Bayesian Receiver Operating Characteristic Estimation of Multiple Tests for Diagnosis of Bovine Tuberculosis in Chadian Cattle

Background

Bovine tuberculosis (BTB) today primarily affects developing countries. In Africa, the disease is present essentially on the whole continent; however, little accurate information on its distribution and prevalence is available. Also, attempts to evaluate diagnostic tests for BTB in naturally infected cattle are scarce and mostly complicated by the absence of knowledge of the true disease status of the tested animals. However, diagnostic test evaluation in a given setting is a prerequisite for the implementation of local surveillance schemes and control measures.

Methodology/Principal Findings

We subjected a slaughterhouse population of 954 Chadian cattle to single intra-dermal comparative cervical tuberculin (SICCT) testing and two recently developed fluorescence polarization assays (FPA). Using a Bayesian modeling approach we computed the receiver operating characteristic (ROC) curve of each diagnostic test, the true disease prevalence in the sampled population and the disease status of all sampled animals in the absence of knowledge of the true disease status of the sampled animals. In our Chadian setting, SICCT performed better if the cut-off for positive test interpretation was lowered from >4 mm (OIE standard cut-off) to >2 mm. Using this cut-off, SICCT showed a sensitivity and specificity of 66% and 89%, respectively. Both FPA tests showed sensitivities below 50% but specificities above 90%. The true disease prevalence was estimated at 8%. Altogether, 11% of the sampled animals showed gross visible tuberculous lesions. However, modeling of the BTB disease status of the sampled animals indicated that 72% of the suspected tuberculosis lesions detected during standard meat inspections were due to other pathogens than Mycobacterium bovis.

Conclusions/Significance

Our results have important implications for BTB diagnosis in a high incidence sub-Saharan African setting and demonstrate the practicability of our Bayesian approach for diagnostic test evaluation.     

丙型肝炎病毒核心重组抗原C_（27）的纯化

高效表达了ＨＣＶ核心区基因抗原之后,对表达蛋白Ｃ_（２７）进行了纯化。经研究,重组蛋白是以包涵体形式存在于宿主菌内的。Ｃ_（２７）重组蛋白分别经过包涵体洗涤、ＤＥＡＥ阴离子交换层析和Ｓ－２００分子筛两步柱层析纯化之后,纯度大于９５％,纯化得率为５３．２％,总回收率为１７．９％。纯化工艺流程简单、得率高,适合向规模化生产发展。     

Detection of Bovine Spongiform Encephalopathy-Related Prion Protein Gene Promoter Polymorphisms in Local Turkish Cattle

Polymorphisms in open reading frames of the prion protein gene (PRNP) have been shown to be associated with prion disease susceptibility in humans, sheep, and mice. Studies in recent years have demonstrated a similar effect of PRNP promoter and intron-1 polymorphisms on bovine spongiform encephalopathy (BSE) susceptibility in cattle. In this study, the deletion/insertion (indel) polymorphisms of the bovine PRNP gene within the promoter sequence (23 bp) and intron 1 (12 bp) were analyzed in local Turkish cattle. For this, 150 animals belonging to three different local breeds--the South Anatolian red, the East Anatolian red, and the Turkish gray--were tested using DNA purification and polymerase chain reaction. The ins allele in the 12 bp indel, which is associated with low susceptibility to BSE, showed a high frequency in all three breeds. The low-susceptibility allele of the 23-bp indel was identified in Turkish gray cattle with a frequency of 0.80. Results of the study have shown that local Turkish cattle might have an important genetic value for selection against BSE.     

Protein Array-based Approaches for Biomarker Discovery in Cancer

Biomarkers are deemed to be potential tools in early diagnosis, therapeutic monitoring, and prognosis evaluation for cancer, with simplicity as well as economic advantages compared with computed tomography and biopsy. However, most of the current cancer biomarkers present insufficient sensitivity as well as specificity. Therefore, there is urgent requirement for the discovery of biomarkers for cancer. As one of the most exciting emerging technologies, protein array provides a versatile and robust platform in cancer proteomics research because it shows tremendous advantages of miniaturized features, high throughput, and sensitive detections in last decades. Here, we will present a relatively complete picture on the characteristics and advance of different types of protein arrays in application for biomarker discovery in cancer, and give the future perspectives in this area of research.     

