Development Of New Molecular Markers Research Articles

Assembly and characterization of the complete mitochondrial genome of Descurainia sophia: a medical plant producing glucosinolate

As a commonly used traditional Chinese medicine, Descurainia sophia has various reported pharmacological activities such as prevention of chronic diseases, cardiovascular protection, neuroprotection, anticancer, antioxidant, and has high nutritional values, but its mitochondrial genome (mitogenome) has not been reported. In this study, the D. sophia mitogenome was sequenced, assembled and annotated using next generation sequencing technologies on the Illumina HiSeq and PacBio Sequel platform. The results showed that the D. sophia mitogenome was a circular DNA molecule with the length of 265,457 bp and the GC content of 44.78%, encoding unique 56 genes, including 35 protein coding genes, 18 tRNA genes and 3 rRNA genes. We analyzed codon preference, repeated sequences, DNA sequence transformation, phylogenetic relationship, RNA editing and synteny in the D. sophia mitogenome. Based on the DNA sequences of mitogenomes, the phylogenetic and synteny analysis indicated that D. sophia was more closely related to Boechera stricta, and the mitogenome of D. sophia underwent frequent genome recombination. In this study, we obtained the complete mitogenome of D. sophia, which can provide valuable data support for future studies on genetic characteristics, phylogenetic relationships, species identification and development of new molecular markers in D. sophia.

Comparing hs-CRP and MPO Biomarkers of Subclinical Atherosclerosis in Metabolic Syndrome Patients

Cardiovascular disorders have been linked to myeloperoxidase, an enzyme generated from leukocytes. MPO creates an antibacterial system and has been many correlations between MPO, hs-CRP and cardiovascular disease. The present study has aimed to assess MPO, hs-CRP and subclinical atherosclerosis in metabolic syndrome patients by using FMD and CIMT parameters. 75 metabolic syndrome affected patients had defined as per the criteria of IDF (International Diabetes Federation) which had been in this study. In addition, ultrasound doppler had been employed for determining the carotid intima medial thickness for both right and left (left and right CIMT) and brachial artery FMD. By employing the Immunoassay MPO and hs-CRP ultrasensitive ELISA kit, the concentration of MPO and hs-CRP is measured. A positive link between MPO with CIMT right and left (r value of right CIMT=0.723, p <0.05 and left CIMT r=0.712, p<0.01), hs-CRP with CIMT right and left (r value of right CIMT=0.613, p<0.05and left CIMT r=0.64, p<0.01)and a significant inverse correlation between MPO with FMD (r= -0.319,p<0.05), hs-CRP with FMD (r= -0.304,p<0.01) in metabolic syndrome patients. Serum MPO and hs-CRP is positively linked with subclinical atherosclerosis in metabolic syndrome patients. According to this finding, understanding the mechanism behind the risk factors for cardiovascular disease can be aided by the development of new molecular markers for metabolic syndrome and subclinical atherosclerosis.

Identification and Analysis of Flax Resistance Genes to Septoria linicola (Speg.) Garassini

ABSTRACT In this study, the flax (Linum usitatissimum L.) genes associated with resistance to the disease pasmo (Septoria linicola (Speg.) Garassini) were mapped using genome resequencing and bulked segregant analysis (BSA) of genomic DNA of the pasmo-resistant parent y62–9, pasmo-susceptible parent y64–5, and F2 generation segregants. Pasmo resistance genes were identified using Gene Ontology (GO) functional prediction and gene annotation methods. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed the biological information and molecular mechanisms associated with the flax-pathogen interaction. The results of a quantitative real-time PCR analysis revealed that the levels of expression of the three genes Lus10003106, Lus10022077, and Lus10021999 differed between the y62–9 (pasmo-resistant) and y64–5 (pasmo-susceptible) parental flax lines after the inoculation of plants with the pasmo pathogen. Thus, these genes may play key roles in the resistance of flax to pasmo. The results of this study provide a foundation to support future studies of the pathogenesis of flax disease and the discovery and cloning of resistance genes and development of new molecular markers toward the development of pasmo-resistant flax varieties.

