Jessica torres
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This document discusses incorporating unnatural amino acids into proteins to expand their functions. It describes how pyrrolysine is used as an orthogonal system to incorporate unnatural amino acids specified by an amber stop codon. Various unnatural amino acids containing alkene and norbornene functional groups were successfully incorporated into GFP and other proteins in E. coli and mammalian cells. These modified proteins could then be site-specifically labeled using bioorthogonal reactions like the thiol-ene and Diels-Alder reactions. This allows proteins to be labeled and studied in live cells with new functions.
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This paper focuses on automated procedures to reduce the dimensionality of protein structure prediction datasets by simplifying the way in which the primary sequence of a protein is represented. The potential benefits of this procedure are faster and easier learning process as well as the generation of more compact and human-readable classifiers. The dimensionality reduction procedure we propose consists on the reduction of the 20-letter amino acid (AA) alphabet, which is normally used to specify a protein sequence, into a lower cardinality alphabet. This reduction comes about by a clustering of AA types accordingly to their physical and chemical similarity. Our automated reduction procedure is guided by a fitness function based on the Mutual Information between the AA-based input attributes of the dataset and the protein structure feature that being predicted. <br />
To search for the optimal reduction, the Extended Compact Genetic Algorithm (ECGA) was used, and afterwards the results of this process were fed into (and validated by) BioHEL, a genetics-based machine learning technique. BioHEL used the reduced alphabet to induce rules for protein structure prediction features. BioHEL results are compared to two standard machine learning systems. Our results show that it is possible to reduce the size of the alphabet used for prediction from twenty to just three letters resulting in more compact, i.e. interpretable, rules. Also, a protein-wise accuracy performance measure suggests that the loss of accuracy accrued by this substantial alphabet reduction is not statistically significant when compared to the full alphabet.
output
This document is Denis Malyshev's PhD thesis presented to The Scripps Research Institute in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemical Biology. The thesis is dedicated to Sergey Semenov, the principal of the Moscow Chemical Lyceum and Malyshev's teacher. It acknowledges the contributions of his research advisor Floyd Romesberg and many colleagues who assisted with his research projects, which focused on expanding the genetic alphabet by developing unnatural base pairs that can be replicated in vitro and in vivo.
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2. Vaccines produced using recombinant DNA techniques, such as vaccines for hepatitis B. This involves inserting the gene for the hepatitis B surface antigen protein into yeast which then produces the protein for the vaccine.
3. Production of other proteins through recombinant DNA like cytokines and interferons, which help modulate the immune system and can be used as treatments for various conditions. Overall, recombinant DNA technology has generated many commercially useful proteins and
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Automated alphabet reduction with evolutionary algorithms for protein structu...
This paper focuses on automated procedures to reduce the dimensionality of protein structure prediction datasets by simplifying the way in which the primary sequence of a protein is represented. The potential benefits of this procedure are faster and easier learning process as well as the generation of more compact and human-readable classifiers. The dimensionality reduction procedure we propose consists on the reduction of the 20-letter amino acid (AA) alphabet, which is normally used to specify a protein sequence, into a lower cardinality alphabet. This reduction comes about by a clustering of AA types accordingly to their physical and chemical similarity. Our automated reduction procedure is guided by a fitness function based on the Mutual Information between the AA-based input attributes of the dataset and the protein structure feature that being predicted. <br />
To search for the optimal reduction, the Extended Compact Genetic Algorithm (ECGA) was used, and afterwards the results of this process were fed into (and validated by) BioHEL, a genetics-based machine learning technique. BioHEL used the reduced alphabet to induce rules for protein structure prediction features. BioHEL results are compared to two standard machine learning systems. Our results show that it is possible to reduce the size of the alphabet used for prediction from twenty to just three letters resulting in more compact, i.e. interpretable, rules. Also, a protein-wise accuracy performance measure suggests that the loss of accuracy accrued by this substantial alphabet reduction is not statistically significant when compared to the full alphabet.
output
This document is Denis Malyshev's PhD thesis presented to The Scripps Research Institute in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemical Biology. The thesis is dedicated to Sergey Semenov, the principal of the Moscow Chemical Lyceum and Malyshev's teacher. It acknowledges the contributions of his research advisor Floyd Romesberg and many colleagues who assisted with his research projects, which focused on expanding the genetic alphabet by developing unnatural base pairs that can be replicated in vitro and in vivo.
Genetic code2
1. The genetic code is composed of nucleotide triplets called codons that specify individual amino acids.
2. Experiments confirmed that the genetic code is a triplet code and that each codon corresponds to a specific amino acid, with some codons coding for the same amino acid (degenerate).
