Overview of molecular signatures of senescence and associated resources: pros and cons.

Groupers belong to the subfamily Epinephelinae of the family Serranidae. They are an economically important marine fisheries resource and are commercially cultivated throughout the tropical and temperate regions of the world. The aquaculture industry relies on artificial breeding of groupers in order to obtain fingerlings which are free of pathogens and demonstrate a uniform growth rate. Rapid validation of sperm and eggs is a major challenge to breeders. Single locus DNA markers are ideal for the authentication of germplasm as they generate single PCR amplicons which do not require further sequencing. This study focused on the development of single locus DNA markers for genotyping of sperm samples derived from two species of grouper, the Giant grouper (Epinephelus lanceolatus) and the Tiger grouper (E. fuscoguttatus). Single locus molecular markers were developed using DNA sequences obtained from shotgun genomic libraries and tested against sperm samples derived from each of the species and the closely related groupers E. coioides and E. corallicola. A total of 54 molecular markers were developed of Research Article Annual Research & Review in Biology, 4(1): 93-104, 2014 94 which six were found to be specific to E. fuscoguttatus and seven to E. lanceolatus. The remaining markers generated PCR products in all of the four species and were rejected as suitable candidates for genotyping. The markers developed as a result of this study are relevant to fish breeders and fish farmers as they species specific, inexpensive and augment traditional methods of identification based on phenotypic characterization.

Provenance of Mytilus food products in Europe using SNP genetic markers

All living organisms are subject to progressive loss of function and damage to their tissues, a process known as aging. At the cellular level, the accumulation of damage to DNA, proteins, and organelles induces cellular senescence, a stress-response pathway that likely influence the aging process, because of its involvement in age-related pathologies and in reducing the lifespan of transgenic mice affected by a progeroid syndrome. Aging can be delayed by single gene mutations in the Insulin/IGF-1 and TOR pathways. These mutations affect the activity of cellular pathways that increase cellular homeostasis, such as stress-resistance, protein folding, and protein and organelle degradation. Among these pathways, autophagy plays a critical role in mediating the anti-aging effects of long-lived mutations in the Insulin/IGF-1 and TOR pathways. Autophagy of damaged proteins and organelles is mediated by p62/SQSTM1, a multi-domain protein involved in several signaling and degradation pathways. Loss of p62/SQSTM1 reduces lifespan and causes age-related pathologies in mouse, suggesting its involvement in the aging process. Nevertheless, it remains unknown whether p62/SQSTM1 is required to extend lifespan in response to reduced Insulin/IGF1 and TOR signaling, nor whether these pathways extend lifespan by modulating cellular senescence. We explored the role of the IGF-1 and mTOR signaling pathways in cellular senescence. Prolonged exposure to IGF-1 activates mTOR, promotes cellular senescence and reduces proliferative potential in quiescent human fibroblasts by reducing the autophagy of depolarized mitochondria. Similarly, proliferating cells progressively accumulate depolarized mitochondria and show increased signaling through mTOR as they approach replicative senescence. Inhibiting mTOR with rapamycin restores the autophagy of depolarized mitochondria, restores proliferative potential in cells treated with IGF-1, and delays the onset of cellular senescence in quiescent and proliferating cells. In addition, rapamycin reduces the accumulation of reactive oxygen species and increases resistance to exogenous stress by inducing the NFE2L2 anti-oxidant response. Reducing the expression of p62/SQSTM1 abrogates mitochondrial clearance and the activation of NFE2L2 in cells treated with rapamycin, and promotes the expression of markers of senescence. Our results provide a link between mTOR signaling and cellular senescence, and establish p62/SQSTM1 as a mediator of longevity in response to mTOR inhibition.

