PANGENOME – Fixing God’s Mistakes?

What makes you YOU? Why are you who you are? What makes you tick and moves your heart?  Why are some people gentle and kind where others are hateful and evil?  What hurts you? saddens you? Fills you with joy?  Why are some people great with children and others don’t care for them at all?  What makes one person trust in GOD, and another turn his back?

Everything about you is in your genes!!  You carry it with you and pass it on to your children.  There are many things in you life that naturally affect your DNA through things you experience and choices you make.  But then there are things that change your DNA through methods and madness out of your control.  Those who perpetrate these assaults on your being are the folks you idolize, trust and obey.  Folks who should be looking out for your best interest.

They tell you that is what they are doing.  They claim that they are busily building a better future for you and your children.  They assert that all of their testing, studying, inventing and producing will ultimately be of immense benefit.  They find all kinds of rationalization for the things they do and the things they pawn off on the public.  However, the underlying TRUTH is always that they are NOT AT ALL INTERESTED IN YOUR WELL BEING.   They devoted to their own agenda which is to promote the Kingdom of the Anti-Christ.
There are really only two kinds of people in this world.  There are those who know and love the GOD who created them and there are those who do not even know him nor do they even want to.
YOU have an enemy who hates you with more rabid a hatred than you can ever imagine.  The Devil and his followers and servants have NO HOPE of SALVATION.  The crimes that they committed were so heinous that our Heavenly Father cannot pardon them and remain righteous and just.  So, the Devil and all his followers despise the children of GOD who are forgiven and enter to into Eternity with GOD.   They want nothing but to KILL, STEAL and DESTROY everything and everyone who belongs to GOD.

THE MOST HEINOUS CRIME the Fallen Angels committed was to alter the DNA of God’s creation,  transmute the life forms and corrupt all flesh.  This was the reason for the flood.  ALL FLESH was so badly corrupted that they could not be saved.THIS IS HAPPENING AGAIN IN OUR WORLD TODAY!!  WE are reliving the DAYS OF NOAH.  The Devil knows his time is short. He is about to unleash all of his power, his creatures, and his weapons upon humanity.

HIS PRIMARY FOCUS is US!  He wants to change us completely from the inside out.  He is pulling out all the stops and coming after our bodies, minds and spirits.  CONTROL… he wants full control.  He wants all of us to be his slaves or die.

Those who call themselves Scientists think they are developing new ideas, creations, inventions…not so my friends.  There is nothing new under the SUN.
The Fallen Angels taught mankind all the skills, arts and crafts and are stilling working at the same thing today.  They are the force behind all the evil in the world.  They are behind all the “advances” in the area of manipulation of DNA and the applications and uses for stem cells.
When CRISPR was revealed to the public, I new it was over for humanity.  They have been messing with the DNA of plants and animals for a long time now.  I don’t know how long they were actually using CRSPR before we were allowed to know about it.  But, you could already see the changes in our world.  All the new diseases and birth defects, all the new bacteria and algae, all the issues with pregnancy and childbirth, all the hormonal changes and the blending of the sexes.  IT was not normal, organic or natural.
Now, they want you to believe that they are mapping the human genome for your benefit.  Though they don’t really have any solid justification.  You have to know that mapping is the last step to control in the field of “Science”.  They tell us that until know they have only mapped the genome of one human and that it does not provide information on ALL the differences in the various races and nationalities.  But, apparently the genomes of 350 people would cover it, though there are over 8 billion people in the world.  How ridiculous!  ALL human beings have pretty much the same genes.  We are all descended from Adam and Eve through NOAH.  Though there are subtle differences.  The biggest differences between humans is not in our Genes.  It is in our Spirit.  Our nature, our behavior, our values, our choices come out of the abundance of our heart and from the source of our morality.  Whether we are Children of the Most High who live according to HIS SPIRIT or we are children of the DEVIL and we live according to his order.
If you have never read my posts on CHISPR, you might want to check them out, as well a my series on It’s in the Blood:

updated: May 16, 2023


CRISPR (short for “clustered regularly interspaced short palindromic repeats”) is a technology that research scientists use to selectively modify the DNA of living organisms. CRISPR was adapted for use in the laboratory from naturally occurring genome editing systems found in bacteria.

Mike Smith

Mike Smith, Ph.D.
Former Program Director, Genome Technology Program
Division of Genome Sciences

CRISPR. When I first learned about CRISPR about a decade ago, the technology and the future possibilities were just amazing. A few years after that, I had the joy of meeting Dr. Jennifer Doudna at a small meeting at NHGRI, and we knew at that time that we were talking to a future Nobel Prize winner and, indeed, she got that very recently. This class of enzymes from bacteria has many, many uses, and I thought I’d pick one just for its timeliness. It provided the simple method for detection of COVID ribonucleic acid — or RNA — without making copies up front or performing gene amplification, or sometimes called PCR. And that’s just a nice impactful example of so many places that this discovery has been important.


The Scientific Method vs. Types of Research

Think of the years you’ve spent in science classes and the hundreds of hours you’ve faced teachers drilling you on the “scientific method” (who can forget the poor lima beans squished into dirt-filled paper cups and shoved into dark closets while their siblings enjoyed sunny places on the first-grade window sill?). Do you understand the difference between the “scientific method” and the “types” of research methods?

Think of the scientific method as having four goals (description, prediction, explanation and control). It is important to remember that these goals are the same for anything that can be studied via the scientific method (a chemical compound, a biological organism, or in the case of psychology, behavior). Each goal can be understood in terms of the question that it answers about the entity under investigation. For psychology, each goal answers a particular question with respect to behavior:

  1. Description: What are the characteristics of the behavior?
  2. Prediction: How likely is it that the behavior will occur?
  3. Explanation: What causes the behavior?
  4. Control: Can I make the behavior happen/ not happen?



James K. Feibleman

If science is still taught by the apprentice method, it is because the scientific method has never been properly abstracted. Full abstraction discloses that there is only one scientific method. Although its employment in the separate experimental sciences is always mediated by extenuating circumstances, essentially the same set of procedures, conducted in approximately the same order can be discovered in laboratory practices. The scientific method is an on-going process, which nevertheless lends itself to analysis into six well-defined stages. These stages are : observation, hypothesis, experiment, theory, prediction and control. Each of these stages except the first emerges logically from the one before, and each except the last leads logically into the next. Observations are for the purpose of discovering hypotheses; and hypotheses are established in order to test them against fact by experiment, against theory by mathematical calculations, against the application of laws to future particulars by prediction, and finally against the application to practice by the control over fact.

Until the sixteenth century, people believed in magic as a way of explaining how the world worked. Indeed Queen Elizabeth I had a court magician, John Dee. However during the reign of the Stuart kings magic was killed and science took its place. This change came about because a group of men met in London and decided to set up a society to study the mechanisms of nature.
Freemasonry and the Birth of Modern Science. Paperback – November 22, 2015.   I have the book, in it they state that the goal of modern science is ALWAYS CONTROL.  The “scientific method” was created as the plan to get from a hypothesis to CONTROL.

 Goals of Science: Describe, Explain, Predict, Control

Concept mapping is a method to determine the achievement of knowledge. Concepts are linked with labelled lines to proposition. The concepts create a graphical structured meaningful relationship. The method is also proved to be effective for testing, indicating well students’ mentality and its structure. This article describes three case studies using concept maps as assessment tools. Two studies measured the necessity of animations describing abstract topics in chemistry. Memorizing time period, different learning materials, topics, and structure of animation were used as parameters. The third study detected the time when higher taxonomy scored concept maps were created. Could students find concept themselves from the exercise, or should they be given by the instructor? We argue that concept mapping method gives a unique possibility to visualize the structure of students’ knowledge.


Scientists have mapped just about everything on earth and gained control over weather, energy, chemicals, minerals, the ocean, etc… NOW, they want to CONTROL YOU.   Every aspect of you, including your body, mind and soul/spirit.  They are mapping humanity.  Our habits, our interests, our personalities, our bodily functions, our thought processes, our emotions and our spirits.  Mapping is the LAST STEP before total control.  Are you prepared?


Sequencing 101: Looking Beyond the Single Reference Genome to a pangenome for every species
APRIL 30, 2020  |  SEQUENCING 101

What is a pangenome?

 A pangenome identifies which portions of the genome are unique and which overlap and are therefore core to the species.

Note the familiar symbol of the Trinity.  This is a very ancient and esoteric symbol.

Unless you have an identical twin, no other person has a genome that is identical to yours. The same is true for other animal, plant, and microbial species that reproduce sexually: the genomes of individuals are unique. Less well known, but equally true, is that individual members of a species do not always share even the exact same genes. Nevertheless, scientists mostly use a single reference genome to represent an entire species:

                • one human genome
                • one maize genome
                • one Staphylococcus aureus genome


Staphylococcus aureus Infections – Infections – Merck Manuals Consumer …
Staphylococcus aureus is the most dangerous of all of the many common staphylococcal bacteria. These gram-positive , sphere-shaped (coccal) bacteria (see figure How Bacteria Shape Up ) often cause skin infections but can cause pneumonia, heart valve infections, and bone infections and may be resistant to treatment with some antibiotics.
So, why did they select that genome?

The coining of the “pangenome”
Around 2005, geneticists started to explore the concept of the pangenome, originally defined as the entire set of genes possessed by all members of a particular species and then extended to refer to a collection of all the DNA sequences that occur in a species.

