Pizza club - March 2017 - Ursula
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A. Hughes, DE Gottschling, An early age increase in vacuolar pH limits mitochondrial function and lifespan in yeast, Nature 492, 261–265 (13 December 2012), doi:10.1038/nature11654 Adam L. Hughes & Daniel E. Gottschling
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doi: 10.1016/j.freeradbiomed.2017.06.006. Epub 2017 Jun 9.
Mod 5 Poster
The CCK-8 cell viability assay showed that wortmannin has a dose-dependent cytotoxic effect on DU-145 prostate cancer cells, with an IC50 of approximately 100 nM. Flow cytometry analysis of cells treated with 100 nM wortmannin found a decrease in single activation of the PI3K pathway, an increase in dual PI3K/MAPK pathway activation, and a small increase in MAPK pathway activation. Phase contrast images suggest the cells underwent apoptosis rather than lysis in response to wortmannin, as there was little cell debris present. These results indicate wortmannin affects signaling cross-talk in DU-145 cells and may increase apoptosis through impacts on the MAPK and dual PI3
Carbohydrate metabolism- a quick revision.pdf
A quick revision of pathways of carbohydrate metabolism
Final IP Poster
This study examined the effect of linolenic acid concentration on the expression of fatty acid biosynthetic genes in female C57BL/6j mouse livers. Mice were fed either a soybean or cottonseed diet with different linolenic acid levels during gestation and lactation. Their offspring were sacrificed at 21 days, and liver gene expression was analyzed. The genes fatty acid synthase (Fasn), elongation of very long chain fatty acids family member 6 (Elovl6), and stearoyl-CoA desaturase-1 (Scd1) showed higher expression in pups from the soybean diet group, and expression of Elovl6 was statistically significant. The results suggest that
NetBioSIG2014-Keynote by Marian Walhout
This document summarizes research on how the nematode C. elegans is affected by different bacterial diets, and the role of interspecies systems biology in understanding this. Studies found that a Comamonas bacterial diet caused different effects on C. elegans' development, fertility and lifespan compared to an E. coli diet. Further work identified vitamin B12 as a key metabolite produced at much higher levels by Comamonas that mimics the effects of this diet. Vitamin B12 was found to regulate C. elegans gene expression and accelerate development via the methionine/SAM cycle, while also mitigating toxicity from propionic acid, another metabolite affected by the bacterial diets. This research demonstrates how studying
Microtubule inhibiting drugs
This document summarizes information about microtubule inhibiting drugs. It discusses the history of these drugs, including that the first known compound to bind tubulin was colchicine. It also describes the two main types of microtubule inhibitors - stabilizing agents like taxanes and destabilizing agents like vinca alkaloids. Specific drugs from each class are explained in terms of their source, structure, mechanism of action, pharmacokinetics, and clinical applications.
Rubisco Lab Report
This document discusses tracing the evolution of the human body through analyzing the chemical evolution of proteins and other molecules in the body over time. It notes that tracking changes in conserved proteins that control fundamental processes, like the Pax6 gene which regulates eye development, can reveal how closely related different organisms are. It recommends using the human arrestin protein sequence as an example, performing BLAST searches to find the arrestin sequence in the human genome and other organism genomes, then aligning the protein sequences to compare percentages and determine evolutionary relationships.
Role of apoptosis in cancer progression
it gives you answer to the question that why does cell proceed towards carcinogenesis when there are mechanisms to remove cells unfit for survival?
Mitochondrial dynamics and cancer (2)
Mitochondria are double membranous organelle, the inner membrane is more larger than the outer one. For this reason the inner membrane of the mitochondria folds inside forming a special figure called creasteae. The inner mitochondrial membrane (IMM) contains the subunits for oxidative phosphorylation (OXPHOS). And this inner mitochondrial membrane coverd by a second membrane called the outer mitochondrial membrane (OMM). We called mitochondria as a power house of cell not only they generates ATP via oxidative phosphorylation they also take part in various biochemical pathways such as- pyrimidine and purine biosynthesis, heme biosynthesis, the regulation of N2 balance in urea cycle, gluconeogenesis, keton body production and fatty acid degradation and elongation. They also take part in cell signalling via regulating the protein-protein interaction or by regulating the cellular concentration of calcium ion(Ca2+) and reactive oxygen species(ROS).
