This document discusses indoor microbial ecology and DNA sequencing approaches to studying microbiomes. It provides an overview of sequencing technologies and their applications to microbial studies. It also outlines current and future challenges, such as data overload from massive sequencing datasets, limitations of short read lengths, lack of reference data, and challenges in turning data into knowledge. Solutions proposed include new algorithms, automated analysis, distributed data sharing, expanding reference databases, and linking 'omics data to other fields.
Introduction to molecular genetic. ADN an ARN, structure and function.
Central dogma of molecular biology. Replication, transcription and translation.
Mutation, causes and classification
Introduction to molecular genetic. ADN an ARN, structure and function.
Central dogma of molecular biology. Replication, transcription and translation.
Mutation, causes and classification
Perl - die Taschenkettensäge unter den Programmiersprachen - Vortrag 2003Brigitte Jellinek
Vorstellung der Programmiersprache Perl auf drei Ebenen: für Programmier-Anfänger, für Fortgechrittene und für Profis. inkl. Buchtipps zu Perl.
Ein Vortrag den ich ursprünglich am Chaos Communication Congress 2000 in Berlin gehalten habe, hier in der Version von 2003.
INTRODUCTION
RIBOZYME CATALYSIS
SMALL SELF CLEAVING RIBOZYME
HAMMERHEAD
HAIRPIN
HDV
COMPLEX RIBOZYME
GROUP I INTRON
GROUP II INTRON
RNaseP
CONCLUSION
REFERENCE
Perl - die Taschenkettensäge unter den Programmiersprachen - Vortrag 2003Brigitte Jellinek
Vorstellung der Programmiersprache Perl auf drei Ebenen: für Programmier-Anfänger, für Fortgechrittene und für Profis. inkl. Buchtipps zu Perl.
Ein Vortrag den ich ursprünglich am Chaos Communication Congress 2000 in Berlin gehalten habe, hier in der Version von 2003.
INTRODUCTION
RIBOZYME CATALYSIS
SMALL SELF CLEAVING RIBOZYME
HAMMERHEAD
HAIRPIN
HDV
COMPLEX RIBOZYME
GROUP I INTRON
GROUP II INTRON
RNaseP
CONCLUSION
REFERENCE
Ribotyping
Introduction
History
Ribosomes
Ribosomal RNA
Principle of ribotyping
16S rRNA
Procedure of ribotyping
Types of ribotyping
Use of ribotyping
Advantage and disadvantage of ribotyping
Reference
Innovations in Sequencing & Bioinformatics
Talk for
Healthy Central Valley Together Research Workshop
Jonathan A. Eisen University of California, Davis
January 31, 2024 linktr.ee/jonathaneisen
Thoughts on UC Davis' COVID Current ActionsJonathan Eisen
Slides I used for a presentation to Chancellor May's leadership council about the current state of UC Davis' response to COVID and how it could be improved
Basavarajeeyam is an important text for ayurvedic physician belonging to andhra pradehs. It is a popular compendium in various parts of our country as well as in andhra pradesh. The content of the text was presented in sanskrit and telugu language (Bilingual). One of the most famous book in ayurvedic pharmaceutics and therapeutics. This book contains 25 chapters called as prakaranas. Many rasaoushadis were explained, pioneer of dhatu druti, nadi pareeksha, mutra pareeksha etc. Belongs to the period of 15-16 century. New diseases like upadamsha, phiranga rogas are explained.
263778731218 Abortion Clinic /Pills In Harare ,sisternakatoto
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Basavarajeeyam is a Sreshta Sangraha grantha (Compiled book ), written by Neelkanta kotturu Basavaraja Virachita. It contains 25 Prakaranas, First 24 Chapters related to Rogas& 25th to Rasadravyas.
Recomendações da OMS sobre cuidados maternos e neonatais para uma experiência pós-natal positiva.
Em consonância com os ODS – Objetivos do Desenvolvimento Sustentável e a Estratégia Global para a Saúde das Mulheres, Crianças e Adolescentes, e aplicando uma abordagem baseada nos direitos humanos, os esforços de cuidados pós-natais devem expandir-se para além da cobertura e da simples sobrevivência, de modo a incluir cuidados de qualidade.