Serological, fragmentomic, and epigenetic characteristics of cell-free DNA in patients with lupus nephritis.

The biological characteristics of plasma circulating cell-free DNA (cfDNA) are related to the pathogenesis of lupus nephritis (LN). The aim of this study was to explore the biological characteristics of cfDNA in patients with LN in terms of serology, fragment omics, and epigenetics, and to discuss the possibility of liquid biopsy for cfDNA as an alternative to conventional tissue biopsy. cfDNA was extracted from plasma samples of 127 patients with systemic lupus erythematosus (64 with LN, 63 without LN). The cfDNA concentration was determined using the Qubit method. Next-generation sequencing cfDNA methylation profiling was performed for three LN patients and six non-LN patients. The methylation panel was designed based on data from The Cancer Genome Atlas cohort. The fragmentation index, motif score, and DELFI score were calculated to explore the fragmentation profile of cfDNA in patients with LN. Statistical and machine learning methods were used to select features to calculate the methylation scores of the samples. Patients with LN had significantly lower cfDNA concentrations (P = 0.0347) than those without LN. This may be associated with the presence of anti-double-stranded DNA antibodies (r = -0.4189; P = 0.0296). The mean DELFI score (proportion of short fragments of cfDNA) in patients with LN was significantly higher than that in patients without LN (P = 0.0238). Based on the pan-cancer data, 73, 66, 8, and 10 features were selected and used to calculate the methylation scores. The mean methylation scores of these features in patients with LN differed significantly from those in patients without LN (P = 0.0238). The specificity of cfDNA in patients with LN was identified using serological, fragmentomic, and epigenetic analyses. The findings may have implications for the development of new molecular markers of LN.

Imaging Hallmarks of Sarcoma Progression Via X-ray Computed Tomography: Beholding the Flower of Evil.

Simple SummarySarcomas represent the largest group of rare solid tumors that arise from mesenchymal stem cells and are a leading cause of cancer death in individuals younger than 20 years of age. There is an immediate need for the development of an algorithm for the early accurate diagnosis of sarcomas due to the high rate of diagnostic inaccuracy, which reaches up to 30%. X-ray computed tomography is a non-invasive imaging technique used to obtain detailed internal images of the human or animal body in clinical practice and preclinical studies. We summarized the main imaging features of soft tissue and bone sarcomas, and noted the development of new molecular markers to reach tumor type-specific imaging. Also, we demonstrated the possibility of the use X-ray computed microtomography for non-destructive 3D visualization of sarcoma progression in preclinical studies. Finding correlations between X-ray computed tomography modalities and the results of the histopathological specimen examination may significantly increase the accuracy of diagnostics, which leads to the initiation of appropriate management in a timely manner and, consequently, to improved outcomes.Sarcomas are a leading cause of cancer death in individuals younger than 20 years of age and represent the largest group of rare solid tumors. To date, more than 100 morphological subtypes of sarcomas have been described, among which epidemiology, clinical features, management, and prognosis differ significantly. Delays and errors in the diagnosis of sarcomas limit the number of effective therapeutic modalities and catastrophically worsen the prognosis. Therefore, the development of an algorithm for the early accurate diagnosis of sarcomas seems to be as important as the development of novel therapeutic advances. This literature review aims to summarize the results of recent investigations regarding the imaging of sarcoma progression based on the use of X-ray computed tomography (CT) in preclinical studies and in current clinical practice through the lens of cancer hallmarks. We attempted to summarize the main CT imaging features of soft-tissue and bone sarcomas. We noted the development of new molecular markers with high specificity to antibodies and chemokines, which are expressed in particular sarcoma subtypes to reach tumor type-specific imaging. We demonstrate the possibility of the use of X-ray computed microtomography (micro-CT) for non-destructive 3D visualization of solid tumors by increasing the visibility of soft tissues with X-ray scattering agents. Based on the results of recent studies, we hypothesize that micro-CT enables the visualization of neovascularization and stroma formation in sarcomas at high-resolution in vivo and ex vivo, including the novel techniques of whole-block and whole-tissue imaging. Finding correlations between CT, PET/CT, and micro-CT imaging features, the results of the histopathological specimen examination and clinical outcomes may significantly increase the accuracy of soft-tissue and bone tumor diagnostics, which leads to the initiation of appropriate histotype-specific management in a timely manner and, consequently, to improved outcomes.

