Closing a gap in the physical map of the ovine major histocompatibility complex

A 184 kb gap in an ovine MHC physical map was successfully closed by identification of two overlapping clones (304C7 and 222G18) from a Chinese fine wool merino sheep BAC library. The location and tiling path of the two clones were confirmed by BAC-end sequencing and PCR amplification of loci in overlapping regions. Full-length sequencing of the clones identified 13 novel ovine genes in the gap between loci Notch4 and Btnl2, and eight of them belonging to the Butyrophilin-like (Btn-like or Btnl) gene family. The scattered distribution of the Btnl gene cluster at the gap provided a clue to explain the difficulties previously experienced in closing the gap. Completed BAC contigs of the ovine MHC will facilitate sequencing of the entire ovine leukocyte antigen (OLA) region, providing detailed information for comparative studies of MHC evolution.

Paradoxical effects of all-trans-retinoic acid on lupus-like disease in the MRL/lpr mouse model

Roles of all-trans-retinoic acid (tRA), a metabolite of vitamin A (VA), in both tolerogenic and immunogenic responses are documented. However, how tRA affects the development of systemic autoimmunity is poorly understood. Here we demonstrate that tRA have paradoxical effects on the development of autoimmune lupus in the MRL/lpr mouse model. We administered, orally, tRA or VA mixed with 10% of tRA (referred to as VARA) to female mice starting from 6 weeks of age. At this age, the mice do not exhibit overt clinical signs of lupus. However, the immunogenic environment preceding disease onset has been established as evidenced by an increase of total IgM/IgG in the plasma and expansion of lymphocytes and dendritic cells in secondary lymphoid organs. After 8 weeks of tRA, but not VARA treatment, significantly higher pathological scores in the skin, brain and lung were observed. These were accompanied by a marked increase in B-cell responses that included autoantibody production and enhanced expression of plasma cell-promoting cytokines. Paradoxically, the number of lymphocytes in the mesenteric lymph node decreased with tRA that led to significantly reduced lymphadenopathy. In addition, tRA differentially affected renal pathology, increasing leukocyte infiltration of renal tubulointerstitium while restoring the size of glomeruli in the kidney cortex. In contrast, minimal induction of inflammation with tRA in the absence of an immunogenic environment in the control mice was observed. Altogether, our results suggest that under a predisposed immunogenic environment in autoimmune lupus, tRA may decrease inflammation in some organs while generating more severe disease in others.

Gene silencing of non-obese diabetic receptor family (NLRP3) protects against the sepsis-induced hyper-bile acidaemia in a rat model

The role of NOD-like receptor family (NLRP3) has been confirmed in various inflammatory diseases. The association between NLRP3 and hyper-bileacidaemia during the sepsis remains unclear. We aimed to investigate whether NLRP3 silencing protects against the sepsis-induced hyper-bileacidaemia. Sepsis was induced by caecum ligation and puncture (CLP). Gene silencing of NLRP3 was performed by injecting rats with NLRP3 short hairpin RNA plasmids (NLRP3 shRNA) 48 h before surgery. Rats were divided into four groups: group 1: sham; group 2: sepsis; group 3: NLRP3 shRNA + sepsis (called the 'NLRP3 shRNA' group); and group 4: scrambled shRNA + sepsis (called the 'scrambled shRNA' group). The serum levels of bile acids, hepatic expression of hepatocyte membrane transporters, hepatic cytokine levels and behaviours of immune cells were compared among the groups. Hepatic NLRP3 expression was increased dramatically during the sepsis, but was suppressed by pretreatment with NLRP3 shRNA. Compared with rats in the sepsis and the scrambled shRNA groups, rats in the NLRP3 shRNA group exhibited significantly decreased serum levels of glycine and taurine conjugated-bile acids, with rehabilitated expression of hepatocyte transporters, suppressed hepatic cytokine levels, decreased hepatic neutrophils infiltration and attenuated macrophages pyroptosis. Gene silencing of NLRP3 ameliorates sepsis-induced hyper-bileacidaemia by rehabilitating hepatocyte transporter expression, reducing hepatic cytokine levels, neutrophil infiltration and macrophages pyroptosis. NLRP3 may be a pivotal target for sepsis management.

