serial analysis gene expression is a transcriptomic technique used by molecular biologists to produce a snapshot of the messenger RNA population in a sample of interest in the form of small tags that correspond to fragments of those transcripts.
DNA SEQUENCING METHODS AND STRATEGIES FOR GENOME SEQUENCINGPuneet Kulyana
This presentation will give you a brief idea about the various DNA sequencing methods and various strategies used for genome sequencing and much more vital information related to gene expression and analysis
Yeast two-hybrid is based on the reconstitution of a functional transcription factor (TF) when two proteins or polypeptides of interest interact. Upon interaction between the bait and the prey, the DBD and AD are brought in close proximity and a functional TF is reconstituted upstream of the reporter gene.
DNA SEQUENCING METHODS AND STRATEGIES FOR GENOME SEQUENCINGPuneet Kulyana
This presentation will give you a brief idea about the various DNA sequencing methods and various strategies used for genome sequencing and much more vital information related to gene expression and analysis
Yeast two-hybrid is based on the reconstitution of a functional transcription factor (TF) when two proteins or polypeptides of interest interact. Upon interaction between the bait and the prey, the DBD and AD are brought in close proximity and a functional TF is reconstituted upstream of the reporter gene.
In shotgun sequencing the genome is broken randomly into short fragments (1 to 2 kbp long) suitable for sequencing. The fragments are ligated into a suitable vector and then partially sequenced. Around 400–500 bp of sequence can be generated from each fragment in a single sequencing run. In some cases, both ends of a fragment are sequenced. Computerized searching for overlaps between individual sequences then assembles the complete sequence.
Genome annotation, NGS sequence data, decoding sequence information, The genome contains all the biological information required to build and maintain any given living organism.
CD Genomics provides a fast, one-stop bacterial RNA sequencing solution from the quality control of sample to comprehensive data analysis. Please contact us for more information and a detailed quote.
In shotgun sequencing the genome is broken randomly into short fragments (1 to 2 kbp long) suitable for sequencing. The fragments are ligated into a suitable vector and then partially sequenced. Around 400–500 bp of sequence can be generated from each fragment in a single sequencing run. In some cases, both ends of a fragment are sequenced. Computerized searching for overlaps between individual sequences then assembles the complete sequence.
Genome annotation, NGS sequence data, decoding sequence information, The genome contains all the biological information required to build and maintain any given living organism.
CD Genomics provides a fast, one-stop bacterial RNA sequencing solution from the quality control of sample to comprehensive data analysis. Please contact us for more information and a detailed quote.
As a pioneer biotechnology company in the world, Creative Biogene can provide high quality cDNA libraries construction service to customers worldwide.
https://www.creative-biogene.com/Services/cDNA-Library-Construction-Service
Creation of a cDNA library starts with mRNA instead of DNA. Messenger RNA carries encoded information from DNA to ribosomes for translation into protein. To create a cDNA library, these mRNA molecules are treated with the enzyme reverse transcriptase, which is used to make a DNA copy of an mRNA (i.e., cDNA). A cDNA library represents a sampling of the transcribed genes, but a genomic library includes untranscribed regions.
The study of the complete set of RNAs (transcriptome) encoded by the genome of a specific cell or organism at a specific time or under a specific set of conditions is called Transcriptomics.
Transcriptomics aims:
I. To catalogue all species of transcripts, including mRNAs, noncoding RNAs and small RNAs.
II. To determine the transcriptional structure of genes, in terms of their start sites, 5′ and 3′ ends, splicing patterns and other post-transcriptional modifications.
III. To quantify the changing expression levels of each transcript during development and under different conditions.
The complete genome sequences of a number of organisms, including mammals, have recently become available because of rapid advances in DNA sequencing technology. Nevertheless, the analysis of transcripts still plays a crucial role in bridging the gap between the genome and the proteome, particularly in mammals. Therefore, as a method for the analysis of transcripts, cDNA library construction is crucial, even in the post-genome sequencing era.
https://www.creative-biogene.com/Services/cDNA-Library-Construction-Service
Creative Biogene’s goal is to provide you with the most affordable and high-quality cDNA libraries construction service to ensure your satisfaction in a timely and professional manner. https://www.creative-biogene.com/Services/cDNA-Library-Construction-Service
A class of DNA sequencing techniques currently in active development is third-generation sequencing, commonly referred to as long-read sequencing. In comparison to second generation sequencing, also referred to as next generation sequencing, third generation sequencing technologies have the capacity to create noticeably longer reads.
This pdf is about the DNA Libraries / Genomic DNA vs cDNA.
