Machine learning-based identification of a consensus immune-derived gene signature to improve head and neck squamous cell carcinoma therapy and outcome.

Background: Head and neck squamous cell carcinoma (HNSCC), an extremely aggressive tumor, is often associated with poor outcomes. The standard anatomy-based tumor-node-metastasis staging system does not satisfy the requirements for screening treatment-sensitive patients. Thus, an ideal biomarker leading to precise screening and treatment of HNSCC is urgently needed. Methods: Ten machine learning algorithms-Lasso, Ridge, stepwise Cox, CoxBoost, elastic network (Enet), partial least squares regression for Cox (plsRcox), random survival forest (RSF), generalized boosted regression modelling (GBM), supervised principal components (SuperPC), and survival support vector machine (survival-SVM)-as well as 85 algorithm combinations were applied to construct and identify a consensus immune-derived gene signature (CIDGS). Results: Based on the expression profiles of three cohorts comprising 719 patients with HNSCC, we identified 236 consensus prognostic genes, which were then filtered into a CIDGS, using the 10 machine learning algorithms and 85 algorithm combinations. The results of a study involving a training cohort, two testing cohorts, and a meta-cohort consistently demonstrated that CIDGS was capable of accurately predicting prognoses for HNSCC. Incorporation of several core clinical features and 51 previously reported signatures, enhanced the predictive capacity of the CIDGS to a level which was markedly superior to that of other signatures. Notably, patients with low CIDGS displayed fewer genomic alterations and higher immune cell infiltrate levels, as well as increased sensitivity to immunotherapy and other therapeutic agents, in addition to receiving better prognoses. The survival times of HNSCC patients with high CIDGS, in particular, were shorter. Moreover, CIDGS enabled accurate stratification of the response to immunotherapy and prognoses for bladder cancer. Niclosamide and ruxolitinib showed potential as therapeutic agents in HNSCC patients with high CIDGS. Conclusion: CIDGS may be used for stratifying risks as well as for predicting the outcome of patients with HNSCC in a clinical setting.

Ultrafast underwater self-healing piezo-ionic elastomer via dynamic hydrophobic-hydrolytic domains.

The development of advanced materials capable of autonomous self-healing and mechanical stimulus sensing in aquatic environments holds great promise for applications in underwater soft electronics, underwater robotics, and water-resistant human-machine interfaces. However, achieving superior autonomous self-healing properties and effective sensing simultaneously in an aquatic environment is rarely feasible. Here, we present an ultrafast underwater molecularly engineered self-healing piezo-ionic elastomer inspired by the cephalopod's suckers, which possess self-healing properties and mechanosensitive ion channels. Through strategic engineering of hydrophobic C-F groups, hydrolytic boronate ester bonds, and ions, the material achieves outstanding self-healing efficiencies, with speeds of 94.5% (9.1 µm/min) in air and 89.6% (13.3 µm/min) underwater, coupled with remarkable pressure sensitivity (18.1 kPa-1) for sensing performance. Furthermore, integration of this mechanosensitive device into an underwater submarine for signal transmission and light emitting diode modulation demonstrates its potential for underwater robotics and smarter human-machine interactions.

The feasibility of level Ib-sparing intensity-modulated radiation therapy in patients with nasopharyngeal carcinoma and high-risk factors classified based on the International Guideline.

BACKGROUND AND PURPOSE: To examine the feasibility of level Ib-sparing intensity-modulated radiation therapy (IMRT) in patients with nasopharyngeal carcinoma (NPC) who had high-risk factors classified based on the International Guideline (IG). MATERIALS AND METHODS: We evaluated 961 non-metastatic NPC cases based on IG recommendations for prophylactic Ib irradiation. Four high-risk factors were used to categorise patients into three cohorts: A, B, and C. Propensity score matching was used to balance baseline characteristics in Cohort C, resulting in a matched Cohort C. Recurrence rates at level Ib and regional relapse-free survival (RRFS) rates were evaluated. RESULTS: Among patients with negative Ib lymph nodes (LNs), 18, 54, 420, and 444 exhibited involvement of structures that drain to level Ib as the first echelon (FES), involvement of the submandibular gland (SMG), level II LNs with radiologic extranodal extension (rENE), and level II nodes with a maximal axial diameter (MAD) ≥ 2 cm, respectively. The recurrence rate was highest in Cohort A (11.1 %). Cohort B had no level Ib recurrence. In matched Cohort C, recurrence rates were low in both groups (Ib-sparing group: 0.6 % vs. Ib-covering group: 0.6 %, P > 0.999). No significant differences were observed in 5-year RRFS rates between the two groups in cohort A (p = 0.208), cohort B (p = 0.905), and matched cohort C (p = 0.423). CONCLUSIONS: Level Ib-sparing IMRT could be performed safely for NPC patients with level II LNs who had rENE and/or MAD ≥ 2 cm. Further research should determine the necessity of level Ib prophylactic irradiation for patients with FES or SMG involvement.

