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PubMed2006

Ochrobactrum oryzae sp. nov., an endophytic bacterial species isolated from deep-water rice in India.

A non-pigmented, motile, Gram-negative bacterium designated MTCC 4195(T) was isolated from surface-sterilized seeds and plant tissue from deep-water rice (Oryza sativa) cultivated in Suraha Tal Lake in northern India. This isolate was shown to reinfect and colonize deep-water rice endophytically. The highest level of 16S rRNA sequence similarity (96.8 %) to strain MTCC 4195(T) was shown by Ochrobactrum gallinifaecis DSM 15295(T). Strain MTCC 4195(T) utilized gamma-hydroxybutyric acid, adonitol, d-glucosaminic acid and arabinose as carbon sources, but failed to use gentiobiose or citrate. The cell-wall fatty acids of strain MTCC 4195(T) were characterized by the presence of a relatively large proportion of C(18 : 1)omega7c and a relative small proportion of C(16 : 0) in comparison with Ochrobactrum species. DNA-DNA relatedness studies showed less than 52 % binding with the DNAs of type strains of other species of the genus Ochrobactrum. On the basis of phenotypic and genotypic characteristics and the results of 16S rRNA gene sequence analysis, the novel species Ochrobactrum oryzae sp. nov. is proposed, with MTCC 4195(T) (=DSM 17471(T)) as the type strain.

Carbohydrate Metabolism↗
PubMed1987

Phylogenetic diversity and position of the genus Campylobacter.

RNA sequence analysis has been used to examine the phylogenetic position and structure of the genus Campylobacter. A complete 5S rRNA sequence was determined for two strains of Campylobacter jejuni and extensive partial sequences of the 16S rRNA were obtained for several strains of C. jejuni and Wolinella succinogenes. In addition limited partial sequence data were obtained from the 16S rRNAs of isolates of C. coli, C. laridis, C. fetus, C. fecalis, and C. pyloridis. It was found that W. succinogenes is specifically related to, but not included, in the genus Campylobacter as presently constituted. Within the genus significant diversity was noted. C. jejuni, C. coli and C. laridis are very closely related but the other species are distinctly different from one another. C. pyloridis is without question the most divergent of the Campylobacter isolates examined here and is sufficiently distinct to warrant inclusion in a separate genus. In terms of overall position in bacterial phylogeny, the Campylobacter/Wolinella cluster represents a deep branching most probably located within an expanded version of the Division containing the purple photosynthetic bacteria and their relatives. The Campylobacter/Wolinella cluster is not specifically includable in either the alpha, beta or gamma subdivisions of the purple bacteria.

Base Sequence↗
PubMed1999

Varied appearance of cornea of patients with corneal dystrophy associated with R124H mutation in the BIGH3 gene.

PURPOSE: To evaluate the corneal phenotype of patients with corneal dystrophy and the R124H mutation in the BIGH3 gene. METHODS: We examined the corneas of 24 unrelated Japanese individuals who had an R124H mutation in the BIGH3 gene. Large, discrete, granular deposits were present in the anterior stroma of all patients. They were subdivided into two types according to the appearance of the cornea. Histologic examination of the cornea after Masson trichrome and Congo red staining also was performed in specimens from patients who underwent keratoplasty. RESULTS: The first and the most common type of corneal findings on slit-lamp examination (20 of 24 patients) were discrete granular deposits in the anterior stromal layer and star-shaped opacities in the mid-to-deep stroma. The central subepithelial diffuse opacity increased with age. Amyloid deposits were seen mainly in the mid-to-deep stroma in five of the seven such patients evaluated. The second type of corneal appearance (four of 24 patients) was the presence of diffuse subepithelial opacities in the anterior stroma predominantly, rather than granular or linear opacities. Amyloid deposits were present in the anterior cornea of three of these four patients. CONCLUSION: The corneal lesions documented in patients with the R124H mutation were not unique to that disease but could be divided into two types, which likely represent a disease continuum. The lesion location, amount of amyloid deposition, or an interaction between the granular materials and amyloid may influence the varied appearance of the corneal lesion in patients with this disease.

Aged↗
PubMed2000

Day-flying butterflies remain day-flying in a Polynesian, bat-free habitat.

