The objective of the experiment is for students to become familiar with databases that can be used to investigate gene sequences and to construct cladograms that provide evidence for evolutionary relatedness among species.
In this investigation, students will:
1. Create cladograms that depict evolutionary relationships among organisms.
2. Analyze biological data with online bioinformatics tools.
3. Connect and apply concepts pertaining to genetics and evolution.
A description of how technology has changed the face of Biology, specially in the fields of genetics, proteomics, and evolution.
It includes a brief history, examples of usage, and a look into the future.
This HIBB presentation provides background information on bases, amino acids, proteins, nucleotides and DNA. The presentation then explains what bioinformatics is, lists some examples, and demonstrates some tools. It demonstrates tools which compare parts of human and chimp genes, and illustrate drug resistance analysis and HIV subtype analysis. It then discusses some ethical and clinical aspects to bioinformatics.
NCBI has developed a powerful suite of online biomedical and bioinformatics resources, including old friends like PubMed and OMIM and newer resources such as Genome. This collection of databases and tools are widely used by scientists and medical professionals across the world. With such a wealth of information, it is easy to get overwhelmed. Join us for an overview to NCBI resources for the information professional with an emphasis on biodata connectivity. No science degree required!
A description of how technology has changed the face of Biology, specially in the fields of genetics, proteomics, and evolution.
It includes a brief history, examples of usage, and a look into the future.
This HIBB presentation provides background information on bases, amino acids, proteins, nucleotides and DNA. The presentation then explains what bioinformatics is, lists some examples, and demonstrates some tools. It demonstrates tools which compare parts of human and chimp genes, and illustrate drug resistance analysis and HIV subtype analysis. It then discusses some ethical and clinical aspects to bioinformatics.
NCBI has developed a powerful suite of online biomedical and bioinformatics resources, including old friends like PubMed and OMIM and newer resources such as Genome. This collection of databases and tools are widely used by scientists and medical professionals across the world. With such a wealth of information, it is easy to get overwhelmed. Join us for an overview to NCBI resources for the information professional with an emphasis on biodata connectivity. No science degree required!
Lecture given for the Data Mining course at Uppsala university in October 2013. The presentation talks about data analysis in the context of genomics, next-generation sequencing, metagenomics etc.
The NCBI Boot Camp for Beginners was designed to offer an overview of the NCBI suite of resources. In the first half of the presentation, highlighted databases were covered in four main categories: literature, sequences, genes & genomes and expression & structure. The second half of the class used the apolipoprotein A as a query that was explored through many of the NCBI databases, from identifying the reference sequences to a structural analysis of the Cys130Arg variant.
DNA IMAGE SEGMENTATION – A COMPARISON OF EDGE DETECTION TECHNIQUESijbbjournal
Bioinformatics is a computer-assisted interface discipline dealing with the acquisition, storage,
management, access and processing of molecular biology data. It is an interdisciplinary scientific tool
without barriers among various disciplines of science like biology, mathematics, computer science and
information technology. Bioinformatics has become an important part of many areas of biology.
Bioinformatics tools aid in the comparison of genetic and genomic data and more generally in the
understanding of evolutionary aspects of molecular biology. In structural biology, it aids in the simulation
and modelling of DNA, RNA and Protein structures as well as molecular interactions. The most important
feature of DNA is that it is usually composed of two polynucleotide chains twisted around each other in the
form of a double helix. In this paper we have easily identified the complicated structure of DNA images for
using several techniques of edge detection in image processing .we consider various well known Algorithms
and metrics used in image processing applied to DNA images in this comparison .
The DNA Data Bank of Japan (DDBJ) is a biological database that collects DNA sequences. It is located at the National Institute of Genetics (NIG) in the Shizuoka prefecture of Japan. It is also a member of the International Nucleotide Sequence Database Collaboration or INSDC.
NCBI; Introduction, Homepage and about
Tools and database of NCBI
BLAST; Introduction, Homepage and types of BLAST
Some databases of NCBI
References
Acknowledgements
Next Generation Sequencing Informatics - Challenges and OpportunitiesChung-Tsai Su
Genetic data is the foundation of precision medicine. Next Generation Sequencing(NGS) enable us to get our whole genome data in affordable cost. How to process huge amount of NGS data effectively ?
This proposed method focus on these issues by developing a novel classification algorithm by combining Gene Expression Graph (GEG) with Manhattan distance. This method will be used to express the gene expression data. Gene Expression Graph provides the optimal view about the relationship between normal and unhealthy genes. The method of using a graph-based gene expression to express gene information was first offered by the authors in [1] and [2], It will permits to construct a classifier based on an association between graphs represented for well-known classes and graphs represented for samples to evaluate. Additionally Euclidean distance is used to measure the strength of relationship which exists between the genes.