Prognostic value of the cervical lymph node necrosis ratio in nasopharyngeal carcinoma.

PURPOSE: Whether cervical lymph node necrosis (CNN) is an independent adverse prognostic factor in nasopharyngeal carcinoma (NPC) has not been determined. In this study, the CNN ratio was graded quantitatively to explore the prognostic value in NPC. PARTICIPANTS AND METHODS: We retrospectively reviewed a total of 648 pathologically confirmed as NPC. We outlined metastatic lymph nodes and necrotic area of lymph nodes slice by slice on the magneticresonanceimages (MRI) cross section, and calculated the corresponding CNN ratio. RESULTS: The median CNN ratio (17.37 %) was taken as the cut-off point, 256 (39.51 %) patients were divided into CNN1 group (<17.37 %, n = 128) and CNN2 group (≥17.37 %, n = 128), 392 (60.49 %) patients without lymph nodes necrosis were CNN0. Among the CNN0, CNN1 and CNN2 groups, five-year overall survival (OS) was 82.4 %, 76.6 % and 71.1 %, locoregional recurrence-free survival (LRRFS) was 91.3 %, 91.1 % and 90.5 %, distant metastasis-free survival (DMFS) was 83.7 %, 78.5 % and 68.7 %, progression-free survival (PFS) was 78.3 %, 71.7 % and 61.6 % respectively. By multivariate analysis, CNN was an independent prognostic factor for OS (P = 0.003), DMFS (P = 0.019) and PFS (P = 0.007). More than 3 cycles of chemotherapy significantly increased OS (P = 0.024) and DMFS (P = 0.015) in the CNN1 group. CONCLUSIONS: This study indicated that CNN is one of the factors with the negative prognosis of NPC. The CNN ratio might be used as one of the reference factors in the formulation of individualized treatment plan.

Effects of Chinese gallnut tannic acid on growth performance, blood parameters, antioxidative status, intestinal histomorphology, and cecal microbial shedding in broilers challenged with aflatoxin B1.

The objective of the present study was to investigate the effects of tannic acid (TA) on growth performance, blood parameters, antioxidant capacity, and intestinal health in broilers challenged with aflatoxin B1 (AFB1). A total of 480 broilers aged 1 d were randomly allotted into four treatments: 1) CON, control diet; 2) AF, CON + 60 µg/kg AFB1 of feed during days 1 to 21, CON + 120 µg/kg AFB1 of feed during days 22 to 42; 3) TA1, AF + 250 mg/kg TA; and 4) TA2, AF + 500 mg/kg TA. Average daily gain (ADG) and average daily feed intake (ADFI) were increased in the TA1 during days 1 to 21, days 22 to 42, and days 1 to 42 compared with CON and AF treatments (P < 0.05). Broilers fed the TA2 diet had greater ADG and ADFI than those fed the CON and AF diets during the finisher and the whole period (P < 0.05). Administration of TA decreased the relative weight of liver and kidney compared with broilers fed the AF diet on day 42 (P < 0.05). The blood activity of alanine transferase (ALT) and gamma-glutamyl transferase (GGT) was increased in the AF treatment compared with the CON (P < 0.05). Broilers fed the TA1 decreased the ALT content on day 21, and the level of ALT and GGT was decreased in the TA2 compared with the AF group on day 42 (P < 0.05). The activity of total superoxide dismutase (T-SOD) and glutathione peroxidase (GSH-Px) in plasma, and the hepatic glutathione S-transferase (GST) was decreased in the AF group compared with the CON group (P < 0.05). The TA decreased plasma malondialdehyde concentration, and increased plasma T-SOD, GSH-Px, total antioxidant capacity, and hepatic GST activity compared with the AF (P < 0.05). The crypt depth of the jejunum was decreased in the TA1 treatment on day 21, and the villus height of the ileum was increased in the TA2 group on day 42 compared with the AF treatment (P < 0.05). The cecal Lactobacillus counts on day 21 were tended to increase in the TA treatments compared with the AF (P = 0.061). In conclusion, dietary inclusion of 250 and 500 mg/kg TA could improve the growth, antioxidant capacity, and partially protected the intestinal health of broilers challenged with AFB1.