3. Key properties of the genetic code include it being triplet-based, non-overlapping, unambiguous, degenerate, and nearly universal across organisms.
Xenobiology
so we can conclude that xenobiology can give various answers of life and also can help to discover various biochemical reaction as well as can increas economy of one country
DNA new alphabet
Toward the expansion of the genetic alphabet of DNA, several artificial third base pairs (unnatural base pairs) have been created. Organisms are defined by the information encoded in their genomes, and since the origin of life this information has been encoded using a two-base-pair genetic alphabet (A–T and G–C). In vitro, the alphabet have been expanded to include several unnatural base pairs (UBPs). A class of UBPs formed between nucleotides bearing hydrophobic nucleobases, exemplified by the pair formed between d5SICS and dNaM (d5SICS–dNaM) was developed, which is efficiently PCR-amplified and transcribed in vitro, and whose unique mechanism of replication has been characterized. However, expansion of an organism’s genetic alphabet presents new and unprecedented challenges: the unnatural nucleoside triphosphates must be available inside the cell; endogenous polymerases must be able to use the unnatural triphosphates to faithfully replicate DNA containing the UBP within the complex cellular milieu; and finally, the UBP must be stable in the presence of pathways that maintain the integrity of DNA. In a major breakthrough, it was reported that an exogenously expressed algal nucleotide triphosphate transporter efficiently imports the triphosphates of both d5SICS and dNaM (d5SICSTP and dNaMTP) into Escherichia coli, and that the endogenous replication machinery uses them to accurately replicate a plasmid containing d5SICS–dNaM was already reported. Neither the presence of the unnatural triphosphates nor the replication of the UBP introduces a notable growth burden. Thus, the resulting bacterium is the first semi-synthetic organism to propagate stably an expanded genetic alphabet. The unnatural base pair systems now have high potential to open the door to next generation biotechnology.
The French Revolution of 1789
An introduction of events leading the French Revolution of 1789, beginning with a discussion of the Old Regime and ending with the Women's March on Versailles
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Omics in plant breeding
This document discusses the use of various "omics" technologies in crop breeding, including genomics, transcriptomics, proteomics, metabolomics, phenomics, and ionomics. It provides examples of each type of omics analysis in crop plants like potato and wheat. Integrating multi-omics datasets can provide a powerful tool for crop improvement by identifying genes and networks controlling important traits. However, future work is still needed to reduce costs and develop bioinformatic tools to fully leverage omics technologies in breeding programs.
Altered substrate-specificity-of-the-pterygoplichthys-sp.-loricariidae-cyp1 a...
This study investigated the substrate specificity of the CYP1A enzyme from Pterygoplichthys sp., a species of catfish. The CYP1A gene from Pterygoplichthys sp. was expressed in yeast cells. The catalytic activity of the expressed enzyme was then tested against 15 potential substrates. Results showed that the enzyme had a much higher activity for coumarin derivatives than resorufin derivatives, unlike most other vertebrate CYP1As. The enzyme was also able to metabolize some flavones and ethoxyfluorescein but not resveratrol. These findings suggest the Pterygoplichthys sp. CYP1A has a divergent substrate
Winnetal
1) Researchers developed transgenic medaka (fish) carrying multiple copies of a bacteriophage vector containing the cII gene, which serves as a target for detecting mutations.
2) They adapted an assay used in transgenic rodents to efficiently recover cII mutants from fish genomic DNA and detect them by infecting bacteria.
3) Spontaneous mutant frequencies in liver, whole fish, and testes of medaka were comparable to frequencies observed in transgenic rodents. Treatment with ethylnitrosourea induced cII mutations in the medaka in a tissue-specific and time-dependent manner consistent with known mutagen mechanisms.
Thesis Poster
The document describes the development of an HPLC-MS/MS method to isolate and identify inositol phosphate isomers from Chlamydomonas reinhardtii. Solid phase extraction was optimized to remove trichloroacetic acid contaminants. A WAX column with a methanol gradient eluted higher inositol phosphates. Post-column dilution reduced ion suppression caused by salts. The fully assembled method separated and identified inositol phosphate isomers from standards and C. reinhardtii extracts from IP1 to IP6 based on mass detection. Future work will quantify isomers in biological samples and further separate IP7 and IP8 isomers.
Domains of unknown function are essential in yeast
Presented in the Synthetic Biology & Gene Editing strand of the 4Bio Summit. For more information, visit:
www.global-engage.com
~25% of yeast essential domains of unknown function (yeDUFs) are broadly conserved across all kingdoms of life (including Bacteria), while a small number are found in large numbers of proteins in mammals. In this presentation, Norman Goodacre from the FDA discusses 68 yeDUFs and their roles in alternative carbohydrate metabolism, mitochondrial transport, nuclear pore complex, mRNA processing, initiation of translation, protein complex assembly, and membrane-binding.
