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PubMed2002

Detection of Mycobacterium avium subspecies paratuberculosis specific IS900 insertion sequences in bulk-tank milk samples obtained from different regions throughout Switzerland.

BACKGROUND: Since Mycobacterium avium subspecies paratuberculosis (MAP) was isolated from intestinal tissue of a human patient suffering Crohn's disease, a controversial discussion exists whether MAP have a role in the etiology of Crohn's disease or not. Raw milk may be a potential vehicle for the transmission of MAP to human population. In a previous paper, we have demonstrated that MAP are found in raw milk samples obtained from a defined region in Switzerland. The aim of this work is to collect data about the prevalence of MAP specific IS900 insertion sequence in bulk-tank milk samples in different regions of Switzerland. Furthermore, we examined eventual correlation between the presence of MAP and the somatic cell counts, the total colony counts and the presence of Enterobacteriaceae. RESULTS: 273 (19.7%) of the 1384 examined bulk-tank milk samples tested IS900 PCR-positive. The prevalence, however, in the different regions of Switzerland shows significant differences and ranged from 1.7% to 49.2%. Furthermore, there were no statistically significant (p >> 0.05) differences between the somatic cell counts and the total colony counts of PCR-positive and PCR-negative milk samples. Enterobacteriaceae occur as often in IS900 PCR-positive as in PCR-negative milk samples. CONCLUSION: This is the first study, which investigates the prevalence of MAP in bulk-tank milk samples all over Switzerland and infers the herd-level prevalence of MAP infection in dairy herds. The prevalence of 19.7% IS900 PCR-positive bulk-milk samples shows a wide distribution of subclinical MAP-infections in dairy stock in Switzerland. MAP can therefore often be transmitted to humans by raw milk consumption.

Animals↗

PubMed1997

Expression of an extracellular calcium-sensing receptor in human and mouse bone marrow cells.

The cloning of a G protein-coupled, extracellular calcium (Ca2+e)-sensing receptor (CaR) from bovine parathyroid provided direct evidence that Ca2+e-sensing can occur through receptor-mediated activation of G proteins and their associated downstream regulators of cellular function. CaR transcripts and protein are present in various tissues of humans and other mammals that are involved in Ca2+e homeostasis, including parathyroid, kidney, and thyroidal C-cells. The present study was performed to determine whether bone marrow cells express the CaR, since cells within the marrow space could be exposed to substantial changes in Ca2+e related to bone turnover. Using DNA and RNA probes from the human parathyroid CaR cDNA, we identified CaR transcripts of 5.2 and approximately 4.0 kilobases by Northern analysis of poly(A+) RNA from low-density mononuclear cells isolated from whole human bone marrow that are putatively enriched in marrow progenitor cells, including bone cell precursors. In situ hybridization also identified CaR transcripts in the same cell preparations. Reverse transcription-polymerase chain reaction demonstrated > 99% nucleotide identity between transcripts from human bone marrow cells and the corresponding regions of the human CaR cDNA. Antisera specific for several different regions within the extracellular domain of the CaR were reactive with low-density human marrow cells that were either adherent or nonadherent to plastic. About one-third of the adherent, CaR-immunoreactive cells were also positive for alkaline phosphatase, a nonspecific marker of preosteoblasts, osteoblasts, and assorted cells of the colony-forming unit-fibroblast lineage. In addition, a substantial fraction (approximately 60%) of low density murine marrow cells cultured for 1 week at 4.8 mM Ca2+e expressed both CaR immunoreactivity and nonspecific esterase, an enzyme expressed by monocyte/macrophages and fibroblasts. Finally, erythroid precursors and megakaryocytes from murine marrow as well as blood platelets expressed abundant CaR immunoreactivity, while peripheral blood erythrocytes and most polymorphonuclear leukocytes did not. These studies indicate that the CaR is present in low-density mononuclear bone marrow cells as well as in cells of several hematopoietic lineages and could potentially play a role in controlling the function of various cell types within the marrow space.

Animals↗

PubMed2000

Genotypic and phenotypic nevirapine resistance correlates with virological failure during salvage therapy including abacavir and nevirapine.

