Zhiheng Pei, M.D., Ph.D.

Oral Microbiome Profiles: 16S rRNA Pyrosequencing and Microarray Assay Comparison
Ahn, Jiyoung; Yang, Liying; Paster, Bruce J; Ganly, Ian; Morris, Luc; Pei, Zhiheng; Hayes, Richard B
2011 ;6(7):e22788-e22788, PLoS ONE
OBJECTIVES: The human oral microbiome is potentially related to diverse health conditions and high-throughput technology provides the possibility of surveying microbial community structure at high resolution. We compared two oral microbiome survey methods: broad-based microbiome identification by 16S rRNA gene sequencing and targeted characterization of microbes by custom DNA microarray. METHODS: Oral wash samples were collected from 20 individuals at Memorial Sloan-Kettering Cancer Center. 16S rRNA gene survey was performed by 454 pyrosequencing of the V3-V5 region (450 bp). Targeted identification by DNA microarray was carried out with the Human Oral Microbe Identification Microarray (HOMIM). Correlations and relative abundance were compared at phylum and genus level, between 16S rRNA sequence read ratio and HOMIM hybridization intensity. RESULTS: The major phyla, Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria were identified with high correlation by the two methods (r = 0.70 approximately 0.86). 16S rRNA gene pyrosequencing identified 77 genera and HOMIM identified 49, with 37 genera detected by both methods; more than 98% of classified bacteria were assigned in these 37 genera. Concordance by the two assays (presence/absence) and correlations were high for common genera (Streptococcus, Veillonella, Leptotrichia, Prevotella, and Haemophilus; Correlation = 0.70-0.84). CONCLUSION: Microbiome community profiles assessed by 16S rRNA pyrosequencing and HOMIM were highly correlated at the phylum level and, when comparing the more commonly detected taxa, also at the genus level. Both methods are currently suitable for high-throughput epidemiologic investigations relating identified and more common oral microbial taxa to disease risk; yet, pyrosequencing may provide a broader spectrum of taxa identification, a distinct sequence-read record, and greater detection sensitivity
— id: 136523, year: 2011, vol: 6, page: e22788, stat: Journal Article,

The effect of H. pylori eradication on meal-associated changes in plasma ghrelin and leptin
Francois, Fritz; Roper, Jatin; Joseph, Neal; Pei, Zhiheng; Chhada, Aditi; Shak, Joshua R; de Perez, Asalia Z Olivares; Perez-Perez, Guillermo I; Blaser, Martin J
2011 ;11:37-37, BMC gastroenterology
ABSTRACT: BACKGROUND: Appetite and energy expenditure are regulated in part by ghrelin and leptin produced in the gastric mucosa, which may be modified by H. pylori colonization. We prospectively evaluated the effect of H. pylori eradication on meal-associated changes in serum ghrelin and leptin levels, and body weight. METHODS: Veterans referred for upper GI endoscopy were evaluated at baseline and >/=8 weeks after endoscopy, and H. pylori status and body weight were ascertained. During the first visit in all subjects, and during subsequent visits in the initially H. pylori-positive subjects and controls, blood was collected after an overnight fast and 1 h after a standard high protein meal, and levels of eight hormones determined. RESULTS: Of 92 enrolled subjects, 38 were H. pylori-negative, 44 H. pylori-positive, and 10 were indeterminate. Among 23 H. pylori-positive subjects who completed evaluation after treatment, 21 were eradicated, and 2 failed eradication. After a median of seven months following eradication, six hormones related to energy homeostasis showed no significant differences, but post-prandial acylated ghrelin levels were nearly six-fold higher than pre-eradication (p = 0.005), and median integrated leptin levels also increased (20%) significantly (p < 0.001). BMI significantly increased (5 +/- 2%; p = 0.008) over 18 months in the initially H. pylori-positive individuals, but was not significantly changed in those who were H. pylori-negative or indeterminant at baseline. CONCLUSIONS: Circulating meal-associated leptin and ghrelin levels and BMI changed significantly after H. pylori eradication, providing direct evidence that H. pylori colonization is involved in ghrelin and leptin regulation, with consequent effects on body morphometry
— id: 132313, year: 2011, vol: 11, page: 37, stat: Journal Article,

Association of overexpression of TIF1gamma with colorectal carcinogenesis and advanced colorectal adenocarcinoma
Jain, Shilpa; Singhal, Shashideep; Francis, Franto; Hajdu, Cristina; Wang, Jin-Hua; Suriawinata, Arief; Wang, Yin-Quan; Zhang, Miao; Weinshel, Elizabeth H; Francois, Fritz; Pei, Zhi-Heng; Lee, Peng; Xu, Ru-Liang
2011 Sep 21;17(35):3994-4000, World journal of gastroenterology : WJG
AIM: To determine the expression and clinical significance of transcriptional intermediary factor 1 gamma (TIF1gamma), Smad4 and transforming growth factor-beta (TGFbetaR) across a spectrum representing colorectal cancer (CRC) development. METHODS: Tissue microarrays were prepared from archival paraffin embedded tissue, including 51 colorectal carcinomas, 25 tubular adenomas (TA) and 26 HPs, each with matched normal colonic epithelium. Immunohistochemistry was performed using antibodies against TIF1gamma, Smad4 and TGFbetaRII. The levels of expression were scored semi-quantitatively (score 0-3 or loss and retention for Smad4). RESULTS: Overexpression of TIF1gamma was detected in 5/26 (19%) HP; however, it was seen in a significantly higher proportion of neoplasms, 15/25 (60%) TAs and 24/51 (47%) CRCs (P < 0.05). Normal colonic mucosa, HP, and TAs showed strong Smad4 expression, while its expression was absent in 22/51 (43%) CRCs. Overexpression of TGFbetaRII was more commonly seen in neoplasms, 13/25 (52%) TAs and 29/51 (57%) CRCs compared to 9/26 (35%) HP (P < 0.05). Furthermore, there was a correlation between TIF1gamma overexpression and Smad4 loss in CRC (Kendall tau rank correlation value = 0.35, P < 0.05). The levels of TIF1gamma overexpression were significantly higher in stage III than in stage I and II CRC (P < 0.05). CONCLUSION: The findings suggest that over-expression of TIF1gamma occurs in early stages of colorectal carcinogenesis, is inversely related with Smad4 loss, and may be a prognostic indicator for poor outcome
— id: 140416, year: 2011, vol: 17, page: 3994, stat: Journal Article,

Metastatic balloon cell malignant melanoma: a case report and literature review
Lee, Lili; Zhou, Fang; Simms, Anthony; Wieczorek, Rosemary; Fang, Yanan; Subietas-Mayol, Antonio; Wang, Beverly; Heller, Patricia; Huang, Hongying; Pei, Zhiheng; Osman, Iman; Meehan, Shane; Lee, Peng
2011 Mar;4(3):315-321, International journal of clinical & experimental pathology
A case of metastatic balloon cell malignant melanoma (BCMM) is presented. The balloon melanoma cells (BMC) were absent in the shave biopsy of the primary lesion and present as a minor component in the wide and deep excision. A subsequent right neck lymph node metastasis showed complete replacement of the lymph node by large, foamy cells. Though the tumor was amelanocytic and Fontana-Masson stain failed to reveal melanin, it stained positively for S-100, HMB-45, and Melan-A. Ultrastructurally, the foamy cells were characterized by cytoplasmic vacuolization and a lack of melanosomes. The differential diagnosis of metastatic balloon cell malignant melanoma is broad, and clinicopathologic correlation may play a critical role in achieving the correct diagnosis
— id: 133175, year: 2011, vol: 4, page: 315, stat: Journal Article,

Association Between Oral Health And Gastric Precancerous Lesions
Salazar CR; Francois F; Li Y; Corby P; Hays R; Leung C; Bedi S; Segers S; Queiroz E; Sun J; Wang B; Ho H; Craig R; Cruz G; Blaser MJ; Perez-Perez G; Hayes RB; Dasanayake A; Pei Z; Chen Y
2011 Dec 1;:399-403 #, Carcinogenesis
Although recent studies have suggested that tooth loss is positively related to the risk of gastric non-cardia cancer, the underlying oral health conditions potentially responsible for the association remain unknown. We investigated whether clinical and behavioral measures of oral health are associated with the risk of gastric precancerous lesions. We conducted a cross sectional study of 131 patients undergoing upper gastrointestinal endoscopy. Cases were defined as those with gastric precancerous lesions including intestinal metaplasia or chronic atrophic gastritis on the basis of standard biopsy review. A validated structured questionnaire was administered to obtain information on oral health behaviors. A comprehensive clinical oral health examination was performed on a subset of 91 patients to evaluate for periodontal disease and dental caries experience. A total of 41 (31%) cases of gastric precancerous lesions were identified. Compared to non-cases, cases were significantly more likely to not floss their teeth (Odds Ratio [OR] = 2.89, 95% Confidence Interval [CI]: 1.09-7.64), adjusting for age, sex, race, BMI, smoking status, educational attainment and Helicobacter pylori status in serum. Among participants who completed the oral examination, cases (n=28) were more likely to have a higher percentage of sites with gingival bleeding than non-cases (OR = 2.63, 95% CI: 1.37-5.05 for a standard deviation increase in bleeding sites [equivalent to 19.7%]), independent of potential confounders. Our findings demonstrate that specific oral health conditions and behaviors such as gingival bleeding and tooth flossing are associated with gastric precancerous lesions
— id: 147670, year: 2011, vol: , page: 399, stat: Journal Article,

