Molecular detection of Chlamydophila abortus, Coxiella burnetii, and Mycoplasma agalactiae in small ruminants' aborted fetuses in southern Iran.

Abortion in sheep and goats has become increasingly important worldwide because of the significant economic losses and potential zoonotic implication of commonly involved pathogens. Therefore, this cross-sectional study was conducted in southern Iran to detect the Chlamydophila abortus and Coxiella burnetii, as zoonotic pathogens, and Mycoplasma agalactiae, as a neglected abortifacient agent in small ruminants' aborted fetuses, by using polymerase chain reaction (PCR). From a total of 300 aborted fetuses (183 sheep and 117 goats), 46 samples (15.5%) were positive by PCR, 11% for C. abortus, 2% for C. burnetii, and 3% for M. agalactiae. Also, the association of suggested risk factors with abortion due to these bacterial agents was investigated using univariable and multivariable logistic regression. Results of the statistical analysis showed significant association of C. abortus with flock size (OR = 2.82, P = 0.014), season (P < 0.05), and the number of pregnancy in the aborted dam (OR = 2.5, P = 0.05). Our results indicated that C. abortus has a relatively substantial role in small ruminant abortions, and C. burnetii and M. agalactiae are likely important abortifacient agents in our region, too. Regarding veterinary and/or public health importance of these bacterial agents, more attention from veterinary and/or human health services and, maybe, a surveillance system for control and prevention of them are recommended.

High-grade B-cell lymphoma, not otherwise specified: a multi-institutional retrospective study.

In this multi-institutional retrospective study, we examined the characteristics and outcomes of 160 patients with high-grade B-cell lymphoma, not otherwise specified (HGBL-NOS)-a rare category defined by high-grade morphologic features and lack of MYC rearrangements with BCL2 and/or BCL6 rearrangements ("double hit"). Our results show that HGBL-NOS tumors are heterogeneous: 83% of patients had a germinal center B-cell immunophenotype, 37% a dual-expressor immunophenotype (MYC and BCL2 expression), 28% MYC rearrangement, 13% BCL2 rearrangement, and 11% BCL6 rearrangement. Most patients presented with stage IV disease, a high serum lactate dehydrogenase, and other high-risk clinical factors. Most frequent first-line regimens included dose-adjusted cyclophosphamide, doxorubicin, vincristine, and etoposide, with rituximab and prednisone (DA-EPOCH-R; 43%); rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP; 33%); or other intensive chemotherapy programs. We found no significant differences in the rates of complete response (CR), progression-free survival (PFS), or overall survival (OS) between these chemotherapy regimens. CR was attained by 69% of patients. PFS at 2 years was 55.2% and OS was 68.1%. In a multivariable model, the main prognostic factors for PFS and OS were poor performance status, lactate dehydrogenase >3 × upper limit of normal, and a dual-expressor immunophenotype. Age >60 years or presence of MYC rearrangement were not prognostic, but patients with TP53 alterations had a dismal PFS. Presence of MYC rearrangement was not predictive of better PFS in patients treated with DA-EPOCH-R vs R-CHOP. Improvements in the diagnostic criteria and therapeutic approaches beyond dose-intense chemotherapy are needed to overcome the unfavorable prognosis of patients with HGBL-NOS.

The DNA sequence, annotation and analysis of human chromosome 3.

After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion.

The finished DNA sequence of human chromosome 12.

Human chromosome 12 contains more than 1,400 coding genes and 487 loci that have been directly implicated in human disease. The q arm of chromosome 12 contains one of the largest blocks of linkage disequilibrium found in the human genome. Here we present the finished sequence of human chromosome 12, which has been finished to high quality and spans approximately 132 megabases, representing approximately 4.5% of the human genome. Alignment of the human chromosome 12 sequence across vertebrates reveals the origin of individual segments in chicken, and a unique history of rearrangement through rodent and primate lineages. The rate of base substitutions in recent evolutionary history shows an overall slowing in hominids compared with primates and rodents.

The DNA sequence of the human X chromosome.

The human X chromosome has a unique biology that was shaped by its evolution as the sex chromosome shared by males and females. We have determined 99.3% of the euchromatic sequence of the X chromosome. Our analysis illustrates the autosomal origin of the mammalian sex chromosomes, the stepwise process that led to the progressive loss of recombination between X and Y, and the extent of subsequent degradation of the Y chromosome. LINE1 repeat elements cover one-third of the X chromosome, with a distribution that is consistent with their proposed role as way stations in the process of X-chromosome inactivation. We found 1,098 genes in the sequence, of which 99 encode proteins expressed in testis and in various tumour types. A disproportionately high number of mendelian diseases are documented for the X chromosome. Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence.

