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Douglas C Youvan

Douglas C Youvan

Ph.D.
(anti-) Biological Warfare Group Leader, and Successor to Richard / Rachel Levine ****

About

138
Publications
40,355
Reads
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5,428
Citations
Introduction
Adverse to all aspects of Biological Warfare, Transhumanism, Organoids, Eugenics, and Fascism
Skills and Expertise
Additional affiliations
January 2015 - June 2015
Youvan Foundation
Position
  • CEO
September 1987 - July 1995
Massachusetts Institute of Technology
Position
  • Professor (Associate)
Description
  • I am very proud of my graduate students: Adam Arkin Simon Delagrave Edward J. Bylina Ellen Goldman George Fuellen Steve Robles and my Postdocs: Mary M. Yang William J. Coleman and my UROP: Christine Goddard
June 1986 - June 1993
Massachusetts Institute of Technology
Position
  • Professor (Associate)
Description
  • In 1993, I was denied tenure, but in 1999 MIT offered that I form and head BioE. MIT's change of heart might have been related to the disappearance of the President, Provost, and Dean of Science as the faculty reacted to the 1988 disbanding of Course 20.
Education
June 1975 - January 1981
University of California, Berkeley
Field of study
  • Biophysics

Publications

Publications (138)
Preprint
Full-text available
Did W. Ian Lipkin, Ralph S. Baric, and Peter Daszak in the US Design COVID 19 Before Linfa Wang Designed COVID 19 in Singapore or Before Shi Zhengli in Wuhan Designed COVID 19?
Preprint
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While looking though the COVID literature, Craig Holland found a sophisticated epidemiological model of COVID infections. He showed this to Douglas C. Youvan who recognized the mathematics as a possible solution to the ToE, and that is expanded upon herein.
Preprint
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Consciousness and Relativity: The human mind is not restricted by lightspeed (c). There are no light cones.
Preprint
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Designated Cube 1, the order: g, a, c, u yields a structure with the most closed-loops. The mirror of this cube (u, c, a, g) is a second solution.
Preprint
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An encryption key is derived by a prime number pointer in the form of XXXW yielding an isotropic cube ordering nucleotides as g, a, c, u on three orthogonal axes. There is an equally good solution of a mirror cube using u, c, a, g. The physical chemistry of the amino acids is related to the topology of the cube. We suggest this is the closest packi...
Preprint
Full-text available
The WEF elites are actively depopulating us with lab leaks of pathogens and blaming it on zoonoses. Then they will replace us with Harari’s Homo Deus. Because of Intelligent Design, they won’t be able to engineer brain chemistry properly in their new species. Homo Deus will be more psychotic than the elites. Wild-type humans will become precious.
Preprint
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A view of the world of research and pandemics.
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PRELUDE TO A PROPOSED CONGRESSIONAL BILL National Bio and Agro-Defense Facility (NBAF) Directive
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Graphics created for our (anti-) Biological Warfare Group from April, 2021 to January, 2022. https://www.facebook.com/groups/1154470481693356
Preprint
Full-text available
COVID-19 Virus Vaccines Variants ADE WEF Depopulation Nuremburg Eugenics
Technical Report
See www.youvan.com A Solution to P v NP using Einstein's Time Dilation Equation
Article
Correlations between protein sequences and phenotypes were explored using databases of combinatorial cassette mutants of pigment-protein complexes. Heuristically formulated decision algorithms and computer implemented neural networks were compared to determine their accuracy in classification of phenotypic categories. For the databases examined, de...
Chapter
The increasing sophistication of mutagenesis and screening technologies has led to the isolation of many biophysically important mutants of the photosynthetic reaction center and light harvesting antennae. Site-directed mutagenesis and structural motif rearrangements of these proteins have accelerated our understanding of the fundamental mechanisms...
Article
Full-text available
Abstract Molecular reagents, software algorithms, and optics are described for calibrating an epifluorescence microscope,for fluorescence resonance,energy transfer (FRET) imagery. This MicroFRETsystem compensates for overlap among donor, acceptor, and FRET spectra. The effectiveness of this new method,relies on the use of well characterized fluores...
Conference Paper
A new digital imaging spectrophotometer and a series of colorimetric solid phase assays have been developed to screen bacterial libraries expressing mutagenized enzymes undergoing directed evolution. This high-throughput solid-phase assay system (known as 'Kcat Technology') can detect less than a 20% difference in enzyme rates within microcolonies...
Article
Full-text available
Directed evolution has become an important enabling technology for the development of new enzymes in the chemical and pharmaceutical industries. Some of the most interesting substrates for these enzymes, such as polymers, have poor solubility or form highly viscous solutions and are therefore refractory to traditional high-throughput screens used i...