It started with bacteria, as many things do. Genomic activity like recombination, mobile genetic elements, and horizontal gene transfer were clearly contributing to individual diversity across the bacterial domain. Some scientists discovered dozens, if not hundreds, of unknown genes when they sequenced new strains.

Generating pangenomes reveals more diversity than expected.

In 2007, MIT microbiologist Sallie Chisholm (@ChisholmLab_MIT) set out to determine the extent of genetic variation in the marine cyanobacterium  Prochlorococcus. Each strain contains approximately 2,000 genes, and Chisholm estimated that a pangenome for Prochlorococcus  would be around 6,000 genes, based on an initial set of 12 genome sequences. Eight years later, with 45 strains sequenced, she revised that estimate up to at least 80,000 genes — around four times the number of genes in the human genome with the core genome for the species comprising only about 1,000 genes, or less than 2 percent of the total gene pool.

“That’s a lot of information shaping that collective,” Chisholm told The Scientist. “[The pangenome view] changes the way you think about what an organism is.”

Why is it important to capture the full range of genetic diversity? 
Those looking to create vaccines need to understand the genomic variation and versatility of disease-causing microbes, especially if they are hoping to develop universal vaccines that could provide protection against more than one strain in a species.  (Or, if they are looking to create pandemics)

Those studying adaptation to climate change would benefit from a comparison of genes absent or in abundance within species found in different geographic locations and/or environmental conditions. In crop plants, differences in variable genes could have implications on disease resistance, metabolite production, and stress responses.

And with differences in gene number increasingly being associated with disorders including autism, Parkinson’s, and Alzheimer’s diseases, there are strong medical justifications for taking a more variation-centric view of the human species. Variants cannot be identified within regions completely missing from the reference sequence, many of which have been found to be more common than previously thought.  (Since they have been studying and experimenting with DNA and with Disease and Immunology, there have been more and more birth defects, chronic diseases, epidemics and vaccine side effects, reactions and deaths.  There have also been more algae and aquatic bacteria, as well as more foodborne illnesses. For instance, we had never seen the waters turn blood red before, now it is common, we see it all the time and everywhere.)

What is being done to generate pangenomes?
To answer this question, we sat down with a few scientists to talk about the era of the pangenome and what’s to come.

Sequencing 101: Looking Beyond the Single Reference Genome to a ...
Pangenomes have revealed more genetic diversity within the maize species than between human and chimpanzees.  They can and do claim all different animals and plants who share 94% of our genetic makeup… Naturally, lol, we are all made of the earth!!  But, God created HUMANS in his own IMAGE and Likeness.  No other life form can claim that.  Vesica Pisces – Symbol of Woman’s Vagina, Fertility, Sex.    Note the visual of the snake eye, split in the middle.


meno: 1. a combining form borrowed from Greek, where it meant “month,” used with reference to menstruation in the formation of compound words: menopause.  The vagina looks like a mouth.


video image 16.2K29:41



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Old video I made showing one of the many meanings of these symbols, one other is our plane of existance is the vesica pisces and the obelisk is the pole star polaris in the middle 1 year, 3 months ago


Original Article continued

One particularly important crop that has haunted geneticists and breeders for years is maize. It is challenging to sequence because the vast majority of its 2.3 Gb genome, a staggering 85 percent, is made up of highly repetitive transposable elements. Maize is also incredibly diverse in its DNA makeup. As an example, a study comparing genome segments from two inbred lines revealed that half of the sequence and one-third of the gene content was not sharedthat’s much more diversity within the species than between humans and chimpanzees, which exhibit around 94 percent sequence similarity.

Maize is a cultigen; human intervention is required for it to propagate. Whether or not the kernels fall off the cob on their own is a key piece of evidence used in archaeology to distinguish domesticated maize from its naturally-propagating teosinte ancestor.[4] Genetic evidence can also be used to determine when various lineages split. [12  Wikipedia 
cultigen (from Latin cultus ‘cultivated’, and gens ‘kind’) or cultivated plant[note 1] is a plant that has been deliberately altered or selected by humans;

Cultigens arise in the following ways:

  • through the selection of variants from the wild or cultivation, including vegetative sports (aberrant growth that can be reproduced reliably in cultivation)
  • from plants that are theplant breeding result of plant breeding and selection programs
  • from genetically modified plants (plants modified by the deliberate implantation of genetic material)
  • from graft-chimaeras (plants grafted to produce mixed tissue with graft material from wild plants, special selections, or hybrids).     WIKIPEDIA

The whole notion of a single reference genome for crop plants is an antiquated concept borne out of necessity from the technological limitations of the past. Now with the capability to rapidly generate high-quality references for even the largest crop genomes, we can readily access the full complement of sequence diversity and structural variation within a crop,” says Kevin Fengler, Comparative Genomics Lead at Corteva Agriscience.

So the field was delighted when a collective of 33 scientists released a 26-line maize pangenome reference collection earlier this year. The collection was created using PacBio sequencing, and includes comprehensive, high-quality assemblies of 26 inbreds known as the NAM founder lines. These include the most extensively researched maize lines that represent a broad cross section of modern maize diversity, as well as an additional line containing an abnormal chromosome 10.

It turns out it’s not just maize biology that can be informed by pangenomes. “The high level of diversity in maize is well known, but we see a lot of diversity and structural variation underlying traits of interest in all the crop plants we work on. Creating the first reference genome for a crop genome is a great first step, but things get really interesting as you begin to add more genomes and a more comprehensive view emerges,” adds Fengler.

As for our own species, the current reference genome (GRCh38) — an update of the genome produced by the international Human Genome Project in 2000 and based mostly on DNA from one person — has been added to and annotated through the years, but is still an incomplete sequence and woefully inadequate as a representation of human diversity and genetic variation. Scientists estimate that up to 40 megabases of sequence, including protein-coding regions, are absent from the reference genome.

Several studies using PacBio long reads have reported an average of ~20,000 structural variants (SV) per human genome, most of which fall within repetitive elements and segmental duplications. Furthermore, it does not represent the diploid structure of human genomes. Rather, it is an arbitrary linear combination of different haplotypes, or a mosaic of multiple individuals.


Several groups have undertaken efforts to ensure certain populations are better represented in genomic databases, from Sweden to Tibet to Japan.

When asked the value a pangenome could bring to human research, Fritz Sedlazeck (@sedlazeck), Assistant Professor at Baylor College of Medicine, said, “the pangenome has the potential to represent the diversity of the human population or any species. This eases the re-identification of complex alleles or even haplotypes.”

And it seems the National Human Genome Research Institute agrees, recently committing $30 million towards the creation of a new human pangenome based on high-quality sequencing of 350 individuals from across the human population, to capture all genomic variation observed in human populations.

One human genome cannot represent all of humanity. The human pangenome reference will be a key step forward for biomedical research and personalized medicine. Not only will we have 350 genomes representing human diversity, they will be vastly higher quality than previous genome sequences,” said David Haussler, director of the University of California Santa Cruz Genomics Institute, which is leading the project.

4 days agoDefinition. The genome is the entire set of DNA instructions found in a cell. In humans, the genome consists of 23 pairs of chromosomes located in the cell’s nucleus, as well as a small chromosome in the cell’s mitochondria. A genome contains all the information needed for an individual to develop and function.

How to generate a pangenome
So, what are the most important things to keep in mind when creating a pangenome reference?

First, Fengler says that being able to be confident in your results is really important. “Ideally, all of the references in the pangenome collection will be built with a similar recipe to enable direct comparisons without artifacts from different technologies.” This points to the need for a reliable technology that can be used to generate equivalent quality genomes for many samples with little variability.

Sequel sequencer
HiFi reads from the Sequel II system enable fast, reliable results.

Second, the data must be high quality. When asked the importance of long reads to pangenome efforts, Sedlazeck said, “they will be important to distinguish between different alleles/paths in the graph and to characterize novel mutations. Thus, being able to cope with graphs that encode a much higher number of variations to better represent the population.” Along those lines, Fengler adds, “the approach for assembly needs to be robust and accurate such that mis-assembly and sequence errors are not interpreted as structural variation and sequence diversity.”

Lastly, cost and speed have to be taken into account. With the high accuracy of HiFi sequencing, only 10- to 15-fold coverage per haplotype is needed for a high-quality resulting genome assembly, and the analysis time can be cut in half.

“Now researchers no longer need to wait for actionable sequence data,” says Fengler. “For maize, we can generate a high-quality reference genome the same day that the sequencing finishes.”

What’s next in pangenomes?

Pangenome workflow
Questions remain as to how to fully utilize pangenomes to better understand biology.

As pangenome collections grow, scientists have to tackle questions around how to represent a pangenome.Which variations should be included into a pangenome? Is it all of them? Then you lose specificity in regions. Is it only the common variations? Then you have a problem with disease-causing variations and other complex regions like HLA,” asks Sedlazeck, highlighting the continued work that needs to be done.

In addition, tackling things like annotation, visualization, and relationship management are on Fengler’s mind. “A variety of new pangenome analysis and visualization tools are needed to fully realize the value of having a pangenome collection for each crop.”

And then we have to move into functional and translational analysis. Scientists need to be able to take their newfound understanding of variation at the genome level and see how it impacts phenotypes, and whether the variation can be introduced artificially to influence agronomic traits, for instance.