To test the theory that insectivorous bats have selected for diurnality in earless butterflies I compared the nocturnal flight patterns of three species of nymphalid butterflies on the bat-free Pacific island of Moorea with those of three nymphalids in the bat-inhabited habitat of Queensland, Australia. Nocturnal flight, measured as the ratio of deep night (1 h following sunset to 1 h preceding sunrise) to twilight night (1 h before sunset to 30 min after sunrise) activity did not differ significantly between the two locations, nor did the percentage of individuals active and I conclude that living in a bat-released habitat has not produced nocturnal flight in these insects. This result is surprising considering the potential advantages of escaping diurnally active predators and suggests that physiological adaptations (e.g. thermoregulation and/or vision) currently constrain these insects to diurnal flight. Since taxonomic records suggest that gene flow does not exist with bat-exposed conspecifics, I suggest that insufficient time has elapsed since these species migrated to Moorea to have resulted in major phenotypic changes such as diel flight preferences.

Animals↗
PubMed2007

Toxicogenomics applied to predictive and exploratory toxicology for the safety assessment of new chemical entities: a long road with deep potholes.

Toxicology is the perturbation of metabolism by external factors such as xenobiotics, environmental factors or drugs. As such, toxicology covers a broad range of fields from studies of the whole organism responses to minute biochemical events. Mechanistic toxicogenomics is an attempt to harness genomic tools to understand the physiological basis for a toxic event based on an analysis of transcriptional, translational or metabolomic profiles. These studies are complicated by non-toxic adaptive responses in transcript, protein or metabolite expression levels that have to be distinguished from those that are proximally related to the toxic event. Substantial progress has been made on the identification of biomarkers and the establishment of screens derived from such toxicogenomics studies. The ultimate goal, of course, is predictive toxicogenomics, which is an attempt to infer the likelihood of occurrence of a toxic event with exposure to a new agent based upon comparative responses with large databases of gene, protein or metabolite expression data. Gene expression databases are currently limited by the fact that measurable toxic phenotypes generally precede or at best coincide with the earliest observable changes in transcriptional profiles. Unfortunately, predictive protein databases have been limited by technical difficulties. Metabonomics-based databases, which would probably have the highest predictive value, are limited in turn by the inability to perform high dose studies in humans. This chapter will conclude by reviewing those elements of toxicogenomics that apply specifically to the development of anti-infectives and the potential for accurately modelling the toxicity of future drugs.

Animals↗
PubMed1999

Bacteriological studies of blood, tissue fluid, lymph and lymph nodes in patients with acute dermatolymphangioadenitis (DLA) in course of 'filarial' lymphedema.

Filarial lymphedema is complicated by frequent episodes of dermatolymphangioadenitis (DLA). Severe systemic symptoms during attacks of DLA resemble those of septicemia. The question we asked was whether bacterial isolates can be found in the peripheral blood of patients during the episodes of DLA. Out of 100 patients referred to us with 'filarial' lymphedema 14 displayed acute and five subacute symptoms of DLA. All were on admission blood microfilariae negative but had a positive test in the past. Blood bacterial isolates were found in nine cases, four acute (21%) and five subacute (26%). In 10 acute cases blood cultures were found negative. Six blood isolates belonged to Bacilli, four to Cocci and one was Sarcina. To identify the sites of origin of bacterial dissemination, swabs taken from the calf skin biopsy wounds and tissue fluid, lymph and lymph node specimens were cultured. Swabs from the calf skin biopsy wound contained isolates in nine (47%) cases. They were Bacilli in nine, Cocci in three, Acinetobacter and Erwinia in two cases. Tissue fluid was collected from 10 patients and contained Bacilli in four (40%) and Staphylococci in three (30%). Lymph was drained in four patients and contained isolates in all samples (100%). They were Staphylococcus epidermis, xylosus and aureus, Acinetobacter, Bacillus subtilis and Sarcina. Three lymph nodes were biopsied and contained Staphylococcus chromogenes, xylosus, Enterococcus and Bacillus cereus. In six cases the same phenotypically defined species of bacteria were found in blood and limb tissues or fluids. In the 'control' group of patients with lymphedema without acute or subacute changes all blood cultures were negative. Interestingly, swabs from biopsy wound of these patients contained isolates in 80%, tissue fluid in 68%, lymph in 70% and lymph nodes in 58% of cases. In healthy controls, tissue fluid did not contain bacteria, and lymph isolates were found only in 12% of cases. This study demonstrates that patients with acute episodes of DLA reveal bacteremia in a high percentage of cases. Diversity of blood and tissue bacterial isolates in these patients points to a breakdown of the skin immune barrier in lymphedema and subsequently indiscriminate bacterial colonization of deep tissues and spread to an blood circulation.