Comparative Genomic Analysis Uncovers the Chloroplast Genome Variation and Phylogenetic Relationships of Camellia Species.

Camellia is the largest genus in the family Theaceae. Due to phenotypic diversity, frequent hybridization, and polyploidization, an understanding of the phylogenetic relationships between Camellia species remains challenging. Comparative chloroplast (cp) genomics provides an informative resource for phylogenetic analyses of Camellia. In this study, 12 chloroplast genome sequences from nine Camellia species were determined using Illumina sequencing technology via de novo assembly. The cp genome sizes ranged from 156,545 to 157,021 bp and were organized into quadripartite regions with the typical angiosperm cp genomes. Each genome harbored 87 protein-coding, 37 transfer RNA, and 8 ribosomal RNA genes in the same order and orientation. Differences in long and short sequence repeats, SNPs, and InDels were detected across the 12 cp genomes. Combining with the complete cp sequences of seven other species in the genus Camellia, a total of nine intergenic sequence divergent hotspots and 14 protein-coding genes with high sequence polymorphism were identified. These hotspots, especially the InDel (~400 bp) located in atpH-atpI region, had sufficient potential to be used as barcode markers for further phylogenetic analysis and species identification. Principal component and phylogenetic analysis suggested that regional constraints, rather than functional constraints, strongly affected the sequence evolution of the cp genomes in this study. These cp genomes could facilitate the development of new molecular markers, accurate species identification, and investigations of the phylogenomic relationships of the genus Camellia.

A First Genome Survey and Genomic SSR Marker Analysis of Trematomus loennbergii Regan, 1913.

Simple SummaryThe scaly rockcod (Trematomus loennbergii) is distributed in the Antarctic Ocean and this area is isolated by the Antarctic Circumpolar Current. It is important region to study evolutionary diversity. Trematomus is the main genus, having 11 species, and their habit distribution is well known. However, their genetic and genomic information is not studied. In addition, some species have similar morphology. In this study, a genome survey of T. loennbergii and microsatellite motif analysis were conducted to obtain genomic profile. The fundamental data such as genome size, heterozygosity ratio, duplication ration and microsatellite motifs were obtained. These data will provide a foundation for further whole-genome sequencing and the development of new molecular markers of T. loennbergii.Trematomus loennbergii Regan, 1913, is an evolutionarily important marine fish species distributed in the Antarctic Ocean. However, its genome has not been studied to date. In the present study, whole genome sequencing was performed using next-generation sequencing (NGS) technology to characterize its genome and develop genomic microsatellite markers. The 25-mer frequency distribution was estimated to be the best, and the genome size was predicted to be 815,042,992 bp. The heterozygosity, average rate of read duplication, and sequencing error rates were 0.536%, 0.724%, and 0.292%, respectively. These data were used to analyze microsatellite markers, and a total of 2,264,647 repeat motifs were identified. The most frequent repeat motif was di-nucleotide with 87.00% frequency, followed by tri-nucleotide (10.45%), tetra-nucleotide (1.94%), penta-nucleotide (0.34%), and hexa-nucleotide (0.27%). The AC repeat motif was the most abundant motif among di-nucleotides and among all repeat motifs. Among microsatellite markers, 181 markers were selected and PCR technology was used to validate several markers. A total of 15 markers produced only one band. In summary, these results provide a good basis for further studies, including evolutionary biology studies and population genetics of Antarctic fish species.

