Microarray gene expression classification with few genes: Criteria to combine attribute selection and classification methods

Microarray data classification is a task involving high dimensionality and small samples sizes. A common criterion to decide on the number of selected genes is maximizing the accuracy, which risks overfitting and usually selects more genes than actually needed. We propose, relaxing the maximum accuracy criterion, to select the combination of attribute selection and classification algorithm that using less attributes has an accuracy not statistically significantly worst that the best. Also we give some advice to choose a suitable combination of attribute selection and classifying algorithms for a good accuracy when using a low number of gene expressions. We used some well known attribute selection methods (FCBF, ReliefF and SVM-RFE, plus a Random selection, used as a base line technique) and classifying techniques (Naive Bayes, 3 Nearest Neighbor and SVM with linear kernel) applied to 30 data sets involving different cancer types.     

Antimicrobial resistance and virulence genes of Arcobacter isolates recovered from edible bivalve molluscs

The goals of this study were to assess the prevalence, antimicrobial susceptibility and the presence of virulence genes of arcobacters recovered from edible bivalve molluscs. A total of 106 samples (21 clams, 18 mussels, 20 oysters, 20 razor clams, 11 scallops and 16 surf clams) were analysed by culture between 2010 and 2013. The obtained colonies were identified by multiplex PCR and PCR-RFLP and genotyped by ERIC-PCR. Furthermore, nine putative virulence genes (cadF, ciaB, cjl349, irgA, hecA, hecB, mviN, pldA and tlyA) were assessed by PCR and the antimicrobial resistance was tested by the dilution agar method. The global prevalence was 40.5%, with the highest value in surf clams (87.5%) followed by razor clams (65.0%), mussels (33.3%), clams (23.8%), scallops (18.0%) and oysters (15.0%). The most commonly found species was Arcobacter butzleri (62%) followed by Arcobacter cryaerophilus (21%), Arcobacter skirrowii (16%) and Arcobacter defluvii (1%). A high resistance was found to nalidixic acid and ampicillin, while the predominant detected virulence genes were mviN (83.8%), ciaB (82.8%) and tlyA (72.7%). Our results indicate a high prevalence of arcobacters in shellfish and the pathogenic potential of the recovered isolates suggests that this type of food could be a plausible transmission route of virulent strains to humans.     

Stabilization of the Single-Chain Fragment Variable by an Interdomain Disulfide Bond and Its Effect on Antibody Affinity

The interdomain instability of single-chain fragment variable (scFv) might result in intermolecular aggregation and loss of function. In the present study, we stabilized H4—an anti-aflatoxin B₁ (AFB₁) scFv—with an interdomain disulfide bond and studied the effect of the disulfide bond on antibody affinity. With homology modeling and molecular docking, we designed a scFv containing an interdomain disulfide bond between the residues H44 and L100. The stability of scFv (H4) increased from a GdnHCl₅₀ of 2.4 M to 4.2 M after addition of the H44-L100 disulfide bond. Size exclusion chromatography revealed that the scFv (H44-L100) mutant existed primarily as a monomer, and no aggregates were detected. An affinity assay indicated that scFv (H4) and the scFv (H44-L100) mutant had similar IC₅₀ values and affinity to AFB₁. Our results indicate that interdomain disulfide bonds could stabilize scFv without affecting affinity.     

Prevalence and characterization of Escherichia coli O157:H7 from samples along the production line in Chinese beef-processing plants

This work investigated the prevalence of Escherichia coli O157:H7 and the antibiotic susceptibility, genetic diversity and virulence genes of isolated strains from four beef slaughter plants in China. A total of 510 samples (feces, hide, carcasses and raw meat) were tested for E. coli O157:H7 using enrichment, immunomagnetic separation, and plating on selective media. The prevalence of E. coli O157:H7 in the feces, hide, pre-evisceration carcass, post-evisceration carcass, post-washing carcass, chilled carcass, and raw meat samples was 1.43%, 1.43%, 0%, 0%, 0%, 1.25%, and 0%, respectively. Multiplex PCR assays were used for serotype confirmation and virulence gene detection. stx₂, eaeA and EHEC-hlyA genes were present in all six of the strains, and the stx₁ gene was not present. Fluorescence amplified fragment length polymorphism (FAFLP) was used to determine the genetic diversity of E. coli O157:H7 and revealed a high similarity between the strains isolated from feces and those isolated from carcasses. None of the isolated strains were found to be resistant to sixteen commonly used antimicrobial agents. The results of this study indicate that although E. coli O157:H7 contamination in the Chinese beef industry is sporadic and not as common as reported in other counties, all of the isolates contained three major virulence genes, presenting a high risk of disease for humans. The current research provides baseline information on E. coli O157:H7 prevalence and character profiles in Chinese beef-processing plants that can be used for future studies.     

