Genome structure of Halobacterium halobium: plasmid dynamics in gas vacuole deficient mutants

1989 ◽  
Vol 35 (1) ◽  
pp. 96-100 ◽  
Author(s):  
Felicitas Pfeifer ◽  
Ulrike Blaseio ◽  
Mary Horne
Keyword(s):  
Genome Structure ◽  
Gene Mutations ◽  
Halobacterium Halobium ◽  
Chromosomal Dna ◽  
Insertion Element ◽  
Deletion Event ◽  
High Frequencies ◽  
Insertion Elements ◽  
The Difference ◽  
Gas Vacuole

Halobacterium halobium contains two gas vacuole protein genes that are located in plasmid pHH1 (p-vac) and in the chromosomal DNA (c-vac). The mutation frequency for these genes is different: the constitutively expressed p-vac gene is mutated with a frequency of 10−2, while the chromosomal gene expressed in the stationary phase of growth is mutated with a frequency of 10−5. The difference in the mutation susceptibility is due to the dynamics of plasmid pHH1. p-vac gene mutations are caused (i) by the integration of an insertion element or (ii) by a deletion event encompassing the p-vac gene region. In contrast, c-vac mutants analyzed to date incurred neither insertion elements nor deletions. Deletion events within pHH1 occur at high frequencies during the development of a H. halobium culture. The investigation of the fusion regions resulting from deletion events indicates that insertion elements are involved. The analysis of pHH1 deletion variants led to a 4 kilobase pair DNA region containing the origin of replication of the pHH1 plasmid.Key words: gas vacuole protein gene, plasmid dynamics, deletions, insertion elements.

scholarly journals THE PECULIARITIES OF THE SOUND FIELD ENERGY DECAY IN A ROOM WITH THE USE OF DIFFERENT PULSED SOUND SOURCES/GARSO LAUKO ENERGIJOS SLOPIMO PATALPOJE YPATUMAI, NAUDOJANT SKIRTINGUS IMPULSINIUS GARSO ŠALTINIUS

1999 ◽  
Vol 5 (2) ◽  
pp. 135-140
Author(s):  
Vytautas Stauskis
Keyword(s):  
Noise Level ◽  
Sound Field ◽  
Maximum Energy ◽  
Reverberation Time ◽  
Frequency Range ◽  
Sound Sources ◽  
Low Frequencies ◽  
High Frequencies ◽  
The Difference ◽  
Field Decay

The paper deals with the differences between the energy created by four different pulsed sound sources, ie a sound gun, a start gun, a toy gun, and a hunting gun. A knowledge of the differences between the maximum energy and the minimum energy, or the signal-noise ratio, is necessary to correctly calculate the frequency dependence of reverberation time. It has been established by investigations that the maximum energy excited by the sound gun is within the frequency range of 250 to 2000 Hz. It decreases by about 28 dB at the low frequencies. The character of change in the energy created by the hunting gun differs from that of the sound gun. There is no change in the maximum energy within the frequency range of 63–100 Hz, whereas afterwards it increases with the increase in frequency but only to the limit of 2000 Hz. In the frequency range of 63–500 Hz, the energy excited by the hunting gun is lower by 15–30 dB than that of the sound gun. As frequency increases the difference is reduced and amounts to 5–10 dB. The maximum energy of the start gun is lower by 4–5 dB than that of the hunting gun in the frequency range of up to 1000 Hz, while afterwards the difference is insignificant. In the frequency range of 125–250 Hz, the maximum energy generated by the sound gun exceeds that generated by the hunting gun by 20 dB, that by the start gun by 25 dB, and that by the toy gun—by as much as 35 dB. The maximum energy emitted by it occupies a wide frequency range of 250 to 2000 Hz. Thus, the sound gun has an advantage over the other three sound sources from the point of view of maximum energy. Up until 500 Hz the character of change in the direct sound energy is similar for all types of sources. The maximum energy of direct sound is also created by the sound gun and it increases along with frequency, the maximum values being reached at 500 Hz and 1000 Hz. The maximum energy of the hunting gun in the frequency range of 125—500 Hz is lower by about 20 dB than that of the sound gun, while the maximum energy of the toy gun is lower by about 25 dB. The maximum of the direct sound energy generated by the hunting gun, the start gun and the toy gun is found at high frequencies, ie at 1000 Hz and 2000 Hz, while the sound gun generates the maximum energy at 500 Hz and 1000 Hz. Thus, the best results are obtained when the energy is emitted by the sound gun. When the sound field is generated by the sound gun, the difference between the maximum energy and the noise level is about 35 dB at 63 Hz, while the use of the hunting gun reduces the difference to about 20–22 dB. The start gun emits only small quantities of low frequencies and is not suitable for room's acoustical analysis at 63 Hz. At the frequency of 80 Hz, the difference between the maximum energy and the noise level makes up about 50 dB, when the sound field is generated by the sound gun, and about 27 dB, when it is generated by the hunting gun. When the start gun is used, the difference between the maximum signal and the noise level is as small as 20 dB, which is not sufficient to make a reverberation time analysis correctly. At the frequency of 100 Hz, the difference of about 55 dB between the maximum energy and the noise level is only achieved by the sound gun. The hunting gun, the start gun and the toy gun create the decrease of about 25 dB, which is not sufficient for the calculation of the reverberation time. At the frequency of 125 Hz, a sufficiently large difference in the sound field decay amounting to about 40 dB is created by the sound gun, the hunting gun and the start gun, though the character of the sound field curve decay of the latter is different from the former two. At 250 Hz, the sound gun produces a field decay difference of almost 60 dB, the hunting gun almost 50 dB, the start gun almost 40 dB, and the toy gun about 45 dB. At 500 Hz, the sound field decay is sufficient when any of the four sound sources is used. The energy difference created by the sound gun is as large as 70 dB, by the hunting gun 50 dB, by the start gun 52 dB, and by the toy gun 48 dB. Such energy differences are sufficient for the analysis of acoustic indicators. At the high frequencies of 1000 to 4000 Hz, all the four sound sources used, even the toy gun, produce a good difference of the sound field decay and in all cases it is possible to analyse the reverberation process at varied intervals of the sound level decay.

