The First High-quality Reference Genome of Sika Deer Provides Insights into High-tannin Adaptation.

Sika deer are known to prefer oak leaves, which are rich in tannins and toxic to most mammals; however, the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear. In identifying the mechanism responsible for the tolerance of a highly toxic diet, we have made a major advancement by explaining the genome of sika deer. We generated the first high-quality, chromosome-level genome assembly of sika deer and measured the correlation between tannin intake and RNA expression in 15 tissues through 180 experiments. Comparative genome analyses showed that the UGT and CYP gene families are functionally involved in the adaptation of sika deer to high-tannin food, especially the expansion of the UGT family 2 subfamily B of UGT genes. The first chromosome-level assembly and genetic characterization of the tolerance to a highly toxic diet suggest that the sika deer genome may serve as an essential resource for understanding evolutionary events and tannin adaptation. Our study provides a paradigm of comparative expressive genomics that can be applied to the study of unique biological features in non-model animals.

Chaperonin containing TCP1 subunit 5 is a tumor associated antigen of non-small cell lung cancer.

Novel tumor antigens and their related autoantibodies have tremendous potential for early diagnosis of non-small cell lung cancer (NSCLC). In this study, we identify antigens from NSCLC tissue and autoantibodies in sera of patients with NSCLC using a modified proteomics-based approach. We seperated and identified four NSCLC-associated proteins extracted from the cytosol in tumor tissues by mini-two-dimensional gel electrophoresis, followed by Western blot and hybridization with individual sera for confirmation of antibody binding. Of the proteins we identified, we selected 58 kDa chaperonin containing TCP1(T-Complex Protein 1) subunit 5 (CCT5) for validation. Serum levels of carcinoembryonic antigen (CEA) and cytokeratin 19 fragments (CYFRA 21-1) were measured in all serum samples with an immunoluminometric assay and a receiver operating characteristic (ROC) curve was analyzed for autoantibodies against CCT5, CEA and CYFRA 21-1. The results show that CCT5 can induce an autoantibody response in NSCLC sera and show higher expression in NSCLC tissues by immunohistochemistry and Western blot. Anti-CCT5 autoantibody was found in 51% (23/45) of patients with NSCLC, but only 2.5% (1/40) in non-tumor individual controls. A receiver operating characteristic curve constructed with a panel of autoantibodies against CCT5 (AUC=0.749), CEA (AUC=0.6758), and CYFRA 21-1(AUC=0.760) show a sensitivity of 51.1% and 97.5% specificity in discriminating NSCLC from matched controls. These results indicate the potential utility of screening autoantibodies in sera, show that CCT5 could be used as a biomarker in cancer diagnosis.

Comparative Transcriptome Analysis of Mink (Neovison vison) Skin Reveals the Key Genes Involved in the Melanogenesis of Black and White Coat Colour.

Farmed mink (Neovison vison) is one of the most important fur-bearing species worldwide, and coat colour is a crucial qualitative characteristic that contributes to the economic value of the fur. To identify additional genes that may play important roles in coat colour regulation, Illumina/Solexa high-throughput sequencing technology was used to catalogue the global gene expression profiles in mink skin with two different coat colours (black and white). RNA-seq analysis indicated that a total of 12,557 genes were differentially expressed in black versus white minks, with 3,530 genes up-regulated and 9,027 genes down-regulated in black minks. Significant differences were not observed in the expression of MC1R and TYR between the two different coat colours, and the expression of ASIP was not detected in the mink skin of either coat colour. The expression levels of KITLG, LEF1, DCT, TYRP1, PMEL, Myo5a, Rab27a and SLC7A11 were validated by qRT-PCR, and the results were consistent with RNA-seq analysis. This study provides several candidate genes that may be associated with the development of two coat colours in mink skin. These results will expand our understanding of the complex molecular mechanisms underlying skin physiology and melanogenesis in mink and will provide a foundation for future studies.

Epidemiology and antifungal susceptibilities of yeast isolates causing invasive infections across urban Beijing, China.

AIM: To investigate the species distribution and antifungal susceptibility profiles of yeast isolates causing invasive infections across Beijing. MATERIALS & METHODS: A total of 1201 yeast isolates recovered from blood and other sterile body fluids were correctly identified by matrix-assisted laser desorption/ionization TOF MS supplemented by DNA sequencing. Antifungal susceptibility testing was performed according to the Clinical and Laboratory Standards Institute broth microdilution method. RESULTS: Candida (95.5%) remained the most common yeast species isolated; Candida albicans (38.8%) and Candida parapsilosis (22.6%) were the leading species of candidemia. Azole resistances were mainly observed in Candida glabrata and Candida tropicalis isolates. CONCLUSION: This study outlined the epidemiologic data of invasive yeast infections and highlighted the need for continuous monitoring of azole resistances among C. glabrata and C. tropicalis isolates in Beijing.

