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

Agaricus sinodeliciosus is a rare wild edible mushroom from northwest China, and grows naturally in mild saline-alkali soil, which is also unusual in mushrooms. A. sinodeliciosus 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 A. sinodeliciosus. Comparative genomic analyses reveal A. sinodeliciosus has numerous changes to its genome organization after a solitary evolutionary history under saline-alkali environments, such as gene family contraction, retrotransposon expansion and rapid evolution of adaptative genes. Our saline and alkali tolerance tests show that mycelium growth and fruit body formation of this species are effected by mild alkalinity. Transcriptomic analyses reveal that genes involved in carbon and nitrogen utilization, cell stability and fruit body formation of A. sinodeliciosus could be activated under mildly alkaline conditions. In particular, the 'starch and sucrose metabolism', 'biosynthesis of amino acids' and 'phenylpropanoid biosynthesis' pathways are important for mildly alkaline tolerance of A. sinodeliciosus. Like plants and arbuscular mycorrhizal fungi, in the rot fungus A. sinodeliciosus, the biosynthesis of intracellular small molecules could be enhanced to counter osmotic and oxidative stresses caused by mild alkalinity, and the biosynthesis of monolignol could be suppressed to increase cell wall infiltrates under mildly alkaline conditions. This research provides an understanding of the genomic evolution and mechanisms of A. sinodeliciosus in tolerance to saline-alkali environments. The A. sinodeliciosus genome constitutes a valuable resource for evolutionary and ecological studies of Agaricus.

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. They were analysed by a new exon group sequencing method. Single nucleotide polymorphisms (SNPs) were screened by using databases, such as dbSNP and HAPMAP, and then the candidate genes were selected. Genes were analysed, and finally, the most likely mutation sites were screened. The results were examined by Sanger sequencing.

Results

In this TSC family, we identified c.913+2T>G, a splicing site mutation in the 9th intron region of TSC1. Family members without TSC did not have this mutation.

Conclusion

The mutations in the intron regions cannot be ruled out as a pathogenic factor for TSC.

Comparison of peripheral artery plaque characteristics between ACS patients with plaque rupture and plaque erosion in culprit coronary artery: an OCT and ultrasound study

Background

Recent research has found that the characteristics of peripheral arterial plaque are related to the increased risk of cardiovascular disease, however, the relationship of plaque characteristics between peripheral artery and coronary is still unknown.

Purpose

To assess the correlation between coronary plaque characteristics assessed by optical coherence tomography (OCT) and peripheral artery plaque characteristics assessed by ultrasound.

Methods

150 patients with acute coronary syndrome (ACS) underwent coronary angiography were prospectively enrolled. OCT imaging of culprit vessel were performed during the procedure and ultrasound examination of bilateral carotid, iliofemoral and popliteal arteries was performed during hospitalization after procedure. Panvascular disease was defined as the presence of observable plaques in two or more vascular beds. Patients were divided into plaque rupture (PR) group and plaque erosion (PE) group according to culprit plaque characteristics on OCT.

Results

There were 132 (88%) ACS patients had panvascular disease in which 36 (24%) with generalized atherosclerosis (4 sites) and the prevalence of panvascular atherosclerosis in PR group was significantly higher than in PE group especially in carotid arteries and iliofemoral arteries (Figure 1, Figure 2). Compared to PE group, PR group had higher carotid plaque score (p=0.001) which indicates more plaques and severer atherosclerosis. Moreover, there were larger intima-media thickness (IMT) of iliofemoral arteries (6.9±1.4mm vs. 6.5±1.1mm, p=0.036) and more calcified plaques in PR group.

Conclusions

Panvascular disease is highly prevalent in ACS patients especially in patients with plaque rupture in culprit vessel, in which more than half of the patients had plaques in more than 3 sites of vascular beds. In addition, patients with plaque rupture had thicker iliofemoral IMT and higher panvascular atherosclerosis burden, which indicates that characteristics of coronary plaques are the focal expression of plaques in the whole panvcascular system.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): National Key R&D Program of China Figure 1. Prevalence of panvascular disease in ACSFigure 2. Comparison of peripheral artery plaques

Identification of a SCN4A 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 (SCN4A), 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. The patients in this pedigree did not respond to saline treatment, but calcium gluconate treatment was effective.

