electrophoresis of reserve proteins in acidic PAAG, the PCR method is much easier to interpret the results, but it does not allow to detect all the polymorphism obtained on electrophoregrams of reserve proteins.

SDPS-45 PROGNOSTIC CHARACTERIZATION OF GENETIC MARKERS IN GLIOMA-ASSOCIATED EPILEPSY

Abstract BACKGROUND High-grade gliomas are often associated with seizures, which impair quality of life and cause deleterious neurocognitive effects. Few molecular markers characterized in high-grade gliomas have prognostic capacity for glioma-associated epilepsy. Mutations in isocitrate-dehydrogenase 1 (IDH1) have been associated with glioma-associated epilepsy (Chen et al. Neurology 2017;88(19):1805–13), but other genetic and cell proliferation markers in glioma biopsies have inconclusive connections with glioma-associated epilepsy. Current AAN guidelines advise against prophylactic administration of anti-seizure medications in patients with newly diagnosed brain tumors. We sought to characterize common molecular markers in high-grade glioma-associated epilepsy. METHODS We retrospectively reviewed 241 patients diagnosed with grade IV gliomas between 2018 and 2021 at our institution. Analysis of genetic biomarkers in tumor biopsies included chromosome 1p/19q deletion, ki-67 expression, p53 expression, MGMT methylation, IDH1 mutation, and EGFR amplification. Multiple logistic regressions were utilized to examine the association between genetic biomarkers and seizure incidence at three intervals: preoperative, postoperative, and six months post-surgery. Other variables examined were age, tumor location (lobe, laterality, eloquence), and treatment type (radiation therapy, chemotherapy, immunotherapy). RESULTS Of 241 patients analyzed, 104 (43%) patients experienced seizures. EGFR amplification in high-grade gliomas was associated with preoperative seizures (β = .92, p = .013) but was not associated with postoperative seizures nor seizures six months post-surgery. Chromosome 1p/19q deletion, ki-67 expression, p53 expression, MGMT methylation, and IDH1 mutation were all not associated with seizure incidence. CONCLUSION The study results indicate that EGFR amplification is associated with preoperative seizures, suggesting EGFR to promote glioma epileptiform activity. As EGFR amplification is characteristic of the classical subtype of glioblastoma, these results further suggest that the pathogenesis of glioma-associated epilepsy is likely related to specific molecular tumor characteristics. These preliminary results will be expanded upon with further analyses that increase sample size and include next-generation sequencing RESULTS

T2-FLAIR Mismatch Sign in Pediatric Low-Grade Glioma.

No qualitative imaging feature currently predicts molecular alterations of pediatric low-grade gliomas with high sensitivity or specificity. The T2-FLAIR mismatch sign predicts IDH-mutated 1p19q noncodeleted adult gliomas with high specificity. We aimed to assess the significance of the T2-FLAIR mismatch sign in pediatric low-grade gliomas. Pretreatment MR images acquired between January 2001 and August 2018 in pediatric patients with pediatric low-grade gliomas were retrospectively identified. Inclusion criteria were the following: 1) 0-18 years of age, 2) availability of molecular information in histopathologically confirmed cases, and 3) availability of preoperative brain MR imaging with non-motion-degraded T2-weighted and FLAIR sequences. Spinal cord tumors were excluded. Three hundred forty-nine patients were included (187 boys; mean age, 8.7 [SD, 4.8] years; range, 0.5-17.7 years). KIAA1549-B-Raf proto-oncogene (BRAF) fusion and BRAF p.V600E mutation were the most common molecular markers (n = 148, 42%, and n = 73, 20.7%, respectively). The T2-FLAIR mismatch sign was present in 25 patients (7.2%). Of these, 9 were dysembryoplastic neuroepithelial tumors; 8, low-grade astrocytomas; 5, diffuse astrocytomas; 1, a pilocytic astrocytoma; 1, a glioneuronal tumor; and 1, an angiocentric glioma. None of the 25 T2-FLAIR mismatch pediatric low-grade gliomas were BRAF p.V600E-mutated. Fourteen of 25 pediatric low-grade gliomas with the T2-FLAIR mismatch sign had rare molecular alterations, while the molecular subtype was unknown for 11 tumors. The T2-FLAIR mismatch sign was not observed in the common molecular alterations, BRAF p.V600E-mutated and KIAA1549-BRAF fused pediatric low-grade gliomas, while it was encountered in pediatric low-grade gliomas with rare pediatric molecular alterations.

