Genetic diversity and population structure of Clavibacter michiganensis subsp. nebraskensis

2011 ◽  
Vol 57 (5) ◽  
pp. 366-374 ◽  
Author(s):  
I.V. Agarkova ◽  
P.A. Lambrecht ◽  
A.K. Vidaver

Clavibacter michiganensis subsp. nebraskensis (CMN) is a gram-positive bacterium and an incitant of Goss’s bacterial wilt and leaf blight or “leaf freckles” in corn. A population structure of a wide temporal and geographic collection of CMN strains (n = 131), originating between 1969 and 2009, was determined using amplified fragment length polymorphism (AFLP) analysis and repetitive DNA sequence-based BOX-PCR. Analysis of the composite data set of AFLP and BOX-PCR fingerprints revealed two groups with a 60% cutoff similarity: a major group A (n = 118 strains) and a minor group B (n = 13 strains). The clustering in both groups was not correlated with strain pathogenicity. Group A contained two clusters, A1 (n = 78) and A2 (n = 40), with a linkage of 75%. Group A strains did not show any correlation with historical, geographical, morphological, or physiological properties of the strains. Group B was very heterogeneous and eight out of nine clusters were represented by a single strain. The mean similarity between clusters in group B varied from 13% to 63%. All strains in group B were isolated after 1999. The percentage of group B strains among all strains isolated after 1999 (n = 69) was 18.8%. Implications of the findings are discussed.

1998 ◽  
Vol 16 (4) ◽  
pp. 1397-1406 ◽  
Author(s):  
M Adachi ◽  
T Taki ◽  
T Konishi ◽  
C I Huang ◽  
M Higashiyama ◽  
...  

PURPOSE The transmembrane-4 superfamily (TM4SF) is a recently discovered family of genes. Of the TM4SF members, MRP-1/CD9, KAI1/CD82, and ME491/CD63 have been reported to modulate tumor progression or metastasis. In this study, we investigated the relationships between these three genes, MRP-1, KAI1, and ME491, in patients with non-small-cell lung cancers (NSCLCs). Moreover, we assessed the prognostic value of evaluating the expressions of MRP-1, KAI1, and ME491 simultaneously in NSCLCs. PATIENTS AND METHODS One hundred seventy-two patients up to stage IIIB NSCLC underwent radical surgery during the period of January 1991 through June 1994. Using a quantitative reverse-transcriptase polymerase chain reaction (RT-PCR) analysis, we studied the expression of MRP-1, KAI1, and ME491 genes in these patients. RESULTS We found that 109 patients (63.4%) had MRP-1-positive tumors and 42 patients (24.4%) had KAl1-positive tumors. Conversely, all 172 patients expressed ME491. No relationship was found between MRP-1 expression and KAI1 expression. We classified these patients into three groups. The 36 patients who were positive for both MRP-1 and KAI1 were defined as group A; the 79 patients with reduced expression of either MRP-1 or KAI1 were defined as group B, and the remaining 57 patients with reduced expression of both MRP-1 and KAI1 were defined as group C. This new classification was correlated with nodal status, tumor status, and pathologic stage (P = .0056, P = .0003, and P < .0001, respectively). In NSCLC patients, the 5-year survival rate of group A patients was significantly better than that of group B patients and much better than that of group C patients (86.8%, 53.9%, and 31.5%, respectively; P < .0001). Cox multivariate regression analysis showed that this new classification in NSCLCs was a significant prognostic factor, as was the nodal status (P < .0001). CONCLUSION Our results suggest that a low MRP-1 and KAI1 expression by tumors of the lung may be associated with poor prognosis. It is conceivable that the evaluation for MRP-1 and KAI1 expression may identify node-negative lung cancer patients who are at high risk for early disease recurrence, and thus need intensive adjuvant therapy.


Plant Disease ◽  
2018 ◽  
Vol 102 (2) ◽  
pp. 300-308 ◽  
Author(s):  
Yusuf Sen ◽  
Yesim Aysan ◽  
Mustafa Mirik ◽  
Duygu Ozdemir ◽  
Fien Meijer-Dekens ◽  
...  