For more details visit on YouTube; @SELF-EXPLANATORY; https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos Thanks...!
Transcriptomics is the study of RNA, single-stranded nucleic acid, which was not separated from the DNA world until the central dogma was formulated by Francis Crick in 1958, i.e., the idea that genetic information is transcribed from DNA to RNA and then translated from RNA into protein.
Ribosomes are complex structures found in all living cells which functions in protein synthesis machinery. Basically ribosome’s consists of two subunits, each of which is composed of protein and a type of RNA, known as ribosomal RNA (rRNA). Prokaryotic ribosomes consist of 30S subunit (small sub unit) and 50S subunit (large sub unit) which together make up the complete 70S ribosome, where S stands for Svedberg unit non-SI unit for sedimentation rate. 30S subunit is composed of 16S ribosomal RNA and 21 polynucleotide chains while 50S subunit is composed of two rRNA species, the 5S and 23S rRNAs. The presence of hyper variable regions in the 16S rRNA gene provides a species specific signature sequence which is useful for bacterial identification process. 16S Ribosomal RNA sequencing is widely used in microbiology studies to identify the diversities in prokaryotic organisms as well as other organisms and thereby studying the phylogenetic relationships between them. The advantages of using ribosomal RNA in molecular techniques are as follows
Ribosomes and ribosomal RNA are present in all cells.
RNA genes are highly conserved in nature.
Culturing of microbial cells is absent in the sequencing techniques.
Most probable number or multiple tube fermentation techniqueSamsuDeen12
multiple tube fermentation or most probable number is a microbiological technique used to check the portability of water. microbial analysis of water is determined, and distinguished between faecal and non faecal contaminated water.
herpes simplex virus is a double stranded DNA virus causing many symptoms all over the body. it affects globally all over the world .
neonatal hsv attacks even the baby and made them to a fatal conditions.
cDNA library construction using mRNA which are derived from DNA. cDNA is formed from the reverse transcription of single stranded mRNA. cDNA contains only the exons, it donot not contains introns. The mRNA consists of poly A tail in which the tRNA and rRNA donot contains poly A tail. A short oligo nucleotide of Poly T is used to isolate mRNA seperately thereby single stranded mRNA is then converted into cDNA by using reverse transcriptase enzyme.
Production of tetracyclin and cephalosporinSamsuDeen12
Tetracyclin and cephalosporins are one of the major used antibiotics commonly all around the world. They are used to treat against microorganisms as a bactericidal, these eliminates those organisms in the host through various mechanism. These antibiotics are produced in a large scale using a bioreactors in many countries.
Fish is the major economically exported source. There are various products are there based on fish. The major products are exported to other countries than utilizing in India such as oyster which are more preferred for eaten by Germans and Italians.
paramecium is a microscopic organism. it is an protozoan that comes under ciliates. they are even visible under naked eyes. Paramecium are unicellular organism they lives in aquatic environment. they are used as live feed for fishes.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
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.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
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.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
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 .
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
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.
1. SERIAL ANALYSIS OF GENESERIAL ANALYSIS OF GENE
EXPRESSIONEXPRESSION ( (SAGESAGE))
-SAMSUDEEN.
S
2. Serial analysis of gene expression
(SAGE) is a transcriptomic
technique used by molecular biologists to
produce a snapshot of the messenger
RNA population in a sample of interest in
the form of small tags that correspond to
fragments of those transcripts.
3. SAGESAGE EXPERIMENTSEXPERIMENTS PROCEED AS FOLLOWS:PROCEED AS FOLLOWS:
The mRNA of an input sample is isolated and
a reverse transcriptase and biotinylated primers
are used to synthesize cDNA from mRNA.
The cDNA is bound to Streptavidin beads via
interaction with the biotin attached to the
primers, and is then cleaved using a restriction
endonuclease called an anchoring enzyme (AE).
The location of the cleavage site and thus the
length of the remaining cDNA bound to the
bead will vary for each individual cDNA
(mRNA).
5. SAGESAGE EXPERIMENTSEXPERIMENTS PROCEED AS FOLLOWS:PROCEED AS FOLLOWS:
The cleaved cDNA downstream from the
cleavage site is then discarded, and the
remaining immobile cDNA fragments
upstream from cleavage sites are divided in
half and exposed to one of two adapter
oligonucleotides (A or B) containing several
components in the following order upstream
from the attachment site:
6. A) Sticky ends with the anchoring enzyme
cut site to allow for attachment to cleaved
cDNA.
B) A recognition site for a restriction
endonuclease known as the tagging enzyme
(TE), which cuts about 15 nucleotides
downstream of its recognition site.
