El 12 de mayo de 2017 celebramos en la Fundación Ramó Areces una jornada con IS Global y Unitaid sobre enfermedades transmitidas por vectores, como la malaria, entre otras.
A knockout mouse is a mouse in which a specific gene has been inactivated or“knocked out” by replacing it or disrupting it with an artificial piece of DNA.
The loss of gene activity often causes changes in a mouse's phenotype and thus provides valuable information on the function of the gene.
A gene knockout is a genetic technique in which one of an organism's genes is made inoperative ("knocked out" of the organism). However, gene knockout can also refer to the gene that is knocked out or the organism that carries the gene knockout. Knockout organisms or simply knockouts are used to study gene function, usually by investigating the effect of gene loss. Researchers draw inferences from the difference between the knockout organism and normal individuals.
Transgensis: The process of transfer of gene from one organism to another organism.
Transgene: the gene responsible for transfer
Transgenic Mice: can be done by three methods
1)Retroviral Method: by using retroviral vector transgene is inserted into the egg
2) Dna Microinjection: Direct inoculation of transgene into the male pronuclues
3) Embryonic Stem cell: transgene is inserted during embryonic stage of the embryo
There are many applications, limitations .
Introduction
History
Landmarks Events in Transgenic Livestock Research
Techniques/ Method for Gene Transfer
Examples of transgenesis
Importance
Application
Limitation
Issue related to Transgenic Technology
Ethical concerns and how to Overcome
This slides include projects analyzed using next-generation sequencing method in genomic imprinting, X chromosome dosage compensation and DNA methylome in bovine early embryos.
El 12 de mayo de 2017 celebramos en la Fundación Ramó Areces una jornada con IS Global y Unitaid sobre enfermedades transmitidas por vectores, como la malaria, entre otras.
A knockout mouse is a mouse in which a specific gene has been inactivated or“knocked out” by replacing it or disrupting it with an artificial piece of DNA.
The loss of gene activity often causes changes in a mouse's phenotype and thus provides valuable information on the function of the gene.
A gene knockout is a genetic technique in which one of an organism's genes is made inoperative ("knocked out" of the organism). However, gene knockout can also refer to the gene that is knocked out or the organism that carries the gene knockout. Knockout organisms or simply knockouts are used to study gene function, usually by investigating the effect of gene loss. Researchers draw inferences from the difference between the knockout organism and normal individuals.
Transgensis: The process of transfer of gene from one organism to another organism.
Transgene: the gene responsible for transfer
Transgenic Mice: can be done by three methods
1)Retroviral Method: by using retroviral vector transgene is inserted into the egg
2) Dna Microinjection: Direct inoculation of transgene into the male pronuclues
3) Embryonic Stem cell: transgene is inserted during embryonic stage of the embryo
There are many applications, limitations .
Introduction
History
Landmarks Events in Transgenic Livestock Research
Techniques/ Method for Gene Transfer
Examples of transgenesis
Importance
Application
Limitation
Issue related to Transgenic Technology
Ethical concerns and how to Overcome
This slides include projects analyzed using next-generation sequencing method in genomic imprinting, X chromosome dosage compensation and DNA methylome in bovine early embryos.
Osteoblasts remotely supply lung tumors with cancer-promoting SiglecFhigh neu...Gul Muneer
Systemic cross-talk between lung tumors and bones
Bone marrow–derived myeloid cells can accumulate within tumors and foster
cancer outgrowth. Local immune-neoplastic interactions have been intensively
investigated, but the contribution of the systemic host environment to tumor growth
remains poorly understood. Here, we show in mice and cancer patients (n = 70) that
lung adenocarcinomas increase bone stromal activity in the absence of bone
metastasis. Animal studies reveal that the cancer-induced bone phenotype involves
bone-resident osteocalcin-expressing (Ocn+) osteoblastic cells. These cells promote
cancer by remotely supplying a distinct subset of tumor-infiltrating SiglecFhigh
neutrophils, which exhibit cancer-promoting properties. Experimentally reducing
Ocn+ cell numbers suppresses the neutrophil response and lung tumor outgrowth.
These observations posit osteoblasts as remote regulators of lung cancer and
identify SiglecFhigh neutrophils as myeloid cell effectors of the osteoblast-driven
protumoral response
Next Generation Sequencing and its Applications in Medical Research - Frances...Sri Ambati
The so-called “next-generation” sequencing (NGS) technologies allows us, in a short time and in parallel, to sequence massive amounts of DNA, overcoming the limitations of the original Sanger sequencing methods used to sequence the first human genome. NGS technologies have had an enormous impact on biomedical research within a short time frame. This talk will give an overview of these applications with specific examples from Mendelian genomics and cancer research. #h2ony
Los días 20 y 21 de octubre de 2016, la Fundacion Ramón Areces organizó un simposio internacional para analizar las 'Enfermedades raras de la piel: de la clínica al gen y viceversa'. El doctor Fernando Larcher Laguzzi, del CIEMAT-Universidad Carlos III de Madrid-IIS Fundación Jiménez Díaz, ejerció de coordinador.