Estas diretrizes visam melhorar a qualidade dos cuidados pós-natais essenciais e de rotina prestados às mulheres e aos recém-nascidos, com o objetivo final de melhorar a saúde e o bem-estar materno e neonatal.
Uma “experiência pós-natal positiva” é um resultado importante para todas as mulheres que dão à luz e para os seus recém-nascidos, estabelecendo as bases para a melhoria da saúde e do bem-estar a curto e longo prazo. Uma experiência pós-natal positiva é definida como aquela em que as mulheres, pessoas que gestam, os recém-nascidos, os casais, os pais, os cuidadores e as famílias recebem informação consistente, garantia e apoio de profissionais de saúde motivados; e onde um sistema de saúde flexível e com recursos reconheça as necessidades das mulheres e dos bebês e respeite o seu contexto cultural.
Estas diretrizes consolidadas apresentam algumas recomendações novas e já bem fundamentadas sobre cuidados pós-natais de rotina para mulheres e neonatos que recebem cuidados no pós-parto em unidades de saúde ou na comunidade, independentemente dos recursos disponíveis.
É fornecido um conjunto abrangente de recomendações para cuidados durante o período puerperal, com ênfase nos cuidados essenciais que todas as mulheres e recém-nascidos devem receber, e com a devida atenção à qualidade dos cuidados; isto é, a entrega e a experiência do cuidado recebido. Estas diretrizes atualizam e ampliam as recomendações da OMS de 2014 sobre cuidados pós-natais da mãe e do recém-nascido e complementam as atuais diretrizes da OMS sobre a gestão de complicações pós-natais.
O estabelecimento da amamentação e o manejo das principais intercorrências é contemplada.
Recomendamos muito.
Vamos discutir essas recomendações no nosso curso de pós-graduação em Aleitamento no Instituto Ciclos.
Esta publicação só está disponível em inglês até o momento.
Prof. Marcus Renato de Carvalho
www.agostodourado.com
Lung Cancer: Artificial Intelligence, Synergetics, Complex System Analysis, S...Oleg Kshivets
RESULTS: Overall life span (LS) was 2252.1±1742.5 days and cumulative 5-year survival (5YS) reached 73.2%, 10 years – 64.8%, 20 years – 42.5%. 513 LCP lived more than 5 years (LS=3124.6±1525.6 days), 148 LCP – more than 10 years (LS=5054.4±1504.1 days).199 LCP died because of LC (LS=562.7±374.5 days). 5YS of LCP after bi/lobectomies was significantly superior in comparison with LCP after pneumonectomies (78.1% vs.63.7%, P=0.00001 by log-rank test). AT significantly improved 5YS (66.3% vs. 34.8%) (P=0.00000 by log-rank test) only for LCP with N1-2. Cox modeling displayed that 5YS of LCP significantly depended on: phase transition (PT) early-invasive LC in terms of synergetics, PT N0—N12, cell ratio factors (ratio between cancer cells- CC and blood cells subpopulations), G1-3, histology, glucose, AT, blood cell circuit, prothrombin index, heparin tolerance, recalcification time (P=0.000-0.038). Neural networks, genetic algorithm selection and bootstrap simulation revealed relationships between 5YS and PT early-invasive LC (rank=1), PT N0—N12 (rank=2), thrombocytes/CC (3), erythrocytes/CC (4), eosinophils/CC (5), healthy cells/CC (6), lymphocytes/CC (7), segmented neutrophils/CC (8), stick neutrophils/CC (9), monocytes/CC (10); leucocytes/CC (11). Correct prediction of 5YS was 100% by neural networks computing (area under ROC curve=1.0; error=0.0).