During various biological diseasesmitochondrial morphology altered, as in the case when there is lack of nutrient in our body mitochondria combine together to share their nutrient and alo their DNA and ETC components to maintain their OXPHOS. But in case of high energy demand of a part of body mitochondria undergo division or called fission because they move rapidly than lager one (Zhao et al., 2013). Fission also occur in mitotic cell to share equal amount of mitochondria to the daughter cells. Many questions arise in mitochondrial dinamics but here I am going to answer a most doubtful question- Is mitochondrial dynamics play any role in tumorigenic process? Is any oncogenic signalling play crucial role in morphological alteration of mitochondria?
Cell cycle
Lee Hartwell used temperature sensitive cell division cycle (cdc) mutants in the budding yeast Saccharomyces cerevisiae to develop a model of the eukaryotic cell cycle. He found that cdc28 is required early in the cell cycle before bud emergence and DNA replication, representing a commitment to a new cell division cycle called Start. Passing Start commits the cell to completing the entire cell cycle. Cyclin levels correlate with progression through the cell cycle, rising and falling at each stage. Work from Paul Nurse and Tim Hunt showed that cyclin and the maturation promoting factor (MPF) are conserved regulators of mitosis across species.
BIO Philadelphia yeast expression 2005
This document discusses novel solutions for recombinant protein expression in yeast. It summarizes that whole 2μm plasmids are very stable expression vectors in yeast. Significant variation exists between yeast strains in terms of secretion capacity, and strain engineering through chemical mutagenesis and selection can increase protein expression and control proteolysis. High levels of various recombinant proteins have been expressed intracellularly and secreted from yeast, including albumin fusions up to 8 g/L. Mitotically stable vector systems and optimization of yeast strains through mutagenesis allows improved productivity, control of post-translational modifications, and enhanced downstream processing.
NGUYENTHINHI-W9.pptx
1. The document reports on a study investigating the role of insulin signaling in pancreatic β cells using Cre-loxP mediated recombination to generate βIRKO mice lacking the insulin receptor in β cells.
2. Results showed βIRKO mice exhibited impaired glucose tolerance and insulin secretion compared to controls. Expression of genes CENP-A and PLK1 were decreased in βIRKO cells.
3. Further experiments demonstrated insulin stimulates FoxM1 binding to the CENP-A and PLK1 genes, and CENP-A expression is reduced in type 2 diabetes patient islets. Knockout of CENP-A in β cells decreased proliferation.
OTHERS.pdf
1. The document contains calculations and questions related to pharmacology, physiology, structures, and pharmaceutical topics.
2. Key concepts covered include enzyme kinetics, glomerular filtration rate calculation, central tendency measures, drug clearance, pharmacokinetics, drug metabolism, organ systems, electromagnetic waves, and pharmaceutical compounding.
3. Various questions test knowledge of drug dosage forms, routes of administration, stability considerations, sterilization methods, and pharmaceutical calculations.
Shivaputra
Mitochondria are organelles found in plant cells that provide energy and regulate important metabolic processes. Plant mitochondrial genomes vary significantly in size but generally encode proteins involved in oxidative phosphorylation as well as rRNAs and tRNAs. These genomes often contain introns, open reading frames, and chloroplast DNA sequences. Mutations in mitochondrial DNA can impact plant development and cause cytoplasmic male sterility. Expression of chimeric mitochondrial genes is associated with some cases of male sterility. Studies examine the role of mitochondrial proteins like uncoupling proteins and alternative oxidases in conferring stress tolerance in plants. The WA352 mitochondrial gene is implicated in cytoplasmic male sterility in rice through interaction with the nuclear-encoded protein COX11.