Iridium(III) Luminescent Probe for Detection of the Malarial Protein Biomarker Histidine Rich Protein-II

This work outlines the synthesis of a non-emissive, cyclometalated Ir(III) complex, Ir(ppy)₂(H₂O)₂⁺ (Ir1), which elicits a rapid, long-lived phosphorescent signal when coordinated to a histidine-containing protein immobilized on the surface of a magnetic particle. Synthesis of Ir1, in high yields,is complete O/N and involves splitting of the parent cyclometalated Ir(III) chloro-bridged dimer into two equivalents of the solvated complex.To confirm specificity, several amino acids were probed for coordination activity when added to the synthesized probe, and only histidine elicited a signal response. Using BNT-II, a branched peptide mimic of the malarial biomarker Histidine Rich Protein II (pfHRP-II), the iridium probe was validated as a tool for HRP-II detection. Quenching effects were noted in the BNT-II/Ir1 titration when compared to L-Histidine/Ir1, but these were attributed to steric hindrance and triplet state quenching. Biolayer interferometry was used to determine real-time kinetics of interaction of Ir1 with BNT-II. Once the system was optimized, the limit of detection of rcHRP-II using the probe was found to be 12.8 nM in solution. When this protein was immobilized on the surface of a 50 µm magnetic agarose particle, the limit of detection was 14.5 nM. The robust signal response of this inorganic probe, as well as its flexibility of use in solution or immobilized on a surface, can lend itself toward a variety of applications, from diagnostic use to imaging.     

Analysis and Frequency of Bovine Lymphocyte Antigen (BoLA-DRB3) Alleles in Iranian Holstein Cattle

The bovine lymphocyte antigen (BoLA-DRB3) gene encodes cell surface glycoproteins that initiate immune response by presenting processed antigenic peptides to CD4 T helper cells. DRB3 is the most polymorphic bovine MHC class II gene which encodes the peptide-binding groove. DRB3 gene has been extensively evaluated as a candidate marker for association with various bovine diseases and immunological traits. This study describes genetic variability in the BoLA-DRB3 in Iranian Holstein cattle. This is the first study of the DNA polymorphism of the BoLA-DRB3 gene in Iranian Holstein cattle. Hemi-nested PCR-RFLP method is used for identification the frequency of BoLA-DRB3 alleles. The BoLA-DRB3 locus is highly polymorphic in the studied herd (26 alleles). Almost 67% of the alleles were accounted for four alleles (BoLA-DRB3.2*8, *24, *11, and *16) in Iranian Holstein cattle. The DRB3.2*8 allele frequency (26.6%) was higher than the others. The frequencies of the DRB3.2*54, *37, *36, *28, *25, *14, *13, *10, *1 alleles were lower than 1%. Significant distinctions have been found between Iranian Holstein cattle and other cattle breeds studied. In Iranian Holstein cattle the alleles (BoLA-DRB3.2*22, *2, and *16) associated with a lower risk of cystic ovarian disease in Holstein cattle are found. The alleles associated with the resistance to mastitis and to bovine leukemia virus infection BoLA-DRB3.2*11 and *23 are detected with the frequencies 10.4 and 4.4%, respectively. Thus, in the Iranian Holstein cows studied alleles associated with resistance to various diseases are found. The method of DNA-typing of animals can be used in agricultural practice for BoLA-DRB3 allele genotyping of cattle in order to reduce spreading of alleles providing susceptibility to mastitis or leukemia in cattle herds.__________From Genetika, Vol. 41, No. 6, 2005, pp. 817–822.Original English Text Copyright © 2005 by Nassiry, Eftekhar Shahroodi, Mosafer, Mohammadi, Manshad, Ghazanfari, Mohammad Abadi, Sulimova.The article was submitted by the authors in English.     