CONCLUSIONS: 5YS of LCP after radical procedures significantly depended on: 1) PT early-invasive cancer; 2) PT N0--N12; 3) cell ratio factors; 4) blood cell circuit; 5) biochemical factors; 6) hemostasis system; 7) AT; 8) LC characteristics; 9) LC cell dynamics; 10) surgery type: lobectomy/pneumonectomy; 11) anthropometric data. Optimal diagnosis and treatment strategies for LC are: 1) screening and early detection of LC; 2) availability of experienced thoracic surgeons because of complexity of radical procedures; 3) aggressive en block surgery and adequate lymph node dissection for completeness; 4) precise prediction; 5) adjuvant chemoimmunoradiotherapy for LCP with unfavorable prognosis.
Knee anatomy and clinical tests 2024.pdfvimalpl1234
This includes all relevant anatomy and clinical tests compiled from standard textbooks, Campbell,netter etc..It is comprehensive and best suited for orthopaedicians and orthopaedic residents.
These simplified slides by Dr. Sidra Arshad present an overview of the non-respiratory functions of the respiratory tract.
Learning objectives:
1. Enlist the non-respiratory functions of the respiratory tract
2. Briefly explain how these functions are carried out
3. Discuss the significance of dead space
4. Differentiate between minute ventilation and alveolar ventilation
5. Describe the cough and sneeze reflexes
Study Resources:
1. Chapter 39, Guyton and Hall Textbook of Medical Physiology, 14th edition
2. Chapter 34, Ganong’s Review of Medical Physiology, 26th edition
3. Chapter 17, Human Physiology by Lauralee Sherwood, 9th edition
4. Non-respiratory functions of the lungs https://academic.oup.com/bjaed/article/13/3/98/278874
Title: Sense of Smell
Presenter: Dr. Faiza, Assistant Professor of Physiology
Qualifications:
MBBS (Best Graduate, AIMC Lahore)
FCPS Physiology
ICMT, CHPE, DHPE (STMU)
MPH (GC University, Faisalabad)
MBA (Virtual University of Pakistan)
Learning Objectives:
Describe the primary categories of smells and the concept of odor blindness.
Explain the structure and location of the olfactory membrane and mucosa, including the types and roles of cells involved in olfaction.
Describe the pathway and mechanisms of olfactory signal transmission from the olfactory receptors to the brain.
Illustrate the biochemical cascade triggered by odorant binding to olfactory receptors, including the role of G-proteins and second messengers in generating an action potential.
Identify different types of olfactory disorders such as anosmia, hyposmia, hyperosmia, and dysosmia, including their potential causes.
Key Topics:
Olfactory Genes:
3% of the human genome accounts for olfactory genes.
400 genes for odorant receptors.
Olfactory Membrane:
Located in the superior part of the nasal cavity.
Medially: Folds downward along the superior septum.
Laterally: Folds over the superior turbinate and upper surface of the middle turbinate.
Total surface area: 5-10 square centimeters.
Olfactory Mucosa:
Olfactory Cells: Bipolar nerve cells derived from the CNS (100 million), with 4-25 olfactory cilia per cell.
Sustentacular Cells: Produce mucus and maintain ionic and molecular environment.
Basal Cells: Replace worn-out olfactory cells with an average lifespan of 1-2 months.
Bowman’s Gland: Secretes mucus.
Stimulation of Olfactory Cells:
Odorant dissolves in mucus and attaches to receptors on olfactory cilia.
Involves a cascade effect through G-proteins and second messengers, leading to depolarization and action potential generation in the olfactory nerve.
Quality of a Good Odorant:
Small (3-20 Carbon atoms), volatile, water-soluble, and lipid-soluble.
Facilitated by odorant-binding proteins in mucus.
Membrane Potential and Action Potential:
Resting membrane potential: -55mV.
Action potential frequency in the olfactory nerve increases with odorant strength.
Adaptation Towards the Sense of Smell:
Rapid adaptation within the first second, with further slow adaptation.
Psychological adaptation greater than receptor adaptation, involving feedback inhibition from the central nervous system.
Primary Sensations of Smell:
Camphoraceous, Musky, Floral, Pepperminty, Ethereal, Pungent, Putrid.
Odor Detection Threshold:
Examples: Hydrogen sulfide (0.0005 ppm), Methyl-mercaptan (0.002 ppm).
Some toxic substances are odorless at lethal concentrations.
