Time and Money: Techniques for Neural Gene Expression Profiling
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This was the very first talk I gave in front of a classroom based heavily on my research own personal research. It was 2013, and my audience was a group of students at the Marine Biological Lab in Woods Hole, MA and a group of students who Skyped in from Uruguay. The goal of this talk is to help students better understand when candidate gene approaches are preferred of whole genome approaches and vice versa. You can watch this talk here: http://videocenter.mbl.edu/videos/video/630/in/channel/21/
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This master's thesis project involves studying small regulatory peptides and alternative translation initiation sites using techniques like ribosome profiling, mass spectrometry, and sequencing. Specific topics being investigated include micropeptides, non-ATG translation start sites, nuclear translation, evolutionary epigenetics, imprinted loci identification, and cardiovascular epigenomics. The student is welcome to contribute to tool development for analyzing ribosome profiling and mass spectrometry data, or help with computational analysis and data integration. Potential collaborators mentioned include labs at VIB, VITO, and international institutions studying related topics.
Recombinant DNA Technology
1. Recombinant DNA technology involves manipulating genetic material from different sources to create chimeric DNA molecules. This is done using various tools like restriction enzymes, DNA ligase, cloning, and gene transfer methods.
2. Medical biotechnology applies recombinant DNA technology to research and produce pharmaceuticals and diagnostic products to treat and prevent human diseases. This includes producing insulin, growth hormones, antibodies, and vaccines.
3. Techniques like PCR, blotting, hybridization, and DNA sequencing are used in recombinant DNA technology applications such as gene mapping, understanding disease mechanisms, DNA-based diagnostics, forensics, and gene therapy.
Catalyzing Plant Science Research with RNA-seq
RNA-seq is a revolutionary tool for transcriptomics that has advantages over previous methods like microarrays. It allows for single-base resolution expression profiling, detection of splicing variants and gene fusions, and can detect a wider dynamic range of expression levels. RNA-seq is being used to improve genome annotations by characterizing alternative splicing events and verifying gene boundaries. It is also useful for generating genetic resources for non-model species by performing de novo transcriptome sequencing and annotation. Additionally, RNA-seq can help advance proteomics by providing a reference database to match peptide spectra. Studies are using RNA-seq to examine spatial and temporal transcriptome landscapes in various plants.
Microarry andd NGS.pdf
A microarray is a laboratory tool used to detect the expression of thousands of genes at the same time. DNA microarrays are microscope slides that are printed with thousands of tiny spots in defined positions, with each spot containing a known DNA sequence or gene.
2017 molecular profiling_wim_vancriekinge
The document discusses various topics related to molecular profiling and personalized medicine. It describes first generation molecular profiling techniques like gene sequencing, microarrays, and PCR. It then covers next generation sequencing technologies like Roche 454, Illumina, and ABI SOLID. It also discusses second generation techniques for DNA and RNA profiling including exome sequencing, ChIP-seq, and RNA-seq. Finally, it briefly mentions third generation sequencing and epigenetic profiling.
Tools for lncRNA research in cancer
The human genome is pervasively transcribed, giving rise to an increasing number of long non-coding RNA genes. Most of these genes are novel or poorly characterized, and their relevance in human health and disease remains elusive. In our lab, we have developed various tools to study lncRNAs, amongst others to assess their role in cancer. As such, we are looking for novel biomarkers and therapeutic targets. I will describe various tools and ongoing research programs, including a comprehensive annotated catalog of human lncRNAs (LNCipedia), a targeted screen for focal lncRNA copy number alterations, a web tool for antisense oligonucleotide design, Zipper plot to visualize the transcriptional activity of lncRNAs in their genomic context, decodeRNA functional context mapping, and probe based lncRNA capture sequencing in body fluids.
DNA and RAN based taxonomy in animals
This document discusses molecular taxonomy and DNA barcoding for species identification. It provides background on using DNA and RNA data for taxonomy rather than just morphological characters. DNA barcoding involves identifying species by sequencing a short, standardized region of mitochondrial DNA. The COI gene is commonly used as it varies more between species than within. DNA barcoding allows identification of all life stages, works with fragments, and increases accuracy in applications like food safety, invasive species control, forensics, agriculture, conservation, and education.