Aflatoxin B1 (AFB1) is well known for its growth retardation, hepatotoxic, immunosuppressive, and other negative effects both in humans and poultry. Plant extracts such as tannic acid (TA) have been demonstrated as effective agents to control AFB1 contamination. The objective of this study was to evaluate the effects of Chinese gallnut TA in preventing aflatoxicosis in broilers. Broilers received one of four treatments: CON, control diet; AF, control diet with AFB1; TA1, AF + 250 mg/kg TA; TA2, AF + 500 mg/kg TA. Although AF did not decrease the growth performance of broilers, 250 and 500 mg/kg TA had greater average daily gain and average daily feed intake than those in the CON and AF. The relative weight of liver and kidney, blood alanine transferase, and gamma-glutamyl transferase activity were increased, and the antioxidant status was depressed in chicks fed the AF diet compared with the CON group. Dietary supplementation with 250 and 500 mg/kg TA ameliorated all the above-mentioned negative effects of AFB1. Moreover, the crypt depth of the jejunum was decreased, and the villus height of the ileum was increased in TA treatments compared with the AF. Conclusively, Chinese gallnut TA could be considered as a potential natural agent for the prevention of AFB1-induced oxidative and intestinal damage of broilers.

Failure Patterns of Recurrence and Metastasis After Intensity-Modulated Radiotherapy in Patients With Nasopharyngeal Carcinoma: Results of a Multicentric Clinical Study.

PURPOSE: This study aimed to explore factors associated with recurrence and metastasis after intensity-modulated radiotherapy (IMRT) in patients with nasopharyngeal carcinoma (NPC) and provide evidence for NPC treatment. METHODS: We retrospectively analysed the treatment dose and survival outcomes of 645 patients with nasopharyngeal carcinoma without distant metastases treated with IMRT for the first time at three treatment centres in the Guangxi Zhuang Autonomous Region, China, between January 2009 and December 2012. RESULTS: There were 9.3% of patients (60/645) had recurrence and 17.5% (113/645) had distant metastasis 5 years after treatment. The 1-year, 3-year and 5-year local recurrence rates were 0.9%, 6.5% and 9.0% respectively. And the 1-year, 3-year and 5-year distant metastasis rates were 3.4%, 10% and 17.2%, respectively. In the 60 patients with recurrence, the in-field, marginal-field, and out-field recurrence rates were 93.3% (56/60), 5.0% (3/60) and 1.7% (1/60), respectively. Recurrence failures occurring within the first three years after treatment accounted for 81.7% (49/60). In the 113 patients with metastasis, the size of the cervical lymph node, the presence of lower cervical lymph node metastasis, the residual cervical lymph node size and the time of residual cervical lymph node complete response (CR) were independent prognostic factors for DMFS (P <0.05). CONCLUSION: Most recurrences occured in the first three years after IMRT. In-field recurrence was the most common pattern for loco-regional failure of NPC treatment. The risk of distant metastasis was positively correlated with higher N stage, lower neck nodal metastasis, larger size of cervical lymph nodes, and longer time to response for residual NPC in cervical adenopathy.

Individualized cumulative cisplatin dose for locoregionally-advanced nasopharyngeal carcinoma patients receiving induction chemotherapy and concurrent chemoradiotherapy.