Meta-analysis of Correlation between Peripheral Serum MIC-1 level and Lung Cancer

Lung cancer (LC) is a common malignant tumor with high morbidity and mortality. The development of new molecular markers and the early diagnosis of LC and the exploration of emerging targeted therapies are of great significance. Therefore, this study systematically evaluates the correlation between peripheral serum MIC-1 levels and LC. Search PubMed, Web of Science, Medline and other databases, the search time is from the establishment of the database to July 2021. The LC group included LC patients, the Non-cancer group included patients with benign lung diseases (BLD), and the control group included healthy people. The serum MIC-1 levels of LC group and control group, LC group and Non-cancer group were compared respectively, and the correlation between serum MIC-1 and clinical characteristics of LC patients was evaluated and analyzed, and the ROC curve of MIC-1 in prediction of LC. Finally, 5 articles were included, including 1179 patients with LC, 109 patients with BLD, and 1020 healthy people. Meta-analysis results: the level of MIC-1 in LC group was overtop that in healthy group, and the difference was obvious [SMD=1.97, 95%CI (1.35, 2.59), PC0.00001]. The level of MIC-1 in LC group was overtop that in Non-cancer group, and the difference was obvious [SMD=382.97,95%CI (313.74, 452.19), PC0.00001]. The descriptive evaluation analyzes the correlation between MIC-1 and the clinical characteristics of LC group, and the results show that MIC-1 has a certain correlation with the stage of LC group. The AUC of serum MIC-1 in the identification of LC group and the control group was greater than 0.5. The AUC value of MIC-1 in the diagnosis of LC was 0.851-0.906, and the best sensitivity range was 63.50%-99.00%. The best specificity is in the range of 70.4%-95.80%. The Meta-analysis indicated that the serum MIC-1 level in LC group is overtop that in BLD and healthy people, and has a obvious correlation with LC stage staging; and the ROC curve shows that it has important significance in the diagnosis and prognosis of LC.

How to Choose a Good Marker to Analyze the Olive Germplasm (Olea europaea L.) and Derived Products.

The olive tree (Olea europaea L.) is one of the most cultivated crops in the Mediterranean basin. Its economic importance is mainly due to the intense production of table olives and oil. Cultivated varieties are characterized by high morphological and genetic variability and present a large number of synonyms and homonyms. This necessitates the introduction of a rapid and accurate system for varietal identification. In the past, the recognition of olive cultivars was based solely on analysis of the morphological traits, however, these are highly influenced by environmental conditions. Therefore, over the years, several methods based on DNA analysis were developed, allowing a more accurate and reliable varietal identification. This review aims to investigate the evolving history of olive tree characterization approaches, starting from the earlier morphological methods to the latest technologies based on molecular markers, focusing on the main applications of each approach. Furthermore, we discuss the impact of the advent of next generation sequencing and the recent sequencing of the olive genome on the strategies used for the development of new molecular markers.

Genome survey and microsatellite motif identification of Pogonophryne albipinna.

The genus Pogonophryne is a speciose group that includes 28 species inhabiting the coastal or deep waters of the Antarctic Southern Ocean. The genus has been divided into five species groups, among which the P. albipinna group is the most deep-living group and is characterized by a lack of spots on the top of the head. Here, we carried out genome survey sequencing of P. albipinna using the Illumina HiSeq platform to estimate the genomic characteristics and identify genome-wide microsatellite motifs. The genome size was predicted to be ∼883.8 Mb by K-mer analysis (K = 25), and the heterozygosity and repeat ratio were 0.289 and 39.03%, respectively. The genome sequences were assembled into 571624 contigs, covering a total length of ∼819.3 Mb with an N50 of 2867 bp. A total of 2217422 simple sequence repeat (SSR) motifs were identified from the assembly data, and the number of repeats decreased as the length and number of repeats increased. These data will provide a useful foundation for the development of new molecular markers for the P. albipinna group as well as for further whole-genome sequencing of P. albipinna.