Human Microbiome and HIV/AIDS
Saxena D; Li Y; Yang L; Pei Z; Poles M; Abrams WR; Malamud D
2011 Dec 23;:44-51 #, Current HIV/AIDS reports
Understanding of the human microbiome continues to grow rapidly; however, reports on changes in the microbiome after HIV infection are still limited. This review surveys the progress made in methodology associated with microbiome studies and highlights the remaining challenges to this field. Studies have shown that commensal oral, gut, vaginal, and penile bacteria are vital to the health of the human immune system. Our studies on crosstalk among oral and gastrointestinal soluble innate factors, HIV, and microbes indicated that the oral and gut microbiome was altered in the HIV-positive samples compared to the negative controls. The importance of understanding the bacterial component of HIV/AIDS, and likelihood of 'crosstalk' between viral and bacterial pathogens, will help in understanding the role of the microbiome in HIV-infected individuals and facilitate identification of novel antiretroviral factors for use as novel diagnostics, microbicides, or therapeutics against HIV infection
— id: 149845, year: 2011, vol: , page: 44, stat: Journal Article,

Distinct function of androgen receptor coactivator ARA70alpha and ARA70beta in mammary gland development, and in breast cancer
Wu, Xinyu; Chen, Fei; Sahin, Aysegul; Albarracin, Constance; Pei, Zhiheng; Zou, Xuanyi; Singh, Baljit; Xu, Ruliang; Daniels, Garrett; Li, Yirong; Wei, Jianjun; Blake, Marvin; Schneider, Robert J; Cowin, Pamela; Lee, Peng
2011 Jul;128(2):391-400, Breast cancer research & treatment
Steroid receptor coactivators are important in regulating the function of the receptors in endocrine organ development and in cancers, including breast. Androgen receptor (AR) coactivator ARA70, was first identified as a gene fused to the ret oncogene and later characterized as an AR coactivator. We previously reported that the full length ARA70alpha functions as a tumor suppressor gene and that ARA70beta functions as an oncogene in prostate cancer. Here we show that both ARA70alpha and ARA70beta function as AR and estrogen receptor (ER) coactivators in breast cancer cells. However, ARA70alpha and ARA70beta serve different functions in mammary gland development and breast cancer tumorigenesis. We observed hypoplastic development of mammary glands in MMTV driven ARA70alpha transgenic mice and overgrowth of mammary glands in ARA70beta transgenic mice at virgin and pregnant stages. We determined that ARA70alpha inhibited cell proliferation, and that ARA70beta promotes proliferation in MCF7 breast cancer cells. These effects were observed in hormone-free media, or in media with androgen or estrogen, though to varying degrees. Additionally, we observed that ARA70beta strongly enhanced the invasive ability of MCF7 breast cancer cells in in vitro Matrigel assays. Significantly, decreased ARA70alpha expression is associated with increased tendency of breast cancer metastasis. In summary, ARA70alpha and ARA70beta have distinct effects in mammary gland development and in the progression of breast cancer
— id: 138162, year: 2011, vol: 128, page: 391, stat: Journal Article,

Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome
Nossa, Carlos W; Oberdorf, William E; Yang, Liying; Aas, Jorn A; Paster, Bruce J; Desantis, Todd Z; Brodie, Eoin L; Malamud, Daniel; Poles, Michael A; Pei, Zhiheng
2010 Sep 7;16(33):4135-4144, World journal of gastroenterology : WJG
AIM: To design and validate broad-range 16S rRNA primers for use in high throughput sequencing to classify bacteria isolated from the human foregut microbiome. METHODS: A foregut microbiome dataset was constructed using 16S rRNA gene sequences obtained from oral, esophageal, and gastric microbiomes produced by Sanger sequencing in previous studies represented by 219 bacterial species. Candidate primers evaluated were from the European rRNA database. To assess the effect of sequence length on accuracy of classification, 16S rRNA genes of various lengths were created by trimming the full length sequences. Sequences spanning various hypervariable regions were selected to simulate the amplicons that would be obtained using possible primer pairs. The sequences were compared with full length 16S rRNA genes for accuracy in taxonomic classification using online software at the Ribosomal Database Project (RDP). The universality of the primer set was evaluated using the RDP 16S rRNA database which is comprised of 433 306 16S rRNA genes, represented by 36 phyla. RESULTS: Truncation to 100 nucleotides (nt) downstream from the position corresponding to base 28 in the Escherichia coli 16S rRNA gene caused misclassification of 87 (39.7%) of the 219 sequences, compared with misclassification of only 29 (13.2%) sequences with truncation to 350 nt. Among 350-nt sequence reads within various regions of the 16S rRNA gene, the reverse read of an amplicon generated using the 343F/798R primers had the least (8.2%) effect on classification. In comparison, truncation to 900 nt mimicking single pass Sanger reads misclassified 5.0% of the 219 sequences. The 343F/798R amplicon accurately assigned 91.8% of the 219 sequences at the species level. Weighted by abundance of the species in the esophageal dataset, the 343F/798R amplicon yielded similar classification accuracy without a significant loss in species coverage (92%). Modification of the 343F/798R primers to 347F/803R increased their universality among foregut species. Assuming that a typical polymerase chain reaction can tolerate 2 mismatches between a primer and a template, the modified 347F and 803R primers should be able to anneal 98% and 99.6% of all 16S rRNA genes in the RDP database. CONCLUSION: 347F/803R is the most suitable pair of primers for classification of foregut 16S rRNA genes but also possess universality suitable for analyses of other complex microbiomes
— id: 112048, year: 2010, vol: 16, page: 4135, stat: Journal Article,

Diversity of 16S rRNA genes within individual prokaryotic genomes
Pei, Anna Y; Oberdorf, William E; Nossa, Carlos W; Agarwal, Ankush; Chokshi, Pooja; Gerz, Erika A; Jin, Zhida; Lee, Peng; Yang, Liying; Poles, Michael; Brown, Stuart M; Sotero, Steven; Desantis, Todd; Brodie, Eoin; Nelson, Karen; Pei, Zhiheng
2010 Jun;76(12):3886-3897, Applied & environmental microbiology
Analysis of intragenomic variation of 16S rRNA genes is a unique approach to examining the concept of ribosomal constraints on rRNA genes; the degree of variation is an important parameter to consider for estimation of the diversity of a complex microbiome in the recently initiated Human Microbiome Project (http://nihroadmap.nih.gov/hmp). The current GenBank database has a collection of 883 prokaryotic genomes representing 568 unique species, of which 425 species contained 2 to 15 copies of 16S rRNA genes per genome (2.22 +/- 0.81). Sequence diversity among the 16S rRNA genes in a genome was found in 235 species (from 0.06% to 20.38%; 0.55% +/- 1.46%). Compared with the 16S rRNA-based threshold for operational definition of species (1 to 1.3% diversity), the diversity was borderline (between 1% and 1.3%) in 10 species and >1.3% in 14 species. The diversified 16S rRNA genes in Haloarcula marismortui (diversity, 5.63%) and Thermoanaerobacter tengcongensis (6.70%) were highly conserved at the 2 degrees structure level, while the diversified gene in B. afzelii (20.38%) appears to be a pseudogene. The diversified genes in the remaining 21 species were also conserved, except for a truncated 16S rRNA gene in 'Candidatus Protochlamydia amoebophila.' Thus, this survey of intragenomic diversity of 16S rRNA genes provides strong evidence supporting the theory of ribosomal constraint. Taxonomic classification using the 16S rRNA-based operational threshold could misclassify a number of species into more than one species, leading to an overestimation of the diversity of a complex microbiome. This phenomenon is especially seen in 7 bacterial species associated with the human microbiome or diseases
— id: 133520, year: 2010, vol: 76, page: 3886, stat: Journal Article,

Streptococcus gallolyticus subspecies pasteurianus (biotype II/2), a newly reported cause of adult meningitis
Sturt, Amy S; Yang, Liying; Sandhu, Kuldip; Pei, Zhiheng; Cassai, Nicholas; Blaser, Martin J
2010 Jun;48(6):2247-2249, Journal of clinical microbiology
We report the first case of adult meningitis confirmed to be due to Streptococcus gallolyticus subsp. pasteurianus. Phenotypically reported as Streptococcus bovis biotype II/2, 16S rRNA sequencing revealed S. gallolyticus subsp. pasteurianus. Because of taxonomic uncertainties, S. gallolyticus subsp. pasteurianus may be an underrecognized agent of systemic infections
— id: 133500, year: 2010, vol: 48, page: 2247, stat: Journal Article,