Effect of vitrification on meiotic maturation, mitochondrial distribution and glutathione synthesis in immature silver fox cumulus oocyte complexes.

The present study was designed to investigate the effects of vitrifying oocytes obtained from silver foxes on nuclear maturation, mitochondrial distribution and glutathione (GSH) synthesis after in vitro culture for 72 h. Immature oocytes were randomly divided into three groups: (1) fresh GV (germinal vesicle) oocytes (Control group), (2) exposure to the equilibration and vitrification solution but without being plunged into liquid nitrogen (exposed group), and (3) vitrification by the cryoloop method (vitrified-warmed group). The number of survival oocytes was not decreased by either being exposed to the cryoprotectant or being vitrified-warmed compared with the control group (P > 0.05). After IVM, the percentage of resumption of meiosis for vitrified-warmed oocytes (41.9%) was significantly lower than in the control (81.2%) and exposed (79.1%) groups (P < 0.05). However, the proportion of oocytes reaching the metaphase II (MII) stage was similar among the different groups (11.4%, 9.3% and 5.2%, respectively, P > 0.05). The translocation of active mitochondria during fox oocyte maturation was revealed using MitoTracker Red staining and confocal laser microscopy. For fresh oocytes at the GV stage, active mitochondria were distributed around the entire cortex with small granulations and various-sized cavities (no MitoTracker signals). After IVM, the mitochondria formed large granulations and clumps throughout the cytoplasm. Vitrification significantly decreased the proportion of MII oocytes with normal mitochondrial distribution compared with the control and exposed groups (35.4%, 71.9% and 59.2%, respectively, P < 0.05). Similarly, the GSH content was significantly lower in vitrified-warmed oocytes compared with the control and exposed oocytes after IVM (3.4, 5.7 and 4.7 pM/oocyte, respectively, P < 0.05). However, no significant difference was observed between the cryoprotectant exposed and control groups with regard to the normal mitochondrial distribution or GSH content (P > 0.05). These results indicate that vitrification of fox immature oocytes using a cryoloop allows them to resume meiosis and develop to the MII stage. The damage to mitochondria and the GSH synthesis deficiency may be associated with the reduced developmental competence of cryopreserved oocytes.

Serum GROß: a potential tumor-associated biomarker for colorectal cancer.

OBJECTIVE: This study aimed to confirm the potential of growth-related gene product ß (GROß) as a biomarker for colorectal cancer. We compared serum GROß levels in patients with colorectal cancer, healthy individuals and individuals with non-tumor diseases. METHODS: We measured serum GROß levels with enzyme-linked immunosorbent assay in patients with colorectal cancer (123 preoperative samples and 66 postoperative samples), 88 healthy controls and 125 individuals with other diseases. Serum levels of carcinoembryonic antigen (CEA) and carbohydrate antigen 19-9 (CA19-9) were measured in all samples with an immunoluminometric assay. Statistical analyses were performed to determine associations between serum GROß levels and clinical parameters for colorectal cancer. A receiver operating characteristic (ROC) curve was analyzed for GROß, CEA and CA19-9. RESULTS: The serum GROß levels were much higher in patients with colorectal cancer (median: 96.15 pg/ml) than those in healthy controls (median: 43.28 pg/ml, P < 0.01) and other disease controls (median: 57.30 pg/ml, P < 0.01). Serum GROß levels in colorectal cancer were correlated positively with tumor-node-metastasis staging (P < 0.01) and the depth of infiltration (P < 0.05), but not with the histological grade, tumor embolus, lymph node metastasis, gross pathologic tumor type, or patient gender. The sensitivity and specificity of the assay for serum GROß were 56.1% (69/123) and 95.31% (203/213), respectively. The area under the ROC curve constructed with GROß (0.834) was larger than that constructed with CEA (0.739) or CA19-9 (0.676) for discriminating colorectal cancer from matched controls. CONCLUSION: These preliminary results suggested that the serum GROß level could be a useful biomarker for colorectal cancer diagnoses.

Novel amdoparvovirus infecting farmed raccoon dogs and arctic foxes.

