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At least 829 records · Page 46Linked to original sources
PubMed2000

Mutational spectrum analysis of RNase H(35) deficient Saccharomyces cerevisiae using fluorescence-based directed termination PCR.

Mutational spectrum analysis has become an informative genetic tool to understand those protein functions involved in mutation avoidance pathways since specific types of mutations are often associated with particular protein defects involved in DNA replication and repair. In this study, we describe a novel, fluorescence-based procedure for direct determination of deletions and insertions with 100% accuracy. We performed two complementary directed termination PCR with near infrared dye-labeled primers, followed by visualization of termination fragments using an automated Li-cor DNA sequencer. This method is used for rapid analysis of mutational spectra generated in nuclease-defective strains of Saccharomyces cerevisiae to elucidate the role of RNase H(35) in RNA primer removal during DNA replication and in mutation avoidance. Strains deficient in RNH35 displayed a distinct spontaneous mutation spectrum of deletions characterized by a unique 4 bp deletion in a lys2-Bgl allele. This was in sharp contrast to strains deficient in rad27 that displayed duplication mutations. Further analysis of mutations in a rnh35/rad27 double mutant revealed a mixed spectrum. These results indicate that RNase H(35) may participate in a redundant pathway in Okazaki fragment processing and that mutational spectra caused by protein deficiencies may be more intermediate-specific than pathway-specific.

DNA Mutational Analysis↗
PubMed2004

siRNA relieves chronic neuropathic pain.

Double stranded, short interfering RNAs (siRNA) of 21-22 nt length initiate a sequence-specific, post-trancriptional gene silencing in animals and plants known as RNA interference (RNAi). Here we show that RNAi can block a pathophysiological pain response and provide relief from neuropathic pain in a rat disease model by down regulating an endogenous, neuronally expressed gene. Rats, intrathecally infused with a 21 nt siRNA perfectly complementary to the pain-related cation-channel P2X3, showed diminished pain responses compared to missense (MS) siRNA-treated and untreated controls in models of both agonist-evoked pain and chronic neuropathic pain. This form of delivery caused no adverse effects in any of the animals receiving P2X3 siRNA, MS siRNA or vehicle. Molecular analysis of tissues revealed that P2X3 mRNA expressed in dorsal root ganglia, and P2X3 protein translocated into the dorsal horn of the spinal cord, were significantly diminished. These observations open a path toward use of siRNA as a genetic tool for drug target validation in the mammalian central nervous system, as well as for proof of concept studies and as therapeutic agents in man.

Animals↗
PubMed2002

Yeast protein kinase C.

The mammalian protein kinase C (PKC) superfamily plays regulatory roles in many different cellular processes. However, due to the many members that exist in cells, it is very complicated to present experimental evidence of the particular function of each member. In contrast, yeasts have only one or two PKC members and genetic tools have unveiled their role as main regulators of cell integrity. In this review, we will discuss the function of yeast protein kinase C homologues, their mechanism of activation and the signalling pathways that they regulate in two model yeasts, Saccharomyces cerevisiae and Schizosaccharomyces pombe.

Fungal Proteins↗
PubMed2005

Application of RNA interference to root-knot nematode genes encoding esophageal gland proteins.

Plant parasitic nematodes have been, so far, refractory to transformation or mutagenesis. The functional analysis of nematode genes relies on the development of reverse genetic tools adapted to these obligate parasites. Here, we describe the application of RNA interference (RNAi) to the root-knot nematode Meloidogyne incognita for the knock-down of two genes expressed in the subventral esophageal glands of the nematode and potentially involved in parasitism, the calreticulin (Mi-crt) and the polygalacturonase (Mi-pg-1) genes. Incubation in 1% resorcinol for 4 h induced double-stranded RNA uptake through the alimentary track of the nematodes and led to up to 92% depletion of Mi-crt transcripts. Timecourse analysis of the silencing showed different temporal patterns for Mi-crt and Mi-pg-1. The silencing of Mi-crt was optimal 20 h after soaking, whereas the silencing of Mi-pg-1 was optimal 44 h after soaking. For the two genes, the silencing effect was highly time-limited, since no transcript depletion was detectable 68 h after soaking.

