Lior I. Schenk1, Praseeda Venugopalan1,2, Xiong Zhang1, and Jeffrey L. Goldberg1,3
1 University of California, San Diego, La Jolla, CA; 2 University of Miami, Miami, FL; 3 UCSD Shiley Eye Center, La Jolla, CA
Bioo Scientific - Absolute Quantitation for RNA-SeqBioo Scientific
Accurate quantitation is a critical issue for most RNA-Seq analysis. As the efficiency of PCR amplification is sequence-dependent, with some transcripts being preferentially amplified over others, PCR amplification introduces bias during NGS library construction. The traditional approach to removing these artifacts, introduced during PCR, involves removing all fragments with identical start and stop sites. However, detailed analyses have shown that many original fragments have identical start and stop sites, and this method can incorrectly eliminate unique fragments from NGS data, thus reducing its accuracy. Bioo Scientific has incorporated Molecular Indexes™ into its NEXTflex™ Rapid Directional qRNA-Seq™ Kit, allowing for a more accurate resolution of duplicates introduced during PCR amplification. This presentation describes how Molecular Indexes can be used to increase the accuracy of RNA-Seq analysis.
Bioo Scientific - Simplify and Reduce Cost of mtDNA Isolation and Library PrepBioo Scientific
Mutations in mitochondrial DNA (mtDNA) have been implicated in various human disorders and in aging, making NGS analysis of mtDNA a priority for a number of labs. However, accurately determining the diversity of mtDNA has been difficult for a number of reasons. The standard methods for mitochondrial DNA extraction have a number of limitations making them inferior solutions for NGS library preparation. Bioo Scientific has commercialized a kit which overcomes these limitations of mtDNA isolation by selectively digesting linear nuclear DNA (nDNA) while leaving circular mtDNA intact. This technology has been incorporated into the NEXTflex mtDNA-Seq Kit which includes optimized reagents for the isolation of mtDNA and for the construction of Illumina mtDNA libraries. Libraries constructed using the NEXTflex mtDNA-Seq Kit are ideal for many NGS applications including heteroplasmy analysis.
The evolution of antimicrobial resistance: a Darwinian perspectiveThe Royal Institution
Sir Richard Sykes presented this Friday Evening Discourse at the Royal Institution of Great Britain on Friday 6 May 2011.
Microbes have evolved over 3.5 billion years and are arguably the most adaptable organisms on earth. Restricted genetically by their inability to reproduce sexually, bacteria have acquired several additional mechanisms by which to exchange genetic material. Such mechanisms have allowed bacteria to inhabit some of the most inhospitable environments on earth. It is then hardly surprising that when faced with a barrage of inimical chemicals (antibiotics) they have responded with an equal and opposite force.
Sir Richard compared and contrasted the evolution of antimicrobial resistance to B-lactam antibiotics over the last 70 years in two bacterial species, namely Staphylococcus aureus, a highly evolved human pathogen, and Pseudomonas aeruginosa, an opportunistic nosocomial pathogen.
Find out more at www.rigb.org
As the COVID-19 pandemic continues, people are becoming infected at an alarming rate, individuals are unknowingly spreading disease, and more lives are lost every day. There is
an immediate need for a simple, rapid, early, and sensitive point-of-care testing for COVID-
19 disease. Recently,
clustered regularly interspaced short palindromic repeats (CRISPR)-based detection methods have received substantial attention for nucleic acid-based molecular testing due to their simplicity, high sensitivity and specificity. This review explores the various CRISPR-based COVID-19 detection methods and related diagnostic devices. As with any emerging technology, CRISPR/Cas-based nucleic acid testing methods have several
challenges that must be overcome for practical applications in clinics and hospitals. More importantly, these detection methods are not limited to COVID-19 but can be applied to detect any type of pathogen, virus, and fungi that may threaten humans, agriculture, and food industries in resource-limited settings. CRISPR/Cas-based detection methods have the potential to become simpler, more reliable, more affordable, and faster in the near future, which is highly important for achieving point-of-care diagnostics.