Cloud bioinformatics 2
This document provides an overview of cloud bioinformatics and the challenges of analyzing large datasets from next-generation sequencing (NGS). It discusses how bioinformatics uses computational methods to study genes, proteins, and genomes. The advent of NGS has led to huge datasets that require high-performance computing. Cloud computing provides access to pooled computing resources in a cost-effective manner and helps address the bioinformatics challenge of assembling and analyzing NGS data. The document also outlines common bioinformatics software and resources available through WestGrid and Galaxy that can be used for sequence assembly, annotation, and other applications.
20170209 ngs for_cancer_genomics_101
This document provides an overview of next generation sequencing (NGS) for cancer genomics. It discusses how NGS allows sequencing of whole genomes or targeted regions to identify genetic changes between normal and tumor DNA. Analysis involves aligning DNA reads to reference genomes, detecting mutations, and categorizing them as silent, non-silent, oncogenic drivers, or signatures of mutational processes. RNA sequencing can also profile gene expression and detect fusion genes. The data requires specialized bioinformatics analysis to interpret genetic changes driving cancer.
Sequencing @ BitLab
The document describes the author's experience sequencing the genome of Acinetobacter Baumannii using 454 sequencing. Key points include:
- The genome was sequenced to 23x coverage using 900,000 reads from GS20 and GS FLX platforms, yielding 96 million base pairs.
- The sequence was assembled into 1,036 contigs with a maximum length of 200,000 bp using Newbler, and further assembled into 47 scaffolds using paired end reads.
- Repeated regions and plasmids posed challenges for assembly and required additional work like manual inspection and PCR to resolve.
- General issues discussed include original experimental design, managing multiple assemblies over time, and improving communication between bioinformaticians and microbiologists
Functional genomics
Functional genomics uses genome-wide experimental approaches to assess gene function on a large scale. It analyzes gene expression through techniques like transcriptomics and proteomics. Transcriptomics analyzes gene expression profiles through RNA sequencing or microarray analysis. Microarray analysis involves hybridizing fluorescently-labeled cDNA or cRNA to microarrays containing DNA probes to measure gene expression levels across thousands of genes simultaneously. Functional genomics provides a global understanding of gene function and molecular interactions through integrated omics approaches.
Lecture 4.ppt
- Hi-C has determined the 3D structure of genomes. Transposons and retroelements are mobile genetic elements that can copy and insert into new genome regions.
- Mutations can occur through nucleotide changes or changes at the codon/protein level, causing missense, nonsense, or silent mutations. A single nucleotide change is a point mutation.
- Gene identification in eukaryotes considers promoters, introns/exons, splice sites, polyA signals, and codon usage bias. Experimental validation is needed to prove a sequence is truly a gene.
Polymerase chain reactions
The document discusses polymerase chain reaction (PCR), a laboratory technique used to amplify a specific segment of DNA. It was invented in 1983 by Kary Mullis, who was awarded the Nobel Prize in 1993. PCR works by repeating cycles of heating and cooling of the DNA sample to separate the double helix, followed by use of DNA polymerase to make copies of the targeted region. This process can generate millions of copies of the targeted DNA sequence. The document outlines the components and steps of PCR, including primers, DNA polymerase, and thermal cycling. It discusses some applications of PCR such as detecting low-abundance DNA sequences, forensic analysis, and prenatal diagnosis.
Kim Pruitt trainingbiocuration2015
The document discusses curating sequence and literature data for RefSeq and Gene at the National Center for Biotechnology Information. It provides an overview of RefSeq, describing what RefSeq is, how it compares to GenBank, its advantages, and how the RefSeq dataset is built through curated data and sequence analysis. It then discusses the curation process in depth, including examples of curating genes, transcripts, proteins, and literature. It also describes the tools and quality assurance checks used in curation.
The UCSC genome browser: A Neuroscience focused overview
An self guided tutorial based overview of the UCSC genome browser for accessing public neuroscience data, in particular data from the ENCODE project. Including additional transcriptomic resources for the Neurosciences.