A new insertion element, ISH26, from Halobacterium halobium

1987 ◽  
Vol 206 (1) ◽  
pp. 81-87 ◽  
Author(s):  
Klaus Ebert ◽  
Christian Hanke ◽  
Hajo Delius ◽  
Werner Goebel ◽  
Felicitas Pfeifer
Keyword(s):  
Halobacterium Halobium ◽  
Insertion Element

Phylogeny in the genus Hordeum based on nucleotide sequences closely linked to the vrs1 locus (row number of spikelets)

Genome ◽  
1999 ◽  
Vol 42 (5) ◽  
pp. 973-981 ◽  
Author(s):  
Takao Komatsuda ◽  
Ken-ichi Tanno ◽  
Björn Salomon ◽  
Tomas Bryngelsson ◽  
Roland von Bothmer
Keyword(s):  
Nuclear Dna ◽  
Sister Group ◽  
Single Copy ◽  
Nucleotide Sequences ◽  
Restriction Maps ◽  
Deletion Event ◽  
Single Base ◽  
Genome Group ◽  
The Difference ◽  
Hordeum Species

The phylogenetic relationship between four basic genomes designated H, I, Xa, and Xu in the genus Hordeum was studied using a nuclear DNA sequence. The sequence, cMWG699, is single copy in the H. vulgare genome, and tightly linked to the vrs1 locus which controls two- and six-rowed spikes. DNA fragments homologous to cMWG699 were amplified from diploid Hordeum species and the nucleotide sequences were determined. A phylogeny based on both base substitutions and an insertion-deletion event showed that the H- and Xa-genome groups are positioned in one monophyletic group indicating that the Xa-genome taxa should be included in the H-genome group. The large H-genome group is highly homogeneous. The I and Xu genomes are distinctly separated from H and Xa, and form sister groups. Another phylogeny pattern based on data excluding the insertion-deletion gave a result that the Xa genome forms a sister group to the H-genome group. The difference between the H and Xa genomes was affected only by a single base insertion-deletion event, thus the H and Xa genomes are likely to be closely related. The I and Xu genomes were again distinctly separated from the H and Xa genomes.Key words: genome DNA, molecular markers, restriction maps, barley, Psathyrostachys.

Mutational Spectrum Analysis of Interesting Correlation and Interrelationship Between RNA Splicing Pathway and Commonly Targeted Genes in Myelodysplastic Syndrome

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 273-273 ◽  
Author(s):  
Yasunobu Nagata ◽  
Masashi Sanada ◽  
Ayana Kon ◽  
Kenichi Yoshida ◽  
Yuichi Shiraishi ◽  
...  
Keyword(s):  
Rna Splicing ◽  
Genetic Basis ◽  
De Novo ◽  
Gene Mutations ◽  
Myeloid Neoplasms ◽  
Disease Subtypes ◽  
The Difference ◽  
De Novo Aml ◽  
Insight Into ◽  
Splicing Machinery