Assessment of heavy metals in surface sediments from Gansu section of Yellow River, China

The concentrations of Cu, Fe, Mn, Ni, Zn, Cr, Pb, and Cd in 28 samples collected from bottom sediments in the Gansu section of Yellow River, China, were investigated in order to evaluate their distribution and pollution level. The measured metals in the sediments were found to be in the range of Cu 15.52∼57.50 mg/kg, Fe 19593.24∼69963.42 mg/kg, Mn 472.70∼1491.67 mg/kg, Ni 5.10∼74.28 mg/kg, Zn 64.61∼173.83 mg/kg, Cr 57.68∼183.47 mg/kg, Pb 1.21∼28.36 mg/kg, and Cd 0.35∼4.25 mg/kg. The mean values of the heavy metal contents were arranged in the following decreasing order: Fe > Mn > Cr > Zn > Ni > Cu > Pb > Cd. There were significantly positive correlations between Cu, Fe, Mn, and Zn. However, principal component analysis (PCA) extracted two factors with Eigenvalues explaining 62.15 % of the total variance. Cu, Fe, Mn, Zn, and Cr had a natural origin controlled by the first factor. Ni and Pb could originate anthropogenic sources controlled by the second factor. Cd could be affected by natural geological background and human activity. It was attributed principally to anthropogenic activities that the geo-accumulation index, enrichment factor, and pollution load index of Cr were all higher than other measured metals. Zn appears to pose no risk at all of the sites of the system. The pollution class of sediment from the Gansu section in the upstream of Yellow River was 0∼1, from unpolluted to moderately polluted degree.

Genome-wide association study identifies QTLs for EBV of backfat thickness and average daily gain in Duroc pigs

Backfat thickness (BFT) and average daily gain (ADG) are two important economic traits in commercial swine production. Identifying QTLs and uncovering the molecular mechanism for BFT and ADG would greatly help to speed up the breeding progress. In current breeding program, EBV for these two traits are calculated and formulated a comprehensive breeding index, which then be used to improve pig performance. Using Illumina PorcineSNP60 BeadChip, a pilot genomewide association studies (GWAS) for BFT and ADG in 83 Duroc pigs were performed. A total of 31 genome-wise significant SN Ps were detected to be associated with BFT on SSC 4, 9, 11, 12 and 14, ten of which were coincident with previously reported QTL regions. There are two genome-wise loci prominently associated with ADG on SSC2 and SSC13, respectively. The two loci on SSC2 are well overlapped with the QTL regions previously reported. All the 31 significant SNPs associated with BFT are verified on 219 outbreed pigs, six SN Ps reach an extreme significant level and seven SNP reaches a significant level, CACNA1E and ACBD6 are chosen as positional candidate genes. Our findings not only confirmed previously findings, but also revealed a number of novel SNPs associated with BFT and ADG. Two positional candidate genes CACNA1E and ACBD6 were identified for further study. These results would facilitate the identification of causative genes for BFT and ADG.

Recent vaccine development for human metapneumovirus

Human metapneumovirus (hMPV) and respiratory syncytial virus, its close family member, are two major causes of lower respiratory tract infection in the paediatric population. hMPV is also a common cause of worldwide morbidity and mortality in immunocompromised patients and older adults. Repeated infections occur often, demonstrating a heavy medical burden. However, there is currently no hMPV-specific prevention treatment. This review focuses on the current literature on hMPV vaccine development. We believe that a better understanding of the role(s) of viral proteins in host responses might lead to efficient prophylactic vaccine development.

