Insights into the genomic evolution and the alkali tolerance mechanisms of by comparative genomic and transcriptomic analyses.

is a rare wild edible mushroom from northwest China, and grows naturally in mild saline-alkali soil, which is also unusual in mushrooms. represents a potential model organism for explaining saline-alkali tolerance mechanisms and revealing related physiological processes in mushrooms. Here, we provide a high-quality genome of .

Preliminary Screening of a Familial Tuberous Sclerosis Complex Pathogenic Gene.

Purpose: The aim of this study was to screen the possible pathogenic genes of one family with tuberous sclerosis complexes (TSCs).

Patients And Methods: All family members were examined through detailed clinical evaluations, auxiliary examinations and CT. Then, we selected five members from this TSC family as the test samples.

Genetic factors related to the widespread dissemination of ST11 extensively drug-resistant carbapenemase-producing Klebsiella pneumoniae strains within hospital.

Background: Carbapenemase-producing Klebsiella pneumoniae (CP-Kp) poses distinct clinical challenges due to extensively drug resistant (XDR) phenotype, and sequence type (ST) 11 is the most dominant blaKPC-2-bearing CP-Kp clone in China. The purpose of this current retrospective study was to explore the genetic factors associated with the success of XDR CP-Kp ST11 strains circulated in the intensive care unit (ICU) of a Chinese tertiary hospital.

Methods: Six ST11 XDR CP-Kp strains were identified between May and December 2014 and validated by minimum inhibitory concentration examination, polymerase chain reaction, and pyrosequencing.

Identification of a mutation in a large Chinese family with atypical normokalemic periodic paralysis using whole-exome sequencing.

Objectives: Normokalemic periodic paralysis (NormoKPP) of skeletal muscle is an autosomal dominant disorder caused by mutations in the gene encoding voltage-gated sodium channel protein type 4 subunit alpha (), which leads to ion channel dysfunction. Little is known about the relationship between genotype and the clinical symptoms of NormoKPP. The present study aimed to evaluate the genetic variation in a large Chinese family with NormoKPP.

[Advances of sequencing and assembling technologies for complex genomes].

Complex genomes are noted to be extremely difficult to sequence or assemble by using ordinary methods. Complex genomes are typically characterized as being highly repetitive, highly heterozygous, extremely GC biased, or naturally contaminated, i.e.

Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging.

Oral squamous cell carcinoma (OSCC) is a highly aggressive cancer and the fourth leading malignancy among males in Taiwan. Some pathogenic bacteria are associated with periodontitis and oral cancer. However, the comprehensive profile of the oral microbiome during the cancer's progression from the early stage to the late stage is still unclear.

Immune tolerance of vector beetle to its partner plant parasitic nematode modulated by its insect parasitic nematode.

Immune response of insect vectors to transmitted pathogens or insect hosts against parasites are well studied, whereas the mechanism of tripartite interactions remains elusive. In this study, we investigated the immune interactions of the vector beetle Monochamus alternatus ( Ma) to the devastating plant parasitic nematode Bursaphelenchus xylophilus ( Bx) and the insect parasitic nematode Howardula phyllotretae ( Hp). We report the unique immune mechanism by which the vector beetle tolerates many devastating Bx in its trachea, yet that immune tolerance is compromised by the parasitic nematode Hp.

Comparative analysis of the Monochamus alternatus immune system.

The pine sawyer beetle, Monochamus alternatus, is regarded as a notorious forest pest in Asia, vectoring an invasive pathogenic nematode, Bursaphelenchus xylophilus, which is known to cause pine wilt disease. However, little sequence information is available for this vector beetle. This hampered the research on its immune system.

The calcium-dependent protein kinase (CDPK) and CDPK-related kinase gene families in -comparison with five other plant species in structure, evolution, and expression.