METHODS

We performed a series of clinical examinations and genetic analyses, using whole-exome and Sanger sequencing, to examine the mutation status of SCN4A in a Chinese family segregating for NormoKPP.

RESULTS

Whole-exome sequencing revealed a c.2111C>T substitution in SCN4A in most of the affected family members. This mutation results in the amino acid substitution p.T704M.

CONCLUSIONS

These results support a causative role of this mutation in SCN4A in NormoKPP, and provide information about the relationship between genotype and atypical clinical symptoms.

[Expression discordances and clinical values of ER, PR, HER-2 and Ki-67 in primary and metastatic breast cancer]

Objective: To investigate the expression discordances of estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor2 (HER-2) and Ki-67 in primary and metastatic breast cancer specimens and explore the clinical significances. Methods: Biopsies of metastatic lesions were performed in 203 patients with breast cancer recurrence and metastasis indicated by physical examination and/or imaging examination. We confirmed pathological properties and assessed the expressions of ER, PR, HER-2 and Ki-67 in primary and metastatic lesions, their relationships with prognosis were also analyzed. Results: Biopsy failed in 3 patients, the pathology and immunohistochemitry results of metastatic lesions were not obtained. One person was diagnosed as tuberculosis and another was primary lung cancer. Among the 198 cases of primary and metastatic lesions, the discordance rates of ER, PR, HER-2 and Ki-67 were 27.3%, 34.3%, 11.8% and 15.1%, respectively.The expressions of ER, HER-2 and Ki-67 were not significantly different between the primary and metastatic lesions, however, the expressions of PR were more likely to turn negative in the metastases (P<0.001). The disease-free survival (DFS) of patients with ER, PR positive, HER-2 negative and low expression of Ki-67 in metastatic lesion was much longer (P<0.05). Conclusions: The expressions of ER, PR, HER-2 and Ki-67 in metastatic lesions are associated with the prognosis of breast cancer patients.Their expression discordances between primary and metastatic lesions can guide the treatment and evaluate the risks of recurrence and prognosis.

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. Based on the transcriptome of M. alternatus, we have identified and characterized 194 immunity-related genes in M. alternatus, and compared them with homologues molecules from other species known to exhibit immune responses against invading microbes. The lower number of putative immunity-related genes in M. alternatus were attributed to fewer C-type lectin, serine protease (SP) and anti-microbial peptide (AMP) genes. Phylogenetic analysis revealed that M. alternatus had a unique recognition gene, galectin3, orthologues of which were not identified in Tribolium castaneum, Drosophila melanogastor, Anopheles gambiae and Apis mellifera. This suggested a lineage-specific gene evolution for coleopteran insects. Our study provides the comprehensive sequence resources of the immunity-related genes of M. alternatus, presenting valuable information for better understanding of the molecular mechanism of innate immunity processes in M. alternatus against B. xylophilus.

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. We profiled the oral microbiota and identified bacteria biomarkers associated with OSCC. The microbiota of an oral rinse from 51 healthy individuals and 197 OSCC patients at different stages were investigated using 16S rRNA V3V4 amplicon sequencing, followed by bioinformatics and statistical analyses. The oral microbiota communities from stage 4 patients showed significantly higher complexity than those from healthy controls. The populations also dynamically changed with the cancer's progression from stage 1 to stage 4. The predominant phyla in the oral samples showed variation in the relative abundance of Fusobacteria, Bacteroidetes, and Actinobacteria. The abundance of Fusobacteria increased significantly with the progression of oral cancer from the healthy controls (2.98%) to OSCC stage 1 (4.35%) through stage 4 (7.92%). At the genus level, the abundance of Fusobacterium increased, while the number of Streptococcus, Haemophilus, Porphyromonas, and Actinomyces decreased with cancer progression. Fusobacterium periodonticum, Parvimonas micra, Streptococcus constellatus, Haemophilus influenza, and Filifactor alocis were associated with OSCC, and they progressively increased in abundance from stage 1 to stage 4. The abundances of Streptococcus mitis, Haemophilus parainfluenzae, and Porphyromonas pasteri were inversely associated with OSCC progression. We selected a bacterial marker panel of three bacteria (upregulated F. periodonticum, down-regulated S. mitis, and P. pasteri), which had an AUC of 0.956 (95% CI = 0.925-0.986) in discriminating OSCC stage 4 from the healthy controls. Furthermore, the functional prediction of oral bacterial communities showed that genes involved in carbohydrate-related metabolism, such as methane metabolism, and energy-metabolism-related parameters, such as oxidative phosphorylation and carbon fixation in photosynthetic organisms, were enriched in late-stage OSCC, while those responsible for amino acid metabolism, such as folate biosynthesis and valine, leucine, and isoleucine biosynthesis, were significantly associated with the healthy controls. In conclusion, our results provided evidence of oral bacteria community changes during oral cancer progression and suggested the possibility of using bacteria as OSCC diagnostic markers.