Article
A new digital imaging spectrophotometer and a series of colorimetric solid phase assays have been developed to screen bacterial libraries expressing mutagenized enzymes undergoing directed evolution. This high-throughput solid-phase assay system (known as 'Kcat Technology') can detect less than a 20% difference in enzyme rates within microcolonies...
Article
Full-text available
rRNA-based molecular phylogenetic techniques were used to identify the bacterial species present in the ear fluid from a female patient with otitis externa. We report the identification of Staphylococcus intermedius from the patient and a possible route of transmission. Analysis of 16S ribosomal DNA restriction fragment length polymorphisms indicat...
Article
Full-text available
A multispectral optical technique was developed to simultaneously classify individual bacterial cells within mixed populations. Multispectral Bacterial Identification (mBID) combines innovations in microscopy with a software analysis program to measure and categorize the fluorescence signals from multiplexed 16S ribosomal RNA probes hybridized to p...
Article
Full-text available
Digital imaging spectroscopy (DIS) combines image processing and optical spectroscopy such that each picture element (pixel) or group of pixels in a two dimensional scene also includes additional dimension(s) of spectral and/or temporal information. Imaging spectrophotometers developed at KAIROS are literally equivalent to hundreds of thousands of...
Article
Full-text available
A new digital imaging spectrophotometer and a series of colorimetric solid phase arrays have been developed to screen bacterial libraries expressing mutagenized enzymes undergoing directed evolution. This high-throughput solid- phase array system (known as `Kcat Technology') can detect less than a 20% difference in enzyme rates within microcolonies...
Article
The electron transfer reactions involving QA and QB were investigated in Rb. capsulatus RCs where the QB site was mutated to contain 42 residues from the QA site. The RCs have M220–M261 in the QA site substituted for L193–L227 in the QB site plus the M subunit second-site mutations, M144MI and M145AS, which had been found to restore the ability of...
Article
Full-text available
Biotechnology et alia 8:1-16 2 ABSTRACT We have used 16S rRNA phylogenetic analysis to investigate the microbial diversity of sulfur-rich black mud marine sediments. Two distinct environments were examined: mud from a hypersaline marsh and mud from a brackish marsh. Only two out of one hundred cloned 16S rDNA sequences were identical, indicating a...
Article
Steady-state absorption and fluorescence excitation spectra together with ps-fluorescence and fs-absorption measurements have identified an important relaxation channel of excited states in Green Fluorescent Protein (GFP). GFP derivatives with (1) shortened lifetimes of the protonated chromophore RH* state and deprotonated chromophore R−* state, an...
Article
We have investigated the spectroscopic properties of two classes of light-harvesting 2 (LH2, B800-850) mutants of Rhodobacter capsulatus obtained by combinatorial mutagenesis to the C-terminal half of the beta-apoprotein: a pseudoLH2 (pLH2) class, in which the 800-nm absorption was normal but the 850-nm peak was blue-shifted by up to 14 nm, and the...
Article
Full-text available
The High Resolution Imaging Microscope (HIRIM) is a microspectrophotometer which is capable of determining the individual absorption spectra of complex groupings of microscopic features in a massively parallel manner. We demonstrate here the feasibility of obtaining high resolution spectra of pigmented or stained biological material with this instr...
Article
Steady-state absorption and fluorescence excitation spectra together with ps-fluorescence and fs-absorption measurements have identified an important relaxation channel of excited states in Green Fluorescent Protein (GFP). GFP derivatives with (1) shortened lifetimes of the protonated chromophore RH* state and deprotonated chromophore R−* state, an...
Article
We have engineered a photosynthetically competent mutant of the purple non-sulfur bacterium Rhodobacter capsulatus which seeks to mimic the behavior of the primary electron donor (P) of the plant photosystem II (PS II) reaction center (RC). To construct this mutant (denoted D1-ILMH), four residues in the bacterial L subunit were mutagenized, such t...
Article
Recently steady-state and picosecond time-resolved absorption and fluorescence spectroscopy on the Green Fluorescent Protein (GFP) have been interpreted by a mechanism where the key process is an excited state deprotonation of the chromophore (M. Chattoraij, B.A. King, G.U. Bublitz and S.G. Boxer, Proc. Natl. Acad. Sci. USA, 93 (1996) 8362–8367). S...
Article
The green fluorescent protein (GFP) from the jellyfish, Aequorea victoria, has become a versatile reporter for monitoring gene expression and protein localization in a variety of cells and organisms. GFP emits bright green light (lambda max = 510 nm) when excited with ultraviolet (UV) or blue light (lambda max = 395 nm, minor peak at 470 nm). The c...
