Legionella Laboratory Testing | Biosan LaboratoriesAnthony Lewis
With increasing legionella contamination in Michigan-based businesses, it has become necessary for all commercial and residential properties in the state to opt for legionella laboratory testing from a reliable microbiological laboratory.
For More Details Visit: http://www.biosan.com/
CRISPR ……is a family of DNA sequences in bacteria. The sequences contain snippets of DNA from viruses that have attacked the bacterium. These snippets are used by the bacterium to detect and destroy DNA from similar viruses during subsequent attacks. These sequences play a key role in a bacterial defense system, and form the basis of a technology known as CRISPR/Cas9 that effectively and specifically changes genes within organisms
Accelerating Scientific Research Through Machine Learning and GraphNeo4j
Miroculus is a molecular diagnostics company that leverages the potential of microRNAs as biomarkers and has created the most easy-to-use and automated platform for their detection. MicroRNAs are small non-coding RNA molecules, whose primary role is to regulate the expression of our genes. Their discovery in circulation of body fluids such as blood plasma/serum, urine and saliva has been followed up by a multitude of studies, providing evidence that detection of specific microRNA molecules can give clues about a person’s health status and may therefore be used as biomarkers for various conditions.
Loom is an up-to-date snapshot of the scientific literature landscape focused on microRNAs that we built to expedite our own research. As of today, there is no compelling way to access much of the microRNA research. By using Loom's easy-to-use, interactive UI, the researcher is able to quickly locate the relevant sentences across many publications relating specific microRNAs with her disease or gene of interest. With this tool, our objective is to provide a visually compelling and complete overview of how microRNAs relate to specific diseases and genes.
At the backend, Loom is comprised of 4 microservices. The first one is a listener that fetches new publications daily that are available in the NCBI databases: PubMed for abstracts and PMC for full-text, open-access publications. Then, a natural language processor scans the publication, breaking them down into their constituent sentences and detecting mentions of microRNAs, genes and diseases.
Within each sentence, a machine learning scorer evaluates the strength and type of relationship on a scale from 0 to 1 and outputs the results in a graph database. The resulting graph database is then queried in real-time by the UI to retrieve the sentences and relationships the user is interested in.
Rapid 16S Next Generation Sequencing for Bacterial Identification in Polymicr...Thermo Fisher Scientific
In order to identify prokaryotic species in a sample, it is often necessary to culture the sample for hours or days to increase the abundance of bacteria to assayable levels. This often precludes the rapid identification of infectious species.
Furthermore, some species are not easily culturable. We
have developed a facile research method for identifying
bacterial species by 16S ribosomal RNA sequencing on the
Ion Torrent platform. The Ion 16S™ Metagenomics Kit is
designed to PCR amplify the hypervariable regions of the 16S
gene of bacteria. We used this kit to construct libraries from
15 retrospective samples of synovial fluid with various
bacterial species either spiked in or present at collection.
Libraries were sequenced on the Ion PGM™ system and the
data analysis performed using the Ion Reporter™ workflow
which provides an automated analysis solution. Bacteria
present in the samples were correctly identified in samples
containing a single spiked-in species, mixed-species samples,
and in infected samples. Thus, the Ion Torrent™ platform
provides a mechanism for rapidly identifying bacteria that are
present in research samples without culturing.
Legionella Laboratory Testing | Biosan LaboratoriesAnthony Lewis
With increasing legionella contamination in Michigan-based businesses, it has become necessary for all commercial and residential properties in the state to opt for legionella laboratory testing from a reliable microbiological laboratory.
For More Details Visit: http://www.biosan.com/
CRISPR ……is a family of DNA sequences in bacteria. The sequences contain snippets of DNA from viruses that have attacked the bacterium. These snippets are used by the bacterium to detect and destroy DNA from similar viruses during subsequent attacks. These sequences play a key role in a bacterial defense system, and form the basis of a technology known as CRISPR/Cas9 that effectively and specifically changes genes within organisms
Accelerating Scientific Research Through Machine Learning and GraphNeo4j
Miroculus is a molecular diagnostics company that leverages the potential of microRNAs as biomarkers and has created the most easy-to-use and automated platform for their detection. MicroRNAs are small non-coding RNA molecules, whose primary role is to regulate the expression of our genes. Their discovery in circulation of body fluids such as blood plasma/serum, urine and saliva has been followed up by a multitude of studies, providing evidence that detection of specific microRNA molecules can give clues about a person’s health status and may therefore be used as biomarkers for various conditions.