The calcium-dependent protein kinase (CDPK) and CDPK-related kinase gene families in Hevea brasiliensis-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 Hevea brasiliensis (the Para rubber tree). Here, we characterize the entire H. brasiliensis CDPK and CDPK‐related kinase (CRK) gene families comprising 30 CDPK genes (HbCPK1 to 30) and nine CRK genes (HbCRK1 to 9). Structure and phylogeny analyses of these CDPK and CRK genes demonstrate evolutionary conservation in these gene families across H. brasiliensis and other plant species. The expression of HbCPK and HbCRK genes was investigated via Solexa sequencing in a range of experimental conditions (different tissues, phases of leaf development, ethylene treatment, and various abiotic stresses). The results suggest that HbCPK and HbCRK genes are important components in growth, development, and stress responses of H. brasiliensis. Parallel studies on the CDPK and CRK gene families were also extended to five other plant species (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Manihot esculenta, and Ricinus communis). The CDPK and CRK genes from different plant species that exhibit similar expression patterns tend to cluster together, suggesting a coevolution of gene structure and expression behavior in higher plants. The results serve as a foundation to further functional studies of these gene families in H. brasiliensis as well as in the whole plant kingdom.

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. A total of 21,558 Bailinggu mycelia unigenes were de novo assembled and annotated from four libraries (control at 25 °C, plus cold stimulation treatments at -3 °C for a duration of 1-2 days, 5-6 days, and 9-10 days). GO and KEGG pathway analysis indicated that functional groups of differentially expressed unigenes associated with cell wall and membrane stabilization, calcium signaling and mitogen-activated protein kinases (MAPK) pathways, and soluble sugars and protein biosynthesis and metabolism pathways play a vital role in Bailinggu's response to cold stimulation. Six hundred and seven potential EST-based SSRs loci were identified in these unigenes, and 100 EST-SSR primers were randomly selected for validation. The overall polymorphism rate was 92% by using 10 wild strains of Bailinggu. Therefore, these results can serve as a valuable resource for a better understanding of the molecular mechanisms associated with Bailinggu's response to cold stimulation.

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 time-course analysis of the fat body transcriptome was performed to explore the host immune response to O. sinensis infection. In total, 50,164 unigenes were obtained by assembling the reads from two high-throughput approaches: 454 pyrosequencing and Illumina Hiseq2000. Hierarchical clustering and functional examination revealed four major gene clusters. Clusters 1-3 included transcripts markedly induced by the fungal infection within 72 h. Cluster 4, with a lower number of transcripts, was suppressed during the early phase of infection but returned to normal expression levels sometime before 1 year. Based on sequence similarity to orthologs known to participate in immune defenses, 258 candidate immunity-related transcripts were identified, and their functions were hypothesized. The genes were more primitive than those in other Lepidopteran insects. In addition, lineage-specific family expansion of the clip-domain serine proteases and C-type lectins were apparent and likely caused by selection pressures. Global expression profiles of immunity-related genes indicated that H. xiaojinensis was capable of a rapid response to an O. sinensis challenge; however, the larvae developed tolerance to the fungus after prolonged infection, probably due to immune suppression. Specifically, antimicrobial peptide mRNAs could not be detected after chronic infection, because key components of the Toll pathway (MyD88, Pelle and Cactus) were downregulated. Taken together, this study provides insights into the defense system of H. xiaojinensis, and a basis for understanding the molecular aspects of the interaction between the host and the entomopathogen.