Article
Full-text available
We report fluorescent resonance energy transfer (FRET) between two linked variants of the green fluorescent protein (GFP). The C terminus of a red-shifted variant of GFP (RSGFP4) is fused to a flexible polypeptide linker containing a Factor Xa protease cleavage site. The C terminus of this linker is in turn fused to the N terminus of a blue variant...
Article
Many invertebrates produce bioluminescence using green-fluorescent proteins (GFPs) as energy-transfer acceptors. GFPs fluoresce in vivo upon receiving energy from either a luciferase-oxyluciferin excited-state complex or a Ca(2+)-activated photoprotein depending upon the organism. These highly fluorescent proteins are unique due to the chemical nat...
Article
This correspondence debates the efficiency and application of genetic algorithms (GAs) to search protein sequence space. The important experimental point is that such sparse searches utilize physically realistic syntheses. In this regard, all GA-based technologies are very similar; they {open_quotes}learn{close_quotes} from their initial sparse sea...
Article
Two different combinatorial mutagenesis experiments on the light-harvesting II (LH2) protein of Rhodobacter capsulatus indicate that heuristic rules relating sequence directly to phenotype are dependent on which sets or groups of residues are mutated simultaneously. Previously reported combinatorial mutagenesis of this chromogenic protein (based on...
Article
Full-text available
Using optimized combinatorial mutagenesis techniques and Digital Imaging Spectroscopy (DIS), we have isolated mutants of the cloned Aequorea victoria green fluorescent protein (GFP) that show red-shifted excitation spectra similar to that of Renilla reniformis GFP. Selective excitation of wild-type versus Red-Shifted GFP (RSGFP) enables spectral se...
Article
The applications of Digital Imaging Spectroscopy (DIS) have illustrated the differentiation of mutant colonies based either on ground state absorption spectra or fluorescence emission spectra. Clearly, these first experiments on chlorophyll-based systems are generalizable to other biological targets producing chromogenic natural substances. Extrins...
Article
Digital imaging spectrophotometers can simultaneously measure the spectra of hundreds of features in a two-dimensional scene. While a variety of applications can be anticipated, a colorimetric analysis of mutants expressing pigmented proteins has already led to the development of efficient algorithms for optimizing combinatorial mutagenesis.
Article
We describe an efficient method for generating combinatorial libraries with a high percentage of unique and functional mutants. Combinatorial libraries have been successfully used in the past to express ensembles of mutant proteins in which all possible amino acids are encoded at a few positions in the sequence. However, as more positions are mutag...
Article
Combinatorial cassette mutagenesis was used to substitute randomly nine amino acid residues in the vicinity of the active branch monomeric bacteriochlorophyll in the photosynthetic reaction center of Rhodobacter capsulatus. The bacteriochlorophyll environment was targeted because of the potential role of this cofactor in the initial charge separati...
Article
We have developed a generally applicable experimental procedure to find functional proteins that are many mutational steps from wild type. Optimization algorithms, which are typically used to search for solutions to certain combinatorial problems, have been adapted to the problem of searching the 'sequence space' of proteins. Many of the steps norm...
Article
Combinatorial cassettes based on a phylogenetic "target set" were used to simultaneously mutagenize seven amino acid residues on one face of a transmembrane alpha helix comprising a bacteriochlorophyll binding site in the light harvesting II antenna of Rhodobacter capsulatus. This pigmented protein provides a model system for developing complex mut...
Chapter
Light-induced FTIR difference spectroscopy is used to monitor structural changes in genetically modified reaction centers (RC) of Rhodobacter (Rb.) capsulatus. In the photosynthetic bacterial RC, His M200 and His L173 are the axial ligands to the central Mg of each of the two bacteriochlorophylls (BChl) constituting the primary electron donor P. Th...
Article
Light-induced P+QB-/PQB FTIR difference spectra of reaction centers (RCs) have been obtained from chromatophores lacking light-harvesting B800-850 antenna for Rhodobacter capsulatus wild type (WT) and for the two mutants HisM200-->Leu and HisL173-->Leu. The primary donor (P) in both mutants consists of a bacteriochlorophyll-bacteriopheophytin heter...
Article
Full-text available
An algorithm for protein engineering, termed recursive ensemble mutagenesis, has been developed to produce diverse populations of phenotypically related mutants whose members differ in amino acid sequence. This method uses a feedback mechanism to control successive rounds of combinatorial cassette mutagenesis. Starting from partially randomized "wi...
Article
In random mutagenesis, synthesis of an NNN triplet (i.e. equiprobable A, C, G, and T at each of the three positions in the codon) could be considered an optimal nucleotide mixture because all 20 amino acids are encoded. NN(G,C) might be considered a slightly more intelligent "dope" because the entire set of amino acids is still encoded using only h...