Loom is an up-to-date snapshot of the scientific literature landscape focused on microRNAs that we built to expedite our own research. As of today, there is no compelling way to access much of the microRNA research. By using Loom's easy-to-use, interactive UI, the researcher is able to quickly locate the relevant sentences across many publications relating specific microRNAs with her disease or gene of interest. With this tool, our objective is to provide a visually compelling and complete overview of how microRNAs relate to specific diseases and genes.
At the backend, Loom is comprised of 4 microservices. The first one is a listener that fetches new publications daily that are available in the NCBI databases: PubMed for abstracts and PMC for full-text, open-access publications. Then, a natural language processor scans the publication, breaking them down into their constituent sentences and detecting mentions of microRNAs, genes and diseases.
Within each sentence, a machine learning scorer evaluates the strength and type of relationship on a scale from 0 to 1 and outputs the results in a graph database. The resulting graph database is then queried in real-time by the UI to retrieve the sentences and relationships the user is interested in.
Rapid 16S Next Generation Sequencing for Bacterial Identification in Polymicr...Thermo Fisher Scientific
In order to identify prokaryotic species in a sample, it is often necessary to culture the sample for hours or days to increase the abundance of bacteria to assayable levels. This often precludes the rapid identification of infectious species.
Furthermore, some species are not easily culturable. We
have developed a facile research method for identifying
bacterial species by 16S ribosomal RNA sequencing on the
Ion Torrent platform. The Ion 16S™ Metagenomics Kit is
designed to PCR amplify the hypervariable regions of the 16S
gene of bacteria. We used this kit to construct libraries from
15 retrospective samples of synovial fluid with various
bacterial species either spiked in or present at collection.
Libraries were sequenced on the Ion PGM™ system and the
data analysis performed using the Ion Reporter™ workflow
which provides an automated analysis solution. Bacteria
present in the samples were correctly identified in samples
containing a single spiked-in species, mixed-species samples,
and in infected samples. Thus, the Ion Torrent™ platform
provides a mechanism for rapidly identifying bacteria that are
present in research samples without culturing.
Sequencing your poo with a usb stick - Linux.conf.au 2016 miniconf - mon 1 ...Torsten Seemann
This talk introduces a Linux Professional audience to bacterial genomics and modern sequencing technology. The title is slightly misleading and is a bit of clickbait. The diagrams are good.
WGS in public health microbiology - MDU/VIDRL Seminar - wed 17 jun 2015Torsten Seemann
How genomics is changing the practice of public health microbiology. The role of whole genome sequencing as the "one true assay". Another powerful tool for the epidemiologist.
Metagenomics is the study of metagenomes, genetic material recovered directly from environmental samples. The broad field was referred to as environmental genomics, ecogenomics or community genomics. Recent studies use "shotgun" Sanger sequencing or next generation sequencing (NGS) to get largely unbiased samples of all genes from all the members of the sampled communities.
Lecture on nano_biotech and art by Victoria Vesna, media artist and professor. She is joined by Siddharth Ramakrishnan, research scientist, Columbia University and Romie Littrell, graduate student in bioengineering, UCLA.
A cloning vector is a genome that can accept the target DNA and increase the number of copies through its own autonomous replication.
An adapter or adaptor, or a linker in genetic engineering is a short, chemically synthesized, single-stranded or double-stranded oligonucleotide that can be ligated to the ends of other DNA or RNA molecules. It may be used to add sticky ends to cDNA allowing it to be ligated into the plasmid much more efficiently.
Assessment of microbial population diversity in polymicrobial research sample...Thermo Fisher Scientific
Analysis of 16S sequences in microbial populations using NGS gives a rapid overview of the community diversity, and is usually performed by sequencing one or two hypervariable regions (V-regions), out of the nine present in the 16S rRNA gene. In this study we compared the community structure of fecal, oral and water microbiomes by analyzing sequences from a single variable region, or from the seven V-regions (V2, V3, V4, V6-7, V8 and V9) included into Ion 16S™ Metagenomics Kit (multi-V analysis)
Viral metagenomics is the study of viral genetic material sourced directly from the environment rather than from a host or natural reservoir. The goal is to ascertain the viral diversity in the environment that is often missed in studies targeting specific potential reservoirs.