Calcium-dependent protein kinases (CDPKs or CPKs) play important roles in various physiological processes of plants, including growth and development, stress responses and hormone signaling. Although the CDPK gene family has been characterized in several model plants, little is known about this gene family in (the Para rubber tree). Here, we characterize the entire CDPK and CDPK-related kinase (CRK) gene families comprising 30 genes ( to ) and nine genes ( to ).

De Novo Sequencing and Transcriptome Analysis of Pleurotus eryngii subsp. tuoliensis (Bailinggu) Mycelia in Response to Cold Stimulation.

Cold stimulation of Bailinggu's mycelia is the main factor that triggers primordia initiation for successful production of fruiting bodies under commercial cultivation. Yet, the molecular-level mechanisms involved in mycelia response to cold stimulation are still unclear. Here, we performed comparative transcriptomic analysis using RNA-Seq technology to better understand the gene expression regulation during different temporal stages of cold stimulation in Bailinggu.

Genome-wide mapping of 5-hydroxymethylcytosine in three rice cultivars reveals its preferential localization in transcriptionally silent transposable element genes.

5-Hydroxymethylcytosine (5hmC), a modified form of cytosine that is considered the sixth nucleobase in DNA, has been detected in mammals and is believed to play an important role in gene regulation. In this study, 5hmC modification was detected in rice by employing a dot-blot assay, and its levels was further quantified in DNA from different rice tissues using liquid chromatography-multistage mass spectrometry (LC-MS/MS/MS). The results showed large intertissue variation in 5hmC levels.

Transcriptomic insight into the immune defenses in the ghost moth, Hepialus xiaojinensis, during an Ophiocordyceps sinensis fungal infection.

Hepialus xiaojinensis is an economically important species of Lepidopteran insect. The fungus Ophiocordyceps sinensis can infect its larvae, which leads to mummification after 5-12 months, providing a valuable system with which to study interactions between the insect hosts and pathogenic fungi. However, little sequence information is available for this insect.

A Critical Role for CLSP2 in the Modulation of Antifungal Immune Response in Mosquitoes.

Entomopathogenic fungi represent a promising class of bio-insecticides for mosquito control. Thus, detailed knowledge of the molecular mechanisms governing anti-fungal immune response in mosquitoes is essential. In this study, we show that CLSP2 is a modulator of immune responses during anti-fungal infection in the mosquito Aedes aegypti.

MicroRNA profiles and potential regulatory pattern during the early stage of spermatogenesis in mice.

Spermatogenesis is a complicated and poorly understood process that relies on the precise regulation of the self-renewal and differentiation of spermatogonia. In many organisms, microRNAs (miRNAs) are involved in multiple developmental processes as critical regulators of transcriptional and post-transcriptional gene silencing. This study investigated the expression pattern of miRNAs in type B spermatogonia cells (BSc) and primary spermatocytes (PSc) of mice, using a high-throughput small RNA sequencing system.

Transcriptomic analysis reveals key regulators of mammogenesis and the pregnancy-lactation cycle.

An organ unique to mammals, the mammary gland develops 90% of its mass after birth and experiences the pregnancylactation-involution cycle (PL cycle) during reproduction. To understand mammogenesis at the transcriptomic level and using a ribo-minus RNA-seq protocol, we acquired greater than 50 million reads each for the mouse mammary gland during pregnancy (day 12 of pregnancy), lactation (day 14 of lactation), and involution (day 7 of involution). The pregnancy-, lactation- and involution-related sequencing reads were assembled into 17344, 10160, and 13739 protein-coding transcripts and 1803, 828, and 1288 non-coding RNAs (ncRNAs), respectively.

A large-scale gene discovery for the red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae).

The red palm weevil (RPW; Rhynchophorus ferrugineus) is a devastating pest of palms, prevalent in the Middle East as well as many other regions of the world. Here, we report a large-scale de novo complementary DNA (cDNA) sequencing effort that acquired ∼5 million reads and assembled them into 26 765 contigs from 12 libraries made from samples of different RPW developmental stages based on the Roche/454 GS FLX platform. We annotated these contigs based on the publically available known insect genes and the Tribolium castaneum genome assembly.