Aijrfans14 244
This document summarizes a study on the effects of Pallisentis nagpurensis infection on protein and free amino acid metabolism in two commercially important fish species, Catla catla and Labeo rohita. The study found that total protein content and free amino acid levels increased in the liver and intestine tissues of both infected fish species compared to normal uninfected fish. This suggests the parasitic infection altered the protein metabolism of the fish, likely to support tissue repair mechanisms in response to the parasite invasion. Overall, the study demonstrates that P. nagpurensis infection biochemically impacts the host fish by changing their protein and amino acid metabolism.
The Importance Of Animal Uses In Animals
This document discusses using bromophenols as potential therapeutics for treating type 2 diabetes mellitus (T2DM). Bromophenols have been identified as inhibitors of the enzyme tyrosine phosphatase 1B (PTP1B), which is involved in insulin signaling. A series of new bromophenol analogs will be synthesized and tested for PTP1B inhibitory activity using in vitro enzyme assays to elucidate their mechanism of action. Bromophenols occur naturally in marine organisms and have attracted interest as anti-diabetic agents due to their suspected PTP1B inhibitory activity. However, quinone species formed from bromophenols could be toxic, so further study is needed to
Radiation protection,protease inhibition.
Radiation, inhibition, protease, toxicity, acute radiation syndromes, antiradiation antidote, public health, countermeasure
development.
JBEI Highlights May 2015
- Researchers studied the roles of three major prolyl-4-hydroxylase (P4H) isoforms expressed in Arabidopsis roots.
- P4H5 was found to have an essential function different from P4H2 and P4H13, which are partly redundant.
- Protein-protein interaction studies revealed the P4H proteins form homodimers and heterodimers, and P4H5 is necessary for the targeting of P4H2 to the Golgi.
- Understanding the complex regulation and interactions of P4H isoforms impacts root hair expansion and cell wall formation.
s41598-020-71015-9.pdf
This document describes a study that investigated the seminal plasma proteome of Holstein bulls with low and high sperm freezability. Label-free mass spectrometry identified 1,445 seminal plasma proteins. There were 338 proteins differentially expressed between bulls with low and high freezability. Specific proteins were identified as markers of each phenotype, with BSP5 and seminal ribonuclease associated with high freezability and spermadhesin-1, gelsolin, and peroxiredoxin-5 associated with low freezability. Regression models found sperm freezability scores were related to levels of peroxiredoxin-5, spermadhesin-1, and their interaction. This research provides insights
1 s2.0-s105046481300034 x-main
This document summarizes research purifying and characterizing a novel antioxidant peptide from the hard-shelled mussel Mytilus coruscus. Enzymatic hydrolysis was used to generate hydrolysates from M. coruscus, which were screened for antioxidant activity. The papain hydrolysate showed the highest free radical scavenging activity. Further purification using chromatography yielded a novel 10 amino acid peptide. In vitro and in vivo assays found the peptide to have potent antioxidant effects, inhibiting oxidative stress markers and enhancing antioxidant enzyme activity in mice. This is the first report of an antioxidant peptide from M. coruscus with potential anti-inflammatory properties.
CV_Michiko Sumiya
Michiko Sumiya has extensive experience in biomedical research and academia. She has over 25 years of experience conducting research on topics such as the mannose binding protein, coagulation factor VIII, and sodium/potassium channels. She has worked in both academic and industrial settings in Japan, the UK, and the US. Dr. Sumiya has authored over 15 peer-reviewed publications and has presented her work at numerous international conferences. She is highly skilled in molecular biology, genetics, and biochemical techniques.
Hu cal platnimm alis adds
The document provides an overview of HuCAL Platinum, a synthetic antibody library produced by Morphosys. It describes the 7 step process for generating monoclonal antibodies from the library, which includes immobilizing the antigen, panning the library, subcloning and screening colonies, sequencing antibodies, and purification. Key advantages of HuCAL Platinum are that it does not require animals, has a diverse selection of 45 billion antibody genes produced in E. coli, and has over a 90% success rate. Applications include drug discovery, structural analysis, and Morphosys has several antibodies in clinical trials for diseases like cancer and rheumatoid arthritis.