Abstract Abstract 273 Myelodysplastic syndromes (MDS) are a heterogeneous group of myeloid neoplasms showing a frequent transition to acute myeloid leukemia. Although they are discriminated from de novo AML by the presence of a preleukemic period and dysplastic cell morphology, the difference in molecular genetics between both neoplasms has not been fully elucidated because of the similar spectrum of gene mutations. In this regards, the recent discovery of frequent pathway mutations (45∼90%) involving the RNA splicing machinery in MDS and related myeloid neoplasm with their rare mutation rate in de novo AML provided a novel insight into the distinct molecular pathogenesis of both neoplasms. Thus far, eight components of the RNA splicing machinery have been identified as the targets of gene mutations, among which U2AF35, SF3B1, SRSF2 and ZRSR2 show the highest mutation rates in MDS and CMML. Meanwhile, the frequency of mutations shows a substantial variation among disease subtypes, although the genetic/biological basis for these differences has not been clarified; SF3B1 mutations explain >90% of the spliceosome gene mutations in RARS and RCMD-RS, while mutations of U2AF35 and ZRSR2 are rare in these categories (< 5%) but common in CMML (16%) and MDS without increased ring sideroblasts (20%). On the other hand, SRSF2 mutations are most frequent in CMML (30%), compared with other subtypes (<10 %) (p<0.001) (Yoshida K, et al, unpublished data). So to obtain an insight into the genetic basis for these difference, we extensively explored spectrums of gene mutations in a set of 161 samples with MDS and related myeloid neoplasms, in which mutations of 10 genes thus far identified as major targets in MDS were examined and their frequencies were compared with regard to the species of mutated components of the splicing machinery. The mutation status of the 161 specimens was determined using the target exon enrichment followed by massively parallel sequencing. In total, 86 mutations were identified in 81(50%) in the 8 components of the splicing machinery. The mutations among 4 genes, U2AF35 (N = 20), SRSF2 (N = 31), SF3B1 (N = 15) and ZRSR2 (N = 10), explained most of the mutations with a much lower mutational rate for SF3A1 (N = 3), PRPF40B (N = 3), U2AF65 (N = 3) and SF1 (N = 1). Conspicuously, higher frequency 4 components of the splicing machinery were mutated in 76 out of the 161 cases (47.2%) in a mutually exclusive manner. On the other hand, 172 mutations of the 10 common targets were identified among 117, including 41 TET2 (25%), 32 RUNX1 (20%), 26 ASXL1 (16%), 24 RAS (NRAS/KRAS) (15%), 22 TP53 (14%), 17 IDH1/2 (10%), 10 CBL (6%) and 10 EZH2 (6%) mutations. We examined the difference between the major spliceosome mutations in terms of the number of the accompanying mutations in the 10 common gene targets. The possible bias from the difference in disease subtypes was compensated by multiple regressions. The SRSF2 mutations are more frequently associated with accompanying gene mutations with a significantly higher number of those mutations (N=29; OR 6.2; 95%CI 1.1–35) compared with that of the U2AF35 mutations (N=14) (p=0.038). Commonly involving the E/A splicing complexes, these splicing pathway mutations lead to compromised 3' splice site recognition. However, individual mutations may still have different impacts on cell functions, which could contribute to the determination of discrete disease phenotypes. It was demonstrated that SRSF2 was involved in the regulation of DNA stability and that depletion of SRSF2 can lead to DNA hypermutability, which may explain the higher number of accompanying gene mutation in SRSF2-mutated cases than cases with other spliceosome gene mutations. In conclusion, it may help to disclosing the genetic basis of MDS and related myeloid neoplasms that highly paralleled resequencing was confirmed SRSF2 mutated case significantly overlapped common mutations. Disclosures: No relevant conflicts of interest to declare.

A large plasmid from Halobacterium halobium carrying genetic information for gas vacuole formation

Plasmid ◽  
1979 ◽  
Vol 2 (3) ◽  
pp. 377-386 ◽  
Author(s):  
Gottfried Weidinger ◽  
Günther Klotz ◽  
Werner Goebel
Keyword(s):  
Genetic Information ◽  
Halobacterium Halobium ◽  
Large Plasmid ◽  
Vacuole Formation ◽  
Gas Vacuole

Air and Bone Conduction Change after Stapedotomy and Partial Stapedectomy for Otosclerosis

2005 ◽  
Vol 133 (1) ◽  
pp. 116-120 ◽  
Author(s):  
Nicola Quaranta ◽  
Gaspare Besozzi ◽  
Rosa Anna Fallacara ◽  
Antonio Quaranta
Keyword(s):  
Conductive Hearing Loss ◽  
Bone Conduction ◽  
Neck Surgery ◽  
Closure Rate ◽  
High Frequencies ◽  
Results Of Treatment ◽  
The Difference ◽  
Similar Good ◽  
Conductive Hearing ◽  
Air Conduction