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. With a fungal infection, the expression of the CLSP2 gene is elevated. CLSP2 is cleaved upon challenge with Beauveria bassiana conidia, and the liberated CLSP2 CTL-type domain binds to fungal cell components and B. bassiana conidia. Furthermore, CLPS2 RNA interference silencing significantly increases the resistance to the fungal challenge. RNA-sequencing transcriptome analysis showed that the majority of immune genes were highly upregulated in the CLSP2-depleted mosquitoes infected with the fungus. The up-regulated immune gene cohorts belong to melanization and Toll pathways, but not to the IMD or JAK-STAT. A thioester-containing protein (TEP22), a member of α2-macroglobulin family, has been implicated in the CLSP2-modulated mosquito antifungal defense. Our study has contributed to a greater understanding of immune-modulating mechanisms in mosquitoes.

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. We find that over 80% of coding sequences (CDS) from the RPW contigs have high-identity homologs to known proteins with complete CDS. Gene expression analysis shows that the pupa and larval stages have the highest and lowest expression levels, respectively. In addition, we also identified more than 60 000 single nucleotide polymorphisms and 1 200 simple sequence repeat markers. This study provides the first large-scale cDNA dataset for RPW, a much-needed resource for future molecular studies.

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. mongholica are commonly used as Radix Astragali in several Asian countries, including China, Japan, and Korea. However, in addition to the two species recorded in the Chinese Pharmacopoeia, there are twenty-three species from different genera including Astragalus, Oxytropis, Hedysarum, and Glycyrrhiza, which have been used as adulterants not only in trading markets but also by the herbal medicine industry. Therefore, a simple, reliable, and accurate classification method is important for distinguishing authentic Radix Astragali from its adulterants. In this study, we acquired data for 37 samples from four related genera within the family Fabaceae. Then we compared four candidate DNA barcoding markers using ITS, matK, rbcL, and coxI sequences from nuclear, chloroplast, and mitochondrial genomes, all commonly used for plants to identify genetic variations among genera, intraspecies, and interspecies. We observed higher divergences among genera and interspecies for ITS, which have the average Kimura 2-parameter distances of 4.5% and 14.1%, respectively, whereas matK was found to have sufficient divergence at the intraspecific level. Moreover, two indels detected in the matK sequence are useful for PCR studies in distinguishing Radix Astragali from its adulterants. This study suggests that the combined barcoding regions of ITS and matK are superior barcodes for Radix Astragali and further studies should focus on evaluating the applicability and accuracy of such combined markers for a wide range of traditional Chinese herbs.

Functional annotation and analysis of expressed sequence tags from the hepatopancreas of mitten crab (Eriocheir sinensis)

Due to its popularity as a traditional food, intensive harvesting of the mitten crab (Eriocheir sinensis) is common and has lead to an increase in disease incidence, resulting in catastrophic losses to crab aquaculture. The hepatopancreas of E. sinensis is not only an important digestive organ but also an indispensable immune organ. We constructed a nonnormalized cDNA library from the hepatopancreas of E. sinensis and acquired 3,297 high-quality expressed sequence tags representing 1,178 unigenes. More than half of these unigenes were novel genes for this species; the remaining had homologs in public databases, which is of great importance for future functional research. We also investigated the association of these genes with immune processes for insight into one of the main functions of the hepatopancreas besides metabolism. Despite the relatively low sampling scalar of our cDNA library, we were able to demonstrate several important properties of the hepatopancreatic transcriptome and identified numerous genes that were closely associated with immune responses. These results might serve as the basis for an in-depth genomics study of E. sinensis, including transcriptome analysis, physical mapping, and whole genome sequencing.

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. paratyphi C, cause typhoid, a potentially fatal systemic infection. It is not known whether the typhoid agents have evolved from a common ancestor (by divergent processes) or acquired similar pathogenic traits independently (by convergent processes). Comparison of different typhoid agents with non-typhoidal Salmonella lineages will provide excellent models for studies on how similar pathogens might have evolved.