Animals↗
PubMed2001

Pediatric inflammatory bowel disease: clinical and therapeutic aspects.

Epidemiologic data suggest that the incidences of pediatric ulcerative colitis and Crohn disease continue to evolve with geographic variations. One study suggests that children with autism have a unique inflammatory bowel disorder that is associated with gastrointestinal symptoms. The appropriate use of new diagnostic tests and novel treatments for inflammatory bowel disease (IBD) needs to be clarified in the pediatric population. Because of concerns regarding sensitivity and specificity, serologic markers measuring anti-Saccharomyces cerevisiae antibodies and perinuclear antineutrophil cytoplasmic antibodies cannot yet replace conventional diagnostic testing for screening or diagnosis of pediatric IBD. Large, prospective, pediatric population-based studies still need to be performed to ascertain their use as a noninvasive screening tool. Genetic studies using thiopurine methyl transferase and measurement of 6-mercaptopurine metabolites appear to be valuable for management of pediatric patients with IBD, in assisting clinicians in optimizing therapeutic response to 6-mercaptopurine, and in identifying individuals at increased risk for drug-induced toxicity. Newer immunomodulatory agents also are being explored in pediatric IBD. Open pilot trials of infliximab (Remicade; Centocor, Malvern, PA) for the treatment of children with Crohn disease that does not respond to conventional management have demonstrated short-term efficacy and safety. Trials of tacrolimus for treatment of fulminant colitis in children have been disappointing.

Journal Article↗
PubMed2002

Transgenic over-expression of galanin in injured primary sensory neurons.

The 29 amino acid neuropeptide galanin is normally expressed in < 5% of sensory neurons in the adult dorsal root ganglia. After nerve transection (axotomy), the galanin content of the dorsal root ganglia rises 120-fold and the peptide is then expressed in > 50% of neurons. Published data suggest that galanin plays a role in the modulation of pain processing and may be involved in the regeneration of sensory neurons. Here we describe the initial characterisation of a new line of transgenic mice that selectively over-express galanin in the dorsal root ganglia in an inducible manner following axotomy of the sciatic nerve, but not in the uninjured state. Results of acute thermal or mechanosensory pain tests are normal in intact transgenic animals when compared to wild-type controls. The generation of these novel transgenic animals will be most useful as genetic tools to further elucidate the role played by galanin in the adaptive response of the peripheral nervous system to injury.

Animals↗
PubMed2004

Rodent models for treatment of spinal cord injury: research trends and progress toward useful repair.

PURPOSE OF REVIEW: In this review, we have documented some current research trends in rodent models of spinal cord injury. We have also catalogued the treatments used in studies published between October 2002 and November 2003, with special attention given to studies in which treatments were delayed for at least 4 days after injury. RECENT FINDINGS: Most spinal cord injury studies are performed with one of three general injury models: transection, compression, or contusion. Although most treatments are begun immediately after injury, a growing number of studies have used delayed interventions. Mice and the genetic tools they offer are gaining in popularity. Some researchers are setting their sights beyond locomotion, to issues more pressing for people with spinal cord injury (especially bladder function and pain). SUMMARY: Delayed treatment protocols may extend the window of opportunity for treatment of spinal cord injury, whereas continued progress in the prevention of secondary cell death will reduce the severity of new cases. The use of mice will hopefully accelerate progress towards useful regeneration in humans. Researchers must improve cross-study comparability to allow balanced decisions about potentially useful treatments.

Adult↗
PubMed2003

PTEN as a molecular marker to distinguish metastatic from primary synchronous endometrioid carcinomas of the ovary and uterus.