Chan & Roth 2008
When yeast cells are exposed to anoxia (no oxygen) on a non-fermentable carbon source, they enter a state of suspended animation where all observable life processes reversibly halt until oxygen is restored. Transcriptional profiling revealed differences in gene expression between yeast exposed to carbon monoxide (CO) gas versus nitrogen (N2) gas. CO can mimic oxygen binding and led to derepression of aerobic metabolism genes compared to N2 exposure. Mutants lacking components of the mitochondrial retrograde signaling pathway recovered normally from CO but not N2 exposure, indicating its importance in the cellular response to different anoxic conditions. The study establishes yeast as a model for investigating suspended animation and oxygen-regulated gene expression.
Waksman Student Scholars Program Poster
The document describes an experiment to sequence the DNA of the duckweed plant Landoltia punctata and analyze the protein encoded. Researchers used PCR to amplify duckweed DNA inserted into bacteria. Restriction digest isolated the duckweed DNA, which was sequenced. Analysis identified the protein as Mitogen-Activated Protein Kinase (MAPK), which regulates cellular responses to stimuli and contains conserved domains. The 3D structure of this protein is similar to the human MAPK protein, indicating an evolutionary advantage across kingdoms.
Advantages And Disadvantages Of Reverse Sequence Syphilis...
Here are the key conclusions I can draw from the results of this experiment:
- The chemotherapeutic drug was effective at reducing cell viability in a dose-dependent manner across all three cancer cell lines tested (HEPG2, PANC-1, PC-3). Higher drug concentrations led to lower percentages of viable cells.
- PANC-1 and PC-3 cell lines appeared to be more sensitive to the drug, as viability decreased more sharply with increasing concentration compared to HEPG2. This suggests the drug may be more effective against pancreatic and prostate cancers.
- Even at the highest concentration of 40μM, the drug did not reduce HEPG2 viability below 60%. This indicates HEPG2 may be more
Abstract conference mbsmb 2009
Abstract conference MBSMB 2009
(Poster presentation @ Malaysian Biochemistry Society and Molecular Biology)
Research Project Report
This study investigates the localization and function of VDAC4, a porin protein in Tetrahymena thermophila mitochondria. Bioinformatics analysis predicted VDAC4 contains a conserved Porin3 domain found in mitochondrial porins and Tom40 proteins. The researcher amplified and cloned the VDAC4 gene, created a YFP fusion construct, transformed Tetrahymena cells, and observed YFP localization using microscopy. YFP localized to punctate structures consistent with mitochondrial localization, supporting VDAC4 involvement in mitochondrial membrane processes.
Fungal Contamination
Fungal contamination of food can occur accidentally but also intentionally for bioterrorism purposes. The mycotoxins aflatoxin B1 and T-2 toxin produced by fungi are particularly toxic and chemically stable, making them suitable for bioweapons. Cereals are globally important foods that are highly susceptible to fungal growth in fields and storage. T-2 toxin inhibits protein synthesis and disrupts DNA and RNA synthesis, affecting rapidly dividing cells like those in the gastrointestinal tract.
1-s2.0-S0014480015000970-main
1) Betacellulin (BTC) transgenic mice were studied to examine the effects of constitutive BTC overexpression on the urinary bladder.
2) BTC was detected in microvascular structures and umbrella cells of the uroepithelium lining. ERBB1 and ERBB4 receptors were also present in the uroepithelium.
3) BTC transgenic mice and mice that were double transgenic for BTC and a dominant kinase-dead EGFR mutant developed hyperplasia of the uroepithelium at 5 months of age, suggesting BTC signaling was not solely dependent on ERBB1/EGFR.
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Domains of unknown function are essential in yeast
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Annotated bibliographies wp
This document summarizes three research articles on the use of cannabis to treat Crohn's disease. The first article finds that 21 out of 30 Crohn's patients saw improved symptoms after treatment with cannabis. It also found reductions in drug usage and surgeries. The second article determines that cannabidiol selectively inhibits inflammatory hypermotility in mice when an inflammatory stimulus is present. The third article surveys Crohn's and ulcerative colitis patients and finds that cannabis helped relieve common symptoms like abdominal pain and diarrhea for most users.
Drug discovery strategy final draft
The document discusses in silico drug discovery methods including identifying potential drug targets, generating pharmacophore models, screening compound databases, and analyzing top hits through molecular docking simulations. A drug discovery strategy is outlined involving primary and secondary screening to identify lead compounds. The work plan describes using AutoDock Vina to dock and rank compounds, selecting the top 14 hits, and analyzing their binding interactions with HIV proteases. Nilotinib, lopinavir, ergoloid, and zafirlukast were evaluated in more detail and found to have high binding affinity to the target proteins.
Em zombage
Bacteriophage Zombage was isolated and characterized using electron microscopy. Pictures were taken of the phage using electron microscopy to view its structure and morphology at high magnification. The electron microscopy images provide detailed views of Zombage's capsid, tail fibers, and other viral structures.
