Isolation and characterization of S genome specific sequences from Aegilops sect. sitopsis species

Genome ◽  
2003 ◽  
Vol 46 (3) ◽  
pp. 478-489 ◽  
Author(s):  
D Giorgi ◽  
R D'Ovidio ◽  
O A Tanzarella ◽  
C Ceoloni ◽  
E Porceddu
Keyword(s):  
Genomic Library ◽  
Low Frequency ◽  
Repeated Sequence ◽  
Aegilops Speltoides ◽  
Sequencing Analysis ◽  
Wheat Evolution ◽  
Isolation And Characterization ◽  
Close Relationship ◽  
Partial Genomic Library ◽  
Specific Sequences

Three S genome specific sequences were isolated from Aegilops sect. sitopsis species using different experimental approaches. Two clones, UTV86 and UTV39, were isolated from a partial genomic library obtained from DNA of Aegilops sharonensis, whereas a third clone, UTV5, was isolated from Aegilops speltoides. The three clones were characterized by sequencing, analysis of methylation, and sequence organization and abundance in some Aegilops and Triticum species. The clones UTV39 and UTV5 belong to the same family of tandem repeated sequences and showed high homology with a sequence already present in nucleotide databases. The UTV86 clone from Ae. sharonensis corresponded to an interspersed low frequency repeated sequence and did not show any significant homology with reported sequences. Southern hybridization experiments, using the cloned sequences as probes, detected polymorphism in the restriction patterns of all the five Aegilops species in section sitopsis. Aegilops speltoides showed the most divergent hybridization pattern. A close relationship was detected between the S genome of Ae. speltoides and the G genome of the wild Triticum timopheevii. In situ hybridization revealed a telomeric and (or) subtelomeric location of the sequences UTV39 and UTV5.Key words: Aegilops, genome-specific sequences, sitopsis, wheat evolution.

Isolation and characterization of a developmentally regulated homeobox sequence in the Mexican axolotl Ambystoma mexicanum

1990 ◽  
Vol 68 (3) ◽  
pp. 622-629 ◽  
Author(s):  
Mary Whiteley ◽  
John B. Armstrong
Keyword(s):  
Genomic Dna ◽  
Genomic Library ◽  
Ambystoma Mexicanum ◽  
Tail Bud ◽  
Developmentally Regulated ◽  
Mexican Axolotl ◽  
Isolation And Characterization ◽  
Partial Genomic Library ◽  
Homeobox Sequence

A homeobox-containing genomic DNA fragment was isolated from the Mexican axolotl. This clone was obtained from a partial genomic library enriched for sequences that cross-hybridized with the Drosophila Antp homeobox under low stringency hybridization conditions. DNA sequence analysis revealed that this sequence (Ahox1) was 66% homologous to the Antp homeobox sequence and was most closely related to the mouse Hox-1.6 (84% identity) and Drosophila lab (79% identity) homeobox sequences. Several cross-hybridizing fragments to Ahox1 were detected in both mouse and axolotl genomic DNA. This sequence was also shown to be conserved in other Ambystoma species. Northern blot analysis revealed that genes containing this sequence are developmentally regulated. Transcripts hybridizing to the Ahox1 homeobox probe were detected during the neurula and tail bud stages of development.Key words: axolotl, homeobox, mouse, Drosophila, gene expression.

scholarly journals Structural characterization of the DRF1 gene of Aegilops speltoides and comparison of its sequence with those of B and other Triticeae genomes

Euphytica ◽  
2020 ◽  
Vol 216 (10) ◽  
Author(s):  
Karthikeyan Thiyagarajan ◽  
Arianna Latini ◽  
Cristina Cantale ◽  
Patrizia Galeffi
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analyses ◽  
Aegilops Speltoides ◽  
Species Variation ◽  
Regulation Mechanism ◽  
Isolation And Characterization ◽  
Close Relationship ◽  
Wheat Gene ◽  
Processed Pseudogene

Abstract The genus Aegilops L. has been intensively investigated due to its close relationship with wheat (Triticum L.) as contributor of B and D subgenomes. Because of their vast genetic diversity, Aegilops species represent a rich source of alleles of agronomic interest, which could be used to widen the wheat gene pool and improve tolerance to diseases, pests, drought, cold and other environmental stresses. We report the isolation and characterization of the Dehydration Responsive Factor 1 (DRF1) gene in three accessions of Ae. speltoides coming from different regions of the Fertile Crescent. The DRF1 gene belongs to the DREB gene family and encodes transcription factors which play a key role in plant response to water stress. As in other cereals, the DRF1 gene in Aegilops speltoides consists of four exons and three introns and undergoes alternative splicing. A processed pseudogene was also identified and compared with the sequence of an actual mRNA transcript, breaking new ground in the understanding of the complex regulation mechanism of this gene. The genetic diversity was evaluated by comparison of inter- and intra-species variation among some Aegilops and Triticeae, by considering both the whole gene and exon 4 sequences. The phylogenetic analyses were able to cluster the sequences in well-supported clades attributable to the genomes analysed. The overall results suggest that there is a high similarity between the B and S genome copies of the DRF1 gene but also features indicating that the two genomes have evolved independently.