Methodologies/Principal Findings

We sequenced a strain of S. paratyphi C, RKS4594, and compared it with previously sequenced Salmonella strains. RKS4594 contains a chromosome of 4,833,080 bp and a plasmid of 55,414 bp. We predicted 4,640 intact coding sequences (4,578 in the chromosome and 62 in the plasmid) and 152 pseudogenes (149 in the chromosome and 3 in the plasmid). RKS4594 shares as many as 4346 of the 4,640 genes with a strain of S. choleraesuis, which is primarily a swine pathogen, but only 4008 genes with another human-adapted typhoid agent, S. typhi. Comparison of 3691 genes shared by all six sequenced Salmonella strains placed S. paratyphi C and S. choleraesuis together at one end, and S. typhi at the opposite end, of the phylogenetic tree, demonstrating separate ancestries of the human-adapted typhoid agents. S. paratyphi C seemed to have suffered enormous selection pressures during its adaptation to man as suggested by the differential nucleotide substitutions and different sets of pseudogenes, between S. paratyphi C and S. choleraesuis.

Conclusions

S. paratyphi C does not share a common ancestor with other human-adapted typhoid agents, supporting the convergent evolution model of the typhoid agents. S. paratyphi C has diverged from a common ancestor with S. choleraesuis by accumulating genomic novelty during adaptation to man.

[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. Six other genes are obtained encoding auxin-regulated protein, auxin response factor 4 and auxin-repressed protein in the roots of American ginseng. In addition, thirteen expressed transcripts are stress-connected proteins and twelve expressed other transcripts are closely related to plant defense in four-year-old American ginseng roots. Furthermore, 62 genes no hit in BLAST and in Interproscan may be new genes. These results indicate EST is an useful tool for research on functional genomics of P. quinquefolium and it can be applied to the molecular modification of the ginsenosides biosynthetic pathway ultimately for improving the quality of American ginseng germplasm.

Analysis of 10,000 ESTs from lymphocytes of the cynomolgus monkey to improve our understanding of its immune system

BACKGROUND

The cynomolgus monkey (Macaca fascicularis) is one of the most widely used surrogate animal models for an increasing number of human diseases and vaccines, especially immune-system-related ones. Towards a better understanding of the gene expression background upon its immunogenetics, we constructed a cDNA library from Epstein-Barr virus (EBV)-transformed B lymphocytes of a cynomolgus monkey and sequenced 10,000 randomly picked clones.

RESULTS

After processing, 8,312 high-quality expressed sequence tags (ESTs) were generated and assembled into 3,728 unigenes. Annotations of these uniquely expressed transcripts demonstrated that out of the 2,524 open reading frame (ORF) positive unigenes (mitochondrial and ribosomal sequences were not included), 98.8% shared significant similarities (E-value less than 1e-10) with the NCBI nucleotide (nt) database, while only 67.7% (E-value less than 1e-5) did so with the NCBI non-redundant protein (nr) database. Further analysis revealed that 90.0% of the unigenes that shared no similarities to the nr database could be assigned to human chromosomes, in which 75 did not match significantly to any cynomolgus monkey and human ESTs. The mapping regions to known human genes on the human genome were described in detail. The protein family and domain analysis revealed that the first, second and fourth of the most abundantly expressed protein families were all assigned to immunoglobulin and major histocompatibility complex (MHC)-related proteins. The expression profiles of these genes were compared with that of homologous genes in human blood, lymph nodes and a RAMOS cell line, which demonstrated expression changes after transformation with EBV. The degree of sequence similarity of the MHC class I and II genes to the human reference sequences was evaluated. The results indicated that class I molecules showed weak amino acid identities (<90%), while class II showed slightly higher ones.

CONCLUSION

These results indicated that the genes expressed in the cynomolgus monkey could be used to identify novel protein-coding genes and revise those incomplete or incorrect annotations in the human genome by comparative methods, since the old world monkeys and humans share high similarities at the molecular level, especially within coding regions. The identification of multiple genes involved in the immune response, their sequence variations to the human homologues, and their responses to EBV infection could provide useful information to improve our understanding of the cynomolgus monkey immune system.