DRAQ5-based, no-lyse, no-wash bone marrow aspirate evaluation by flow cytometry.

Flow cytometry (FC) is a powerful tool for objective phenotyping of hematolymphoid neoplasia. Analysis of bone marrow aspirates and peripheral blood specimens by FC typically requires an erythrocyte lysis or gradient separation method to remove erythrocytes prior to analysis, which may result in the loss of certain populations, in particular nucleated erythroid cells. We developed a method to analyze bone marrow aspirates (BMAs) by FC without erythrocyte lysis or washing to minimize cell loss by exploiting the nuclear DRAQ5 fluorescence as a gating parameter (DRAQ5 protocol). We analyzed a total of 31 BMAs from patients with a variety of diagnoses utilizing the DRAQ5 protocol in combination with CD71 and CD45 antibodies to determine the marrow differentials. These were compared with differential counts obtained by morphologic study and erythrocyte lysis FC. The DRAQ5 protocol preserved the nucleated erythrocytes, allowing calculations of the myeloid to erythroid ratio and of blasts/abnormal cells that better reflect the morphologic nucleated cell differential than erythrocyte lysis FC.

Acute bilineal leukemia: a rare disease with poor outcome.

Most cases of acute leukemia can be assigned to the myeloid, B or T lineage. In a few cases, definitive assignment cannot be achieved because blasts express antigens of more than one lineage. A subset of these, referred to as acute bilineal leukemias (aBLLs), is characterized by the presence of more than one population of blasts, each comprising a single lineage. We identified 19 cases of aBLL, including 10 mixed T and myeloid (T-My) and nine mixed B and myeloid (B-My); no mixed B and T cases were identified. Cytogenetic data were available for 16 patients. Three of seven patients with B-My had a t(9;22)(q34q11.2), two had 11q23 translocations and one had del(9). Two of nine patients with T-My had 2p13 translocations; five had other unrelated abnormalities. Of 16 patients with outcome data, only six achieved complete remission and only two remain free of disease 2.5 and 4.5 years after chemotherapy or stem cell transplantation. aBLL is a rare disease that combines B or T and myeloid blasts. Cytogenetic abnormalities of t(9;22) and 11q23 are common in, and may be restricted to, B-My cases, while T-My cases have frequent but generally non-recurring abnormalities. Both types of aBLL are associated with poor outcome.

Antibody response of chickens to serotype 1, 2, or 3 Marek's disease vaccines based on ELISA with infected cells as antigen.

An enzyme-linked immunosorbent assay (ELISA) was applied to evaluate the antibody response of commercial White Leghorn chickens to vaccination against Marek's disease (MD) at hatch (day 0) with serotype-1 (Rispens), -2 (SB-1), or -3 (turkey herpesvirus, HVT) vaccine virus and to challenge on day 21 with MD virus. Antigens for the test were whole chicken embryo fibroblast cells infected with Rispens, SB-1, or HVT. The chickens were progeny of stock that had been vaccinated with HVT, and on day 21 the nonvaccinated group had higher levels of maternal antibodies to HVT than to other antigens (P < 0.05). Only SB-1 vaccine had induced antibodies by day 21, and this was detected only against homologous antigens. On day 49, all three vaccines had induced higher levels of antibodies to homologous than to heterologous antigens. Marek's Disease virus (MDV) induced antibodies to all three antigens, but challenging vaccinated chicks did not significantly increase levels of antibodies on day 81 to any of the three antigens. It was concluded that an ELISA using whole cells as antigens would have potential value for monitoring the antibody response induced by MD vaccines and virulent MDV.

Detection of human papillomavirus in cervical lymph nodes: a highly effective strategy for localizing site of tumor origin.