OBJECTIVE: To study the development of resistance during 8 weeks of salvage therapy with abacavir and nevirapine in combination with other reverse transcriptase inhibitors (RTIs) and protease inhibitors (PIs). METHODS: Samples obtained at baseline and after 8 weeks of therapy from 16 heavily pretreated patients were analysed for genotypic and phenotypic resistance. Genotypic resistance was analysed in cell-associated DNA and plasma HIV-RNA using direct sequencing. Phenotypic resistance was analysed in a PBMC-based assay and in a recombinant virus assay. Plasma viral load was measured at baseline and after 2, 4 and 8 weeks of therapy. RESULTS: The majority of patients was genotypically and phenotypically resistant to lamivudine, abacavir, zidovudine and PIs, whereas 50% of the patients showed resistance to nevirapine at baseline in at least one of the methods used. After 8 weeks of salvage therapy, no additional development of resistance against nucleoside reverse transcriptase inhibitors and PIs could be detected. However, the amount of patients resistant to nevirapine increased to 83%. When the patients were divided into two groups according to baseline resistance against nevirapine, a significantly higher transient reduction in viral load was observed in patients with nevirapine-sensitive HIV at baseline compared to patients with resistant HIV at baseline. CONCLUSION: The transient effect of salvage therapy including abacavir and nevirapine was due to the effect of nevirapine. The lack of effect of abacavir was most likely due to cross-resistance between abacavir and lamivudine/zidovudine used in previous treatment.

Anti-HIV Agents↗

PubMed2003

DARP-36aa selectively promotes survival and morphological development of cultured mesencephalic neurons.

We examined the effects of DARP-36aa on the survival and morphological development of embryonic rat mesencephalic neurons. Treatment of mesencephalic cultures with DARP-36aa, a synthetic peptide corresponding to the N terminal of dopamine-releasing protein (DARP), resulted in a 1.8-fold increase in neuron survival. Morphological analysis revealed that DARP-36aa-treated neurons contained 48% more branching points per neuron compared with controls. DARP-36aa selectively affected mesencephalic cultures; diencephalic and C6 glioma cells were not affected by DARP-36aa treatments. Mesencephalic cultures were also incubated with polyclonal antibodies against DARP-36aa (anti-DARP-36aa) to assess the effect of immunoneutralization of endogenous DARP on these cells. Mesencephalic cultures treated with anti-DARP-36aa contained 43% fewer neurons, and the number of branching points per neuron was decreased by nearly twofold compared with cultures grown with medium alone. Similar to cultures treated with DARP-36aa, immunoneutralization of DARP had no effect on any parameters examined in primary diencephalic and C6 glioma cultures. Mesencephalic cultures maintained in the presence of DARP-36aa had a 3.2-fold increase in the number of tyrosine hydroxylase (TH)-immunoreactive neurons, whereas anti-DARP-36aa incubations decreased TH-immunoreactive neurons by 40% compared with control cultures. Finally, coincubation of the specific tyrosine kinase inhibitor genistein with DARP-36aa resulted in a complete attenuation of DARP-36aa-mediated neuron survival and development in mesencephalic cultures. The findings indicate that DARP-36aa is a novel neurotrophic peptide that selectively promotes the survival and development of mesencephalic neurons.

Amino Acid Sequence↗

PubMed1994

Enhancer sequences of the DF3 gene regulate expression of the herpes simplex virus thymidine kinase gene and confer sensitivity of human breast cancer cells to ganciclovir.

A potentially novel therapeutic strategy for breast cancer treatment involves sensitization of tumor cells to chemotherapy through gene transfer. Clinical application of this approach, however, may be limited by the lack of target cell specificity of currently available gene delivery techniques. Development of vectors with tumor-selective gene expression could overcome this problem. The DF3/MUC1 gene encodes a high molecular weight mucin-like glycoprotein which is overexpressed at the transcriptional level in the majority of human breast cancers. To develop a breast tumor-selective enhancer, we cloned the upstream region of the DF3 gene and have identified a 114-base pair enhancer region that can modulate transcription from heterologous promoters. The present studies demonstrate that the DF3 enhancer sequences can direct selective gene expression in DF3-positive breast carcinoma cells. DF3-positive breast carcinoma cell lines transfected with herpes simplex virus thymidine kinase gene expression cassettes modified by the DF3 enhancer were markedly more sensitive to killing by ganciclovir than were the same cells transfected with the expression cassettes lacking the DF3 enhancer. DF3-negative cell lines transfected with the DF3 enhancer constructs, however, were no more sensitive to ganciclovir than were cells treated with the unmodified expression plasmids. Consistent with an innocent bystander effect, nontransfected human breast carcinoma cells were susceptible in a cell density-dependent manner to ganciclovir-induced cell killing when adjacent to transfected cells. The results also demonstrate that the DF3 enhancer sequences can be effectively incorporated into a retroviral vector to mediate selective gene expression following retroviral infection. These findings suggest that the DF3 promoter/enhancer may be useful for incorporation into vectors designed for gene therapy of breast cancer.