HER-2, EGFR, Cox-2 and Ki67 expression in lymph node metastasis of canine mammary carcinomas: Association with clinical-pathological parameters and overall survival

As phylogenomic approach becomes a common practice for constructing true bacterial phylogenies, it has become apparent that single molecular markers such as 16S ribosomal DNA often lead to misclassification of species. In this study, we present a program called Popmarker that uses the true species phylogeny and identifies a minimum set of molecular markers reflecting the bacterial evolution history and phylogenetic relationship at the resolution of populations. Popmarker ranks the proteome according to the correlation of whole species tree or subtree branch length against orthologous sequence distances. We demonstrate that 5 proteins of 2 top ranks achieve the same resolution as concatenation of 2203 single-copy orthologous genes and the right species classification as well as correct split of the 2 groups of Vibrio campbellii. The top-ranking genes selected by Popmarker are candidates that lead to speciation and are useful in distinguishing close related species in microbiome study.

Quantitative Monitoring By RT-PCR of Molecular Markers on Day +100 after Allogeneic Stem Cell Transplantation Predicts Outcome in Patients with Acute Myeloid Leukemia

BackgroundHigher numbers of senescent cells have been implicated in age-related disease pathologies. However, whether different diseases have different senescent phenotypes is unknown. Here we provide a systematic overview of the current available evidence of senescent cells in age-related diseases pathologies in humans and the markers currently used to detect senescence levels in humans. MethodsPubMed, Web of Science and EMBASE were systematically searched from inception to the 29th of September 2019, using keywords related to ‘senescence’, ‘age-related diseases’ and ‘biopsies’. ResultsIn total 12,590 articles were retrieved of which 103 articles were included in this review. The role of senescence in age-related disease has been assessed in 9 different human organ system and 27 different age-related diseases of which heart (27/103) and the respiratory systems (18/103) are the most investigated. Overall, 27 different markers of senescence have been used to determine cellular senescence and the cell cycle regulator p16ink4a is most often used (23/27 age-related pathologies). ConclusionThis review demonstrates that a higher expression of senescence markers are observed within disease pathologies. However, not all markers to detect senescence have been assessed in all tissue types.

One concern associated with pancreatic diseases is the poor prognosis of pancreatic cancer. Even with advances in diagnostic modalities, risk stratification of premalignant lesions and differentiation of pancreatic cysts are challenging. Pancreatic lesions of concern include intraductal papillary mucinous neoplasms, mucinous cystic neoplasms, serous cystadenomas, pseudocysts, and retention cysts, as well as cystic degeneration of solid tumors such as solid pseudopapillary neoplasms and pancreatic neuroendocrine neoplasms. Pancreatic juice obtained during endoscopic retrograde cholangiopancreatography has previously been used for the detection of KRAS mutation. Recently, duodenal fluid, which can be obtained during the relatively minimally invasive procedures of endoscopic ultrasound (EUS) and esophagogastroduodenoscopy, and cyst fluid collected by EUS-guided fine-needle aspiration (FNA) were used for molecular biological analysis. Furthermore, advanced analytic methods with high sensitivity were used for the detection of single and multiple markers. Early detection of malignant pancreatic tumors and risk stratification of premalignant tumors can be performed using duodenal fluid samples with a single marker with high sensitivity. Technological advances in simultaneous detection of multiple markers allow for the differentiation of cystic pancreatic tumors. One thing to note is that the clinical guidelines do not recommend pancreatic cyst fluid and pancreatic juice (PJ) sampling by EUS-FNA and endoscopic retrograde cholangiopancreatography, respectively, in actual clinical practice, but state that they be performed at experienced facilities, and duodenal fluid sampling is not mentioned in the guidelines. With improved specimen handling and the combination of markers, molecular markers in PJ samples may be used in clinical practice in the near future.

Molecular markers are the fragments of DNA sequences associated with the genome that are used to identify particular DNA sequence. Markers are very much useful in the identification of microorganisms and in determining plant microbe interactions. This chapter deals with the molecular markers used in the diagnosis of Arbuscular Mycorrhizal Fungi (AMF). Conventional methods of AMF identification and classification have been done with the spore characters such as size, colour, spore wall layer, spore-hyphal attachment and spore germination. However, the problem associated with the availability of well-trained taxonomist and the difficulties in distinguishing the minor differences in the spore wall layers mislead the identification. Nowadays, with the explosive growth of genetic research and marker development improved our knowledge on AMF identity, diversity, role in the ecosystem functioning and plant growth promotion. Molecular markers may be grouped into non-PCR and PCR based approaches. Each of them has their advantages and disadvantages. Therefore, different markers are needed for the identification of AMF. It has been reported that combining two or more genetic markers to identify or classify AMF are more reliable than using single marker. Many molecular markers are biased, as some of the primers used to detect only parts of the community and the level of taxonomic resolution in most cases are uncertain. Species-level community analyses based on rDNA regions should be feasible, but no single molecular marker or DNA barcode is yet suitable for species-level resolution of all AMF genera. Discovery of new molecular markers (DNA or non-DNA based), in the field of AMF identification and plant-AMF interactions are very much desirable.

