Antibacterial Treatment Against Diarrhea in Oral Rehydration Solution
(by T4 phage)
Randomized, Double Blind Placebo-controlled Studies to Evaluate the Effect of an Orally-fed Escherichia Coli (E. Coli) Phage in the Management of ETEC and EPEC Induced Diarrhea in Children.
This study hopes to demonstrate the potentials of a new form of therapy for childhood diarrhea, a major cause of morbidity and deaths in Bangladesh and other developing countries, and thus a priority for improving child health.
Scientific works:
T4 phages against Escherichia coli diarrhea: Potential and problems
Nestle´ Research Centre, CH-1000 Lausanne 26 Vers-chez-les-Blanc, Switzerland
Phage therapy: the Escherichia coli experience
Harald Brüssow
Nestle´ Research Centre, CH-1000 Lausanne 26 Vers-chez-les-Blanc, Switzerland
Human Volunteers Receiving Escherichia coli Phage T4 Orally:
a Safety Test of Phage Therapy
Anne Bruttin and Harald Brüssow,
Nestle´ Research Center, Nestec Ltd., Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland
Saturday, 26 December 2009
Thursday, 24 December 2009
Cds from D29,L5,BXZ2 and TM4 mycobacterium phages
I have investigated the genomes of these phages searching for a relationship of cause and effect (D29,Bxz2,L5 and TM4 phages grow on M.ulcerans and M.smegmatis).
These are the results after the comparisons(D29,BXZ2,L5 and TM4):
Blue=% identity
Orange =% similarity
Each time two genomes are compared by BugView software ( Smith Waterman algorithm ).
The results obtained are(cds from files .gbk):
| D29 on L5:31,39,85/on BXZ2:3,4,38/on TM4:24,27,39 |
| L5 on D29:34,39,82/on BXZ2:3,4,38/on TM4:24,27,39 |
| BXZ2 on D29:34,39,51/on L5:31,39,85/on TM4:24,27,39 |
| TM4 on D29:34,39,80/on L5:31,39,85/on BXZ2:4,2,38 |
By Sockeye software I have showed all genomes and each cds:
cds 4 from Bxz2 genome
cds 24 from TM4 genome
cds 31 from L5 genome
cds 34 from D29 genome
Dot Plot by Serolis software:
Which is the Phage receptor? Fourth part.
Fourth comparison:TM4 phage genome
1- this is the result of Local (Smith-Waterman) comparison between the whole TM4 sequence and Proteins of Mycobacterium ulcerans Agy99:
By BugView:
4208 comparisons for user's query sequence and
Mycobacterium ulcerans Agy99
Finished in 4629 seconds.
Highest score = 1695 for cds_3629 (118619508)
Second score = 1217 for cds_2549 (118618448)
Third score = 1094 for cds_3641 (118619519)
2-I have compared ,one by one, the indicated M.ulcerans cds with the TM4 phage genome:
1°cds_3629
cds_3629 is (MUL_4367):
PE-PGRS family protein (Mycobacterium ulcerans Agy99)
Other Aliases: MUL_4367
Annotation: NC_008611.1 (4845511..4848744, complement)
GeneID: 4550406
By BugView:
89 comparisons for cds_3629 (118619508)
Finished in 1 seconds.
Highest score = 266 for cds_24 (18496911)
Second score = 150 for cds_22 (18496909)
Third score = 128 for cds_8 (18496895)
cds_24
TM4_gp25
similar to L5 gp32 [Mycobacterium phage TM4]
Other Aliases: TM4_gp25, TM4_25
Other Designations: hypothetical protein
Annotation: NC_003387.1 (21422..22426)
GeneID: 932261
Name.............................Start.....End. Strand. Length... Accession... GeneID........ Locus_tag
| hypothetical protein TM4_gp25 | 21422 | 22426 | 334 | NP_569761.1 | 932261 | - | TM4_gp25 |
I have compared , the indicated cds 24 with the M.ulcerans genome:
By BugView:
4208 comparisons for cds_24 (18496911)
Finished in 48 seconds.
Highest score = 299 for cds_331 (118616247)
Second score = 279 for cds_3309 (118619191)
Third score = 277 for cds_620 (118616526)
2°cds_2549
By BugView:
89 comparisons for cds_2549 (118618448)
Finished in 1 seconds.
Highest score = 244 for cds_24 (18496911)
Second score = 171 for cds_22 (18496909)
Third score = 137 for cds_28 (18496915)
3°cds_3641
By BugView:
89 comparisons for cds_3641 (118619519)
Finished in 1 seconds.