Molecular marker technologies in food plant genetic diversity studies: An overview

Marker-assisted technologies in the field of plant biotechnology have attracted great interest of scientists seeking to determine the genetic variety and improve specific characteristics of species. Among several types, molecular markers hold great promise due to their high efficiency, adequate accuracy, and good reproducibility. This review aimed to present different molecular markers used in genetic biodiversity studies of common food plants, including potato, corn, and tomato.
 We presented some of the most frequent molecular markers in terms of their methodologies, advantages, challenges, and applications. We also reviewed the latest advances in the genetic diversity studies of common food plants that contribute to agricultural activities.
 According to latest progress, Simple Sequence Repeats, Sequence Characterized Amplified Region, and Single Nucleotide Polymorphism are the most common molecular markers in plant diversity studies due to their co-dominancy, high level of polymorphism, great reproducibility, and adequate specificity. Considering common food plants like potato, corn, and tomato, Simple Sequence Repeats and Single Nucleotide Polymorphisms provide detailed information about polymorphisms, resistance to pathogens or diseases, genome maps, and population dynamics. However, more research should be conducted to apply the latest and more efficient technologies, such as Next Generation Sequencing, Diversity Array Technologies, and omics, to the genetic diversity studies of plant species.
 Within the scope of recent progress, this review has a strong potential in providing relevant material for further research. It can serve as a guide to adopt the latest and most efficient sequencing platforms for examining various plant species, primarily potato, corn, and tomato.

Atherosclerosis-related biomarker PABPC1 predicts pan-cancer events

BackgroundAtherosclerosis (AS) and tumours are the leading causes of death worldwide and share common risk factors, detection methods and molecular markers. Therefore, searching for serum markers shared by AS and...

Human umbilical cord mesenchymal stem cell treatment alleviates symptoms in an atopic dermatitis-like mouse model

BackgroundAtopic dermatitis (AD) is one of the most common immune and inflammatory skin disorders, leading to insufferable itching and skin abnormalities that seriously affect life quality of patients. There are still huge unmet needs for long-term and effective disease control, despite currently available therapies. Evidenced by some preclinical and clinical studies of AD treatment with stem cells, stem cell treatment could significantly and effectively ameliorate AD symptoms.ObjectivesTo elucidate underlying mechanisms of how stem cells therapy alleviates AD-like symptoms.MethodsAn AD-like mouse model was constructed and treated with mesenchymal stem cells (MSCs) subcutaneously or subcutaneously combined with intravenously. The differentially expressed genes were sorted out from RNA sequencing results of dorsal skin and blood.ResultsTwo injection routes of MSCs could alleviate AD-like symptoms and pathologic changes of the skin and immune organs. RNA sequencing of dorsal skin sections and blood provided gene expression signatures for amelioration of skin defects, inflammatory and immune modulation by MSCs, as well as common AD molecular markers for the skin and blood, which may benefit for clinical diagnosis. IL-1β and its signaling pathway were specifically found to be associated with the development of AD-like dermatitis lesions. MSC treatment effectively inhibited the JAK-STAT pathway and receptors of IL-4, IL-13, IL-17, and IgE.ConclusionsMSC therapy could regulate abnormal immune and inflammatory status in AD. Mechanistic exploration will contribute to the development of personalized AD treatment based on MSCs.