The pathogenic gram-positive bacterium Clavibacter michiganensis subsp. michiganensis (Smith) Davis et al. is the most harmful bacterium to tomatoes in many countries with a cooler climate. Multilocus sequence analysis was performed on five housekeeping genes (bipA, gyrB, kdpA, ligA, and sdhA) and three virulence-related genes (ppaA, chpC, and tomA) to determine evolutionary relationships and population structure of 108 C. michiganensis subsp. michiganensis strains collected from Turkey between 1996 and 2012. Based on these analyses, we concluded that C. michiganensis subsp. michiganensis in Turkey is highly uniform. However, at least four novel C. michiganensis subsp. michiganensis strains were recently introduced, possibly at the beginning of the 1990s. The singletons might point to additional sources or to strains that have evolved locally in Turkey.


2011 ◽  
Vol 75 (3) ◽  
pp. 245-251 ◽  
Author(s):  
Elżbieta Cieślak ◽  
Wojciech Paul ◽  
Michał Ronikier

An extremely endangered population of <em>Viola uliginosa</em> Besser at the classical locality of this taxon has been studied. The AFLP analysis was based on 18 specimens of <em>V. uliginosa</em> (about 10% of preserved individuals); additionally, two individuals of <em>V. riviniana</em> were included in the data set as the out group. A high genetical uniformity of the whole population (similarity indexes close to 1) was detected. It was not correlated significantly with the spatial distribution of the plants. The study serves as a basis for practical conservation measures and at the same time as a starting point for a more extensive research on the genetical variability of the species throughout its range.


Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 5415-5415 ◽  
Author(s):  
Alexander H. Schmidt ◽  
Andrea Stahr ◽  
Daniel Baier ◽  
Gerhard Ehninger ◽  
Claudia Rutt

Abstract In strategic stem cell donor registry planning, it is of special importance to decide how to type newly registered donors. This question refers to both the selection of HLA loci and the resolution (low, intermediate, or high) of HLA typings. In principle, high-resolution typings of all transplant-relevant loci are preferable. However, cost considerations generally lead to incomplete typings (only selected HLA loci with low or intermediate typing resolution) in practice. Here, we present results of a project in which newly recruited donors are typed for the HLA-A, -B, -C, and -DRB1 loci with high resolution by sequencing. Efficiency of these typings is measured by subsequent requests for confirmatory typings (CTs) and stem cell donations. Results for donors who were included in the project (Donor Group A) are compared to requests for donors with other, less complete typing levels: HLA-A and HLA-B at intermediate resolution, HLA-DRB1 at high resolution (Group B); HLA-A, -B, -C, and -DRB1 at intermediate resolution (Group C); HLA-A, -B, and -DRB1 at intermediate resolution (Group D). All data are taken from the donor file of DKMS German Bone Marrow Donor Center. Since the four groups differ considerably regarding their age and sex distributions, calculations are also carried through for restricted data sets that include only male donors up to age 25. Results are shown in Table 1. Donors of Groups A and B have similar CT request frequencies of 5.90 and 5.92 requests per 100 donors per year in the resctricted data sets, respectively. These frequencies significantly exceed the corresponding frequencies of the other groups with less complete typing levels. For donation requests, the frequency is signifcantly higher for Group A than for Group B (restricted data sets): 1.45 vs 1.02 requests per donor per year (p<0.05). Obviously, the additional HLA information for Group A donors leads to a higher ratio between donations and CT requests. Again, figures are much lower for Groups C and D. These results are based on a high number of requests even for the restricted data sets, namely between 44 and 90 donation requests and between 227 and 619 CT requests per group. Our results show that full (HLA-A, -B, -C, and -DRB1) high-resolution typings at donor recruitment lead to significantly higher probabilities for donation requests. Donor centers and registries should carefully take into account these higher probabilities when they consider full high-resolution typings for newly recruited donors. However, the final decision regarding the typing strategy at recruitment must also depend on the individual cost structure of a donor center or registry. The presented results are based on a donor file that consists mainly (≈99%) of Caucasian donors. It should be subject to further analyses if these results also apply to other, more heterogeneous donor pools. Table 1: Requests per 100 donors per year by donor group CT requests Donation requests Donor Group Full data set Only male donors≤ 25 Full data set Only male donors≤ 25 A 5.14 5.90 1.45 1.45 B 4.60 5.92 0.84 1.02 C 2.50 3.03 0.58 0.67 D 2.36 2.80 0.38 0.48


Plant Disease ◽  
2015 ◽  
Vol 99 (11) ◽  
pp. 1569-1577 ◽  
Author(s):  
Qinggang Guo ◽  
Shezeng Li ◽  
Xiuyun Lu ◽  
Hui Gao ◽  
Xiaoguang Wang ◽  
...  