Transcriptome profiling of the developing postnatal mouse testis using next-generation sequencing.

Mammalian testis development is a complex and highly sophisticated process. To study the dynamic change of normal testis development at the transcriptional level, we investigated mouse testes at three postnatal ages: 6 days postnatal, 4 weeks old, and 10 weeks old, representing infant (PN1), juvenile (PN2), and adult (PN3) stages, respectively. Using ultra high-throughput RNA sequencing (RNA-seq) technology, we obtained 211 million reads with a length of 35 bp.

Molecular identification of Diphyllobothrium latum and a brief review of diphyllobothriosis in China.

Two tapeworm specimens collected in northeast China in 2009 and 2011 were identified as Diphyllobothrium latum based on morphological criteria. Molecular methods were used to confirm their identity and analyze genetic variations compared with published data for this species. Species identity was confirmed by molecular characterization of the 18S rDNA partial sequence, complete sequences of internal transcribed spacers (ITSs) and 5.

Pyrosequencing the Bemisia tabaci transcriptome reveals a highly diverse bacterial community and a robust system for insecticide resistance.

Background: Bemisia tabaci (Gennadius) is a phloem-feeding insect poised to become one of the major insect pests in open field and greenhouse production systems throughout the world. The high level of resistance to insecticides is a main factor that hinders continued use of insecticides for suppression of B. tabaci.

Comparative transcriptome analysis of transporters, phytohormone and lipid metabolism pathways in response to arsenic stress in rice (Oryza sativa).

• Arsenic (As) contamination of rice (Oryza sativa) is a worldwide concern and elucidating the molecular mechanisms of As accumulation in rice may provide promising solutions to the problem. Previous studies using microarray techniques to investigate transcriptional regulation of plant responses to As stress have identified numerous differentially expressed genes. However, little is known about the metabolic and regulatory network remodelings, or their interactions with microRNA (miRNA) in plants upon As(III) exposure.

DNA barcoding provides distinction between Radix Astragali and its adulterants.

Based on variable nuclear and/or organellar DNA sequences among vastly divergent species as well as morphologically indistinguishable species, DNA barcoding is widely applicable in species identification, biodiversity studies, forensic analyses, and authentication of medicinal plants. The roots of Astragalus membranaceus and A. membranaceus var.

Identification of microRNA in the protist Trichomonas vaginalis.

MicroRNAs (miRNAs) are a class of small noncoding RNAs that have important regulatory roles in multicellular organisms. However, miRNA has never been identified experimentally in protist. Direct cloning of 438 expressed miRNA tags by microRNA serial analysis of gene expression from the parasitic protist Trichomonas vaginalis identified nine candidate miRNAs.

Salmonella paratyphi C: genetic divergence from Salmonella choleraesuis and pathogenic convergence with Salmonella typhi.

Background: Although over 1400 Salmonella serovars cause usually self-limited gastroenteritis in humans, a few, e.g., Salmonella typhi and S.

Analysis of expressed sequence tags in porcine uterus tissue.

Two non-normalized cDNA libraries of uteri from Danish Landrace and Chinese Erhualian pigs were constructed, and 13,756 expressed sequence tags (ESTs) were randomly sequenced. The ESTs were clustered by Phrap software, and 6,139 distinct tentative consensus sequences were produced, including 2,730 contigs and 3,409 singlets. Using Blast tools, these 6,139 candidate genes were compared to the nr and nt databases; 5,210 of them were assigned putative functions, whereas 929 potentially represent new genes.

[Analysis of expressed sequence tags (EST) from Panax quinquefolium root].

To investigate the profile of gene expression in American ginseng (Panax quinquefolium L.) and discover its functional genes, for the first time, expressed sequence tags (EST) library of four-year-old American ginseng roots has been established. According to BLAST and Gene Ontology analysis, eleven genes, encoding cytochrome P450, glucosyltransferase, farnesyltransferase and cyclase family protein, are found to be associated with ginsenosides biosynthesis.