Adolescent↗
PubMed2000

Human melanoma progression in skin reconstructs : biological significance of bFGF.

Human skin reconstructs are three-dimensional in vitro models consisting of epidermal keratinocytes plated onto fibroblast-contracted collagen gels. Cells in skin reconstructs more closely recapitulate the in situ phenotype than do cells in monolayer culture. Normal melanocytes in skin reconstructs remained singly distributed at the basement membrane which separated the epidermis from the dermis. Cell lines derived from biologically early primary melanomas of the radial growth phase proliferated in the epidermis and the basement membrane was left intact. Growth and migration of the radial growth phase melanoma cells in the dermal reconstruct and tumorigenicity in vivo were only observed when cells were transduced with the basic fibroblast growth factor gene, a major autocrine growth stimulator for melanomas. Primary melanoma cell lines representing the more advanced stage vertical growth phase invaded the dermis in reconstructs and only an irregular basement membrane was formed. Metastatic melanoma cells rapidly proliferated and aggressively invaded deep into the dermis, with each cell line showing typical invasion and growth characteristics. Our results demonstrate that the growth patterns of melanoma cells in skin reconstructs closely correspond to those in situ and that basic fibroblast growth factor is critical for progression.

Basement Membrane↗
PubMed2026

SynFlow: an interactive online genome structural variant viewer.

MOTIVATION: Structural variations (SVs), including inversions, translocations (TRAs), duplications, and large insertions or deletions, are key drivers of genome evolution and phenotypic diversity. With the increasing number of high-quality, chromosome-scale genome assemblies, the ability to detect and interpret SVs has become a crucial aspect of modern genomics. While SV detection has advanced, most visualization methods produce static plots that fall short when researchers, particularly in comparative genomics, need to interactively explore large datasets, zoom into specific genomic regions, or dynamically filter structural events in real time. RESULTS: To address this gap, we introduce SynFlow, a lightweight, web-based interactive application specifically designed for exploring and visualizing SVs identified by SyRI. We demonstrate that SynFlow can reproduce complex static synteny plots published in literature, but transforms them into dynamic, shareable visualizations that support real-time filtering, reordering, and deep exploration of specific SVs, including TRAs. SynFlow is available as a web server and offers multiple entry points: browsing precomputed datasets (e.g. banana and grapevine genomes), uploading user-provided SyRI outputs, or running an integrated workflow to produce and visualize SVs on the fly. AVAILABILITY AND IMPLEMENTATION: https://synflow.southgreen.fr; source code https://github.com/SouthGreenPlatform/synflow; preprocessing Snakemake workflow https://gitlab.cirad.fr/agap/cluster/snakemake/synflow.

Software↗
PubMed1993

The fates of cells in the developing cerebral cortex of normal and methylazoxymethanol acetate-lesioned mice.

We are interested in the mechanisms that generate the mature cerebral cortex. We used bromodeoxyuridine (BrdU) to label cortical cells as they were being born. We followed the fates of specific sets of cortical precursors in normal mice and in mice in which other groups of cortical progenitors had been destroyed with the antimitotic agent methylazoxymethanol acetate (MAM Ac). In normal mice, most cells destined for the cerebral cortex were produced from embryonic day 12 (E12) to E16 in the expected inside-to-outside sequence (deep layers first, superficial layers last). Injection of MAM Ac at E13 killed cells that would normally have contributed to the deep cortical layers. As a consequence, the cortex was thinned by approximately 25% at postnatal day 21 (P21). However, all laminae were present and had normal connections with subcortical structures, although all were proportionately thinner. BrdU injected on E16 labelled a normally sized complement of cells that spanned a larger proportion of the depth of the thinned cortex. Thus, the deep cortical layers comprised many cells that were born several days later than normal. At embryonic ages prior to E12, a transient set of cells is produced in the early telencephalon. After injection with MAM Ac at E10, the cortex appeared histologically and histochemically normal at P21. However, many cells that would normally have contributed to superficial cortex (born on E15) were significantly deeper than normal. These results suggest that, during the early stages of cortical development, the nervous system is sufficiently plastic to compensate to some extent for the destruction of specific precursor cells by altering the fates of neurons born later. They indicate that the embryonic date on which a cortical cell is born does not necessarily determine its eventual phenotype.