Jattir Emerging Scholars Poster
This study compared the cytotoxicity and induction of genes encoding metabolic enzymes in cells exposed to different alkylated polycyclic aromatic hydrocarbons (PAHs). An SRB assay showed little cell death between exposures of 1uM naphthalene, 1uM dimethyl naphthalene, 1uM BAP, and the vehicle control, except for 5uM BAP. RT-PCR analysis found that 1uM BAP induced expression of CYP1A1 and CYP1B1 genes, but 1uM naphthalene and dimethyl naphthalene did not induce gene expression. Comparing responses to the parent naphthalene and dimethylated naphthalene,
Cell cycle checkpoints, apoptosis and cancer
1. The document discusses various aspects of the cell cycle, including its key phases and regulating molecules. It notes that the cell cycle includes growth, DNA replication, chromosome separation, and cytokinesis.
2. Major regulatory molecules discussed include cyclins, CDKs, Rb protein, and checkpoints like START that ensure DNA damage is repaired before progression.
3. External factors like nutrients and growth signals regulate the cell cycle at transition points like the G1/S boundary through pathways involving cyclins, CDKs, and Rb.
Ketosis 2011 samiei
This document discusses factors that can cause stress in dairy cows around calving and impact their health and milk production. It notes that the period from 3 weeks before to 3 weeks after calving is the most challenging as cows face metabolic, digestive, and calving stresses. Reduced dry matter intake pre-calving can predispose cows to health disorders post-calving. The document reviews biomarkers like non-esterified fatty acids and beta-hydroxybutyrate that can indicate negative energy balance and ketosis in cows during this transition period. It also examines the liver's role in ketone body production and clearance from the bloodstream when cows produce more fatty acids than can be utilized.
Metalloprotease's Power Point
The document discusses a study on metalloproteases (MP), enzymes that shape the extracellular matrix. The researchers aim to control irregularities in MP activity by inhibiting the MP gene. They plan to obtain and sequence the MP gene from the Bornean orangutan (Pongo pygmaeus) to gain information on a global health issue. Their goals are to purify and sequence the MP gene, transform E. coli with the gene for expression, and perform protease detection assays.
Similar to Pizza club - March 2017 - Ursula (20)
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Pizza club - January 2017 - Kamil
This document discusses epithelial-mesenchymal transition (EMT) and its role in cancer metastasis. It summarizes findings from a study using a triple-transgenic mouse model of breast cancer metastasis that found: 1) Primary tumor cells disseminated and formed metastases while maintaining their epithelial phenotype, not undergoing EMT. 2) Inhibiting EMT with miR-200 had no effect on metastasis. 3) Non-EMT tumor cells were sensitive to chemotherapy, whereas mesenchymal cells were resistant. The study provides evidence that EMT may not be required for cancer metastasis in this model.
Pizza club - January 2017 - Alberto
This document discusses biological networks such as metabolic, regulatory, signaling, and protein-protein interaction networks. It specifically focuses on metabolic networks, describing Recon 2 as a global reconstruction of the human metabolic network containing over 7,000 reactions and 2,000 genes. ReconMap is introduced as a Google Maps interface to visualize and interact with Recon 2 integrated with omics data and simulation results. The document then discusses Leigh Syndrome, a progressive neurodegenerative disorder, and how a gene-phenotype network map is being built to help provide accurate diagnoses for patients by combining the map with whole exome sequencing data and metabolic testing.
Pizza club - October 2016 - Eugen
This document discusses comparing microbial communities to multicellular organisms. It explores whether microbial communities can be understood as multicellular organisms and vice versa. The document notes some similarities in their evolution of multicellularity, such as both utilizing spatial and temporal gradients to drive differentiation. However, it also outlines some key differences, such as differentiated microbes being more autonomous than differentiated eukaryotic cells. The document concludes that while microbial communities and multicellular organisms share some common patterns in their development, different modeling approaches may be needed to represent their differing levels of cellular dependencies and interactions.