Highest score = 252 for cds_24 (18496911)
Second score = 163 for cds_22 (18496909)
Third score = 140 for cds_8 (18496895)
Which is the Phage receptor? Third part.
Third comparison:BXZ2 phage genome
The Third comparison is with BXZ2 phage genome:
1- this is the result of Local (Smith-Waterman) comparison between the whole BXZ2 sequence and Proteins of Mycobacterium ulcerans Agy99:
By BugView:
4208 comparisons for user's query sequence and Mycobacterium ulcerans Agy99.
Finished in 4376 seconds.
Highest score = 1516 for cds_3629 (118619508)
Second score = 1108 for cds_967 (118616873)
Third score = 979 for cds_3641 (118619519)
2-I have compared ,one by one, the indicated M.ulcerans cds with the BXZ2 phage genome:
1°cds_3629
cds_3629 is (MUL_4367):
PE-PGRS family protein (Mycobacterium ulcerans Agy99)
Other Aliases: MUL_4367
Annotation: NC_008611.1 (4845511..4848744, complement)
GeneID: 4550406
By BugView:
89 comparisons for cds_3629 (118619508)
Finished in 1 seconds.
Highest score = 406 for cds_3 (29566025)
Second score = 247 for cds_4 (29566026)
Third score = 110 for cds_26 (29566045)
Bxz2_gp4
cds_3
gp4 [Mycobacterium phage Bxz2]
Other Aliases: Bxz2_gp4, Bxz2p04
Annotation: NC_004682.1 (1692..2726)
GeneID: 1259216
Name.Start..End. Strand. Length... Accession... GeneID........ Locus_tag
| gp4 | 1692 | 2726 | 344 | NP_817595.1 | 1259216 | - | Bxz2_gp4 |
I have compared , the indicated cds 3 with the M.ulcerans genome:
By BugView:
4208 comparisons for cds_3 (29566025)
Finished in 46 seconds.
Highest score = 414 for cds_3076 (118618968)
Second score = 413 for cds_620 (118616526)
Third score = 406 for cds_3629 (118619508)
2°cds_967
By BugView:
89 comparisons for cds_967 (118616873)
Finished in 0 seconds.
Highest score = 281 for cds_3 (29566025)
Second score = 212 for cds_4 (29566026)
Third score = 111 for cds_26 (29566045)
3°cds_3641
By BugView:
89 comparisons for cds_3641 (118619519)
Finished in 1 seconds.
Highest score = 383 for cds_3 (29566025)
Second score = 208 for cds_4 (29566026)
Third score = 118 for cds_26 (29566045)
In the cluster is present the gp5 from cds 4. But the gp4 from cds 3 is correlated to the gp5.
Name.,,,,,,Start..End. Strand. Length... Accession...,,, GeneID.......... ..Locus_tag
| gp5 | 2730 | 3362 | 210 | NP_817596.1 | 1259217 | - | Bxz2_gp5 | - |
Which is the Phage receptor? Second part.
Second comparison :L5 phage genome
The second comparison is with L5 phage genome:
1- this is the result of Local (Smith-Waterman) comparison between the whole L5 sequence and Proteins of Mycobacterium ulcerans Agy99:
By BugView:
4208 comparisons for user's query sequence and Mycobacterium ulcerans Agy99.Finished in 4126 seconds.
Highest score = 1559 for cds_3629 (118619508)
Second score = 1108 for cds_2549 (118618448)
Third score = 993 for cds_3641 (118619519)
2-I have compared ,one by one, the indicated M.ulcerans cds with the L5 genome:
1°cds_3629
PE-PGRS family protein (Mycobacterium ulcerans Agy99)
Other Aliases: MUL_4367
Annotation: NC_008611.1 (4845511..4848744, complement)
GeneID: 4550406
By BugView:
88 comparisons for cds_3629 (118619508)
Finished in 1 seconds.
Highest score = 244 for cds_31 (9625462)
Second score = 126 for cds_27 (9625458)
Third score = 104 for cds_9 (9625440
L5p32
cds_31
gene 32 [Mycobacterium phage L5]
Other Aliases: L5p32
Other Designations: predicted 21.3kd protein
Annotation: NC_001335.1 (23536..24198)
GeneID: 2942918
Product Name.................. Start.. End.... Strand.. Length... Accession... GeneID... Locus_tag
| predicted 21.3kd protein | 23536 | 24198 | 220 | NP_039696.1 | 2942918 | - | L5p32 |
I have compared , the indicated cds 31 with the M.ulcerans genome:
By BugView:
4208 comparisons for cds_31 (9625462).