Em shockage
Bacteriophage Shockage was isolated and characterized. Electron microscopy pictures were taken of the phage particles. The pictures show the structure of Shockage, which includes an icosahedral capsid and long, non-contractile tail.
Lab summaries complete
1. This laboratory focused on practicing proper micropipetting techniques. Students mixed solutions of water and dyes to practice using micropipettes accurately and safely. This helped prepare them for upcoming labs requiring precise measurements.
2. Students learned different microscopy techniques, including fluorescence and bright field microscopy. They took photomicrographs using a camera attached to the microscope.
3. Over three days, students extracted their own DNA from mouth cells, ran PCR tests to determine if a patient sample had diabetes, and used gel electrophoresis to analyze protein biomarkers and diagnose a lysosomal storage disorder.
Phages presentation final final final
This document describes the isolation of mycobacteriophages from soil samples in Puerto Rico. Two students isolated three unique phages and characterized them through plaque assays, enrichment techniques, and SDS-PAGE gel electrophoresis. Two distinct phages, named Shockage and Zombage, were identified based on their protein band patterns and plaque morphology. Further sequencing of the phage genomes was proposed to better characterize the newly discovered viruses.
Microscopy. nostoc. brightfield.
This document contains 4 images of the blue-green algae Nostoc viewed under a microscope using Bright Field techniques at magnifications of 200x and 400x. The images show Nostoc in its natural state as well as using a squash technique to better view its structure.
14.anaeli and nicolle. mycobacteriophages paper.
Two mycobacteriophages were isolated from a soil sample collected in Gurabo, Puerto Rico. Following enrichment and plaque purification, two distinct phages (named Shockage and Zombage) were isolated based on differences in morphology and protein band patterns. Shockage had a distinct protein profile while Zombage and another initially isolated phage had nearly identical protein bands, indicating they were the same phage. Further DNA sequencing would help fully characterize these newly isolated phages and determine if they represent unique viruses. Overall, this experiment demonstrated a method for isolating new mycobacteriophages from environmental samples.
Art orieliz
This document summarizes research on a two-component nanoparticle system that uses communication to amplify targeting of nanoparticles to tumors. The system consists of "signalling" nanoparticles that first target tumors and activate the coagulation cascade locally, and "receiving" nanoparticles that target areas of coagulation activation to deliver diagnostic or therapeutic agents. Two types of signalling nanoparticles are investigated - gold nanorods that activate coagulation when heated with near-infrared light, and engineered tissue factor proteins that activate coagulation upon binding to tumor receptors. Both are shown to induce localized fibrin deposition in tumors. Receiving nanoparticles containing imaging or drug payloads are then able to target the coagulated tumor sites for enhanced delivery.
Ss third
This article discusses a study that surveyed patients with inflammatory bowel diseases like Crohn's disease and ulcerative colitis about their use of cannabis. The researchers hypothesized that cannabis works as an anti-inflammatory through receptors called endocannabinoids. The survey found that in most cases, patients reported cannabis helped relieve abdominal pain, diarrhea and reduced appetite. While cannabis has side effects, it improved quality of life for these patients and could be a viable treatment option.
Ss second
This research paper studied whether cannabidiol inhibits inflammatory hypermotility in mice. Researchers induced intestinal inflammation in mice using croton oil, then tested the effects of different doses of cannabidiol. They found that cannabidiol effectively reduced hypermotility when inflammation was present, and higher doses produced greater inhibition. The study concluded that cannabidiol can help normalize intestinal motility during inflammation.
Ss first
This article describes a study of 30 Crohn's disease patients who used cannabis as a treatment. Cannabis is known to have anti-inflammatory properties, and a symptom of Crohn's is bowel inflammation. The study found that 21 of the 30 patients experienced great improvement in their condition after using cannabis. The results show that cannabis treatment can reduce symptoms of Crohn's disease like bowel inflammation.
Yaddilette
Galsulfase is a recombinant form of human N-acetylgalactosamine 4-sulfatase that was approved by the FDA in May 2005 for the treatment of mucopolysaccharidosis type VI (MPS-VI), a rare lysosomal storage disorder. MPS-VI is caused by a deficiency of N–acetylgalactosamine 4-sulfatase, which leads to the accumulation of dermatan sulfate. Clinical trials found that patients treated with galsulfase showed improvements in walking and stair-climbing ability compared to placebo. Galsulfase represents the first approved treatment for MPS-VI and provides an important new therapy for patients suffering from this rare disease.