One thing is for sure: the pangenome era is upon us, and whether you need a pangenome to understand important traits or you build tools to interpret those traits, there will be plenty to work on in the coming years.

Interested in finding out more about HiFi data for pangenome sequencing your organism of interest? Get in touch with a PacBio scientist to scope out your project.


   I found this image very interesting.  A key shaped genome?

KeyGene’s two-part webinar about PanGenomes, Part 2: Constructing and use of a pangenome

PanGenomes describe the available genetic diversity within, for instance, plant species, crops or germplasm collections (or humans) . Because of diminishing costs of genome sequencing, increasing speed of reference genomes construction and advances in bioinformatics, PanGenomes have become an accessible tool. The genome insights delivered by PanGenomes can spectacularly speed up and contribute to plant breeding and research.

KeyGene is well known for its unique combination of extensive expertise in wet lab and in silico research. We offer optimized techniques for high molecular weight plant DNA isolation, the most advanced DNA sequencing platforms and breakthrough bioinformatics pipelines and tools. This combination has already allowed KeyGene to successfully support partners in building and applying plant PanGenomes.

At KeyGene, we underpin the value of PanGenomes and support partners in constructing and using it. Therefore, we organize this two-part webinar on PanGenomes, where we explain what one needs to be able to construct PanGenomes and highlight their value in breeding and research. The two-part webinar will also show KeyGene capabilities in successfully generating and using PanGenomes.

Participation is free of charge.

=> Register here for Part 2 of KeyGene’s two-part webinar on PanGenomes

Part 2: Construction and use of a PanGenome, Thursday 18 March 2021, 16-17h CET

  • State-of-the art tools for PanGenome construction at KeyGene, Erwin Datema, Senior Scientist Genome Informatics, KeyGene
  • Applications of PanGenome in breeding and research, René Hofstede, Program Scientist, KeyGene
  • The value of a PanGenome for crop breeding, Allen Sessions, Senior Principle Scientist and Crop Genetics Team Lead, BASF

Dr Allen Sessions holds a PhD in Plant Biology from the University of California, Berkeley. He has held leading positions at Syngenta and Bayer CropScience working on genotyping, marker-trait associations and next-generation sequencing applications in cotton, maize, and soybean. Currently, Dr Sessions is a senior principal scientist and Group Leader of Crop Genetics at BASF where his team focuses on trait discovery and deployment for cotton and soybean breeding while applying various NGS technologies.

=> Register now for Part 2 of KeyGene’s two-part webinar on PanGenomes

Throughout the world’s existence the fallen Angels and those who serve them have worked very hard to convince humanity that they can thrive without the intervention of the Creator.  They have had thousands of years to erase the truth, and fill the world with deception.  They have been very successful as most of the world today does not even believe that God exists, or that the Devils exist, or that judgement is coming.  
There are many pagan religions once again in our world.  Too many to go into here, but all religions really fall somewhere under the following:

Pantheism is the belief that God and the universe are one and the same. There is no dividing line between the two. Pantheists believe that everything is part of an all-encompassing, immanent God. All forms of reality may then be considered either modes of that Being, or identical with it.  They view God as immanent and impersonal. This belief system grew out of the Scientific Revolution, and pantheists generally are strong supporters of scientific inquiry, as well as religious toleration. Pantheists don’t believe there is a God that made the earth or defined gravity, but, rather, God is the earth and gravity and everything else in the universeBecause God is uncreated and infinite, the universe is likewise uncreated and infinite and ever changing.. God did not choose one day to make the universe. Rather, it exists precisely because God exists, since the two are the same thing. Because all things are ultimately God, all approaches to God can conceivably lead to an understanding of God. Each person should be allowed to pursue such knowledge as they wish. This does not mean, however, that pantheists believe every approach is correct. They generally do not believe in an afterlife, for example, nor do they find merit in strict dogma and ritual. Pantheist thought can be found within animistic beliefs and tribal religions throughout the world as an expression of unity with the divine, specifically in beliefs that have no central polytheist or monotheist personas.  Pantheism  derives from the Greek word πᾶν pan (meaning “all, of everything”) and θεός theos (meaning “god, divine”). 

Animism (from Latinanima meaning ‘breathspiritlife‘) is the belief that objects, places, and creatures all possess a distinct spiritual essence. Animism perceives all thingsanimalsplantsrocksriversweather systems, human handiwork, and in some cases wordsas animated and alive. Animism is used as a term for the belief system of many Indigenous peoples. Although each culture has its own mythologies and rituals, animism is said to describe the most common, foundational thread of indigenous peoples’ “spiritual” or “supernatural” perspectives.   Animists believe that all material phenomena have agency, that there exists no categorical distinction between the spiritual and physical world, and that soul, spirit, or sentience exists not only in humans but also in other animals, plants, rocks, geographic features (such as mountains and rivers), and other entities of the natural environment. Examples include water spritesvegetation deities, and tree spirits, among others. Animism may further attribute a life force to abstract concepts such as words, true names, or metaphors in mythology. The origin of the word comes from the Latin word anima, which means life or soul.

Polytheism is the belief in many divine beings, who typically have to beworshippedor, if malevolent, warded off with appropriate rituals. Like some other religions Polytheism identifies natural forces and objects as divinitiesclassified in three categories celestial, atmospheric, and earthly.  In pastoral times when people survived through hunting and agriculture the forces of nature were vital to survival.  Ancient peoples developed  religions that exhibit rites connected with fertility. The sun’s vitality was seen in the cyclical effects of causing things to grow and wither. Because of its dominance over the world, the sun was often seen as all-knowing, and thus sky gods of various cultures were seen as highly powerful and knowledgeable. The sky was associated with creation in contrast the moon was rarely seen as important (though in Ur, a city of ancient southern Babylonia, the moon god Sin was supreme). The role of the sky god in ensuring food and in providing light and warmth, over against the chaotic effects of darkness, was a theme of various myths of the cosmic drama and was one main reason for the connection in mythic thought between creation and light. Important in the development of fertility religion were the dying and rising” gods, such as AdonisAttisOsiris, and Tammuz. Their cults had a new life in the mystery cults of the Greco-Roman world, where the original agricultural significance of the rites was transformed into more personal and psychological terms. On earth, besides the divine mother out of whose womb plant life has its birth, there are a host of divinities connected with agricultural and pastoral life. In addition, sacred significance is often attached to features of the particular environment in which a given group finds itself. Thus, sacred mountains, such as Olympus in Greece, have their resident deities, and a river, such as the Ganges (Ganga), may be divinized. Underground rivers have special significance in connecting with the underworld, or nether regions, which can be important as the place of repose of the dead but also as the matrix for the re-creation of life. Geographical locations can also have cosmic significance; e.g., Delphi, Greece, was known as the navel of the earth. Further, many cultures have gods and goddesses associated with the sea.

Scientists, Technologists, Scholars and the Wealthy Elite want you to believe that they do not believe in GOD or are not religious at all…they are developed beyond such nonsense.  That is a flat out lie.  They serve their gods and goddesses faithfully, and don’t make a move without them.  This is clearly demonstrated in their symbolism and numerology.  

The TRUTH is that there is ONLY ONE TRUE and LIVING GOD who CREATED ALL THINGS.  Those who know him enjoy the peace that passes all understanding.  They are comforted in knowing that there is no lack with GOD and that He is always in control.

God created us in His image.  That means that our bodies were designed to be like His.  Everything about our bodies was designed to function properly, to be self healing, to work together as single whole.

The elite do all that they can to reduce us to nothing more than a lump of cells thrown together by accident and with no more importance that a stone or plant or spec of dust.  DON’T BUY THEIR LIES.  

Here you will see that the have terms for the precious gift of new life created by GOD that reduce it to insignificant, disposable tissue.

Human Pangenome Reference Consortium

The Human Pangenome Reference Consortium (HPRC) is a project funded by the National Human Genome Research Instititue to sequence and assemble genomes from individuals from diverse populations in order to better represent genomic landscape of diverse human populations.

We have released a new high-quality collection of reference human genome sequences that includes genome sequences of 47 people, with the the goal of increasing that number to 350 by mid-2024.

Link to Publications:
A draft human pangenome reference;
Increased mutation rate and gene conversion within human segmental duplications;
Recombination between heterologous human acrocentric chromosomes;
Pangenome graph construction from genome alignment with minigraph-cactus.

No single genome can represent the diversity in the human population. Using a single reference genome creates reference biases, adversely affecting variant discovery, gene–disease association studies and the accuracy of genetic analyses.

The HPRC was started to help migrate common genomic analysis to use a pangenome so diverse populations are better represented.

What are we doing?

Sequencing from diverse set of samples with the newest, long read, technologies
Creating and releasing high-quality assemblies and pangenomes
Embedding a team of scholars to address ethical, legal and social implications (ELSI) of the HPRC’s work


Year 1
Current Production
Next Round
Usable Mature
The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny).
phylogeny fī-lŏj′ə-nē – noun
  1. The evolutionary development and history of a species or trait of a species or of a higher taxonomic grouping of organisms.
  2. A model or diagram delineating such an evolutionary history.
  3. A similar model or diagram delineating the development of a cultural feature.

Taxonomy Definition & Meaning – Merriam-Webster
taxonomy: [noun] the study of the general principles of scientific classification : systematics.

