Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications.

The epitranscriptome embodies many new and largely unexplored functions of RNA. A significant roadblock hindering progress in epitranscriptomics is the identification of more than one modification in individual transcript molecules. We address this with CHEUI (CH3 (methylation) Estimation Using Ionic current). CHEUI predicts N6-methyladenosine (m6A) and 5-methylcytosine (m5C) in individual molecules from the same sample, the stoichiometry at transcript reference sites, and differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals to achieve high single-molecule, transcript-site, and stoichiometry accuracies in multiple tests using synthetic RNA standards and cell line data. CHEUI's capability to identify two modification types in the same sample reveals a co-occurrence of m6A and m5C in individual mRNAs in cell line and tissue transcriptomes. CHEUI provides new avenues to discover and study the function of the epitranscriptome.

Vaginal neutrophils eliminate sperm by trogocytosis.

STUDY QUESTION: What is the vaginal polymorphonuclear (PMN) spermicidal mechanism to reduce the excess of sperm? SUMMARY ANSWER: We show that PMNs are very efficient at killing sperm by a trogocytosis-dependent spermicidal activity independent of neutrophil extracellular traps (NETs). WHAT IS KNOWN ALREADY: Trogocytosis has been described as an active membrane exchange between immune cells with a regulatory purpose. Recently, trogocytosis has been reported as a mechanism which PMNs use to kill tumour cells or Trichomonas vaginalis. STUDY DESIGN, SIZE, DURATION: We used in vivo murine models and human ex vivo sperm and PMNs to investigate the early PMN-sperm response. PARTICIPANTS/MATERIALS, SETTING, METHODS: We set up a live/dead sperm detection system in the presence of PMNs to investigate in vivo and ex vivo PMN-spermicidal activity by confocal microscopy, flow cytometry and computer-assisted sperm analysis (SCA). MAIN RESULTS AND THE ROLE OF CHANCE: We revealed that PMNs are highly efficient at killing sperm by way of a NETs-independent, contact-dependent and serine proteases-dependent engulfment mechanism. PMNs 'bite' sperm and quickly reduce sperm motility (within 5 min) and viability (within 20 min) after contact. LARGE SCALE DATA: N/A. LIMITATIONS, REASONS FOR CAUTION: This study was conducted using murine models and healthy human blood PMNs; whether it is relevant to human vaginal PMNs or to cases of infertility is unknown. WIDER IMPLICATIONS OF THE FINDINGS: Vaginal PMNs attack and immobilize excess sperm in the vagina by trogocytosis because sperm are exogenous and may carry pathogens. Furthermore, this mechanism of sperm regulation has low mucosal impact and avoids an exacerbated inflammatory response that could lead to mucosal damage or infertility. STUDY FUNDING/COMPETING INTEREST(S): This work was partially supported by Ministry of Economy and Competitiveness ISCIII-FIS grants, PI16/00050, and PI19/00078, co-financed by ERDF (FEDER) Funds from the European Commission, 'A way of making Europe' and IiSGM intramural grant II-PI-MRC-2017. M.R. holds a Miguel Servet II contract (CPII14/00009). M.C.L. holds IiSGM intramural contract. There are no competing interests.

Legumes display common and host-specific responses to the rhizobial cellulase CelC2 during primary symbiotic infection.

Primary infection of legumes by rhizobia involves the controlled localized enzymatic breakdown of cell walls at root hair tips. Previous studies determined the role of rhizobial CelC2 cellulase in different steps of the symbiotic interaction Rhizobium leguminosarum-Trifolium repens. Recent findings also showed that CelC2 influences early signalling events in the Ensifer meliloti-Medicago truncatula interaction. Here, we have monitored the root hair phenotypes of two legume plants, T. repens and M. sativa, upon inoculation with strains of their cognate and non-cognate rhizobial species, R. leguminosarum bv trifolii and E. meliloti, (over)expressing the CelC2 coding gene, celC. Regardless of the host, CelC2 specifically elicited 'hole-on-the-tip' events (Hot phenotype) in the root hair apex, consistent with the role of this endoglucanase in eroding the noncrystalline cellulose found in polarly growing cell walls. Overproduction of CelC2 also increased root hair tip redirections (RaT phenotype) events in both cognate and non-cognate hosts. Interestingly, heterologous celC expression also induced non-canonical alterations in ROS (Reactive Oxygen Species) homeostasis at root hair tips of Trifolium and Medicago. These results suggest the concurrence of shared unspecific and host-related plant responses to CelC2 during early steps of symbiotic rhizobial infection. Our data thus identify CelC2 cellulase as an important determinant of events underlying early infection of the legume host by rhizobia.