Detection of DNA Damage Using Comet Assay Image AnalysisIJRST Journal
Reactive species such as free radicals are constantly produced in vivo and DNA is the very important target of oxidative stress. Oxidative DNA damage is considered as a predictive biomarker to monitor the risk of development of many diseases. The comet assay is widely used for specifying oxidative DNA damage at a single cell level. The analysis of comet assay output images, however, poses considerable challenges. The comet assay, also known as single-cell gel electrophoresis (SCGE), is a simple, sensitive and reliable method for studying DNA damage caused by physical and chemical agents. So the comet assay is a well-established, simple, versatile, visual, rapid, and sensitive method used extensively to assess DNA damage quantitatively and qualitatively at single cell level. The comet assay is most frequently used to analyze white blood cells or lymphocytes in human bio monitoring studies. So through the analysis of comet assay image we can detect edge of damaged DNA comet isolating it from undamaged DNA.
Lecture given for the Data Mining course at Uppsala university in October 2013. The presentation talks about data analysis in the context of genomics, next-generation sequencing, metagenomics etc.
The NCBI Boot Camp for Beginners was designed to offer an overview of the NCBI suite of resources. In the first half of the presentation, highlighted databases were covered in four main categories: literature, sequences, genes & genomes and expression & structure. The second half of the class used the apolipoprotein A as a query that was explored through many of the NCBI databases, from identifying the reference sequences to a structural analysis of the Cys130Arg variant.
DNA IMAGE SEGMENTATION – A COMPARISON OF EDGE DETECTION TECHNIQUESijbbjournal
Bioinformatics is a computer-assisted interface discipline dealing with the acquisition, storage,
management, access and processing of molecular biology data. It is an interdisciplinary scientific tool
without barriers among various disciplines of science like biology, mathematics, computer science and
information technology. Bioinformatics has become an important part of many areas of biology.
Bioinformatics tools aid in the comparison of genetic and genomic data and more generally in the
understanding of evolutionary aspects of molecular biology. In structural biology, it aids in the simulation
and modelling of DNA, RNA and Protein structures as well as molecular interactions. The most important
feature of DNA is that it is usually composed of two polynucleotide chains twisted around each other in the
form of a double helix. In this paper we have easily identified the complicated structure of DNA images for
using several techniques of edge detection in image processing .we consider various well known Algorithms
and metrics used in image processing applied to DNA images in this comparison .
The DNA Data Bank of Japan (DDBJ) is a biological database that collects DNA sequences. It is located at the National Institute of Genetics (NIG) in the Shizuoka prefecture of Japan. It is also a member of the International Nucleotide Sequence Database Collaboration or INSDC.
NCBI; Introduction, Homepage and about
Tools and database of NCBI
BLAST; Introduction, Homepage and types of BLAST
Some databases of NCBI
References
Acknowledgements
Next Generation Sequencing Informatics - Challenges and OpportunitiesChung-Tsai Su
Genetic data is the foundation of precision medicine. Next Generation Sequencing(NGS) enable us to get our whole genome data in affordable cost. How to process huge amount of NGS data effectively ?
This proposed method focus on these issues by developing a novel classification algorithm by combining Gene Expression Graph (GEG) with Manhattan distance. This method will be used to express the gene expression data. Gene Expression Graph provides the optimal view about the relationship between normal and unhealthy genes. The method of using a graph-based gene expression to express gene information was first offered by the authors in [1] and [2], It will permits to construct a classifier based on an association between graphs represented for well-known classes and graphs represented for samples to evaluate. Additionally Euclidean distance is used to measure the strength of relationship which exists between the genes.
Detection of DNA Damage Using Comet Assay Image AnalysisIJRST Journal
Reactive species such as free radicals are constantly produced in vivo and DNA is the very important target of oxidative stress. Oxidative DNA damage is considered as a predictive biomarker to monitor the risk of development of many diseases. The comet assay is widely used for specifying oxidative DNA damage at a single cell level. The analysis of comet assay output images, however, poses considerable challenges. The comet assay, also known as single-cell gel electrophoresis (SCGE), is a simple, sensitive and reliable method for studying DNA damage caused by physical and chemical agents. So the comet assay is a well-established, simple, versatile, visual, rapid, and sensitive method used extensively to assess DNA damage quantitatively and qualitatively at single cell level. The comet assay is most frequently used to analyze white blood cells or lymphocytes in human bio monitoring studies. So through the analysis of comet assay image we can detect edge of damaged DNA comet isolating it from undamaged DNA.
A Study on DNA based Computation and Memory DevicesEditor IJCATR
The present study delineates Deoxyribonucleic Acid (DNA) based computing and storage devices which have good future in the vast era of information technology. The traditional devices mostly used are made up of silicon. The devices are costly and have physical limitations to cause leakage of electrons and circuit to shorten. So, there is a need of materials which are capable of doing fast processing and have vast memory storage. DNA which is a bio-molecule has all these characteristics capable of providing ample storage. In classical computing devices, electronic logic gates are elements which allow storing and transforming of information. Designing of an appropriate sequence or a net of “store” and “transform” operations (in a sense of building a device or writing a program) is equivalent to preparing some computations. In DNA based computation, the situation is analogous. The main difference is the type of computing devices since in this new method of computing instead of electronic gates, DNA molecules have been deployed for the processing of dossier. Moreover, the inherent massive parallelism of DNA computing may lead to methods solving some intractable computational problems. The aim of this research study is to analyze the logical features and memory formation using DNA bio molecules in order to achieve proliferated speed, accuracy and vast storage.