Goals of the Tree of Life

The Tree of Life Web Project is an online database that compiles information about biodiversity and the evolutionary relationships of all organisms.  Content for the project is compiled collaboratively by hundreds of biologists and amateur contributors from all over the world. The project is non-profitfunded by the U. S. National Science Foundation and the University of Arizona.  All of our services are free and open to the public.

We envisage the Tree of Life being used by people interested in locating information about a particular group of organisms, by biologists seeking identification keys, figures, phylogenetic trees, and other systematic information for a group of organisms, and by educators teaching about organismal diversity. The ToL project was originally designed for biologists. However, given the response of other people to the project, including middle and high school students, we are encouraging authors to include information of interest to non-biologists, and we now also accept contributions from students and other amateur scientists and nature lovers. For more information, please see Contributing Images and Other Media to the Tree of Life and Learning with the Tree of Life.

The basic goals of the Tree of Life project are:

  • To present information about every species and significant group of organisms on Earth, living and extinct, authored by experts in each group.
  • To present a modern scientific view of the evolutionary tree that unites all organisms on Earth.
  • To aid learning about and appreciation of biological diversity and the evolutionary Tree of Life.
  • To share information with other databases and analytical tools, and to phylogenetically link information from other databases.

About the ToL Navigation Picture

We’ve been getting a lot of inquiries about the tree of life picture on our home page. It is important to note that the major function of this picture is to help visitors to the ToL web site to quickly navigate to pages of some of the major groups of organisms. In order to serve this purpose, we had to use a greatly simplified representation of the tree of life.

They are REBUILDING us.  THE BUILDERS.   They are forming us in their image with demonic spirits ruling over us from the inside.  They are corrupting our flesh in every way possible.

Practical Graphical Pangenomics

Nov 15, 2022 High-throughput’ in sequencing refers to the amount of DNA molecules read at the same time. Technologies are now capable of sequencing many fragments of DNA in parallel. This enables scientists to read hundreds of millions of DNA fragments and generate more data, with less time and costs than ever before.
Aug 6, 2022 High-throughput genome sequencing is rapidly being adapted in clinical settings, and is revolutionizing patient care in a variety of human diseases. The age of Big Genomics is only the beginning. The rate at which sequencing technologies are being developed and adopted in research and clinic setting is increasing exponentially.spacer

Parts of the pangenome

In the pangenome, we can identify three sets of genes: Core, Shell, and Cloud genome. The Core genome comprises the genes that are present in all genomes analyzed. To avoid dismissing families due to sequencing artifacts some authors consider the softcore (>95% occurrence). The Shell genome consists of the genes shared by the majority of genomes (10-95% occurrence). The gene families present in only one genome or <10% occurrence are described as Dispensable or Cloud genome.


Is the part of the pangenome that is shared by every genome in the tested set. Some authors have divided the core pangenome in hard core, those families of homologous genes that has at least one copy of the family shared by every genome (100% of genomes) and the soft core or extended core,[15] those families distributed above a certain threshold (90%). In a study that involves the pangenomes of Bacillus cereus and Staphylococcus aureus, some of them isolated from the international space station, the thresholds used for segmenting the pangenomes were as follows: “Cloud,” “Shell,” and “Core” corresponding to gene families with presence in <10%, 10 to 95%, and >95% of the genomes, respectively.[16]

The core genome size and proportion to the pangenome depends on several factors, but it is especially dependent on the phylogenetic similarity of the considered genomes. For example, the core of two identical genomes would also be the complete pangenome. The core of a genus will always be smaller than the core genome of a species. Genes that belong to the core genome are often related to house keeping functions and primary metabolism of the lineage, nevertheless, the core gene can also contain some genes that differentiate the species from other species of the genus, i.e. that may be related pathogenicity to niche adaptation.[17]


Is the part of the pangenome shared by the majority of the genomes in a pangenome.[18] There is not a universally accepted threshold to define the shell genome, some authors consider a gene family as part of the shell pangenome if it shared by more than 50% of the genomes in the pangenome.[19] A family can be part of the shell by several evolutive dynamics, for example by gene loss in a lineage where it was previously part of the core genome, such is the case of enzymes in the tryptophan operon in Actinomyces,[20] or by gene gain and fixation of a gene family that was previously part of the dispensable genome such is the case of trpF gene in several Corynebacterium species.[21]


The cloud genome consists of those gene families shared by a minimal subset of the genomes in the pangenome,[22] it includes singletons or genes present in only one of the genomes. It is also known as the peripheral genome. Gene families in this category are often related to ecological adaptation.[citation needed]


Roary: Analysis of Prokaryote Pan Genome on a large-scale


The Microbial Pan Genome is the union of genes shared by genomes of interest. This term was first used by Medini in 2005.

Since then, microbial genome data has been enormously increased, so to study processes such as selection and evolution, the construction of pan genome of species is required. But construction of pan genome from the real data available is very difficult and would not be accurate due to fragmented assemblies, poor annotation and also the contamination,i.e., microbial organisms can rapidly acquire genes from other organisms. Therefore, Andrew J. Page et al have developed

a new method to generate the pan genome of a set of related prokaryotic isolates and named the tool as ‘Roary’. It deals with thousands of isolates in a feasible time.

How Roary Works?

One annotated assembly per sample is input in the Roary from which coding regions are extracted and converted in to protein sequences, and all the partial sequences are removed and pre clustered using CD-HIT (a fast program for clustering and comparing). This produces a reduced set of protein sequences. These reduced sequences are compared all-against-all with the help of BLASTP with a user defined percentage sequence identity (default 95%). Now, by using conserved neighborhood genes, homologous groups are split in to true orthologs. Finally, a graph is constructed showing the  relationships of the clusters based on the order of occurrence in the input sequences.

Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life.Two segments of DNA can have shared ancestry because of three phenomena: either a speciation event (orthologs), or a duplication event (paralogs), or else a horizontal (or lateral) gene transfer event (xenologs).

Fig.1  Effect of dataset size on the wall time of multiple applications.

That’s how the orthologous genes of prokaryotes can be easily identified and the microbial evolution can be well studied. It is done on a large scale covering a large data set to analyse the pan genomes of prokaryotes. Other tools have also been made earlier than Roary for the same purpose,namely, PanOCT and PGAP, but Roary is more fast, heuristic and most feasible tool among them.

Key points: Prokaryotesare single-celled organisms belonging to the domains Bacteria and Archaea. Prokaryotic cells are much smaller than eukaryotic cells, have no nucleus, and lack organelles. All prokaryotic cells are encased by a cell wall. Many also have a capsule or slime layer made of polysaccharide.


A linear and circular plot can also be tied together so that manipulation of one will cause a mirror alteration in the other, such as zooming or changing the visible region of the genome. A specific region can be recentre to focus. Many other features have been introduced in GenomeD3 Plot for easy visualization and interpretation of genomes
From the picture below, you should be able to discern that they want to blend your DNA not only with all other human DNA but with the DNA of EVERYTHING IN/ON the EARTH, SEA and SKY.
Building the Pangenome for human genetic variation
An imaginary interpretation of the diversity of the human species. Like a flowering garden under a multi-colored sky, your genome holds undiscovered variety, offering a treasure of possibilities.
Building a beautiful Pangenome

Cool tech and ingenuity are building a beautiful Pangenome. It’s a reference genome representing the full spectrum of human genetic variation.

For twenty years, geneticists at the Human Genome Project have built the Reference Genome to give “the world a resource of detailed information about the structure, organization, and function of the complete set of human genes.”

Looking into the nano-spaces of our genome to get precious information has been tough because DNA is bundled tightly into chromosomes and packed into the tiny nucleus in the cell. Especially difficult to unravel are the telomeres and centromeres.

What Are Telomeres?
Telomeres are segments of DNA at the end of our chromosomes. Scientists frequently compare them to the plastic tips of shoelaces that keep the laces together. (1) Telomeres function similarly, preventing chromosomes from fraying or tangling with one another. When that happens, it can cause genetic information to get mixed up or destroyed, leading to cell malfunction, increasing the risk of disease or even shortening lifespans.Each time a cell divides, its telomeres become shorter. After years of splicing and dicing, telomeres become too short for more divisions. At this point, cells are unable to divide further and become inactive, die or continue dividing anyway — an abnormal process that’s potentially dangerous.

Centromere – Definition, Function and Types | Biology Dictionary
Centromere Definition. The centromere is the point on a chromosome where mitotic spindle fibers attach to pull sister chromatids apart during cell division. When a cell seeks to reproduce itself, it must first make a complete copy of each of its chromosomes, to ensure that their daughter cell receives a full complement of the parent cell’s DNA.

Telomeres cap the end of our chromosomes. Centromeres are the knotted-looking section in the middle. Both have thousands of tightly wrapped, repeated segments of DNA and hold essential information.

Chromosome number one showing the centromere and telomeres

During the past two decades, scientists used NexGen technology to “see” and “read” the exact ATCG sequence on the chromosomes. But Nexgen is a short-read method with fundamental limitations. There are gaps in the sequence data. It can’t make sense of the tightly wrapped telomeres and centromeres, nor can it fully sequence non-coding regions.

With long-read tech, scientists can “see every crater, every color, from something that only had the blurriest understanding of before.” And make thrilling discoveries, “researchers have uncovered more than 100 new genes that may be functional and have identified millions of genetic variations between people. Some of those differences probably play a role in diseases.”