Finished in 37 seconds.
Highest score = 264 for cds_3679 (118619555)
Second score = 261 for cds_3560 (118619440)
Third score = 261 for cds_2695 (118618593)
2°cds_2549
88 comparisons for cds_2549 (118618448)
Finished in 0 seconds.
Highest score = 234 for cds_31 (9625462)
Second score = 119 for cds_30 (9625461)
Third score = 107 for cds_27 (9625458)
3°cds_3641
88 comparisons for cds_3641 (118619519)
Finished in 1 seconds.
Highest score = 234 for cds_31 (9625462)
Second score = 111 for cds_11 (9625442)
Third score = 109 for cds_27 (9625458)
Tuesday, 22 December 2009
Which is the Phage receptor? First part.
organism.......................................................accession...... length... proteins .RNAs .genes
Mycobacterium smegmatis str. MC2 155 .. ... NC_008596... 6988209 nt ...6716..... 54 .... 6938
Mycobacterium ulcerans Agy99....................... NC_008611 .. 5631606 nt... 4160..... 50..... 4981
Mycobacterium phage D29............................. NC_001900..... 49136 nt........ 79....... 5........ 84
Mycobacterium phage L5 ...............................NC_001335...... 52297 nt........ 85....... 3....... 88
Mycobacterium phage Bxz2........................... NC_004682 .....50913 nt......... 86 .......3....... 89
Mycobacterium phage TM4............................ NC_003387...... 52797 nt ........89........ 0.......89
Which is the Phage receptor?
This is my question... but before some information about Smith–Waterman algorithm.
The Smith-Waterman algorithm is a dynamic programming method for determining similarity between nucleotide or protein sequences.
From NCBI I find now this Cluster (Cluster VOGp0048 Uncharacterized). I have found by Bug View this protein Cluster before without knowing while I was finding the Phage receptor.
My intuition here is the comparison between each gene of this cluster with M.ulcerans genome.
By BugView I have compared the genome of M.ulcerans with each mycobacterium phage genome present in the list.
First comparison:D29 phage genome
The first comparison is with D29 phage genome:
1- this is the result of Local (Smith-Waterman) comparison between the whole D29 sequence and Proteins of Mycobacterium ulcerans Agy99:
By BugView:
4208 comparisons for user's query sequence and Mycobacterium ulcerans Agy99. Finished in 4107 seconds.
Highest score = 1581 for cds_3629 (118619508)
Second score = 1141 for cds_2549 (118618448)
Third score = 1044 for cds_3641 (118619519)
2-I have compared ,one by one, the indicated M.ulcerans cds with the D29 genome:
1°cds_3629
PE- PGRS proteins family (Mycobacterium ulcerans Agy99)
Other Aliases: MUL_4367
Annotation: NC_008611.1 (4845511..4848744, complement)
GeneID: 4550406
PE and PPE proteins family
The PE family of proteins all contain an amino-terminal region of about 110 amino acids.
The carboxyl terminus of this family are variable and fall into several classes. The largest class of PE proteins is the highly repetitive PGRS class which have a high glycine content. The function of these proteins is uncertain but it has been suggested that they may be related to antigenic variation of Mycobacterium tuberculosis.
These glycine-rich gene families code for PE and PPE proteins.
PE family has two subfamilies, PE and PE PGRS.
All the 99 members of PE family have a highly conserved N-terminal domain of 110 amino acid residues, whereas the C-terminal domain show marked heterogeneity, showing variation in size, sequence and repeat copy numbers.
The members of PE PGRS subfamily have a polyglycine-rich sequence at the C-terminus, along with the conserved amino terminus.
The C-terminal extension is characterized by the presence of multiple tandem repetitions of Gly–Gly–Ala or Gly–Gly–Asn encoded by PGRS motif.
The PPE family consists of 68 members and has a conserved N-terminal domain of 180 amino acid residues with varying carboxy terminal domains. The polymorphism of these two gene families is the major source of variation in M. tuberculosis complex in an otherwise genetically homogeneous bacterium[. Though the sub cellular localization of these proteins is still a mystery, a few of PE PGRS proteins have been considered as possible virulence factors in M. marinum , and some are cell surface constituents, involved in interaction of mycobacteria and macrophage.
By BugView:
84 comparisons for cds_3629 (118619508)
Finished in 1 seconds.