Adenomatoid Tumor of the Adrenal Gland Case Report of a Rare Adrenal Lesion
Chaudhry, S; Lubitz, S; Newman, K; Pei, ZH; Shepard, T; Danoff, A
2009 SEP-OCT ;19(5):233-236, Endocrinologist
Objective: To report a rare case of an adenomatoid tumor (AT) of the adrenal gland. Methods: We present a case report, including clinical, radiologic, and pathologic findings, and review the relevant literature. Results: We describe a 60-year-old man in whom an AT of the adrenal gland was discovered incidentally, and review the literature. Fewer than 20 cases of these tumors are reported. The tumors range in size from 0.5 to 11 cm, are more common in men, and are more frequently located in the left adrenal gland. A specific imaging phenotype has not been characterized. Histologic features, including infiltration into the surrounding tissue, and presence of signet ring cells, may raise concern of a more aggressive neoplasm. Immunologic staining for mesothelial and endothelial markers may be necessary to establish a definitive diagnosis. Conclusion: ATs of the adrenal gland are rare benign lesions. They are difficult to differentiate from more common adrenal tumors by computerized tamography (CT) or magnetic resonance imaging (MRI). Pathologic findings also can present challenges in distinguishing these lesions from more aggressive neoplasms. ATs should be considered in the differential diagnosis of adrenal masses, whether discovered as incidental radiologic, surgical, or pathologic findings, or at autopsy, so that the potential consequences of misdiagnosis may be avoided
— id: 102951, year: 2009, vol: 19, page: 233, stat: Journal Article,

Pancreatic carcinoma with multilineage (acinar, neuroendocrine, and ductal) differentiation
Newman, Kia; Stahl-Herz, Jay; Kabiawu, Oluyomi; Newman, Elliot; Wieczorek, Rosemary; Wang, Beverly; Pei, Zhiheng; Bannan, Michael; Lee, Peng; Xu, Ruliang
2009 ;2(6):602-607, International journal of clinical & experimental pathology
The preponderance of pancreatic tumors is adenocarcinoma of the ductal type; carcinomas with multiple lineage differentiation are extremely rare. We report an unusual case of pancreatic carcinoma with combined acinar and neuroendocrine differentiation and minor ductal component with concurrent acinar-ductal metaplasia (ADM), an early lesion implicated in ductal carcinogenesis. The patient is a 56-year-old man with vague complaints of dull left upper quadrant pain with radiation across the mid-portion of his abdomen. A computer tomography scan revealed an irregular enlargement of the distal 3.2 cm of the pancreatic body. A distal pancreatectomy was then performed. Histologic examination revealed a pancreatic carcinoma with cellular features of eosinophilic granular cytoplasm and salt-pepper nuclei. The acinar differentiation of the carcinoma was confirmed by positivity on periodic acid-Schiff stain resistant to diastase digestion (dPAS), positivity for antitrypsin on immunohistochemistry (IHC), and presence of zymogen granules on electron microscopy (EM). The neuroendocrine differentiation was evident by positive synaptophysin and chromogranin stain on IHC and neuroendocrine granules on EM. The ductal component was only visible by PAS stain and immunostains for CEA and CK19A and accompanied by a number of the acinar-ductal metaplasia lesions adjacent to the main tumor. Thus, the histological, histochemical, immunohistochemical and electron-microscopic evidence all suggested that the pancreatic carcinoma underwent trilineage differentiation
— id: 101289, year: 2009, vol: 2, page: 602, stat: Journal Article,

Diversity of 23S rRNA genes within individual prokaryotic genomes
Pei, Anna; Nossa, Carlos W; Chokshi, Pooja; Blaser, Martin J; Yang, Liying; Rosmarin, David M; Pei, Zhiheng
2009 ;4(5):e5437-e5437, PLoS ONE
BACKGROUND: The concept of ribosomal constraints on rRNA genes is deduced primarily based on the comparison of consensus rRNA sequences between closely related species, but recent advances in whole-genome sequencing allow evaluation of this concept within organisms with multiple rRNA operons. METHODOLOGY/PRINCIPAL FINDINGS: Using the 23S rRNA gene as an example, we analyzed the diversity among individual rRNA genes within a genome. Of 184 prokaryotic species containing multiple 23S rRNA genes, diversity was observed in 113 (61.4%) genomes (mean 0.40%, range 0.01%-4.04%). Significant (1.17%-4.04%) intragenomic variation was found in 8 species. In 5 of the 8 species, the diversity in the primary structure had only minimal effect on the secondary structure (stem versus loop transition). In the remaining 3 species, the diversity significantly altered local secondary structure, but the alteration appears minimized through complex rearrangement. Intervening sequences (IVS), ranging between 9 and 1471 nt in size, were found in 7 species. IVS in Deinococcus radiodurans and Nostoc sp. encode transposases. T. tengcongensis was the only species in which intragenomic diversity >3% was observed among 4 paralogous 23S rRNA genes. CONCLUSIONS/SIGNIFICANCE: These findings indicate tight ribosomal constraints on individual 23S rRNA genes within a genome. Although classification using primary 23S rRNA sequences could be erroneous, significant diversity among paralogous 23S rRNA genes was observed only once in the 184 species analyzed, indicating little overall impact on the mainstream of 23S rRNA gene-based prokaryotic taxonomy
— id: 106442, year: 2009, vol: 4, page: e5437, stat: Journal Article,

Inflammation and intestinal metaplasia of the distal esophagus are associated with alterations in the microbiome
Yang, Liying; Lu, Xiaohua; Nossa, Carlos W; Francois, Fritz; Peek, Richard M; Pei, Zhiheng
2009 Aug;137(2):588-597, Gastroenterology
BACKGROUND & AIMS: Gastroesophageal reflux causes inflammation and intestinal metaplasia and its downstream sequelum adenocarcinoma in the distal esophagus. The incidence of esophageal adenocarcinoma has increased approximately 6-fold in the United States since the 1970s, accompanied with a significant increase in the prevalence of gastroesophageal reflux disease (GERD). Despite extensive epidemiologic study, the cause for GERD and the unexpected increases remain unexplainable. Microbes are among the environmental factors that may contribute to the etiology of GERD, but very little research has been done on the esophageal microbiome, particularly in its relation to GERD. This is the first comprehensive reported correlation between a change in the esophageal microbiome and esophageal diseases. METHODS: Biopsy samples of the distal esophagus were collected from 34 patients. Host phenotypes were histologically defined as normal, esophagitis, or Barrett's esophagus (intestinal metaplasia). Microbiomes from the biopsy samples were analyzed by bacterial 16S ribosomal RNA gene survey and classified into types using unsupervised cluster analysis and phenotype-guided analyses. Independence between host phenotypes and microbiome types were analyzed by Fisher exact test. RESULTS: Esophageal microbiomes can be classified into 2 types. The type I microbiome was dominated by the genus Streptococcus and concentrated in the phenotypically normal esophagus. Conversely, the type II microbiome contained a greater proportion of gram-negative anaerobes/microaerophiles and primarily correlated with esophagitis (odds ratio, 15.4) and Barrett's esophagus (odds ratio, 16.5). CONCLUSIONS: In the human distal esophagus, inflammation and intestinal metaplasia are associated with global alteration of the microbiome. These findings raise the issue of a possible role for dysbiosis in the pathogenesis of reflux-related disorders
— id: 101280, year: 2009, vol: 137, page: 588, stat: Journal Article,

Interobserver variability in differentiation of nodal nevus from melanoma micrometastasis in sentinel lymph adenectomy specimens
Celin, N; Bannan, M; Darvishian, F; Hajdu, C; Nonaka, D; Ye, W; Pei, Z; Melamed, J
2008 ;21(2):409-409, Modern pathology
— id: 100682, year: 2008, vol: 21, page: 409, stat: Journal Article,