Base Sequence↗

PubMed1995

Hormonal regulation of the cholesterol 7 alpha-hydroxylase gene (CYP7).

The transcriptional regulation of the rat cholesterol 7 alpha-hydroxylase gene (CYP7) by hormones and signal transduction pathways was studied by transient transfection assay of the promoter activity. HepG2 cells were transfected with deletion mutants of the CYP7 upstream region linked to the luciferase reporter gene. The transcription of CYP7/luciferase chimeric genes was higher in confluent than in subconfluent cultures of HepG2 cells. Glucocorticoid receptors, in the presence of dexamethasone, up-regulated the CYP7 gene through two regions located between -3262 and -2803, and between -344 and -222, respectively. Thyroid hormones did not have any effect on the promoter activity. Insulin inhibited the promoter activity through sequences located between -344 and -222, and abolished the stimulation by dexamethasone. Hence, the insulin effect was dominant over that of glucocorticoids. Treatment of transfected HepG2 cells with phorbol 12-myristate 13-acetate (PMA), a known activator of protein kinase C (PKC), resulted in a time-dependent inhibition of the CYP7 promoter activity. The negative phorbol ester-response sequences were mapped between -344 and -222, and between -200 and -161, respectively. The CYP7 promoter activity was induced nearly 5-fold by all-trans-retinoic acid through sequences in the region from -200 to -129. Finally, cyclic AMP and protein kinase A (PKA) stimulated the expression of the CYP7/luciferase gene through multiple sequences in the distal and proximal regions, and both positive and negative response regions were mapped. Our results revealed that the -416 fragment of the rat CYP7 gene confers the activation by glucocorticoids and retinoic acid, and inhibition by insulin, phorbol esters and cAMP. It appears that this proximal promoter may contain a pleiotropic domain that regulates the effects of multiple signals.

Animals↗

PubMed2006

Estrogen receptor alpha promoter polymorphism: stronger estrogen action is coupled with lower sperm count.

BACKGROUND: Although the importance of estrogens in male reproduction is indisputable, little attention has been paid to the role of estrogen receptor (ER) gene mutations in male infertility. Significant correlation between (TA)n repeat allelic variants and lumbar bone mineral density was previously observed in the promoter region of the ERalpha gene, indicating that allelic combinations with higher number of (TA)n repeats are functionally more active genetic variants. METHODS: We studied the (TA)n repeat polymorphism situated in the promoter region of the ERalpha gene in a large group of infertile and normospermic men (n = 347). RESULTS: Although the (TA)n polymorphism failed to show a significant association with male infertility, we found a significant effect of this polymorphism on sperm count. In the group of infertile men, the mean TA repeat number and sperm concentration (P = 0.022) and total sperm number (P = 0.043) were inversely correlated, showing an association between higher TA repeat number (genotype A) and lower sperm production. In line with this observation, normospermic subjects with genotype A had a significantly lower mean sperm concentration with respect to men bearing genotype B with shorter TA alleles (P < 0.05) and a lower total sperm count (P < 0.01). CONCLUSIONS: Our data indicate that specific allelic combinations of the ERalpha, which confer a stronger estrogen effect, may negatively influence human spermatogenesis.

Alleles↗

PubMed1997

Semiparametric regression analysis for recurrent event interval counts.