[Detection of a novel mutation in COL4A5 gene from a Chinese family with X-linked alport syndrome]

By means of PCR and direct sequencing, all 51 exons and their neighbouring intronic sequences of the COL4A5 gene were analyzed to detect mutations in 17 members from a Chinese family with X-linked Alport syndrome(XLAS). At the position 2240 in exon 26, a single-base deletion(2240deIC) is found in all male patients, and a heterozygous deletion is found in all female patients, whereas no mutation is found in normal and 80 control individuals. Meanwhile, the corresponding PCR products of female patients are cloned and sequenced to confirm the results. It is concluded that the 2240deIC mutation is the underlying cause of XLAS in this family,not a polymorphism. Furthermore,this single-base deletion mutation in COL4A5 gene is first reported in X-linked Alport syndrome.

[Sequencing and analyzing of expressed sequence tags (ESTs) of pig fat tissue]

In this paper,the ESTs of pig fat tissue were sequenced and analyzed using the large-scale DNA sequencing method, 7790 high quality ESTs were gained,from which 4354 genes were obtained using cluster analysis with the STACK-PACK software, including 3609 singlet genes and 745 multicopy genes. The 4354 candidate genes were compared with BLASTN to the nr library (e =1e-10), of which 2712 were known genes, containing 1 987 singlet genes and 725 multicopy genes,there are 2 109 unknown genes and new ESTs. Based on the results of BlastN and the index of GenBank Accenssion No., the known gene expression profile of pig fat were constructed. It showed that the genes participating in metabolism held the highest proportion in the 7 sorts, and in some aspects showed the hearty metabolism activity of fat tissue. 257 total reads of the Major Histocompatibility Complex (MHC) genes in the pig fat tissue were found,including 181 singlet genes and 44 multicopy genes. They account for 44.9% of the cell and organism defense, and 5.4% of all known genes,from this we can see that the MHC has a fairly high expression degree. Comparing all ESTs related with MHC (257reads) with known pig BAC we found the partial sequences (approximately 200 bp) of the ESTs distributing to every exon of. We can predict that the ESTs in MHC contain approximately 200 bp highly consistent regions and every exon possesses one of these regions. Although these MHC sequences in different BAC have different protein domains,they are highly consistent and related with immune functions. When the MHC genes transfer to the next generation,they can duplicate repeatly and inherit stably.

[Analysis of gene expression profiles in heart tissues from two breeds of pigs]

To study the expression profiles in the heart tissues of domestic pigs,five un-normalized cDNA libraries from Danish adult female Landrace heart, biceps femoris, aorta, left ventricle tissues and Chinese adult female Erhualian heart tissue were constructed. Totally 35 180 expressed sequence tags (ESTs) were randomly sequenced. Using functional clustering and statistic methods, three gene clusters and 47 genes highly expressed in Landrace heart tissue were found. These genes are corresponding to the chaperone activity, motor activity and physiology process, implying the functional importance of the protection and movement process in heart. Between the two pig breeds, most of the differentially expressed genes are related with energy metabolism and catalytic activity, of which the majority are highly expressed in Landrace. The results indicate that the physiological activities of Landrace heart are more active and effective than Erhualian heart.

[Comparing gene density and GC content between two large genomic blocks at short arm of chromosome 3]

The present paper is to investigate gene distribution at different genomic region with different local GC content. With shout-gun technology, we sequencing two sequences at 3p25.1 and 3p26.1, at genome size 328 kb and 753 kb respectively. The 328 kb sequence,with an average GC content as high as 47.57%, has high gene density (13.7 gene/100 kb). However, another sequence at 3p26.1 only includes one exon and one intron of large gene GRM7 and the coding sequence size is 11 520 bp only taking a small part (1.31%) of the whole genome region. High percentage distribution of GC-rich repeats of SINEs explain high GC genomic region at 3p25.1 and high concentration of AT-rich repeats of LINEs at 3p26.1 lead to low GC content of the region. Our results suggest isochore structure is the result of coevolution between gene and genome.