OBJECTIVES: To screen subgroup potentially benefiting from cumulative cisplatin dose (CCD) ≥ 200 mg/m2 during concurrent chemoradiotherapy (CCRT) of patients with locoregionally-advanced nasopharyngeal carcinoma (LA-NPC) receiving induction chemotherapy (IC) and CCRT. MATERIALS AND METHODS: In total, 2 063 patients with non-disseminated LA-NPC diagnosed from 2009 to 2015 receiving IC plus CCRT were enrolled. Patients were restaged based on proposed stage groupings and risk groupings was established. After propensity score matching, survival outcomes were compared within different risk groupings with 200 mg/m2 CCD. Post-IC gross primary tumor (GTVp) and lymph node (GTVnd) volumes were calculated from planning computed tomography. The role of risk groupings and post-IC tumor volume to CCD was explored. RESULTS: Compared with the low-risk group, the high-risk group showed poor survival outcomes in terms of 5-year progression-free survival (PFS), overall survival (OS), distant metastasis-free survival (DMFS), and locoregional relapse-free survival (LRRFS). CCD ≥ 200 mg/m2 improved survival in terms of 5-year PFS, OS and DMFS in the high-risk group but not in the low-risk group. High-risk patients with unfavorable response to IC benefited from CCD ≥ 200 mg/m2 with respect to PFS and DMFS; while those in low-risk group or with favorable response to IC didn't. CONCLUSIONS: Risk groupings was effective for risk stratification. Combining risk groupings and post-IC tumor volume is a simple and useful method to guide individualized CCD treatment of CCRT for patients with LA-NPC receiving IC and CCRT. CCD ≥ 200 mg/m2 may be indicated for high-risk patients with unfavorable response to IC.

Characterization of Salt-Induced Epigenetic Segregation by Genome-Wide Loss of Heterozygosity and its Association with Salt Tolerance in Rice (Oryza sativa L.).

In a breeding effort to develop salt tolerant (ST) rice varieties by designed QTL pyramiding, large numbers of progenies derived from four crosses between salt- or drought- tolerant BC2F5 IR64 introgression lines, were subjected to severe salt stress, resulting in 422 ST plants. The progeny testing of the selected F3 lines under more severe salt stress resulted in identification of 16 promising homozygous lines with high levels of ST. Genetic characterization of the 422 ST F3 progeny and 318 random F2 plants from the same four crosses using 105 segregating SSR markers lead to three interesting discoveries: (1) salt stress can induce genome-wide epigenetic segregation (ES) characterized by complete loss of heterozygosity (LOH) and nearly complete loss of an allele (LOA) in the F3 progenies of four rice populations in a single generation; (2) ∼25% of the stress-induced ES loci were transgenerational and inherited from their salt- and drought- selected parents; and (3) the salt-induced LOH and LOA loci (regions) appeared to contain genes/alleles associated with ST and/or drought tolerance. 32 genomic regions that showed one or more types of salt-induced ES in the random and salt-selected progenies from these crosses. The same or different types of ES were detected with two large genomic regions on chromosomes 1 and 6 where more and the strongest ES were found across different populations. 14 genomic regions were found where the salt-induced ES regions were overlapping with QTL affecting ST related traits. The discovery of the three types of salt-induced ES showed several interesting characteristics and had important implications in evolution and future breeding for developing stress-resilient rice and crops.

BTLA-expressing CD11c antigen presenting cells in patients with active tuberculosis exhibit low capacity to stimulate T cell proliferation.

Despite past extensive studies on B and T lymphocyte attenuator (BTLA)-mediated negative regulation of T cell activation, the role of BTLA in antigen presenting cells (APCs) in patients with active pulmonary tuberculosis (ATB) remains poorly understood. Here, we demonstrate that BTLA expression on CD11c APCs increased in patients with ATB. Particularly, BTLA expression in CD11c APCs was likely associated with the attenuated stimulatory capacity on T cells (especially CD8+ T cell) proliferation. BTLA-expressing CD11c APCs showed lower antigen uptake capacity, lower CD86 expression, higher HLA-DR expression, and enhanced IL-6 secretion, compared to counterpart BTLA negative CD11c APCs in healthy controls (HC). Interestingly, BTLA-expressing CD11c APCs from ATB patients displayed lower expression of HLA-DR and less IL-6 secretion, but higher expression of CD86 than those from HC volunteers. Mixed lymphocyte reaction suggests that BTLA expression is likely associated with positive rather than conventional negative regulation of CD11c APCs stimulatory capacity. This role is impaired in ATB patients manifested by low expression of HLA-DR and low production of IL-6. This previous unappreciated role for BTLA may have implications in the prevention and treatment of patients with ATB.