Advanced sequencing technology also plays a role in addressing the diversity problem. The current Reference Genome DNA is from mostly European populations. It lacks the full spectrum of worldwide genetic variation. So scientists are building a Human Pangenome with long-read tech.  They’re accumulating so much data that two projects are set up to sequence, map, and analyze it:  (ALWAYS REMEMBER MAPPING IS THE LAST STEP TO CONTROL)

Telomere to Telomere Project fills the gaps by sequencing chromosomes end-to-end from people worldwide with diverse ancestry. They’ve already identified “hundreds of thousands of novel variants per sample — a new frontier for evolutionary and biomedical discovery.” More about the T2T project here.

Human Genome Reference Program will gather “high-quality gapless sequences from ancestrally diverse people.” It will consolidate data from many sources, such as the T2T project. Other researchers are improving sequence technology, and bioinformatics scientists are designing tools for better data analysis. More about the program here.

The Human Pangenome Reference Consortium “aims to issue a new pangenome reference assembly to the international community that reflects the full range of genomic diversity across the globe. We are committed to achieving this goal in a responsible and ethical manner, with explicit attention to community engagement, inclusion, and fair representation.” More about the consortium here.

Put them together, and voila! Pulling data from a wide variety of sources will take years to sort and analyze. The result won’t be just one Reference Genome. What started more than twenty years ago with “the one” will expand into a worldwide compilation of hundreds of data sets — beautiful Pangenomes for a unified representation of the human species.

Finding wonder and beauty in the science of us. From an artistic perspective, we could say scientists are gathering all the subtle hues of human variation. And we are mining the new data for hidden gems. What can we imagine with the full spectrum of human genetic diversity? What would you write, draw, compose, sing about your genome?

One thing is for sure: the pangenome era is upon us, and whether you need a pangenome to understand important traits or you build tools to interpret those traits, there will be plenty to work on in the coming years.

Thomas Lin Pedersen @thomasp85 · Super excited to team up with a Danish design juggernaut with art, sound, and visuals in their DNA and help them enter web3. Along with fellow artists @shavonnewong_ and @Hackatao Quote Tweet Bang & Olufsen @BangOlufsen · It’s official. The #DNACollection is here. Read more about it below:

juggernaut – jŭg′ər-nôt″ – noun
  1. An overwhelming or unstoppable force.
  2. The popular form of Jagannatha, the name of the famous Hindu idol. See Jagannatha, 2.
  3. Figuratively, something, as an idea, custom, fashion, requirement, etc., to which one either devotes himself or is blindly sacrificed.
Thomas Lin Pedersen studied at Technical  University  of  DenmarkTechnical University of Denmark Ph.D Bioinformatics 2012 2016 Events Number of Events 1 Thomas Lin Pedersen has participated in 1 event, PLOTCON on May 2, 2017. PLOTCON Speaker Oakland, California, United States, North America May 2, 2017 Recent News and Activity
Born in Roskilde, Denmark in 1970, Thomas Sunn Pedersen studied applied physics engineering at the Technical University of Denmark (DTU) in Lyngby. He graduated with a M. Sc. degree in 1995 having completed his Master’s thesis at Risø National Laboratory in computational plasma physics and spent a semester at JET in England.
Roskilde – etymology

roseens (Danish)

Noun – roseens (common)

  1. Genitive singular definite of rose

This is the meaning of rose:

rose (Danish)  Origin & history I

From late Old Norse rósrósa, from Middle Low German rōse, from Latin rosa (“rose”).

Pronunciation   IPA: /roːsə/ Noun rose

  1. rose (flower, shrub of the genus Rosa)

Origin & history II  From French rosé.

Alternative forms  rosé

Pronunciation  IPA: /rose/ Noun  rose

  1. rosé (a pale pink wine)

Origin & history III

From Old Norse hrósa, whence dialectal English roose.

Pronunciation  IPA: /roːsə/ Verb

  1. praisecommend
Etymology 1 . From Old Norse kelda, from Proto-Germanic *kaldijǭ, cognate with Norwegian kjelde, Swedish källa. Derived from *kaldaz (” kold “). Noun . kilde c (singular definite kilden, plural indefinite kilder) spring, fountain, source (a place where water emerges from the ground)

·Since 2003, all humans on Earth have been compared to only one reference genome. We need reference genomes for every ancestry – a pangenome.

Massive Science
In 2003, biologists created the first ever human genome sequence. The 3 billion DNA letter sequence, called the reference genome, was mostly made up of DNA donated from people in the city of Buffalo, New York. So far, when clinicians and researchers study an individual’s genome, they compare it to the reference genome to identify differences. But can you compare all of humanity to one genome? No, because one reference genome does not convey the genomic diversity of the human species. We need many reference genomes–a pangenome. This monumental undertaking is already taking place and is poised to redefine the future of genomic research and human health.


The microbial pangenome is the union of genes shared by genomes of interest. The core genome is the intersection of genes of these genomes, thus core genes are genes present in all strains. The accessory genome (also: variable, flexible, dispensable genome) refers to genes not present in all strains of a species. These include genes present in two or more strains or even genes unique to a single strain. Acquired antibiotic resistance genes are typically genes of the accessory genome.


Pangenome analysis

Comparing every gene of every genome to every other gene in the dataset is an enourmous task, and takes a long time even if automated. Roary is a pipeline to determine genes of the core and pangenome. It takes a few short-cuts such as clustering instead of pair-wise alignment and can perform this task in a relatively short time frame. An excellent step-by-step tutorial can be found here


Some genes are present in all genomes, some are present in some and absent in others. Data on presence and absence of genes was collected in a matrix called gene_presence_absence.csv. Clustering of this information was used to build a tree (available as accessory_binary_genes.fa.newick). As a next step we are going to visualize this clustering.

Key Points

  • The microbial pangenome is the union of genes in genomes of interest.
  • The microbial core genome is the intersection of genes shared by genomes of interest.
  • Roary is a pipeline to determine genes of the pangenome.

 An illustration of the globe ribbons of bright color wrapped around it, representing the newly drafted human pangenome
An illustration of the globe ribbons of bright color wrapped around it, representing the newly drafted human pangenome

Scientists have published the first human “pangenome” — a full genetic sequence that incorporates genomes from not just one individual, but 47.

These 47 individuals hail from around the globe and thus vastly increase the diversity of the genomes represented in the sequence, compared to the previous full human genome sequence that scientists use as their reference for study. The first human genome sequence was released with some gaps in 2003 and only made “gapless” in 2022. If that first human genome is a simple linear string of genetic code, the new pangenome is a series of branching paths.

The ultimate goal of the Human Pangenome Reference Consortium, which published the first draft of the pangenome on Wednesday (May 10) in the journal Nature, is to sequence at least 350 individuals from different populations around the world. Although 99.9% of the genome is the same from person to person, there is a lot of diversity found in that final 0.1%.

“Rather than using a single genome sequence as our coordinate system, we should instead have a representation that is based on the genomes of many different people so we can better capture genetic diversity in humans,” Melissa Gymrek, a genetics researcher at the University of California, San Diego, who was not involved in the project, told Live Science.

Related: More than 150 ‘made-from-scratch’ genes are in the human genome. 2 are totally unique to us.

Depiction of the old human reference genome, mostly based on one person&#39;s DNA, alongside the new pangenome, based on 47 people&#39;s dna
Depiction of the old human reference genome, mostly based on one person’s DNA, alongside the new pangenome, based on 47 people’s dna

A reference for health

The first full human genome sequence was completed in 2003 by the Human Genome Project and was based on one person’s DNA. Later, bits and pieces from about 20 other individuals were added, but 70% of the sequence scientists use to benchmark genetic variation still comes from a single person.

Geneticists use the reference genome as a guide when sequencing pieces of people’s genetic codesArya Massarat, a doctoral student in Gymrek’s lab who co-authored an editorial about the new research with her in the journal Nature, told Live Science. They match the newly decoded DNA snippets to the reference to figure out how they fit within the genome as a whole. They also use the reference genome as a standard to pinpoint genetic variations — different versions of genes that diverge from the reference — that might be linked with health conditions.

But with a single reference mostly from one person, scientists have only a limited window of genetic diversity to study.

The first pangenome draft now doubles the number of large genome variants, known as structural variants, that scientists can detect, bringing them up to 18,000. These are places in the genome where large chunks have been deleted, inserted or rearranged. The new draft also adds 119 million new base pairs, meaning the paired “letters” that make up the DNA sequence, and 1,115 new gene duplication mutations to the previous version of the human genome.

It really is understanding and cataloging these differences between genomes that allow us to understand how cells operate and their biology and how they function, as well as understanding genetic differences and how they contribute to understanding human disease,” study co-author Karen Miga, a geneticist at the University of California, Santa Cruz, said at a press conference held May 9.

The pangenome could help scientists get a better grasp of complex conditions in which genes play an influential role, such as autism, schizophrenia, immune disorders and coronary heart disease, researchers involved with the study said at the press conference.

For example, the Lipoprotein A gene is known to be one of the biggest risk factors for coronary heart disease in African Americans, but the specific genetic changes involved are complex and poorly understood, study co-author Evan Eichler, a genomics researcher at the University of Washington in Seattle, told reporters. With the pangenome, researchers can now more thoroughly compare the variation in people with heart disease and without, and this could help clarify individuals’ risk of heart disease based on what variants of the gene they carry.

