Objective To observe the value of virtual tough tissue imaging quantification (VTIQ) in differential diagnosis of thyroid imaging reporting and data system(TI-RADS) 4 thyroid nodules.Methods A total of 185 patients with 192 TI-RADS 4 nodules were included in this study.The nodules were divided into three groups according to the maximum size as follows:Group Ⅰ,the maximum size≤0.6 cm;Group Ⅱ,0.6 cm＜ the maximum size≤ 1.0 cm;Group Ⅲ,the maximum size ＞ 1.0 cm.Shear wave velocities (SWV) of nodules were measured by means of VTIQ technique.With pathological diagnosis as the gold standard,SWV value of benign and malignant nodules were analyzed and ROC curve was drawn to assess the diagnostic efficiency.Results By the ROC curve test,at SWV cut-off values of 2.44 m/s for group Ⅰ and group Ⅱ,2.49 m/s for group Ⅲ,the sensitivity were 79.0 ％,76.0 ％,88.6％,specificity were 88.6％,89.5 ％,93.7 ％,accuracy were 83.5 ％,81.8 ％,90.1％,Youden index were 0.68,0.66,0.82,respectively.Conclusions VTIQ can reflect the hardness of TI-RADS 4 nodules,the value of the differential diagnosis of such nodules is high,convenient,noninvasive and not limited by the size of nodules.

Objective To explore the ultrasonographic features and diagnostic value of the appendix diseases. Methods Ultrasonographic findings of 6 093 cases confirmed suffering from appendix disease by surgery, pathology or clinical were analyzed retrospectively. Results All cases were classified as follows, 1 073 cases of acute simple appendicitis, 2 810 cases of acute suppurative appendicitis, 521 cases of acute gangrene appendicitis, 679 cases of appendix ab-scess, 976 cases of chronic appendicitis, 2 cases of appendix diverticulitis, 15 cases of appendix mucous cyst, 9 cases of appendix bursae adenoma, 3 cases of appendix mucous cyst-adenocarcinoma, 2 cases of adenocarcinoma of the ap-pendix, 3 cases of carcinoid appendix. All of which had certain ultrasonographic features and those features in ultra-sonographic findings played a decisive role in the differential diagnosis. Diagnosis coincide rate of ultrasound was 86.9%(5 295/6 093). Conclusion Ultrasonic examination is valuable in diagnosis of the appendix diseases.

Objective To explore the ultrasonographic features and diagnostic value of the axillary masses. Methods Ultrasonographic findings of 275 cases confirmed suffering from axillary mass by operation or puncture biopsy and pathology were analyzed retrospectively. Results All cases were classified as follows, 86 cases of accessory, 158 cases of lesions of lymph node, 23 cases of benign tumor, 2 cases of abscess, 6 cases of radical mastectomy of breast cancer axillary effusion. Diagnosis sensitivity rate of ultrasound was 98.2%, diagnosis coincide rate of ultrasound was 97.1%. Conclusion Axillary masses have certain ultrasonographic features, Ultrasonic examination can be used as an important means of the diagnosis of axillary mass.

Since pig is an important livestock species worldwide, its gene expression has been investigated intensively, but rarely in brain. In order to study gene expression profiles in the pig central nervous system, we sequenced and analyzed 43,122 highquality 5′ end expressed sequence tags (ESTs) from porcine cerebellum, cortex cerebrum, and brain stem cDNA libraries, involving several different prenatal and postnatal developmental stages. The initial ESTs were assembled into 16,101 clusters and compared to protein and nucleic acid databases in GenBank. Of these sequences, 30.6% clusters matched protein databases and represented function known sequences; 75.1% had significant hits to nucleic acid databases and partial represented known function; 73.3% matched known porcine ESTs; and 21.5% had no matches to any known sequences in GenBank. We used the categories defined by the Gene Ontology to survey gene expression in the porcine brain.