PURPOSE: Patients with head and neck squamous cell carcinoma (HNSCC) often come to clinical attention with a neck mass due to metastatic spread to lymph nodes. Treatment is dictated by the subsequent determination of primary tumor site and stage. However, the primary site remains elusive in some patients even after an exhaustive examination. Human papillomavirus type 16 (HPV-16) is an important etiologic agent for HNSCCs that arise within the oropharynx but less so for tumors from nonoropharyngeal sites. Detection of HPV-16 or a surrogate marker may be useful in localizing tumor origin in patients who present with metastatic HNSCC. EXPERIMENTAL DESIGN: We performed in situ hybridization (ISH) for HPV-16 on lymph node metastases from 68 patients with HNSCC. P16 immunohistochemistry was also performed because HPV-16 integration disrupts the retinoblastoma pathway and induces an overexpression of p16. RESULTS: HPV-16 was detected in 22 of the 68 (32%) cases by ISH. When stratified by site of origin, HPV-16 was detected in 22 of 31 (71%) metastases from the oropharynx, but in none of the 37 (0%) metastases from other sites (P < 0.001; Fisher's exact). P16 expression was associated with the presence of HPV-16 by ISH: 21 of 22 HPV-16 positive tumors exhibited p16 expression, whereas only 4 of the 46 HPV-16-negative tumors were p16 positive (95% versus 9%; P < 0.001; Fisher's exact). P16 expression in the node metastases also correlated with site of tumor origin: 24 of 31 oropharyngeal tumors were p16 positive, whereas only 1 of 37 nonoropharyngeal tumors was p16 positive (77% versus 3%; P < 0.001; Fisher's exact). CONCLUSIONS: For patients with metastatic HNSCC, detection of HPV-16 is a reliable way to establish origin from the oropharynx, either directly by ISH or indirectly by immunohistochemistry for p16 overexpression.

Histologic and histomorphometric changes of testis following oral exposure to methyl tertiary-butyl ether in adult rat.

Methyl tertiary-butyl ether (MTBE) is used to reduce carbon monoxide and ozone in urban air and to boost fuel octane. There is a lack of knowledge in the literature about the histomorphometric changes of the testis following exposure to MTBE. Therefore, this experimental study was performed to determine the effect of oral exposure to MTBE on histologic and histomorphometric changes of testis in adult rat. A total of 25 adult male Sprague-Dawley rats were randomly divided into five equal experimental groups: control, almond oil and three treatment groups which received 400, 800 and 1600 mg/kg/day MTBE in almond oil by gavages for 30 consecutive days. Histomorphometric analysis showed no significant difference in absolute and relative testis weight, connective tissue thickness, germinal epithelium height, tunica albuginea thickness and Sertoli cell numbers between experimental groups (P>0.05). However, trend analysis showed that the seminiferous tubule diameter increased and interstitial cell numbers as well as spermatocyte and spermatid cell numbers decreased significantly in MTBE treated groups (P<0.05). It may be concluded that MTBE could exert adverse effects on spermatogenic cells in adult rat. Whether the observed changes in the present study are due to the direct effect of MTBE via passing blood-testis barrier or its indirect effect through another mechanism should be elucidated in future studies.

The genomic organization of Isopeptidase T-3 (ISOT-3), a new member of the ubiquitin specific protease family (UBP).

A novel Isopeptidase T gene (ISOT-3) has been identified on human mosome 3q26.2--q26.3. gene shows 67.3% nucleotide identity and 54.8% amino acid identity to n Isopeptidase (ISOT-1). Northern blot analysis has shown that ISOT-3 is highly essed in ovary and testes, low-level expression in six other tissues tested. In contrast, ISOT-1 is essed at high levels in brain, and there is no detectable expression in ovary. The exonic nization of these two genes highly conserved with only one variant intron position. Intron 15 in -3 is absent in ISOT-1, there is an alternate splice site at the same location. Although the --intron structure has been erved between the two genes, ISOT-3 has significantly larger intronic ons, and the overall of this gene is at least 90 kb compared to 15 kb for ISOT-1. These data suggest that both ISOT-1 and ISOT-3 have descended from a common ancestor. In addition, the low overall sequence identity and different expression patterns may reflect differences in substrate specificity.

Genomic organization of the mouse double minute 2 gene.

Transfection of the mouse double minute 2 (Mdm2) oncogene has been found to induce immortalization of primary cells and to transform cultured cells. Amplification and/or overexpression of human MDM2 has been documented in a large percentage of human cancers. Mouse and human Mdm2 cDNA have been cloned from transformed cells and the cDNA sequence of both genes have been reported previously. In this report, we present the gene structure of mouse Mdm2. Comparison of the coding sequences of the Mdm2 gene with the previously reported cDNA sequence and with Mdm2 sequences obtained from an Mdm2-bearing cosmid clone capable of inducing transformation revealed that the reported cDNA sequence was in error, and that Mdm2-induced transformation of cells does not require an activating mutation in Mdm2. Ligation-anchor PCR analysis of transcripts produced from the P1 and P2 promoters indicates that transcription initiates at sites upstream of those reported previously for both promoters.