Causal Genomic and Epigenomic Network Analysis emerges as a New Generation of Genetic Studies of Complex Diseases.

Fusarium head blight (FHB) incited by Fusarium graminearum Schwabe is a devastating disease of barley and other cereal crops worldwide. Fusarium head blight is associated with trichothecene mycotoxins such as deoxynivalenol (DON), which contaminates grains, making them unfit for malting or animal feed industries. While genetically resistant cultivars offer the best economic and environmentally responsible means to mitigate disease, parent lines with adequate resistance are limited in barley. Resistance breeding based upon quantitative genetic gains has been slow to date, due to intensive labor requirements of disease nurseries. The production of a high-throughput genome-wide molecular marker assembly for barley permits use in development of genomic prediction models for traits of economic importance to this crop. A diverse panel consisting of 400 two-row spring barley lines was assembled to focus on Canadian barley breeding programs. The panel was evaluated for FHB and DON content in three environments and over 2 years. Moreover, it was genotyped using an Illumina Infinium High-Throughput Screening (HTS) iSelect custom beadchip array of single nucleotide polymorphic molecular markers (50 K SNP), where over 23 K molecular markers were polymorphic. Genomic prediction has been demonstrated to successfully reduce FHB and DON content in cereals using various statistical models. Herein, we have studied an alternative method based on machine learning and compare it with a statistical approach. The bi-allelic SNPs represented pairs of alleles and were encoded in two ways: as categorical (–1, 0, 1) or using Hardy-Weinberg probability frequencies. This was followed by selecting essential genomic markers for phenotype prediction. Subsequently, a Transformer-based deep learning algorithm was applied to predict FHB and DON. Apart from the Transformer method, a Residual Fully Connected Neural Network (RFCNN) was also applied. Pearson correlation coefficients were calculated to compare true vs. predicted outputs. Models which included all markers generally showed marginal improvement in prediction. Hardy-Weinberg encoding generally improved correlation for FHB (6.9%) and DON (9.6%) for the Transformer network. This study suggests the potential of the Transformer based method as an alternative to the popular BLUP model for genomic prediction of complex traits such as FHB or DON, having performed equally or better than existing machine learning and statistical methods.

Molecular genetic markers represent one of the most powerful tools for the analysis of genomes. Molecular marker technology has developed rapidly over the last decade, and two forms of sequence-based markers, simple sequence repeats (SSRs), also known as microsatellites, and single nucleotide polymorphisms (SNPs), now predominate applications in modern genetic analysis. The availability of large sequence data sets permits mining for SSRs and SNPs, which may then be applied to genetic trait mapping and marker-assisted selection. Here, we describe Web-based automated methods for the discovery of these SSRs and SNPs from sequence data. SSRPrimer enables the real-time discovery of SSRs within submitted DNA sequences, with the concomitant design of PCR primers for SSR amplification. Alternatively, users may browse the SSR Taxonomy Tree to identify predetermined SSR amplification primers for any species represented within the GenBank database. SNPServer uses a redundancy-based approach to identify SNPs within DNA sequence data. Following submission of a sequence of interest, SNPServer uses BLAST to identify similar sequences, CAP3 to cluster and assemble these sequences, and then the SNP discovery software autoSNP to detect SNPs and insertion/deletion (indel) polymorphisms.