C) A short primer sequence unique to
either adapter A or B, which will later be
used for further amplification via PCR.
7. After adapter ligation, cDNA are cleaved
using tagging enzyme (TE) to remove them
from the beads, leaving only a short "tag" of
about 11 nucleotides of original cDNA.
The cleaved cDNA tags are then repaired
with DNA polymerase to produce blunt
end cDNA fragments.
8. These cDNA tag fragments are ligated,
sandwiching the two tag sequences together,
and flanking adapters A and B at either end.
These new constructs, called ditags, are then
PCR amplified using anchor A and B specific
primers.
The ditags are then cleaved using the original
anchoring enzyme, and allowed to link
together with other ditags, which will be
ligated to create a cDNA concatemer with each
ditag being separated by the Anchoring
Enzyme recognition site.
9. These concatemers are then transformed into
bacteria for amplification through bacterial
replication.
The cDNA concatemers can then be isolated
and sequenced using modern high-
throughput DNA sequencers and these
sequences can be analysed with computer
programs which quantify the recurrence of
individual tags.
10. In 1995, the idea of reducing the tag length from
100 to 800 bp down to tag length of 10 to 22 bp
helped reduce the cost of mRNA surveys. In this
year, the original SAGE protocol was published
by Victor Velculescu at the Oncology Center of
Johns Hopkins University. Although SAGE was
originally conceived for use in cancer studies, it has
been successfully used to describe
the transcriptome of other diseases and in a wide
variety of organisms.
12. LONG SAGELONG SAGE
LongSAGE was a more robust version of the
original SAGE developed in 2002 which had a
higher throughput, using 20 μg of mRNA to
generate a cDNA library of thousands of
tags. Robust LongSage (RL-SAGE) Further
improved on the LongSAGE protocol with the
ability to generate a library with an insert size of 50
ng mRNA, much smaller than previous LongSAGE
insert size of 2 μg mRNA and using a lower number
of ditag polymerase chain reactions (PCR) to
obtain a complete cDNA library.
13.
14. SUPER SAGESUPER SAGE
SuperSAGE is a derivative of SAGE that uses
the type III-endonuclease EcoP15I
of phage P1, to cut 26 bp long sequence
tags from each transcript's cDNA, expanding
the tag-size by at least 6 bp as compared to
the predecessor techniques SAGE and
LongSAGE. The longer tag-size allows for a
more precise allocation of the tag to the
corresponding transcript, because each
additional base increases the precision of the
annotation considerably.
15. Like in the original SAGE protocol, so-called
ditags are formed, using blunt-ended tags. By
direct sequencing with high-throughput
sequencing techniques, hundred thousands or
millions of tags can be analyzed simultaneously,
producing very precise and quantitative gene
expression profiles. Therefore, tag-based gene
expression profiling also called "digital gene
expression profiling" (DGE) can today
provide most accurate transcription profiles that
overcome the limitations of microarrays.
16. MASSIVE ANALYSIS OF CDNA ENDSMASSIVE ANALYSIS OF CDNA ENDS
In the mid 2010s several techniques combined with
Next Generation Sequencing were developed that
employ the "tag" principle for "digital gene
expression profiling" but without the use of the
tagging enzyme. The "MACE" approach, (Massive
Analysis of cDNA Ends) generates tags
somewhere in the last 1500 bps of a transcript. The
technique does not depend on restriction enzymes
anymore and thereby circumvents bias that is
related to the absence or location of the restriction
site within the cDNA.
17. cDNA is randomly fragmented and the
3'ends are sequenced from the 5' end of the
cDNA molecule that carries the poly-A tail.
The sequencing length of the tag can be
freely chosen. Because of this, the tags can be
assembled into contigs and the annotation of
the tags can be drastically improved.
Therefore, MACE is also use for the analyses
of non-model organisms. In addition, the
longer contigs can be screened for
polymorphisms.
18. MACE does only require 3’ ends of
transcripts, even partly degraded RNA can be
analyzed with less degradation dependent
bias. The MACE approach uses unique
molecular identifiers to allow for
identification of PCR bias.
20. RESULT ANALYSIS:RESULT ANALYSIS:
The output of SAGE is a list of short sequence tags
and the number of times it is observed.
Using sequence databases a researcher can usually
determine, with some confidence, from which
original mRNA (and therefore which gene) the tag
was extracted.
Statistical methods can be applied to tag and count
lists from different samples in order to determine
which genes are more highly expressed. For
example, a normal tissue sample can be compared
against a corresponding tumor to determine
which genes tend to be more (or less) active.