Genetic engineering
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This document summarizes a student group project on designing antisense RNA for the HBA1 and HBA2 genes involved in alpha thalassemia. The group searched literature to identify the relevant genes, retrieved the FASTA sequence for the HBA1 gene from NCBI, and used the OligoWalk tool to predict efficient siRNA candidates. OligoWalk output showed the top siRNA candidates and their free energy changes. The sequence with the highest score was selected as the most efficient antisense RNA design.
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Bob Reedy - Nitrate in Texas Groundwater.pdf
Presented at June 6-7 Texas Alliance of Groundwater Districts Business Meeting
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The binding of cosmological structures by massless topological defects
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
light in the same manner as an equipotential (isothermal) sphere. Thus, the need for dark matter or modified gravity theory is
mitigated, at least in part.
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.
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/
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.
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...University of Maribor
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/Equivariant neural networks and representation theory
Or: Beyond linear.
Abstract: Equivariant neural networks are neural networks that incorporate symmetries. The nonlinear activation functions in these networks result in interesting nonlinear equivariant maps between simple representations, and motivate the key player of this talk: piecewise linear representation theory.
Disclaimer: No one is perfect, so please mind that there might be mistakes and typos.
dtubbenhauer@gmail.com
Corrected slides: dtubbenhauer.com/talks.html
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.
Cytokines and their role in immune regulation.pptx
This presentation covers the content and information on "Cytokines " and their role in immune regulation .
bordetella pertussis.................................ppt
Bordettela is a gram negative cocobacilli spread by air born drop let
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Immersive Learning That Works: Research Grounding and Paths Forward
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8.Isolation of pure cultures and preservation of cultures.pdf
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Basics of crystallography, crystal systems, classes and different forms
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Authoring a personal GPT for your research and practice: How we created the Q...
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Sharlene Leurig - Enabling Onsite Water Use with Net Zero Water
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The binding of cosmological structures by massless topological defects
The binding of cosmological structures by massless topological defects
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptx
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptx
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...
Compexometric titration/Chelatorphy titration/chelating titration
Compexometric titration/Chelatorphy titration/chelating titration
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...
Equivariant neural networks and representation theory
Equivariant neural networks and representation theory
The debris of the ‘last major merger’ is dynamically young
The debris of the ‘last major merger’ is dynamically young
Cytokines and their role in immune regulation.pptx
Cytokines and their role in immune regulation.pptx
bordetella pertussis.................................ppt
bordetella pertussis.................................ppt
Genetic engineering
- 1. The Design of Antisense RNA from Alpha Thalassemia HBA1 & HBA2 Gene Deletion GROUP MEMBERS SOHEL RANA (18MSB0003) MOVVA HARSHAVARDHAN (18MSB0041) TANVI SINGH(18MSB0044) RITOBRATA SENGUPTA(18MSB0048) SANGEETHA M (18MSB0052)
- 9. Introduction: Designing Anti-Sense RNA • Antisense RNA is a single stranded RNA that is complementary to a protein coding messenger RNA (mRNA) with which it hybridizes, and there by blocks its translation into protein. • One way of designing Antisense RNA in vitro is by annealing mechanism. • On the other hand, the basal biochemical mechanisms underlying the relationship between RNA structure and efficient annealing could allow one to derive more general rules for the design of in vivo effective antisense RNA.
- 10. Methodology Diagram 1: Diagrammatic representation of flow of work Literature search in order to find out the genes (HBA1 & HBA2) responsible for Alpha Thalassemia Selection of coding sequence of Homo sapiens chromosome 16, GRCh38.p12 Primary Assembly for HBA1 gene on NCBI Retrieval of FASTA format for HBA1 gene using NCBI database Prediction of efficient siRNA candidates for the FASTA sequence using OligoWalk web server
- 11. Methodology • Online Tool Used: • In order to facilitate Antisense RNA designing , FASTA sequence of HBA1 gene was retrieved using NCBI database. • The National Centre for Biotechnology Information is part of the United States National Library of Medicine, a branch of the National Institutes of Health. • The computational tool used to perform Antisense RNA designing was OligoWalk. • OligoWalk is a web server constructed to predict efficient siRNA candidates for an mRNA sequence on the basis of the statistical mechanics of the siRNA-target interaction.
- 15. Discussion • Alpha thalassemia is a blood disorder results from deletions involving the HBA1 & HBA2 genes. • Both of these genes provide instructions for making a protein called alpha globin which is a component of hemoglobin. • Based on the results obtained using OligoWalk, the below sequence was found to be the most efficient siRNA and the selection of sequence relies on the score generated(Highest score selected).
- 16. References • SCZAKIEL, G. (1997). The Design of Antisense RNA. Antisense and Nucleic Acid Drug Development, 7(4), 439–444. • Huesken D, Lange J, Mickanin C, Weiler J, Asselbergs F, Warner J, Meloon B, Engel S, Rosenberg A, Cohen D, Labow M, Reinhardt M, Natt F, Hall J. (2005). Design of a genome-wide siRNA library using an artificial neural network. Nat Biotechnol 23:995-1001.