This paper deals with analysis of data from longitudinal studies where the rate of a recurrent event characterizing morbidity is the primary criterion for treatment evaluation. We consider clinical trials which require patients to visit their clinical center at successive scheduled times as part of follow-up. At each visit, the patient reports the number of events that occurred since the previous visit, or an examination reveals the number of accumulated events, such as skin cancers. The exact occurrence times of the events are unavailable and the actual patient visit times typically vary randomly about the scheduled follow-up times. Each patient's record thus consists of a sequence of clinic visit dates, event counts corresponding to the successive time intervals between clinic visits, and baseline covariates. We propose a semiparametric regression model, extending the fully parametric model of Thall (1988, Biometrics 44, 197-209), to estimate and test for covariate effects on the rate of events over time while also accounting for the possibly time-varying nature of the underlying event rate. Covariate effects enter the model parametrically, while the underlying time-varying event rate is modelled nonparametrically. The method of Severini and Wong (1992, Annals of Statistics 20, 1768-1802) is used to construct asymptotically efficient estimators of the parametric component and to specify their asymptotic distribution. A simulation study and application to a data set are provided.

Biometry↗

PubMed2025

CNV-Finder: Streamlining Copy Number Variation Discovery.

Copy Number Variations (CNVs) play pivotal roles in the etiology of complex diseases and are variable across diverse populations. Understanding the association between CNVs and disease susceptibility is significant in disease genetics research and often requires analysis of large sample sizes. One of the most cost-effective and scalable methods for detecting CNVs is based on normalized signal intensity values, such as Log R Ratio (LRR) and B Allele Frequency (BAF), from Illumina genotyping arrays. In this study, we present CNV-Finder, a novel pipeline integrating deep learning techniques on array data, specifically a Long Short-Term Memory (LSTM) network, to expedite the large-scale identification of CNVs within predefined genomic regions. This facilitates efficient prioritization of samples for time-consuming or costly subsequent analyses such as Multiplex Ligation-dependent Probe Amplification (MLPA), short-read, and long-read whole genome sequencing. We incorporate four genes to establish our methods-Parkin (PRKN), Leucine Rich Repeat And Ig Domain Containing 2 (LINGO2), Microtubule Associated Protein Tau (MAPT), and alpha-Synuclein (SNCA)-which may be relevant to neurological diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), Progressive Supranuclear Palsy (PSP), or related disorders such as essential tremor (ET). By training our models on expert-annotated samples and validating them across diverse cohorts, including those from the Global Parkinson's Genetics Program (GP2) and additional dementia-specific databases, we demonstrate the efficacy of CNV-Finder in accurately detecting deletions and duplications. Our pipeline outputs app-compatible files for visualization within CNV-Finder's interactive web application. This interface enables researchers to review predictions and filter displayed samples by model prediction values, LRR range, and variant count in order to explore or confirm results. Our pipeline integrates this human feedback to enhance model performance and reduce false positive rates. Through a series of comprehensive analyses and validations using visual inspection, MLPA, short-read, and long-read sequencing data, we demonstrate the robustness and adaptability of CNV-Finder in identifying CNVs with regions of varied size, probe density, and noise. Our findings highlight the significance of contextual understanding and human expertise in enhancing the precision of CNV identification, particularly in complex genomic regions like 17q21.31. The CNV-Finder pipeline is a scalable, publicly available resource for the scientific community, available on GitHub (https://github.com/GP2code/CNV-Finder; DOI 10.5281/zenodo.14182563). CNV-Finder not only expedites accurate candidate identification but also significantly reduces the manual workload for researchers, enabling future targeted validation and downstream analyses in regions or phenotypes of interest.

Copy Number Variation (CNV)↗

PubMed2004

Genotype and phenotype patterns of human immunodeficiency virus type 1 resistance to enfuvirtide during long-term treatment.

The human immunodeficiency virus type 1 (HIV-1) fusion inhibitor enfuvirtide has recently been introduced into clinical practice and has exhibited efficient anti-HIV-1 activity in combination with other antiretroviral agents. In the present study, we addressed the effect of long-term treatment with enfuvirtide on the intrahost evolution of HIV-1. The genotype and phenotype patterns and the relative replication capacity (rRC) of enfuvirtide-resistant HIV-1 mutants were evaluated in samples from 11 subjects (7 virological nonresponders and 4 responders) who received the compound for more than 1 year in combination with different regimens. Selection of one or more mutations clustering in a sequence (amino acids 36 to 45) of the gp41 N-terminal heptad repeat was observed in samples from the seven virological nonresponders but not in those from responders. In two subjects who discontinued enfuvirtide, reversion of the resistant genotype was detected within 3 months. Recombinant clones bearing mutated gp41 sequences displayed reduced susceptibilities to enfuvirtide, with the 50% inhibitory concentrations (IC(50)s) ranging from 0.6 to 12.8 microg/ml, whereas the IC(50) for isolates with baseline sequences was 0.013 +/- 0.010 microg/ml. Interestingly, long-term monitoring of resistant variants provided evidence that ongoing adaptation to the drug is paralleled by phenotypic changes. A limited drop in the rRC in the absence of drug was observed for clones from four of the seven nonresponders bearing mutations associated with resistance. Overall, the data indicate that the different genotype patterns associated with a detectable degree of HIV-1 resistance to enfuvirtide generated during long-term treatments are characterized by a substantially low genetic barrier, possible ongoing adaptation with increased degrees of resistance, and limited influence on the viral rRC.