Morphology of the esophagus of ferrets and expression profile of molecular markers

To examine the morphological characteristics and the expression profile of molecular markers of ferret esophagus and assess the feasibility of using ferrets as animal models for studying human esophageal diseases. Frozen sections and paraffin- embedded specimens of the esophageal tissues were obtained from adult ferrets (aged 6 to 8 months) and ferrets aged 1 day, 3 days, 5 days, 1 week and 2 weeks. HE staining and periodic acid-Schiff (PAS) staining were used for morphological analysis of the esophageal submucosal glands (SMGs) of adult ferrets, and the expressions of MUC5B and MUC5AC were tested using Mucin staining; The expressions of cytokeratins (CK4, CK5, CK7, CK8, CK14, CK17, CK18, CK19, and CK20) in adult ferret esophagus were examined using HE staining and immunofluorescence assay. The expressions of LEF1 in the esophageal epithelium and SMGs were detected with immunofluorescence assay. In adult ferrets, the esophageal SMGs were connective tissues below the muscularis mucosa of the esophagus with secretory functions. Cytokeratins were expressed differentially in different esophageal cells: CK4, CK8 and CK20 were expressed mainly in the mucous cells, ductal cells and epithelial cells, respectively, while the mucous cells expressed the largest variety of cytokeratins. Mucin staining showed positive MUC5B and MUC5AC expression in the cytoplasm and lumen of adult ferret esophageal glands. Lectin from DBA, ECL, GSLI, GSL Ⅱ, SBA, Tacalin bioylated, ULEX, WGA, GSL Ⅰ and GSL Ⅱ were expressed on ductal cell membrane, and ECL, PNA and WGA were detected on epithelial cell membrane. Lectin with ConA, PHA-E and PHA-L were expressed on serous cell membrane. Immunofluorescence assay showed that LEF1 in the developing glands were visible from 3 days to 1 week of age and then disappeared as the glands matured. The intensity of LEF1 expression in the esophageal glands differed significantly between ferrets aged 1 to 7 days and those aged two weeks. Ferrets and human share similar esophageal tissue structures and some common molecular markers, suggesting the possibility of using ferrets as animal models of human esophageal diseases.

Computational Insight into Intraspecies Distinctions in Pseudoalteromonas distincta: Carotenoid-like Synthesis Traits and Genomic Heterogeneity

Advances in the computational annotation of genomes and the predictive potential of current metabolic models, based on more than thousands of experimental phenotypes, allow them to be applied to identify the diversity of metabolic pathways at the level of ecophysiology differentiation within taxa and to predict phenotypes, secondary metabolites, host-associated interactions, survivability, and biochemical productivity under proposed environmental conditions. The significantly distinctive phenotypes of members of the marine bacterial species Pseudoalteromonas distincta and an inability to use common molecular markers make their identification within the genus Pseudoalteromonas and prediction of their biotechnology potential impossible without genome-scale analysis and metabolic reconstruction. A new strain, KMM 6257, of a carotenoid-like phenotype, isolated from a deep-habituating starfish, emended the description of P. distincta, particularly in the temperature growth range from 4 to 37 °C. The taxonomic status of all available closely related species was elucidated by phylogenomics. P. distincta possesses putative methylerythritol phosphate pathway II and 4,4'-diapolycopenedioate biosynthesis, related to C30 carotenoids, and their functional analogues, aryl polyene biosynthetic gene clusters (BGC). However, the yellow-orange pigmentation phenotypes in some strains coincide with the presence of a hybrid BGC encoding for aryl polyene esterified with resorcinol. The alginate degradation and glycosylated immunosuppressant production, similar to brasilicardin, streptorubin, and nucleocidines, are the common predicted features. Starch, agar, carrageenan, xylose, lignin-derived compound degradation, polysaccharide, folate, and cobalamin biosynthesis are all strain-specific.

Differentially Expressed Genes and Molecular Susceptibility to Human Age-Related Diseases.