Evaluation of epithelial mesenchymal transition markers snail and slug as predictor of nodal metastasis in oral squamous cell carcinoma

<p><strong>Background: </strong>Presence of regional neck node metastasis in head and neck cancer is a major determinant of overall survival. In patients presenting with neck node metastasis, there is a fifty percent decrease in overall survival, irrespective of the treatment modality. Tumor, nodes, metastases staging system, based on the anatomical extent of disease is used to predict patient prognosis and need for adjuvant treatment. Advent of immune based therapy has led to development of new molecular markers which can predict the disease aggressiveness by predicting lymph node and distal metastasis. Epithelial mesenchymal transition<strong> (</strong>EMT) in cancer is thought to convert the stable epithelial cells to mesenchymal cells that acquire properties of invasion with regional and distal metastasis.</p><p><strong>Methods:</strong> In the current study we evaluated the expression of EMT markers snail and slug in oral squamous cell carcinoma with and without neck node metastasis in 86 patients.</p><p><strong>Results:</strong> In this study, snail positivity was observed in 72 cases (83.72%), slug positivity was observed in 52 cases (60.46%) and either of the two expressions was observed in 77 cases (89.53%). Found that snail was significantly associated with clinical nodal status (p=0.037) and post-op histopathological nodal status (p=0.003). Also found that slug was significantly associated with clinical nodal status (p<0.001), post-op histopathological nodal status (p=0.001) and perineural invasion (p=0.003).</p><p><strong>Conclusions:</strong> Snail and slug positivity correlates with clinical and post-op histopathological nodal status and thus can be used as a predictor of nodal metastasis in oral squamous cell carcinoma.</p>

Comparative chloroplast genome analysis of Artemisia (Asteraceae) in East Asia: insights into evolutionary divergence and phylogenomic implications

BackgroundArtemisia in East Asia includes a number of economically important taxa that are widely used for food, medicinal, and ornamental purposes. The identification of taxa, however, has been hampered by insufficient diagnostic morphological characteristics and frequent natural hybridization. Development of novel DNA markers or barcodes with sufficient resolution to resolve taxonomic issues of Artemisia in East Asia is significant challenge.ResultsTo establish a molecular basis for taxonomic identification and comparative phylogenomic analysis of Artemisia, we newly determined 19 chloroplast genome (plastome) sequences of 18 Artemisia taxa in East Asia, de novo-assembled and annotated the plastomes of two taxa using publicly available Illumina reads, and compared them with 11 Artemisia plastomes reported previously. The plastomes of Artemisia were 150,858–151,318 base pairs (bp) in length and harbored 87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNA genes in conserved order and orientation. Evolutionary analyses of whole plastomes and 80 non-redundant protein-coding genes revealed that the noncoding trnH-psbA spacer was highly variable in size and nucleotide sequence both between and within taxa, whereas the coding sequences of accD and ycf1 were under weak positive selection and relaxed selective constraints, respectively. Phylogenetic analysis of the whole plastomes based on maximum likelihood and Bayesian inference analyses yielded five groups of Artemisia plastomes clustered in the monophyletic subgenus Dracunculus and paraphyletic subgenus Artemisia, suggesting that the whole plastomes can be used as molecular markers to infer the chloroplast haplotypes of Artemisia taxa. Additionally, analysis of accD and ycf1 hotspots enabled the development of novel markers potentially applicable across the family Asteraceae with high discriminatory power.ConclusionsThe complete sequences of the Artemisia plastomes are sufficiently polymorphic to be used as super-barcodes for this genus. It will facilitate the development of new molecular markers and study of the phylogenomic relationships of Artemisia species in the family Asteraceae.