Application of Whole Genome Sequencing in the infectious disease’ in vitro di...ExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Applications of WGS in industry. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management -23-25 May 2016, Rome, Italy.
Web Apollo: Lessons learned from community-based biocuration efforts.Monica Munoz-Torres
This presentation tries to highlight the importance and relevance of community-based curation of biological data. It describes the results of harvesting expertise from dispersed researchers assigning functions to predicted and curated peptides, as well as collaborative efforts for standardization of genes and gene product attributes across species and databases.
Sequencing your poo with a usb stick - Linux.conf.au 2016 miniconf - mon 1 ...Torsten Seemann
This talk introduces a Linux Professional audience to bacterial genomics and modern sequencing technology. The title is slightly misleading and is a bit of clickbait. The diagrams are good.
WGS in public health microbiology - MDU/VIDRL Seminar - wed 17 jun 2015Torsten Seemann
How genomics is changing the practice of public health microbiology. The role of whole genome sequencing as the "one true assay". Another powerful tool for the epidemiologist.
Metagenomics is the study of metagenomes, genetic material recovered directly from environmental samples. The broad field was referred to as environmental genomics, ecogenomics or community genomics. Recent studies use "shotgun" Sanger sequencing or next generation sequencing (NGS) to get largely unbiased samples of all genes from all the members of the sampled communities.
Lecture on nano_biotech and art by Victoria Vesna, media artist and professor. She is joined by Siddharth Ramakrishnan, research scientist, Columbia University and Romie Littrell, graduate student in bioengineering, UCLA.
A cloning vector is a genome that can accept the target DNA and increase the number of copies through its own autonomous replication.
An adapter or adaptor, or a linker in genetic engineering is a short, chemically synthesized, single-stranded or double-stranded oligonucleotide that can be ligated to the ends of other DNA or RNA molecules. It may be used to add sticky ends to cDNA allowing it to be ligated into the plasmid much more efficiently.
Assessment of microbial population diversity in polymicrobial research sample...Thermo Fisher Scientific
Analysis of 16S sequences in microbial populations using NGS gives a rapid overview of the community diversity, and is usually performed by sequencing one or two hypervariable regions (V-regions), out of the nine present in the 16S rRNA gene. In this study we compared the community structure of fecal, oral and water microbiomes by analyzing sequences from a single variable region, or from the seven V-regions (V2, V3, V4, V6-7, V8 and V9) included into Ion 16S™ Metagenomics Kit (multi-V analysis)
Viral metagenomics is the study of viral genetic material sourced directly from the environment rather than from a host or natural reservoir. The goal is to ascertain the viral diversity in the environment that is often missed in studies targeting specific potential reservoirs.
Application of Whole Genome Sequencing in the infectious disease’ in vitro di...ExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Applications of WGS in industry. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management -23-25 May 2016, Rome, Italy.
Web Apollo: Lessons learned from community-based biocuration efforts.Monica Munoz-Torres
This presentation tries to highlight the importance and relevance of community-based curation of biological data. It describes the results of harvesting expertise from dispersed researchers assigning functions to predicted and curated peptides, as well as collaborative efforts for standardization of genes and gene product attributes across species and databases.
Forensic investigation involves the collecting, assembling, and analysis of all crime-related evidence with the aim of getting to a conclusion about a suspect. Humans have microorganisms present in the gut, mouth, and skin, unique to each individual. Individual microbiome can be distinguished based on the bacterial 16S rRNA to tell the bacterial species diversity between and among persons. Sterilized swab-sticks were used to sample fifteen individuals’ fingertips, their personal items, office doorknob and a college photocopier. Skin-associated bacteria were readily recovered from surfaces and the structure of these bacterial communities can be used to link individuals to the objects they had touched. We compared the bacterial communities on objects and skin to match the objects to the individual. The 16S rRNA gene PCR polymorphism was used to analyze the bacterial community for each person and object. The higher similarity of bacterial community between individuals’ and personal laptop keyboards, office chairs and office member’s fingertips were evident than between the doorknob and the photocopier. Highest bacterial species diversity was observed in doorknob followed by the photocopier. Hence, an individual’s bacterial profile can be used as a human identification tool alongside other tools in forensic fields especially in cases where there is evidence of deficiency.