Bioo Scientific - Absolute Quantitation for RNA-SeqBioo Scientific
Accurate quantitation is a critical issue for most RNA-Seq analysis. As the efficiency of PCR amplification is sequence-dependent, with some transcripts being preferentially amplified over others, PCR amplification introduces bias during NGS library construction. The traditional approach to removing these artifacts, introduced during PCR, involves removing all fragments with identical start and stop sites. However, detailed analyses have shown that many original fragments have identical start and stop sites, and this method can incorrectly eliminate unique fragments from NGS data, thus reducing its accuracy. Bioo Scientific has incorporated Molecular Indexes™ into its NEXTflex™ Rapid Directional qRNA-Seq™ Kit, allowing for a more accurate resolution of duplicates introduced during PCR amplification. This presentation describes how Molecular Indexes can be used to increase the accuracy of RNA-Seq analysis.
Bioo Scientific - Simplify and Reduce Cost of mtDNA Isolation and Library PrepBioo Scientific
Mutations in mitochondrial DNA (mtDNA) have been implicated in various human disorders and in aging, making NGS analysis of mtDNA a priority for a number of labs. However, accurately determining the diversity of mtDNA has been difficult for a number of reasons. The standard methods for mitochondrial DNA extraction have a number of limitations making them inferior solutions for NGS library preparation. Bioo Scientific has commercialized a kit which overcomes these limitations of mtDNA isolation by selectively digesting linear nuclear DNA (nDNA) while leaving circular mtDNA intact. This technology has been incorporated into the NEXTflex mtDNA-Seq Kit which includes optimized reagents for the isolation of mtDNA and for the construction of Illumina mtDNA libraries. Libraries constructed using the NEXTflex mtDNA-Seq Kit are ideal for many NGS applications including heteroplasmy analysis.
The evolution of antimicrobial resistance: a Darwinian perspectiveThe Royal Institution
Sir Richard Sykes presented this Friday Evening Discourse at the Royal Institution of Great Britain on Friday 6 May 2011.
Microbes have evolved over 3.5 billion years and are arguably the most adaptable organisms on earth. Restricted genetically by their inability to reproduce sexually, bacteria have acquired several additional mechanisms by which to exchange genetic material. Such mechanisms have allowed bacteria to inhabit some of the most inhospitable environments on earth. It is then hardly surprising that when faced with a barrage of inimical chemicals (antibiotics) they have responded with an equal and opposite force.
Sir Richard compared and contrasted the evolution of antimicrobial resistance to B-lactam antibiotics over the last 70 years in two bacterial species, namely Staphylococcus aureus, a highly evolved human pathogen, and Pseudomonas aeruginosa, an opportunistic nosocomial pathogen.
Find out more at www.rigb.org
As the COVID-19 pandemic continues, people are becoming infected at an alarming rate, individuals are unknowingly spreading disease, and more lives are lost every day. There is
an immediate need for a simple, rapid, early, and sensitive point-of-care testing for COVID-
19 disease. Recently,
clustered regularly interspaced short palindromic repeats (CRISPR)-based detection methods have received substantial attention for nucleic acid-based molecular testing due to their simplicity, high sensitivity and specificity. This review explores the various CRISPR-based COVID-19 detection methods and related diagnostic devices. As with any emerging technology, CRISPR/Cas-based nucleic acid testing methods have several
challenges that must be overcome for practical applications in clinics and hospitals. More importantly, these detection methods are not limited to COVID-19 but can be applied to detect any type of pathogen, virus, and fungi that may threaten humans, agriculture, and food industries in resource-limited settings. CRISPR/Cas-based detection methods have the potential to become simpler, more reliable, more affordable, and faster in the near future, which is highly important for achieving point-of-care diagnostics.
