Shuting Li

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000-40,000. Only 2%-3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.

The objective of the present study was to differentiate the sarcoplasmic proteome of color-stable (Longissimus lumborum; LL) and color-labile (Psoas major; PM) beef muscles. LL and PM muscles from seven beef carcasses (24 h post-mortem) were fabricated into 2.54 cm steaks, aerobically packaged, and assigned to refrigerated retail display for 9 days. LL steaks demonstrated greater (P < 0.05) color stability and lower (P < 0.05) lipid oxidation than PM steaks. Proteome analyses identified 16 differentially abundant proteins in LL and PM, including antioxidant proteins and chaperones. Proteins demonstrating positive correlation with redness (aldose reductase, creatine kinase, and β-enolase) and color stability (peroxiredoxin-2, peptide methionine sulfoxide reductase, and heat shock protein-27 kDa) were overabundant in LL, whereas the protein overabundant in PM (mitochondrial aconitase) exhibited negative correlation with redness. The color stability of LL could be attributed to the overabundance of antioxidant proteins and chaperones, and this finding suggests the necessity of developing muscle-specific processing strategies to improve beef color.

Elucidating the cellular organization of the cerebral cortex is critical for understanding brain structure and function. Using large-scale single-nucleus RNA sequencing and spatial transcriptomic analysis of 143 macaque cortical regions, we obtained a comprehensive atlas of 264 transcriptome-defined cortical cell types and mapped their spatial distribution across the entire cortex. We characterized the cortical layer and region preferences of glutamatergic, GABAergic, and non-neuronal cell types, as well as regional differences in cell-type composition and neighborhood complexity. Notably, we discovered a relationship between the regional distribution of various cell types and the region's hierarchical level in the visual and somatosensory systems. Cross-species comparison of transcriptomic data from human, macaque, and mouse cortices further revealed primate-specific cell types that are enriched in layer 4, with their marker genes expressed in a region-dependent manner. Our data provide a cellular and molecular basis for understanding the evolution, development, aging, and pathogenesis of the primate brain.

The clinical outcomes and therapeutic strategies for infiltrating ductal carcinoma (IDC) and infiltrating lobular carcinoma (ILC) are not uniform. The primary objectives of this study were to identify the differences in the clinical characteristics and prognoses between ILC and IDC, and identify the high-risk population based on the hormone receptor status and metastasis sites. The Surveillance, Epidemiology, and End Results Program database was searched and patients diagnosed with ILC or IDC from 1990 to 2013 were identified. In total,796,335 patients were analyzed, including 85,048 withILC (10.7%) and 711,287 withIDC (89.3%). The ILC group was correlatedwith older age, larger tumor size, later stage, lower grade, metastasis disease(M1) disease, and greater counts ofpositive lymph nodesandestrogen-receptor-positive (ER)/progesterone receptor-positive (PR) positive nodes. The overall survival showed an early advantage for ILC but a worse outcome after 5 years. Regarding the disease-specific survival, the IDC cohort had advantages over the ILC group, both during the early years and long-term. In hormone status and metastasis site subgroup analyses, the ER+/PR+ subgroup had the best survival, while the ER+/PR- subgroup had the worst outcome, especially the ILC cohort. ILC and IDC had different metastasis patterns. The proportion of bone metastasis was higher in the ILC group (91.52%) than that in the IDC (76.04%), and the ILC group was more likely to have multiple metastasis sites. Survival analyses showed patients with ILC had a higher risk of liver metastasis (disease-specific survival[DSS]; P = 0.046), but had a better overall survival than the bone metastasis group (P<0.0001). We concluded that the long-term prognosis for ILC was poorer than that for IDC, and the ER+/PR- subgroup had the worst outcome. Therefore, the metastasis pattern and prognosis must be seriously evaluated, and a combination of endocrine therapy and chemotherapy should be considered.

// Shuting Li 1 , Yanwei Shen 1 , Mengying Wang 2, 3 , Jiao Yang 1 , Meng Lv 1 , Pan Li 1 , Zheling Chen 1 , Jin Yang 1 1 Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, P.R. China 2 Institute of Endemic Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, P.R. China 3 Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, P.R. China Correspondence to: Jin Yang, email: 1473106133@qq.com Keywords: PTEN, breast cancer, prognosis, meta-analysis Received: January 17, 2017&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Accepted: March 22, 2017&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Published: March 31, 2017 ABSTRACT Various studies have evaluated the significance of PTEN (phosphatase and tensin homolog deleted from chromosome 10) expression in breast cancer, but their results remain controversial. We conducted a meta-analysis to evaluate the associations of PTEN expression with clinicopathological characteristics and prognosis in breast cancer. PubMed, Embase, Web of Science, and China National Knowledge Infrastructure were searched to identify relevant publications. The associations between PTEN expression and clinicopathological parameters, disease-free survival (DFS), and overall survival (OS) were then assessed via meta-analyses of odds ratio (ORs) and hazard ratio (HRs) with 95% confidence intervals (CIs). Based on 27 studies involving 10,231 patients, the pooled results revealed that PTEN loss was significantly more common in breast cancer than in normal tissues (OR = 12.15, 95% CI = 6.48&ndash;22.79, P &lt; 0.00001) and that PTEN loss had clear associations with larger tumor size (&gt; 2 cm, OR = 0.62, 95% CI = 0.48&ndash;0.82, P = 0.0006), lymph node metastasis(OR = 0.61, 95% CI = 0.45&ndash;0.82, P = 0.0001), later TNM stage(stage III&ndash;IV, OR = 0.55, 95% CI = 0.35&ndash;0.86, P = 0.009), poor differentiation(OR = 0.37, 95% CI = 0.24&ndash;0.59, P &lt; 0.0001), and the highly aggressive triple-negative phenotype (OR = 1.62, 95% CI = 1.23&ndash;2.12, P = 0.0005). Moreover, patients with PTEN loss exhibited significantly worse DFS and OS(HR = 1.63, 95% CI = 1.04&ndash;2.22, P &lt; 0.00001; HR = 1.41, 95% CI = 1.08&ndash;1.73, P &lt; 0.0001; respectively). In conclusion, PTEN loss might predict more aggressive behavior and worse outcomes in patients with breast cancer.