Persistently high prevalence of primary resistance and multidrug resistance of tuberculosis in Heilongjiang Province, China.

BACKGROUND: The spread of multidrug-resistant tuberculosis (MDR-TB) Mycobacterium tuberculosis (M. tuberculosis) strains has been a big challenge to the TB control and prevention in China. Knowledge about patterns of drug resistance in TB high-burden areas of China is crucial to develop appropriate control strategies. We conducted a comprehensive investigation of the resistance pattern of M. tuberculosis in Heilongjiang Province. METHODS: 1427 M. tuberculosis clinical strains were isolated from pulmonary TB patients hospitalized between 2007 and 2012. The susceptibility of the isolates to the first-line anti-TB drugs and the resistance of MDR M. tuberculosis to fluoroquinolones were examined. We also performed a statistical analysis to identify the correlated risk factors for high burden of MDR-TB. RESULTS: The global resistance rates of 2007-2012 to the first-line drugs and MDR were 57.0 and 22.8 %, respectively. Notably, the primary MDR-TB and pan-resistance rates were as high as 13.6 and 5.0 %, respectively. Of MDR M. tuberculosis isolates (2009), approximately 13 % were not susceptible to any of the fluoroquinolones tested. Being age of 35 to 54, high re-treatment proportion, the presence of cavity lesion, and high proportion of shorter hospitalization are correlated with the development of MDR-TB. CONCLUSIONS: The high prevalence of drug resistant, MDR-TB, and fluoroquinolone-resistant MDR-TB is a big concern for TB control. More importantly, in order to control the development of MDR-TB effectively, we need to pay more attention to the primary resistance. Targeting reducing the prevalence of the risk factors may lead to better TB control in China.

Complex molecular mechanisms underlying seedling salt tolerance in rice revealed by comparative transcriptome and metabolomic profiling.

To understand the physiological and molecular mechanisms underlying seedling salt tolerance in rice (Oryza sativa L.), the phenotypic, metabolic, and transcriptome responses of two related rice genotypes, IR64 and PL177, with contrasting salt tolerance were characterized under salt stress and salt+abscisic acid (ABA) conditions. PL177 showed significantly less salt damage, lower Na(+)/K(+) ratios in shoots, and Na(+) translocation from roots to shoots, attributed largely to better salt exclusion from its roots and salt compartmentation of its shoots. Exogenous ABA was able to enhance the salt tolerance of IR64 by selectively decreasing accumulation of Na(+) in its roots and increasing K(+) in its shoots. Salt stress induced general and organ-specific increases of many primary metabolites in both rice genotypes, with strong accumulation of several sugars plus proline in shoots and allantoin in roots. This was due primarily to ABA-mediated repression of genes for degradation of these metabolites under salt. In PL177, salt specifically up-regulated genes involved in several pathways underlying salt tolerance, including ABA-mediated cellular lipid and fatty acid metabolic processes and cytoplasmic transport, sequestration by vacuoles, detoxification and cell-wall remodeling in shoots, and oxidation-reduction reactions in roots. Combined genetic and transcriptomic evidence shortlisted relatively few candidate genes for improved salt tolerance in PL177.

Temporal profiling of primary metabolites under chilling stress and its association with seedling chilling tolerance of rice (Oryza sativa L.).

BACKGROUND: Chilling stress is a major factor limiting rice production. Rice genotypes differ greatly in their seedling chilling tolerance (CT), which is known to involve differential expression of large numbers of genes and proteins. To further understand the metabolomic responses of rice to chilling stress, profiles of the 106 primary metabolites of a CT japonica variety, Lijiangxintuanhegu (LTH) and a chilling sensitive indica line, IR29, were investigated under a time-series of chilling stress and non-stress control conditions at the seedling stage. RESULTS: We identified 106 primary metabolites that were temporally and genotype-dependently regulated in LTH and IR29 under the time-series chilling stress and subsequent recovery. Three major groups of primary metabolites, amino acids (AAs), organic acids (OAs) and sugars, showed distinct change patterns in both genotypes in response to the chilling stress: a more general accumulation of most AAs, more dramatic decreased levels of most OAs, and greatly reduced levels for most sugars at early time points of stress but increased levels of specific sugars at the later time points of stress. Compared to IR29, LTH had more metabolites showing chilling induced changes, greater levels of these metabolomic changes and a greater ability to recover after stress, implying that LTH used a positive energy-saving strategy against chilling stress. During subsequent recovery, more metabolites were significantly and exclusively up-regulated in LTH, indicating their positive role in chilling tolerance. A comparative analysis of these metabolites data and differentially expressed genes data allowed identification of 7 AAs and related genes that were both chilling responsive and contributed greatly to the CT of LTH. CONCLUSIONS: The metabolomic responses of rice to chilling stress at the seedling stage were dynamic and involved large numbers of the metabolites. The chilling induced changes of three major groups of metabolites, AAs, OAs and sugars, in rice were well coordinated. The high level seedling CT of LTH was apparently attributed to its increased levels of most AAs and reduced energy consumption that resulted in increased glycolysis and strong resilience on recovery. The results of this study extend our understanding of molecular mechanisms of chilling stress tolerance in rice.