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Toward Single Neuron Gene Expression Analysis for Studying Behavior
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Polymerase Chain Reaction (PCR) and The Application.pptx
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The UCSC genome browser: A Neuroscience focused overview
The UCSC genome browser: A Neuroscience focused overview
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Bob Reedy - Nitrate in Texas Groundwater.pdf
Presented at June 6-7 Texas Alliance of Groundwater Districts Business Meeting
Immersive Learning That Works: Research Grounding and Paths Forward
We will metaverse into the essence of immersive learning, into its three dimensions and conceptual models. This approach encompasses elements from teaching methodologies to social involvement, through organizational concerns and technologies. Challenging the perception of learning as knowledge transfer, we introduce a 'Uses, Practices & Strategies' model operationalized by the 'Immersive Learning Brain' and ‘Immersion Cube’ frameworks. This approach offers a comprehensive guide through the intricacies of immersive educational experiences and spotlighting research frontiers, along the immersion dimensions of system, narrative, and agency. Our discourse extends to stakeholders beyond the academic sphere, addressing the interests of technologists, instructional designers, and policymakers. We span various contexts, from formal education to organizational transformation to the new horizon of an AI-pervasive society. This keynote aims to unite the iLRN community in a collaborative journey towards a future where immersive learning research and practice coalesce, paving the way for innovative educational research and practice landscapes.
Thornton ESPP slides UK WW Network 4_6_24.pdf
ESPP presentation to EU Waste Water Network, 4th June 2024 “EU policies driving nutrient removal and recycling
and the revised UWWTD (Urban Waste Water Treatment Directive)”
SAR of Medicinal Chemistry 1st by dk.pdf
In this presentation include the prototype drug SAR on thus or with their examples .
Syllabus of Second Year B. Pharmacy
2019 PATTERN.
THEMATIC APPERCEPTION TEST(TAT) cognitive abilities, creativity, and critic...
THEMATIC APPERCEPTION TEST(TAT) cognitive abilities, creativity, and critic...Abdul Wali Khan University Mardan,kP,Pakistan
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skillsDescribing and Interpreting an Immersive Learning Case with the Immersion Cub...
Current descriptions of immersive learning cases are often difficult or impossible to compare. This is due to a myriad of different options on what details to include, which aspects are relevant, and on the descriptive approaches employed. Also, these aspects often combine very specific details with more general guidelines or indicate intents and rationales without clarifying their implementation. In this paper we provide a method to describe immersive learning cases that is structured to enable comparisons, yet flexible enough to allow researchers and practitioners to decide which aspects to include. This method leverages a taxonomy that classifies educational aspects at three levels (uses, practices, and strategies) and then utilizes two frameworks, the Immersive Learning Brain and the Immersion Cube, to enable a structured description and interpretation of immersive learning cases. The method is then demonstrated on a published immersive learning case on training for wind turbine maintenance using virtual reality. Applying the method results in a structured artifact, the Immersive Learning Case Sheet, that tags the case with its proximal uses, practices, and strategies, and refines the free text case description to ensure that matching details are included. This contribution is thus a case description method in support of future comparative research of immersive learning cases. We then discuss how the resulting description and interpretation can be leveraged to change immersion learning cases, by enriching them (considering low-effort changes or additions) or innovating (exploring more challenging avenues of transformation). The method holds significant promise to support better-grounded research in immersive learning.
Applied Science: Thermodynamics, Laws & Methodology.pdf
When I was asked to give a companion lecture in support of ‘The Philosophy of Science’ (https://shorturl.at/4pUXz) I decided not to walk through the detail of the many methodologies in order of use. Instead, I chose to employ a long standing, and ongoing, scientific development as an exemplar. And so, I chose the ever evolving story of Thermodynamics as a scientific investigation at its best.
Conducted over a period of >200 years, Thermodynamics R&D, and application, benefitted from the highest levels of professionalism, collaboration, and technical thoroughness. New layers of application, methodology, and practice were made possible by the progressive advance of technology. In turn, this has seen measurement and modelling accuracy continually improved at a micro and macro level.
Perhaps most importantly, Thermodynamics rapidly became a primary tool in the advance of applied science/engineering/technology, spanning micro-tech, to aerospace and cosmology. I can think of no better a story to illustrate the breadth of scientific methodologies and applications at their best.
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptx
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).
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...
Context. With a mass exceeding several 104 M⊙ and a rich and dense population of massive stars, supermassive young star clusters
represent the most massive star-forming environment that is dominated by the feedback from massive stars and gravitational interactions
among stars.
Aims. In this paper we present the Extended Westerlund 1 and 2 Open Clusters Survey (EWOCS) project, which aims to investigate
the influence of the starburst environment on the formation of stars and planets, and on the evolution of both low and high mass stars.
The primary targets of this project are Westerlund 1 and 2, the closest supermassive star clusters to the Sun.