Estradiol impairs epithelial CXCL1 gradient in the cervix to delay neutrophil transepithelial migration during insemination.

Female reproductive mucosa must allow allogenic sperm survival whereas at the same time, avoid pathogen infection. To preserve sperm from neutrophil attack, neutrophils disappear from the vagina during the ovulatory phase (high estradiol); although the mechanisms that regulate neutrophil influx to the vagina during insemination remain controversial. We investigated the sex hormone regulation of the neutrophil migration through the cervix during insemination and revealed that ovulatory estradiol dose fades the CXCL1 epithelial expression in the ectocervix and fornix; hence, retarding neutrophil migration and retaining them in the epithelium. These mechanisms spare sperm from neutrophil attack to preserve reproduction, but might compromise immunity. However, luteal progesterone dose promotes the CXCL1 gradient expression to restore neutrophil migration, to eliminate sperm and prevent sperm associated pathogen dissemination. Surprisingly, these mechanisms are hormone dependent and independent of the insemination. Thus, sex hormones orchestrate tolerance and immunity in the vaginal lumen by regulating neutrophil transepithelial migration in the fornix and ectocervix.

Nodal FDG-PET/CT uptake influences outcome and relapse location among esophageal cancer patients submitted to chemotherapy or radiochemotherapy.

PURPOSE: Our aim was investigate whether lymph node uptake is associated with survival and regional relapses, and relapse patterns with respect to the radiotherapy fields in esophageal cancer (EC). MATERIALS AND METHODS: The FDG-PET/CT image datasets of 56 patients were analyzed. All patients underwent definitive or neoadjuvant radio/chemotherapy (RCT). All patients suffering from persistent or recurrent local/regional-only disease after RCT were considered for salvage resection. Patients with adenocarcinoma without metastatic disease were considered for planned resection (usually within 3 months of treatment). RESULTS: Patients with PET-positive lymph nodes before treatment had a worse overall survival and a shorter disease-free survival than those without PET-positive nodes. They also had worse node and metastatic relapse-free survival. N2 patients had statistically significant poorer outcomes than N1-N0 patients and a better survival if the involved nodes were closer to the esophageal tumor. Involved node location by PET/CT also affected global, nodal and metastatic relapses. In addition, an increment of SUVmax value increased relative risk of death and increased relative risk of node and metastatic relapses. The first site of relapse was metastatic recurrence and, second, local recurrence. The most frequent were "in-field" loco/regional recurrence. We observed a relationship between patients classified-N1 and out-field nodal recurrence (p = 0.024), and between patients-N2 and in-field nodal recurrence. The number of PET-positive nodes was an independent significant prognostic predictor for relapse (p < 0.001). CONCLUSION: Our study shows that only FDG-PET/CT can provide prognostic information in EC. Nodal PET/CT uptake influences outcome and relapse location among EC patients.

Melatonin expression in periodontitis and obesity: An experimental in-vivo investigation.

BACKGROUND AND OBJECTIVE: Melatonin deficiency has been associated with obesity and systemic inflammation. This study aims to evaluate whether melatonin could interfere with the mechanisms of co-morbidity linking obesity and periodontitis. MATERIAL AND METHODS: Twenty-eight male Wistar rats were randomly divided in 4 groups: control group (Con) (fed with standard diet); high-fat diet group (HFD) (fed with a diet containing 35.2% fat); Con group with induced periodontitis (Con-Perio) and HFD group with induced periodontitis (HFD-Perio). To induce periodontitis, the method of oral gavages with Porphyromonas gingivalis ATCC W83K1 and Fusobacterium nucleatum DMSZ 20482 was used. Circulating melatonin levels were analyzed by multiplex immunoassays. Periodontitis was assessed by alveolar bone loss (micro-computed tomography and histology) and by surrogate inflammatory outcomes (periodontal pocket depth, modified gingival index and plaque dental index). RESULTS: Plasma melatonin levels were significantly decreased (P < .05) in the obese rats with periodontitis when compared with controls or with either obese or periodontitis rats. Alveolar bone loss increased 27.71% (2.28 µm) in HFD-Perio group compared with the Con group. The histological analysis showed marked periodontal tissue destruction with osteoclast activity, particularly in the HFD-Perio group. A significant negative correlation (P < .05) was found between periodontal pocket depth, modified gingival index and circulating melatonin levels. CONCLUSION: Obese and periodontitis demonstrated significantly lower melatonin concentrations when compared with controls, but in obese rats with periodontitis these concentrations were even significantly lower when compared with either periodontitis or obese rats. These results may indicate that melatonin deficiency could be a key mechanism explaining the co-morbidity effect in the association between obesity and periodontitis.