Seminar yadilette rivera_amherst,mass_oct.18-1 copy
The Biology Honor Society will provide refreshments from 10:30-10:40 in room 106 MMM on Thursday. Yadilette Rivera, an alumna from Univ. of Massachusetts Amherst, will then give a seminar from 10:40-11:20 in room 106 MMM about the challenges of protein crystallography and graduate school.
Reflection on the third seminar
Yadilette's research focuses on treating lysosomal storage disorders, which cause bone abnormalities, through enzyme replacement therapy rather than bone marrow transplantation. Her treatment involves purifying proteins through crystallization and x-ray analysis to determine the replacement enzyme, then injecting patients weekly and monitoring their progress through tests, with some patients showing increased mobility based on walking and climbing tests. This research helps improve the lives of those suffering from these diseases and creates more awareness.
Art. jessica
This document describes a new method for site-specifically labeling proteins using genetically encoded norbornene and rapidly reactive tetrazine probes. Key points:
1) A norbornene-containing amino acid is genetically encoded in E. coli and mammalian cells using the pyrrolysyl tRNA synthetase system.
2) A series of tetrazine probes are developed that react rapidly and specifically with norbornene via an inverse electron demand Diels-Alder reaction.
3) The tetrazine-norbornene reaction is shown to be much faster than established bioorthogonal reactions, allowing specific labeling of proteins both in vitro and on mammalian cell surfaces.
Ad jessica torres seminar
Jessica Torres from North Carolina State University will give a seminar on incorporating unnatural amino acids into proteins. Unnatural amino acids allow the expression of proteins with new functions and enable a wide range of studies by using diverse functional groups beyond the 20 common amino acids. Examples include incorporating fluorescent and spectroscopic probes to study biological processes in live cells. The seminar will discuss how introducing unnatural amino acids into proteins, both in vitro and in vivo, is a promising technique that can provide insights into answering biomedical questions relevant to human health. Refreshments will be provided before the talk at 10:30am on Thursday September 20 in room MMM 106.
Second seminar reflection
An improved method of protein labeling uses unnatural amino acids inserted during protein synthesis, which do not interfere with the organism's natural systems. The unnatural amino acids are chosen for their similarity to natural amino acids but are distinct enough to avoid incorporation elsewhere. By adding a stop codon to the unnatural amino acid and inserting it into tRNA, only the desired protein will be labeled without affecting other proteins.
Olga gonzalez1
Rta is a key transcriptional activator that is required for reactivation of Kaposi's sarcoma-associated herpesvirus (KSHV) from latency. Rta stimulates DNA binding of the transcription factor RBP-Jk to KSHV promoter regions containing RBP-Jk binding sites. The interaction between Rta and RBP-Jk leads to recruitment of additional factors and transactivation of immediate early and delayed early genes, establishing the lytic replication cycle. Precise cis-elements including CANT repeats and [A/T]3 motifs that flank the RBP-Jk site contribute to the strength of Rta/RBP-Jk mediated transactivation. Understanding this molecular mechanism of
First seminar. reflection kshv
Ms. Olga González presented on the Kaposi sarcoma-associated herpesvirus (KSHV). KSHV has two stages - the lytic cycle where infection occurs, and the lysogenic cycle where the virus establishes latency. It infects people through saliva, blood or sexual contact, and only causes harm in those with weak immune systems, allowing the virus to reactivate, switch cycles, and reproduce to create cancerous tumors. Her research aims to find and stop the molecular trigger of reactivation, which could help other scientists attack the virus at its source without killing healthy cells, as well as create awareness for those susceptible to infection.
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Removing Uninteresting Bytes in Software Fuzzing
Imagine a world where software fuzzing, the process of mutating bytes in test seeds to uncover hidden and erroneous program behaviors, becomes faster and more effective. A lot depends on the initial seeds, which can significantly dictate the trajectory of a fuzzing campaign, particularly in terms of how long it takes to uncover interesting behaviour in your code. We introduce DIAR, a technique designed to speedup fuzzing campaigns by pinpointing and eliminating those uninteresting bytes in the seeds. Picture this: instead of wasting valuable resources on meaningless mutations in large, bloated seeds, DIAR removes the unnecessary bytes, streamlining the entire process.
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Climate Impact of Software Testing at Nordic Testing Days
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Webinar Recording: https://www.panagenda.com/webinars/hcl-notes-and-domino-license-cost-reduction-in-the-world-of-dlau/
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Monitoring and observability aren’t traditionally found in software curriculums and many of us cobble this knowledge together from whatever vendor or ecosystem we were first introduced to and whatever is a part of your current company’s observability stack.
While the dev and ops silo continues to crumble….many organizations still relegate monitoring & observability as the purview of ops, infra and SRE teams. This is a mistake - achieving a highly observable system requires collaboration up and down the stack.