Random RNA interactions control protein expression in prokaryotesPaul Gardner
Presented at the NZSBMB/NZMS Conference in Christchurch 2016
CustomScience Award
A core assumption of gene expression analysis is that mRNA abundances broadly correlate with protein abundance, but these two can be imperfectly correlated. Some of the discrepancy can be accounted for by two important mRNA features: codon usage and mRNA secondary structure. We present a new global factor, called mRNA:ncRNA avoidance, and provide evidence that avoidance increases translational efficiency. We demonstrate a strong selection for the avoidance of stochastic mRNA:ncRNA interactions across prokaryotes, and that these have a greater impact on protein abundance than mRNA structure or codon usage. By generating synonymously variant green fluorescent protein (GFP) mRNAs with different potential for mRNA:ncRNA interactions, we demonstrate that GFP levels correlate well with interaction avoidance. Therefore, taking stochastic mRNA:ncRNA interactions into account enables precise modulation of protein abundance.
Genetic Engineering andResistance to VirusesBiotech Online
Resistance to viruses has been achieved by transforming susceptible plant varieties with genes or gene sequences derived from viral genomes.
This approach is known as pathogen-derived resistance (PDR)
See more in slides
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.
Tag-based transcript sequencing: Comparison of SAGE and CAGEMatthias Harbers
Talk given at the European Meeting on Next Generation Sequencing, August 29 to September 1, 2010, at Leiden University Medical Center, The Netherland.
Data have been published in: Hestand et al.: “Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies.” Nucleic Acids Res. 2010 Sep;38(16):e165.
PMID: 20615900
Visualizing SNVs to quantify allele-specific expression in single cellsArjun Raj
We present a FISH-based method for detecting single- nucleotide variants (SNVs) in exons and introns on individual RNA transcripts with high efficiency. We used this method
to quantify allelic expression in cell populations and in single cells, and also to distinguish maternal from paternal chromosomes in single cells.
Regenerative Medicine is the revolution of the future. We are proud to use these technologies with great success in patients with orthopedic needs. Learn more about the science here.
Random RNA interactions control protein expression in prokaryotesPaul Gardner
Presented at the NZSBMB/NZMS Conference in Christchurch 2016
CustomScience Award
A core assumption of gene expression analysis is that mRNA abundances broadly correlate with protein abundance, but these two can be imperfectly correlated. Some of the discrepancy can be accounted for by two important mRNA features: codon usage and mRNA secondary structure. We present a new global factor, called mRNA:ncRNA avoidance, and provide evidence that avoidance increases translational efficiency. We demonstrate a strong selection for the avoidance of stochastic mRNA:ncRNA interactions across prokaryotes, and that these have a greater impact on protein abundance than mRNA structure or codon usage. By generating synonymously variant green fluorescent protein (GFP) mRNAs with different potential for mRNA:ncRNA interactions, we demonstrate that GFP levels correlate well with interaction avoidance. Therefore, taking stochastic mRNA:ncRNA interactions into account enables precise modulation of protein abundance.
Genetic Engineering andResistance to VirusesBiotech Online
Resistance to viruses has been achieved by transforming susceptible plant varieties with genes or gene sequences derived from viral genomes.
This approach is known as pathogen-derived resistance (PDR)
See more in slides
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.
Tag-based transcript sequencing: Comparison of SAGE and CAGEMatthias Harbers
Talk given at the European Meeting on Next Generation Sequencing, August 29 to September 1, 2010, at Leiden University Medical Center, The Netherland.
Data have been published in: Hestand et al.: “Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies.” Nucleic Acids Res. 2010 Sep;38(16):e165.
PMID: 20615900
Visualizing SNVs to quantify allele-specific expression in single cellsArjun Raj
We present a FISH-based method for detecting single- nucleotide variants (SNVs) in exons and introns on individual RNA transcripts with high efficiency. We used this method
to quantify allelic expression in cell populations and in single cells, and also to distinguish maternal from paternal chromosomes in single cells.