Amino Acid Sequence↗

PubMed2006

Genetic attributes of cerebrospinal fluid-derived HIV-1 env.

HIV-1 often invades the CNS during primary infection, eventually resulting in neurological disorders in up to 50% of untreated patients. The CNS is a distinct viral reservoir, differing from peripheral tissues in immunological surveillance, target cell characteristics and antiretroviral penetration. Neurotropic HIV-1 likely develops distinct genotypic characteristics in response to this unique selective environment. We sought to catalogue the genetic features of CNS-derived HIV-1 by analysing 456 clonal RNA sequences of the C2-V3 env subregion generated from CSF and plasma of 18 chronically infected individuals. Neuropsychological performance of all subjects was evaluated and summarized as a global deficit score. A battery of phylogenetic, statistical and machine learning tools was applied to these data to identify genetic features associated with HIV-1 neurotropism and neurovirulence. Eleven of 18 individuals exhibited significant viral compartmentalization between blood and CSF (P < 0.01, Slatkin-Maddison test). A CSF-specific genetic signature was identified, comprising positions 9, 13 and 19 of the V3 loop. The residue at position 5 of the V3 loop was highly correlated with neurocognitive deficit (P < 0.0025, Fisher's exact test). Antibody-mediated HIV-1 neutralizing activity was significantly reduced in CSF with respect to autologous blood plasma (P < 0.042, Student's t-test). Accordingly, CSF-derived sequences exhibited constrained diversity and contained fewer glycosylated and positively selected sites. Our results suggest that there are several genetic features that distinguish CSF- and plasma-derived HIV-1 populations, probably reflecting altered cellular entry requirements and decreased immune pressure in the CNS. Furthermore, neurological impairment may be influenced by mutations within the viral V3 loop sequence.

Amino Acid Sequence↗

PubMedDate not supplied

Characterization of the regulatory region of Adra2c, the gene encoding the murine alpha2C adrenoceptor subtype.

The 5' flanking sequence (3,227 base pairs, bp) of the mouse Adra2c subtype gene was determined and characterized. The transcription start site was mapped to nucleotide 'A' of two initiator motifs in tandem array, i.e. 1,159 and 1,153 bp upstream from the initiation codon of the open reading frame (ORF) of Adra2c, respectively. One structural feature salient to the 5' regulatory region of Adra2c is present in the sequence 1 kb immediately upstream from the receptor ORF, which is highly enriched in GC content (76%) and CpG island counts (i.e. CpG/GpC, 146:177), and thus rich in Sp1-binding motifs. At the 3' flanking region, the polyadenylation signal was mapped to 481 bp downstream from the termination codon. The transcript defined by sequence data thereby is consistent with a size of 3 kb (brain form) determined by Northern blot analysis. The transgene, Adra2c-NN- lacZ, which links the promoter region of Adra2c to the lacZ reporter gene, was constructed in order to evaluate the functional capacity of the promoter and the putative motifs residing within the defined regulatory region (1.9 kb upstream from the ORF) in directing the reporter gene expression in vitro in transiently transfected cells and in vivo in transgenic (Tg) mice. Permissive cell types to Adra2c-NN include those derived from neural and kidney lineages. Significant Adra2c-NN-driven reporter expression in Tg mice established suggests that alpha2C adrenoceptor expression is permissive under Adra2c-NN in central (cerebral cortex, hippocampus, subthalamus, hypothalamus, superior colliculus, cerebellum, and brain stem) and peripheral (pancreatic beta-islets) tissues.

Amino Acid Motifs↗

PubMed1989

Effectiveness of measures requiring and not requiring prior sequence alignment for estimating the dissimilarity of natural sequences.