Methods. The project is based primarily on recent observations conducted with the Chandra and JWST observatories. Specifically,
the Chandra survey of Westerlund 1 consists of 36 new ACIS-I observations, nearly co-pointed, for a total exposure time of 1 Msec.
Additionally, we included 8 archival Chandra/ACIS-S observations. This paper presents the resulting catalog of X-ray sources within
and around Westerlund 1. Sources were detected by combining various existing methods, and photon extraction and source validation
were carried out using the ACIS-Extract software.
Results. The EWOCS X-ray catalog comprises 5963 validated sources out of the 9420 initially provided to ACIS-Extract, reaching a
photon flux threshold of approximately 2 × 10−8 photons cm−2
s
−1
. The X-ray sources exhibit a highly concentrated spatial distribution,
with 1075 sources located within the central 1 arcmin. We have successfully detected X-ray emissions from 126 out of the 166 known
massive stars of the cluster, and we have collected over 71 000 photons from the magnetar CXO J164710.20-455217.
waterlessdyeingtechnolgyusing carbon dioxide chemicalspdf
The technology uses reclaimed CO₂ as the dyeing medium in a closed loop process. When pressurized, CO₂ becomes supercritical (SC-CO₂). In this state CO₂ has a very high solvent power, allowing the dye to dissolve easily.
8.Isolation of pure cultures and preservation of cultures.pdf
Isolation of pure culture, its various method.
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Bordettela is a gram negative cocobacilli spread by air born drop let
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...
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Slides from talk:
Aleš Zamuda: Remote Sensing and Computational, Evolutionary, Supercomputing, and Intelligent Systems.
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Inter-Society Networking Panel GRSS/MTT-S/CIS Panel Session: Promoting Connection and Cooperation
https://www.etran.rs/2024/en/home-english/The debris of the ‘last major merger’ is dynamically young
The Milky Way’s (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
‘last major merger.’ Hypotheses for the origin of this component include Gaia-Sausage/Enceladus (GSE), where the progenitor
collided with the MW proto-disc 8–11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
MW disc within the last 3 Gyr. These two scenarios make different predictions about observable structure in local phase space,
because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
at late times. Roughly 20 per cent of the stars in the prograde local stellar halo are associated with the observed caustics. Based
on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1–2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
measurement of phase mixing (2D causticality). The observed local phase-space distribution best matches the simulated data
1–2 Gyr after collision, and certainly not later than 3 Gyr. This is further evidence that the progenitor of the ‘last major merger’
did not collide with the MW proto-disc at early times, as is thought for the GSE, but instead collided with the MW disc within
the last few Gyr, consistent with the body of work surrounding the VRM.
Authoring a personal GPT for your research and practice: How we created the Q...
Thematic analysis in qualitative research is a time-consuming and systematic task, typically done using teams. Team members must ground their activities on common understandings of the major concepts underlying the thematic analysis, and define criteria for its development. However, conceptual misunderstandings, equivocations, and lack of adherence to criteria are challenges to the quality and speed of this process. Given the distributed and uncertain nature of this process, we wondered if the tasks in thematic analysis could be supported by readily available artificial intelligence chatbots. Our early efforts point to potential benefits: not just saving time in the coding process but better adherence to criteria and grounding, by increasing triangulation between humans and artificial intelligence. This tutorial will provide a description and demonstration of the process we followed, as two academic researchers, to develop a custom ChatGPT to assist with qualitative coding in the thematic data analysis process of immersive learning accounts in a survey of the academic literature: QUAL-E Immersive Learning Thematic Analysis Helper. In the hands-on time, participants will try out QUAL-E and develop their ideas for their own qualitative coding ChatGPT. Participants that have the paid ChatGPT Plus subscription can create a draft of their assistants. The organizers will provide course materials and slide deck that participants will be able to utilize to continue development of their custom GPT. The paid subscription to ChatGPT Plus is not required to participate in this workshop, just for trying out personal GPTs during it.
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Immersive Learning That Works: Research Grounding and Paths Forward
Immersive Learning That Works: Research Grounding and Paths Forward
THEMATIC APPERCEPTION TEST(TAT) cognitive abilities, creativity, and critic...
THEMATIC APPERCEPTION TEST(TAT) cognitive abilities, creativity, and critic...
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Describing and Interpreting an Immersive Learning Case with the Immersion Cub...