Distinction of endocervical and endometrial adenocarcinomas: immunohistochemical p16 expression correlated with human papillomavirus (HPV) DNA detection.

Determining the origin of uterine adenocarcinomas can be difficult in biopsy and curettage specimens because the morphologic spectrum of endocervical and endometrial adenocarcinomas overlaps. In hysterectomy specimens, the primary site is often equivocal for tumors that involve the lower uterine segment and endocervix and lack identifiable precursor lesions. Most endocervical adenocarcinomas (ECAs) contain high-risk human papillomavirus (HPV) DNA, whereas endometrial adenocarcinomas (EMAs) rarely do. p16 is an inhibitor ofcyclin-dependent kinases, and overexpression of p16 has been observed in cervical intraepithelial lesions and invasive carcinomas associated with high-risk HPV types. We evaluated the utility of immunohistochemistry for p16 in the distinction of ECAs and EMAs. p16 expression was assessed in 24 unequivocal EMAs and 19 unequivocal ECAs and correlated with HPV DNA detection by in situ hybridization and polymerase chain reaction. These assays were then used to assist in the classification of four lower uterine segment/upper endocervical adenocarcinomas (LUS/EC-A) of equivocal origin. p16 expression was moderate-strong and diffuse in 18 ECAs (median 90% of tumor cells positive, range 90%-100%), and weak and diffuse in one. Fourteen of these were positive for HPV DNA, whereas 5 lacked detectable HPV DNA by in situ hybridization; one of these 5 was positive by polymerase chain reaction. In contrast, EMAs displayed weaker staining with patchy distribution (median 30% of tumor cells positive, range 5%-70%) and none contained HPV DNA by in situ hybridization. Two LUS/EC-As, which were positive for HPV, exhibited strong, diffuse p16 expression, consistent with endocervical origin of the tumors. The remaining 2 LUS/EC-As showed patchy p16 staining and did not contain detectable HPV DNA, consistent with the endometrial origin of the tumors. The p16 expression pattern can distinguish ECAs from EMAs. Compared with HPV DNA detection by in situ hybridization, p16 immunohistochemistry appears to be a more sensitive and easier to perform method for distinguishing ECAs from EMAs, can be used to assist in the classification of LUS/EC-As of equivocal origin, and should be evaluated for its utility in the prospective classification of uterine adenocarcinomas in curettage specimens prior to hysterectomy.

Immunohistochemical p53 expression patterns in sarcomatoid carcinomas of the upper respiratory tract.

Sarcomatoid carcinoma of the upper respiratory tract is a phenotypically complex neoplasm that has triggered much thoughtful discussion regarding histogenic origin and morphologic classification. In particular, its putative epithelial lineage and distinction from a pseudosarcomatous reaction are sometimes questioned. Little is known about the genetic alterations underlying sarcomatoid carcinoma. Although about 45% of conventional squamous cell carcinomas of the upper respiratory tract harbor p53 mutations, the p53 status of sarcomatoid carcinomas is not well established. p53 immunohistochemical analysis using the monoclonal antibody D07 was performed on 23 sarcomatoid carcinomas of the upper respiratory tract. Twenty tumors were biphasic, having dual epithelial and spindled components. In four of these biphasic tumors, the epithelial and spindled components were separately analyzed for p53 gene mutations by sequence analysis. p53 immunohistochemistry was also performed on 19 cases of postradiation stromal atypia. Strong and diffuse p53 staining was detected in 18 (78%) of the 23 sarcomatoid carcinomas. When the spindled component was compared with its corresponding epithelial component, identical patterns of p53 protein expression were noted in 19 (95%) of the 20 biphasic tumors. Weak p53 staining was observed in one (5%) of the 19 cases of postradiation stromal atypia. In the four biphasic tumors evaluated by DNA sequence analysis, p53 status was always the same in the paired epithelial and spindle cell components. These findings help further dispel the notion that sarcomatoid carcinoma represents a reactive spindle cell proliferation (pseudosarcoma) or a collision between a carcinoma and a sarcoma (collision tumor). Instead, the epithelial and spindled components share a common pathway of tumorigenesis despite their conspicuous divergence at the phenotypic level.

Quantitation of mixed-base populations of HIV-1 variants by automated DNA sequencing with BODIPY dye-labeled primers.