The genetic diversity and population structure of shallots (Allium cepa var. aggregatum) in Indonesia based on R gene-derived markers

Abstract. Herlina L, Reflinur, Sobir, Maharijaya A, Wiyono S. 2019. The genetic diversity and population structure of shallots (Allium cepa var. aggregatum) in Indonesia based on R gene-derived markers. Biodiversitas 20: 696-703. Molecular markers are very useful for determining plant genetic diversity, especially when they are associated with useful traits. In shallots, type of markers still very limited. Therefore, development of new molecular markers is challenging if the future demand for this crop is to be met. The present study reports the genetic diversity analysis of 36 accessions of shallots using molecular markers derived from partial R gene sequences. Six polymorphic R gene-derived markers (Acepa-1, Acepa-2, Acepa-3, Acepa-4, Acepa-5, and Acepa-6) were developed and applied to analyze the genetic diversity of shallots in Indonesia. These loci produced a total of 963 alleles with an average of 0.51 + 0.77 alleles per marker. The polymorphic information content value ranged from 0.2784 to 0.5236 with an average of 0.36015. The markers were able to differentiate the shallot genotypes into three major clusters, suggesting that shallots are characterized by poor levels of genetic diversity in Indonesia. After further validation, the markers will be very useful, serving as tools to support the breeding of disease-resistant shallot varieties.

东北亚地区鼩鼱科动物分子生态学研究进展

PDF HTML阅读 XML下载 导出引用 引用提醒 东北亚地区鼩鼱科动物分子生态学研究进展 DOI: 10.5846/stxb201807251594 作者: 作者单位: 牡丹江师范学院生命科学与技术学院;牡丹江师范学院生命科学与技术学院;牡丹江师范学院生命科学与技术学院,东北林业大学野生动物资源学院 哈尔滨;牡丹江师范学院生命科学与技术学院,东北林业大学野生动物资源学院 哈尔滨;牡丹江师范学院生命科学与技术学院;牡丹江师范学院生命科学与技术学院;牡丹江师范学院生命科学与技术学院 作者简介: 通讯作者: 中图分类号: 基金项目: 黑龙江省教育厅备案项目（1354ZD004，1354PT005，1354PT006）；黑龙江省自然基金项目（C2017065）；牡丹江师范学院项目（PT2018007） Current progress and prospects in the molecular ecology of Soricidae in Northeast Asia Author: Affiliation: College of Life Science and Technology, Mudanjiang Normal University,, Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:在东北亚地区（中国的东北地区和内蒙古东北部、日本、朝鲜半岛、蒙古国、俄罗斯的远东地区）具有较为丰富的鼩鼱科类群。分子生物学方法的快速发展，使东北亚地区鼩鼱科动物分子生态学研究不断深入。对鼩鼱科动物的分子系统发育、遗传多样性和分子系统地理学等分子生态学内容进行了综述。提出鼩鼱科动物分子生态学研究未来的发展：1）东北亚地区第四纪冰期避难所的研究；2）同域分布的鼩鼱科动物比较系统地理学研究；3）中国东北地区鼩鼱科动物在东北亚分布区的系统地理学地位；4）新型分子标记和分析方法的发展。 Abstract:In Northeast Asia (Northeast China and the northeast of Inner Mongolia, Japan, the Korean Peninsula, Mongolia, and the Russian Far East), there are a wealth of species in the family Soricidae. In Northeast Asia, studies on the molecular ecology of the Soricidae have increased rapidly along with on going advances in molecular biology methods. In this study, we review the molecular phylogeny, genetic diversity, and molecular phylogeography of the Soricidae. Four expectations regarding future developments in the molecular ecology of Soricidae are proposed in this paper:(1) the study of Quaternary glacial refugia in Northeast Asia; (2) study of the comparative phylogeography of Soricidae distributed in the same region; (3) the phylogeographical status of Soricidae in Northeast Asia and Northeast China; and (4) the development of new molecular markers and new analytical methods. 参考文献 相似文献 引证文献

Molecular genotyping, diversity studies and high-resolution molecular markers unveiled by microsatellites in Giardia duodenalis.