The association of gastric leptin with oesophageal inflammation and metaplasia
Francois, F; Roper, J; Goodman, A J; Pei, Z; Ghumman, M; Mourad, M; de Perez, A Z Olivares; Perez-Perez, G I; Tseng, C-H; Blaser, M J
2008 Jan;57(1):16-24, Gut: journal of the British Society of Gastroenterology
BACKGROUND: Gastro-oesophageal reflux disease complications may reflect imbalances between protective and injurious factors. Through its effects on cell growth, leptin may influence oesophageal mucosal homeostasis. AIMS: To determine whether leptin receptors are present in the oesophagus, and whether serum or gastric leptin levels are associated with oesophageal inflammation and metaplasia. METHODS: From patients referred for upper endoscopy, biopsies were obtained from the stomach and distal oesophagus, and serum samples were collected. Patients were classified as having normal, inflamed or Barrett's oesophagus. Quantitative immunohistochemistry was performed on representative sections, and leptin levels in plasma and gastric biopsy samples were determined by specific immunoassay. RESULTS: Of 269 individuals enrolled, 105 were Helicobacter pylori-negative. Of the 88 patients with complete oesophageal biopsies, 44 were normal, 24 were inflamed and 20 were Barrett's oesophagus. Receptors for leptin were highly expressed on oesophageal epithelial cells, with similar density and staining pattern in all three conditions, and plasma and antral leptin levels did not differ significantly. Patients with Barrett's had significantly (p = 0.01) higher fundic leptin levels (median 202 (interquartile range 123-333) pg/mg) compared with normal (126 (78-221) pg/mg) or inflamed (114 (76-195) pg/mg) oesophagus. In multivariate analysis, for every twofold increase in fundic leptin, the odds of having Barrett's was 3.4 times (95% CI 1.5 to 7.6) higher compared with having a normal oesophagus. CONCLUSIONS: Leptin receptor expression on oesophageal epithelial cells provides a pathway for leptin-mediated signal transduction. Variation in gastric leptin production could contribute to differential oesophageal healing and metaplasia progression
— id: 75709, year: 2008, vol: 57, page: 16, stat: Journal Article,

Substantial alterations of the cutaneous bacterial biota in psoriatic lesions
Gao, Zhan; Tseng, Chi-hong; Strober, Bruce E; Pei, Zhiheng; Blaser, Martin J
2008 ;3(7):e2719-e2719, PLoS ONE
For psoriasis, an idiopathic inflammatory disorder of the skin, the microbial biota has not been defined using cultivation-independent methods. We used broad-range 16S rDNA PCR for archaea and bacteria to examine the microbiota of normal and psoriatic skin. From 6 patients, 19 cutaneous samples (13 from diseased skin and 6 from normal skin) were obtained. Extracted DNA was subjected to the broad range PCR, and 1,925 cloned products were compared with 2,038 products previously reported from healthy persons. Using 98% sequence identity as a species boundary, 1,841 (95.6%) clones were similar to known bacterial 16S rDNA, representing 6 phyla, 86 genera, or 189 species-level operational taxonomic unit (SLOTU); 84 (4.4%) clones with <98% identity probably represented novel species. The most abundant and diverse phylum populating the psoriatic lesions was Firmicutes (46.2%), significantly (P<0.001) overrepresented, compared to the samples from uninvolved skin of the patients (39.0%) and healthy persons (24.4%). In contrast, Actinobacteria, the most prevalent and diverse phylum in normal skin samples from both healthy persons (47.6%) and the patients (47.8%), was significantly (P<0.01) underrepresented in the psoriatic lesion samples (37.3%). Representation of Propionibacterium species were lower in the psoriatic lesions (2.9+/-5.5%) than from normal persons (21.1+/-18.2%; P<0.001), whereas normal skin from the psoriatic patients showed intermediate levels (12.3+/-21.6%). We conclude that psoriasis is associated with substantial alteration in the composition and representation of the cutaneous bacterial biota
— id: 86553, year: 2008, vol: 3, page: e2719, stat: Journal Article,

Bacterial community in the crop of the hoatzin, a neotropical folivorous flying bird
Godoy-Vitorino, Filipa; Ley, Ruth E; Gao, Zhan; Pei, Zhiheng; Ortiz-Zuazaga, Humberto; Pericchi, Luis R; Garcia-Amado, Maria A; Michelangeli, Fabian; Blaser, Martin J; Gordon, Jeffrey I; Dominguez-Bello, Maria G
2008 Oct;74(19):5905-5912, Applied & environmental microbiology
The hoatzin is unique among known avian species because of the fermentative function of its enlarged crop. A small-bodied flying foregut fermenter is a paradox, and this bird provides an interesting model to examine how diet selection and the gut microbiota contribute to maximizing digestive efficiency. Therefore, we characterized the bacterial population in the crop of six adult hoatzins captured from the wild. A total of 1,235 16S rRNA gene sequences were grouped into 580 phylotypes (67% of the pooled species richness sampled, based on Good's coverage estimator, with C(ACE) and Chao1 estimates of 1,709 and 1,795 species-level [99% identity] operational taxonomic units, respectively). Members of 9 of the approximately 75 known phyla in Bacteria were identified in this gut habitat; the Firmicutes were dominant (67% of sequences, belonging to the classes Clostridia, Mollicutes, and Bacilli), followed by the Bacteroidetes (30%, mostly in the order Bacteroidales), Proteobacteria (1.8%), and Lentisphaerae, Verrucomicrobia, TM7, Spirochaetes, Actinobacteria, and Aminanaerobia (all <0.1%). The novelty in this ecosystem is great; 94% of the phylotypes were unclassified at the 'species' level and thus likely include novel cellulolytic lineages
— id: 95160, year: 2008, vol: 74, page: 5905, stat: Journal Article,

Case report: Paenibacillus thiaminolyticus: a new cause of human infection, inducing bacteremia in a patient on hemodialysis
Ouyang, Jie; Pei, Zhiheng; Lutwick, Larry; Dalal, Sharvari; Yang, Liying; Cassai, Nicholas; Sandhu, Kuldip; Hanna, Bruce; Wieczorek, Rosemary L; Bluth, Martin; Pincus, Matthew R
2008 Autumn;38(4):393-400, Annals of clinical & laboratory science
Paenibacilli are gram-positive, aerobic bacteria that are related to Bacilli but differ in the DNA encoding their 16S rRNA. Until recently, these organisms were not known to cause human disease. There are now several reports of human infection caused by a few members of this genus, most commonly by P. alvei. We report a human infection in a patient with a permacath for chronic hemodialysis who was found to have bacteremia caused by P. thiaminolyticus, which is an environmental bacterium that has never been found to cause human disease. We identified this bacterium by biochemical tests, cloning, sequencing the genomic DNA encoding its 16S rRNA, growth characteristics, and electron microscopic studies. This constitutes the first report of a human infection caused by this organism
— id: 140207, year: 2008, vol: 38, page: 393, stat: Journal Article,

Androgen receptor coactivator ARA70alpha and ARA70beta isoform-specific antibodies: new tools for studies of expression and immunohistochemical localization
Peng, Yi; Chiriboga, Luis; Yee, Herman; Pei, Zhiheng; Wang, Zhenxing; Lee, Peng
2008 Jan;16(1):7-12, Applied immunohistochemistry & molecular morphology
ARA70 is a coactivator of androgen receptor (AR), a ligand-dependent transcription factor that plays an important role in prostate cancer. There are 2 variants of ARA70, the full length 70 kd ARA70alpha isoform and the internally spliced 35 kd ARA70beta isoform. Recent studies have suggested different expression and roles of the 2 isoforms in several endocrine malignancies, including prostate, breast, and ovarian cancers. To study the roles of these isoforms in cancers, we produced isoform-specific polyclonal antibodies. The anti-ARA70alpha antibody was raised in rabbits against 326 amino acid peptide corresponding to the internal deletion missing from ARA70beta (ARA70id), whereas the anti-ARA70beta antibody was raised against 18 amino acid polypeptide spanning the splice junction, with Gln-Gln motif unique to ARA70beta. The antisera were affinity purified on CNBr-activated sepharose 4B, and their specificity tested against bacterially expressed, Ni-column-purified ARA70alpha, ARA70beta, and ARA70id. The anti-ARA70alpha antibody recognized ARA70alpha and ARA70id, but not ARA70beta. The anti-ARA70beta antibody was specific to ARA70beta and did not cross-react with ARA70alpha or ARA70id. We then used these antibodies to detect ARA70 isoforms in crude extracts made of prostate cancer cell lines and performed immunohistochemical localization of these proteins in prostate tissues. ARA70beta localized to the cytosol, whereas ARA70alpha was found in the nucleus, supporting the notion of their dissimilar functions
— id: 76112, year: 2008, vol: 16, page: 7, stat: Journal Article,