Genetic composition of Fusarium oxysporum f. sp. vasinfectum strains, including race 3, 7, and 8, Australian genotype strain, and 80 strains collected from China, were studied using amplified fragment length polymorphism (AFLP). Based on AFLP analysis, these strains were separated into four groups. Race 3, strain CN3, was the only strain in group A. Race 8, strain CN8, was the only strain in group B. Race 7, strain CN7, was grouped with 75 strains from China in group C. The Australian genotype strain ATCC96291 was grouped with five strains from China in group D. Evolution of the five native strains in group D was studied using multigene genealogies. Phylogenetic tree analysis revealed that the five strains of group D had a closer genetic relationship to the Australian genotype strain than the other races based on the combined elongation factor, β-tubulin, and phosphate permase gene sequence data. Group D was further tested for pathogenicity and virulence on four cotton cultivars from Upland (Gossypium hirsutum) and Sea Island (G. barbadense) cotton. All five strains caused typical Fusarium wilt symptoms on all four cotton cultivars but virulence were relatively low compared with race 3, race 7, and race 8.


2015 ◽  
Vol 105 (2) ◽  
pp. 169-179 ◽  
Author(s):  
Matthew A. Tancos ◽  
Holly W. Lange ◽  
Christine D. Smart

New York Clavibacter michiganensis subsp. michiganensis isolates, collected from disparate bacterial canker of tomato outbreaks over the past 11 years, were characterized with a multilocus sequence analysis (MLSA) scheme that differentiated the 51 isolates into 21 haplotypes with a discriminatory power of 0.944. The MLSA scheme consisted of five housekeeping genes (kdpA, sdhA, dnaA, ligA, and gyrB) and three putative pathogenicity genes (celA, tomA, and nagA). Repetitive polymerase chain reaction (PCR), with the BOX-A1R primer, confirmed the high diversity of C. michiganensis subsp. michiganensis isolates in New York by demonstrating that all six PCR patterns (A, B, 13C, 65C, 81C, and D) were present, with PCR patterns C and A being the most common. The MLSA scheme provided higher resolving power than the current repetitive-PCR approach. The plasmid profiles of New York isolates were diverse and differed from reference strain NCPPB382. PCR analysis indicated that the presence of putative pathogenicity genes varied between isolates and highlighted the ephemeral nature of pathogenicity genes in field populations of C. michiganensis subsp. michiganensis. Analysis of molecular variance between Serbian and New York C. michiganensis subsp. michiganensis isolates demonstrated that the two populations were not significantly different, with 98% genetic variation within each population and only 2% genetic variation between populations.


1994 ◽  
Vol 8 (3) ◽  
pp. 113-116 ◽  
Author(s):  
Jukka I. Sipilä ◽  
Jouko T. Suonpää ◽  
Pekka T. Laippala

Correlation between active anterior rhinomanometry and subjective sensation of nasal obstruction was studied in three groups of patients. Group A included patients with marked septal deviation causing high nasal resistance. Group B represented cases where there was minor septal deviation, but normal resistance. Group C consisted of cases with chronic rhinitis causing nasal stuffiness, but normal septum and normal decongestion resistance. The patient's response as to the more obstructed side of the nose was correlated with the rhinomanometrically recorded less patent nostril. The results show that the correlation was good in Group A, but did not exist in the other groups. The reason for this is that, when the side difference of resistance between the two nasal cavities was less than 60–70%, it was very difficult for the patient to estimate the more obstructed side. This was especially the case in Group C, where mucosal swelling often changes sides. The conclusion is that patients’ capability to detect a minor side difference is poorer than rhinomanometry's. Furthermore, if rhinomanometry and subjective sensation do not agree, the reason may be that the patient's nasal complaint is dominated by the mucosal disease, rather than by a structural deformity and therefore, treatment other than surgery may be preferred.


Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 17-18
Author(s):  
Hannah Seemann ◽  
Nadja Jaekel ◽  
Susann Schulze ◽  
Juliane Grimm ◽  
Ole Vollstaedt ◽  
...  