Various measures of sequence dissimilarity have been evaluated by how well the additive least squares estimation of edges (branch lengths) of an unrooted evolutionary tree fit the observed pairwise dissimilarity measures and by how consistent the trees are for different data sets derived from the same set of sequences. This evaluation provided sensitive discrimination among dissimilarity measures and among possible trees. Dissimilarity measures not requiring prior sequence alignment did about as well as did the traditional mismatch counts requiring prior sequence alignment. Application of Jukes-Cantor correction to singlet mismatch counts worsened the results. Measures not requiring alignment had the advantage of being applicable to sequences too different to be critically alignable. Two different measures of pairwise dissimilarity not requiring alignment have been used: (1) multiplet distribution distance (MDD), the square of the Euclidean distance between vectors of the fractions of base signlets (or doublets, or triplets, or ...) in the respective sequences, and (2) complements of long words (CLW), the count of bases not occurring in significantly long common words. MDD was applicable to sequences more different than was CLW (noncoding), but the latter often gave better results where both measures were available (coding). MDD results were improved by using longer mutliplets and, if the sequences were coding, by using the larger amino acid and codon alphabets rather than the nucleotide alphabet. The additive least squares method could be used to provide a reasonable consensus of different trees for the same set of species (or related genes).

Animals↗

PubMed2005

Global Pseudomonas aeruginosa biodiversity as reflected in a Belgian river.

The biodiversity of the bacterium Pseudomonas aeruginosa in an aquatic environment (the Woluwe River, Brussels, Belgium) was analysed. Surface water was sampled bimonthly over a 1-year period (2000-2001) at seven sites evenly dispersed over the river. Total bacterial counts were performed and P. aeruginosa strains were isolated on a selective medium. A weighed out sample of 100 randomly chosen presumptive P. aeruginosa isolates was further analysed. A set of data consisting of the nucleotide sequence of the oprL gene, a DNA-based fingerprint (amplified fragment length polymorphism, AFLP), serotype, pyoverdine type and antibiogram (MICs of 21 clinically relevant antibiotics) was assembled. These data were integrated with those previously obtained for 73 P. aeruginosa clinical and environmental isolates collected across the world. The combined results were analysed and compared using biological data analysis software. Our findings indicate a positive relationship between the extent of pollution and the prevalence of P. aeruginosa. Surprisingly, the Woluwe River P. aeruginosa community was almost as diverse as the global P. aeruginosa population. Indeed, the Woluwe River harboured members of nearly all successful clonal complexes. With the exception of one multidrug-resistant (MDR) strain, belonging to a ubiquitous and clinically relevant serotype O11 clone, antibiotic resistance levels were relatively low. These findings illustrate the significance of river water as a reservoir and source of distribution of potentially pathogenic P. aeruginosa strains and could have repercussions on antinosocomial infection strategies.

Anti-Bacterial Agents↗

PubMed1996

Changes in the cellularity of the cortex of human hairs as an indicator of radiation exposure.

Growing hair follicles with their rapid cell proliferation would be expected to be sensitive organs to cytotoxic agents such as radiation. Various abnormalities in the hair and hair follicles have been reported in the past. Changes in the number of cells in the newly forming hair cortex have been shown in the mouse to be one of the more sensitive assays for radiation effects, and this approach could provide a basis for a biological dosimeter. Here we show for the first time using hair cortex cell counts some preliminary data indicating that the number of cell nuclei in a unit of length (140 microns) of the cortex of human hairs from the chest and scalp of patients undergoing fractionated radiotherapy falls significantly (P = 0.005) by 5%-10% 3 days after the first dose in a fractionated sequence of irradiations. The first dose was delivered on a Friday, and no further exposures were delivered until after the hair sample was taken on the 3rd day (Monday). No significant effect of radiation dose could be detected over the available. limited range of doses studied (5-6.5 Gy with one exit dose sample at 2.6 Gy). Also, the width varies from hair to hair. If the width of the hair is taken into account and the cortical nuclei counts are normalised to the width of each hair, the effects seen at day 3 become slightly more significant (P = 0.002), and those at day 5 also become significant (P = 0.012). Samples taken on the 5th day after the first (Friday) exposure were also 2 days after the second exposure and 1 day after the third exposure. However, little expression of damage attributable to the 2nd and 3rd exposures was anticipated since their effects would take some time to be expressed in the cortical region examined, which is some distance from the proliferative region of the follicle.