Regenerative Medicine is the revolution of the future. We are proud to use these technologies with great success in patients with orthopedic needs. Learn more about the science here.
Chronic myelogenous leukemia (CML) - pluripotential stem cell disease
A malignancy the treatment of which has been revolutionised over the last decade.
Here is a comprehensive discussion on the disease
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.
A CRISPR/Cas9, works like a biological version of a word-processing programme’s “find and replace”. Its simplicity and extremely low cost of implementation is the reason to use. How Cas 9 is activated and its mechanism (DNA binding and cleavage), it's regulation and application in human disease therapy, new drug screening, agriculture and biofuel etc.
understanding of the human immune system, and thereby cancer immunology.
αβT-cells are the primary constituents of human cell-mediated adaptive immunity.
The antigen specificity of each αβT-cell is encoded in the 500-600 bp transcript
encompassing the variable portion of the rearranged TCRα and TCRβ subunits,
which can be read via NGS in a process termed repertoire sequencing. Until now,
the main challenge the field faces is the lack of a technology that can provide a
contiguous read of 600 bp to minimize the complexity of designing bias-prone
primers and informatics challenges of stitching short reads. Here we leverage the
long read capability of Ion 530™ chip to comprehensively sequence all three CDR
domains of the TCRβ chain. The Ion 530™ chip offers greater than 15 M productive
reads, allowing a multiplex of 2-4 samples with sufficient coverage for most repertoire
profiling studies. Initial testing with leukocyte total RNA demonstrates that this
multiplex PCR assay produced repertoires that were much more similar to data
derived from 5’-RACE protocol than the commonly used BIOMED-2 primer set. This
result suggested that the use of long reads minimizes bias by allowing targeting of
less variable regions. To further assess the performance of the assay, we designed a
model system of 30 plasmid controls containing common human T-cell CDR3
sequences. Each plasmid was amplified individually and sequenced to confirm the
detection of a single clonal population. Analytical sensitivity of the assay and
accuracy of the accompanied analysis solution were further evaluated by spiking in
plasmid concentrations from 10 pg to 0.0001 pg (5 million to 50 copies) in a
background of 100 ng cDNA reverse transcribed from leukocyte total RNA. Results
showed the assay offers linearity over 5 orders of magnitude of decreasing input
concentration. In summary, we have demonstrated a NGS workflow for TCRβ
sequencing that offers multiplex flexibility on Ion S5 with sample to answer in less
than 48 hours.
this is a presentation on molecular markers that include what is molecular marker, it's types, biochemical markets (alloenzyme), it's classification, data analysis and it's applications
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...Travis Hills MN
Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptxMAGOTI ERNEST
Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024).
Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).
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.
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.
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
Nucleophilic Addition of carbonyl compounds.pptxSSR02
Nucleophilic addition is the most important reaction of carbonyls. Not just aldehydes and ketones, but also carboxylic acid derivatives in general.
Carbonyls undergo addition reactions with a large range of nucleophiles.
Comparing the relative basicity of the nucleophile and the product is extremely helpful in determining how reversible the addition reaction is. Reactions with Grignards and hydrides are irreversible. Reactions with weak bases like halides and carboxylates generally don’t happen.
Electronic effects (inductive effects, electron donation) have a large impact on reactivity.
Large groups adjacent to the carbonyl will slow the rate of reaction.
Neutral nucleophiles can also add to carbonyls, although their additions are generally slower and more reversible. Acid catalysis is sometimes employed to increase the rate of addition.
ANAMOLOUS SECONDARY GROWTH IN DICOT ROOTS.pptxRASHMI M G
Abnormal or anomalous secondary growth in plants. It defines secondary growth as an increase in plant girth due to vascular cambium or cork cambium. Anomalous secondary growth does not follow the normal pattern of a single vascular cambium producing xylem internally and phloem externally.