Mainstream transcriptome profiling of susceptibility versus resistance to age-related diseases (ARDs) is focused on differentially expressed genes (DEGs) specific to gender, age, and pathogeneses. This approach fits in well with predictive, preventive, personalized, participatory medicine and helps understand how, why, when, and what ARDs one can develop depending on their genetic background. Within this mainstream paradigm, we wanted to find out whether the known ARD-linked DEGs available in PubMed can reveal a molecular marker that will serve the purpose in anyone's any tissue at any time. We sequenced the periaqueductal gray (PAG) transcriptome of tame versus aggressive rats, identified rat-behavior-related DEGs, and compared them with their known homologous animal ARD-linked DEGs. This analysis yielded statistically significant correlations between behavior-related and ARD-susceptibility-related fold changes (log2 values) in the expression of these DEG homologs. We found principal components, PC1 and PC2, corresponding to the half-sum and the half-difference of these log2 values, respectively. With the DEGs linked to ARD susceptibility and ARD resistance in humans used as controls, we verified these principal components. This yielded only one statistically significant common molecular marker for ARDs: an excess of Fcγ receptor IIb suppressing immune cell hyperactivation.

Genetic Diversity and Geographical Distribution of the Red Tide Species Coscinodiscus granii Revealed Using a High-Resolution Molecular Marker

Diatoms are responsible for approximately 40% of the global primary photosynthetic production and account for up to 20% of global carbon fixation. Coscinodiscus granii is a red tide forming species of the phylum Bacillariophyta that has been detected in a wide range of coastal regions, suggesting the possibility of the existence of high genetic diversity with differential adaptation. Common molecular markers including 18S rDNA, 16S rDNA, ITS, cox1, and rbcL do not provide sufficient resolution for distinguishing intra-species genetic diversity, hindering in-depth research on intra-species genetic diversity and their spatial and temporal dynamics. In this project, we aimed to develop molecular markers with high resolution and specificity for C. granii, attempting to identify different taxa of this species, which will set up a stage for subsequent functional assays. Comparative genomics analysis of the mtDNAs of C. granii strains identified a genomic region with high genomic variations, which was used to guide the development of a molecular marker with high resolution and high specificity. This new molecular marker, which was named cgmt1 (C. granii mitochondrial 1), was 376 bp in size and differentiated C. granii samples collected in coastal regions of China into three different clades. Preliminary analysis of field samples collected in various coastal regions in China revealed that C. granii clades were almost exclusively found in the Bohai Sea and the north Yellow Sea. This newly developed molecular marker cgmt1 could be used for tracking intra-species genetic diversity and biogeographic distribution of C. granii in different ecosystems.

SARS-CoV-2 infection increases the gene expression profile for Alzheimer’s disease risk

The coronavirus disease 2019 (COVID-19) pandemic has caused over 600,000,000 infections globally thus far. Up to 30% of individuals with mild to severe disease develop long COVID, exhibiting diverse neurologic symptoms including dementias. However, there is a paucity of knowledge of molecular brain markers and whether these can precipitate the onset of Alzheimer’s disease (AD). Herein, we report the brain gene expression profiles of severe COVID-19 patients showing increased expression of innate immune response genes and genes implicated in AD pathogenesis. The use of a mouse-adapted strain of SARS-CoV-2 (MA10) in an aged mouse model shows evidence of viral neurotropism, prolonged viral infection, increased expression of tau aggregator FKBP51, interferon-inducible gene Ifi204, and complement genes C4 and C5AR1. Brain histopathology shows AD signatures including increased tau-phosphorylation, tau-oligomerization, and α-synuclein expression in aged MA10 infected mice. The results of gene expression profiling of SARS-CoV-2-infected and AD brains and studies in the MA10 aged mouse model taken together, for the first time provide evidence suggesting that SARS-CoV-2 infection alters expression of genes in the brain associated with the development of AD. Future studies of common molecular markers in SARS-CoV-2 infection and AD could be useful for developing novel therapies targeting AD.

Comparative Analysis of Bacillariophyceae Chloroplast Genomes Uncovers Extensive Genome Rearrangements Associated with Speciation.