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In the rapidly evolving landscape of technologies, XML continues to play a vital role in structuring, storing, and transporting data across diverse systems. The recent advancements in artificial intelligence (AI) present new methodologies for enhancing XML development workflows, introducing efficiency, automation, and intelligent capabilities. This presentation will outline the scope and perspective of utilizing AI in XML development. The potential benefits and the possible pitfalls will be highlighted, providing a balanced view of the subject.
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By highlighting the potential advantages and challenges of integrating AI with XML development tools and languages, the presentation seeks to inspire thoughtful conversation around the future of XML development. We’ll not only delve into the technical aspects of AI-powered XML development but also discuss practical implications and possible future directions.
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Jessica torres
- 1. Incorporation of Unnatural Amino Acids for the Expression of Proteins with New Function Jessica Torres-Kolbus, Chungjung Chou, Kathrin Lang, Lloyd Davis, Jason Chin, and Alexander Deiters* University of Puerto Rico, Cayey RISE Seminar September 20, 2012
- 2. Proteins: Many Structures, Many Functions Nature Chemical Biology 1, 13 - 21 (2005) • Compose over 50% of the cellular dry mass • Involved in all cellular functions: • Signaling • Transport • Defense • Catalysis • Maintenance • Stability • Tens of thousands of different proteins Green Fluorescent Protein (GFP) Bright green fluorescence Aequorea victoria 238 AAs Myoglobin (Mb) Binds to iron and oxigen Found in muscle tissue of most vertebrates 154 AAs
- 3. Why Study Proteins? • understand protein structure-function relationships • investigate protein-involved biological processes • many diseases are caused by errors in proteins, e.g.: cystic fibrosis – one amino acid deletion sickle cell anemia – one incorrect amino acid position Huntington disease – expansion repeat of an amino acid • manipulate proteins, protein-based drugs, generate proteins and organisms with new properties
- 4. How Study Proteins? • many proteins undergo post-translational modifications or bind to cofactors to extend their properties • biological processes are very complex and are regulated in both space and time • many of these processes cannot be observed and studied when the protein involved is isolated • study of biological processes in their native environments • reporter tags are required for the trafficking and detection of biomolecules
- 5. Strategies for Chemical Modification of Proteins Protein Labeling Labeled proteins (e.g. fluorescent tags) provide exciting new tools for studying proteins and their function in the cell
- 6. The Genetic Alphabet: 20 Common Amino Acids
- 7. Expanding The Genetic Alphabet: Unnatural Amino Acids
- 8. An Orthogonal Biosynthetic Machinery
- 9. Stealing Parts from other Organisms → large differences between archaea, bacteria, and eukaryotes in tRNA genes and their aminoacyl tRNA synthetases → engineer a synthetase to specifically recognize an UAA PylRS is found in some methanogenic archea and bacteria, charges its cognate tRNA with pyrrolysine. The unique and large substrate binding pocket of pyrrolysyl synthetase (PylRS) shows that it may recognize a broad spectrum of lysine UAA. Pyrrolysyl synthetase (PylRS) binding pocket Yokoyama, S. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006, 62 (Pt 10), 1031-3.
- 10. A Pyrrolysyl-Based Facile System The PylRS/tRNA pair is orthogonal in E. coli, S. cerevisiae , mammalian cells, and C. elegans. Pyrrolysine is naturally encoded by an amber stop codon
- 11. Promiscuity of the PylRS Effective Pyl mimics: Ineffective Pyl mimics: pyrrolysine
- 12. Promiscuity of the PylRS Effective Pyl mimics: Ineffective Pyl mimics:
- 13. Unnatural Amino Acids as Bioorthogonal Chemical Reporters Bertozzi, C. R. Nat. Chem. Bio. 2005, 1 (1): 13–21. 1. Site-specific incorporation of UAA with reactive handle. 2. Highly selective reaction with exogenously delivered probe. Bioorthogonal reaction refers to any reaction that takes place inside of biological systems with selective reactivity and biocompatibility. Physiological conditions No-cross reaction Non-toxic Low concentrations High yields Fast The reaction results in a stable covalent bond between the protein and the probe.
- 14. Genetically Encoded Alkenes for the Expression of Protein with New Function
- 15. Introduction of the Alkene Functionality into Proteins • Rarely found in natural proteins. • Versatile in organic transformations. Alloc-L-lysine is incorporated via the wild-type PylRS.
- 16. Bioconjugation with Alkene Lysine via the Thiol-ene Reaction
- 17. Incorporation Efficiency of Alkene Lysine Library 100% (AllocLys) 80% 109% 82% 86% 14% 9% 3.8% 102% 45% Each amino acid was tested as PylRS substrate for incorporation into protein. Incorporation efficiency relative to AllocLys.