Animals↗
PubMed2001

Genetic heterogeneity of Borrelia burgdorferi sensu lato in the southern United States based on restriction fragment length polymorphism and sequence analysis.

Fifty-six strains of Borrelia burgdorferi sensu lato, isolated from ticks and vertebrate animals in Missouri, South Carolina, Georgia, Florida, and Texas, were identified and characterized by PCR-restriction fragment length polymorphism (RFLP) analysis of rrf (5S)-rrl (23S) intergenic spacer amplicons. A total of 241 to 258 bp of intergenic spacers between tandemly duplicated rrf (5S) and rrl (23S) was amplified by PCR. MseI and DraI restriction fragment polymorphisms were used to analyze these strains. PCR-RFLP analysis results indicated that the strains represented at least three genospecies and 10 different restriction patterns. Most of the strains isolated from the tick Ixodes dentatus in Missouri and Georgia belonged to the genospecies Borrelia andersonii. Excluding the I. dentatus strains, most southern strains, isolated from the ticks Ixodes scapularis and Ixodes affinis, the cotton rat (Sigmodon hispidus), and cotton mouse (Peromyscus gossypinus) in Georgia and Florida, belonged to Borrelia burgdorferi sensu stricto. Seven strains, isolated from Ixodes minor, the wood rat (Neotoma floridana), the cotton rat, and the cotton mouse in South Carolina and Florida, belonged to Borrelia bissettii. Two strains, MI-8 from Florida and TXW-1 from Texas, exhibited MseI and DraI restriction patterns different from those of previously reported genospecies. Eight Missouri tick strains (MOK-3a group) had MseI patterns similar to that of B. andersonii reference strain 21038 but had a DraI restriction site in the spacer. Strain SCGT-8a had DraI restriction patterns identical to that of strain 25015 (B. bissettii) but differed from strain 25015 in its MseI restriction pattern. Strain AI-1 had the same DraI pattern as other southern strains in the B. bissettii genospecies but had a distinct MseI profile. The taxonomic status of these atypical strains needs to be further evaluated. To clarify the taxonomic positions of these atypical Borrelia strains, the complete sequences of rrf-rrl intergenic spacers from 20 southeastern and Missouri strains were determined. The evolutionary and phylogenetic relationships of these strains were compared with those of the described genospecies in the B. burgdorferi sensu lato species complex. The 20 strains clustered into five separate lineages on the basis of sequence analysis. MI-8 and TXW-1 appeared to belong to two different undescribed genospecies, although TXW-1 was closely related to Borrelia garinii. The MOK-3a group separated into a distinct deep branch in the B. andersonii lineage. PCR-RFLP analysis results and the results of sequence analyses of the rrf-rrl intergenic spacer confirm that greater genetic heterogeneity exists among B. burgdorferi sensu lato strains isolated from the southern United States than among strains isolated from the northern United States. The B. andersonii genospecies and its MOK-3a subgroup are associated with the I. dentatus-cottontail rabbit enzootic cycle, but I. scapularis was also found to harbor a strain of this genospecies. Strains that appear to be B. bissettii in our study were isolated from I. minor and the cotton mouse, cotton rat, and wood rat. The B. burgdorferi sensu stricto strains from the south are genetically and phenotypically similar to the B31 reference strain.

Animals↗
PubMed2026

A Foundation Model Based CT Biomarker for Non-Invasive Prediction of Response to Neoadjuvant Immunochemotherapy in Non-Small Cell Lung Cancer.