New steady-state quiescent high-confinement plasma in an experimental advanced superconducting tokamak

A critical challenge facing the basic long-pulse high-confinement operation scenario (H mode) for ITER is to control a magnetohydrodynamic (MHD) instability, known as the edge localized mode (ELM), which leads to cyclical high peak heat and particle fluxes at the plasma facing components. A breakthrough is made in the Experimental Advanced Superconducting Tokamak in achieving a new steady-state H mode without the presence of ELMs for a duration exceeding hundreds of energy confinement times, by using a novel technique of continuous real-time injection of a lithium (Li) aerosol into the edge plasma. The steady-state ELM-free H mode is accompanied by a strong edge coherent MHD mode (ECM) at a frequency of 35-40 kHz with a poloidal wavelength of 10.2 cm in the ion diamagnetic drift direction, providing continuous heat and particle exhaust, thus preventing the transient heat deposition on plasma facing components and impurity accumulation in the confined plasma. It is truly remarkable that Li injection appears to promote the growth of the ECM, owing to the increase in Li concentration and hence collisionality at the edge, as predicted by GYRO simulations. This new steady-state ELM-free H-mode regime, enabled by real-time Li injection, may open a new avenue for next-step fusion development.

Novel host genetic variations associated with spontaneous clearance of a single-source outbreak of HCV1b infections

Background and aims

A total of 105 patients were identified as accidentally infected with hepatitis C virus genotype 1b (HCV1b) through blood transfusion from a single blood donor. This group provides a unique patient population to study host factors involved in the spontaneous clearance of HCV and disease progression.

Methods

Clinical markers, HCV RNA and eight single nucleotide polymorphisms (SNPs) of interleukin-28B (IL-28B) were detected. Exome capture and sequencing were analysed for association with HCV clearance.

Results

Among the 85 patients with the positive HCV antibody, 27 cases (31.8%) were HCV RNA negative over a period of 9–12 years. Of the 58 patients with positive HCV RNA, 22.4% developed chronic hepatitis, and 5.2% developed cirrhosis. Age was found to be associated with HCV1b clearance. IL-28 rs10853728 CC showed the trend. By exon sequencing, 39 SNPs were found to be significantly different in spontaneous clearance patients (p<0.001). Two SNPs in the tenascin receptor (TNR), five in the transmembrane protease serine 11A (TMPRSS11A), and one in the serine peptidase inhibitor kunitz type 2 (SPINT2) showed the closest associations (p<10⁻⁵).

Conclusions

Host genetic analyses on the unique, single source HCV1b-infected patient population has suggested that age and mutations in TNR, TMPRSS11A and SPINT2 genes may be factors associated with HCV clearance.

A flowing liquid lithium limiter for the Experimental Advanced Superconducting Tokamak

A program involving the extensive and systematic use of lithium (Li) as a "first," or plasma-facing, surface in Tokamak fusion research devices located at Institute of Plasma Physics, Chinese Academy of Sciences, was started in 2009. Many remarkable results have been obtained by the application of Li coatings in Experimental Advanced Superconducting Tokamak (EAST) and liquid Li limiters in the HT-7 Tokamak-both located at the institute. In furtherance of the lithium program, a flowing liquid lithium (FLiLi) limiter system has been designed and manufactured for EAST. The design of the FLiLi limiter is based on the concept of a thin flowing film which was previously tested in HT-7. Exploiting the capabilities of the existing material and plasma evaluation system on EAST, the limiter will be pre-wetted with Li and mechanically translated to the edge of EAST during plasma discharges. The limiter will employ a novel electro-magnetic pump which is designed to drive liquid Li flow from a collector at the bottom of limiter into a distributor at its top, and thus supply a continuously flowing liquid Li film to the wetted plasma-facing surface. This paper focuses on the major design elements of the FLiLi limiter. In addition, a simulation of incoming heat flux has shown that the distribution of heat flux on the limiter surface is acceptable for a future test of power extraction on EAST.

Elevated expression of CX3C chemokine receptor 1 mediates recruitment of T cells into bone marrow of patients with acquired aplastic anaemia

OBJECTIVE

Acquired aplastic anaemia (AA) is a T-cell-mediated, organ-specific autoimmune disease characterized by haematopoietic stem cell destruction in the bone marrow. The exact molecular mechanism of T-cell trafficking into the bone marrow is unclear in AA. Very late activation antigen-4 (VLA-4) and CX3C chemokine receptor 1 (CX3CR1) play active roles in many autoimmune diseases. Therefore, we investigated whether VLA-4 and CX3CR1 also contribute to T-cell migration into the bone marrow in acquired AA.