Three genetic systems controlling growth, development and productivity of rice (Oryza sativa L.): a reevaluation of the 'Green Revolution'.

The Green Revolution (GR-I) included worldwide adoption of semi-dwarf rice cultivars (SRCs) with mutant alleles at GA20ox2 or SD1 encoding gibberellin 20-oxidase. Two series of experiments were conducted to characterize the pleiotropic effects of SD1 and its relationships with large numbers of QTLs affecting rice growth, development and productivity. The pleiotropic effects of SD1 in the IR64 genetic background for increased height, root length/mass and grain weight, and for reduced spikelet fertility and delayed heading were first demonstrated using large populations derived from near isogenic IR64 lines of SD1. In the second set of experiments, QTLs controlling nine growth and yield traits were characterized using a new molecular quantitative genetics model and the phenotypic data of the well-known IR64/Azucena DH population evaluated across 11 environments, which revealed three genetic systems: the SD1-mediated, SD1-repressed and SD1-independent pathways that control rice growth, development and productivity. The SD1-mediated system comprised 43 functional genetic units (FGUs) controlled by GA. The SD1-repressed system was the alternative one comprising 38 FGUs that were only expressed in the mutant sd1 backgrounds. The SD1-independent one comprised 64 FGUs that were independent of SD1. GR-I resulted from the overall differences between the former two systems in the three aspects: (1) trait/environment-specific contributions; (2) distribution of favorable alleles for increased productivity in the parents; and (3) different responses to (fertilizer) inputs. Our results suggest that at 71.4 % of the detected loci, a QTL resulted from the difference between a functional allele and a loss-of-function mutant, whereas at the remaining 28.6 % of loci, from two functional alleles with differentiated effects. Our results suggest two general strategies to achieve GR-II (1) by further exploiting the genetic potential of the SD1-repressed and SD1-independent pathways and (2) by restoring the SD1-mediated pathways, or 'back to the nature' to fully exploit the genetic diversity of those loci in the SD1-mediated pathways which are virtually inaccessible to most rice-breeding programs worldwide that are exclusively based on sd1.

[Comparison of two interferon-gamma release assays in the diagnosis of tuberculosis].

OBJECTIVE: To compare the diagnostic performance of A.TB, an ELISA-based interferon-gamma release assay (IGRA), and T-SPOT.TB, an ELISPOT-based IGRA, and therefore to evaluate the value of A.TB assay in the routine clinical practice. METHODS: From March to May of the year of 2011, 112 hospitalized patients were enrolled from 2 chest hospitals in Beijing and Harbin, including 75 cases in the TB group (43 male and 32 female) with the average age of (44 ± 18) years, spanning from 28 to 57 years, and 37 cases in the non-TB group (21 male and 16 female) with the average age of (54 ± 10) years, spanning from 24 to 82 years. During the same period, 34 healthy volunteers (4 male and 30 female), with the average age of (20 ± 0.6) years, spanning from 19 to 22 years, were recruited in Beijing Chest Hospital. A head-to-head comparison of the 2 IGRAs was performed on the 146 subjects to evaluate their overall diagnostic performance. Chi-square test or Fisher's exact test was used for statistical analysis of enumeration data. RESULTS: The sensitivity and specificity of A.TB were 81.3% (61/75, 95%CI = 72.5 - 90.2) and 83.1% (59/71, 95%CI = 74.4 - 91.8) respectively, compared to 90.7% (68/75, 95%CI = 84.1 - 97.3) and 78.9% (56/71, 95%CI = 69.4 - 88.4) for T-SPOT.TB. There was no significant difference in sensitivity or specificity (chi square values were 2.77 and 0.17 respectively, both P > 0.05). The area under the ROC curve was 0.90 (95%CI = 0.84 - 0.95) for A.TB and 0.91 (95%CI = 0.86 - 0.96) for T-SPOT.TB. The observation agreement between the 2 methods was 87.2% (123/141), with a kappa value of 0.74. T-SPOT.TB produced indeterminate results at a rate of 3.4% (5/146). CONCLUSIONS: There was comparable diagnostic performance between the 2 assays. However, when compared to T-SPOT.TB, the A.TB testing procedure, with less technical demand and without requirement of well-equipped lab, is simpler and the interpretation of results is less subjective.