MspI Allelic Pattern of Bovine Growth Hormone Gene in Indian Zebu Cattle (Bos indicus) Breeds

The MspI allelic variation in intron III of the bovine growth hormone (bGH) gene was explored using PCR-RFLP in 750 animals belonging to 17 well-recognized breeds of Indian zebu cattle (Bos indicus) reared in different geographic locations of the country. Restriction digestion analysis of a 329-bp PCR fragment of the bGH intron III region with MspI restriction enzyme revealed two alleles (MspI− and MspI+) and two genotypes (−/− and +/−) across the 17 cattle breeds studied. The allelic frequency varied from 0.67 to 0.94 for MspI (−) and from 0.06 to 0.33 for MspI (+) across the 17 breeds, with a combined average frequency of 0.87 and 0.13, respectively. No animal with +/+ genotype was detected across the samples analyzed. The chi-square test showed that the difference in MspI allelic frequency was not significant (p > 0.05), regardless of the geographic origin, coat color, or utility of the cattle breed. The high MspI (−) allele frequencies obtained for Indian zebu cattle in this study are in sharp contrast to those reported for taurine breeds from northern Europe, Mediterranean countries, and America. Findings of this study further substantiate the hypothesis that the MspI (−) allele has an Indian origin.     

Large-Scale Preparation of Biologically Active Recombinant Chicken Obese Protein (Leptin)

Prokaryotic expression vector pMON3401 encoding full size A(−1) chicken leptin (AF012727) was prepared by PCR of previously described cDNA.Escherichia colicells transformed with this vector overexpressed large amounts of chicken leptin upon induction with nalidixic acid. The expressed protein found in the inclusion bodies was refolded and purified to homogeneity on a Q-Sepharose column, yielding two electrophoretically pure fractions (leptin-1 and leptin-2), eluted from the column by 100 and 125 mM NaCl. Both fractions showed a single band of the expected molecular mass of 16 kDa and were composed of over 95% of monomeric protein. The biological activity of both fractions, resulting from proper renaturation, was further evidenced by their ability to stimulate proliferation of leptin-sensitive BAF/3 cells transfected with a long form of human leptin–receptor construct and by lowering the food intake of starved chicken following intravenal or intraperitoneal injections.     

Iron Is a Sensitive Biomarker for Inflammation in Multiple Sclerosis Lesions

MRI phase imaging in multiple sclerosis (MS) patients and in autopsy tissue have demonstrated the presence of iron depositions in white matter lesions.The accumulation of iron in some but not all lesions suggests a specific, potentially disease-relevant process, however; its pathophysiological significance remains unknown.Here, we explore the role of lesional iron in multiple sclerosis using multiple approaches: immunohistochemical examination of autoptic MS tissue, an in vitro model of iron-uptake in human cultured macrophages and ultra-highfield phase imaging of highly active and of secondary progressive MS patients.Using Perls'' stain and immunohistochemistry, iron was detected in MS tissue sections predominantly in non-phagocytosing macrophages/microglia at the edge of established, demyelinated lesions. Moreover, iron-containing macrophages but not myelin-laden macrophages expressed markers of proinflammatory (M1) polarization.Similarly, in human macrophage cultures, iron was preferentially taken up by non-phagocytosing, M1-polarized macrophages and induced M1 (super) polarization. Iron uptake was minimal in myelin-laden macrophages and active myelin phagocytosis led to depletion of intracellular iron.Finally, we demonstrated in MS patients using GRE phase imaging with ultra-highfield MRI that phase hypointense lesions were significantly more prevalent in patients with active relapsing than with secondary progressive MS.Taken together, our data provide a basis to interpret iron-sensitive GRE phase imaging in MS patients: iron is present in non-phagocytosing, M1-polarized microglia/macrophages at the rim of chronic active white matter demyelinating lesions. Phase imaging may therefore visualize specific, chronic proinflammatory activity in established MS lesions and thus provide important clinical information on disease status and treatment efficacy in MS patients.     