SPK1 is an essential S-phase-specific gene of Saccharomyces cerevisiae that encodes a nuclear serine/threonine/tyrosine kinase

1993 ◽  
Vol 13 (9) ◽  
pp. 5829-5842
Author(s):  
P Zheng ◽  
D S Fay ◽  
J Burton ◽  
H Xiao ◽  
J L Pinkham ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Cycle ◽  
Dna Damage ◽  
Dna Synthesis ◽  
Genomic Library ◽  
Excision Repair ◽  
Low Frequency ◽  
S Phase ◽  
Upstream Region ◽  
Specific Gene

SPK1 was originally discovered in an immunoscreen for tyrosine-protein kinases in Saccharomyces cerevisiae. We have used biochemical and genetic techniques to investigate the function of this gene and its encoded protein. Hybridization of an SPK1 probe to an ordered genomic library showed that SPK1 is adjacent to PEP4 (chromosome XVI L). Sporulation of spk1/+ heterozygotes gave rise to spk1 spores that grew into microcolonies but could not be further propagated. These colonies were greatly enriched for budded cells, especially those with large buds. Similarly, eviction of CEN plasmids bearing SPK1 from cells with a chromosomal SPK1 disruption yielded viable cells with only low frequency. Spk1 protein was identified by immunoprecipitation and immunoblotting. It was associated with protein-Ser, Thr, and Tyr kinase activity in immune complex kinase assays. Spk1 was localized to the nucleus by immunofluorescence. The nucleotide sequence of the SPK1 5' noncoding region revealed that SPK1 contains two MluI cell cycle box elements. These elements confer S-phase-specific transcription to many genes involved in DNA synthesis. Northern (RNA) blotting of synchronized cells verified that the SPK1 transcript is coregulated with other MluI box-regulated genes. The SPK1 upstream region also includes a domain highly homologous to sequences involved in induction of RAD2 and other excision repair genes by agents that induce DNA damage. spk1 strains were hypersensitive to UV irradiation. Taken together, these findings indicate that SPK1 is a dual-specificity (Ser/Thr and Tyr) protein kinase that is essential for viability. The cell cycle-dependent transcription, presence of DNA damage-related sequences, requirement for UV resistance, and nuclear localization of Spk1 all link this gene to a crucial S-phase-specific role, probably as a positive regulator of DNA synthesis.

scholarly journals Isolation and characterization of a repeated sequence (RPS1) of Candida albicans

1992 ◽  
Vol 138 (9) ◽  
pp. 1893-1900 ◽  
Author(s):  
S.-I. Iwaguchi ◽  
M. Homma ◽  
H. Chibana ◽  
K. Tanaka
Keyword(s):  
Candida Albicans ◽  
Repeated Sequence ◽  
Isolation And Characterization

scholarly journals Isolation and characterization of PEP3, a gene required for vacuolar biogenesis in Saccharomyces cerevisiae

1991 ◽  
Vol 11 (12) ◽  
pp. 5801-5812
Author(s):  
R A Preston ◽  
M F Manolson ◽  
K Becherer ◽  
E Weidenhammer ◽  
D Kirkpatrick ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Gene Product ◽  
Zinc Finger ◽  
Genomic Library ◽  
Sequence Similarity ◽  
Carboxypeptidase Y ◽  
Lag Phase ◽  
Significant Similarity ◽  
Reading Frame ◽  
Isolation And Characterization