Related: As little as 1.5% of our genome is ‘uniquely human’

A diverse understanding

The current pangenome draft used data from participants in the 1000 Genomes Project, which was the first attempt to sequence genomes from a large number of people from around the world. The included participants had agreed for their genetic sequences to be anonymized and included in publicly available databases.

The new study also used advanced sequencing technology called “long-read sequencing,” as opposed to the short-read sequencing that came before. Short-read sequencing is what happens when you send your DNA to a company like 23andMe, Eichler said. Researchers read out small segments of DNA and then stitch them together into a whole. This kind of sequencing can capture a decent amount of genetic variation, but there can be poor overlap between each DNA fragment. Long-read sequencing, on the other hand, captures big segments of DNA all at once.


Humans’ big-brain genes may have come from ‘junk DNA’

Rosalind Franklin knew DNA was a helix before Watson and Crick, unpublished material reveals

Smallest genome of living creature discovered

While it’s possible to sequence a genome with short-read sequencing for about $500, long-read sequencing is still expensive, costing about $10,000 a genome, Eichler said. The price is coming down, however, and the pangenome team hopes to sequence their next batches of genomes at half that cost or less.

The researchers are working to recruit new participants to continue to fill in diversity gaps in the pangenome, study co-author Eimear Kenny, a professor of medicine and genetics at  the Institute for Genomic Health at Icahn School of Medicine at Mount Sinai in New York City, told reporters. Because genetic information is sensitive and because different rules govern data-sharing and privacy in different countries, this is delicate work. Issues include privacy, informed consent, and the possibility of discrimination based on genetic information, Kenny said.

Already, researchers are uncovering new genetic processes with the draft pangenome. In two papers published in Nature alongside the work, researchers looked at highly repetitive segments of the genome. These segments have traditionally been difficult to study, biochemist Brian McStay of the National University of Ireland Galway, told Live Science, because sequencing them via short-read technology makes it hard to understand how they fit together. The long read technology allows for long chunks of these repetitive sequences to be read at once.

The studies found that in one type of repetitive sequence, known as segmental duplications, there is a larger than expected amount of variation, potentially a mechanism for the long-term evolution of new functions for genes. In another type of repetitive sequence that is responsible for building the cellular machines that create new proteins, though, the genome stays remarkably stable. The pangenome allowed researchers to discover a potential mechanism for how these key segments of DNA stay consistent over time.

“This is just the start,” McStay said. “There will be a whole lot of new biology that will come out of this.

spacerPangenome overview. The Venn diagram showing the core genome and the ...
The first draft of a human pangenome has been published, bringing together sequences from dozens of people at once to provide a better atlas of human genetic variety Depositphotos
Pangenome overview. The Venn diagram showing the core genome and the genes specific of the strains L. pneumophila Alcoy, Philadelphia, Lens, Paris and Corby. Genes overlapping at least 70% length and 80% of similarity were considered orthologs.
Source publication
Diversity-generating retroelements (DGRs) are a unique family of retroelements that confer selective advantages to their hosts by facilitating localized DNA sequence evolution through a specialized error-prone reverse transcription process. We characterized a DGR in Legionella pneumophila, an opportunistic human pathogen that causes Legionnaires disease…


The CRISPR-Cas is an adaptive immune system composed of CRISPR arrays and Cas genes, and the types IC, IF, and IIB have been reported in Legionella [32][33][34]. The CRISPR arrays contain short palindromic repeats (repeats) and spacers that separate the repeats. …
… The repeats in CRISPR are almost identical, but the spacers are different and determine the specificity of the immune function of the CRISPR-Cas system. Previous studies have reported the CRISPR-Cas system is not present in Corby [32,35], but type IF was detected in the recently isolated Corby (ICDC) isolate, and two sets of CRISPR sequences were found to be present. Analysis of its spacers revealed abundant spacer-matched gene-encoded products, indicating that Corby (ICDC) was invaded by many kinds of bacteria, plasmids, viruses, and phages in the external environment; the major capsid protein encoded is a viral gene product, which has virus-specific antigenicity and stimulates the body to mount an antigenic viral immune response. …
Full-text available

Clostridium baratii strains are rare opportunistic pathogens associated with botulism intoxication. They have been isolated from foods, soil and be carried asymptomatically or cause botulism outbreaks. Is not taxonomically related to Clostridium botulinum, but some strains are equipped with BoNT/F7 cluster. Despite their relationship with diseases, our knowledge regarding the genomic features and phylogenetic characteristics is limited. We analyzed the pangenome of C. baratii to understand the diversity and genomic features of this species. We compared existing genomes in public databases, metagenomes, and one newly sequenced strain isolated from an asymptomatic subject. The pangenome was open, indicating it comprises genetically diverse organisms. The core genome contained 28.49% of the total genes of the pangenome. Profiling virulence factors confirmed the presence of phospholipase C in some strains, a toxin capable of disrupting eukaryotic cell membranes. Furthermore, the genomic analysis indicated significant horizontal gene transfer (HGT) events as defined by the presence of prophage genomes. Seven strains were equipped with BoNT/F7 cluster. The active site was conserved in all strains, identifying a missing 7-aa region upstream of the active site in C. baratii genomes. This analysis could be important to advance our knowledge regarding opportunistic clostridia and better understand their contribution to disease.