OBJECTIVE: The aim of this study was to analyze and compare the results obtained in otosclerosis patient undergoing stapedotomy and partial stapedectomy. STUDY DESIGN AND SETTINGS: Retrospective review of surgical series. The guidelines of the American Academy of Otolaryngology-Head and Neck Surgery for the evaluation of results of treatment of conductive hearing loss were used. RESULTS: Pure tone average (0.5 to 3 kHz) air-bone gap was 6.1 dB in the partial stapedectomy and 6 dB in the stapedotomy group. The air-bone gap (ABG) closure rate did not differ between the 2 groups, except at 4 kHz, where stapedotomy group showed greater closure ( P 0.003). Mean postoperative ABG gain was significantly ( P <0.05) higher in the stapedotomy group at 2, 3, and 4 kHz. Mean postoperative air-conduction gain did not differ significantly. Mean postoperative bone conduction (BC) change (1, 2, and 4 kHz) was 3.68 dB in partial stapedectomy and −0.02 dB in stapedotomy group, the difference being significant ( P 0.007). Differences in BC change between the 2 groups were significant at each frequency. CONCLUSIONS: Similar good results can be obtained in experienced hands using either partial stapedectomy or stapedotomy technique. ABG closure rates were analogous in the 2 techniques as well as the complication rate. Although stapedotomy obtain better results at high frequencies, partial stapedectomy is associated with increased BC threshold at all frequencies.

277 PRELIMINARY STUDY OF THE DIFFERENCE IN THE GENOME-WIDE METHYLATION PROFILES BETWEEN GERM CELLS AND SOMATIC CELLS OF BULLS

2007 ◽  
Vol 19 (1) ◽  
pp. 254
Author(s):  
N. Phutikanit ◽  
J. Suwimonteerabutr ◽  
D. Harrison ◽  
M. J. D'Occhio ◽  
B. J. Carroll ◽  
...  
Keyword(s):  
Germ Cells ◽  
Genome Structure ◽  
Somatic Cells ◽  
Cell Types ◽  
Methylation Pattern ◽  
Arbitrary Sequence ◽  
Chi Square ◽  
Short Oligonucleotide ◽  
Genome Wide ◽  
The Difference

DNA methylation is tissue-specific and is thought to be one of the factors that regulates gene expression. This recent study was carried out in order to examine the difference of the genome-wide methylation profiles at the HpaII sites in germ cells and somatic cells of bulls. Ejaculated spermatozoa, leukocytes, and ear fibroblasts were collected from 3 Holstein bulls of ages 1 to 3 years. The genomic DNA was extracted and treated overnight with a methylation-sensitive restriction endonuclease (HpaII) to digest unmethylated sites throughout the genome. Both undigested and digested DNA samples were used as templates in the PCR-based technique developed by researchers at the University of Queensland, which allows the amplification of the methylation sites by short oligonucleotide primers of arbitrary sequence containing the HpaII recognition site (CCGG). The amplicons were separated in 4% polyacrylamide gel by electrophoresis and the gel was stained with silver nitrate. The results were evaluated on the basis of the presence–absence of the band(s) in the digested template compared with the undigested counterpart, and the difference between types of marker was analyzed using the chi-square test. From 10 sets of primer, approximately 400 markers in the genomic samples could be scored. The samples from the 3 bulls showed similar but not identical patterns. Statistical analysis showed that the difference between marker types was dependent on the individual. Generally, most of the markers were digestion-resistant markers signifying that most of the HpaII sites in the genome of both germ cells and somatic cells are methylated. Leukocytes had a significantly higher methylation content compared to fibroblasts (94.1 vs. 90.1%; P = 0.0004), but did not differ from those in sperm (92.3%; P = 0.09). Sperm cells showed a slightly higher percentage of unmethylated sites than did somatic cells (3.5 vs. 2.6% in leukocytes and 3.3% in fibroblasts), and yet the difference was non-significant. Moreover, fibroblastic cells had a higher portion of the digestion-dependent markers than did other cell types, and this difference was statistically significant (6.6 vs. 4.2% in sperm, P = 0.009, and 3.3% in leukocytes, P = 0.001). In conclusion, the DNA of the germ cells and somatic cells is highly methylated at the HpaII sites, with some variation in methylation pattern between the 2 cell lineages. The markers found only in the digested template of the ear fibroblasts suggest the difference in genome structure between the versatile cell types and the fully differentiated ones. Further investigation is required to elucidate any possible relationship between the variation of the methylation pattern found in sperm and fibroblasts and the failure of the reprogramming process in cloned animals derived from somatic cell nuclear transfer. This study was supported by The Faculty of Veterinary Science, Chulalongkorn University, and The Royal Golden Jubilee PhD program of Thailand Research Fund.

Sign in / Sign up

Export Citation Format

Share Document