The distinction between two primary carcinomas on the one hand and a metastatic disease on the other hand in patients suffering from synchronous endometrioid carcinomas of the uterus and ovary is difficult. Exclusive histopathologic analysis appears to be insufficient and sometimes misleading. The tumor suppressor PTEN was found to be important in early neoplastic transformation in endometrioid carcinomas of the uterus. In this study, we screened synchronous endometrioid carcinomas of the uterus and ovary of 10 patients for loss of heterozygosity using seven different microsatellite markers at 10q23.3 and for mutations in the entire coding region of PTEN. Point mutations or microdeletions/insertions were found in six patients. Allelic loss at 10q23.3 was detected in eight patients. Based on conventional histology, a metastatic disease was diagnosed in seven patients and a concomitant uterine and ovarian carcinoma in three patients. After molecular analysis, the histopathologic diagnosis of three patients had to be revised. Histopathology represents the standard method to process tumor specimens from these patients. Nevertheless, mutation screen for PTEN and LOH analysis at 10q23.3 provide helpful genetic tools to establish a correct final diagnosis, which is important in view of prognosis and therapeutic implications.

Aged↗
PubMed1999

Novel findings about 24,25-dihydroxyvitamin D: an active metabolite?

The physiological role of 24,25-dihydroxyvitamin D remains controversial. Recent results suggest that 24,25-dihydroxyvitamin D is essential for fracture healing, and binding sites for 24,25-dihydroxyvitamin D have been identified in fracture callus tissue. Mice deficient in the 25-hydroxyvitamin D-24-hydroxylase enzyme provide novel genetic tools in which to study the role of 24,25-dihydroxyvitamin D in bone development and fracture repair.

24,25-Dihydroxyvitamin D 3↗
PubMed2005

Leptospirosis.

PURPOSE OF REVIEW: Leptospirosis, a spirochaetal zoonotic disease, has been recognized as an important emerging infectious disease in the last 10 years. This review addresses the issues in the epidemiology, diagnosis and clinical management which confront public health responses, and highlights the progress made towards understanding the Leptospira genome, biology and pathogenesis. RECENT FINDINGS: Leptospirosis has spread from its traditional rural base to become the cause of epidemics in poor urban slum communities in developing countries. Mortality from severe disease forms, Weil's disease and severe pulmonary haemorrhage syndrome, is high (>10% and >50%, respectively) even when optimal treatment is provided. Moreover, the overall disease burden is underestimated, since leptospirosis is a significant cause of undifferentiated fever and frequently not recognized. Barriers to addressing this problem have been the lack of an adequate diagnostic test and effective control measures. China and Brazil, countries in which leptospirosis is a major health problem, have completed the sequence of the Leptospira interrogans genome. Together with new genetic tools and proteomics, new insights have been made into the biology of Leptospira and the mechanisms used to adapt to host and external environments. Surface-exposed proteins and putative virulence determinants have been identified which may serve as sub-unit vaccine candidates. SUMMARY: Major progress has been made in the basic research of leptospirosis. Future challenges will be to translate these advances into public health measures for developing countries. Yet the most effective responses may be interventions that directly address the determinants of poverty, such as poor sanitation, which are often responsible for transmission.

Genome, Bacterial↗
PubMed2000

Salmonella interactions with host cells: in vitro to in vivo.

Salmonellosis (diseases caused by Salmonella species) have several clinical manifestations, ranging from gastroenteritis (food poisoning) to typhoid (enteric) fever and bacteraemia. Salmonella species (especially Salmonella typhimurium) also represent organisms that can be readily used to investigate the complex interplay that occurs between a pathogen and its host, both in vitro and in vivo. The ease with which S. typhimurium can be cultivated and genetically manipulated, in combination with the availability of tissue culture models and animal models, has made S. typhimurium a desirable organism for such studies. In this review, we focus on Salmonella interactions with its host cells, both in tissue culture (in vitro) and in relevant animal models (in vivo), and compare results obtained using these different models. The recent advent of sophisticated imaging and molecular genetic tools has facilitated studying the events that occur in disease, thereby confirming tissue culture results, yet identifying new questions that need to be addressed in relevant disease settings.