Leptin and ghrelin in relation to Helicobacter pylori status in adult males
Roper, Jatin; Francois, Fritz; Shue, Peter L; Mourad, Michelle S; Pei, Zhiheng; Olivares de Perez, Asalia Z; Perez-Perez, Guillermo I; Tseng, Chi-Hong; Blaser, Martin J
2008 Jun;93(6):2350-2357, Journal of clinical endocrinology & metabolism
Context: Leptin and ghrelin, hormones involved in human energy homeostasis, are both produced in the stomach. Objective: We sought to determine whether the presence of Helicobacter pylori affects local and systemic levels of leptin and ghrelin. Design: Prospective Setting: Veterans Affairs outpatient endoscopy center Patients: 256 patients referred for upper endoscopy Outcomes: We obtained fasting serum, fundic and antral biopsies, and gastric juice. Based on histological, biochemical and serological assays, patients were categorized as H. pylori+ or H. pylori-. Leptin and total ghrelin levels in serum, gastric biopsies and gastric juice were determined by specific ELISAs. Results: Of the 256 subjects, 120 were H. pylori+ and 96 were H. pylori-; 40 patients of indeterminant status were excluded. Serum and fundic leptin levels correlated with Body Mass Index in the H. pylori+ (R=0.35, p<0.0001 and R=0.35, p<0.0001, respectively) and H. pylori- (R=0.65, p<0.0001 and R=0.41, p<0.0001, respectively) groups, but H. pylori+ subjects had significantly lower serum leptin levels [median 2.2 ng/ml, IQR (0.9-4.6) vs. 4.0 ng/ml, (1.7-7.2); p=0.0003]. Serum ghrelin levels were similar in the H. pylori+ and H. pylori- groups [median 1651 pg/ml, IQR (845-2247) vs. 1629 pg/ml, (992-2886); p=0.23]. H. pylori status did not significantly affect gastric biopsy leptin and ghrelin levels. Ghrelin levels in gastric juice varied over 4 log10 (<80-776,000 pg/ml) and correlated with gastric juice pH in the H. pylori+ group (R=0.68, p<0.0001). Conclusions: These findings provide evidence that H. pylori status affects leptin and ghrelin homeostasis, presumably via intragastric interactions
— id: 78624, year: 2008, vol: 93, page: 2350, stat: Journal Article,

Molecular analysis of human forearm superficial skin bacterial biota
Gao, Zhan; Tseng, Chi-hong; Pei, Zhiheng; Blaser, Martin J
2007 Feb 20;104(8):2927-2932, Proceedings of the National Academy of Sciences of the United States of America
The microbial ecology of human skin is complex, but little is known about its species composition. We examined the diversity of the skin biota from the superficial volar left and right forearms in six healthy subjects using broad-range small subunit rRNA genes (16S rDNA) PCR-based sequencing of randomly selected clones. For the initial 1,221 clones analyzed, 182 species-level operational taxonomic units (SLOTUs) belonging to eight phyla were identified, estimated as 74.0% [95% confidence interval (C.I.), approximately 64.8-77.9%] of the SLOTUs in this ecosystem; 48.0 +/- 12.2 SLOTUs were found in each subject. Three phyla (Actinobacteria, Firmicutes, and Proteobacteria) accounted for 94.6% of the clones. Most (85.3%) of the bacterial sequences corresponded to known and cultivated species, but 98 (8.0%) clones, comprising 30 phylotypes, had <97% similarity to prior database sequences. Only 6 (6.6%) of the 91 genera and 4 (2.2%) of the 182 SLOTUs, respectively, were found in all six subjects. Analysis of 817 clones obtained 8-10 months later from four subjects showed additional phyla (numbering 2), genera (numbering 28), and SLOTUs (numbering 65). Only four (3.4%) of the 119 genera (Propionibacteria, Corynebacteria, Staphylococcus, and Streptococcus) were observed in each subject tested twice, but these genera represented 54.4% of all clones. These results show that the bacterial biota in normal superficial skin is highly diverse, with few well conserved and well represented genera, but otherwise low-level interpersonal consensus
— id: 71419, year: 2007, vol: 104, page: 2927, stat: Journal Article,

Radiographic determination of tissue thickness in paraffin blocks: application to the construction of tissue microarrays
Kong, Xiangtian; Zhao, Yan; Ksionsk, Marti; Zhou, Meisheng; Walden, Paul; Bosland, Maarten; Pei, Zhiheng; Lee, Peng; Melamed, Jonathan
2007 Mar;15(1):108-112, Applied immunohistochemistry & molecular morphology
The determination of tissue thickness in paraffin blocks in the histology laboratory has been largely based on visual estimates. More accurate methods are required for the construction of tissue microarrays (TMAs) to assure a greater yield of cores in sections through the TMA block. We describe an accurate radiographic method to determine tissue thickness in donor paraffin blocks and have validated its application to TMA construction. Individual radiographic analysis was performed on paraffin donor blocks used for the construction of TMAs for determination of donor block tissue thickness. Consecutive numbered slide sections through the TMA block were then examined for the presence or loss of cores in the 150th TMA slide (from the final third of the TMA block) and correlated with the thickness of the individual donor blocks determined radiographically. At the 150th TMA slide, 202 of 1340 cores (15.1%) were depleted. Radiographic measurement showed a greater thickness of the donor paraffin block tissue (2.02 mm) corresponding to the retained cores as compared with the donor tissue (1.54 mm) of the depleted cores (P < 0.001). With progressive slide sections through a TMA block, the retention of tissue cores shows a significant correlation with donor block tissue thickness. Radiographic determination of tissue thickness in donor paraffin blocks can be used in TMA construction. Prior knowledge of tissue thickness in TMA construction can prompt compensatory steps that can enhance the yield of valuable samples and assure sufficient numbers of adequate cores for statistical analysis in biomarker evaluations
— id: 73238, year: 2007, vol: 15, page: 108, stat: Journal Article,

Fasting gastric leptin levels are elevated in diabetics independent of BMI
Young, B; Roper, H; Mourad, M; Olivares de Perez, AZ; Perez-Perez, GI; Pei, ZH; Blaser, MJ; Francois, F
2007 SEP ;102(6):S163-S163, American journal of gastroenterology
— id: 74153, year: 2007, vol: 102, page: S163, stat: Journal Article,

Myxoid lipoadenoma of parathyroid gland: a case report and literature review
Fischer, Ingeborg; Wieczorek, Rosemary; Sidhu, Gurdip S; Pei, Zhiheng; West, Brian; Lee, Peng
2006 Oct;10(5):294-296, Annals of diagnostic pathology
Myxoid lipoadenoma of the parathyroid gland is a rare variant of parathyroid adenoma. We present the case of a 40-year-old man with asymptomatic hypercalcemia who underwent surgical removal of a parathyroid adenoma. Histologically, the tumor consisted of monomorphous round-to-oval chief cells arranged in several architectural patterns including solid sheet-like, trabecular, and follicular. The tumor stroma was prominently myxoid with interspersed mature adipose tissue. Immunohistochemistry confirmed expression of thyroid transcription factor and parathyroid hormone by all tumor cells and a low proliferation rate with a Ki-67 labeling index of at most 5%. Although the lesion exhibited characteristics that have been previously associated with 'atypical parathyroid adenoma,' such as dense fibrous bands within the tumor and a trabecular growth pattern, there was no further evidence, neither histologically nor clinically, for malignant behavior of the tumor
— id: 68682, year: 2006, vol: 10, page: 294, stat: Journal Article,

Bacterium-macrophage interaction in gastroesophageal reflux disease
Lu, X; Yang, L; Pei, Z
2006 JAN ;19(4):113A-113A, Modern pathology
— id: 61436, year: 2006, vol: 19, page: 113A, stat: Journal Article,

Bacterium-macrophage interaction in gastroesophageal reflux disease
Lu, X; Yang, L; Pei, Z
2006 JAN ;86(4):113A-113A, Laboratory investigation
— id: 62617, year: 2006, vol: 86, page: 113A, stat: Journal Article,

Bacteria, inflammation, and colon cancer
Yang, Liying; Pei, Zhiheng
2006 Nov 14;12(42):6741-6746, World journal of gastroenterology : WJG
Our relationship with the colonic bacterial flora has long been viewed as benign, but recent studies suggest that this symbiosis has risks as well as benefits. This relationship requires that the host not only provide a supportive environment for the symbiotic bacteria, but also actively maintain intact mechanisms for properly managing the physiologic stresses that are closely associated with the symbiont's essential survival functions. Failure to do so breaches the host-symbiont contract, and can result in serious effects on the health of the host. Recent investigations that employ several knockout mouse models reveal the consequences of genetic deficiency in the host regarding these mechanisms, and the latent, pro-inflammatory, tumorigenic nature of normal bacterial flora. Further study of the interactions between normal bacterial flora and hosts could shed light on the etiologies and pathogenesis of inflammatory diseases and related cancers, with implications for human health
— id: 79201, year: 2006, vol: 12, page: 6741, stat: Journal Article,

Recent advances in the rapid detection of Bacillus anthracis
Levine, SA; Tang, YW; Pei, ZH
2005 OCT ;16(4):125-133, Reviews in medical microbiology
Bacillus anthracis is a Gram-positive, spore-forming rod that causes anthrax. Culture-based methods are the gold standard for the identification of virulent B. anthracis strains but these require days for completion. The experience from the anthrax attacks in September and October of 2001 revealed the urgent need for methods that can rapidly detect this pathogen with high reliability. Because of the extensive homology among non-anthrax Bacillus sp. at the chromosomal level, rapid detection of virulent B. anthracis strains depends oil markers associated with the two plasmids, pXO1 and pXO2, responsible for its virulence. Genes encoding toxins and capsules have been used as markers for pXO1 and pXO2, respectively, in methods that are designed for rapid and sensitive detection of B. anthracis DNA, Such as real-time polymerase chain reaction, direct liquid phase hybridization, and DNA microarrays. A variety of platforms can be modified to suit the needs for rapid detection of B. anthracis antigens, but little is known about plasmid-encoded antigens expressed in spores. Future studies should be aimed at detecting markers for pXO1 and pXO2in viable spores. (c) 2005 Lippincott Williams & Wilkins
— id: 62536, year: 2005, vol: 16, page: 125, stat: Journal Article,