Radiotherapy volume delineation using 18F-FDG-PET/CT modifies gross node volume in patients with oesophageal cancer.

PURPOSE: Evidence supporting the use of 18F-FDG-PET/CT in the segmentation process of oesophageal cancer for radiotherapy planning is limited. Our aim was to compare the volumes and tumour lengths defined by fused PET/CT vs. CT simulation. MATERIALS AND METHODS: Twenty-nine patients were analyzed. All patients underwent a single PET/CT simulation scan. Two separate GTVs were defined: one based on CT data alone and another based on fused PET/CT data. Volume sizes for both data sets were compared and the spatial overlap was assessed by the Dice similarity coefficient (DSC). RESULTS: The gross tumour volume (GTVtumour) and maximum tumour diameter were greater by PET/CT, and length of primary tumour was greater by CT, but differences were not statistically significant. However, the gross node volume (GTVnode) was significantly greater by PET/CT. The DSC analysis showed excellent agreement for GTVtumour, 0.72, but was very low for GTVnode, 0.25. CONCLUSIONS: Our study shows that the volume definition by PET/CT and CT data differs. CT simulation, without taking into account PET/CT information, might leave cancer-involved nodes out of the radiotherapy-delineated volumes.

In vivo adhesion of malignant B cells to bone marrow microvasculature is regulated by α4ß1 cytoplasmic-binding proteins.

Multiple myeloma (MM) and chronic lymphocytic leukemia (CLL) cells must attach to the bone marrow (BM) microvasculature before lodging in the BM microenvironment. Using intravital microscopy (IVM) of the BM calvariae we demonstrate that the α4ß1 integrin is required for MM and CLL cell firm arrest onto the BM microvasculature, while endothelial P-selectin and E-selectin mediate cell rolling. Talin, kindlin-3 and ICAP-1 are ß1-integrin-binding partners that regulate ß1-mediated cell adhesion. We show that talin and kindlin-3 cooperatively stimulate high affinity and strength of α4ß1-dependent MM and CLL cell attachment, whereas ICAP-1 negatively regulates this adhesion. A functional connection between talin/kindlin-3 and Rac1 was found to be required for MM cell attachment mediated by α4ß1. Importantly, IVM analyses with talin- and kindlin-3-silenced MM cells indicate that these proteins are needed for cell arrest on the BM microvasculature. Instead, MM cell arrest is repressed by ICAP-1. Moreover, MM cells silenced for talin and kindlin-3, and cultured on α4ß1 ligands showed higher susceptibility to bortezomib-mediated cell apoptosis. Our results highlight the requirement of α4ß1 and selectins for the in vivo attachment of MM and CLL cells to the BM microvasculature, and indicate that talin, kindlin-3 and ICAP-1 differentially control physiological adhesion by regulating α4ß1 activity.

Name analysis to classify populations by ethnicity in public health: validation of Onomap in Scotland.

OBJECTIVES: Health inequalities between ethnic minorities and the general population are persistent. Addressing them is hampered by the inability to classify individuals' ethnicity accurately. This is addressed by a new name-based ethnicity classification methodology called 'Onomap'. This paper evaluates the diagnostic accuracy of Onomap in identifying population groups by ethnicity, and discusses applications to public health practice. STUDY DESIGN: Onomap was applied to three independent reference datasets (birth registration, pupil census and register of Polish health professionals) collected in Britain and Poland at individual level (n = 260,748). METHODS: Results were compared with the reference database ethnicity 'gold standard'. Outcome measures included sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV). Ninety-five percent confidence intervals and Chi-squared tests were used. RESULTS: Onomap identified the majority of those in the British participant group with high sensitivity and PPV (>95%), and low misclassification (<5%), although specificity and NPV were lowest in this group (56-87%). Outcome measures for all other non-British groupings were high for specificity and NPV (>98%), but variable for sensitivity and PPV (17-89%). Differences in misclassification by gender were statistically significant. Using maiden name rather than married name in women improved classification outcomes for those born in the British Isles (0.53%, 95% confidence interval 0.26-0.8%; P < 0.001) but not for South Asian or Polish groups. CONCLUSIONS: Onomap offers an effective methodology for identifying population groups in both health-related and educational datasets, categorizing populations into a variety of ethnic groups. This evaluation suggests that it can successfully assist health researchers, planners and policy makers in identifying and addressing health inequalities.