- 18. Expression of Alkene-modified sfGFP 100% (AllocLys) 10 80% 109% 82% 3 86% 4 14% 9% 3.8% 102% 45% Each amino acid was tested as PylRS substrate for incorporation into protein. Incorporation efficiency relative to AllocLys. 58 30 46 M -AA WT +10 +3 +4 25 Incorporation in sfGFP in E. coli
- 19. Fluorescent labeling of sfGFP Fluorescence Comassie Light activated, site-specific labeling of sfGFP bearing an alkene with a thiol-containing fluorescent probe via the thiol-ene reaction Samples were irradiated at 365 nm for 5 min 10 3 Dansyl-thiol (fluorescent)Alkene-modified protein
- 20. Bioconjugation of sfGFP and lysozyme M 58 30 46 25 1 2 3 4 5 6 7 8 M. Marker 1. wt sfGFP 2. +10, - lysozyme 3. wt sfGFP + lysozyme, - UV 4. +10 + lysozyme, - UV 5. +3 + lysozyme, - UV 6. wt sfGFP + lysozyme, + UV 7. +10 + lysozyme, + UV 8. +3 + lysozyme, + UV sfGFP increased from ~28 kDa to ~44 kDa after conjugating to the lysozyme with UV light Samples were irradiated at 365 nm for 5 min
- 21. Diels-Alder reaction. • High selectivity • High yields • Fast reaction in aqueous media Synthesis of Norbornene Lysine and Protein Expression Nature Chem. 2012, 4, 298-304
- 22. Diels-Alder reaction. • High selectivity • High yields • Fast reaction in aqueous media Synthesis of Norbornene Lysine and Protein Expression Nature Chem. 2012, 4, 298-304 Expression in E. coli
- 23. Bioconjugation with ‘Turn-on’ Fluorescence Non-fluorescent Fluorescent 9 Nature Chem. 2012, 4, 298-304
- 24. Site-Specific Protein Labeling via Bioorthogonal Cycloaddition with Genetically Encoded Norbornene in Mammalian Cells Labeling of EGFR-(TAG)-GFP in HEK293 cells. Nature Chem. 2012 , 4, 298-304 TAMRA
- 25. Summary and Conclusions • Site-specific incorporation of UAAs into proteins in both bacteria and mammalian cells. • Labeled proteins via bioorthogonal reactions. • A library of aliphatic alkene lysines was generated for genetic encoding into proteins. • The alkene-modified protein was successfully subjected to bioorthogonal labeling via the thiol-ene reaction. • A norbornene-containing amino acid was synthesized and encoded into protein for fast ‘turn-on’ fluorescence labeling in both bacterial and mammalian cells.
- 26. Acknowledgements Deiters Lab Dr. Alexander Deiters Dr. Chungjung (Hank) Chou Collaborators: Jason Chin Lab (MRC, Cambridge, UK) Kathrin Lang, Lloyd Davis NSF Graduate Fellowship
- 27. Duke University UNC-Chapel Hill NCSU RTP • largest university in the state, with almost 30,000 students • more than 1,700 faculty members, many of them nationally recognized • offers master's degrees in 101 fields, and doctoral degrees in 59 fields, in addition to the Doctor of Veterinary Medicine degree • has 10 colleges and schools: Colleges of Agriculture and Life Sciences, Design, Education, Engineering, Natural Resources, Humanities and Social Sciences, Management, Physical and Mathematical Sciences, Textiles, and Veterinary Medicine • located west of downtown Raleigh, a part of the state’s technology-rich Research Triangle area North Carolina State University http://www.ncsu.edu/ http://www.rtp.org/ http://www.unc.edu/index.htm http://www.duke.edu/
- 28. Department of Chemistry at NCSU Dabney Hall Main Campus http://www.ncsu.edu/chemistry/ • Over 120 graduate students and 27 research faculty • 20 to 40 new graduate students each year • Analytical, Biological Chemistry, ChemEd, Inorganic, Magnetic resonance, Materials, Nanoscience, Organic, Physical, Polymers, Theoretical
- 29. Join the Department of Chemistry at NCSU • Bachelor’s degree in Chemistry or related fields • GPA of at least 3.0 (out of 4.0) in the sciences • GRE General Test scores are required and the Subject Test is recommended • Application – opens online Aug 15, closes Dec 15 http://www.ncsu.edu/grad/applygrad.htm • Statement of Purpose • One official transcript • Three reference letters • No application fee http://www.ncsu.edu/chemistry/graduate/application.html