Systemic mastocytosis (SM) is reported to be a rare myeloid disease. The true incidence is unknown as the diagnosis is often missed due to the diversity of symptoms and signs. In the HRYD study, we hypothesized that the reported incidence of around 1/100000/year is too low and the assumed underdiagnosis could be reduced if serum tryptase, although only a minor criterion for the diagnosis of SM, would be measured in patients (pts) with cytopenia and/or leukocytosis. Methods: HRYD was a prospective single-center trial. The protocol was approved by the local ethics committee. The primary endpoint was the incidence of SM in a consecutive cohort of 100 unselected pts with unclear cytopenia and/or leukocytosis at the University Hospital Halle. Pts with suspected or known SM or cutaneous mastocytosis were excluded. Serum tryptase levels were measured at initial presentation (normal &lt; 11 ng/ml). The diagnosis and classification of SM were based on the 2016 WHO classification where a baseline tryptase level &gt; 20 ng/mL is considered as a minor criterion for SM. Routine diagnostic work-up included medical history, physical examination, blood analyses (blood picture, differential count, liver and renal function, albumin, and further tests as needed), and if indicated a bone marrow biopsy and aspiration for cytology, immunophenotyping, karyotyping, and molecular diagnostics as appropriate. Mutational profiling from a peripheral blood sample with next-generation sequencing (NGS) was done if required. All pts gave informed consent. Results: 100 pts (51% males) &gt; 18 years (y) were recruited between February, 2019 and June, 2020. Median age was 64.5 (range 18-88) y. Based on the final diagnosis, pts were allocated to five subgroups (group A: SM, group B: non-SM malignant hematological diseases, group C: benign hematological diseases, group D: non-hematological diseases, group E: unclear diagnosis at data-cut-off) (table 1). For the entire cohort, fatigue (n=46), weight loss (n=25), and dyspnea (n=15) were the most frequent symptoms at presentation. A non-SM malignant disease (group B) was most frequently diagnosed (n=49) followed by a non-hematological cause (n=24) (figure1). With a median age of 70 (31-88) y, pts in group B tended to be older compared to those in groups C and D. Serum tryptase &gt; 20 ng/ml was detected in 9 pts (median level 53.4, range 21.6-200) ng/ml. SM was diagnosed in 4 (4%) pts (group A). The remaining 5 pts belonged to group B, n=4 and group D, n=1. A history of allergies, skin lesions, hepatomegaly, and/or splenomegaly were not predictive for the diagnosis of SM. The median tryptase level in SM pts was 163 (range 32.1-200) ng/ml. All pts in group A suffered from SM with associated hematologic neoplasm (SM-AHN). The AHN were MDS, n=1; MPN, n=1; AML, n=2. A KIT point mutation at codon 816 was detected in one of the SM-AHN pts. Overall, a diagnosis of SM could be excluded with a probability of 85.4% and a specificity of 95% if the tryptase level was &lt; 20 ng/ml. On the other hand and although sensitivity was 100%, the positive predictive value of a serum tryptase &gt; 20 ng/ml for SM was only 44.4%. WBC, Hb, and platelets did not correlate with tryptase levels or the final diagnosis in all groups. In group B, three pts with BCR-ABL positive CML were diagnosed. In contrast to SM-AHN pts, marked leukocytosis with a WBC &gt;100x109/L was present in the CML pts. NGS was performed in 27 pts. A median of 3 (range 0-8) somatic mutations were detected. From a diagnostic point of view, the added value of NGS was met in 8/27 (30%) pts. Conclusions: In an unselected cohort of pts with undiagnosed cytopenia and/or leucocytosis, the incidence of SM-AHN was higher than that for BCR-ABL positive CML. Our data question the low reported epidemiological data to SM. Because of the prognostic and therapeutic consequences of a correct diagnosis and despite the low positive predictive value of an elevated tryptase for the diagnosis of SM, including the cheap serum tryptase test in the work-up of pts with unclear clinical scenarios and abnormal hematological parameters is a simple tool to increase awareness of physicians to SM as a differential diagnosis. SM is highly unlikely if the tryptase level is below 20 ng/ml. Disclosures Niederwieser: Amgen: Speakers Bureau; Daiichi: Research Funding; Cellectis: Membership on an entity's Board of Directors or advisory committees; Novartis: Speakers Bureau. Al-Ali:Celgene: Honoraria, Research Funding; Novartis: Honoraria, Research Funding.


