Species specificity of musty odor producing Phormidium tenue in Lake Kamafusa

2004 ◽  
Vol 49 (9) ◽  
pp. 41-46 ◽  
Author(s):  
E. Oikawa ◽  
Y. Ishibashi
Keyword(s):  
Phylogenetic Tree ◽  
Dna Sequences ◽  
Lake Biwa ◽  
Detection Method ◽  
Species Specificity ◽  
The Third ◽  
16S Ribosomal Dna ◽  
Base Sequences ◽  
Dot Hybridization ◽  
Musty Odor

16S ribosomal DNA sequences of various strains of Phormidium tenue (P. tenue) in Lake Kamafusa were determined. Such P. tenue could not be distinguished under microscopic examination. From the results of the analyses of base sequences, and using a phylogenetic tree, several P. tenue with different species specificity on the sequence were found in the lake. P. tenue were divided into three groups. The first produced 2-methylisoborneol (MIB) and was close to a species from the moat of Nagoya castle. The second produced MIB and was characteristic of Lake Kamafusa. The third had a brown color like a Lake Biwa strain and was MIB non-producing. From the phylogenetic tree, it was revealed that species had not changed recently by mutation. Moreover, a detection method for P. tenue by PCR and dot hybridization was established.

The relationship between musty-odor-causing organisms and water quality in Lake Biwa

1995 ◽  
Vol 31 (11) ◽  
pp. 153-158 ◽  
Author(s):  
M. Kajino ◽  
K. Sakamoto
Keyword(s):  
Water Quality ◽  
Data Analysis ◽  
Green Algae ◽  
Analytical Methods ◽  
Lake Biwa ◽  
Blue Green Algae ◽  
Odor Compounds ◽  
Musty Odor ◽  
The Relationship

Musty odor has occurred annually in Lake Biwa since 1969. Osaka municipal waterworks, which is located downstream of Lake Biwa, has made many efforts to treat musty-odor compounds produced in Lake Biwa from spring through autumn. With the development of analytical methods for the determination of musty-odor compounds, we have been able to confirm that planktonic blue-green algae are the major causes of the musty-odor occurrences. The relationship between the growth of blue-green algae and the water quality was not so apparent. However, through our data analysis focusing on the relationship between musty-odor occurrences due to Phormidium tenue or Oscillatoria tenuis and some nutrients in Lake Biwa, we found that the concentration of nitrate in water may be an important parameter for the estimation of growth of the algae and the musty-odor behavior.

scholarly journals VARIABILITY OF EVOLUTIONARY RATES OF DNA

Genetics ◽  
1986 ◽  
Vol 113 (4) ◽  
pp. 1077-1091
Author(s):  
John H Gillespie
Keyword(s):  
Dna Sequences ◽  
Significant Excess ◽  
Ergodic Markov Chain ◽  
The Third ◽  
Markov Chain Models ◽  
Rate Of Molecular Evolution ◽  
The Mean ◽  
Nuclear Loci ◽  
The Individual ◽  
Evolution Of Proteins

ABSTRACT A statistical analysis of DNA sequences from four nuclear loci and five mitochondrial loci from different orders of mammals is described. A major aim of the study is to describe the variation in the rate of molecular evolution of proteins and DNA. A measure of rate variability is the statistic R, the ratio of the variance in the number of substitutions to the mean number. For proteins, R is found to be in the range 0.16 < R < 35.55, thus extending in both directions the values seen in previous studies. An analysis of codons shows that there is a highly significant excess of double substitutions in the first and second positions, but not in the second and third or first and third positions. The analysis of the dynamics of nucleotide evolution showed that the ergodic Markov chain models that are the basis of most published formulas for correcting for multiple substitutions are incompatible with the data. A bootstrap procedure was used to show that the evolution of the individual nucleotides, even the third positions, show the same variation in rates as seen in the proteins. It is argued that protein and silent DNA evolution are uncoupled, with the evolution at both levels showing patterns that are better explained by the action of natural selection than by neutrality. This conclusion is based primarily on a comparison of the nuclear and mitochondrial results.

scholarly journals Comparison of 16S Ribosomal DNA Sequences of All Xanthomonas Species

1997 ◽  
Vol 47 (2) ◽  
pp. 328-335 ◽  
Author(s):  
L. HAUBEN ◽  
L. VAUTERIN ◽  
J. SWINGS ◽  
E. R. B. MOORE
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
16S Ribosomal Dna ◽  
Xanthomonas Species

scholarly journals ЦАХИЛДАГНЫ ТӨРЛИЙН УРГАМЛЫН ФИЛОГЕНЕТИК ХОЛБОО

2016 ◽  
pp. 25-31
Author(s):  
Х Алтанзул ◽  
Ю Оюунбилэг
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Relationship ◽  
Dna Sequences ◽  
Fragment Size ◽  
Dna Fragment ◽  
Relationship Of