Predicting pathological complete response (pCR) to neoadjuvant immunochemotherapy in non-small cell lung cancer (NSCLC) is clinically important yet remains challenging. Here, we introduce a foundation model-derived computed tomography (CT) imaging biomarker established from a multi-center cohort of 702 patients. Specifically, we developed and validated a non-invasive baseline CT-based model for risk stratification of pathological response. To address scanner and protocol heterogeneity, we first built a 3D Vision Mamba-based CT super-resolution model trained on 2494 cases for image standardization. We then fine-tuned a lung cancer-specific CT foundation model from a pretrained 3D model (VoCo) using 6643 chest CT scans. Finally, we constructed a multi-task Swin Transformer that jointly performs risk stratification and segments tumors to generate the imaging biomarker. Across five centers, the model achieved consistently strong generalization (AUC: 0.75-0.87) for pCR prediction. Genomic analysis revealed that the biomarker was independent of tumor mutational burden but significantly associated with TP53 mutations, suggesting an association with a radiogenomic phenotype related to this alteration. Together, these results demonstrate a generalizable and biologically meaningful foundation model-based biomarker for non-invasive risk stratification of pathological response in NSCLC.

Female↗
PubMed2005

Maturational differences in superficial and deep zone articular chondrocytes.

To examine whether differences in chondrocytes from skeletally immature versus adult individuals are important in cartilage healing, repair, or tissue engineering, superficial zone chondrocytes (SZC, from within 100 microm of the articular surface) and deep zone chondrocytes (DZC, from 30%-45% of the deepest un-mineralized part of articular cartilage) were harvested from immature (1-4 months) and young adult (18-36 months) steers and compared. Cell size, matrix gene expression and protein levels, integrin levels, and chemotactic ability were measured in cells maintained in micromass culture for up to 7 days. Regardless of age, SZC were smaller, had a lower type II to type I collagen gene expression ratio, and higher gene expression of SZ proteins than their DZC counterparts. Regardless of zone, chondrocytes from immature steers had higher levels of Sox 9 and type II collagen gene expression. Over 7 days in culture, the SZC of immature steers had the highest rate of proliferation. Phenotypically, the SZC of immature and adult steers were more stable than their respective DZC. Cell surface alpha5 and alpha2 integrin subunit levels were higher in the SZC of immature than of adult steers, whereas beta1 integrin subunit levels were similar. Both immature and adult SZC were capable of chemotaxis in response to fetal bovine serum or basic fibroblast growth factor. Our data indicate that articular chondrocytes vary in the different zones of cartilage and with the age of the donor. These differences may be important for cartilage growth, tissue engineering, and/or repair.

Age Factors↗
PubMed2006

High Twist expression is involved in infiltrative endometrial cancer and affects patient survival.

Epithelial-mesenchymal transition (EMT) is critical not only for morphogenesis during embryonic development but also the conversion of early-stage tumors into infiltrative phenotypes. The present study examines the expression of Twist, a highly conserved bHLH transcription factor that is known to promote EMT, and evaluated its prognostic significance in endometrial cancers. Tissue specimens from 70 patients with endometrial cancer who underwent primary surgery were immunohistochemically evaluated for Twist expression. A semiquantitative scoring system was developed based on the intensity and extent of cancer cells with Twist expression. Thirty-six patients (51%) exhibited high Twist expression and 34 (49%) had low expression. Most cases exhibited both cytoplasmic and nuclear staining mainly observed in cancer foci and, preferentially, at the margin but, in some cases, the stromal cells located adjacent to cancer foci as well. Among various clinical variables, high Twist expression was significantly associated with deep myometrial invasion (>1/2) (P = .012) and concurrent with decreased E-cadherin expression (P < .001), a hallmark of EMT. In univariate survival analyses, both myometrial invasion and Twist expression influenced overall survival, but Cox multivariate analyses revealed that only Twist was an independent predictor of patient survival (hazard ratio, 5.12; P = .023). Thus, our data implies that high Twist expression is a potential novel prognostic factor for disease survival of endometrial cancer. Furthermore, the present study implicates Twist as a potential therapeutic target for this tumor type.

Adenocarcinoma↗
PubMed2006

A multi-phase mathematical model of quorum sensing in a maturing Pseudomonas aeruginosa biofilm.