Bacterial biota in reflux esophagitis and Barrettos esophagus
Pei, Zhiheng; Yang, Liying; Peek, Richard M; Jr Levine, Steven M; Pride, David T; Blaser, Martin J
2005 Dec 14;11(46):7277-7283, World journal of gastroenterology : WJG
AIM: To identify the bacterial flora in conditions such as Barrettos esophagus and reflux esophagitis to determine if they are similar to normal esophageal flora. METHODS: Using broad-range 16S rDNA PCR, esophageal biopsies were examined from 24 patients [9 with normal esophageal mucosa, 12 with gastroesophageal reflux disease (GERD), and 3 with Barrettos esophagus]. Two separate broad-range PCR reactions were performed for each patient, and the resulting products were cloned. In one patient with Barrettos esophagus, 99 PCR clones were analyzed. RESULTS: Two separate clones were recovered from each patient (total = 48), representing 24 different species, with 14 species homologous to known bacteria, 5 homologous to unidentified bacteria, and 5 were not homologous (<97% identity) to any known bacterial 16S rDNA sequences. Seventeen species were found in the reflux esophagitis patients, 5 in the Barrettos esophagus patients, and 10 in normal esophagus patients. Further analysis concentrating on a single biopsy from an individual with Barrettos esophagus revealed the presence of 21 distinct bacterial species. Members of four phyla were represented, including Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria. Microscopic examination of each biopsy demonstrated bacteria in intimate association with the distal esophageal epithelium, suggesting that the presence of these bacteria is not transitory. CONCLUSION: These findings provide evidence for a complex, residential bacterial population in esophageal reflux-related disorders. While much of this biota is present in the normal esophagus, more detailed comparisons may help identify potential disease associations
— id: 61597, year: 2005, vol: 11, page: 7277, stat: Journal Article,

False positives and false negatives encountered in diagnostic molecular microbiology
Sefers, S; Pei, ZH; Tang, YW
2005 APR ;16(2):59-67, Reviews in medical microbiology
Nucleic acid-based tests are rapidly expanding in the field of diagnostic microbiology, due to their unique high sensitivity and specificity as well as rapid assay turnaround time. However, the potential of false positives and false negatives can hinder the wide application of these novel techniques. This mini-review article summarizes common causes and potential solutions for false-positives and false-negatives encountered in the field of diagnostic molecular microbiology
— id: 62535, year: 2005, vol: 16, page: 59, stat: Journal Article,

Bacterial biota in the human distal esophagus
Pei, Zhiheng; Bini, Edmund J; Yang, Liying; Zhou, Meisheng; Francois, Fritz; Blaser, Martin J
2004 Mar 23;101(12):4250-4255, Proceedings of the National Academy of Sciences of the United States of America
The esophagus, like other luminal organs of the digestive system, provides a potential environment for bacterial colonization, but little is known about the presence of a bacterial biota or its nature. By using broad-range 16S rDNA PCR, biopsies were examined from the normal esophagus of four human adults. The 900 PCR products cloned represented 833 unique sequences belonging to 41 genera, or 95 species-level operational taxonomic units (SLOTU); 59 SLOTU were homologous with culture-defined bacterial species, 34 with 16S rDNA clones, and two were not homologous with any known bacterial 16S rDNA. Members of six phyla, Firmicutes, Bacteroides, Actinobacteria, Proteobacteria, Fusobacteria, and TM7, were represented. A large majority of clones belong to 13 of the 41 genera (783/900, 87%), or 14 SLOTU (574/900, 64%) that were shared by all four persons. Streptococcus (39%), Prevotella (17%), and Veilonella (14%) were most prevalent. The present study identified approximately 56-79% of SLOTU in this bacterial ecosystem. Most SLOTU of esophageal biota are similar or identical to residents of the upstream oral biota, but the major distinction is that a large majority (82%) of the esophageal bacteria are known and cultivable. These findings provide evidence for a complex but conserved bacterial population in the normal distal esophagus
— id: 42671, year: 2004, vol: 101, page: 4250, stat: Journal Article,

Pneumocystis carinii: an update
Sidhu, Gurdip S; Cassai, Nicholas D; Pei, Zhiheng
2003 Mar-Apr;27(2):115-122, Ultrastructural pathology
Pneumocystis produces respiratory infection in immunocompromised individuals of several species of mammals, including humans. Each mammalian species has its own specific Pneumocystis species, which does not cross-infect other mammals. The species infecting humans has now been renamed P. jerovici, since P. carinii is reserved for one of two species infecting rats. Long believed to be a protozoan, Pneumocystis is now classified as an Archiascomycetous fungus. This is based on new molecular taxonomic techniques using DNA sequence analysis of srRNA genes. Only two of about 140 copies of the gene that exist in Pneumocystis were used for sequencing, so the evidence is not conclusive; however, it is supported by morphological evidence such as fungus-specific nucleus-associated organelles for cell division. There is also ultrastructural evidence of meiotic division and sexual conjugation. Clinically, several lines of evidence suggest the improbability of latent infection. Adult infections appear to be new infections, a fact that invites a new perspective on prevention
— id: 39226, year: 2003, vol: 27, page: 115, stat: Journal Article,

Molecular analysis of sarcoidosis tissues for mycobacterium species DNA
Drake, Wonder Puryear; Pei, Zhiheng; Pride, David T; Collins, Robert D; Cover, Timothy L; Blaser, Martin J
2002 Nov;8(11):1334-1341, Emerging infectious diseases
We performed polymerase chain reaction analysis, for Mycobacterium species 16S rRNA, rpoB, and IS6110 sequences, on 25 tissue specimens from patients with sarcoidosis and on 25 control tissue specimens consisting of mediastinal or cervical lymph nodes and lung biopsies. Mycobacterium species 16S rRNA sequences were amplified from 12 (48%) rpoB sequences and from 6 (24%) of the sarcoidosis specimens. In total, 16S rRNA or rpoB sequences were amplified from 15 sarcoidosis specimens (60%) but were not detected in any of the control tissues (p=0.00002, chi square). In three specimens, the sequences resembled Mycobacterium species other than M. tuberculosis. All specimens with sequences consistent with M. tuberculosis were negative for IS6110. We provide evidence that one of a variety of Mycobacterium species, especially organisms resembling M. tuberculosis, is found in most patients with sarcoidosis
— id: 34575, year: 2002, vol: 8, page: 1334, stat: Journal Article,

Ultrastructural features and TUNEL analysis of glomeruloid adenocarcinoma of the prostate
Yang, GY; Sidhu, GS; Yee, H; Pei, Z; Cassai, N; Wieczorek, R
2001 OCT ;116(4):609-609, American journal of clinical pathology
— id: 54862, year: 2001, vol: 116, page: 609, stat: Journal Article,

Mutation in the peb1A locus of Campylobacter jejuni reduces interactions with epithelial cells and intestinal colonization of mice
Pei Z; Burucoa C; Grignon B; Baqar S; Huang XZ; Kopecko DJ; Bourgeois AL; Fauchere JL; Blaser MJ
1998 Mar;66(3):938-943, Infection & immunity
Campylobacter jejuni is one of the leading causes of bacterial diarrhea throughout the world. We previously found that PEB1 is a homolog of cluster 3 binding proteins of bacterial ABC transporters and that a C. jejuni adhesin, cell-binding factor 1 (CBF1), if not identical to, contains PEB1. A single protein migrating at approximately 27 to 28 kDa was recognized by anti-CBF1 and anti-PEB1. To determine the role that the operon encoding PEB1 plays in C. jejuni adherence, peb1A, the gene encoding PEB1, was disrupted in strain 81-176 by insertion of a kanamycin resistance gene through homologous recombination. Inactivation of this operon completely abolished expression of CBF1, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblotting. In comparison to the wild-type strain, the mutant strain showed 50- to 100-fold less adherence to and 15-fold less invasion of epithelial cells in culture. Mouse challenge studies showed that the rate and duration of intestinal colonization by the mutant were significantly lower and shorter than with the wild-type strain. In summary, PEB1 is identical to a previously identified cell-binding factor, CBF1, in C. jejuni, and the peb1A locus plays an important role in epithelial cell interactions and in intestinal colonization in a mouse model
— id: 19104, year: 1998, vol: 66, page: 938, stat: Journal Article,

