Title: Statistical Approaches to RNA Secondary Structure Prediction and Applications
Speaker: Ye Ding
Wadsworth Center, New York State Department of Health
Abstract
Abstract: RNAs are versatile regulators of gene expression. RNA secondary structures are known to be important for regulatory functions by various types of RNAs. An RNA molecule, particularly a long-chain mRNA, may have a population of structures in the cell. Furthermore, multiple structures have been demonstrated to play important functional roles. Thus a representation of the ensemble of probable structures is of interest. We developed a statistical algorithm to sample rigorously and exactly from the Boltzmann ensemble of secondary structures, and introduced the notion of centroid structures as a new class of structure predictors. These approaches can overcome inherent limitations in conventional algorithms and are the bases for our Sfold RNA folding program (http://sfold.wadsworth.org).
MicroRNAs are small non-coding RNAs that repress protein synthesis by binding to target mRNAs in multicellular eukaryotes. Target identification of microRNA targets is essential to fully understand this new dimension of the complex gene regulatory networks. By employing a two-step model for modeling microRNA:target hybridization, we found that target secondary structure has a major impact on target recognition by microRNAs. Based on analyses of large microRNA targeting data using the model parameters and other sequence and conservation features, we have recently developed a novel computational framework that offers major improvement over established algorithms for prediction of microRNA targets. Computational tools are available through Sfold web server.
http://www.cs.ubc.ca/labs/beta/Courses/BioinfoReadingGroup/winter2011/07Feb2012.html
not really protein structure but mRNA structure ...
Monday, February 6, 2012
Far away friend
"A friend who is far away is sometimes much nearer than one who is at hand. Is not the mountain far more awe-inspiring and more clearly visible to one passing through the valley than to those who inhabit the mountain?"
--Khalil Gibran
--Khalil Gibran
Sunday, February 5, 2012
Remote control (slide changer) for Powerpoint or for OpenOffice
PowerPoint OpenOffice Remote
http://www.vrallev.net/do/apps/android/pptodp_remote/instruction
http://www.vrallev.net/do/download?path=dropbox__ppt_odp_remote&file=PowerPointOpenOfficeRemote_PC_v3.0.0.jar (14 MB)
basically,
1. Download the PC and Android App
2. Run PC App with jar -jar PowerPointOpenOfficeRemote_PC_v3.0.0.jar
3. Run the Android App and read the IP address
4. Enter the IP address in the PC app
5. Open your PowerPoint presentation in full screen, already presenting, don't close, switch back to the PC app
6. Enter the number of slides
7. Connect
8. 'Start Presentation' on your phone
You can toggle buttons in the phone to see back/forward buttons, or just tap on your phone to advance, swipe left to right to go back
dislikes
- large jar file, needs java
- play on watching videos?
- mess up with animations
- setup can be tricky
- the screenshots on the phone doesn't look right, they just look like the desktop for all of them but not important (on linux, openoffice)
Other remote PC apps
http://slodive.com/freebies/android-remote-desktop-apps/ android-vnc-viewer
https://help.ubuntu.com/community/VNC/Servers go to System > Preferences > Remote Desktop
possible issues with these:
- time-outs / disconnects
- hard issue a left arrow key command without a trackball on your phone --> You can actually use the volume button on your phone for this!
http://www.vrallev.net/do/apps/android/pptodp_remote/instruction
http://www.vrallev.net/do/download?path=dropbox__ppt_odp_remote&file=PowerPointOpenOfficeRemote_PC_v3.0.0.jar (14 MB)
basically,
1. Download the PC and Android App
2. Run PC App with jar -jar PowerPointOpenOfficeRemote_PC_v3.0.0.jar
3. Run the Android App and read the IP address
4. Enter the IP address in the PC app
5. Open your PowerPoint presentation in full screen, already presenting, don't close, switch back to the PC app
6. Enter the number of slides
7. Connect
8. 'Start Presentation' on your phone
You can toggle buttons in the phone to see back/forward buttons, or just tap on your phone to advance, swipe left to right to go back
dislikes
- large jar file, needs java
- play on watching videos?
- mess up with animations
- setup can be tricky
- the screenshots on the phone doesn't look right, they just look like the desktop for all of them but not important (on linux, openoffice)
Other remote PC apps
http://slodive.com/freebies/android-remote-desktop-apps/ android-vnc-viewer
https://help.ubuntu.com/community/VNC/Servers go to System > Preferences > Remote Desktop
possible issues with these:
- time-outs / disconnects
- hard issue a left arrow key command without a trackball on your phone --> You can actually use the volume button on your phone for this!
Measuring the microbiome: perspectives on advances in DNA-based techniques for exploring microbial life
http://bib.oxfordjournals.org.proxy.lib.sfu.ca/content/early/2012/02/03/bib.bbr080.abstract
This article reviews recent advances in ‘microbiome studies’: molecular, statistical and graphical techniques to explore and quantify how microbial organisms affect our environments and ourselves given recent increases in sequencing technology. Microbiome studies are moving beyond mere inventories of specific ecosystems to quantifications of community diversity and descriptions of their ecological function. We review the last 24 months of progress in this sort of research, and anticipate where the next 2 years will take us. We hope that bioinformaticians will find this a helpful springboard for new collaborations with microbiologists.