To begin, we systematically searched for CRISPR-Cas systems in over 600 L. pneumophila isolates (Table S1, Fig. S2A) using CRISPRCasFinder (46) and CRISPRDetect (47). Combined with previously identified systems (22,24,25,27,48), we identified a total of 13 isolates with type I-C CRISPR systems, 47 with type I-F systems, and 108 with type II-B systems. Many of these systems contain arrays with conserved spacer content and variance in spacer loss patterns and/ or 59 spacers (Table S5, I-C and I-F). …
… Red dots adjacent to each orthologous group indicate sequence similarity to known phage genes via BLASTp and/or HHpred predictions (Table S4). spacer hits are sequences matching the 5 endogenous plasmids (Paris [48], Lorraine [48], Lens [24,48], Mississauga-2006 [22], and OLDA [51]) previously described in L. pneumophila. Likewise, we observe no matches between spacers and 22 additional endogenous L. pneumophila plasmids deposited into NCBI (Table S1) or even a larger, general database of plasmid sequences (52) ( Table 1). …
Legionella pneumophila is a ubiquitous freshwater pathogen and the causative agent of Legionnaires’ disease. L. pneumophila growth within protists provides a refuge from desiccation, disinfection, and other remediation strategies. One outstanding question has been whether this protection extends to phages. L. pneumophila isolates are remarkably devoid of prophages and to date no Legionella phages have been identified. Nevertheless, many L. pneumophila isolates maintain active CRISPR-Cas defenses. So far, the only known target of these systems is an episomal element that we previously named Legionella Mobile Element-1 (LME-1). The continued expansion of publicly available genomic data promises to further our understanding of the role of these systems. We now describe over 150 CRISPR-Cas systems across 600 isolates to establish the clearest picture yet of L. pneumophila ’s adaptive defenses. By searching for targets of 1,500 unique CRISPR-Cas spacers, LME-1 remains the only identified CRISPR-Cas targeted integrative element. We identified 3 additional LME-1 variants – all targeted by previously and newly identified CRISPR-Cas spacers – but no other similar elements. Notably, we also identified several spacers with significant sequence similarity to microviruses, specifically those within the subfamily Gokushovirinae . These spacers are found across several different CRISPR-Cas arrays isolated from geographically diverse isolates, indicating recurrent encounters with these phages. Our analysis of the extended Legionella CRISPR-Cas spacer catalog leads to two main conclusions: current data argue against CRISPR-Cas targeted integrative elements beyond LME-1, and the heretofore unknown L. pneumophila phages are most likely lytic gokushoviruses. IMPORTANCE Legionnaires’ disease is an often-fatal pneumonia caused by Legionella pneumophila , which normally grows inside amoebae and other freshwater protists. L. pneumophila trades diminished access to nutrients for the protection and isolation provided by the host. One outstanding question is whether L. pneumophila is susceptible to phages, given the protection provided by its intracellular lifestyle. In this work, we use Legionella CRISPR spacer sequences as a record of phage infection to predict that the “missing” L. pneumophila phages belong to the microvirus subfamily Gokushovirinae . Gokushoviruses are known to infect another intracellular pathogen, Chlamydia . How do gokushoviruses access L. pneumophila (and Chlamydia ) inside their “cozy niches”? Does exposure to phages happen during a transient extracellular period (during cell-to-cell spread) or is it indicative of a more complicated environmental lifestyle? One thing is clear, 100 years after their discovery, phages continue to hold important secrets about the bacteria upon which they prey.
… Presently, pan-genome analyses are relevant for determining genetic variability, similarity, essential genes, functional characterization, and prediction of exclusive genes by phenotypic groups to characterize species and strains, in addition to being able to also view the discrepancies between genomes that are not perceived by conventional analyses [43]. Nowadays, there are reports of pan-genome analyses of several pathogens, such as Streptococcus agalactiae [44], Legionella pneumophila [45], Corynebacterium pseudotuberculosis [46], Pasteurella multocida [47], Pseudomonas aeruginosa [48], and Treponema pallidum [49]. …
Acinetobacter baumannii is an important Gram-negative opportunistic pathogen that is responsible for many nosocomial infections. This etiologic agent has acquired, over the years, multiple mechanisms of resistance to a wide range of antimicrobials and the ability to survive in different environments. In this context, our study aims to elucidate the resistome from the A. baumannii strains based on phylogenetic, phylogenomic, and comparative genomics analyses. In silico analysis of the complete genomes of A. baumannii strains was carried out to identify genes involved in the resistance mechanisms and the phylogenetic relationships and grouping of the strains based on the sequence type. The presence of genomic islands containing most of the resistance gene repertoire indicated high genomic plasticity, which probably enabled the acquisition of resistance genes and the formation of a robust resistome. A. baumannii displayed an open pan-genome and revealed a still constant genetic permutation among their strains. Furthermore, the resistance genes suggest a specific profile within the species throughout its evolutionary history. Moreover, the current study performed screening and characterization of the main genes present in the resistome, which can be used in applied research to develop new therapeutic methods to control this important bacterial pathogen.
… And the pan-genome analysis has revealed extensive horizontal transfer in microbial accessory genomes [7]. Pan-genome analysis has been used to study the genetic diversity of a group of related microbial genomes, including gene composition of individual strains, strain tracking, evolutionary impact, niche specialization, antimicrobial target screening, and diagnostic marker identification [5,[8][9][10][11][12][13]. Although pan-genomics is highly informative in profiling microbial diversity and function, it still has limitations. …
Advances in sequencing technology have led to the increased availability of genomes and metagenomes, which has greatly facilitated microbial pan-genome and metagenome analysis in the community. In line with this trend, studies on microbial genomes and phenotypes have gradually shifted from individuals to environmental communities. Pan-genomics and metagenomics are powerful strategies for in-depth profiling study of microbial communities. Pan-genomics focuses on genetic diversity, dynamics, and phylogeny at the multi-genome level, while metagenomics profiles the distribution and function of culture-free microbial communities in special environments. Combining pan-genome and metagenome analysis can reveal the microbial complicated connections from an individual complete genome to a mixture of genomes, thereby extending the catalog of traditional individual genomic profile to community microbial profile. Therefore, the combination of pan-genome and metagenome approaches has become a promising method to track the sources of various microbes and decipher the population-level evolution and ecosystem functions. This review summarized the pan-genome and metagenome approaches, the combined strategies of pan-genome and metagenome, and applications of these combined strategies in studies of microbial dynamics, evolution, and function in communities. We discussed emerging strategies for the study of microbial communities that integrate information in both pan-genome and metagenome. We emphasized studies in which the integrating pan-genome with metagenome approach improved the understanding of models of microbial community profile, both structural and functional. Finally, we illustrated future perspectives of microbial community profile: more advanced analytical techniques, including big-data based artificial intelligence, will lead to an even better understanding of the patterns of microbial communities.
… The importance of pangenome information arises in terms of clinical applications. Pangenomic studies have been helpful to identify drug targets in vaccines and antibacterials [50,62], to investigate pathogens in epidemic diseases [32], to detect strainspecific virulence factors [15] and to distinguish between lineage and niche-specific bacterial population [75]. Core genes are actors of basic biological processes and of the main phenotypic traits, while accessory genes concern functions that can confer selective advantages, such as environmental adaptation. …
Genes – National Geographic Society
May 20, 2022gene carries information in the sequence of its nucleotides, just as a sentence carries information in the sequence of its letters. Although most genes are made of DNA, the genes use RNA to make the proteins that are coded for in the DNA. Genes are located on threadlike structures called chromosomes in the cell nucleus.
Gene | Definition, Structure, Expression, & Facts | Britannica
Genes achieve their effects by directing the synthesis of proteins. In eukaryotes (such as animals, plants, and fungi ), genes are contained within the cell nucleus. The mitochondria (in animals) and the chloroplasts (in plants) also contain small subsets of genes distinct from the genes found in the nucleus.
Genes: Function, makeup, Human Genome Project, and research
Jul 25, 2022 Gene therapy is a medical technique that uses sections of DNA to treat or prevent a disease or medical disorder. Genes are inserted into a patient’s cells and tissues to treat a disease.
Genetics Basics | CDC – Centers for Disease Control and Prevention
Genetics research studies how individual genes or groups of genes are involved in health and disease. Understanding genetic factors and genetic disorders is important in learning more about promoting health and preventing (or causing) disease.
Genetics – National Institute of General Medical Sciences
May 4, 2022 Genetics is the scientific study of genes and heredity—of how certain qualities or traits are passed from parents to offspring as a result of changes in DNA sequence. A gene is a segment of DNA that contains instructions for building one or more molecules that help the body work. DNA is shaped like a corkscrew-twisted ladder, called a double helix.


The first draft of a human pangenome has been published, bringing together sequences from dozens of people at once to provide a better atlas of human genetic variety
Genetic testing involves examining your DNA, the chemical database that carries instructions for your body’s functions. Genetic testing can reveal changes (mutations) in your genes that may cause illness or disease. Although genetic testing can provide important information for diagnosing, treating and preventing illness, there are limitations. 
(The fact that they call DNA a chemical database tells me that they do not have a clue.  Your DNA is determined by GOD.  God can change your DNA, and even bypass it whenever He chooses.  You can affect your DNA by the things to which you put your skills, your focus, your energy and your hands.  Scientists are seeking to play GOD by changing your DNA at their will.)
When genes are close together on the same chromosome, they are said to be linked. That means the alleles, or gene versions, already together on one chromosome will be inherited as a unit more frequently than not. We can see if two genes are linked, and how tightly, by using data from genetic crosses to calculate the recombination frequency.
Jul 25, 2022 Genes do more than just determine the color of our eyes or whether we are tall or short. Genes are at the center of everything that makes us humanGenes are responsible for producing the proteins that run everything in our bodies. Some proteins are visible, such as the ones that compose our hair and skin. Others work out of sight, coordinating …
Oncogenes, Tumor Suppressor Genes, and DNA Repair Genes. Our bodies are made up of trillions of cells, which must work together to keep us healthy. Our cells need to be able to divide to make new cells to help the body grow, or to replace cells that have died. At the same time, cell growth and division need to be controlled, so the cells don …
The term ‘pangenome’ was defined with its current meaning by Tettelin et al. in 2005;[2] it derives ‘pan’ from the Greek word παν, meaning ‘whole’ or ‘everything’, while the genome is a commonly used term to describe an organism’s complete genetic material. Tettelin et al. applied the term specifically to bacteria, whose pangenome “includes a core genome containing genes present in all strains and a dispensable genome composed of genes absent from one or more strains and genes that are unique to each strain.”[2]

It’s a maze in there—and that’s a good thing.

It’s a maze in there—and that’s a good thing.© Yuichiro Chino

The project is still widely understood to be one of the most pivotal in the history of biology. But despite its momentous nature, it was limited. Most of that first human genome was built from the genetic code of one man, and you can simply only extract so much information from a sample set of one. Plus, there were gaps in the original genome, which weren’t completely filled until just last year.

So, researchers have been diligently working to expand this touchstone reference of human genomics, and today, a group of those scientists has made a huge jump forward. Through a series of published papers, the team announced that they have now synthesized almost-complete genomes from 47 individuals across a large range of racial and ethnic backgrounds.

They call it the “pangenome.”

“This complex genomic collection represents significantly more accurate human genetic diversity than has ever been captured before,” Erich Jarvis, one of the primary researchers on the project, said in a press release. “With a greater breadth and depth of genetic data at their disposal, and greater quality of genome assemblies, researchers can refine their understanding of the link between genes and disease traits, and accelerate clinical research.”

Having an understanding of the human genome built on a diverse set of information is critical if you want to understand humanity as a whole. There are genes and conditions in some racial and ethnic groups that never appear in others, and would never be able to be explored if they weren’t added to the genome. There are also genetic differences between male and female humans, which were not taken into account in the original genome and are in the pangenome.

There are also a few genome categories left out. Some cultures, specifically those of Native American and Aboriginal decent, have been reticent to relinquish their genetic material. Historically, many marginalized communities have had medical information taken from them without consent and, understandably, are not jumping at the chance to give up more now. According to an article in the New York Times, the team working on the pangenome is working with some of these groups to set up ethical guidelines around how their genetic information can, and can’t, be used. But it may be a while before some communities see themselves represented in the pangenome—if they ever do.

Still, statistically, this pangenome is a massive step forward. The new sequence shows off over 120 million never-before-seen genetic base pairs, about 90 million of which come from impactful genetic differences called structural variants. In the news release, Jarvis said that structural variants “can have dramatic effects on trait differences, disease, and gene function. With so many new ones identified, there’s going to be a lot of new discoveries that weren’t possible before.”

It’s probably going to take some time before we can access those discoveries, though. Increasing your data set by 47 times is incredibly helpful, but it also makes things more confusing to parse. The pangenome is more like a map than a GPS route, with a whole bunch of different combinations of traits you can make to get to your diagnostic destination. Figuring out how to make sure that the scientists who want to make use of this biological marvel can actually understand it is going to be a whole new, complicated, and challenging task. We have the mapnow we’re developing the key.

Once that key is developed, we’re going to see a whole new wave of genetic investigation. And as the whole project gets even bigger—the team wants to have synthesized genomes from at least 350 people by the middle of next year—we will certainly no longer be lacking in the data department. With hope of being able to probe more genetic traits and maladies than ever before, hopefully, that information converts to new discoveries in short order.