Article
Full-text available
The femtosecond spectral evolution of reaction centers of Rhodobacter sphaeroides R-26 was studied at 10 K. Transient spectra in the near infrared region, obtained with 45-fs pulses (pump pulses centered at 870 nm and continuum probe pulses), were analyzed with associated kinetics at specific wavelengths. The t = 0-fs transient spectrum is very ric...
Chapter
The primary electron transfer in bacterial photosynthetic reaction centers (RCs) involves a fast (≃1–3ps) charge separation between the excited state of the primary electron donor (P) and an acceptor (either BA or HA) along the active pigment branch A. Although this reaction proceeds with a quantum yield close to unity, it must compete with loss ch...
Chapter
The L and M subunits of the reaction center (RC) show sequence homology and structural symmetry, yet paradoxically electron transfer is unidirectional. We have attempted to determine the structural unit of the RC responsible for the unidirectionality of electron transfer by switching homologous regions of the L and M subunits. In the past we report...
Article
Full-text available
It is shown that vibrational coherence modulates the femtosecond kinetics of stimulated emission and absorption of reaction centers of purple bacteria. In the DLL mutant of Rhodobacter capsulatus, which lacks the bacteriopheophytin electron acceptor, oscillations with periods of approximately 500 fs and possibly also of approximately 2 ps were obse...
Article
In the elucidation of the mechanism by which certain photosynthetic bacteria convert light into chemical energy, genetics has become intertwined with biophysical techniques. While X-ray crystallography has yielded an atomic resolution structure of the photosynthetic reaction center (RC), optical spectroscopy remains the most important technique for...
Article
Resonance Raman spectra are reported for RCs from Rb. capsulatus in which the L104 glutamic acid is replaced by glutamine. The skeletal modes of the primary electron acceptor, BPhL, in these RCs undergo temperature-dependent frequency shifts that are identical to those observed for BPhL in RCs from wild-type. This observation suggests that the stre...
Article
Resonance Raman (RR) spectra are reported for the photosynthetic reaction center (RC) proteins from Rhodobacter capsulatus wild type and the genetically modified systems GluL104----Leu and HisM200----Leu. The spectra were obtained with a variety of excitation wavelengths, spanning the UV, violet, and yellow-green regions of the absorption spectrum,...
Article
Digital imaging spectroscopy has been used to obtain the grayscale spectrum of colored bacterial colonies directly from petri dishes. Up to 500 individual colony spectra can be simultaneously recorded and processed from a single plate. Spectra can be obtained in the visible to near infrared region (400nm-900nm) with 10nm resolution. Instrument resp...
Article
Electron paramagnetic resonance (EPR) has been used to investigate the cation and triplet states of Rhodobacter capsulatus reaction centers (RCs) containing amino acid substitutions affecting the primary donor, monomeric bacteriochlorophylls (Bchls), and the photoactive bacteriopheophytin (Bphe). The broadened line width of the cation radical in Hi...
Article
The bacterial photosynthetic reaction center (RC) is a pigmented intrinsic membrane protein that performs the primary charge separation event of photosynthesis, thereby converting light to chemical energy. The RC pigments are bound primarily by two homologous peptides, the L and M subunits, each containing five transmembrane helices. These alpha he...
Article
The effect of an external electric field on the optical absorption spectra of wild-type Rhodobacter capsulatus and two Rb. capsulatus reaction centers that have been genetically modified through site-directed mutagenesis (HisM200----LeuM200 and HisM200----PheM200) was measured at 77 K. The two genetically modified reaction centers replace histidine...
Article
Tryptophan M-250 (TrpM250) in the reaction center (RC) of the purple non-sulfur bacteria occupies a key position between the photoactive pheophytin (HA) and the primary quinone (QA), according to the X-ray crystal structures obtained for Rps. viridis and Rb. sphaeroides (refs. 1,2; Fig. 1). Seven directed mutations have been introduced at this posi...
Chapter
Molecular genetics has rapidly become an integral tool for elucidating the molecular mechanisms of photosynthesis. In the bacterial reaction center (RC) protein, structure/function questions, raised through an inspection of the X-ray crystallographic structure, have been addressed by the combined approaches of genetics and spectroscopy. This system...
Chapter
One of the exciting new techniques available to photosynthetic researchers is the ability to perform site-directed mutagenesis on the photosynthetic apparatus. The X-ray crystal structures of reaction centers (RCs) can be used to identify important amino acid residues (Michel et al., 1986; Chang et al., 1986; Yeates et al., 1988). Genetic manipulat...