A prospective, randomized study on the efficacy of tongue protector in patients with burning mouth syndrome.

OBJECTIVE: To apply a tongue protector with habit-modifying therapy through self-control, in the patients with burning mouth syndrome (BMS). METHODS: A prospective, randomized study was made of 65 consecutive patients with BMS. Fifty subjects were randomized to two groups: group A (informed) and group B (informed and the application of a tongue protector). The symptoms were evaluated by VAS, whereas the psychological profile was assessed using the HAD, with application of the quality of life questionnaires SF-36 and OHIP-49. The duration of treatment was 2 months. RESULTS: Fifty patients (46 females and 4 males) completed the study. The VAS scores in group B were 8.2 at baseline and 4.5 after 2 months. The respective scores in group A were 7.1 and 5.6 - the differences between the two groups being significant (P < 0.001). In group B the OHIP-49 yielded lower scores for most of the scales, with significant differences vs group A. In group B the SF 36 yielded significant differences vs group A in physical role, bodily pain, general health and emotional role. CONCLUSIONS: Parafunctional traumatism of the tongue should be taken into account in the pathogenesis of BMS with a view to exploring new therapeutic options.

Rhizobium cellulase CelC2 is essential for primary symbiotic infection of legume host roots.

The rhizobia-legume, root-nodule symbiosis provides the most efficient source of biologically fixed ammonia fertilizer for agricultural crops. Its development involves pathways of specificity, infectivity, and effectivity resulting from expressed traits of the bacterium and host plant. A key event of the infection process required for development of this root-nodule symbiosis is a highly localized, complete erosion of the plant cell wall through which the bacterial symbiont penetrates to establish a nitrogen-fixing, intracellular endosymbiotic state within the host. This process of wall degradation must be delicately balanced to avoid lysis and destruction of the host cell. Here, we describe the purification, biochemical characterization, molecular genetic analysis, biological activity, and symbiotic function of a cell-bound bacterial cellulase (CelC2) enzyme from Rhizobium leguminosarum bv. trifolii, the clover-nodulating endosymbiont. The purified enzyme can erode the noncrystalline tip of the white clover host root hair wall, making a localized hole of sufficient size to allow wild-type microsymbiont penetration. This CelC2 enzyme is not active on root hairs of the nonhost legume alfalfa. Microscopy analysis of the symbiotic phenotypes of the ANU843 wild type and CelC2 knockout mutant derivative revealed that this enzyme fulfils an essential role in the primary infection process required for development of the canonical nitrogen-fixing R. leguminosarum bv. trifolii-white clover symbiosis.

[Parathyroid cancer in a patient with previous history of hypernephroma: a clinical case]. / Cáncer de paratiroides en paciente con antecedentes de hipernefroma, a propósito de un caso.

We report the clinical case of a 55 year-old male patient, with a previous history of nephrectomy by hypernephroma sixteen years ago, first presenting hypercalcemia and rising of intact parathyroid hormone (iPTH) levels. A localization study revealed an intrathyroid nodule with cystic appearance. After undergoing a hemi-thyroidectomy, the patient is diagnosed with parathyroid carcinoma. This article analyzes previously published cases presenting parathyroidal pathologies associated with hypernephroma. A broader differential diagnosis--including the screening of parathyroidal pathologies should be considered in patients with hypercalcemia and hypernephroma.

Strains of Mesorhizobium amorphae and Mesorhizobium tianshanense, carrying symbiotic genes of common chickpea endosymbiotic species, constitute a novel biovar (ciceri) capable of nodulating Cicer arietinum.