Highest score = 244 for cds_34 (9630416)
Second score = 126 for cds_30 (9630412)
Third score = 90 for cds_13 (9630395)
cds_34
gp32 [Mycobacterium phage D29]
Other Aliases: D29p30
Annotation: NC_001900.1 (24421..25092)
GeneID: 1261559
Name...... Start.. .....End..... Strand. Length.. Accession...... GeneID........... Locus_tag
| gp32 | 24421 | 25092 | 223 | NP_046848.1 | 1261559 | - | D29p30 |
Why the relation between gp32 and collagen protein?
I have compared , the indicated cds 34 with the M.ulcerans genome:
By BugView:
4208 comparisons for cds_34 (9630416)
Finished in 37 seconds.
Highest score = 263 for cds_2549 (118618448)
Second score = 258 for cds_3048 (118618940)
Third score = 258 for cds_3654 (118619532)
By BugView:
2°cds_2549
84 comparisons for cds_2549 (118618448)
Finished in 1 seconds.
Highest score = 263 for cds_34 (9630416)
Second score = 133 for cds_12 (9630394)
Third score = 112 for cds_30 (9630412)
3°cds_3641
By BugView:
Finished in 1 seconds.
Highest score = 223 for cds_34 (9630416)
Second score = 111 for cds_11 (9630393)
Third score = 97 for cds_30 (9630412)
Tuesday, 8 December 2009
Monday, 7 December 2009
Examining Genomes
For examining one or more genomes I describe an easy procedure using some free software packages from the Net:
1- Download the genomes from "The NCBI ftp site " or from other Web site.
2- Go to genome and choise the folder : example Virus.
3- Open the folder and select your genome and store it in your computer.
4- Select only genome file with end: .gbk or .gb or.ffn or Fasta.
5- Download :
BugView (genome browser for comparing the arrangement of genes on a pair of related genomes, and can also be used to view individual genomes).
DAMBE (software package for extensive data analysis in molecular biology and evolution).
e-Workbench (for comparative genome analysis).
(read all user manuals but they are simple and intuitive ):
6- Download the genome file by DAMBE and by e-Workbench.
7- Read by e-Workbench, one by one, the genome features and also check them by DAMBE.
8- Write by Excel programme each information regarding the genes.
9- Repeat points 6,7,8 for another genome.
10- Open BugView and compare two genomes.
Example: D29 and L5 mycobacteriophages
These are the results of my genome analysis using the procedure that I have described above:
1- This is the Excel table where I compare D29 genome against L5 genome.
2- This is the Excel table where I compare L5 genes against D29 genes.
3- This the Gene comparison image between L5 and D29 genes from the Excel table ( point 2).
4- These are the Dot plot images for Gene comparison, in numerical order, from the Excel table (point 2).
These genomes are not circular. They are opened in the circular viewer.
Genome comparison between D29 and L5 mycobacteriophages by BugView.
Genomic skew in D29 and L5 mycobacteriophages
The frequencies of bases in the genome of an organism are not always equiprobable. For example, the composition can have high "GC" content relative to the "AT".
The cause of 'skew' is not understood. Some possibilities include strong biases in mutation or DNA repair.
The minimum and maximum of a GC-skew can be used to predict the origin of replication (minimum) and the terminus location (maximum) in procaryotic genomes. Since the coding strand of bacterial genomic DNA tends to be purine rich and majority of genes are transcribed in the same direction as the movement of the replication fork there is asymmetric nucleotide composition along the
genome such that the DNA composition may
be used to predict the origin and termini of replication.
The origin of replication (ori) and replication terminus (ter) can be deduced by GC skew and cumulative GC skew analyses.
Purine skews are calculated from the first position in the sequence to the last: for each nucleotide, increment a counter if this nucleotide is a purine; decrement it if it is a pyrimidine. The effect is to compute the number of purines minus the number of pyrimidines from the first position to the current one. The X-axis of the skew graph is the position in the sequence; the Y-axis is the value of the counter at this position.
Keto and dinucleotide skews are calculated analogously, with the obvious differences.For a window size of k, every k'th position is drawn
The cumulative dinucleotide skews display the abundance of one nucleotide relative to another across the length of a DNA sequence that may represent a single gene or a complete genome.GC and AT skews have been widely used to predict termini and origins of replication in bacterial and mammalian genomes,
transcription start sites in plants and fungi ,
as well as transcription regions in the human genome .
The "DNA walk" is another method used to study
nucleotide distribution, first described by Lobry and used to detect origins of DNA replication in bacteria genomes.
To graph a DNA walk, a direction (North, South, East, and West) is assigned to each of the four nucleotides and the sequence is then plotted on a graph, beginning at (0,0) and moving one step in the direction specified by each successive nucleotide.
Tuesday, 1 December 2009
Sunday, 29 November 2009
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