Ribonucleic acid (RNA) deserves not only a dedicated field of biological research -- a discipline or branch of knowledge -- but also explicit definitions of its roles in cellular processes and molecular mechanisms. Ribogenomics is to study the biology of cellular RNAs, including their origin, biogenesis, structure and function. On the informational track, messenger RNAs (mRNAs) are the major component of ribogenomes, which encode proteins and serve as one of the four major components of the translation machinery and whose expression is regulated at multiple levels by other operational RNAs. On the operational track, there are several diverse types of RNAs--their length distribution is perhaps the most simplistic stratification--involving in major cellular activ-ities, such as chromosomal structure and organization, DNA replication and repair, transcriptional/post-transcriptional regulation, RNA processing and routing, translation and cellular energy/metabolism regulation. An all-out effort exceeding the magnitude of the Human Genome Project is of essence to construct just mammalian transcriptomes in multiple contexts including embryonic development, circadian and seasonal rhythms, defined life-span stages, pathological conditions and anatomy-driven tissue/organ/cell types.

Objective To construct the UAS-Hey transgenic fly strains to provide a tool for researching the function of Hey gene in the fly development.Methods The Hey gene coding sequence was amplified by reverse transcription PCR and subcloned into pUAST expression vector.The pUAS-Hey recombinant plasmid was constructed and microinjected into the embryos of wild type flies.The UAS-Hey transgenic flies with red eyes were screened out with mini-white marker,then the balancing and mapping of these transgenic strains were performed.The identification was performed by using the PCR amplification method.Results The pUAS-Hey recombinant plasmid was successfully constructed,and seven independent transgenic strains were obtained by microinjection and transgenic fly screening and balance.PCR analysis confirmed that the P[mini-white,UAS-Hey] was integrated into genomes of transgenic strains and was in expressible region.Conclusion The UAS-Hey transgenic flies are successfully constructed,which lays the foundation for further studies of the function and regulation of Hey gene with GAL4/UAS system.

OBJECTIVETo study the severe acute respiratory syndrome (SARS)-associated coronavirus genotype and its characteristics.

METHODSA SARS-associated coronavirus isolate named ZJ01 was obtained from throat swab samples taken from a patient in Hangzhou, Zhejing province. The complete genome sequence of ZJ01 consisted of 29,715 bp (GenBank accession: AY297028, version: gi: 30910859). Seventeen SARS-associated coronavirus genome sequences in GenBank were compared to analyze the common sequence variations and the probability of co-occurrence of multiple polymorphisms or mutations. Phylogenetic analysis of those sequences was done.

RESULTSBy bioinformatics processing and analysis, the 5 loci nucleotides at ZJ01 genome were found being T, T, G, T and T, respectively. Compared with other SARS-associated coronavirus genomes in the GenBank database, an A/G mutation was detected besides the other 4 mutation loci (C:G:C:C/T:T:T:T) involved in this genetic signature. Therefore a new definition was put forward according to the 5 mutation loci. SARS-associated coronavirus strains would be grouped into two genotypes (C:G:A:C:C/T:T:G:T:T), and abbreviated as SARS coronavirus C genotype and T genotype. On the basis of this new definition, the ZJ01 isolate belongs to SARS-associated coronavirus T genotype, first discovered and reported in mainland China. Phylogenetic analysis of the spike protein gene fragments of these SARS-associated coronavirus strains showed that the GZ01 isolate was phylogenetically distinct from other isolates, and compared with groups F1 and F2 of the T genotype, the isolates of BJ01 and CUHK-W1 were more closely related to the GZ01 isolate. It was interesting to find that two (A/G and C/T) of the five mutation loci occurred in the spike protein gene, which caused changes of Asp to Gly and Thr to Ile in the protein, respectively.

CONCLUSIONAttention should be paid to whether these genotype and mutation patterns are related to the virus's biological activities,epidemic characteristics and host clinical symptoms.

