Page 3

Wet Lab and Bioinformatics

Pages
Key Expertise    1
Time Tables    2
Projects    3
Articles    4
eLectures    5
Manuals    6
Miscellaneous    7
Former Time Tables    8
Former Lectures    9
Former Lab Calculations  10
Remarks   11

 Contact: henrik@d-dahlerup.com

Materials 2011-2020

Presenting Materials Generated by Henrik Deber Dahlerup


Projects


Current activity:

Review: Antibiotic resistance ampC: Development and consequences  (pdf) In progress 

Manual Vol 2: Bacterial genomes: DNA sequences etc.  (pdf) In progress


√ Suggestion: Look primarily at ‘Tools applied’ on the right side.

2020

Applying DNA Sequencing During Isolation and Identification of Photobacterium

Tools applied: Traditional Microbiology and Molecular Biology

Analyzing  Food Related Species of Photobacterium:

Isolation and identification of Photobacterium using DNA sequencing on gyrB and 16S rRNA genes :

Identification tests of isolated bacteria and DNA sequencing of isolates using gyrB and 16S rRNA genes.

♦   Lab work with gyrB and 16S rRNA genes:     1 2 3 4 5

♦   Lab work with other approaches:     1 2 3

♦   Other activities:     1 2 3 4 5 6 7

♦   Produced DNA-Sequencing-Methods-Protocol (8 pages)     [ pdf id= 1654 ]

♦   Lab book vol. 1 and 2 (Many pages are removed):


2019

Applying Improved Culture Methods, DNA Sequencing and MALDI-TOF MS During Isolation and Identification of Lactic Acid Bacteria

Tools applied: Traditional Microbiology and Molecular Biology

Analyzing Technologically Food Related Species of Streptococcus, Lactobacillus, Leuconostoc etc.:

Isolation and identification of lactic acid bacteria using improved culture methods, DNA sequencing and MALDI-TOF MS :

Opinion article, LAB Identification

LAB Identification, Suppl. file

Identification tests of isolated bacteria and sequencing of isolates with a technologically related food relevance.

♦   Working with alternative improved culture media (i.e. pectin ‘agar’ etc.), culture media (i.e. improved with antibiotics), sampling and working with isolated DNA from lactic acid bacteria:

Lab work:   1  2  3  4  5  6

♦   Helping students at The Biological Chemistry Course (Lactic acid bacteria: isolation, identification, cloning and detecting/determine gene functions).

Professional help:   1  2

♦   Helping students getting introduced to protein gel assays.

Professional help:   1  2  3

♦   Helping students getting introduced to brewery samples on culture media (improved with antibiotics).

Professional help:   1  2

♦   Helping students getting introduced to isolating, identification and analyzing lactic acid bacteria using culture media and a 96 wells plate reader.

Professional help:   1  2  3  4  5  6  7  8

♦   Helping students improve and test alternative culture media.

Professional help:   1  2  3  4


Detecting and Circumventing Antibiotic Resistance Against New Antibiotics Not Yet Released

Tools applied: Traditional Microbiology, Cloning, Genetic Techniques

Analyzing for Antibiotic Resistance in Mutants of isolate E. coli K12 MG1655:

Investigate how E. coli K12 MG1655 becomes resistant toward specific antimicrobial peptides not yet commercial released as antibiotics.

♦   Working with resistant clones using advanced genetic techniques:

Lab work:   1  2  3  4  5  6  7

Lab book vol. 1 (Many pages are removed from this pdf-file)

(Vol. 2 is not showed)

♦   Helping a friend getting introduced to these assays.

Professional help:   1  2  3  4


Gene Exchange Involving S. aureus, E. coli, and Salmonella

Tools applied: Comparative Genomic Bioinformatics

The New Era of Detailed Insight into Gene Exchange Between Species

Provide detailed information about gene exchange in genomes and plasmids of Staphylococcus and other relevant isolates applying comparative genomic Bioinformatics.

1. Review, Gene Exchange (pdf)

Review, Gene Exchange, Suppl. File (pdf)

2. Review, MRSA (pdf)

Review, MRSA, Suppl. File (pdf)

3. Review, Hot Spots (pdf)

Review, Hot Spots, Suppl. File (pdf)


2018

Conserved Genes and Point Mutations Involving S. aureus, E. coli, and Salmonella

Tools applied: Phylogenetic Trees and Multiple Alignments

A Closer Look at Dynamic and Conserved Antibiotic Resistance Genes of Bacteria

Provide detailed information about changes or a lack of changes in genes of both genomes and plasmids applying comparative genomic Bioinformatics.

1. Research Report, Antibiotic Res. (pdf)

2017


Compare Alternative SCC Transposons of Strain USA300 against Genomes

Tools applied: Comparative Genomics

SCC’s of Strain USA300 Project:

Describe and provide tools to scan a circularized SCC transposon against strain collections by applying comparative genomic bioinformatics.

Research Report, USA300 SCC transposons (pdf)


Horizontal Gene Transfer of Resistance, Virulence and Fitness Factors

Tools applied: Comparative Genomic Bioinformatics

Horizontal Gene Transfer of Staphylococcus:

Investigate relevance and provide locations of future potentials and ‘integration hot spots’ on genomes and plasmids of Staphylococcus and other relevant isolates applying comparative genomic Bioinformatics. The first review provide information which is ‘basics’ for the second review, and the second review provide ‘basics’ for the third review.