BackgroundGiardia duodenalis (synonyms G. lamblia and G. intestinalis) is an enteric protozoan parasite of a wide range of mammalian hosts, including humans and various domestic and wild animals. There is considerable genetic variability in G. duodenalis and isolates of this parasite have been divided into eight genetic assemblages. Microsatellites markers can be used to discriminate isolates with a high level of sensitivity. This study was conducted to identify and characterize genomic microsatellites (simple sequence repeats—SSRs), sequences of one- to six-nucleotide motifs repeated in tandem, present in the available genomes of G. duodenalis and to develop new markers that can serve as a tool for detection and for characterizing the genetic diversity of this parasite.Methodology/ Principal findingsFor each genetic assemblage, polymorphism levels for the microsatellite markers were evaluated. After performing the analysis using the MISA and SciRoKo software, 1,853 simple sequence repeats (SSRs) were identified. In all the genomes, trinucleotide repeats were the most common class followed by tetranucleotide. Many of the SSR loci are assemblage-specific, and 36 SSR loci shared among all the genomes were identified. Together with hypothetical proteins, variant-specific surface proteins represented nearly half of the annotated SSR loci. The results regarding the most common repeat among the SSRs led us to infer that positive selection occurred to avoid frameshift mutations. Additionally, based on inter- and intra-genetic assemblages polymorphism analyses, we unveiled previously undetected genetic variation, indicating that the microsatellite markers we developed are useful molecular tools for epidemiological inferences based on population genetics patterns and processes.ConclusionsThere is increasing demand for the development of new molecular markers and for the characterization of pathogens at a higher resolution level. In this study, we present 60 G. duodenalis microsatellites markers that exhibited high polymerase chain reaction (PCR) amplification efficiency among the different genetic assemblages. Twenty of these markers presented nucleotide sequence polymorphisms and may be used as a genotyping tool. The monomorphic markers can be used for the detection of the parasite at the species and genetic assemblage level. These polymorphic markers revealed a genetic diversity that was previously undetectable, thus they can be considered valuable molecular tools for high resolution markers in future studies investigating Giardia and may also be used for epidemiological inferences based on populations genetics patterns and processes.

Orofacial Malignancies in Relatively Young Nigerians: the need for further investigations of the molecular landscape.

Background: Occurrence of Orofacial malignancies (OFM) is a major global public health issue, being the sixth most common cancer in the world with 500,000 new incidences per year. Pattern of distribution among the younger age group needs to be explored and compared with the pattern among patients in older age groups.Materials and methods: Clinical and histologic information on subjects diagnosed as OFM over a 11-year period was retrieved. Data collected and analyzed with SPSS Statistics version 20 was presented as frequency tables, charts and proportions. A confidence interval of 95% was assumed and the level of significance was set at p 40 years (M: F= 2.35:1). SCC mostly showed mandible site predilection. However, there was a Maxilla site predilection among young subjects ≤ 40 years and a Mandibular site predilection among subjects > 40 years. Salivary gland carcinoma accounted for 40.2% of OFM with site and gender predilections for the palate and female respectively. Peak age of occurrence was in the 6th and 7th decades of life and Adenocarcinoma (AC) was the most common observed type.Sarcoma accounted for 11.8% of OFM and showed a mean age of occurrence of 41 years ±16years, peak age of occurrence in the 5th decade of life and male gender predilection (M:F = 1.2:1) . Conclusion: There is an increasing number of cases of OFM especially SCC, in Nigerians. It is plausible that unidentified factors may trigger genetic mutations that predispose to OFM development in this environment hence an urgent need for exploration of molecular landscape that may lead to the development of new molecular markers for qualitative management.