Animals↗
PubMed2005

Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications.

Marine macroalgae, especially the Rhodophyta, can be notoriously difficult to identify owing to their relatively simple morphology and anatomy, convergence, rampant phenotypic plasticity, and alternation of heteromorphic generations. It is thus not surprising that algal systematists have come to rely heavily on genetic tools for molecular assisted alpha taxonomy. Unfortunately the number of suitable marker systems in the three available genomes is enormous and, although most workers have settled on one of three or four models, the lack of an accepted standard hinders the comparison of results between laboratories. The advantages of a standard system are obvious for practical purposes of species discovery and identification; as well, compliance with a universal marker, such as cox1 being developed under the label 'DNA barcode', would allow algal systematists to benefit from the rapidly emerging technologies. Novel primers were developed for red algae to PCR amplify and sequence the 5' cox1 'barcode' region and were used to assess three known species-complex questions: (i) Mazzaella species in the Northeast Pacific; (ii) species of the genera Dilsea and Neodilsea in the Northeast Pacific; and (iii) Asteromenia peltata from three oceans. These models were selected because they have all caused confusion with regards to species number, distribution, and identification in the field, and because they have all been studied with molecular tools. In all cases the DNA barcode resolved accurately and unequivocally species identities and, with the enhanced sampling here, turned up a variety of novel observations in need of further taxonomic investigation.

Base Sequence↗
PubMed2004

Downregulation of the motA gene delays the escape of the obligate predator Bdellovibrio bacteriovorus 109J from bdelloplasts of bacterial prey cells.

Bdellovibrio bacteriovorus is a Gram-negative bacterium that preys on other Gram-negative bacteria. The lifecycle of B. bacteriovorus alternates between an extracellular flagellated and highly motile non-replicative attack-phase cell and a periplasmic non-flagellated growth-phase cell. The prey bacterium containing periplasmic bdellovibrios becomes spherical but osmotically stable, forming a structure known as the bdelloplast. After completing the growth phase, newly formed bdellovibrios regain their flagellum and escape the bdelloplast into the environment, where they encounter more prey bacteria. The obligate predatory nature of B. bacteriovorus imposes a major difficulty to introducing mutations in genes directly involved in predation, since these mutants could be non-viable. This work reports the cloning of the B. bacteriovorus 109J motAB operon, encoding proteins from the flagellar motor complex, and a genetic approach based on the expression of a motA antisense RNA fragment to downregulate motility. Periplasmic bdellovibrios carrying the plasmid expressing antisense RNA displayed a marked delay in escaping from bdelloplasts, while the released attack-phase cells showed altered motility. These observations suggest that a functionally intact flagellar motor is required for the predatory lifecycle of B. bacteriovorus. Also, the use of antisense RNA expression may be a useful genetic tool to study the Bdellovibrio developmental cycle.

Bacterial Proteins↗
PubMed2006

To have neighbour's fare: extending the molecular toolbox for Streptococcus pneumoniae.

In past years, several useful genetic tools have been developed to study the molecular biology of Streptococcus pneumoniae. In order to extend the existing spectrum of tools, advantage was taken of the toolbox originally developed for the closely related bacterium Lactococcus lactis, which was adapted for the manipulation of S. pneumoniae. The modified tools are as follows. (i) An improved nisin-inducible (over)expression system (NICE). The nisRK genes, encoding a two-component system essential for transcriptional activation in response to nisin, were integrated into the bgaA locus of S. pneumoniae D39. In this strain, D39nisRK, addition of nisin resulted in the overexpression of several genes placed under the control of the nisin-inducible promoter, while no detectable expression was observed in the absence of nisin. (ii) A lacZ reporter system. Using strain D39nisRK, which lacks endogenous beta-galactosidase activity, the usefulness of the lacZ reporter vector pORI13 for the generation of chromosomal transcriptional fusions was demonstrated. In addition, the repA gene, necessary for the replication of pORI13, was introduced into the bgaA locus, thereby generating a background for plasmid-based promoter expression studies. (iii) A simplified chemically defined medium, which supports growth of all sequenced S. pneumoniae strains to a level comparable to that in complex medium. (iv) A system for the introduction of unmarked deletions and mutations into the chromosome, which is independent of the genotype of the target strain. Most of these systems were successfully applied in strains R6 and TIGR4 as well. In addition, the tools offer several improvements and advantages compared to existing ones. Thus, the molecular toolbox for S. pneumoniae has been successfully extended.