Pizza club - October 2016 - Lisa
Midbrain-like organoids from Human Pluripotent Stem Cells contain functional dopaminergic and neuromelanin-producing neurons
Pizza club Zoé 28.09.16
This document summarizes research demonstrating that misfolded alpha-synuclein proteins associated with Multiple System Atrophy (MSA) can behave like prions and be transmitted between cells and laboratory mice. Brain homogenates from 14 MSA patients induced alpha-synuclein aggregation in cultured cells and caused neurological dysfunction in mice. Serial transmission between mice demonstrated replication of the MSA prions. The findings suggest MSA has prion-like properties and raises health concerns.
September Journal Club -Aishwarya
This study used predictive big data analytics to analyze data from the Parkinson's Progression Markers Initiative (PPMI) study. The study:
1) Aggregated and harmonized imaging, genetic, clinical, and demographic data from over 1,000 PPMI participants.
2) Used this complex dataset to test both model-based and model-free machine learning techniques for predicting Parkinson's disease versus healthy controls.
3) Found that combinations of clinical measures, demographics, genetics, and neuroimaging biomarkers provided the most accurate predictions, with classification improved after balancing cohorts.
Nicola Bonzanni - Following Your Passion
The document discusses Nicola Bonzanni's career path in science, which began with challenging himself by pursuing an MSc in Computer Science and a PhD in Bioinformatics. As a post-doc, his monthly routine involved teaching, researching relevant literature, working on personal projects, providing bioinformatics support, and attending meetings and writing grants. Currently, his daily routine at ENPICOM involves business development, customer acquisition, meeting with clients, discussing strategy, managing social media, administration, and working on projects. The document emphasizes managing time, building a network, and finding one's passion.
Magali Michaut - ROCK YOUR SCIENCE!
This document outlines Magali Michaut's career path and experiences in computational biology. It discusses her education history, including completing her PhD in Paris and postdoctoral research in Toronto. It also outlines her current role leading genetic interaction network analysis in Amsterdam. Additionally, it emphasizes the importance of soft skills for scientists, such as communication, collaboration, and networking. It encourages developing these skills in order to advance one's career and maximize contributions to their field.
June 2016 - Zuogong
Statistical inference of regulatory networks fro circadian regulation
Dirk, H., & Marco, G. (2014). Statistical inference of regulatory networks for circadian regulation. Statistical Applications in Genetics and Molecular Biology. http://dx.doi.org/10.1515/sagmb-2013-0051
2016.06 Pizza club - Marco
This document discusses current concepts in cancer mechanics research. It summarizes that mechanical forces play an important role in tumor growth and therapy. Solid stress within tumors is caused by growth and surrounding tissue, and fluid stress includes microvascular and interstitial fluid pressures. Mechanical forces can influence gene expression, proliferation, apoptosis, invasiveness and the extracellular matrix. Experimental platforms are needed to better control stiffness and study its interplay with tumor phenotype. Imaging techniques like elastography and atomic force microscopy can provide insights into biomechanics. Understanding mechanics is key to informing novel treatment approaches.
Pizza club - May 2016 - Shaman
This document summarizes a review article on computational approaches to predict bacteriophage-host relationships using metagenomic data. The review assessed various in silico methods including abundance-based profiles, genetic homology, CRISPR sequences, exact matches, and oligonucleotide profiles on a benchmark dataset of 820 phages and 153 bacterial genomes. The best performing approaches were blast searches and exact sequence matches, which could correctly identify the host around 30-40% of the time. However, most methods could only predict the host to within 1-4 possible bacteria. The predictive power was limited by current knowledge and database gaps as well as the complex dynamics between phages and hosts in environmental communities.
Pizza Club - May 2016 - Anne
- Microbial metabolites from the gut microbiome, especially butyrate, play an important role in modulating intestinal damage and graft-versus-host disease (GvHD) severity.
- In mice that underwent allogeneic stem cell transplantation, butyrate levels decreased significantly in intestinal epithelial cells, likely due to reduced butyrate transporter expression from inflammation.