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
DERIVATION OF MODIFIED BERNOULLI EQUATION WITH VISCOUS EFFECTS AND TERMINAL V...Wasswaderrick3
In this book, we use conservation of energy techniques on a fluid element to derive the Modified Bernoulli equation of flow with viscous or friction effects. We derive the general equation of flow/ velocity and then from this we derive the Pouiselle flow equation, the transition flow equation and the turbulent flow equation. In the situations where there are no viscous effects , the equation reduces to the Bernoulli equation. From experimental results, we are able to include other terms in the Bernoulli equation. We also look at cases where pressure gradients exist. We use the Modified Bernoulli equation to derive equations of flow rate for pipes of different cross sectional areas connected together. We also extend our techniques of energy conservation to a sphere falling in a viscous medium under the effect of gravity. We demonstrate Stokes equation of terminal velocity and turbulent flow equation. We look at a way of calculating the time taken for a body to fall in a viscous medium. We also look at the general equation of terminal velocity.
Characterization of RNA binding protein RBPMS as a novel marker for retinal ganglion cells.
1. Characterization of RNA binding protein RBPMS
as a novel marker for retinal ganglion cells.
ABSTRACT
The recently discovered RNA binding protein
RBPMS appears to be a strong candidate as an
RGC marker. To test its specificity and reliability, we
performed immunostaining for RBPMS and Brn3a
(the latter which labels a large percentage of RGCs),
and compared them to retrogradely labeled RGCs.
Previous studies demonstrate that retrograde
labeling with Fluorogold yields over 99% labeling of
RGCs. Based on FG labeling, results indicate that
RBPMS was expressed specifically in RGCs, and
closely matched Fluorogold's labeling efficiency. This
indicates that RBPMS is expressed in over 99% of
RGCs, unlike Brn3a--which is expressed in only
about 80% of RGCs. Thus, our studies provide
strong evidence that RBPMS is a more reliable and
specific marker for RGCs, compared to other
commonly used markers.
Lior I. Schenk1, Praseeda Venugopalan1,2, Xiong Zhang1, and Jeffrey L. Goldberg1,3
1 University of California, San Diego, La Jolla, CA; 2 University of Miami, Miami, FL; 3 UCSD Shiley Eye Center, La Jolla, CA
FG labeling colocalizes with immunostaining against
RBPMS in over 99% of cells
RBPMS Brn3a
CONCLUSION
Abridged References
Acknowledgements
28
0
Major funding for this work was provided by the National Eye Institute (grant 7R01EY020913-04 ). Thanks
also go to the UCSD Division of Biological Sciences and the Undergraduate Research Scholarship
program for additional funding—and to Ms. W. Kwok (UCSD) for her generous support through the Eureka!
Scholarship to LIS. Original poster layout was provided by Ms. E.K. Nguyen (UCLA). I also thank PV and
XZ for their guidance, Mr. A. Kreymerman for help with editing, Dr. T. Stiles for help with printing, and the
other members of the Goldberg lab for their continual support and good will.
Immunostaining against RBPMS labels RGCs in a
more consistent manner than against current markers
Brn3a RBPMS
Brn3a
DAPI
RBPMS
RBPMS labels more RGCs than other markers do.
Immunostaining against RBPMS yields higher levels
of RGC labeling than staining against other markers
BACKGROUND
How can we identify the cellular impact of retinal
disease? One challenge lies in accurately
quantifying the loss of cells such as retinal ganglion
cells (RGCs). This requires reliable markers that
identify all the different subtypes of RGCs. Several
studies investigating different RGC markers have
been performed--but have yielded varying levels of
success, due to inconsistent expression and
specificity. As such, there is a need in retinal
research for a more efficient RGC marker.
RBPMS yields labeling of RGCs with over 99%
specificity,
in a consistent reliable manner,
and with higher output than that of current
antibodies.