DESIGN, SETTING AND SUBJECTS

Expression levels of CX3CR1 and VLA-4 and their ligands [fractalkine (CX3CL1) and vascular cell adhesion molecule-1 (VCAM-1)] were examined in 63 patients with AA and 21 healthy control subjects. T-cell chemotaxis and adhesion were analysed in 17 patients with severe AA. We also prospectively evaluated the expression pattern of CX3CR1 during treatment with antithymocyte globulin plus cyclosporine in 11 patients with severe AA.

RESULTS

The proportion of peripheral and bone marrow CD4(+) and CD8(+) T cells expressing CX3CR1 and the level of CX3CL1 was increased in patients with AA. However, there was no significant difference in VLA-4 expression or VCAM-1 levels. Functional studies demonstrated that chemotaxis towards autologous bone marrow plasma or soluble CX3CL1 was significantly higher in T cells from AA patients and could be blocked by CX3CR1 inhibitors. CX3CR1-mediated T-cell adhesion was also upregulated in these patients. The expression of CX3CR1 was associated with the efficacy of immunosuppressive therapy.

CONCLUSION

The present findings demonstrate that CX3CR1 plays a pivotal role in recruitment of T cells into the bone marrow in acquired AA and is a potential therapeutic target for treatment of this disorder.

KRAS status and resistance to epidermal growth factor receptor tyrosine-kinase inhibitor treatment in patients with metastatic colorectal cancer: a meta-analysis

AIM

This study reviewed the association between KRAS mutation and resistance to treatment with epidermal growth factor receptor (EGFR) tyrosine-kinase inhibitors (TKIs) in patients with metastatic colorectal cancer (mCRC).

METHOD

A search was carried out of PubMed, MEDLINE, EMBASE and the Cochrane Library databases (to November 2013) without language restrictions.

RESULTS

Ten studies were included in the final meta-analysis, consisting of 1339 patients with mCRC, of whom 427 (32%) had a KRAS mutation. The objective response rate (ORR) of mCRC patients with KRAS mutation was 8% (33/427), whereas the ORR of mCRC patients with wild-type KRAS was 34% (306/912). The overall pooled response rate (RR) for the ORR was 1.297 (95% CI 1.244-1.353, P < 0.01). Subgroup analysis comparing cetuximab monotherapy treatment with cetuximab plus chemotherapy, showed a pooled RR of 1.26 (95% CI 1.12-0.63, P < 0.01) and 1.30 (95% CI 1.25-1.36, P < 0.01), respectively. For patients receiving anti-EGFR with monoclonal antibodies (mAb) given as first-line treatment or not, the pooled RRs were 1.34 (95% CI 1.23-1.46, P < 0.01) and 1.29 (95% CI 1.23-1.35, P < 0.01). The data on progression-free survival from five studies in the meta-analysis gave a hazard ratio (HR) of 1.99 with a 95% CI of 1.69-2.29. Finally, the data for overall survival in mCRC patients were pooled from the only three studies reporting the HR (1.80; 95% CI 1.50-2.10). None of the results had any evidence of heterogeneity.

CONCLUSION

All the results favoured a stronger link between mutant KRAS and anti-EGFR mAb, but due to a mutually exclusive relationship between KRAS and other gene mutations the clinical usefulness of KRAS mutation as a selection marker for sensitivity to EGFR TKIs in mCRC is limited.

Search for a light sterile neutrino at Daya Bay

A search for light sterile neutrino mixing was performed with the first 217 days of data from the Daya Bay Reactor Antineutrino Experiment. The experiment's unique configuration of multiple baselines from six 2.9 GW(th) nuclear reactors to six antineutrino detectors deployed in two near (effective baselines 512 m and 561 m) and one far (1579 m) underground experimental halls makes it possible to test for oscillations to a fourth (sterile) neutrino in the 10(-3) eV(2)<|Δm(41)(2) |< 0.3 eV(2) range. The relative spectral distortion due to the disappearance of electron antineutrinos was found to be consistent with that of the three-flavor oscillation model. The derived limits on sin(2) 2θ(14) cover the 10(-3) eV(2) ≲ |Δm(41)(2)| ≲ 0.1 eV(2) region, which was largely unexplored.