The Saccharomyces cerevisiae PEP3 gene was cloned from a wild-type genomic library by complementation of the carboxypeptidase Y deficiency in a pep3-12 strain. Subclone complementation results localized the PEP3 gene to a 3.8-kb DNA fragment. The DNA sequence of the fragment was determined; a 2,754-bp open reading frame predicts that the PEP3 gene product is a hydrophilic, 107-kDa protein that has no significant similarity to any known protein. The PEP3 predicted protein has a zinc finger (CX2CX13CX2C) near its C terminus that has spacing and slight sequence similarity to the adenovirus E1a zinc finger. A radiolabeled PEP3 DNA probe hybridized to an RNA transcript of 3.1 kb in extracts of log-phase and diauxic lag-phase cells. Cells bearing pep3 deletion/disruption alleles were viable, had decreased levels of protease A, protease B, and carboxypeptidase Y antigens, had decreased repressible alkaline phosphatase activity, and contained very few normal vacuolelike organelles by fluorescence microscopy and electron microscopy but had an abundance of extremely small vesicles that stained with carboxyfluorescein diacetate, were severely inhibited for growth at 37 degrees C, and were incapable of sporulating (as homozygotes). Fractionation of cells expressing a bifunctional PEP3::SUC2 fusion protein indicated that the PEP3 gene product is present at low abundance in both log-phase and stationary cells and is a vacuolar peripheral membrane protein. Sequence identity established that PEP3 and VPS18 (J. S. Robinson, T. R. Graham, and S. D. Emr, Mol. Cell. Biol. 11:5813-5824, 1991) are the same gene.

INFLUENCE OF INTEGRATED APPLICATION OF LASER THERAPY AND LOW-FREQUENCY ELECTROSTATIC FIELD ON BIOCHEMICAL INDICATORS OF ORAL FLUID IN PATIENTS WITH POSTPROTHETIC INFLAMMATORY COMPLICATIONS DURING DENTAL IMPLANTATION

2021 ◽  
pp. 8-17
Author(s):  
Варвара Ильинична Лившиц ◽  
Сергей Николаевич Нагорнев ◽  
Валерий Константинович Фролков ◽  
Галина Анатольевна Пузырева
Keyword(s):  
Lipid Peroxidation ◽  
Laser Therapy ◽  
Oral Fluid ◽  
Dynamic Balance ◽  
Low Frequency ◽  
Clinical State ◽  
Antioxidant Systems ◽  
Physical Factors ◽  
Dental Implantation ◽  
Close Relationship

В статье представлен анализ процессов липопероксидации в ротовой жидкости у пациентов с дентальными периимплантитами при курсовом применении низкоинтенсивной инфракрасной лазеротерапии и низкочастотной электростатической терапии. Полученные результаты позволяют заключить, что развитие воспалительных осложнений, возникающих у пациентов с ортопедическими конструкциями на дентальных имплантатах, характеризуются развитием окислительного стресса, нарушающим динамическое равновесие между про- и антиоксидантными системами. Применение физиотерапевтических факторов (лазера и низкочастотной электротерапии) оказывает выраженное антиоксидантное действие, реализуемое на основе потенцирующего механизма взаимодействия физических факторов и направленное на повышение резервной мощности защитных факторов ротовой жидкости и поддержание окислительного гомеостаза в условиях физиологического равновесия. Установлено, что позитивные сдвиги параметров липопероксидации тесно коррелируют с индексными показателями клинического состояния пациентов, что убедительно свидетельствует не только о патогенетической значимости процессов ПОЛ в развитии постпротетических воспалительных осложнений при дентальной имплантации, но и важности антиоксидантных потенций проводимых лечебных мероприятий в достижении клинической эффективности. Тесная взаимосвязь коэффициента стабильности дентального имплантата с продуктами ПОЛ характеризует собой деструктивное участие липоперекисных процессов в формировании морфологической основы остеоинтеграции имплантатов, а также позволяет рассматривать параметры перекисного метаболизма и значения коэффициента антиоксидантной защиты в качестве информативных индикаторов мониторинга и прогноза устойчивости внутрикостных дентальных конструкций The article presents an analysis of lipid peroxidation processes in the oral fluid in patients with dental peri-implantitis during the course of low-intensity infrared laser therapy and low-frequency electrostatic therapy. The results obtained allow us to conclude that the development of inflammatory complications arising in patients with orthopedic constructions on dental implants are characterized by the development of oxidative stress, which disrupts the dynamic balance between pro- and antioxidant systems. The use of physiotherapeutic factors (laser and low-frequency electrotherapy) has a pronounced antioxidant effect, realized on the basis of a potentiating mechanism of interaction of physical factors and aimed at increasing the reserve power of the protective factors of the oral fluid and maintaining oxidative homeostasis in conditions of physiological equilibrium. It has been established that positive shifts in lipid peroxidation parameters closely correlate with index indicators of the clinical state of patients, which convincingly indicates not only the pathogenetic significance of LPO processes in the development of postprotective inflammatory complications during dental implantation, but also the importance of antioxidant potencies of the therapeutic measures in achieving clinical efficacy. The close relationship of the coefficient of stability of a dental implant with LPO products characterizes the destructive participation of lipoperoxide processes in the formation of the morphological basis of osseointegration of implants, and also allows us to consider the parameters of peroxide metabolism and the value of the coefficient of antioxidant protection as informative indicators for monitoring and predicting the stability of intraosseous dental structures

scholarly journals Identification of an Na+-Dependent Transporter Associated with Saxitoxin-Producing Strains of the Cyanobacterium Anabaena circinalis