PdAu纳米颗粒非标记免疫传感器测定牛奶中的黄曲霉素B_1

用溶剂热法合成Pd Au纳米颗粒,将其修饰在玻碳电极表面,然后根据抗体的自组装作用将黄曲霉素B1的抗体固定在Pd Au/GCE表面,制得免疫传感器。以[Fe(CN)6]3-作为探针对黄曲霉素B1实现灵敏的间接检测。优化了实验条件对传感器性能的影响。结果表明,在电位为0.2V条件下,该传感器检测黄曲霉素B1的线性范围为0.1~12μg/L;其检测限为0.033μg/L。该传感器选择性好、灵敏度高、具有良好的重现性。     

免疫亲和层析净化高效液相色谱法测定澳洲坚果中黄曲霉毒素B_1

建立了一种测定澳洲坚果中黄曲霉毒素B1的免疫亲和层析净化高效液相色谱法。采用甲醇-水提取,提取液经过滤、水稀释、净化,甲醇洗脱溶解,柱后衍生液相色谱仪荧光检测器测定。实验结果表明,澳洲坚果中黄曲霉毒素B1的检出限为0.2μg/kg,在添加水平为5、10、20μg/kg的回收率实验中,平均回收率为81%~96%,相对标准偏差为0.8%~3.7%。     

Identification of Reference Genes for RT-qPCR Data Normalization in Cannabis sativa Stem Tissues

Gene expression profiling via quantitative real-time PCR is a robust technique widely used in the life sciences to compare gene expression patterns in, e.g., different tissues, growth conditions, or after specific treatments. In the field of plant science, real-time PCR is the gold standard to study the dynamics of gene expression and is used to validate the results generated with high throughput techniques, e.g., RNA-Seq. An accurate relative quantification of gene expression relies on the identification of appropriate reference genes, that need to be determined for each experimental set-up used and plant tissue studied. Here, we identify suitable reference genes for expression profiling in stems of textile hemp (Cannabis sativa L.), whose tissues (isolated bast fibres and core) are characterized by remarkable differences in cell wall composition. We additionally validate the reference genes by analysing the expression of putative candidates involved in the non-oxidative phase of the pentose phosphate pathway and in the first step of the shikimate pathway. The goal is to describe the possible regulation pattern of some genes involved in the provision of the precursors needed for lignin biosynthesis in the different hemp stem tissues. The results here shown are useful to design future studies focused on gene expression analyses in hemp.     

Identification of Autophagy in the Pine Wood Nematode Bursaphelenchus xylophilus and the Molecular Characterization and Functional Analysis of Two Novel Autophagy-Related Genes,BxATG1 and BxATG8

The pine wood nematode, Bursaphelenchus xylophilus, causes huge economic losses in pine forests, has a complex life cycle, and shows the remarkable ability to survive under unfavorable and changing environmental conditions. This ability may be related to autophagy, which is still poorly understood in B. xylophilus and no autophagy-related genes have been previously characterized. In this study, transmission electron microscopy was used to confirm that autophagy exists in B. xylophilus. The full-length cDNAs of BxATG1 and BxATG8 were first cloned from B. xylophilus, and BxATG1 and BxATG8 were characterized using bioinformatics methods. The expression pattern of the autophagy marker BxATG8 was investigated using in situ hybridization (ISH). BxATG8 was expressed in esophageal gland and hypodermal seam cells. We tested the effects of RNA interference (RNAi) on BxATG1 and BxATG8. The results revealed that BxATG1 and BxATG8 were likely associated with propagation of nematodes on fungal mats. This study confirmed the molecular characterization and functions of BxATG1 and BxATG8 in B. xylophilus and provided fundamental information between autophagy and B. xylophilus.     

A Glutathione Peroxidase Gene from Litopenaeus vannamei Is Involved in Oxidative Stress Responses and Pathogen Infection Resistance

In shrimp, several glutathione peroxidase (GPX) genes have been cloned and functionally studied. Increasing evidence suggests the genes’ involvement in white spot syndrome virus (WSSV)- or Vibrio alginolyticus-infection resistance. In the present study, a novel GXP gene (LvGPX3) was cloned in Litopenaeus vannamei. Promoter of LvGPX3 was activated by NF-E2-related factor 2. Further study showed that LvGPX3 expression was evidently accelerated by oxidative stress or WSSV or V. alginolyticus infection. Consistently, downregulated expression of LvGPX3 increased the cumulative mortality of WSSV- or V. alginolyticus-infected shrimp. Similar results occurred in shrimp suffering from oxidative stress. Moreover, LvGPX3 was important for enhancing Antimicrobial peptide (AMP) gene expression in S2 cells with lipopolysaccharide treatment. Further, knockdown of LvGPX3 expression significantly suppressed expression of AMPs, such as Penaeidins 2a, Penaeidins 3a and anti-lipopolysaccharide factor 1 in shrimp. AMPs have been proven to be engaged in shrimp WSSV- or V. alginolyticus-infection resistance; it was inferred that LvGPX3 might enhance shrimp immune response under immune challenges, such as increasing expression of AMPs. The regulation mechanism remains to be further studied.