Fusarium head blight (FHB) incited by Fusarium graminearum Schwabe is a devastating disease of barley and other cereal crops worldwide. Fusarium head blight is associated with trichothecene mycotoxins such as deoxynivalenol (DON), where contaminated grains are unfit for malting or animal feed industries. While genetically resistant cultivars offer the best economic and environmentally responsible means to mitigate disease, parent lines with adequate resistance are limited in barley. Resistance-breeding based upon quantitative genetic gains has been slow to date, due to intensive labour requirements of disease nurseries. The development of high throughput genome-wide molecular markers, allow application in genomic prediction models. A diverse genomic panel consisting of 400 two-row spring barley lines was assembled to focus on Canadian barley breeding programs. The panel was evaluated for FHB and DON content in three environments and over two years. Moreover, it was genotyped using an Illumina Infinium HTS iSelect custom beadchip array of single nucleotide polymorphic molecular markers (50K SNP), where over 23K molecular markers were polymorphic. Genomic prediction has been successfully demonstrated for reducing FHB and DON content in cereals using various statistically-based models of different underlying assumptions. Herein, we have studied an alternative method basedon machine learning and compare it with a statistical approach. Two encoding techniques were utilized (categorical or Hardy-Weinberg frequencies), followed by selecting essential genomic markers for phenotype prediction. Subsequently, we applied a transformer-based deep learning algorithm to predict FHB and DON. Apart from the transformer method, we also implemented a Residual Fully Connected Neural Network (RFCNN). Pearson correlation coefficients were calculated to compare true vs. predicted outputs. Under most model scenarios, the use of all markers vs. selected markers marginally improved prediction performance except for RFCNN method for FHB (27.6%). Hardy-Weinberg encoding generally improved correlation for FHB (6.9%) and DON (9.6%) for transformer. This study suggests the potential of the transformer based method for genomic prediction of complex traits such as FHB or DON, having performed better or equally compared with existing machine learning and statistical method.

Accumulation of senescent cells in mitotic tissue of aging primates

BackgroundAs the topologies produced by previous molecular and morphological studies were contradictory and unstable (polytomy), evolutionary relationships within the Diplozoidae family and the Monogenea class (controversial relationships among the Discocotylinea, Microcotylinea and Gastrocotylinea suborders) remain unresolved. Complete mitogenomes carry a relatively large amount of information, sufficient to provide a much higher phylogenetic resolution than traditionally used morphological traits and/or single molecular markers. However, their implementation is hampered by the scarcity of available monogenean mitogenomes. Therefore, we sequenced and characterized mitogenomes belonging to three Diplozoidae family species, and conducted comparative genomic and phylogenomic analyses for the entire Monogenea class.ResultsTaxonomic identification was inconclusive, so two of the species were identified merely to the genus level. The complete mitogenomes of Sindiplozoon sp. and Eudiplozoon sp. are 14,334 bp and 15,239 bp in size, respectively. Paradiplozoon opsariichthydis (15,385 bp) is incomplete: an approximately 2000 bp-long gap within a non-coding region could not be sequenced. Each genome contains the standard 36 genes (atp8 is missing). G + T content and the degree of GC- and AT-skews of these three mitogenome (and their individual elements) were higher than in other monogeneans. nad2, atp6 and nad6 were the most variable PCGs, whereas cox1, nad1 and cytb were the most conserved. Mitochondrial phylogenomics analysis, conducted using concatenated amino acid sequences of all PCGs, indicates that evolutionary relationships of the three genera are: (Eudiplozoon, (Paradiplozoon, Sindiplozoon)); and of the three suborders: (Discocotylinea, (Microcotylinea, Gastrocotylinea)). These intergeneric relationships were also supported by the skewness and principal component analyses.ConclusionsOur results show that nad2, atp6 and nad6 (fast-evolving) would be better candidates than cox1 (slow-evolving) for species identification and population genetics studies in Diplozoidae. Nucleotide bias and codon and amino acid usage patterns of the three diplozoid mitogenomes are more similar to cestodes and trematodes than to other monogenean flatworms. This unusual mutational bias was reflected in disproportionately long branches in the phylogram. Our study offsets the scarcity of molecular data for the subclass Polyopisthocotylea to some extent, and might provide important new insights into the evolutionary history of the three genera and three suborders.