BSA载体蛋白抗体的去除

为了去除抗血清中BSA载体蛋白产生的抗体,一根对BSA载体蛋白抗体高度特异性的亲和柱被构建。结果表明：所构建的亲和柱对BSA载体蛋白抗体具高度特异性和亲和力,能有效地去除BSA载体蛋白产生的抗体。     

重组人卵透明带ZP3蛋白在毕赤酵母中的表达

利用P.pastoris表达人卵透明带ZP3蛋白。设计特定引物从全长hZP3 cDNA上扩增含跨膜区序列的人卵透明带ZP3基因片段,并在N末端接上串联组氨酸编码序列的重组基因序列;扩增片段插入表达载体pPIC9K中;线性化后的重组质粒转入P.pastoris中,用高浓度G418筛选高拷贝菌株,然后甲醇诱导目的蛋白表达。用SDS-PAGE和Western blot分析表达产物。结果发现P.pastoris表达的人ZP3蛋白可以分泌到培养液中,并且可溶性好。纯化前后的重组人ZP3蛋白均能与兔抗猪ZP3蛋白抗体发生交叉反应,证实表达的目的蛋白具有反应原性。     

Subgroup-Based Adaptive (SUBA) Designs for Multi-arm Biomarker Trials

Targeted therapies based on biomarker profiling are becoming a mainstream direction of cancer research and treatment. Depending on the expression of specific prognostic biomarkers, targeted therapies assign different cancer drugs to subgroups of patients even if they are diagnosed with the same type of cancer by traditional means, such as tumor location. For example, Herceptin is only indicated for the subgroup of patients with HER2+ breast cancer, but not other types of breast cancer. However, subgroups like HER2+ breast cancer with effective targeted therapies are rare, and most cancer drugs are still being applied to large patient populations that include many patients who might not respond or benefit. Also, the response to targeted agents in humans is usually unpredictable. To address these issues, we propose subgroup-based adaptive (SUBA), designs that simultaneously search for prognostic subgroups and allocate patients adaptively to the best subgroup-specific treatments throughout the course of the trial. The main features of SUBA include the continuous reclassification of patient subgroups based on a random partition model and the adaptive allocation of patients to the best treatment arm based on posterior predictive probabilities. We compare the SUBA design with three alternative designs including equal randomization, outcome-adaptive randomization, and a design based on a probit regression. In simulation studies, we find that SUBA compares favorably against the alternatives.     

人甲状旁腺激素(1-34)二联体与人血清白蛋白融合蛋白的构建及表达

构建人甲状旁腺激素(1-34)二联体与人血清白蛋白融合蛋白的表达载体,并表达得到该融合蛋白.通过设计强特异性的引物,利用重叠PCR技术,定向定量的拼接得到hPTH(1-34)二联体-HSA融合蛋白的基因;将构建好的融合基因插入表达载体pPIC9K,大量扩增重组质粒,并用Sal I线性化,电击转化毕赤酵母GS115,经组氨酸缺陷和G418抗性双重筛选得到阳性转化子;挑选阳性转化子进行甲醇诱导表达.测序结果表明得到的重组质粒pPIC9K-hPTH(1-34)二联体-HSA与目标设计完全一致;基因组PCR鉴定结果证明成功构建了hPTH(1-34)二联体-HSA融合基因的毕赤酵母(GS115)表达系统;SDS-PAGE电泳表明融合蛋白获得了表达,尿微量白蛋白试剂盒测定甲醇诱导表达3d后融合蛋白的产量为127 mg/L.     