Biotechnology↗
PubMed2025

Tunable, proteolytic dosage control of CRISPR-Cas systems enables precise gene therapy for dosage sensitive disorders.

The ability to modulate gene expression through modular and universal genetic tools like CRISPR-Cas has greatly advanced gene therapy for therapeutics and basic science. Yet, the inherent stochasticity of delivery methods cause variation in target gene expression at the single-cell level, limiting their applicability in systems that require more precise expression. Thus, we implement a modular incoherent feedforward loop based on proteolytic cleavage of Cas to reduce gene expression variability against the variability of vector delivery. We target a genome-integrated marker and demonstrate dosage control of gene activation and repression, post-delivery tuning, and RNA-based compatibility of the system. To illustrate therapeutic relevance, we target the gene RAI1, the haploinsufficiency and triplosensitivity of which cause two autism-related syndromes. We demonstrate dosage-controlled gene activation for both human and mouse Rai1 via viral delivery to patient-derived cell lines and mouse cortical neurons. Overall, we established a robust dosage control circuit for uniform gene expression, beneficial for basic and translational research.

Journal Article↗
PubMed2025

Development of a chemical probe to enable characterization of the casein kinase 1&#x3b3; subfamily.

The casein kinase 1&#x3b3; (CK1&#x3b3;) subfamily, while severely understudied, is implicated in diverse disease-relevant pathways, including WNT signaling and human cytomegalovirus (HCMV) replication. While genetic tools exist to study CK1&#x3b3;, the selective inhibition of CK1&#x3b3; through pharmacological means remains underexplored. Chemical probes, or potent and selective inhibitors, remain one of the most powerful pharmacological tools for uncovering protein biology. Herein, we developed several novel assays for assessing target engagement with the CK1&#x3b3; subfamily in cells. Enabled by these assays, we conducted a comprehensive structure-activity relationship (SAR) campaign to develop the first chemical probe, SGC-CK1&#x3b3;-1, for the CK1&#x3b3; subfamily. SGC-CK1&#x3b3;-1, which was developed alongside a structurally related negative control compound, potently and selectively inhibited the CK1&#x3b3; kinases in living cells, plus inhibited both WNT signaling and human cytomegalovirus replication.

Journal Article↗
PubMed1983

Genetic and voltage-clamp analysis of a Drosophila potassium channel.

These genetic and voltage-clamp studies have produced evidence that strongly supports the hypothesis that the Shaker locus codes for at least one molecular component of the IA channel. Mutations at the Shaker locus have effects that are specific to IA, and thus a general membrane component is not produced by this locus. Regarding the function of the Shaker product itself, there is evidence that it is at least involved in the inactivation and recovery process of the channel. The evidence so far is also consistent with there being a single Shaker product per channel. Regarding its genetic and developmental properties, IA is apparently completely independent of the other major voltage-activated K+ channel in the membrane, IK. However, only after molecular information becomes available will it become clear whether or not these experiments have revealed clues about the molecular nature of these channels. Ultimately, voltage-clamp experiments, even combined with resourceful genetic tools, can only reveal circumstantial information about the molecular structure of channels. It is hoped, however, that these studies have stimulated interest in the Shaker locus and that the way has been well prepared for molecular studies of the IA channel. The actual molecular characterization of the Shaker locus is already under way (cf. Jan et al., this volume; M. Tanouye , pers. comm .).

Animals↗