This article reviews recent advances in ‘microbiome studies’: molecular, statistical and graphical techniques to explore and quantify how microbial organisms affect our environments and ourselves given recent increases in sequencing technology. Microbiome studies are moving beyond mere inventories of specific ecosystems to quantifications of community diversity and descriptions of their ecological function. We review the last 24 months of progress in this sort of research, and anticipate where the next 2 years will take us. We hope that bioinformaticians will find this a helpful springboard for new collaborations with microbiologists.
Saturday, February 4, 2012
Conditional Random Fields applied to protein fold recognition
http://online.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.394
CRFs are “undirected” graphical models (also known as random fields, as opposed to directed graphical models such as HMMs) to compute the conditional likelihood P (y|x) directly.
Protein folds are frequent arrangement pattern of several secondary structure elements: some elements
are quite conserved in sequences or prefer a specific length, while others might form hydrogen bonds with
each other, such as two β-strands in a parallel β-sheet. To model the protein fold better, it would be natural
to think of each secondary structure element as one observation, corresponding to one node in the graph,
and the edges between elements as indicating their interactions in 3-D. Then, given a protein sequence,
we can search for the best segmentation defined by the graph and determine whether the protein adopts
the fold or not.
CRFs are “undirected” graphical models (also known as random fields, as opposed to directed graphical models such as HMMs) to compute the conditional likelihood P (y|x) directly.
Protein folds are frequent arrangement pattern of several secondary structure elements: some elements
are quite conserved in sequences or prefer a specific length, while others might form hydrogen bonds with
each other, such as two β-strands in a parallel β-sheet. To model the protein fold better, it would be natural
to think of each secondary structure element as one observation, corresponding to one node in the graph,
and the edges between elements as indicating their interactions in 3-D. Then, given a protein sequence,
we can search for the best segmentation defined by the graph and determine whether the protein adopts
the fold or not.
Friday, February 3, 2012
Immunology
http://www.microbiology.ubc.ca/system/files/MICB%20302%20-%20Immunology.pdf
Learning objectives: By the end of the course, you should be able to:
1. Identify the major mechanisms (inflammatory responses, cytotoxic T cells, antibodies) by which
immune cells protect us from different types of pathogens (viruses, extracellular bacteria,
intravesicular bacteria, parasites) or from cancer cells.
2. Understand how immune cells detect the presence of pathogens and cancer cells (pattern
recognition receptors, antigen receptors, antigen presentation pathways, NK cell receptors).
3. Describe processes that lead to the elimination of pathogens (e.g. opsonization, phagocytosis,
neutralization, complement activation, cell-mediated cytotoxicity).
4. Describe the structure and function of key molecules that mediate immune responses including
antibodies, antigen receptors, Toll-like receptors, MHC proteins, cytokines, chemokines.
5. Describe the main cell types of the immune system including their development, function, and for lymphocytes, how they generate antigen receptors.
6. Describe how defects in immune cell regulation can lead to immunodeficiency diseases or
autoimmune diseases.
7. Describe the topics of current immunological interest including vaccines, immune tolerance,
allergies, and transplantation.
8. Describe the basis for and application of current experimental approaches in immunology
including flow cytometry, monoclonal antibodies, immunofluorescence, knockout and transgenic
mice, adoptive transfer of immune cells, and gene expression profiling.
9. Relate processes that occur in immune cells to similar processes that occur in all cell types and which have been described in previous cell biology courses (e.g. mRNA splicing, protein
secretion, receptor signaling).
http://www.microbiology.ubc.ca/Murphy
Learning objectives: By the end of the course, you should be able to:
1. Identify the major mechanisms (inflammatory responses, cytotoxic T cells, antibodies) by which
immune cells protect us from different types of pathogens (viruses, extracellular bacteria,
intravesicular bacteria, parasites) or from cancer cells.
2. Understand how immune cells detect the presence of pathogens and cancer cells (pattern
recognition receptors, antigen receptors, antigen presentation pathways, NK cell receptors).
3. Describe processes that lead to the elimination of pathogens (e.g. opsonization, phagocytosis,
neutralization, complement activation, cell-mediated cytotoxicity).
4. Describe the structure and function of key molecules that mediate immune responses including
antibodies, antigen receptors, Toll-like receptors, MHC proteins, cytokines, chemokines.
5. Describe the main cell types of the immune system including their development, function, and for lymphocytes, how they generate antigen receptors.
6. Describe how defects in immune cell regulation can lead to immunodeficiency diseases or
autoimmune diseases.
7. Describe the topics of current immunological interest including vaccines, immune tolerance,
allergies, and transplantation.
8. Describe the basis for and application of current experimental approaches in immunology
including flow cytometry, monoclonal antibodies, immunofluorescence, knockout and transgenic
mice, adoptive transfer of immune cells, and gene expression profiling.