By utilizing this powerful new marker, we can even better visualize each
disease’s pathway of action--putting us one step further in the fight for sight.
METHODS
Retrograde Labeling of RGCs
Fluorogold dye is first applied to the
surface of the superior colliculus.
FG taken up by RGC axon terminals
is transported retrogradely up the
optic nerve to somata in the retina.
Complete FG transport results in
labeling of about 98% of RGCs.
Immunohistochemistry
1. Kwong JM, Caprioli J, Piri N (2010). RNA binding protein with multiple splicing: a new marker for retinal ganglion
cells. Invest Ophthalmol Vis Sci.
2. Nadal-Nicolás FM, Jiménez-López M, Sobrado-Calvo P, Nieto-López L, Cánovas-Martínez I, Salinas-Navarro M,
Vidal-Sanz M, Agudo M (2009). Brn3a as a marker of retinal ganglion cells: qualitative and quantitative time
course studies in naive and optic nerve-injured retinas. Invest Ophthalmol Vis Sci.
3. Chiu K, Lau WM, Yeung SC, Chang RC, So KF (2008). Retrograde labeling of retinal ganglion cells by application of
fluoro-gold on the surface of superior colliculus. J Vis Exp.
All animals were housed, maintained, and examined with
accordance to the IACUC and UCSD’s policies and
procedures as set forth by the Animal Research Committee.
Antibodies:
RBPMS: uniquely expressed in retinal
ganglion cells, for reasons unknown. RNA
binding protein; stains cytoplasm of RGCs.
BRN-3: a family of proteins , each with
various roles in RGC development.
Transcription factors; stain RGC variably
depending on developmental stage (as well
as blood vessels due to peroxidase activity).
DAPI: used as a nuclear and chromosome
counterstain. Binds strongly to A,T regions of
DNA resulting in strong labeling of nuclei.
RESULTS
FG
<1
0
66
5
<1
A B C
D (A,B) More RGCs are present in the
RBPMS stain than in the Brn3a stain.
(B) Brn3a additionally stains blood
vessels, demonstrating a lack of
specificity for RGCs alone. (C) A merged
image with DAPI staining depicts
additional populations of non-RGCs in
the amacrine cell layer. (D) A merged
image compares RPMS and Brn3a IHC.
Arrowheads: Multiple cells were
positive for RBPMS but not for Brn3a.
RBPMS
Brn3a
DAPI
RBPMS RGC labeling (relative to RBPMS)
Brn3a
100%
90%
FG
80%
70%
60%
50%
40%
30%
20%
10%
0%
RBPMS Brn3a
• Over 99% of cells labeled by FG
were also positive for RBPMS.
• RBPMS staining colocalizes
with FG labeling at a higher
rate than Brn3a and FG.
• Though not all cells quantified
were positive for FG or for
Brn3a, over 99% were positive
for RBPMS.
• n=1; more experiments
necessary for conclusive data.
(A) RBPMS immunofluorescence overlayed onto Brn3a
immunofluorescence and FG retrograde labeling. Arrows: Multiple
RGCs (identify confirmed by FG) were positive for RBPMS and FG, but
negative for Brn3a—indicating that RBPMS may be more effective
than Brn3a as an RGC marker. (B) Quantification performed in 4
retinae (stained for RBPMS, Brn3a, and DAPI) demonstrated higher
RBPMS staining overall. On average, and in all zones of the retina,
RBPMS achieved higher RGC labeling than Brn3a.
• A portion of the retina was not labeled
by FG. This could be due to afferents
traveling to areas other than the SC,
such as the LGN and the SCN.
• Though Brn3a staining covered the
entirety of the retina, relevant areas of
examination resulted in higher RBPMS
staining overall.
RBPMS labels RGCs in a highly consistent and reliable manner.
RBPMS
Brn3a
FG
A B
Counterstaining against FG confirms RGC specificity.