It is well known that sessile bacteria have a strong tendency to exist in a biofilm phenotype, whereby bacterial cells aggregate and produce a gel-like extracellular matrix, which, in an infection scenario, offers a significant barrier to attack by conventional antibiotics and the immune system. In this paper we develop a multi-phase model of a maturing Pseudomonas aeruginosa biofilm, allowing for the production and secretion of exopolysaccharide (EPS). The primary quorum-sensing system of P. aeruginosa (namely the lasR system) is believed to be required for full biofilm development, and we thus take the synthesis of EPS to be regulated by the cognate signal molecule, 3-oxo-C12-HSL. We also take EPS and signal production, along with bacterial growth, to be limited by oxygen availability, thus factoring in the nutrient poor conditions deep inside the biofilm. We use simulations to examine the role played by quorum sensing in the biofilm maturation process, and to investigate the effect of anti-quorum sensing and antibiotic treatments on EPS concentration, signal level, bacterial numbers and biofilm growth rate. In addition, we undertake analysis of the associated travelling-wave behaviour.

Biofilms↗
PubMed2006

The neuropeptide tyrosine Y1R is expressed in interneurons and projection neurons in the dorsal horn and area X of the rat spinal cord.

The localization of the neuropeptide tyrosine Y1 receptor was studied with immunohistochemistry in parasagittal and transverse, free-floating sections of the rat lumbar spinal cord. At least seven distinct Y1 receptor-positive populations could tentatively be recognized: Type 1) abundant small, fusiform Y1 receptor-positive neurons in laminae I-II, producing a profuse neuropil; Type 2) Y1 receptor-positive projection neurons in lamina I; Type 3) small Y1 receptor-positive neurons in lamina III, similar to Type 1 neurons, but less densely packed; Type 4) a number of large, multipolar Y1 receptor-positive neurons in the border area between laminae III-IV, with dendrites projecting toward laminae I-II; Type 5) a considerable number of large, multipolar Y1 receptor-positive neurons in laminae V-VI; Type 6) many large Y1 receptor-positive neurons around the central canal (area X); and Type 7) a small number of large Y1 receptor-positive neurons in the medial aspect of the ventral horns (lamina VIII). Many of the neurons present in laminae V-VI and area X produce craniocaudal processes extending for several hundred micrometers. Retrograde tracing using cholera toxin B subunit injected at the 9th thoracic spinal cord level shows that several Type 5 neurons in laminae V-VI, and at least a few Type 2 in lamina I and Type 6 in area X have projections extending to the lower segments of the thoracic spinal cord (and perhaps to supraspinal levels). The present results define distinct subpopulations of neuropeptide tyrosine-sensitive neurons, localized in superficial and deep layers of the dorsal, in the ventral horns and in area X. The lamina II neurons express somatostatin [The neuropeptide Y Y1 receptor is a somatic receptor on dorsal root ganglion neurons and a postsynaptic receptor on somatostatin dorsal horn neurons. Eur J Neurosci 11:2211-2225] and are presumably glutamatergic [Todd AJ, Hughes DI, Polgar E, Nagy GG, Mackie M, Ottersen OP, Maxwell DJ (2003) The expression of vesicular glutamate transporters VGLUT1 and VGLUT2 in neurochemically defined axonal populations in the rat spinal cord with emphasis on the dorsal horn. Eur J Neurosci 17:13-27], that is they are excitatory interneurons under a Y1 receptor-mediated inhibitory influence. The remaining Y1 receptor-positive spinal neurons need to be phenotyped, for example if the large Y1 receptor-positive laminae III-IV neurons (Type 5) are identical to the neurokinin (NK)1R-positive neurons previously shown to receive neuropeptide tyrosine positive dendritic contacts [Polgár E, Shehab SA, Watt C, Todd AJ (1999) GABAergic neurons that contain neuropeptide Y selectively target cells with the NK1 receptor in laminae III and IV of the rat spinal cord. J Neurosci 19:2637-2646]. If so, neuropeptide tyrosine could have an antinociceptive action not only via Y1 receptor-positive interneurons (Type 1) but also projection neurons. The present results show neuropeptide tyrosine-sensitive neuron populations virtually in all parts of the lumbar spinal cord, suggesting a role for neuropeptide tyrosine signaling in many spinal functions, including pain.

Animals↗
PubMed2003

Microvirga subterranea gen. nov., sp. nov., a moderate thermophile from a deep subsurface Australian thermal aquifer.