Key-words: Microbial signature, Forensics, 16S rRNA, Individual person, Skin bacteria, Fingerprint
This presentation was created by Ioanna Leontiou and it is intended as a creative and flexible tool for students on Biological sciences who focus on the chromosome segregation. It is created to facilitate students performing research projects in our lab (especially during Covid restrictions), but it is suitable for every student who wants to learn more about chromosomes and the molecular mechanism controlling chromosome segregation. The presentation includes a generic overview of the cell division, illustrates the chromosome structure and provides molecular details of the spindle assembly checkpoint, an important pathway that ensures high fedility of chromosome segregation through mitosis. It also includes an introduction to some of the molecular biology techniques used in a yeast lab and incoporates some fluorescent microscopy images/videos. At the end of the presentantion there is a list of open access scientific publications for further reading on the the molecular mechanism of spindle checkpoint and some links of some very interesting sites, which include a range of videos on laboratory molecular biology techniques, research talks and guided papers. The purpose of this presentantion is to create a piece of work that students could return to when needed. Diagramms and illustrations are also encouranged to be used by scientists, science communicators and educators.
This presentation is licensed under a Creative Common Attribution-ShareAlike 4.0 (CC BY-SA 4.0), unless otherwise stated on the specific slide.
Forensic Identification using skin bacterial communities
1.
2. Human skin harbors large numbers of
bacteria
Studies have shown skin-associated bacterial
communities are diverse
So diverse that only 13% of bacterial
phylotypes are shared between any given
person.
3. Bacteria communities are actually fairly stable
as well
Communities return to normal within hours
of hand washing.
Individuals have personally unique, temporary
stable, and transferable skin-associated
bacterial colonies.
4. The authors hypothesize that they could use
the residual skin bacteria left on objects for
forensic identification, matching the bacteria
on the object to the skin-associated bacteria
of the individual who touched the object.
5. Three criteria had to be met
◦ The bacteria collected had to allow for adequate
characterization
◦ Skin bacteria had to persist for days to week
◦ Surfaces touched had to be linked to individuals by
a degree of similarity.
6. For the keyboard study, three individuals and
their keyboards were swabbed.
For the mouse study they used nine
individuals.
For the “storage” study they swabbed 2
healthy adults in the right axillary.
7. Target gene 16s rRNA
Used MO BIO PowerSoil DNA Isolation kits.
0.1% Agarose gels were used
DNA staining was done using SYBR sage DNA
gel stain in 0.5xTBE
Pyrosequencing was carried out using454 Life
Sciences genome Sequencer FLX instrument.
8. This image has been created during "DensityDesign
Integrated Course Final Synthesis Studio" at Polytechnic
University of Milan, organized by DensityDesign Research
Lab. Image is released under CC-BY-SA licence.
Attribution goes to "Jacopo Pompilii, DensityDesign
Research Lab"
14. Criteria one and three met.
Bacteria communities resembled that of the
owners hands.
Similarity between the colonies was shown.
Bacteria can be recovered from relatively
small surfaces.
15. Two individuals bacterial communities stayed
relatively similar.
Standard indoor conditions showed the
bacterial community owner could still be
reasonably identified
16. Showed bacterial communities still remained
unique to their owners
They remained unique after time had passed.
Was compared to 270 stored bacterial
community genomes.
17. More studies like this are needed
Forensics is a science that needs to be sure
and certain of results.
Further testing would allow for more accuracy
18. Fierer, Noah, et al. "Forensic identification
using skin bacteria communities."
Proceedings of the National Academy of
Sciences of the United States of America
107.14 (2010): 6477-6481. Web.
Lawley, Rochard. A Revolution in the
Microbiology Labratory. 7 October 2009.
web site. 22 February 2015.
<http://www.foodsafetywatch.org/features
/a-revolution-in-the-microbiology-
laboratory/>.