- Restoring butyrate levels through intragastric gavage improved epithelial integrity, reduced GvHD severity and improved survival. Specific butyrate-producing bacteria were also associated with lower GvHD risk.
20042016_pizzaclub_part1
The document summarizes the African turquoise killifish as a new model organism for studying aging and age-related diseases. It has several advantages over traditional models like worms, flies, mice and zebrafish as it is a short-lived vertebrate with a lifespan of only a few months. Researchers have used killifish to model telomere attrition and genetic anticipation during aging by generating mutants with loss of telomerase activity or point mutations mimicking human diseases. The killifish provides a platform to study conserved aging genes and hallmarks of aging in a naturally short-lived vertebrate model.
20042016_pizzaclub_part2
This document discusses gene regulatory networks (GRNs) and their topology. It introduces concepts like nodes, edges, motifs, and robustness. The key points are:
1) GRNs have specific topologies that allow them to maintain function and recover from perturbations, due to selective pressure for stability.
2) Real transcriptional networks can be modeled as nodes representing genes and edges representing interactions like transcriptional regulation. However, they do not capture post-transcriptional regulations.
3) For a network to be stable, its qualitative topology should not depend on quantitative parameters like protein concentrations. Stability also depends on the presence of certain network motifs like feedback loops.
Resource sharing session
This document provides links to resources from pizza club including slides and materials available at http://rsg-luxembourg.iscbsc.org/. It also lists a site for identifying predatory open access publishers, a text mining tool for miRNA-gene regulation called miRTex, an interactive web tool called Heat*seq for comparing NGS experiments to public data, and a neural network web tool available at http://playground.tensorflow.org/.
160316_pizzaclub_part2
This study identified genetic factors that modify the age of onset of Huntington's disease by conducting a genome-wide association study. They found two single nucleotide variants on chromosome 15 that either delayed or hastened age of onset by 6 or 1.4 years, respectively. A variant on chromosome 8 was also found that hastened onset by 1.6 years. Pathway analysis implicated genes involved in DNA handling and repair, such as MLH1, in modifying disease onset. This study demonstrates that age of onset in Huntington's disease is influenced by genetic modifiers.
160316_pizzaclub_part1
This document summarizes research on microRNAs that confer radioresistance in glioblastoma. Four miRNAs (miR-1, miR-125a, miR-150, miR-425) were identified that limit apoptosis induced by radiation and activate DNA damage checkpoint factors without affecting repair. miR-1 and miR-125a expression is induced by TGF-β signaling. Inhibiting these miRNAs can neutralize radioresistance caused by TGF-β. The miRNAs are expressed in primary glioblastoma samples and targeting them may benefit patients by increasing radiosensitivity.
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Recently uploaded
ESR spectroscopy in liquid food and beverages.pptx
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.
如何办理(uvic毕业证书)维多利亚大学毕业证本科学位证书原版一模一样
原版纸张【微信：741003700 】【(uvic毕业证书)维多利亚大学毕业证】【微信：741003700 】学位证，留信认证（真实可查，永久存档）offer、雅思、外壳等材料/诚信可靠,可直接看成品样本，帮您解决无法毕业带来的各种难题！外壳，原版制作，诚信可靠，可直接看成品样本。行业标杆！精益求精，诚心合作，真诚制作！多年品质 ,按需精细制作，24小时接单,全套进口原装设备。十五年致力于帮助留学生解决难题，包您满意。
本公司拥有海外各大学样板无数，能完美还原海外各大学 Bachelor Diploma degree, Master Degree Diploma
1:1完美还原海外各大学毕业材料上的工艺：水印，阴影底纹，钢印LOGO烫金烫银，LOGO烫金烫银复合重叠。文字图案浮雕、激光镭射、紫外荧光、温感、复印防伪等防伪工艺。材料咨询办理、认证咨询办理请加学历顾问Q/微741003700
留信网认证的作用:
1:该专业认证可证明留学生真实身份
2:同时对留学生所学专业登记给予评定
3:国家专业人才认证中心颁发入库证书
4:这个认证书并且可以归档倒地方
5:凡事获得留信网入网的信息将会逐步更新到个人身份内，将在公安局网内查询个人身份证信息后，同步读取人才网入库信息
6:个人职称评审加20分
7:个人信誉贷款加10分
8:在国家人才网主办的国家网络招聘大会中纳入资料，供国家高端企业选择人才
bordetella pertussis.................................ppt
Bordettela is a gram negative cocobacilli spread by air born drop let
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.