Baylisascaris schroederi,a roundworm(ascaridoid)parasite specific to the bamboo-feeding giant panda(Ailuropoda melanoleuca),represents a leading cause of mortality in wild giant panda populations.Here,we present a 293-megabase chromosome-level genome assembly of B.schroederi to infer its biology,including host adaptations.Comparative genomics revealed an evolutionary trajectory accompanied by host-shift events in ascaridoid parasite lineages after host separations,suggesting their potential for transmission and rapid adaptation to new hosts.Genomic and anatomical lines of evidence,including expansion and positive selection of genes related to the cuticle and basal metabolisms,indicate that B.schroederi undergoes specific adaptations to survive in the sharp-edged bamboo-enriched gut of giant pandas by structurally increasing its cuticle thickness and efficiently utilizing host nutrients through gut parasitism.Additionally,we characterized the secretome of B.schroederi and predicted potential drug and vaccine targets for new control strategies.Overall,this genome resource provides new insights into the host adaptation of B.schroederi to the giant panda as well as the host-shift events in ascaridoid parasite lineages.Our findings on the unique biology of B.schroederi will also aid in the development of prevention and treatment measures to protect giant panda populations from roundworm parasitism.

Genome reannotation aims for complete and accurate characterization of gene models and thus is of critical significance for in-depth exploration of gene function. Although the availability of massive RNA-seq data provides great opportunities for gene model refinement, few efforts have been made to adopt these precious data in rice genome reannotation. Here we reannotate the rice (Oryza sativa L. ssp. japonica) genome based on integration of large-scale RNA-seq data and release a new annotation system IC4R-2.0. In general, IC4R-2.0 significantly improves the completeness of gene structure, identifies a number of novel genes, and integrates a variety of functional annota-tions. Furthermore, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are system-atically characterized in the rice genome. Performance evaluation shows that compared to previous annotation systems, IC4R-2.0 achieves higher integrity and quality, primarily attributable to mas-sive RNA-seq data applied in genome annotation. Consequently, we incorporate the improvedannotations into the Information Commons for Rice (IC4R), a database integrating multiple omics data of rice, and accordingly update IC4R by providing more user-friendly web interfaces and implementing a series of practical online tools. Together, the updated IC4R, which is equipped with the improved annotations, bears great promise for comparative and functional genomic studies in rice and other monocotyledonous species. The IC4R-2.0 annotation system and related resources are freely accessible at http://ic4r.org/.

The rapid development of high-throughput sequencing technologies has led to a dramatic decrease in the money and time required for de novo genome sequencing or genome resequencing projects, with new genome sequences constantly released every week. Among such projects, the plethora of updated genome assemblies induces the requirement of version-dependent annotation files and other compatible public dataset for downstream analysis. To handle these tasks in an efficient manner, we developed the reference-based genome assembly and annotation tool (RGAAT), a flexible toolkit for resequencing-based consensus building and annotation update. RGAAT can detect sequence variants with comparable precision, specificity, and sensitivity to GATK and with higher precision and specificity than Freebayes and SAMtools on four DNA-seq datasets tested in this study. RGAAT can also identify sequence variants based on cross-cultivar or cross-version genomic alignments. Unlike GATK and SAMtools/BCFtools, RGAAT builds the consensus sequence by taking into account the true allele frequency. Finally, RGAAT generates a coordinate conversion file between the reference and query genomes using sequence variants and supports annotation file transfer. Compared to the rapid annotation transfer tool (RATT), RGAAT displays better performance characteristics for annotation transfer between different genome assemblies, strains, and species. In addition, RGAAT can be used for genome modification, genome comparison, and coordinate conversion. RGAAT is available at https://sourceforge.net/projects/rgaat/ and https://github.com/wushyer/RGAAT_v2 at no cost.
Genome ; Genomics ; High-Throughput Nucleotide Sequencing ; methods ; standards ; Humans ; Reference Standards ; Sequence Analysis, DNA ; methods ; standards ; Software