AIMS: To identify several strains of Mesorhizobium amorphae and Mesorhizobium tianshanense nodulating Cicer arietinum in Spain and Portugal, and to study the symbiotic genes carried by these strains. METHODS AND RESULTS: The sequences of 16S-23S intergenic spacer (ITS), 16S rRNA gene and symbiotic genes nodC and nifH were analysed. According to their 16S rRNA gene and ITS sequences, the strains from this study were identified as M. amorphae and M. tianshanense. The type strains of these species were isolated in China from Glycyrrhiza pallidiflora and Amorpha fruticosa nodules, respectively, and are not capable of nodulating chickpea. These strains carry symbiotic genes, phylogenetically divergent from those of the chickpea isolates, whose nodC and nifH genes showed more than 99% similarity with respect to those from Mesorhizobium ciceri and Mesorhizobium mediterraneum, the two common chickpea nodulating species in Spain and Portugal. CONCLUSIONS: The results from this study showed that different symbiotic genes have been acquired by strains from the same species during their coevolution with different legumes in distinct geographical locations. SIGNIFICANCE AND IMPACT OF THE STUDY: A new infrasubspecific division named biovar ciceri is proposed within M. amorphae and M. tianshanense to include the strains able to effectively nodulate Cicer arietinum.

Characterization of xylanolytic bacteria present in the bract phyllosphere of the date palm Phoenix dactylifera.

AIMS: Despite the interest of phyllosphere microbiology, no studies have addressed the bacteria present in bract phyllosphere, an ecosystem that has special characteristics in palm trees because the dry bracts remain on the plant until pruning and may contain polymer-degrading bacteria involved in plant degradation. Therefore, the aim of this work was to characterize xylanolytic bacteria isolated from palm bract phyllosphere. METHODS AND RESULTS: Twelve xylanolytic strains were isolated and characterized by phenotypic features and complete sequencing of 16S rRNA gene. The results showed that the isolates were phenotypically and genotypically diverse. Gram-positive isolates were classified into genus Paenibacillus some of them belonging to hitherto undescribed species of this genus. Gram-negative isolates were classified into genera Pseudomonas and Acinetobacter. CONCLUSIONS: The results of this work confirm the complexity of the bacterial populations present in phyllospheric ecosystems and suggest that bacteria involved in plant degradation are present at the early degradation steps of this process in dry palm tree bracts. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first study on bract phyllospheric bacteria able to hydrolyse vegetal polymers and offers a new perspective in the search of unexplored sources of xylanase-producing strains.

Cellulomonas xylanilytica sp. nov., a cellulolytic and xylanolytic bacterium isolated from a decayed elm tree.

A Gram-positive, aerobic, non-motile bacterium was isolated from a decayed elm tree. Phylogenetic analysis based on 16S rDNA sequences revealed 99.0 % similarity to Cellulomonas humilata. Chemotaxonomic data that were determined for this isolate included cell-wall composition, fatty acid profiles and polar lipids; the results supported the placement of strain XIL11(T) in the genus Cellulomonas. The DNA G+C content was 73 mol%. The results of DNA-DNA hybridization with C. humilata ATCC 25174(T), in combination with chemotaxonomic and physiological data, demonstrated that isolate XIL11(T) should be classified as a novel Cellulomonas species. The name Cellulomonas xylanilytica sp. nov. is proposed, with strain XIL11(T) (=LMG 21723(T)=CECT 5729(T)) as the type strain.

Xylanibacterium ulmi gen. nov., sp. nov., a novel xylanolytic member of the family Promicromonosporaceae.

A bacterial strain designated XIL08(T) was isolated from an elm tree affected by Dutch elm disease. Strain XIL08(T) is Gram-positive, aerobic, rod-shaped and non-motile. The complete 16S rDNA sequence of this micro-organism was obtained and phylogenetic analysis based on the neighbour-joining method indicated that the closest related organism belongs to the genus Xylanimonas of the family Promicromonosporaceae, suborder Micrococcineae. Cell-wall analyses revealed the presence of type A4alpha, L-lys-L-ala-D-Glu peptidoglycan. The cell-wall sugars found were rhamnose in large amounts, fucose, mannose and galactose and traces of arabinose and glucose. HPLC analysis of menaquinones revealed two peaks, the main peak corresponding to MK-9(H(4)) and the smaller one to MK-8(H(4)). The major fatty acid found was anteiso-C(15 : 0). Mycolic acids were absent. The polar lipids detected were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The G+C content of the DNA was 72 mol%. Isolate XIL08(T) hydrolysed xylan but not cellulose. Growth was observed with many carbohydrates including acetate and xylan as the only carbon source. Catalase activity was not detected. The data from this polyphasic study suggest that this bacterium belongs to a novel genus of the family Promicromonosporaceae. It is proposed that isolate XIL08(T) (=LMG 21721(T)=CECT 5731(T)) be classified in a new genus, Xylanibacterium gen. nov., as the type strain of Xylanibacterium ulmi sp. nov.