Dissecting genetic networks underlying complex phenotypes: the theoretical framework.

Great progress has been made in genetic dissection of quantitative trait variation during the past two decades, but many studies still reveal only a small fraction of quantitative trait loci (QTLs), and epistasis remains elusive. We integrate contemporary knowledge of signal transduction pathways with principles of quantitative and population genetics to characterize genetic networks underlying complex traits, using a model founded upon one-way functional dependency of downstream genes on upstream regulators (the principle of hierarchy) and mutual functional dependency among related genes (functional genetic units, FGU). Both simulated and real data suggest that complementary epistasis contributes greatly to quantitative trait variation, and obscures the phenotypic effects of many 'downstream' loci in pathways. The mathematical relationships between the main effects and epistatic effects of genes acting at different levels of signaling pathways were established using the quantitative and population genetic parameters. Both loss of function and "co-adapted" gene complexes formed by multiple alleles with differentiated functions (effects) are predicted to be frequent types of allelic diversity at loci that contribute to the genetic variation of complex traits in populations. Downstream FGUs appear to be more vulnerable to loss of function than their upstream regulators, but this vulnerability is apparently compensated by different FGUs of similar functions. Other predictions from the model may account for puzzling results regarding responses to selection, genotype by environment interaction, and the genetic basis of heterosis.

Genotypes and characteristics of clustering and drug susceptibility of Mycobacterium tuberculosis isolates collected in Heilongjiang Province, China.

For the last decade China has occupied second place, after India, among the top five countries with high burdens of tuberculosis (TB). Heilongjiang Province is located in northeastern China. The prevalence of drug-resistant TB in Heilongjiang Province is higher than the average level in China. To determine the transmission characteristics of Mycobacterium tuberculosis strains isolated in this area and their genetic relationships, especially among the Beijing family strains, we investigated their genotypes. From May 2007 to October 2008, 200 M. tuberculosis isolates from patients presenting pulmonary TB were analyzed by molecular typing using PCR-based methods: spacer-oligonucleotide typing (spoligotyping), Beijing family-specific PCR (detection of the deletion of region of difference 105 [RD105]), and mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) analysis. Different combinations of MIRU-VNTR loci were evaluated to define the genotypes and clustering characteristics of the local strains. We found that Beijing family strains represented 89.5% of the isolates studied. However, the rates of multidrug-resistant (MDR) M. tuberculosis among Beijing and non-Beijing family strains were not statistically different. The 15-locus set is considered the optimal MIRU-VNTR locus combination for analyzing the M. tuberculosis strains epidemic in this area, while the 10-locus set is an ideal set for first-line molecular typing. We found that the clustering rate of all the M. tuberculosis isolates analyzed was 10.0% using the 15-locus set typing. We conclude that the Beijing family genotype is predominant and that highly epidemic TB and MDR TB are less likely associated with the active transmission of M. tuberculosis in the study area.

Drought-induced site-specific DNA methylation and its association with drought tolerance in rice (Oryza sativa L.).