The phylogenetic relationship of eight Iris species (I.flavisimma, I.ventricosa, I.bungei,I.kaempferi, I.tenuifolia, I.lactea, I.tigrida, I.dichotoma) were studied by PCR using six specificprimers (S-523, Z1204R, trnL, trnF and ITS1, ITS4). All species except I.ventricosa wereidentified when using S-523, Z1204R and trnL, trnF primers and the DNA fragment size rangedbetween 500 to 600 bp and 800 bp, respectively. Primers ITS1 and ITS4 produced double bandsin about 500 and 1500 bp to I.bungei, I.kaempferi, and I.lactea species. On the phylogenetic tree, some iris species have close relations based on chloroplastic DNA sequences. The closest relationships showed between I.sanguinea and I.sibirica, I.rutenica and I.uniflora. Also I.tenuifolia, I.ventricosa and I.halophila located on one branch of phylogenetic tree.

scholarly journals Phylogenetic Tree Construction for DNA Sequences using Clustering Methods

2012 ◽  
Vol 38 ◽  
pp. 1362-1366 ◽  
Author(s):  
Gayatri Mahapatro ◽  
Debahuti Mishra ◽  
Kailash Shaw ◽  
Sashikala Mishra ◽  
Tanushree Jena
Keyword(s):  
Phylogenetic Tree ◽  
Dna Sequences ◽  
Clustering Methods ◽  
Phylogenetic Tree Construction ◽  
Tree Construction

Reconstruction of Phylogenetic Tree for COX with DNA Sequences

2020 ◽  
pp. 369-375
Author(s):  
D. Anurag ◽  
Chukka Santhaiah ◽  
N. V. Krishna Rao ◽  
V. JaswanthSai ◽  
P. Akash ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Dna Sequences

More on manipulating text.

2021 ◽  
pp. 257-274
Author(s):  
Donald L. J. Quicke ◽  
Buntika A. Butcher ◽  
Rachel A. Kruft Welton
Keyword(s):  
Phylogenetic Tree ◽  
Dna Sequences ◽  
White Spaces ◽  
Using Data ◽  
Unknown Length

Abstract This chapter provides more information on manipulating text, presenting two examples. Example 1 focuses on standardizing names in a phylogenetic tree description, using R to reformat taxon names, create lists, sort data and use wildcards for when some things you are interested in don't have exactly the same length. The example tree description concerns parasitoids of caterpillars at a study site that have been DNA barcoded and their possible taxonomic identities added automatically. Example 2 deals with substrings of unknown length. This example search for a numeric substring of unknown length but with a standard prefix, using data of some DNA sequences from a set of Aleiodes wasps. The trimming of white spaces and/or tabs, use of wildcards to locate internal letter strings, finding of suffixes, prefixes and specifying of letters, numbers and punctuation, manipulation of character case, ignoring of character case, and specifying of particular and modifiable character classes are briefly described.

THE NATURE OF NUCLEOTIDE SEQUENCE DIVERGENCE BETWEEN BARLEY AND MAIZE CHLOROPLAST DNA

Genetics ◽  
1984 ◽  
Vol 106 (4) ◽  
pp. 735-749
Author(s):  
Gerard Zurawski ◽  
Michael T Clegg ◽  
Anthony H D Brown
Keyword(s):  
Chloroplast Dna ◽  
Dna Sequences ◽  
Large Subunit ◽  
Leader Region ◽  
Coding Region ◽  
Nucleotide Substitutions ◽  
Bisphosphate Carboxylase ◽  
Noncoding Regions ◽  
The Third ◽  
Maize Chloroplast

ABSTRACT Analysis of a 2175-base pair (bp) SmaI-HindIII fragment of barley chloroplast DNA revealed that rbcL (the gene for the large subunit of ribulose 1,5-bisphosphate carboxylase) and atpB (the gene for the β subunit of ATPase) are transcribed divergently and are separated by an untranscribed region of 155-166 bp. The rbcL mRNA has a 320-residue untranslated leader region, whereas the atpB mRNA has a 296- to 309-residue leader region. The sequence of these regions, together with the initial 113 bp of the atpB-coding region and the initial 1279 bp of the rbcL-coding region, is compared with the analogous maize chloroplast DNA sequences. Two classes of nucleotide differences are present, substitutions and insertions/deletions. Nucleotide substitutions show a 1.9-fold bias toward transitions in the rbcL-coding region and a 1.5-fold bias toward transitions in the noncoding region. The level of nucleotide substitutions between the barley and maize sequences is about 0.065/bp. Seventy-one percent of the substitutions in the rbcL-coding region are at the third codon position, and 95% of these are synonymous changes. Insertion/deletion events, which are confined to the noncoding regions, are not randomly distributed in these regions and are often associated with short repeated sequences. The extent of change for the noncoding regions (about 0.093 events/bp) is less than the extent of change at the third codon positions in the rbcL-coding region (about 0.135 events/bp), including insertion/delection events. Limited sequence analysis of the analogous DNA from a wild line (Hordeum spontaneum) and a primitive Iranian barley (H. vulgare) suggested a low rate of chloroplast DNA evolution. Compared to spinach chloroplast DNA, the barley rbcL-atpB untranslated region is extremely diverged, with only the putative rbcL promoters and ribosome-binding site being extensively conserved.