The Bacillariophyceae is a species-rich, ecologically significant class of Bacillariophyta. Despite their critical importance in marine ecosystems as primary producers and in the development of harmful algal blooms (HABs), taxonomic research on Bacillariophyceae species has been hindered because of their limited morphological features, plasticity of morphologies, and the low resolution of common molecular markers. Hence molecular markers with improved resolution are urgently needed. Organelle genomes, which can be constructed efficiently with the recent development of high throughput DNA sequencing technologies and the advancement of bioinformatics tools, have been proposed as super barcodes for their higher resolution for distinguishing different species and intra-species genomic variations. In this study, we tested the value of full-length chloroplast genomes (cpDNAs) as super barcodes for distinguishing diatom species, by constructing cpDNAs of 11 strains of the class Bacillariophyceae, including Nitzschia ovalis, Nitzschia traheaformis, Cylindrotheca spp., Psammodictyon constrictum, Bacillaria paxillifer, two strains of Haslea tsukamotoi, Haslea avium, Navicula arenaria, and Pleurosigma sp. Comparative analysis of cpDNAs revealed that cpDNAs were not only adequate for resolving different species, but also for enabling recognition of high levels of genome rearrangements between cpDNAs of different species, especially for species of the genera Nitzschia, Cylindrotheca, Navicula and Haslea. Additionally, comparative analysis suggested that the positioning of species in the genus Haslea should be transferred to the genus Navicula. Chloroplast genome-based evolutionary analysis suggested that the Bacillariophyceae species first appeared during the Cretaceous period and the diversity of species rose after the mass extinction about 65 Mya. This study highlighted the value of cpDNAs in research on the biodiversity and evolution of Bacillariophyceae species, and, with the construction of more cpDNAs representing additional genera, deeper insight into the biodiversity and evolutionary relationships of Bacillariophyceae species will be gained.

Models and Molecular Markers of Spermatogonial Stem Cells in Vertebrates: To Find Models in Nonmammals.

Spermatogonial stem cells (SSCs) are the germline stem cells that are essential for the maintenance of spermatogenesis in the testis. However, it has not been sufficiently understood in amphibians, reptiles, and fish because numerous studies have been focused mainly on mammals. The aim of this review is to discuss scientific ways to elucidate SSC models of nonmammals in the context of the evolution of testicular organization since rodent SSC models. To further understand the SSC models in nonmammals, we point out common markers of an SSC pool (undifferentiated spermatogonia) in various types of testes where the kinetics of the SSC pool appears. This review includes the knowledge of (1) common molecular markers of vertebrate type A spermatogonia including putative SSC markers, (2) localization of the markers on the spermatogonia that have been reported in previous studies, (3) highlighting the most common markers in vertebrates, and (4) suggesting ways of finding SSC models in nonmammals.

Diatom Biodiversity and Speciation Revealed by Comparative Analysis of Mitochondrial Genomes

Diatoms (Bacillariophyta) constitute one of the most diverse and ecologically significant groups of phytoplankton, comprising 100,000–200,000 species in three classes Bacillariophyceae, Mediophyceae, and Coscinodiscophyceae. However, due to the limited resolution of common molecular markers including 18S rDNA, 28S rDNA, ITS, rbcL, and cox1, diatom biodiversity has not been adequately ascertained. Organelle genomes including mitochondrial genomes (mtDNAs) have been proposed to be “super barcodes” for distinguishing diatom species because of their rich genomic content, and the rapid progress of DNA sequencing technologies that has made it possible to construct mtDNAs with increasing throughout and decreasing cost. Here, we constructed complete mtDNAs of 15 diatom species including five Coscinodiscophyceae species (Guinardia delicatula, Guinardia striata, Stephanopyxis turris, Paralia sulcata, and Actinocyclus sp.), four Mediophyceae species (Hemiaulus sinensis, Odontella aurita var. minima, Lithodesmioides sp., and Helicotheca tamesis), and six Bacillariophyceae species (Nitzschia ovalis, Nitzschia sp., Nitzschia traheaformis, Cylindrotheca closterium, Haslea tsukamotoi, and Pleurosigma sp.) to test the practicality of using mtDNAs as super barcodes. We found that mtDNAs have much higher resolution compared to common molecular markers as expected. Comparative analysis of mtDNAs also suggested that mtDNAs are valuable in evolutionary studies by revealing extensive genome rearrangement events with gene duplications, gene losses, and gains and losses of introns. Synteny analyses of mtDNAs uncovered high conservation among species within an order, but extensive rearrangements including translocations and/or inversions between species of different orders within a class. Duplication of cox1 was discovered for the first time in diatoms in Nitzschia traheaformis and Haslea tsukamotoi. Molecular dating analysis revealed that the three diatom classes split 100 Mya and many diatom species appeared since 50 Mya. In conclusion, more diatom mtDNAs representing different orders will play great dividends to explore biodiversity and speciation of diatoms in different ecological regions.