A strictly aerobic bacterium, strain Fail4T, was isolated from free-flowing geothermal waters of a bore (bore register no. 3768) tapping the Great Artesian Basin of Australia. The non-sporulating, Gram-negative cells of strain Fail4T produced light-pink colonies, were rod-shaped (1 x 1.5-4 microm) and were motile by a single polar flagellum. Strain Fail4T grew optimally at 41 degrees C at a pH of 7.0 and had an absolute requirement for yeast extract. The strain grew on casein hydrolysate, tryptone, gelatin, xylose and acetate in a medium supplemented with 0.06 or 0.006% yeast extract. Weak acid production was detected from glucose and arabinose. Catalase was produced. Nitrite was produced from nitrate. Strain Fail4T was sensitive to antibiotics that inhibit growth of bacteria. The G + C content was 63.5 +/- 0.5 mol%. Strain Fail4T was a member of the class 'Alphaproteobacteria', phylum Proteobacteria, placed almost equidistantly between Methylobacterium species, Chelatococcus asaccharovorans and Bosea thiooxidans (similarity value of 93%) as its nearest phylogenetic relatives. Phylogenetic and phenotypic evidence suggest that strain Fail4T (=ATCC BAA-295T = DSM 14364T) should be placed as the type strain of a species in a newly created genus, for which the name Microvirga subterranea gen. nov., sp. nov. is proposed.

Alphaproteobacteria↗
PubMed2004

A girl with duplication 17p10-p12 associated with a dicentric chromosome.

We report a 7 1/2-year-old girl with an approximately 9.5 Mb duplication of proximal 17p. Her clinical features include moderately severe developmental delay, absence of speech, talipes, congenital dislocation of the hips, premature adrenarche, dysmorphic facial features, deep palmar creases, and signs and symptoms of peripheral neuropathy consistent with Charcot-Marie-Tooth disease type 1A (CMT1A). Chromosome analysis revealed a partially duplicated 17p with two centromeres on the derivative chromosome. Fluorescence in situ hybridization (FISH) analysis demonstrated the tandemly duplicated segment spans 17p10-p12, including the entire Smith-Magenis syndrome (SMS) critical region and a portion of the CMT1A critical region. One breakpoint mapped within the centromere and the second breakpoint mapped within the CMT1A critical region, distal to the PMP22 gene. Microsatellite polymorphism studies showed that the duplicated chromosome is of maternal origin. We compare the clinical features of our patient to those of individuals with partial trisomy of proximal 17p to further delineate the genotype-phenotype correlation associated with segmental duplication of this chromosomal region.

Centromere↗
PubMed1993

Differences in c-fos immunoreactivity due to age and mode of seizure induction.

The aim of this study was to determine whether the regional distribution and time course of immunoreactivity to the c-fos protein varies with maturation and method of seizure induction. The effect of the two chemical convulsants, pentylenetetrazol (PTZ) and flurothyl, on the spatial and temporal pattern of c-fos-like immunoreactivity in immature (postnatal day (P) 10) was compared to that in adult rats. Patterns of c-fos-like immunoreactivity following O2 deprivation were also evaluated at the 2 ages because hypoxia is acutely epileptogenic in immature animals but not adults. C-fos-like immunoreactivity was examined at 2, 4, and 6 h after onset of chemically induced seizures or O2 deprivation at both ages. After PTZ or flurothyl seizures, both ages exhibited similar patterns of IR in amygdala, pyriform cortex, and hypothalamus. Age-dependent regional differences were most prominent in cortex: superficial layers of retrosplenial, cingulate, and neocortex stained in adults; staining was confined to deep layers of neocortex in P10 rats. Intense staining of dentate gyrus and hippocampus occurred with more prolonged seizures, but not brief seizures. PTZ administration resulted in staining at 2 h after seizure onset and was reduced by 4 h in adults, but immunoreactivity was not seen until 4 and 6 h after seizure onset in immature rats, indicating an age effect on the time course of IR. In immature rats, immunoreactivity patterns after hypoxia were markedly different from PTZ or flurothyl: staining was confined to layer VI of neocortex in these animals, and rarely involved limbic structures. These differences in the pattern of c-fos immunoreactivity suggest that the neuronal populations involved in epileptogenesis are influenced by age as well as seizure phenotype and intensity.

Aging↗