Nucleotide sequence and characterization of peb4A encoding an antigenic protein in Campylobacter jejuni
Burucoa C; Fremaux C; Pei Z; Tummuru M; Blaser MJ; Cenatiempo Y; Fauchere JL
1995 Jul-Aug;146(6):467-476, Research in microbiology
The 29-kDa protein PEB4, a major antigen of Campylobacter jejuni, is present in all C. jejuni strains tested and elicits an antibody response in infected patients. By screening a lambda gt11 library of chromosomal DNA fragments of C. jejuni strain 81-176 in Escherichia coli Y1090 cells with antibody raised against purified PEB4, a recombinant phage with a 2-kb insert expressing an immunoreactive protein of 29 kDa was isolated. DNA sequence analysis revealed that the insert contains two complete open reading frames ORF-A and ORF-B. ORF-A (peb4A) encodes a 273-residue protein with a calculated molecular mass of 30,460 daltons. The deduced amino acid sequence, composition and pl of the recombinant mature protein are similar to those determined for purified PEB4. The first 21 residues resemble a signal peptide. Gene bank searches indicated 33.7% identity with protein export protein PrsA of Bacillus subtilis and 23.8% identity with protease maturation protein precursor PrtM of Lactococcus lactis. PCR experiments indicate that peb4A is highly conserved among C. jejuni strains. ORF-B begins 2 bp after the last codon of peb4A and encodes a putative protein of 353 residues with 63.4% identity with E. coli fructose 1,6-biphosphate aldolase. The sequence arrangement suggests that these two genes form an operon
— id: 19164, year: 1995, vol: 146, page: 467, stat: Journal Article,

Pathogenesis of Campylobacter fetus infections: critical role of high-molecular-weight S-layer proteins in virulence
Blaser MJ; Pei Z
1993 Feb;167(2):372-377, Journal of infectious diseases
Wild-type Campylobacter fetus strains possess high-molecular-weight S-layer proteins (S+) and are highly resistant to serum-mediated killing and phagocytosis. Spontaneous mutant strains lacking these proteins (S-) are serum and phagocytosis sensitive and have reduced virulence in a mouse model. Intact S+ cells were treated with pronase, which made them S- although genotypically S+ and had essentially no effect on other cellular proteins or on viability. Treatment with pronase, but not buffer alone, rendered these cells serum and phagocytosis sensitive and reduced mouse virulence to the level observed for the S- mutant cells. In related studies, purified S-layer proteins diminished neutrophil chemoluminescent responses to a heterologous particulate antigen. Finally, passive administration of antiserum to the 97-kDa S-layer protein partially protected mice against lethal challenge with the S+ strain. These studies define the contribution of the S-layer proteins to C. fetus virulence
— id: 19218, year: 1993, vol: 167, page: 372, stat: Journal Article,

Isolation and characterization of two Campylobacter glycine-extracted proteins that bind to HeLa cell membranes
Kervella M; Pages JM; Pei Z; Grollier G; Blaser MJ; Fauchere JL
1993 Aug;61(8):3440-3448, Infection & immunity
Two immunogenic proteins of 27 (CBF1) and 29 (CBF2) kDa from enteropathogenic Campylobacter species appear to bind to mammalian cells. We purified these two proteins from a pathogenic and adherent Campylobacter jejuni strain to homogeneity by using acid extraction, preparative gel electrophoresis, and electroelution. Polyclonal rabbit antisera to these proteins were prepared. Immunologic studies indicate that CBF1 corresponds to the PEB1 and CBF2 corresponds to the PEB4 described by Pei et al. (Z. Pei, R. T. Ellison, and M. Blaser, J. Biol. Chem. 226:16363-16369, 1991). Immunogold labeling of a C. jejuni adherent strain with anti-CBF1, anti-CBF2, and anti-PEB1 suggested that CBF1 (PEB1) is surface exposed while CBF2 (PEB4) is not. Analysis of whole-cell extracts from 14 strains by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis with 7 M urea and immunoblotting with antisera to CBF1 and CBF2 suggests that CBF proteins from adherent and nonadherent strains are different. Use of purified proteins in a microassay of adherence to cellular membranes indicated that CBF1 was much more adherent than CBF2. Adherence of C. jejuni to viable HeLa cells was markedly reduced with the antiserum to CBF1, whereas the CBF2 antiserum was a poor inhibitor. Purified CBF1 competitively inhibited adherence of whole bacteria to HeLa cells, whereas purified CBF2 was no better a competitor than bovine serum albumin. Adherence of CBF2 was markedly reduced in the presence of Tween 20 or SDS, whereas adherence of CBF1 was reduced only by SDS. We conclude that (i) CBF1 (PEB1) is surface exposed and may be the key protein for C. jejuni adhesion and (ii) CBF2 (PEB4) may be complexed with CBF1 and may passively coadhere with CBF1 under certain experimental conditions. Adherent and nonadherent strains contain different isotypes of these two proteins which could be useful markers of C. jejuni adhesion
— id: 19212, year: 1993, vol: 61, page: 3440, stat: Journal Article,

Isolation and Characterization of Two Campylobacter Glycine-Extracted Proteins That Bind to HeLa Cell Membranes
Kervella, Michele; Pages, Jean-Marie; Pei, Zhiheng; Grollier, Chislaine; Blaser, Martin J
[S.l.] : Ft. Belvoir Defense Technical Information Center, 1993,
wo immunogenic proteins of 27 (CBF1) and 29 (CBF2) kDa from enteropathogenic Campylobacter species appear to bind to mammalian cells. We purified these two proteins from a pathogenic and adherent Campylobacter jejuni strain to homogeneity using acid extraction, preparative gel electrophoresis and electroelution. Polyclonal rabbit antisera to these proteins were prepared. Immunologic studies indicate that CBF1 corresponds to the PEB1 and CBF2 corresponds to the PEB4 described by Pei et al
— id: 2035, year: 1993, vol: , page: , stat: ,

PEB1, the major cell-binding factor of Campylobacter jejuni, is a homolog of the binding component in gram-negative nutrient transport systems
Pei Z; Blaser MJ
1993 Sep 5;268(25):18717-18725, Journal of biological chemistry
The protein PEB1 (28 kDa) is a common antigen and a major cell adherence molecule of Campylobacter jejuni and Campylobacter coli. We created a bank of chromosomal DNA fragments of C. jejuni strain 81-176 using lambda gt11. Screening this bank in Escherichia coli Y1090 cells with antibody raised against purified PEB1 enabled us to isolate and to purify a clone with a 2.6-kilobase insert expressing an immunoreactive protein of 28 kDa. DNA sequencing revealed that the insert contains three complete and two partial open reading frames (ORFs), designated 5' to 3' as ORFs A-E. The peb1A gene (ORF D) contains 780 bases encoding a 259-residue polypeptide having a calculated molecular mass of 28,181 Da. The peptide sequence starting at residue 27 matches that determined from aminoterminal sequencing of mature PEB1 from C. jejuni. The first 26 residues contain typical signal peptidase I and II cleavage sites. The deduced amino acid composition and pI of the recombinant mature protein are similar to those determined for purified PEB1. Gene bank searches indicated significant overall homology of peb1A and ORF C with operons for amino acid transport systems in other Gram-negative organisms. peb1A is homologous to the binding components of systems such as glnH (27.8%) and hisJ (28.9%), whereas ORF C has nearly 50% identity to glnQ and hisP. Thus, PEB1 could be involved both in binding to intestinal cells and in amino acid transport
— id: 19206, year: 1993, vol: 268, page: 18717, stat: Journal Article,

Shift in S-layer protein expression responsible for antigenic variation in Campylobacter fetus
Wang E; Garcia MM; Blake MS; Pei Z; Blaser MJ
1993 Aug;175(16):4979-4984, Journal of bacteriology
Campylobacter fetus strains possess regular paracrystalline surface layers (S-layers) composed of high-molecular-weight proteins and can change the size and crystalline structure of the predominant protein expressed. Polyclonal antisera demonstrate antigenic cross-reactivity among these proteins but suggest differences in epitopes. Monoclonal antibodies to the 97-kDa S-layer protein of Campylobacter fetus subsp. fetus strain 82-40LP showed three different reactivities. Monoclonal antibody 1D1 recognized 97-kDa S-layer proteins from all C. fetus strains studied; reactivity of monoclonal antibody 6E4 was similar except for epitopes in S-layer proteins from reptile strains and strains with type B lipopolysaccharide. Monoclonal antibody 2E11 only recognized epitopes on S-layer proteins from strains with type A lipopolysaccharide regardless of size. In vitro shift from a 97-kDa S-layer protein to a 127-kDa S-layer protein resulted in different reactivity, indicating that size change was accompanied by antigenic variation. To examine in vivo variation, heifers were genetically challenged with Campylobacter fetus subsp. venerealis strains and the S-layer proteins from sequential isolates were characterized. Analysis with monoclonal antibodies showed that antigenic reactivities of the S-layer proteins were varied, indicating that these proteins represent a system for antigenic variation
— id: 19213, year: 1993, vol: 175, page: 4979, stat: Journal Article,