scholarly journals Assessment of Pathogenic Potential, Virulent Genes Profile, and Antibiotic Susceptibility of Proteus mirabilis from Urinary Tract Infection

2020 ◽  
Vol 2020 ◽  
pp. 1-5 ◽  
Author(s):  
Emad I. Hussein ◽  
Khalid Al-Batayneh ◽  
Majed M. Masadeh ◽  
Fatina W. Dahadhah ◽  
Mazhar Salim Al Zoubi ◽  
...  
Keyword(s):  
Urinary Tract Infection ◽  
Urinary Tract ◽  
Antimicrobial Susceptibility ◽  
Proteus Mirabilis ◽  
Antibiotic Susceptibility ◽  
Virulence Genes ◽  
Detection Method ◽  
Pathogenic Potential ◽  
The Third ◽  
Urine Specimens

Proteus mirabilis is the third most common bacterium that can cause complicated UTI, especially in catheterized patients. Urovirulence genes of P. mirabilis strains are poorly identified among UTI patients. The aims of the present study were to determine the prevalence of the uropathogenic P. mirabilis strains isolated from UTI patients by the detection of several P. mirabilis virulence genes and to characterize the antibiotic susceptibility profile of P. mirabilis isolates. P. mirabilis isolates were collected from urine specimens of patients suffering from UTI. Virulence genes in P. mirabilis, namely, hpmA, hpmB, rsbA, luxS, ureC1, hlyA, rpoA, atfA, atfC, mrpA, and pm1 were detected in the isolates via PCR detection method. All P. mirabilis virulence genes were detected in more than 90% of the isolates except hlyA gene, which was detected in only 23.8% of the isolates. The rate of susceptibility for ceftriaxone was 96.8%, followed by norfloxacin (82.5%), gentamicin (71.4%), ciprofloxacin (69.8%), cephalexin (52.4%), nalidixic acid (42.9%), sulfamethoxazole (39.7%), ampicillin (36.5%), and nitrofurantoin (3.2%). Significant associations (P<0.05) were detected between antimicrobial susceptibility of each of the following antibiotics and the presence virulence genes. Cephalexin antimicrobial susceptibility was significantly associated with the presence each of ureC1 and atfC. Sulfamethoxazole antimicrobial susceptibility was significantly associated with the presence atfA. Ceftriaxone antimicrobial susceptibility was significantly associated with the presence each of hpmA, ureC1, rpoA, atfC, mrpA, and pm1. Nitrofurantoin antimicrobial susceptibility was significantly associated with the presence each of hpmA, ureC1, rpoA, atfA, atfC, mrpA, and pm1. In conclusion, an association between the presence of urovirulence genes of P. mirabilis and increasing P. mirabilis resistance to antimicrobials has been demonstrated.

Strelitziana sarbhoyi sp. nov. (Strelitzianaceae, Chaetothyriales), from North-Western Himalayas, India, described based on morphology and molecular phylogeny

Phytotaxa ◽  
2019 ◽  
Vol 427 (1) ◽  
pp. 51-59
Author(s):  
SHIWALI RANA ◽  
SANJAY KUMAR SINGH ◽  
PARAS NATH SINGH
Keyword(s):  
Phylogenetic Tree ◽  
Dna Sequences ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Culture Collection ◽  
Fungal Culture ◽  
Western Himalayas ◽  
Holotype Specimen ◽  
North Western

Strelitziana sarbhoyi is established as a new species to accommodate a phylloplane fungus isolated from Mallotus philippensis collected from Kangra region of North-Western Himalayas, Himachal Pradesh. The identity of the fungus is confirmed based on the asexual-morphs, cultural characteristics and phylogenetic analyses of the internal transcribed spacer (ITS) rDNA and partial nuclear ribosomal 28S large subunit (LSU) sequence data. The placement of S. sarbhoyi in the phylogenetic tree was determined based on DNA sequences from authenticated isolates of Strelitziana. Strelitziana sarbhoyi shows nearly 94% similarity with other known species of Strelitziana. Area description is provided for the proposed taxon along with microscopic images, and a phylogenetic tree. This is probably the first report of Strelitziana from India. Holotype specimen (dried voucher culture) is deposited in the Ajrekar Mycological Herbarium (AMH), and an ex-type culture is deposited in National Fungal Culture Collection of India (NFCCI).

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