Compexometric titration/Chelatorphy titration/chelating titration
Classification
Metal ion ion indicators
Masking and demasking reagents
Estimation of Magnisium sulphate
Calcium gluconate
Complexometric Titration/ chelatometry titration/chelating titration, introduction, Types-
1.Direct Titration
2.Back Titration
3.Replacement Titration
4.Indirect Titration
Masking agent, Demasking agents
formation of complex
comparition between masking and demasking agents,
Indicators/Metal ion indicators/ Metallochromic indicators/pM indicators,
Visual Technique,PM indicators (metallochromic), Indicators of pH, Redox Indicators
Instrumental Techniques-Photometry
Potentiometry
Miscellaneous methods.
Complex titration with EDTA.
在线办理(salfor毕业证书)索尔福德大学毕业证毕业完成信一模一样
学校原件一模一样【微信：741003700 】《(salfor毕业证书)索尔福德大学毕业证》【微信：741003700 】学位证，留信认证（真实可查，永久存档）原件一模一样纸张工艺/offer、雅思、外壳等材料/诚信可靠,可直接看成品样本，帮您解决无法毕业带来的各种难题！外壳，原版制作，诚信可靠，可直接看成品样本。行业标杆！精益求精，诚心合作，真诚制作！多年品质 ,按需精细制作，24小时接单,全套进口原装设备。十五年致力于帮助留学生解决难题，包您满意。
本公司拥有海外各大学样板无数，能完美还原。
1:1完美还原海外各大学毕业材料上的工艺：水印，阴影底纹，钢印LOGO烫金烫银，LOGO烫金烫银复合重叠。文字图案浮雕、激光镭射、紫外荧光、温感、复印防伪等防伪工艺。材料咨询办理、认证咨询办理请加学历顾问Q/微741003700
【主营项目】
一.毕业证【q微741003700】成绩单、使馆认证、教育部认证、雅思托福成绩单、学生卡等！
二.真实使馆公证(即留学回国人员证明,不成功不收费)
三.真实教育部学历学位认证（教育部存档！教育部留服网站永久可查）
四.办理各国各大学文凭(一对一专业服务,可全程监控跟踪进度)
如果您处于以下几种情况：
◇在校期间，因各种原因未能顺利毕业……拿不到官方毕业证【q/微741003700】
◇面对父母的压力，希望尽快拿到；
◇不清楚认证流程以及材料该如何准备；
◇回国时间很长，忘记办理；
◇回国马上就要找工作，办给用人单位看；
◇企事业单位必须要求办理的
◇需要报考公务员、购买免税车、落转户口
◇申请留学生创业基金
留信网认证的作用:
1:该专业认证可证明留学生真实身份
2:同时对留学生所学专业登记给予评定
3:国家专业人才认证中心颁发入库证书
4:这个认证书并且可以归档倒地方
5:凡事获得留信网入网的信息将会逐步更新到个人身份内，将在公安局网内查询个人身份证信息后，同步读取人才网入库信息
6:个人职称评审加20分
7:个人信誉贷款加10分
8:在国家人才网主办的国家网络招聘大会中纳入资料，供国家高端企业选择人才
Micronuclei test.M.sc.zoology.fisheries.
Current Ms word generated power point presentation covers major details about the micronuclei test. It's significance and assays to conduct it. It is used to detect the micronuclei formation inside the cells of nearly every multicellular organism. It's formation takes place during chromosomal sepration at metaphase.
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.
Phenomics assisted breeding in crop improvement
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.
20240520 Planning a Circuit Simulator in JavaScript.pptx
Evaporation step counter work. I have done a physical experiment.