Applied Science: Thermodynamics, Laws & Methodology.pdf
Applied Science: Thermodynamics, Laws & Methodology.pdf
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptx
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EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...
mô tả các thí nghiệm về đánh giá tác động dòng khí hóa sau đốt
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8.Isolation of pure cultures and preservation of cultures.pdf
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bordetella pertussis.................................ppt
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...
The debris of the ‘last major merger’ is dynamically young
The debris of the ‘last major merger’ is dynamically young
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Authoring a personal GPT for your research and practice: How we created the Q...
Time and Money: Techniques for Neural Gene Expression Profiling
- 1. TIME AND MONEY: TECHNIQUES FOR NEURAL GENE EXPRESSION PROFILING RAYNA M. HARRIS HOFMANN LAB, THE UNIVERSITY OF TEXAS AT AUSTIN HTTP://VIDEOCENTER.MBL.EDU/VIDEOS/CHANNEL/21/ 1
- 2. RNAlater qRT-PCRRNA-seq O.C.T PFA immunohistochemistryin situ hybridization Common molecular approaches for neural gene expression profiling 2
- 3. Global gene expression profiling with RNA-seq • RNA extraction (1-4 hrs) • Library prep (2 days) • Sequencing (3 days) • Bioinformatics (a few days) • Filter low quality reads • Map to transcriptome • Identify differentially expressed genes • Interpret data (months to years) 3
- 4. Quantitative Real Time PCR • Primer validation (weeks) • Store brains in RNALater or homogenized in buffer • RNA Extraction (1-4 hrs) • cDNA synthesis (2 hrs) – Oligo(dT) for mRNA only – Random hexamers for all RNA • qPCR (3 hours) • Data analysis (~4 hours) RNAlater RNA isolation cDNA synthesis 4 qPCR Data Analysis
- 5. LMDTissue punches Increasing spatial resolution of RNA-seq and qRT-PCR RNAlater qRT-PCRRNA-seq 5
- 6. Tissue punches • A. Freeze in O.C.T (5 min) and section (30 min/brain) • B. Slice fresh tissue (5 min) • Punch regions of interest (5min) • Homogenize and freeze tissue (5 min) 6
- 7. Laser Microdissection • Freeze tissue in O.C.T (5 min) • Prepare membrane slides (20 min) • Histology (5 min/brain) • Laser microdissection (~30min/brain) • RNA extraction (1-4 hrs) • Optional: RNA amplification (1-2 days) 7
- 8. Detecting RNA expression with in situ hybridization • Riboprobe Synthesis (weeks) • Freeze brain in O.C.T. (5 min) • Section brains (hr/brain) • Hybridization & Detection (3 days) • Alternatives – Radioactive – Fluorescent • Visualize the signal – Count silver grains – Map distribution Target RNA Probe & RNA Add HRP Blue signal! 8
- 9. Detecting proteins with Immunohistochemistry • Fix and cryoprotect tissue (2 days) • Section brains (~1hr/brain) • Bind primary and secondary antibodies (3 days) • Visualize the signal • Quantify cell counts or map distribution 9
- 10. From the bench to publication qPCR LMD ISH IHC $ spent $7,620 $4,161 $12,123 $6,695 # papers 2 1 5 5 $ per paper $3,810 $4,161 $2,425 $1,339 10
- 11. A few questions that may help you choose most appropriate technique • What are your molecules of interest? – mRNA or protein? – How soon after the stimulus will its activity be altered? • How big is your experiment? – How many groups, animals, brain regions, genes/proteins? • What resources do you have at your fingertips? – Core facilities and equipment – Validated PCR primers, riboprobes, antibodies? – A mentor who can help you collect & analyze the data? – Bioinformatic and statistical consulting? 11
- 12. Candidate genes vs genomic approaches • Histological approaches allow for co-localization • Histological approaches are low throughput • You may choose the wrong genes • Candidate genes act in networks that are poorly understand • Genomics allows systems level view of brain and behavior • Genomic approaches lack of spatial resolution 12
- 13. Recommended Readings IHC & ISH Mapping: Munchrath &Hofmann (2010) Distribution of Sex Steroid Hormone Receptors in the Brain of an African Cichlid Fish, Astatotilapia burtoni Double IHC: O’Connell LA, Matthews BJ, Hofmann HA (2012) Isotocin regulates fatherhood in a monogamous cichlid fish. qRT-PCR: Matz, Wright, Scott (2013) No Control Genes Required: Bayesian Analysis of qRT-PCR Data Sequencing: https://wikis.utexas.edu/display/GSAF/Pricing 13