Characteristics of Smell:
Odor blindness for single substances due to lack of appropriate receptor protein.
Behavioral and emotional influences of smell.
Transmission of Olfactory Signals:
From olfactory cells to glomeruli in the olfactory bulb, involving lateral inhibition.
Primitive, less old, and new olfactory systems with different path
Flu Vaccine Alert in Bangalore Karnatakaaddon Scans
As flu season approaches, health officials in Bangalore, Karnataka, are urging residents to get their flu vaccinations. The seasonal flu, while common, can lead to severe health complications, particularly for vulnerable populations such as young children, the elderly, and those with underlying health conditions.
Dr. Vidisha Kumari, a leading epidemiologist in Bangalore, emphasizes the importance of getting vaccinated. "The flu vaccine is our best defense against the influenza virus. It not only protects individuals but also helps prevent the spread of the virus in our communities," he says.
This year, the flu season is expected to coincide with a potential increase in other respiratory illnesses. The Karnataka Health Department has launched an awareness campaign highlighting the significance of flu vaccinations. They have set up multiple vaccination centers across Bangalore, making it convenient for residents to receive their shots.
To encourage widespread vaccination, the government is also collaborating with local schools, workplaces, and community centers to facilitate vaccination drives. Special attention is being given to ensuring that the vaccine is accessible to all, including marginalized communities who may have limited access to healthcare.
Residents are reminded that the flu vaccine is safe and effective. Common side effects are mild and may include soreness at the injection site, mild fever, or muscle aches. These side effects are generally short-lived and far less severe than the flu itself.
Healthcare providers are also stressing the importance of continuing COVID-19 precautions. Wearing masks, practicing good hand hygiene, and maintaining social distancing are still crucial, especially in crowded places.
Protect yourself and your loved ones by getting vaccinated. Together, we can help keep Bangalore healthy and safe this flu season. For more information on vaccination centers and schedules, residents can visit the Karnataka Health Department’s official website or follow their social media pages.
Stay informed, stay safe, and get your flu shot today!
1. Microbial Ecology
Indoor Microbial Ecology
(DNA Sequencing Focus)
Indoor Air 2011
Workshop on Microbiomes of the Built Environment
Jonathan A. Eisen, Ph.D.
University of California, Davis
DOE Joint Genome Institute
Twitter: @phylogenomics
2. Outline
• Introduction
• Sequencing in microbial studies
• Sequencing technologies
• Current and future issues
7. A Field Guide to Microbes
• What should be included
• Catalog of types of organism
• Functional diversity
• Biogeography (space and time)
• Niche information
• Means for identification
• “Natural” locations
• “Non natural (i.e., built) locations
8. Microbial Ecology
• Much more than just a field guide
• Interactions of microbes with each other
with macroorganisms, and the
environment
• Mechanisms and rules of such
interactions
• Can be applied to any environment(s)
including built ones
9. I: Sequencing and Microbes
• Sequencing is useful as a tool in studies
of microbial ecology for many reasons
• It is complimentary to other means of
study
10. Era I: rRNA Tree of Life
Bacteria
• Appearance of
microbes not
informative (enough)
• rRNA Tree of Life
Archaea identified two major
groups of organisms
w/o nuclei
• rRNA powerful for
many reasons, though
not perfect
Eukaryotes
Barton, Eisen et al. “Evolution”, CSHL Press. 2007.
Based on tree from Pace 1997 Science 276:734-740
15. PCR & phylogenetic analysis of rRNA
DNA
extraction PCR
Makes lots Sequence
PCR of copies of rRNA genes
the rRNA
genes in
sample
rRNA1
5’...ACACACATAGGTGGAGC
TAGCGATCGATCGA... 3’
Phylogenetic tree Sequence alignment = Data matrix
rRNA2
rRNA1 rRNA2
rRNA1 A C A C A C 5’..TACAGTATAGGTGGAGCT
rRNA4 AGCGACGATCGA... 3’
rRNA3 rRNA2 T A C A G T
rRNA3
rRNA3 C A C T G T 5’...ACGGCAAAATAGGTGGA
E. coli Humans rRNA4 C A C A G T TTCTAGCGATATAGA... 3’
Yeast E. coli A G A C A G rRNA4
5’...ACGGCCCGATAGGTGG
Humans T A T A G T
ATTCTAGCGCCATAGA... 3’
Yeast T A C A G T
16. Era II: rRNA in environment
The Hidden Majority Richness estimates
Hugenholtz 2002 Bohannan and Hughes 2003
17. Era III: Genome Sequencing
Genomes Online
Fleischmann et al. 1995 Science 269:496-512
19. Era IV: Genomes in Environment
shotgun
sequence
Metagenomics
20. Weighted % of Clones
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28. What’s Coming?