(Work in progress.)
Deep Software Variability and Frictionless Reproducibility
Deep Software Variability and Frictionless ReproducibilityUniversity of Rennes, INSA Rennes, Inria/IRISA, CNRS
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
3D Hybrid PIC simulation of the plasma expansion (ISSS-14)
3D Particle-In-Cell (PIC) algorithm,
Plasma expansion in the dipole magnetic field.
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.
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...
The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.
Randomised Optimisation Algorithms in DAPHNE
Slides from talk:
Aleš Zamuda: Randomised Optimisation Algorithms in DAPHNE .
Austrian-Slovenian HPC Meeting 2024 – ASHPC24, Seeblickhotel Grundlsee in Austria, 10–13 June 2024
https://ashpc.eu/
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).
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Pizza club - March 2017 - Ursula
- 1. 1 Ursula Heins Marroquín Journal Club 22.03.17
- 2. 2 Saccharomyces cerevisiae (Budding yeast) unicellular eukaryotic organism small genome comprising about 6000 genes, which has been completely sequenced molecular genetic tools Cost effective model Easy to manipulate High throughput screening 31% of yeast gene has a human homolog
- 3. 3 Introduction S. cerevisiae Aged yeast cells - Mitochondria fragmentation - Increase ROS - Loss of mitochondrial DNA AGEING Chronological life span Replicative life span S. cerevisiae
- 4. 4 Introduction S. cerevisiae Aged yeast cells - Mitochondria fragmentation - Increase ROS - Loss of mitochondrial DNA AGEING Chronological life span Replicative life span S. cerevisiae Number of times an individual cell divides
- 6. 6 Method: Mother enrichment program (MEP) Mother Cell Cell division Daughter Cell
- 7. 7 Method: Mother enrichment program (MEP) Daughter Cell the transcription factor Ace2 Sequester in the cytoplasm Transported into the nucleus
- 8. 8 Method: Mother enrichment program (MEP) Cre- EBD78 SUMO-conjugating enzyme Activator of the anaphase-promoting complex (APC) Arrest in M-phase
- 9. 9 Results: Mitochondrial dysfunction in aged yeast Calcofluor staining of the bud scar TOM70-GFP Mitochondrial marker Nr. Cell division Characterization of age-associated mitochondrial phenotypes
- 10. 10 Results: Decreased of mitochondrial function DiOC6 : ΔΨ-dependent mitochondrial fluorescent dye
- 11. 11 Mitochondrial structure in young cells 250 genes1) 2) Overexpression of the 250 genes MEP strain expressing Tom70-GFP Delayed to the onset of altered mitochondrial morphology in aged cells
- 12. 12 Results: VAM1 and VPH2 VAM1 VPH2 A Catalytic subunit of V-ATPase V-ATPase assembly V-ATPase : Acidification of the vacuole Overexpression of VMA suppressed mitochondrial dysfunction in 93 % Overexpression of VPH2 suppressed mitochondrial dysfunction in 77 % Suppression by VMA1 or VPH2 overexpression required V-ATPase activity
- 13. 13 Results: Vacuolar and mitochondrial function are linked • Overexpression of VMA1 and VPH2 increase both media and maximal replicative lifespan.