9. Relate processes that occur in immune cells to similar processes that occur in all cell types and which have been described in previous cell biology courses (e.g. mRNA splicing, protein
secretion, receptor signaling).
http://www.microbiology.ubc.ca/Murphy
Gastrointestinal flora and gastrointestinal status in children with autism -- comparisons to typical children and correlation with autism severity
http://www.biomedcentral.com/1471-230X/11/22
Due to antibiotics used to treat ASD?
Oral antibiotics were primarily used for treating otitis media (ear infections), which may suggest an impaired immune system. Commonly used oral antibiotics eliminate almost all of the normal gut microbiota, which play an important role in the breakdown of plant polysaccharides, promoting gastrointestinal motility, maintaining water balance, producing some vitamins, and competing against pathogenic bacteria. Loss of normal gut flora can result in the overgrowth of pathogenic flora, which can in turn cause constipation and other problems.
Abstract
Background
Children with autism have often been reported to have gastrointestinal problems that are more frequent and more severe than in children from the general population.
Methods
Gastrointestinal flora and gastrointestinal status were assessed from stool samples of 58 children with Autism Spectrum Disorders (ASD) and 39 healthy typical children of similar ages. Stool testing included bacterial and yeast culture tests, lysozyme, lactoferrin, secretory IgA, elastase, digestion markers, short chain fatty acids (SCFA's), pH, and blood presence. Gastrointestinal symptoms were assessed with a modified six-item GI Severity Index (6-GSI) questionnaire, and autistic symptoms were assessed with the Autism Treatment Evaluation Checklist (ATEC).
Results
Gastrointestinal symptoms (assessed by the 6-GSI) were strongly correlated with the severity of autism (assessed by the ATEC), (r = 0.59, p < 0.001). Children with 6-GSI scores above 3 had much higher ATEC Total scores than those with 6-GSI-scores of 3 or lower (81.5 +/- 28 vs. 49.0 +/- 21, p = 0.00002).
Children with autism had much lower levels of total short chain fatty acids (-27%, p = 0.00002), including lower levels of acetate, proprionate, and valerate; this difference was greater in the children with autism taking probiotics, but also significant in those not taking probiotics. Children with autism had lower levels of species of Bifidobacter (-43%, p = 0.002) and higher levels of species of Lactobacillus (+100%, p = 0.00002), but similar levels of other bacteria and yeast using standard culture growth-based techniques. Lysozyme was somewhat lower in children with autism (-27%, p = 0.04), possibly associated with probiotic usage. Other markers of digestive function were similar in both groups.
Conclusions
The strong correlation of gastrointestinal symptoms with autism severity indicates that children with more severe autism are likely to have more severe gastrointestinal symptoms and vice versa. It is possible that autism symptoms are exacerbated or even partially due to the underlying gastrointestinal problems. The low level of SCFA's was partly associated with increased probiotic use, and probably partly due to either lower production (less sacchrolytic fermentation by beneficial bacteria and/or lower intake of soluble fiber) and/or greater absorption into the body (due to longer transit time and/or increased gut permeability).
Due to antibiotics used to treat ASD?
Oral antibiotics were primarily used for treating otitis media (ear infections), which may suggest an impaired immune system. Commonly used oral antibiotics eliminate almost all of the normal gut microbiota, which play an important role in the breakdown of plant polysaccharides, promoting gastrointestinal motility, maintaining water balance, producing some vitamins, and competing against pathogenic bacteria. Loss of normal gut flora can result in the overgrowth of pathogenic flora, which can in turn cause constipation and other problems.
Thursday, February 2, 2012
Science is refinement thinking
"The whole of science is nothing more than a refinement of everyday thinking."
--Albert Einstein
--Albert Einstein
Roche takeover bid poses challenge to Illumina
http://www.nature.com/news/roche-takeover-bid-poses-challenge-to-illumina-1.9928?WT.ec_id=NATUREjobs-20111219
A merger could stifle innovation, say observers.
for US$5.7 billion
A merger could stifle innovation, say observers.
for US$5.7 billion
Wednesday, February 1, 2012
Covariance vs Correlation
http://www.riskglossary.com/link/correlation.htm
The covariance is defined by the expectation
 |
and 
are the The correlation is defined as
 |
where 
and 
are the standard deviations of 
and 
.
and are the standard deviations of and .The Cell Biology of Synaptic Plasticity
http://www.sciencemag.org/content/334/6056/623.full
Synaptic plasticity is the experience-dependent change in connectivity between neurons that is believed to underlie learning and memory. Here, we discuss the cellular and molecular processes that are altered when a neuron responds to external stimuli, and how these alterations lead to an increase or decrease in synaptic connectivity. Modification of synaptic components and changes in gene expression are necessary for many forms of plasticity. We focus on excitatory neurons in the mammalian hippocampus, one of the best-studied model systems of learning-related plasticity.
Synaptic plasticity is the experience-dependent change in connectivity between neurons that is believed to underlie learning and memory. Here, we discuss the cellular and molecular processes that are altered when a neuron responds to external stimuli, and how these alterations lead to an increase or decrease in synaptic connectivity. Modification of synaptic components and changes in gene expression are necessary for many forms of plasticity. We focus on excitatory neurons in the mammalian hippocampus, one of the best-studied model systems of learning-related plasticity.
Subscribe to:
Posts (Atom)