Cell Count↗

PubMed1995

Phylogenetic identification and in situ detection of individual microbial cells without cultivation.

The frequent discrepancy between direct microscopic counts and numbers of culturable bacteria from environmental samples is just one of several indications that we currently know only a minor part of the diversity of microorganisms in nature. A combination of direct retrieval of rRNA sequences and whole-cell oligonucleotide probing can be used to detect specific rRNA sequences of uncultured bacteria in natural samples and to microscopically identify individual cells. Studies have been performed with microbial assemblages of various complexities ranging from simple two-component bacterial endosymbiotic associations to multispecies enrichments containing magnetotactic bacteria to highly complex marine and soil communities. Phylogenetic analysis of the retrieved rRNA sequence of an uncultured microorganism reveals its closest culturable relatives and may, together with information on the physicochemical conditions of its natural habitat, facilitate more directed cultivation attempts. For the analysis of complex communities such as multispecies biofilms and activated-sludge flocs, a different approach has proven advantageous. Sets of probes specific to different taxonomic levels are applied consecutively beginning with the more general and ending with the more specific (a hierarchical top-to-bottom approach), thereby generating increasingly precise information on the structure of the community. Not only do rRNA-targeted whole-cell hybridizations yield data on cell morphology, specific cell counts, and in situ distributions of defined phylogenetic groups, but also the strength of the hybridization signal reflects the cellular rRNA content of individual cells. From the signal strength conferred by a specific probe, in situ growth rates and activities of individual cells might be estimated for known species. In many ecosystems, low cellular rRNA content and/or limited cell permeability, combined with background fluorescence, hinders in situ identification of autochthonous populations. Approaches to circumvent these problems are discussed in detail.

Bacteria↗

PubMed1995

Microsatellite variation in North American populations of Drosophila melanogaster.

Computer database searching for microsatellites can be particularly effective for organisms like Drosophila melanogaster for which there are extensive sequence data. Here we demonstrate that 17 out of 18 such microsatellites are also highly polymorphic in natural populations of Drosophila, and that this variation is easily scorable with PCR followed by electrophoresis on high-resolution agarose. This form of variation is likely to be of great value in studies of the genomic distribution of polymorphism, population structure, the relation between intraspecific polymorphism and interspecific divergence and the mutation rate and pattern of mutations of microsatellites. In this preliminary survey of 15 lines, we find that the variance in repeat count is most strongly correlated with the maximum count, that perfect repeats are significantly more variable than imperfect repeats and that repeats which are split by an imperfection have unexpectedly low variance given the size of the perfectly repeated portion.

Alleles↗

PubMed2004

Genetic deletion of mouse platelet glycoprotein Ibbeta produces a Bernard-Soulier phenotype with increased alpha-granule size.

Here we report the characterization of a mouse model of the Bernard-Soulier syndrome generated by a targeted disruption of the gene encoding the glycoprotein (GP) Ibbeta subunit of the GP Ib-IX complex. Similar to a Bernard-Soulier model generated by disruption of the mouse GP Ibalpha subunit, GP Ibbeta(Null) mice display macrothrombocytopenia and a severe bleeding phenotype. When examined by transmission electron microscopy, the large platelets produced by a GP Ibbeta(Null) genotype revealed alpha-granules with increased size as compared with the alpha-granules from control mouse platelets. Data are presented linking the overexpression of a septin protein, SEPT5, to the presence of larger alpha-granules in the GP Ibbeta(Null) platelet. The SEPT5 gene resides approximately 250 nucleotides 5' to the GP Ibbeta gene and has been associated with modulating exocytosis from neurons and platelets as part of a presynaptic protein complex. Fusion mRNA transcripts present in megakaryocytes can contain both the SEPT5 and GP Ibbeta coding sequences as a result in an imperfect polyadenylation signal within the 3' end of both the human and mouse SEPT5 genes. We observed a 2- to 3-fold increase in SEPT5 protein levels in platelets from GP Ibbeta(Null) mice. These results implicate SEPT5 levels in the maintenance of normal alpha-granule size and may explain the variant granules associated with human GP Ibbeta mutations and the Bernard-Soulier syndrome.

Animals↗