A new amdoparvovirus, named raccoon dog and fox amdoparvovirus (RFAV), was identified in farmed sick raccoon dogs and arctic foxes. Phylogenetic analyses showed that RFAV belongs to a new species within the genus Amdoparvovirus of the family Parvoviridae. An RFAV strain was isolated in Crandell feline kidney cell culture.

Dietary copper supplementation improves pelt characteristics of female silver fox (Vulpes fulva) during the winter fur-growing season.

Copper has an essential role in normal fur pigmentation and fur quality. This study evaluated the effects of cupric citrate (CuCit) supplementation on growth, nutrients metabolism and pelt characteristics of the female silver fox (Vulpes fulva). Fifty age-matched female silver foxes with similar body weights were randomly divided into five dietary groups for 58 days during the winter fur-growing season. The basal diet contained 4.92 mg/kg copper. Groups I-V were supplemented with 6, 30, 60, 90 or 150 mg Cu from CuCit per 1 kg dry matter basal diet. Serum alkaline phosphatase activity was significantly higher (P<0.05) in those fed 90 mg/kg Cu than those fed 150 mg/kg Cu. Pelt total thickness was significantly higher (P<0.05) in those fed 30 mg/kg Cu than foxes fed 6 mg/kg Cu supplemented diet, but were similar to the other groups. Length of guard hair was significantly lower (P<0.05) in those fed 90 mg/kg Cu than fed 6 mg/kg Cu and 30 mg/kg Cu, but were similar to the other groups. Length of underhair was significantly higher (P<0.05) in those fed 6 mg/kg Cu than those fed 90 mg/kg Cu, but was similar to the other groups. Considering decreasing environmental contamination and improving pelt performance, supplementing 30 mg/kg Cu from CuCit (actual copper 35 mg/kg dry matter) is appropriate for female silver fox.

Evaluation of serum diagnosis of pancreatic cancer by using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry.

Proteomic methods have been widely used in disease marker discovery research. The aim of this study was to discover potential biomarkers for pancreatic cancer (PCa) using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS). Crude serum samples from 132 patients with PCa and 67 healthy controls (HCs) were analyzed in duplicate using SELDI. Support vector machine (SVM) analysis of the spectra was used to generate a predictive algorithm based on proteins that were maximally differentially expressed between patients with PCa and the HCs in the training cohort. This algorithm was tested using leave-one-out cross-validation in the test cohort. From the 4 significant peaks in the training cohort, a classifier for separating patients with PCa from HCs was developed. The classifier was challenged with all samples achieving 96.67% sensitivity and 100% specificity in the training cohort and 93.1% sensitivity and 78.57% specificity in the test cohort. Additionally, the classifier correctly classified 12/12 stage Ia and 13/16 stage IIa PCa cases. The combination of the SELDI panel and CA19-9 was superior to CA19-9 alone in distinguishing individuals with PCa from the healthy subject group. These results suggest that high-throughput proteomic profiling has the capacity to provide new biomarkers for the early detection and diagnosis of PCa.

Identification and expression of a tumor-associated antigen in esophageal squamous cell carcinoma.

OBJECTIVE: To search for novel tumor associated antigens (TAA) in esophageal squamous cell carcinoma (ESCC). METHODS: The proteins extracted from tissues of ESCC were separated by two dimensional polyacrylamide gel electrophoresis and transferred to PVDF membrane. Sera from ESCC patients and healthy individuals were used for primary antibodies for Western blot analysis. The differential spots were excised for trypsin hydrolysis and the tryptic peptides were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The identified TAA of ESCC was validated by immunohistochemical staining (IHC). RESULTS: Sera from ESCC patients yielded multiple positive spots, and one 28 800 Da protein that exhibited positive reactivity with 60% (12/20) sera of ESCC patients and only 5% (1/20) sera of healthy controls (P<0.01). The 28 800 Da protein was identified as phosphoglycerate mutase 1 (PGAM1) by MALDI-TOF-MS. Immunohistochemical analysis showed that PGAM1 was located in both cytoplasm and nucleus, and had a higher expression in cancer tissues. CONCLUSION: PGAM1 maybe a candidate of ESCC.

Determination and analysis of complete mitochondrial genome sequence of mallard (Anas platyrhychos).

The complete mitochondrial genome (mtDNA) of mallard (Anas platyrhychos) was determined by long and accurate polymerase chain reaction and with primer walking sequence method. The entire genome was 16,606 bp in length. Similar to the typical mtDNA of vertebrates, it contained 37 genes (13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes) and a non-coding region (D-loop). The characteristics of the mitochondrial genome were analyzed and discussed in detail.