Toxic effects of heavy metals : Lead and Arsenicsanjana502982
Heavy metals are naturally occuring metallic chemical elements that have relatively high density, and are toxic at even low concentrations. All toxic metals are termed as heavy metals irrespective of their atomic mass and density, eg. arsenic, lead, mercury, cadmium, thallium, chromium, etc.
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.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
ESR spectroscopy in liquid food and beverages.pptxPRIYANKA PATEL
With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
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).
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
Phenomics assisted breeding in crop improvementIshaGoswami9
As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate
change, and increasing global population, crop yield and quality need to be improved in a sustainable way over the coming decades. Genetic improvement by breeding is the best way to increase crop productivity. With the rapid progression of functional
genomics, an increasing number of crop genomes have been sequenced and dozens of genes influencing key agronomic traits have been identified. However, current genome sequence information has not been adequately exploited for understanding
the complex characteristics of multiple gene, owing to a lack of crop phenotypic data. Efficient, automatic, and accurate technologies and platforms that can capture phenotypic data that can
be linked to genomics information for crop improvement at all growth stages have become as important as genotyping. Thus,
high-throughput phenotyping has become the major bottleneck restricting crop breeding. Plant phenomics has been defined as the high-throughput, accurate acquisition and analysis of multi-dimensional phenotypes
during crop growing stages at the organism level, including the cell, tissue, organ, individual plant, plot, and field levels. With the rapid development of novel sensors, imaging technology,
and analysis methods, numerous infrastructure platforms have been developed for phenotyping.
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.
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.
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.
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.
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposé invité Journées Nationales du GDR GPL 2024
Deep Software Variability and Frictionless Reproducibility
Python Meetup2014 (Ying Liu)
1. Unveiling Epigenetic Regulation with
Next Generation Sequencing (NGS) and Python
Ying Liu
Weill Cornell Medical College
The New York Python Meetup, 05-29-2014
2. About Me
• PhD candidate, Weill Cornell Medical College
• Major Area: Stem cell epigenomics, Computational Biology
• Graduation: Fall 2014
• Dream job: data scientist in biomedical informatics
• Email: yingliuyl@gmail.com
• LinkedIn: https://www.linkedin.com/pub/ying-liu/b/669/605
3. Reprogram > 20 days
(Thousands of genes change expression)
Induced pluripotent stem
(iPS) cells
Adult cells
Express pluripotent stem cell
specific genes (4 genes)
2012 Nobel Prize in
Physiology or Medicine
Generate Pluripotent Stem Cells
from Mature Adult Cells
Limitation
• Reprogram efficiency: 0.01 - 0.1%
• Molecular mechanism is not fully understood
?
4. Human Genome Project
• Human genome: ~ 3 billion DNA base pairs
• Complete sequence: 2003
First sequence draft: 2001
5. Nature 454, 711-715
Gene Expression
My project: Histone X
Enriches at expressing genes
Epigenetic Regulation
• Epigenetics: study of heritable changes
in gene activity that are NOT caused by
changes in the DNA sequence
• One of the major epigenetic regulators:
Histone protein
Histone
proteins
DNA
6. Induced pluripotent stem
(iPS) cells
Adult cells
2012 Nobel Prize in
Physiology or Medicine
Project
Detect histone X function in initiating
adult cells reprogramming to iPS cells.
Experiment
• Collect cells at the beginning (Day 0, 3, 6,
10) and after reprogramming (iPS);
• Map genome-wide histone X localization
with Next Generation Sequencing (NGS);
• Analyze the dynamic change of genome-
wide histone X localization with Python
program and framework.
Reprogram > 20 days
(Thousands of genes change expression)
Express pluripotent stem cell
specific genes (4 genes)
Generate Pluripotent Stem Cells
from Mature Adult Cells
7. Next Generation
DNA Sequencing
(Illumina, Inc)
Genome-wide Analysis of Epigenetic Regulation
Computation analysis (by genome)
Tools: Python, R, etc.