重组胰高糖素样肽-1融合蛋白的纯化及其活性测定

主要探讨了发酵液中融合蛋白rh（GLP-1A2G）2-HSA的分离纯化过程。发酵上清液经超滤浓缩、离子交换层析、凝胶过滤分离得高纯度的rh（GLP-1A2G）2-HSA。纯化样品经SDS-PAGE检测为单一条带,HPLC分析纯度达98%,^125I标记后用TCA沉淀法测定放射性纯度达97%,符合药效学和药代动力学研究的需要,整个纯化过程回收率达到48.5%。通过细胞增殖实验表明纯化后的rh（GLP-1A2G）2-HSA具有类似GLP-1的促胰岛β细胞增殖活性,说明该分离过程保护了融合蛋白rh（GLP-1A2G）2-HSA的生物活性。通过融合蛋白rh（GLP-1A2G）2-HSA的纯化方法,可获得高纯度的重组融合蛋白rh（GLP-1A2G）2-HSA,为进一步的药效学和药代动力学研究奠定了基础。     

Analysis of a Urinary Biomarker Panel for Clinical Outcomes Assessment in Cirrhosis

Background

Biomarkers are potentially useful in assessment of outcomes in patients with cirrhosis, but information is very limited. Given the large number of biomarkers, adequate choice of which biomarker(s) to investigate first is important.

Aim

Analysis of potential usefulness of a panel of urinary biomarkers in outcome assessment in cirrhosis.

Patients and Methods

Fifty-five patients with acute decompensation of cirrhosis were studied: 39 had Acute Kidney Injury (AKI) (Prerenal 12, type-1 HRS (hepatorenal syndrome) 15 and Acute Tubular Necrosis (ATN) 12) and 16 acute decompensation without AKI. Thirty-four patients had Acute-on-chronic liver failure (ACLF). A panel of 12 urinary biomarkers was assessed, using a multiplex assay, for their relationship with ATN, ACLF and mortality.

Results

Biomarker with best accuracy for ATN diagnosis was NGAL (neutrophil-gelatinase associated lipocalin): 36 [26-125], 104 [58-208] and 1807 [494-3,716] μg/g creatinine in Prerenal-AKI, type-1 HRS and ATN, respectively; p<0.0001 (AUROC 0.957). Other attractive biomarkers for ATN diagnosis were IL-18, albumin, trefoil-factor-3 (TFF-3) and glutathione-S-transferase-π (GST-π) Biomarkers with less accuracy for ATN AUCROC<0.8 were β2-microglobulin, calbindin, cystatin-C, clusterin and KIM-1 (kidney injury molecule-1). For ACLF, the biomarker with the best accuracy was NGAL (ACLF vs. No-ACLF: 165 [67-676] and 32 [19-40] μg/g creatinine; respectively; p<0.0001; AUROC 0.878). Interestingly, other biomarkers with high accuracy for ACLF were osteopontin, albumin, and TFF-3. Biomarkers with best accuracy for prognosis were those associated with ACLF.

Conclusions

A number of biomarkers appear promising for differential diagnosis between ATN and other types of AKI. The most interesting biomarkers for ACLF and prognosis are NGAL, osteopontin, albumin, and TFF-3. These results support the role of major inflammatory reaction in the pathogenesis of ACLF.     

大肠杆菌重组乳链菌肽抗性蛋白(NSR)的表达纯化及其功能分析

乳链菌肽(Nisin)是由某些乳酸菌产生的一种阳离子抗菌肽, 而Nisin抗性蛋白(Nisin resistance protein, NSR)的表达则使一些非 Nisin产生菌获得Nisin抗性。为深入探索NSR的作用机制, 本研究在大肠杆菌中表达了去除N末端38个氨基酸残基的NSR(NSRΔ38)与GST的融合蛋白GST-NSRΔ38。通过谷胱甘肽(GSH)亲和层析和GST标签的切除后, 得到纯化的NSRΔ38, 并测定了该蛋白可能的nisin降解活性。反应产物的抑菌活性测定结果表明被NSRΔ38作用