1. Introduction:
A few life scientists may mourn the passing of the days when the concept of “one gene, one protein" controlled their professional lives. But most of the colleagues have welcomed the arrival of DNA chips and microarrays that offer researchers the opportunity to run thousands of samples simultaneously in a single experiment under virtually identical conditions. The pharmaceutical industry in particular values the use of microarray technology to screen increasing numbers of molecules in smaller volumes as drug candidates. Alex Szabo, the vice president of Strata gene, says “There’s tremendous excitement about the technology. Everyone realizes that it’s one of the key technologies in the genomic era”.
Microarray technology seems tailor-made for the type of exploration necessary to follow up the initial work on sequencing the genes of humans and other organisms. The professor of Biochemistry, Patrick Brown, at Stanford University says that “Genome projects give you, in a sense, a list of the words in the genome vocabulary”. Jeff Mooney, Business technology manager of Corning Microarray Technologies, extend his thought as “If you want to learn what words mean in a foreign language you look at how they are used. It’s the same of genes. Microarrays as a way of seeing how genes express themselves will be the most widely used application of arrays”. The more we look at the human genome, the more questions people have. Microarray platforms help to answer general and specific questions.
Beyond this, researchers see use of microarrays in such areas as genotyping, studying disease pathways, analysing Single Nucleotide Polymorphisms (SNPs), and examining proteins. “Expression arrays offer researchers the promise of finding the fundamental causes of disease and identifying new, more precise strategies to diagnose, treat, prevent and ultimately cure disease” says Stephen Fodor, Chairman and CEO of Affymetrix, Inc., the first major manufacturer of arrays.
Plenty of vendors have joined Affymetrix in the microarray marketplace. “There are tens, if not hundreds, of companies out there trying to find the next technology” says Andrew Farquharson, executive vice president of Operon Technologies, Inc. Some new comers, such as Nimblegen Systems, Inc., aim to follow the model pioneered by Affymetrix and Incyte Genomics, producing microarrays for core facilities in large industrial and academic departments. Others, such as Corning, plant to enter the market with “theme arrays” targeted at specific diseases. Yet more, including Agilent Technologies and German company Graffinity Pharamaceutical Design, GmbH, provide specific services such as fingerprinting arrays designed and used by individual researchers. CLONTECH Laboratories, subsidiary of BD Bioscience and British firm BioRobotics, Ltd., provide the basic tools necessary for individual researchers to carry out the entire process of producing microarrays, including fingerprinting.
Improving DNA Barcode-based Fish Identification System on Imbalanced Data usi...TELKOMNIKA JOURNAL
Problem in imbalanced data is very common in classification or identification. The problem is
raised when the number of instances of one class far exceeds the other. In the previous research, our
DNA barcode-based Identification System of Tuna and Mackerel was developed in imbalanced dataset.
The number of samples of Tuna and Mackerel were much more than those of other fish samples.
Therefore, the accuracy of the classification model was probably still in bias. This research aimed at
employing Synthetic Minority Oversampling Technique (SMOTE) to yield balanced dataset. We used kmers
frequencies from DNA barcode sequences as features and Support Vector Machine (SVM) as
classification method. In this research we used trinucleotide (3-mers) and tetranucleotide (4-mers). The
training dataset was taken from Barcode of Life Database (BOLD). For evaluating the model, we compared
the accuracy of model using SMOTE and without SMOTE in order to classify DNA barcode sequences
which is taken from Department of Aquatic Product Technology, Bogor Agricultural University. The results
showed that the accuracy of the model in the species level using SMOTE was 7% and 13% higher than
those of non-SMOTE for trinucleotide (3-mers) and tetranucleotide (4-mers), respectively. It is expected
that the use of SMOTE, as one of data balancing technique, could increase the accuracy of DNA barcode
based fish classification system, particularly in the species level which is difficult to be identified.
Learn about enabling next-generation sequencing applications with IBM Storwize V7000 Unified and SONAS Gateway solutions. This paper offers recommendations and guidance to facilitate easy configuration and installation of the solution to ensure an efficient installation with good performance. For more information on IBM Storage Systems, visit http://ibm.co/LIg7gk.
Visit http://on.fb.me/LT4gdu to 'Like' the official Facebook page of IBM India Smarter Computing.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
Astronomy Update- Curiosity’s exploration of Mars _ Local Briefs _ leadertele...
Determining Evolutionary Relationships Using BLAST
1. AP03.170426
Edvo-Kit #AP03
Determining Evolutionary
Relationships Using BLAST
Experiment Objective:
The objective of the experiment is for students to become familiar
with databases that can be used to investigate gene sequences
and to construct cladograms that provide evidence for evolutionary
relatedness among species.
AP03.170426