Align DNA sequence to chromosome
Display in genome browser (by gene)
chromosome
8. 10 kb
Day 0
Day 3
Day 6
Day 10
Day 0
Day 3
Day 6
Day 10
Histone
X
K27me3
Pou5f1 Nanog
Histone X Enriches Near Stem Cell Specific Genes
At the Beginning of Cell Reprogramming
Genome browser (IGV)
Alignment output (BED format)
chr1 3000062 3000113 HWI-1KL117_0134:6:2101:14893:19331#ACAGTG/A..GTG. 37 +
chr1 3000113 3000164 HWI-1KL117_0134:6:2302:6790:10626#ACAGTG/A..GT.. 37 +
chr1 3000146 3000197 HWI-1KL117_0134:6:2303:8145:108924#ACAGTG/A..GT.. 37 -
chr1 3000154 3000205 HWI-1KL117_0134:6:2202:14995:109690#ACAGTG/A..GT.. 37 -
chr1 3000241 3000292 HWI-1KL117_0134:6:1304:12589:77263#ACAGTG/A..GT.. 25 -
chr1 3000311 3000362 HWI-1KL117_0134:6:1101:17212:111473#ACAGTG/A..GT.. 37 -
chr1 3000334 3000385 HWI-1KL117_0134:6:2308:10385:78074#ACAGTG/A..GT.. 25 -
chr1 3000385 3000436 HWI-1KL117_0134:6:2102:20734:102615#ACAGTG/A..GG.. 37 +
chr1 3000498 3000549 HWI-1KL117_0134:6:1203:3146:72739#ACAGTG/A..GTG. 37 -
chr1 3000538 3000589 HWI-1KL117_0134:6:1101:1921:57017#ACAGTG/A..GT.. 37 +
Chrom Start End Strand
9. Computational Pipeline for Genome-wide DNA
Sequence Analysis
Bardet AF, Stark A, Nature Protocols, 2012
Alignment Analysis (Python, Perl)
• BWA
• Picard
• Samtools
• MACS, Cistrome (X. Shirley Liu Lab)
• ChIPseeqer (Olivier Elemento Lab)
10. Peak Identification with Python Program:
Model-based Analysis of ChIP-Seq (MACS)
Zhang Y, Liu XS, et al. Genome Biology 2008
Feng J, Liu XS, et al. Nature Protocol 2012
(1)
(2)
Requirement: ~3 GB of RAM, 1.5 h per data set with
30 million DNA sequence reads.
d: estimated DNA fragment size
5’
3’
3’
5’
d
• Read distribution: Poisson distribution
• Use dynamic λlocal to capture local biases in the genome
λlocal = max (λBG, [λregion, λ1k], λ5k, λ10k)
λBG: constant estimated from the genome background
λregion: estimated from the candidate region
λ1k, λ5k, λ10k: estimated from 1kb, 5kb, 10kb local window in the control
• p-value: default threshold is 10-5
(3)
(4)
12. ChIPseeqer
• Graphical User Interface
• Command-line
http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml
13. 10 kb
Day 0
Day 3
Day 6
Day 10
Day 0
Day 3
Day 6
Day 10
Histone
X
K27me3
Pou5f1 Nanog
Histone X Enriches Near Stem Cell Specific Genes
At the Beginning of Cell Reprogramming
14. Day: 0 3 6 10 iPS E 0 3 6 10 iPS E
L H L H
Expression Histone X
ExpressionChangeExpressionStable
Pou5f1
Sox2
Cdh1
Cldn3
Jag2
Zbtb32
Elf3
Msh6
Lefty1
Piwil2
Notch4
Tjp3
Fbxo15
Cldn6
Foxh1
Zp3
Fgf15
Nodal
Tdgf1
Gdf3
Nanog
Fgf4
Dppa3
Histone X Enriches At Stem Cell Specific Gene Promoters
Prior to Gene Expression Activation
Embryonic placenta development
Stem cell maintenance
Response to nutrient
Cell-cell signaling
DNA metabolic process
DNA recombination
Formation of primary germ layer
Chromosome organization
Mesoderm development
Cell fate commitment
Stem cell differentiation
Blastocyst formation
Meiosis
Sexual reproduction
Thyroid hormone metabolic process
Cellular response to abiotic stimulus
X0
X1
X2
X3
X4
X5
X6
Embryonic placenta development, GO:0001892
Stem cell maintenance, GO:0019827
Response to nutrient, GO:0007584
Cell-cell signaling, GO:0007267
DNA metabolic process, GO:0006259
DNA recombination, GO:0006310
Formation of primary germ layer, GO:0001704
Chromosome organization, GO:0051276
Mesoderm development, GO:0007498
Cell fate commitment, GO:0045165
Stem cell differentiation, GO:0048863
Blastocyst formation, GO:0001825
Meiosis, GO:0007126
Sexual reproduction, GO:0019953
Thyroid hormone metabolic process, GO:0042403
Cellular response to abiotic stimulus, GO:0071214
5
Enrichment
-5
Depletion
X0
X1
X2
X3
X4
X5
X6
Embryonic p
Stem cell m
Response to
Cell-cell s
DNA metabol
DNA recombi
Formation o
Chromosome
Mesoderm de
Cell fate c
Stem cell d
Blastocyst
Meiosis, GO
Sexual repr
Thyroid hor
Cellular re
5
Enrichment
-5
Depletion
Expression Active Stable
Group - a b c a b c
Gene Ontology Analysis
a. Histone X enrich during Day 0 – 10
b. Histone X enrich in iPS (after Day 10)
c. Histone X not Enrich
15. Induced pluripotent stem
(iPS) cells
Adult cells
Limitation
• Reprogram efficiency: 0.01 - 0.1%
• Molecular mechanism is not fully understood
Our Genome-wide analysis suggests:
Histone X participates in stem cell gene activation
at the early stage of adult cell reprogram.
Express pluripotent stem cell
specific genes (4 genes)
Reprogram > 20 days
(Thousands of genes change expression)
Generate Pluripotent Stem Cells
from Mature Adult Cells