Transcriptome sequencing and lncRNA-miRNA-mRNA network construction in cardiac fibrosis and heart failure

ABSTRACT Cardiac fibrosis (CF) and heart failure (HF) are common heart diseases, and severe CF can lead to HF. In this study, we tried to find their common potential molecular markers, which may help the diagnosis and treatment of CF and HF. RNA library construction and high-throughput sequencing were performed. The DESeq2 package in R was used to screen differentially expressed mRNAs (DEmRNAs), differentially expressed lncRNA (DElncRNAs) and differentially expressed miRNA (DEmiRNAs) between different samples. The common DEmRNAs, DElncRNAs and DEmiRNAs for the two diseases were obtained. The ConsensusPathDB (CPDB) was used to perform biological function enrichment for common DEmRNAs. Gene interaction network was constructed to screen out key genes. Subsequently, real-time polymerase chain reaction (RT-PCR) verification was performed. Lastly, GSE104150 and GSE21125 data sets were utilized for expression validation and diagnostic analysis. There were 1477 DEmRNAs, 502 DElncRNAs and 36 DEmiRNAs between CF and healthy control group. There were 607 DEmRNAs, 379DElncRNAs,s and 42 DEmiRNAs between HF and healthy control group. CH and FH shared 146 DEmRNAs, 80 DElncRNAs, and 6 DEmiRNAs. Hsa-miR-144-3p, CCNE2, C9orf72, MAP3K20-AS1, LEF1-AS1, AC243772.2, FLJ46284, and AC239798.2 were key molecules in lncRNA-miRNA-mRNA network. In addition, hsa-miR-144-3p and CCNE2 may be considered as potential diagnostic gene biomarkers in HF. In this study, the identification of common biomarkers of CF and HF may help prevent CF to HF transition as early as possible.

Are Multiple Chemosensory Systems Accountable for COVID-19 Outcome?

Chemosensory systems (olfaction, taste, trigeminus nerve, solitary chemoreceptor cells, neuroendocrine pulmonary cells, and carotid body, etc.) detect molecules outside or inside our body and may share common molecular markers. In addition to the impairment of taste and olfaction, the detection of the internal chemical environment may also be incapacitated by COVID-19. If this is the case, different consequences can be expected. (1) In some patients, hypoxia does not trigger distressing dyspnea (“silent” hypoxia): Long-term follow-up may determine whether silent hypoxia is related to malfunctioning of carotid body chemoreceptors. Moreover, taste/olfaction and oxygen chemoreceptors may be hit simultaneously: Testing olfaction, taste, and oxygen chemoreceptor functions in the early stages of COVID-19 allows one to unravel their connections and trace the recovery path. (2) Solitary chemosensory cells are also involved in the regulation of the innate mucosal immune response: If these cells are affected in some COVID-19 patients, the mucosal innate immune response would be dysregulated, opening one up to massive infection, thus explaining why COVID-19 has lethal consequences in some patients. Similar to taste and olfaction, oxygen chemosensory function can be easily tested with a non-invasive procedure in humans, while functional tests for solitary chemosensory or pulmonary neuroendocrine cells are not available, and autoptic investigation is required to ascertain their involvement.