Presentation Name by lucygriffiths4 on emaze 
A very short but interesting Power Point on BIOETHICS relating to designer babies.  

Babies who have DNA from three different people born in the U.K. for the first time

In 2015, the U.K. became the first country to adopt legislation regulating methods to help prevent women with faulty mitochondria from passing defects on to their babies.
 / Source: Associated Press

LONDON — Britain’s fertility regulator on Wednesday confirmed the births of the U.K.’s first babies created using an experimental technique combining DNA from three people, an effort to prevent the children from inheriting rare genetic diseases.

The Human Fertilization and Embryology Authority said fewer than five babies have been born this way in the U.K. but did not provide further details to protect the families’ identities. The news was first reported by the Guardian newspaper.

In 2015, the U.K. became the first country to adopt legislation regulating methods to help prevent women with faulty mitochondriathe energy source in a cell from passing defects on to their babies. The world’s first baby born using the technique was reported in the U.S. in 2016.


The genetic defects can result in diseases such as muscular dystrophy, epilepsy, heart problems and intellectual disabilities. About one in 200 children in Britain is born with a mitochondrial disorder. To date, 32 patients have been authorized to receive such treatment.

For a woman with faulty mitochondria, scientists take genetic material from her egg or embryo, which is then transferred into a donor egg or embryo that still has healthy mitochondria but had the rest of its key DNA removed.

The fertilized embryo is then transferred into the womb of the mother. The genetic material from the donated egg comprises less than 1% of the child created from this technique.

“Mitochondrial donation treatment offers families with severe inherited mitochondrial illness the possibility of a healthy child,” the U.K. fertility regulator said in a statement Wednesday. The agency said it was still “early days” but it hoped the scientists involved, at Newcastle University, would soon publish details of the treatment.

Concern Growing Over IVF Treatments As States’ Abortion Laws Change

Britain requires every woman undergoing the treatment to receive approval from the Human Fertilization and Embryology Authority. The regulator says that to be eligible, families must have no other available options for avoiding passing on genetic disease.

Many critics oppose the artificial reproduction techniques, arguing there are other ways for people to avoid passing on diseases to their children, such as egg donation or screening tests, and that the experimental methods have not yet been proven safe.

Robin Lovell-Badge, a stem cell expert at the Francis Crick Institute, a biomedical research center in London, said it would be critical to monitor the babies’ future development.

“It will be interesting to know how well the (mitochondrial donation) technique worked at a practical level, whether the babies are free of mitochondrial disease and whether there is any risk of them developing problems later in life,” he said in a statement.

Scientists in Europe published research earlier this year that showed in some cases, the small number of abnormal mitochondria that are inevitably carried over from the mother’s egg to the donor’s can reproduce when the baby is in the uterus, which could ultimately lead to a genetic disease.

Lovell-Badge said the reasons for such problems were not yet understood and that researchers would need to develop methods to reduce the risk.

Previous research assessing another technique to create babies from three people, including an egg donor, found that years later the children were doing well as teenagers, with no signs of unusual health problems and good grades in school.

Doctors in the U.S. were the first to announce the world’s first baby using the mitochondria donation technique, after the treatment was conducted in Mexico.


Jun 6, 2018  On the third floor of a big Soviet-era apartment building in Kharkiv, Ukraine, the mother of one of the world’s first babies created with DNA from three different people cracks open her door

Doctors at the Nadiya Clinic in Kiev, which created her baby, arranged for Tamara to become the first mother of a “three-parent baby” to give an interview to a journalist..

Doctors there told her about something new. “They showed us pictures for how many genes the child would have” from the three parents, she says.

The doctors would fertilize one of her eggs with her husband’s sperm. Next, they would use her husband’s sperm to fertilize an egg from another woman paid to donate eggs. And then the scientists would remove most of the DNA from the other woman’s fertilized egg, and replace it with Tamara’s and her husband’s.

My first reaction was: ‘Whoa! How [has] science got so far?’ ” she says. “It’s unbelievable that they can make such a stuff. It’s wonderful and unbelievable.”

Tamara is one of four women at the Nadiya Clinic who have given birth this way, according to Dr. Valery Zukin, who heads the clinic. Three more women are pregnant, including a woman from Sweden, he says.

Ukrainian women pay about $8,000 to the Nadiya Clinic for the procedure. The clinic is charging women from other countries about $15,000. And the clinic has partnered with the New York clinic to market the procedure to U.S. women.

“I had no doubts,” Tamara says. “We had no doubts. I wanted a child so hard that I didn’t care about how … experimental the procedure would be.”

“I’m so excited. I have a child. And he’s so beautiful. He smiles to me. He’s so cute. He’s so smart. He looks like my mom,” she says.

She is just thrilled to have a baby. “In my point of view, if you can fix something you should fix it,” she says.

While Tamara is thrilled with the outcome, there are big worries about the procedure and its long-term effects. The biggest one: Is it safe? Her son seems perfectly healthy so far. But who knows what might show up months or years from now? Where might routine use of this method lead?

Pronuclear Transfer by Nadiya Clinic

The procedure also raises deeper questions.

What is the importance of the contribution of mitochondrial DNA from a stranger? Philosophically it’s an interesting question,” Kahn says. “It changes your ancestry in a way.”

But that’s not the only concern. The egg donor’s mitochondrial DNA could be passed down by any girls born from the procedure. So any problems inadvertently created could be passed down for generations too.

That’s crossing what had been a bright-line prohibition all across the globe that we would not introduce genetic modifications that would be passed on to future offspring in perpetuity,” Kahn says.

In fact, one of the four babies produced so far with the help of the clinic was a girl, Zukin says.


So, basically, Scientists are claiming that they are smarter than GOD and can do much better at forming and shaping the future of humanity.  Based on what we have seen come out of the Scientific community, I would not trust them for anything.  I prefer that my life and everything about it be in God’s hands. But, Science seeks to rule out that possibility, and deny us the right to choose.

In fact, scientists in Sweden recently began using a powerful genetic cut-and-paste tool known as CRISPR to edit healthy embryos. Those researchers did not let the embryos mature past an early stage of development, but similar techniques could, in theory, be used to design babies that have particular traits. [Controversial Human Embryo Editing: 5 Things to Know]

A separate debate surrounds the safety of fiddling with mitochondrial DNA. Proponents say the technique allows families to avoid passing on deadly conditions to their children.

But mitochondrial DNA is passed from a mother to her children, and her female children will then go on and pass that genetic material to their children. Therefore, creating these hybrid embryos involves deliberately altering the human lineage. Critics have said that the technique has not been sufficiently tested to ensure its safety and that the procedure could add new diseases to the human germ line.

“We know fiddling with mitochondrial DNA may make a massive difference to what happens to nuclear DNA,” Lord Robert Winston, a professor of science and society and a fertility expert at Imperial College Londonpreviously told Live Science. “Abnormal children have been born as result of mitochondrial transfer. … I think, in preventing one genetic disease, you are likely to cause another genetic disease.


Updated on: September 28, 2016 / 8:45 AM / CBS News.In what experts are calling a “revolutionary” medical event, the first baby with DNA from three parents has been born.

The little boy, now nearly six months old, was conceived using a controversial technique meant to help people who carry genes for fatal rare diseases. The procedure received widespread media attention when lawmakers in the U.K. became the first to approve its use last year. It is not approved in the U.S.

As first reported in New Scientist, the baby was born on April 6, 2016 and doctors say he appears healthy. His parents were treated by U.S. fertility specialists in Mexico, where there are no laws prohibiting such methods. His mother carries a genetic mutation for Leigh syndrome, a rare neurological disorder that usually becomes apparent in the first year of life and is generally fatal.

“This mitochondrial disease is usually a very devastating situation for the babies and the family,” Zhang told CBS News.

He opted to try the three-parent IVF technique to ensure that the disease mutation would not be passed along to the baby.

This is the very first time at least in human reproduction that the offspring are produced with three parties – one sperm and different parts of two eggs,” Zhang said. “So this is very revolutionary.”

“If you look at the amount of DNA, it’s almost like it’s 2.001 parents rather than three. But it’s DNA from three different people,” CBS News medical contributor Dr. David Agus noted on “CBS This Morning” Wednesday.

May 10, 2023 The first three-parent babies were born in the 1990s and early 2000s, the products of a then-novel IVF-based technique known as ooplasmic transfer (cytoplasmic transfer). The success of the technique was seen as miraculous, but its use was controversial. It prompted scientists to develop improved techniques and caused regulatory agencies to restrict the use of three-parent IVF. In 2015, following extensive review, MRT was legalized in the United Kingdom for the purpose of preventing genetic disease. The following year a medical scientist in the United States reported the birth of the first three-parent baby produced using MRT; the procedure was carried out in Mexico in order to bypass U.S. regulations. The development was again greeted with excitement and controversy. Much was unknown about the safety of various three-parent IVF techniques, and their use to generate human babies raised ethical and social concerns, among them the possible impacts on health and heredity.
In 2017, the year following the birth of the first baby born using MRT, medical scientists in Ukraine reported the birth of two babies from MRT. The technique has since been applied to treat infertility and genetic diseases in other countries, including Greece. Long-term studies to assess the health of three-parent babies born using MRT are ongoing.