- 14. 14 How vpH affects mitochondrial function? vacuolar protein degradation? Deletion of PEP4 No alteration of mitochondrial structure
- 15. 15 How vpH affects mitochondrial function? Import of vacuolar metabolite? Overexpression of vacuolar importers + ConcA ATV1 Neutral amino acid transporter Prevent mitochondrial dysfunction
- 16. 16 Results: ATV1 prevents mitochondrial fragmentation Overexpression of ATV1 • Prevent alteration of mitochondrial structure • No change in vacuolar acidification
- 17. 17 Results: ATV1 as aging modulator Deletion of ATV1 Development of age-induced mitochondrial dysfunction Overexpression = Extending RLS Deletion = Shortening of RLS
- 18. 18 Conclusion o Yeast is a good model for aging o Link between vacuolar pH and mitochondrial function o Link between metabolite transport and aging o Vacuole functionalion as aging modulator o Reestablishment of acidification in the vacuole in the daughter cells
- 19. 19 Thank you
Editor's Notes
- Expression of the Cre recombinase is restricted by a daughter-specific promoter derived from SCW11 (PSCW11) (Figure 1A). Daughter-specific expression from PSCW11 is regulated by the transcription factor Ace2, which is asymmetrically distributed to daughter cell nuclei prior to cytokinesis Cre activity is also post-transcriptionally regulated by fusion to the estradiol-binding domain (EBD) of the murine estrogen receptor (Cre-EBD78). The EBD sequesters the fusion protein in the cytoplasm until estradiol is introduced, at which point the fusion protein is transported into the nucleus where Cre can act upon its loxP DNA substrates
- Mitochondria—which are normally tubular—fragmented and ultimately aggregated in aged cells (Fig. 1a). Mitochondrial fragmentation was present early in the ageing process (86% of cells at 8 divisions), and progressed to large aggregates and small fragments (93% of cells at 17 divisions) that persisted throughout ageing (median lifespan of 28 divisions).
- Mitochondrial membrane potential decreases in aged cells as indicated by DiOC6 staining of aged cells expressing the mitochondrial outer membrane protein Tom70- mCherry. c, Mitochondrial import is reduced in aged cells. Localization of mitochondrial matrix marker preCox4-mCherry in aged cells that also express Tom70-GFP. pre-Cox4-mCherry is localized to the cytoplasm in cells with reduced mitochondrial import. dependent on the membrane potential for protein import, which is imported into mitochondria proportional to the MMP
- Mitochondrial structure is regulated by 250 identified genes in young cells
- Vma1 is the catalytic subunit of the peripheral-membrane-associated V1 sector of the V-ATPase14. Vph2 is an endoplasmic-reticulum-localized integral membrane protein required for V-ATPase assembly15. Overexpression of VMA1 or VPH2 from a high-copy promoter suppressed age-induced mitochondrial dysfunction in 93% and 77% of aged cells, respectively (17 or 16 divisions) (Fig. 1b and Supplementary Fig. 3a). Importantly, suppression by VMA1 or VPH2 overexpression required V-ATPase activity, as treatment with the specific V-ATPase inhibitor concanamycin A (concA)16 blocked their ability to produce normal, tubular mitochondria (Fig. 1b and Supplementary Fig. 3a).
- that resembled mitochondrial phenotypes present in aged cells.
- If reduced import of a particular amino acid or ion into the vacuole led to mitochondrial dysfunction, then overexpressing the transporter required for import of that metabolite into the vacuole might suppress mitochondrial dysfunction in cells with a low vacuolar proton gradient. To test this, we reduced the vacuolar proton gradient by treating cells with low concentrations of concA, and measured mitochondrial DYwith DiOC6 in cells overexpressing individual vacuolar amino acid or ion transporters. Overexpressing most characterized V-ATPasedependent vacuolar importers22–24 had no (NHX1, VBA1, VBA3) or little (VCX1, VBA2) effect on mitochondrial function. However, overexpressing AVT1, a neutral amino acid transporter25, prevented mitochondrial dysfunction in 60% of cells
- If reduced import of a particular amino acid or ion into the vacuole led to mitochondrial dysfunction, then overexpressing the transporter required for import of that metabolite into the vacuole might suppress mitochondrial dysfunction in cells with a low vacuolar proton gradient. To test this, we reduced the vacuolar proton gradient by treating cells with low concentrations of concA, and measured mitochondrial DYwith DiOC6 in cells overexpressing individual vacuolar amino acid or ion transporters. Overexpressing most characterized V-ATPasedependent vacuolar importers22–24 had no (NHX1, VBA1, VBA3) or little (VCX1, VBA2) effect on mitochondrial function. However, overexpressing AVT1, a neutral amino acid transporter25, prevented mitochondrial dysfunction in 60% of cells