“Review, Multidrug Resistant Strains” presents for the first time Zoom BLAST atlases on plasmids to the authors knowledge.

1. Review, Staphylococci (pdf)

Review, Staphylococci, Suppl. File (pdf)

2. Review, Future Potentials of MRSA (pdf)

Review, Future Potentials of MRSA, Suppl. File (pdf)

3. Review, Multidrug Resistant Strains (pdf)

Review, Multidrug Resistant Strains, Suppl. File (pdf)

4. Review, Mobile Plasmids (pdf)

Review, Mobile Plasmids, Suppl. File (pdf)

Review 4 show in a comprehensive way how to combine our understanding of hot spots (thus integration sites) and lager mechanisms as an example natural selection of MDR-encoded bacteria cells.

 


Compare Plasmid Genes of Strain USA300 against Genomes

Tools applied: Comparative Genomics

Plasmids of Strain USA300 Project:

Describe and provide tools to scan a plasmid against strain collections by applying comparative genomic bioinformatics.

Research Report, USA300 isolates (pdf)


2015

Lectures, Exercises for Students, thus Establishing a Microbiology Lab

Tools applied: Traditional Microbiology

Analyzing for Staphylococcus aureus, E. coli and Salmonella:

I was hired as an academic employee and my work had two goals:

♦   to establish traditional microbiology lectures and exercises for students at a short higher educational level. A non-academic teacher apply them today to teach in this area.

Practical exercises:  1  2  3  4  5  6  7  8  9 

♦   to establish a Microbiology Lab in a rather  large empty room.

The lab under construction:   1  2  3

 


2013

Transfer of SCCmec from CoagulaseNegative Staphylococci to MRSA

Tools applied: Cloning and Traditional Microbiology

SCCmec Projects:

Transfer of SCCmec from CoagulaseNegative Staphylococci to MRSA using cloning and traditional microbiology techniques.

Research Report (Traditional Microbiology, Biofilm) (pdf)

Protocol (Traditional Microbiology, Biofilm) (pdf)

Research Report (MRSA Cloning) (pdf)

Protocol (E. coli strain S171: Producing competent cells) (pdf)

Protocol (S. aureus strain RN4220: Producing competent cells) (pdf)

 


2012

Setting Up and Evaluating Assays

Tools applied: Real Time QPCR

Real Time QPCR Project:

Setting up and evaluating the performance of three different Real Time QPCR assays.

SOP Research Report (Real Time QPCR assays) (pdf)

SOP Protocol (Real Time QPCR assay) (pdf)


Streptococcus equi Subspecies

Tools applied: Comparative Genomic Bioinformatics

The Origin of Streptococcus equi Subspecies:

Discuss the origin of Streptococcus equi subspecies applying comparative genomic bioinformatics.

Opinion Article, Horizontal Gene Transfer (pdf)


SCCmecKeyPC – A noncommercial product

Tools applied: BLAST related Bioinformatics

SCCmec Project:

A bioinformatic project on the automated identification and annotation of the virulence cassette SCCmec in Methicillin Resistant Staphylococcus aureus (MRSA) genomes.

Target group: People who read MRSA articles and with no programming experience.

Research Article, SCCmecKey (pdf) Processed

SCCmecKeyPC Version 0.3.03 (Last updated May 2016):

This Version can preclassify the SCCmec type (i.e. typing SCCmec with a decreased amount of false positives and false negatives compared to Version 0.2).

Short presentations (video):

A SCCmecKeyPC to Large Jobs with Several Whole Genome Sequences (Type 3, 6 min.) Click here

Activate the SCCmecKeyPC and Analyze Your Genome Sequence (Type 2, 8 min.) Click here

Activate the SCCmecKeyPC and Analyze Your Genome Sequence (Type 1, 8 min.) Click here

Instructions (pdf)

A few SCCmec-types (pdf)

Former SCCmecKeyPC Versions


2011

Comparative Microbial Genomics

Tools applied: Comparative Genomic Bioinformatics

Comparative Genomics Project:

Describe and provide tools circumventing (i.e., ‘solving’) events of the evolution (i.e associated with transposon SCCmec and evolutionary ‘bottlenecks’) by applying comparative genomic bioinformatics.

Research Article, MRSA SCCmec type XI (pdf)

Review, Virulence Factors (pdf)


Expression of ccr-genes and SCCmec Allocation

Tools applied: Real Time Reverse Transcription QPCR, Cloning, Traditional Microbiology and Bioinformatics

Methicillin Resistant Staphylococcus aureus (MRSA) associated with ccr expression and SCCmec allocation.
(i.e. SCCmec allocation from the chromosomal DNA and not SCCmec allocation from the cell.)

Article, (Real Time Reverse Transcription QPCR and Traditional Microbiology) (pdf)


Pages
Key Expertise    1
Time Tables    2
Projects    3
Articles    4
eLectures    5
Manuals    6
Miscellaneous    7
Former Time Tables    8
Former Lectures    9
Former Lab Calculations  10
Remarks   11


©2020 Henrik Deber Dahlerup

3