Reattachment of surface array proteins to Campylobacter fetus cells
Yang LY; Pei ZH; Fujimoto S; Blaser MJ
1992 Feb;174(4):1258-1267, Journal of bacteriology
Campylobacter fetus strains may be of serotype A or B, a property associated with lipopolysaccharide (LPS) structure. Wild-type C. fetus strains contain surface array proteins (S-layer proteins) that may be extracted in water and that are critical for virulence. To explore the relationship of S-layer proteins to other surface components, we reattached S-layer proteins onto S- template cells generated by spontaneous mutation or by serial extractions of S+ cells with water. Reattachment occurred in the presence of divalent (Ba2+, Ca2+, Co2+, and Mg2+) but not monovalent (H+, NH4+, Na+, K+) or trivalent (Fe3+) cations. The 98-, 125-, 127-, and 149-kDa S-layer proteins isolated from strains containing type A LPS (type A S-layer protein) all reattached to S- template cells containing type A LPS (type A cells) but not to type B cells. The 98-kDa type B S-layer protein reattached to SAP- type B cells but not to type A cells. Recombinant 98-kDa type A S-layer protein and its truncated amino-terminal 65- and 50-kDa segments expressed in Escherichia coli retained the full and specific determinants for attachment. S-layer protein and purified homologous but not heterologous LPS in the presence of calcium produced insoluble complexes. By quantitative enzyme-linked immunosorbent assay, the S-layer protein copy number per C. fetus cell was determined to be approximately 10(5). In conclusion, C. fetus cells are encapsulated by a large number of S-layer protein molecules which may be specifically attached through the N-terminal half of the molecule to LPS in the presence of divalent cations
— id: 19229, year: 1992, vol: 174, page: 1258, stat: Journal Article,

Identification, purification, and characterization of major antigenic proteins of Campylobacter jejuni
Pei ZH; Ellison RT; Blaser MJ
1991 Sep 5;266(25):16363-16369, Journal of biological chemistry
Evidence from developing countries and volunteer studies indicates that immunity to Campylobacter jejuni and Campylobacter coli may be acquired, but the antigenic basis for this protection is poorly defined. We have purified to homogeneity four proteins with molecular weights of 28,000 (PEB1), 29,000 (PEB2), 30,000 (PEB3), and 31,000 (PEB4) from epidemic C. jejuni strain 81-176 using acid extraction and sequential ion-exchange, hydrophobic interaction, and gel filtration chromatography. The relative amino acid compositions of these four proteins are similar. NH2-terminal sequence analysis indicates that all four proteins are different, although the first 35 amino acids of PEB2 and PEB3 are 51.4% homologous. Isoelectric focusing showed that all four are basic proteins with pI of 8.5 for PEB1 protein and greater than 9.3 for the others. Use of the purified proteins as antigens in an IgG enzyme-linked immunosorbent assay (ELISA) found that seroconversion to the PEB1 or PEB3 proteins occurred in 15 of 19 patients with sporadic C. jejuni or C. coli infection. In comparison, only two, six, and 14 of these patients seroconverted to PEB2, PEB4, or the acid extract antigen. In an ELISA with whole bacterial cells as antigens, antiserum to the acid-extracted antigens showed broad recognition of C. jejuni, C. coli, C. fetus, C. lari, and Helicobacter pylori. Antiserum to PEB1 recognized all 35 C. jejuni and all 15 C. coli strains but none of the isolates of the other three bacterial species. The PEB1 and PEB3 proteins appear to be candidate antigens for both a Campylobacter vaccine and for serological assays for the pathogen
— id: 19239, year: 1991, vol: 266, page: 16363, stat: Journal Article,

Identification, Purification and Characterization of Major Antigenic Proteins of Campylobacter jejuni
Pei, Zhiheng; Ellison, Richard T III; Blaser, Martin J
[S.l.] : Ft. Belvoir Defense Technical Information Center, 1991,
Evidence from developing countries and volunteer studies indicates that immunity to Campylobacter jejuni and Campylobacter coli maybe acquired, but the antigenic basis for this protection is poorly defined. We have purified to homogeneity four proteins with molecular weights of 28,000 (PEB1), 29,000 (PEB2) , 30,000 (PEB3), and 31,000 (PEB4) from epidemic C. jejuni strain 81-176 using acid extraction and sequential ion-exchange, hydrophobic interaction, and gel filtration chromatography. The relative amino acid compositions of these four proteins are similar NH2-terminal sequence analysis indicates that all four proteins are different, although the first 35 amino acids of PEB2 and PEB3 are 51.4% homologous
— id: 2034, year: 1991, vol: , page: , stat: ,

Pathogenesis of Campylobacter fetus infections. Role of surface array proteins in virulence in a mouse model
Pei Z; Blaser MJ
1990 Apr;85(4):1036-1043, Journal of clinical investigation
We developed a mouse model to compare the virulence of Campylobacter fetus strains with (S-plus) and without (S-minus) surface array protein (S-protein) capsules. In adult HA/ICR mice pretreated with ferric chloride, the LD50 for S-plus strain 84-32 was 43.3 times lower than its spontaneous S-minus mutant 84-54. Seven strains of inbred mice were no more susceptible than the outbred strain. In contrast to the findings with Salmonella typhimurium by others, 3 X 10(7) CFU of strain 84-32 caused 90% mortality in C3H/HeN (LPSn) mice and 40% mortality in C3H/HeJ (LPSd) mice. High-grade bacteremia in HA/ICR mice occurred after oral challenge with S-plus C. fetus strains and continued for at least 2 d, but was not present in any mice challenged with S-minus strains. Bacteremia at 30 min after challenge was 51.6-fold lower in mice pretreated with 10 microliters of rabbit antiserum to purified S-protein than after pretreatment with normal rabbit serum. Challenge of mice with a mixture of S-minus strain 84-54 and free S-proteins at a concentration 31.1-fold higher than found in wild-type strain 84-32 caused 30% mortality, compared with 0% with strain 84-54 or S-protein alone. These findings in a mouse model point toward the central role of the S-protein in the pathogenesis of C. fetus infection. The S-protein is not toxic per se, but enhances virulence when present on the bacterial cell surface as a capsule
— id: 19264, year: 1990, vol: 85, page: 1036, stat: Journal Article,

Purification and characterization of a family of high molecular weight surface-array proteins from Campylobacter fetus
Pei Z; Ellison RT; Lewis RV; Blaser MJ
1988 May 5;263(13):6416-6420, Journal of biological chemistry
A variety of Gram-negative and Gram-positive bacteria possess crystalline surface layers, although little is known of their function. We previously have shown that the high molecular weight surface-array proteins of Campylobacter fetus are important in both the pathogenicity and antigenicity of this organism. For biochemical and immunological characterization, we purified high molecular weight (100,000, 127,000, 149,000) surface-array proteins from three C. fetus strains using sequential gel filtration and ion exchange high performance liquid chromatography. These proteins are acidic with pI values between 4.12 and 4.25 and contain large proportions of acidic amino acids (19.7%-22.0%) in addition to hydrophobic amino acids (37.3%-38.5%). They share a novel amino-terminal sequence through at least 19 residues. Carbohydrate analysis using periodic acid-Schiff staining and treatment with trifluoromethanesulfonic acid shows no evidence of glycosylation. Antiserum to a purified Mr = 100,000 protein from C. fetus 82-40 LP cross-reacts with three other purified C. fetus surface-array proteins by enzyme-linked immunosorbent assay with titers greater than 12,800. We conclude that: 1) there is a family of surface-array proteins of C. fetus with common structural and antigenic characteristics; 2) that these molecules have similar biochemical characteristics to surface-array proteins described for other bacteria; but however, 3) by amino-terminal sequence analysis these are unique
— id: 19285, year: 1988, vol: 263, page: 6416, stat: Journal Article,

Purification and Characterization of a Family of High Molecular Weight Surface-Array Proteins from Campylobacter Fetus
Pei Z; Ellison, Richart T II; Lewis, Randolph V; Blaser, Martin J
[S.l.] : Ft. Belvoir Defense Technical Information Center, 1988,
A variety of Gram-negative and Gram-positive bacteria possess crystalline surface layers, although little is known of their function. We previously have shown that the high molecular weight surface-array proteins of Campylobacter fetus are important in both the pathogenicity and antigenicity of this organism. For biochemical and immunological characterization, we purified high molecular weight(100,000, 127,000, 149,000) surface-array proteins from three C. fetus strains using sequential gel filtration and ion exchange high performanc liquid chromatography. These proteins are acidic with pl values between 4.12 and 4.25 and contain large proportions of acidic amino acids (19. 7%-22.0%) in addition to hydrophobic amino acids (37.3%-38.5%). They share a novel amino-terminal sequence through at least 19 residues
— id: 2036, year: 1988, vol: , page: , stat: ,