• Sequencing
• Speed up; cost down
• Mini-sequencers with massive capacity
• Automation of sample processing
• Portable and remote systems
• Massive databases
• Computational changes
• Clusters vs. RAM
• Cloud computing
• GPU acceleration
29. Beyond Sequencing
• Array methods should not be ignored
• Bad gene array
• Phylochips
• High throughput/low cost approaches to
characterizing other macromolecules
• Proteomics
• Metabolomics
• Transcriptomics
30. Challenge 1: Data overload
• Major current issue is massive size of
sequence data sets
• Creates many new challenges not widely
anticipated
• Data transfer and storage
• RAM limits for some processes
• Databases overstretched
31. Solutions?
• Throw away data (analogous to CERN)
• New algorithms to limit RAM needs
• Complete automation of algorithms
• Distributed data (e.g., Biotorrents)
• Emphasis on standards and metadata
32. Challenge 2: Short reads
• Some specific challenges come from
short reads
• Key step in analysis of mixed
communities is “binning”
• Binning methods perform poorly on
short reads
• nucleotide composition
• blast hits
• phylogenetic analysis
33. Solutions
• Longer reads
• More full length reference data
• Reference is annotated
• Reads are used to count
• New algorithms
• Phylogeny w/ short reads
• Cobinning/combining data
• New markers
• Better HMM searches
34. Challenge 3: Real time
• New sequencing and array technologies
allow almost real time data collection
• Analysis generally not done in real time
• e.g., metagenome annotation can take
weeks to months
• e.g., phylogenetics bottleneck
• systems not set up for rapid, open sharing
of results
35. Solutions?
• New automated high throughput
methods
• Must be updated continuously to deal with
new data types
• Need to be tested and verified
• Rapid sharing of results
• PLoS Currents
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36. Challenge 4: Reference Data
• Microbial diversity woefully
undersampled
• Greatly limits ability to
• Identify new organisms from DNA fragments
• Determine if organisms are out of “place” in
some way compared to natural diversity
• Perform reliable attribution/matching
• Understand EIDs
• Know what is “normal”
37. Solution?
• Systematic efforts to sample diversity
• Some decent efforts in this regard in
terms of diversity of known Category
ABC pathogens
• Much more needed
39. Genomic Diversity of Isolates
Bacteria
Archaea
Eukaryotes
Figure from Barton, Eisen et al.
“Evolution”, CSHL Press.
Based on tree from Pace NR, 2003.
40. Gene tree ≠ Genome tree
16s WGT, 23S
Badger et al. 2005 Int J System Evol Microbiol 55: 1021-1026.
43. Challenge 5: Knowledge
• Data collection is of course not enough
• Need to be able to turn the data into
knowledge
• This is difficult to automate
44. Solutions
• More curators
• Populate databases with experimental
information not more predictions
• Bioinformatics expansion
• Better linking with ecology, building
science, etc.
45. Acknowledgements
• $$$
• Sloan Foundation
• DOE
• NSF
• GBMF
• DARPA
• People, places
• DOE JGI: Eddy Rubin, Phil Hugenholtz et al.
• UC Davis: Aaron Darling, Dongying Wu
• Other: Jessica Green, Katie Pollard, Martin
Wu, Tom Slezak, Jack Gilbert
Editor's Notes
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Send it out for sequencing, do an alignment with your gene and blast it (search for other organisms) with a similar sequence\n