Plant Disease ◽  
2006 ◽  
Vol 90 (12) ◽  
pp. 1550-1550 ◽  
Author(s):  
R. J. Holguín-Peña ◽  
R. C. Vázquez-Juárez ◽  
E. O. Rueda-Puente

During the 2005 tomato-growing (Lycopersicon esculentum Mill.) season, an apparent bacterial disease with cankers on the stems and bird's eye lesions on the fruit appeared in commercial fields and greenhouses in the San Quintin and San Simon areas (a 60-mile long coastal plain) near the central region of the Baja California Peninsula of Mexico. The disease was found in midseason, especially when plants were flowering, and the mature and ripe stage. Incidence ranged from 4 to 46%, which represented an important loss in field and greenhouse production. Symptomatic plants showed reddish brown cavities in the stem, discoloration, and water soaking of vascular tissue. Diseased tissues were washed with phosphate buffer and placed on semiselective Clavibacter medium (SCM) (1), and a gram-positive, nonmotile, nonspore-forming, aerobic, curved rod bacterium was consistently isolated and morphologically characterized. Twenty-eight isolates were identified as Clavibacter michiganensis subsp. michiganensis by polymerase chain reaction (PCR) technology with primers CMM5/CMM6 to amplify a fragment of approximately 6.2 kb (2). The isolates were also identified by REP-PCR (repetitive extragenic palindromic PCR) genomic fingerprinting techniques (3) with REP and BOX primer sets (4). Pathogenicity tests consisting of three replicates of 4-week-old tomato seedlings (cv. Tequila) were performed by spraying (twice, 2 days apart) inocula at 108 CFU/ml. Control seedlings were sprayed with sterile water. Inoculated plants previously covered in polyethylene bags were incubated in a growth chamber at 25°C for 48 h. Within 3 weeks, symptoms of reddish-brown cavities, water-soaked lesions, and asymmetrical wilting appeared on inoculated plants and were similar to those symptoms observed in the field. No symptoms were observed on control plants. Confirmation of the causal agent was done by culturing the bacteria on SCM and PCR analysis. Occurrence of the disease in San Quintin Valley is relevant because the disease is one of the five most serious tomato diseases in the peninsula. Moreover, the potential spread of the pathogen by tomato seedlings represents a permanent risk to other pathogen-free areas in the peninsula. Although bacterial canker has been observed in Baja California (Punta Colonet, Vicente Guerrero, San Quintin, and San Simon), to our knowledge, this is the first confirmation of C. michiganensis subsp. michiganensis in Baja, Mexico. References: (1). C. Alarcon et al. Phytopathology 88:306, 1998. (2) J. Dreier et al. Phytopathology 85:462, 1995. (3) F. J. Louws et al. Phytopathology 88:862, 1998. (4) J. Versalovic et al. Methods Mol. Cell. Biol. 5:25, 1994.


Pathogens ◽  
2019 ◽  
Vol 8 (1) ◽  
pp. 18 ◽  
Author(s):  
Alexander Malko ◽  
Pavel Frantsuzov ◽  
Maksim Nikitin ◽  
Natalia Statsyuk ◽  
Vitaly Dzhavakhiya ◽  
...  

Viral and bacterial diseases of potato cause significant yield loss worldwide. The current data on the occurrence of these diseases in Russia do not provide comprehensive understanding of the phytosanitary situation. Diagnostic systems based on disposable stationary open qPCR micromatrices intended for the detection of eight viral and seven bacterial/oomycetal potato diseases have been used for wide-scale screening of target pathogens to estimate their occurrence in 11 regions of Russia and to assess suitability of the technology for high-throughput diagnostics under conditions of field laboratories. Analysis of 1025 leaf and 725 tuber samples confirmed the earlier reported data on the dominance of potato viruses Y, S, and M in most regions of European Russia, as well as relatively high incidences of Clavibacter michiganensis subsp. sepedonicus, Pectobacterium atrosepticum, and P. carotovorum subsp. carotovorum, and provided detailed information on the phytosanitary status of selected regions and geographical spread of individual pathogens. Information on the occurrence of mixed infections, including their composition, was the first data set of this kind for Russia. The study is the first large-scale screening of a wide range of potato pathogens conducted in network mode using unified methodology and standardized qPCR micromatrices. The data represent valuable information for plant pathologists and potato producers and indicate the high potential of the combined use of matrix PCR technology and network approaches to data collection and analysis with the view to rapidly and accurately assess the prevalence of certain pathogens, as well as the phytosanitary state of large territories.


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