An indica pyramiding line, DK151, and its recurrent parent, IR64, were evaluated under drought stress and non-stress conditions for three consecutive seasons. DK151 showed significantly improved tolerance to drought. The DNA methylation changes in DK151 and IR64 under drought stress and subsequent recovery were assessed using methylation-sensitive amplified polymorphism analysis. Our results indicate that drought-induced genome-wide DNA methylation changes accounted for ∼12.1% of the total site-specific methylation differences in the rice genome. This drought-induced DNA methylation pattern showed three interesting properties. The most important one was its genotypic specificity reflected by large differences in the detected DNA methylation/demethylation sites between DK151 and IR64, which result from introgressed genomic fragments in DK151. Second, most drought-induced methylation/demethylation sites were of two major types distinguished by their reversibility, including 70% of the sites at which drought-induced epigenetic changes were reversed to their original status after recovery, and 29% of sites at which the drought-induced DNA demethylation/methylation changes remain even after recovery. Third, the drought-induced DNA methylation alteration showed a significant level of developmental and tissue specificity. Together, these properties are expected to have contributed greatly to rice response and adaptation to drought stress. Thus, induced epigenetic changes in rice genome can be considered as a very important regulatory mechanism for rice plants to adapt to drought and possibly other environmental stresses.

Genome-wide gene responses in a transgenic rice line carrying the maize resistance gene Rxo1 to the rice bacterial streak pathogen, Xanthomonas oryzae pv. oryzicola.

BACKGROUND: Non-host resistance in rice to its bacterial pathogen, Xanthomonas oryzae pv. oryzicola (Xoc), mediated by a maize NBS-LRR type R gene, Rxo1 shows a typical hypersensitive reaction (HR) phenotype, but the molecular mechanism(s) underlying this type of non-host resistance remain largely unknown. RESULTS: A microarray experiment was performed to reveal the molecular mechanisms underlying HR of rice to Xoc mediated by Rxo1 using a pair of transgenic and non-transgenic rice lines. Our results indicated that Rxo1 appeared to function in the very early step of the interaction between rice and Xoc, and could specifically activate large numbers of genes involved in signaling pathways leading to HR and some basal defensive pathways such as SA and ET pathways. In the former case, Rxo1 appeared to differ from the typical host R genes in that it could lead to HR without activating NDR1. In the latter cases, Rxo1 was able to induce a unique group of WRKY TF genes and a large set of genes encoding PPR and RRM proteins that share the same G-box in their promoter regions with possible functions in post-transcriptional regulation. CONCLUSIONS: In conclusion, Rxo1, like most host R genes, was able to trigger HR against Xoc in the heterologous rice plants by activating multiple defensive pathways related to HR, providing useful information on the evolution of plant resistance genes. Maize non-host resistance gene Rxo1 could trigger the pathogen-specific HR in heterologous rice, and ultimately leading to a localized programmed cell death which exhibits the characteristics consistent with those mediated by host resistance genes, but a number of genes encoding pentatricopeptide repeat and RNA recognition motif protein were found specifically up-regulated in the Rxo1 mediated disease resistance. These results add to our understanding the evolution of plant resistance genes.

Up-regulated expression of peroxisome proliferator-activated receptor gamma in the hypothalamic-pituitary-adrenal axis of weaned pigs after Escherichia coli lipopolysaccharide challenge.

The expression of peroxisome proliferator-activated receptor gamma (PPARgamma) was investigated in the hypothalamic-pituitary-adrenal (HPA) axis of weaned pigs after injection with 100 microg/kg bodyweight Escherichia coli lipopolysaccharide (LPS) (n=6) and control pigs injected with sterile saline (n=6). LPS increased PPARgamma mRNA and protein expression in the hypothalamus (23.8 and 3.1-fold relative to controls, respectively), pituitary gland (9.2 and 2.0-fold, respectively) and adrenal gland (3.5 and 2.3-fold, respectively) (P<0.05). LPS also induced an increase in PPARgamma immunohistochemical staining in the hypothalamus (1.3-fold), adenohypophysis (1.3-fold), adrenal cortex (1.4-fold) and adrenal medulla (1.6-fold) (P<0.05). Concurrent with up-regulated expression of PPARgamma, LPS increased the concentrations of plasma corticotrophin-releasing hormone (2.1-fold) and adrenocorticotrophin (1.4-fold) (P<0.05). LPS also induced elevations of interleukin 6 and tumour necrosis factor alpha mRNA levels in the hypothalamus (4.0 and 3.2-fold, respectively), pituitary gland (20.7 and 5.1-fold, respectively) and adrenal gland (3.9 and 3.3-fold, respectively) (P<0.05). PPARgamma may play a role in the regulation of neuroendocrine responses associated with immunological stress in pigs.