Malaria Epigenetics

Organisms with identical genome sequences can show substantial differences in their phenotypes owing to epigenetic changes that result in different use of their genes. Epigenetic regulation of gene expression plays a key role in the control of several fundamental processes in the biology of malaria parasites, including antigenic variation and sexual differentiation. Some of the histone modifications and chromatin-modifying enzymes that control the epigenetic states of malaria genes have been characterized, and their functions are beginning to be unraveled. The fundamental principles of epigenetic regulation of gene expression appear to be conserved between malaria parasites and model eukaryotes, but important peculiarities exist. Here, we review the current knowledge of malaria epigenetics and discuss how it can be exploited for the development of new molecular markers and new types of drugs that may contribute to malaria eradication efforts.

Identification and characterization of REC66, a Ty1-copia-like retrotransposon in the genome of red flower of Mirabilis jalapa L.

Mirabilis jalapa Lis the most commonly grown ornamental species of Mirabilis and is available in a range of brilliant colors. However, genetic research on Mirabilis jalapa Lis limited. Using fluorescent differential display (FDD) screening, we report the identification of a novel Ty1-copia-like retrotransposon in the genome of the red flower of Mirabilis jalapa L, and we named it REC66based on its sequence homology to the GAG protein from Ty1-copiaretrotransposon. Using degenerate primers based on the DNA sequence of REC66, a total of fourteen different variants in reverse transcriptase (RT) sequence were recovered from the genomic DNA. These RT sequences show a high degree of heterogeneity characterized mainly by deletion mutation; they can be divided into three subfamilies, of which the majority encode defective RT. This is the first report of a Ty1-copiaretrotransposon in Mirabilis jalapa L. The finding could be helpful for the development of new molecular markers for genetic studies, particularly on the origin and evolutionary relationships of M. jalapa L, and the study of Ty1-copiaretrotransposons and plant genome evolution in the genus Mirabilisor family Nyctaginaceae.

Three Molecular Subtypes of Gastric Adenocarcinoma Have Distinct Histochemical Features Reflecting Epstein-Barr Virus Infection Status and Neuroendocrine Differentiation.

Current histopathologic classification schemes for gastric adenocarcinoma have limited clinical utility and are difficult to apply due to tumor heterogeneity. Elucidation of molecular subtypes of gastric cancer may contribute to our understanding of gastric cancer biology and to the development of new molecular markers that may lead to improved diagnosis, therapy, or prognosis. We previously demonstrated that Epstein-Barr virus (EBV)-infected gastric cancers have a distinct human gene expression profile compared with uninfected cancers. We now examine the histopathologic features characterizing infected (n=14) and uninfected (n=89) cancers; the latter of which are now further divided into 2 major molecular subtypes based on expression patterns of 93 RNAs. One uninfected gastric cancer subtype was distinguished by upregulation of 3 genes with neuroendocrine (NE) function (CHGA, GAST, and REG4 encoding chromogranin, gastrin, and the secreted peptide REG4 involved in epithelial cell regeneration), implicating hormonal factors in the pathogenesis of a major class of gastric adenocarcinomas. Evidence of NE differentiation (molecular, immunohistochemical, or morphologic) was mutually exclusive of EBV infection. EBV-infected tumors tended to have solid-type morphology with lymphoid stroma. This study reveals novel molecular subtypes of gastric cancer and their associated morphologies that demonstrate divergent NE features.

Complete chloroplast genome of the orchid Cattleya crispata (Orchidaceae:Laeliinae), a Neotropical rupiculous species

A partial genome dataset was sequenced for the orchid Cattleya crispata using both Illumina and 454 technologies. The chloroplast genome was assembled using iterative runs of MIRA software that yielded a circular molecule with 148,343 bp in length and deposited in GenBank database (Accession Number KP168671). The plastid genome conserved the quadripartite structure present in most Orchidaceae chloroplasts and was composed by 79 protein-coding genes, 39 tRNAs and 8 rRNAs. Genome structure, gene order and orientation were similar to previously described chloroplasts for Cymbidium orchids, differing in gene order for petN and psbM genes. Data described here contain the first report of a complete chloroplast for the Neotropical subtribe Laeliinae and may contribute to improve the phylogenetic resolution and allow the development of new molecular markers for population genetic studies of orchids.