Direct DNA sequencing of human immunodeficiency virus type 1 (HIV-1) pol and env gene regions was characterized for accuracy and precision. Restricted maximum likelihood (REML) analysis of molecular clone reconstruction experiments using a primer-walking strategy showed that the BODIPY and BODIPY energy-transfer (BET) dye primers sets were significantly more accurate in quantitating heterogenous base mixtures than the fluorescein/rhodamine dye primers. Of the three sets examined, the BET dye primers were the most accurate. The improved accuracy correlated with the reduced emission band-widths of BODIPY and BET dye primers and the more uniform signal intensities of BET dye primers. However, comparing % coefficients of variation (CV) for the three dye primer sets, revealed that BODIPY dye primers gave better precision than both BET and fluorescein/rhodamine dye primer sets. Several sequence-dependent motifs were identified that showed specific nucleotide-biased incorporation and were determined to be the major variable component of the total %CV. Taken together, these results show that BODIPY and BET direct DNA sequencing can accurately and precisely characterize complex mixed-base populations.

Analysis of HIV type 1 reverse transcriptase expression in a human cell line.

The functional analysis of human immunodeficiency virus type-1 (HIV-1) reverse transcriptase (RT) subunits on transient and constitutive expression, in the absence or presence of the HIV-1 protease (PR) expression, in a human cell line is described. HIV-1 RT is a heterodimer composed of a 51-kDa subunit (p51) and a 66-kDa subunit (p66). Cloning and expression of the RT region of the HIV-1 pol gene in the HT-1080 human fibrosarcoma cell line yielded p66 without any detectable p51 and a low level of RT activity could be measured. Transient expression of PR and RT in cis generated p51 and p66, but when RT and PR were expressed in trans only p66 was produced. Attempts to establish a stable cell line expressing the PR-RT region of the pol gene were hampered by an apparent intolerance of HT-1080 cells to the HIV-1 PR expression. Therefore, to generate p51 independent of PR expression, the 51-kDa subunit was cloned separately. p51 lacked detectable RT activity. Coexpression of p51 and p66 resulted in a dramatic increase in RT activity. Stable HT-1080 cells producing both p51 and p66 exhibited on average a 15-fold increase in RT activity compared to the parental cell line. Immunofluorescence revealed a diffuse cytoplasmic localization of p51 and p66. To date, this is the first example of a human cell line that is constitutively expressing HIV-1 RT in the absence of HIV-1 infection.

Immature granulocyte measurement using the Sysmex XE-2100. Relationship to infection and sepsis.

We determined the usefulness of immature granulocyte measurement as a predictor of infection or positive blood culture and compared the results with total WBC count and absolute neutrophil count (ANC). Blood samples from 102 infected and 69 noninfected patients were analyzed using the Sysmex XE-2100 automated blood cell counter (Sysmex, Kobe, Japan). The percentage of immature granulocytes was significantly higher in infected than in noninfected patients and in patients with positive than patients with negative blood cultures. Receiver operating characteristic curves showed that the percentage of immature granulocytes was a better predictor of infection than the WBC count and comparable to the ANC. Automated immature granulocyte measurements reflect a biologically and clinically relevant phenomenon but are not sensitive enough to be used as screening assays for prediction of infection or bacteremia. However, although infrequently encountered, a percentage of immature granulocytes of more than 3 was a very specific predictor of sepsis and might help expedite microbiologic laboratory evaluation of a subset of patients.

Influence of GSTT1 null genotype on the offspring sex ratio of gasoline filling station workers.

The aim of this study was to investigate whether the occupational exposure to gasoline of men employed at filling stations affects the sex of their children. Altogether 115 offspring (47 males, 68 females) were identified within families of 49 men working in filling stations in Shiraz (Fars province, south of Iran) and 345 offspring (178 males, 167 females) from 147 families of unexposed persons from the general population of Shiraz, which were matched by age of fathers (+/-2 years) and number of children as a control group. The offspring sex ratio at birth (male proportion) in the filling station workers was significantly lower than the ratio in control group (OR = 0.65; 95% confidence intervals (CI) 0.42 to 0.99). Genotypes of glutathione S-transferase M1 (GSTM1) and T1 (GSTT1) were investigated on extracted genomic DNA of 37 exposed workers using the polymerase chain reaction based method. In exposed group with active GSTM1 and GSTT1 genes, offspring sex ratio was the same as the ratio in the control group (OR = 0.66; 95% CI 0.34 to 1.28). However, in the exposed group with active GSTM1 and null genotype of GSTT1, the offspring sex ratio statistically decreased (OR = 0.45; 95% CI = 0.21 to 0.96). It seems that the GSTT1 null genotype has an effect on offspring sex ratio in the filling station workers.