[Genetic polymorphism of 9 STR loci in Zhuang national minority of China]

Genetic distribution for nine STR loci were determined in a Chinese Guangxi Zhuang national minority group based on STR gene scan marked by fluorescence. Sixty-two alleles and 169 genotypes were observed in 91 unrelated Zhuang individuals. The corresponding gene frequency and genotype frequency were 0.0054-0.5495 and 0.0110-0.3297 respectively. The expected and observed genotype frequency of nine STR loci was in accordance with the Hardy-Weinberg equilibrium (P > 0.05). The statistical analysis of nine STR loci showed PIC (polymorphic information content) > or = 0.6088, H (heterozygosity) > or = 0.6174, DP (discrimination power) > or = 0.8028, PPE (probability of paternity exclusion) > or = 0.8165. The genetic distance figured with 9 STR genetic data showed that there were significant differences between Chinese Zhuang national minority and the American White and the American Black, and there was little difference between Zhuang national minority and the Chinese Xi'an Han. The result of clusting showed that the present data were divided into three groups: the Black, the White and the Yellow (the Chinese).

[Genetic polymorphisms of 9 STR loci in Dongxiang ethnic group of China]

Genetic distribution for nine STR loci was determined in a Chinese Dongxing ethnic group based on STR genescan marked by fluorescence. Seventy-two alleles and 182 genotypes were observed in 94 unrelated Chinese Dongxiang individuals,with the corresponding gene frequency and genotype frequency being 0.0053-0.5825 and 0.0106-0.2660 respectively. The genotypes of nine STR loci were in accordance with the Hardy-Weinberg equilibrium (P>0.05). The statistical analysis of nine STR loci showed PIC (polymorphism information content, PIC) = or > 0.6378, H(heterozygosity, H) = or > 0.6500, DP (discrimination power, DP) = or > 0.8216, PPE (probabilities of paternity exculation, PPE) = or > 0.4903. The result indicated that there was a significant difference between Dongxiang ethnic group and the white and the black. There was no significant difference in Han nationality. These result filled the Dongxiang ethnic group-a specific group of Chinese into the genetic database and played an important role in Chinese population genetic study and forensic medicine application.

[Immunohistochemical study of S-100 protein in degenerative nerve after different pathological brachial plexus injuries]

OBJECTIVE

To explore the regularity of the change of S-100 protein in degenerative nerve after different pathological brachial plexus injuries.

METHODS

Eighty SD rats were randomly divided into two groups, right C5, C6 preganglionic injury, and postganglionic injury. The distribution and content of S-100 protein in distal degenerative nerve were detected after 1, 2, 3 and 6 months of injury by immunohistochemical methods.

RESULTS

The S-100 protein was mainly distributed along the axons. The S-100 protein positive axons of each time interval decreased after operation, with significant difference from normal nerves (P < 0.01). There was no statistically significant difference among 1, 2, 3 and 6 months group (P > 0.05). The S-100 protein stain of postganglionic group was negative.

CONCLUSION

In preganglionic injury, the functional expression of Schwann's cells in the distal stump keeps at a certain level and for a certain period. Since Schwann's cell has inductive effect on nerve regeneration, it suggests that the distal nerve stump in preganglionic injury can be used as nerve grafts.

Pulmonary arteriolar muscularization in coal workers' pneumoconiosis and its correlation with right ventricular hypertrophy

The relationship between the thickness of the walls of small pulmonary arteries (the medial wall thickness as a percentage of external diameter, percentage of medial thickness) in coal miners and control subjects were studied using morphometric techniques and correlated with the degree of right ventricular hypertrophy, severity of coal workers' pneumoconiosis, emphysema, and other chronic lung diseases. Pulmonary arteries less than 100 microns in external diameter were identified and the external diameter, medial thickness, and intimal thickness were quantitatively measured in the lung tissues of 57 coal miners and 15 control subjects with and without other chronic lung diseases. Coal workers' pneumoconiosis, emphysema, and right ventricular hypertrophy were assessed uniformly in all cases. The arterial wall thickness correlated with right ventricular hypertrophy, progressive massive fibrosis, and other chronic lung diseases. Severity of emphysema also showed a weak correlation. Although the functional significance of these findings is not known, we conclude that the muscularization of pulmonary arterioles provides a structural basis for the development of right ventricular hypertrophy in coal miners.