Regulatory role of tetraspanin CD9 in tumor-endothelial cell interaction during transendothelial invasion of melanoma cells.

Heterotypic interaction among tumor cells (TCs) and endothelial cells (ECs) may play a critical role during the vascular dissemination of neoplastic cells and during pathologic angiogenesis in tumors. To identify molecules involved in these processes, the distribution of vascular junctional proteins was first studied by immunofluorescence at sites of heterologous intercellular contact using TC-EC mosaic monolayers grown on 2-dimensional collagen. Several members of the tetraspanin superfamily, including CD9, CD81, and CD151, were found to localize at the TC-EC contact area. The localization of tetraspanins to the TC-EC heterologous contact area was also observed during the active transmigration of TCs across EC monolayers grown onto 3-dimensional collagen matrices. Dynamic studies by time-lapse immunofluorescence confocal microscopy showed an active redistribution of endothelial CD9 to points of melanoma insertion. Anti-CD9 monoclonal antibodies were found to specifically inhibit the transendothelial migration of melanoma cells; the inhibitory effect was likely caused by a strengthening of CD9-mediated heterotypic interactions of TCs to the EC monolayer. These data support a novel mechanism of tetraspanin-mediated regulation of TC transcellular migration independent of TC motility and growth during metastasis and a role for these molecules in the formation of TC-EC mosaic monolayers during tumor angiogenesis.

Expression of functional chemokine receptors CXCR3 and CXCR4 on human melanoma cells.

Chemokines are secreted into the tumor microenvironment by tumor-infiltrating inflammatory cells as well as by tumor cells. Chemokine receptors mediate agonist-dependent cell responses, including migration and activation of several signaling pathways. In the present study we show that several human melanoma cell lines and melanoma cells on macroscopically infiltrated lymph nodes express the chemokine receptors CXCR3 and CXCR4. Using the highly invasive melanoma cell line BLM, we demonstrate that the chemokine Mig, a ligand for CXCR3, activates the small GTPases RhoA and Rac1, induces a reorganization of the actin cytoskeleton, and triggers cell chemotaxis and modulation of integrin VLA-5- and VLA-4-dependent cell adhesion to fibronectin. Furthermore, the chemokine SDF-1alpha, the ligand of CXCR4, triggered modulation of beta(1) integrin-dependent melanoma cell adhesion to fibronectin. Additionally, Mig and SDF-1alpha activated MAPKs p44/42 and p38 on melanoma cells. Expression of functional CXCR3 and CXCR4 receptors on melanoma cells indicates that they might contribute to cell motility during invasion as well as to regulation of cell proliferation and survival.

An effective, rapid and simple method for total RNA extraction from bacteria and yeast.

In this work, we describe a rapid and simple method for total RNA extraction from bacteria and yeast. The method allows for the acquirement of high RNA yields while avoiding the use of phenol or other toxic reagents and is less expensive than other methods previously described. The extracted RNA is suitable for applications such as RT-PCR, Northern blot hybridization and low molecular weight RNA (LMW RNA) electrophoresis.

Analysis of stable low molecular weight (LMW) RNA profiles of hydrocarbon metabolizing bacteria by staircase electrophoresis.

Staircase electrophoresis (SCE) in polyacrilamide gels was used to analyze the stable low-molecular weight (LMW) RNA profiles of several propane and butane oxidizing bacteria belonging to different species and genera. Differences in the number and distribution of the RNA bands in these profiles allowed us to differentiate among them. Congruent results were found between the established classification of these bacteria and results obtained by LMW RNA profiling and moreover, some misclassified strains can be assigned to the correct genus and species using this technique. LMW RNA profiling by staircase electrophoresis, which makes possible the analysis of a large number of strains in a short time, permits rapid identification of hydrocarbon metabolizing species when compared with LMW RNA profiles of reference strains.