2004 ◽  
Vol 70 (8) ◽  
pp. 4711-4719 ◽  
Author(s):  
Francesco Pomati ◽  
Brendan P. Burns ◽  
Brett A. Neilan
Keyword(s):  
Genomic Structure ◽  
Repeated Sequence ◽  
Subtractive Hybridization ◽  
Molecular Probe ◽  
Ph Homeostasis ◽  
Important Health ◽  
Cyanobacterium Anabaena ◽  
Specific Sequences ◽  
Anabaena Circinalis

ABSTRACT Blooms of the freshwater cyanobacterium Anabaena circinalis are recognized as an important health risk worldwide due to the production of a range of toxins such as saxitoxin (STX) and its derivatives. In this study we used HIP1 octameric-palindrome repeated-sequence PCR to compare the genomic structure of phylogenetically similar Australian isolates of A. circinalis. STX-producing and nontoxic cyanobacterial strains showed different HIP1 (highly iterated octameric palindrome 1) DNA patterns, and characteristic interrepeat amplicons for each group were identified. Suppression subtractive hybridization (SSH) was performed using HIP1 PCR-generated libraries to further identify toxic-strain-specific genes. An STX-producing strain and a nontoxic strain of A. circinalis were chosen as testers in two distinct experiments. The two categories of SSH putative tester-specific sequences were characterized by different families of encoded proteins that may be representative of the differences in metabolism between STX-producing and nontoxic A. circinalis strains. DNA-microarray hybridization and genomic screening revealed a toxic-strain-specific HIP1 fragment coding for a putative Na+-dependent transporter. Analysis of this gene demonstrated analogy to the mrpF gene of Bacillus subtilis, whose encoded protein is involved in Na+-specific pH homeostasis. The application of this gene as a molecular probe in laboratory and environmental screening for STX-producing A. circinalis strains was demonstrated. The possible role of this putative Na+-dependent transporter in the toxic cyanobacterial phenotype is also discussed, in light of recent physiological studies of STX-producing cyanobacteria.

scholarly journals Isolation and Characterization of vicH, Encoding a New Pleiotropic Regulator in Vibrio cholerae

2000 ◽  
Vol 182 (7) ◽  
pp. 2026-2032 ◽  
Author(s):  
Christian Tendeng ◽  
Cyril Badaut ◽  
Evelyne Krin ◽  
Pierre Gounon ◽  
Saravuth Ngo ◽  
...  
Keyword(s):  
Amino Acid ◽  
Vibrio Cholerae ◽  
Genomic Library ◽  
Single Gene ◽  
Wild Type ◽  
Semisolid Medium ◽  
E Coli ◽  
Isolation And Characterization ◽  
Serovar Typhimurium

ABSTRACT During the last decade, the hns gene and its product, the H-NS protein, have been extensively studied in Escherichia coli. H-NS-like proteins seem to be widespread in gram-negative bacteria. However, unlike in E. coli and inSalmonella enterica serovar Typhimurium, little is known about their role in the physiology of those organisms. In this report, we describe the isolation of vicH, an hns-like gene in Vibrio cholerae, the etiological agent of cholera. This gene was isolated from a V. cholerae genomic library by complementation of different phenotypes associated with anhns mutation in E. coli. It encodes a 135-amino-acid protein showing approximately 50% identity with both H-NS and StpA in E. coli. Despite a low amino acid conservation in the N-terminal part, VicH is able to cross-react with anti-H-NS antibodies and to form oligomers in vitro. ThevicH gene is expressed as a single gene from two promoters in tandem and is induced by cold shock. A V. choleraewild-type strain expressing a vicHΔ92 gene lacking its 3′ end shows pleiotropic alterations with regard to mucoidy and salicin metabolism. Moreover, this strain is unable to swarm on semisolid medium. Similarly, overexpression of the vicH wild-type gene results in an alteration of swarming behavior. This suggests that VicH could be involved in the virulence process in V. cholerae, in particular by affecting flagellum biosynthesis.

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