Gene 320

454 Life Sciences SEQUENCING-POPULAR TODAY

--• 1 Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA. • 454 Life Sciences, is a biotechnology company based in Branford, Connecticut It is a subsidiary of Roche and specializes in high-throughput DNA sequencing. Jim project: Led to the identification of 3.3 million 3 type polymorphisms that make up phenotype functional differences 1) single nucleotide polymorphisms, of which 10,654 cause amino-acid substitution within the coding sequence. 2) insertions and deletions ( INS/indal) In addition, we accurately identified smallscale (2-40,000 base pair (bp)) insertion and deletion polymorphismas well as (generated throughout human genome) 3) copy number variation resulting in the large-scale gain and loss of chromosomal segments ranging from 26,000 to1.5 million bas - within population, noraml variation that occur to give phenotypic changes The first nearly complete human genomes sequenced were J. Craig Venter Caucasian at 7.5-fold average coverage) and James Watson(Caucasian male at 7.4- fold)a Han Chinese (YH at 36-fold), a Yoruban from Nigeria (at 30-fold),a female leukemia patient (at 33 and 14-fold coverage for tumor and normal tissues),and Seong-Jin Kim (Korean at 29-fold).[13] Other full genomes have been sequenced but not published, and as of June 2009, commercialization of full genome sequencing is in an early stage and growing rapidly . james watson- first person with genome sequenced and published *3.3 mil single nucleotide polymorphism between people (snip are gentic basis of who you are)

Meiosis Cellular Stages:

-Meiosis 1 AKA Reduction Division: -Prophase I: is long with 5 steps. To produce VARIATION homologous chromosome exchange genetic material in the 3rd step (Pachytene) via chromosome non sister chromatid crossover and exchange in a region called "Synaptonemal complex (SC)" assembled in 2nd step called (Zygotene). The site of exchange is called chiasma. In sex chromosomes exchange happens only in two pseudo autosomal regions called PAR1 and PAR 2 present in both X and Y chromosome Prometaphase I: Nucleolus disappear and nuclear membrane degrade, meotic spindle fibers start to form. Metaphase 1: Spindle fibers pull the condensed homologous chromosome pair (with exchanged genetic material towards the poles. The centromere is not divided. - 2 particles that come at periphery of cell and start sending spindle fibers that attach at centromere. nucleosomes formed in cytoplasm and bind spindle at the core of centromere * centrosome in cytoplasm that sends spindle fibers into the centromere which is in the chromosome Anaphase: The homologous moves to the poles Telophase 1: The homologous chromosomes are separated into 2 daughter cells via cytokinesis the pinching or inundation of cell membrane takes place to give two daughter cells. The cytoplasm and organelles are shared among the two daughter cells. Reminder: 4C has become 2C egg at this stage.

Quickly reduced Cost

0.00003 cents/bp 24 hours, 750$/Genome (30X= gold standard) HiSeq X (Illumina) Ten just one machine will therefore be capable of sequencing 18,000 human genomes per year insurance pays for it and in a short time all human genomes will be sequences ( ethical and legal issues not technical issues)

Genes in PAR and adjoining regions and Mutation and Consequences:

1) SHOX (short stature homeo box) gene: Height variation normal, mutation= dwarfism ( X and Y) 2) SRY gene (male determining region Y) borders PAR1 region (Y ). When SRY from Y crossed over (small translocation) to X results in 46, XX male and XY female when Y losses SRY region phenotypes. In X the homolog is SRY like HMG box 3 (X and Y); homolog of SRY but not sex determining. *male determining gene Deletions or mutations of the human SRY gene occur in about 15% to 20% of 46,XY females with complete XY gonadal dysgenesis and 90% of 46,XX males have a Y to X translocation which includes the SRY gene SOX9 Gene in chr: 17q has 60% homology to SRY, works downstream of SRY and is involved in testicular development and mutations may cause ambiguous genitalia in 46XY ( even with functioning SRY). - interacts with sry - absence of sox9 ambiguous male genitalia 3) PAR 1 del cause Turners stigmata (X and Y) 4) GCY (Growth control gene on the Y chromosome): (Y) 5) TSPY (testes-specific protein Y coded) Mutation leads to testicular malformation and gonadoblastoma (Y) ** only present in males 6) DAZ deleted in azoospermia ( absence sperm Y)

CHROMOSOMAL ABNORMALITIES A.NUMERICAL:

1. PLOIDY: Abnormal # of Chr. Set (haploid set) Major developmental Defects and early embryonic death. - whole set of chromosomes 2. TRIPLOIDY: three sets (69 chr.). 80% of the times due to dispermy (one egg fertilized by two sperms), and 20% of the times due to diploid gamete. This accounts for 1% of recognized human conception. - - 80% due to disperm, 20% due to diploid gamete 3. TETRAPLOIDY: 4 sets (92 chr.): failure of first mitotic division in a normal diploid zygote. - early zygote failure of first mitotic division 4.ANEUPLOIDY: less than a whole set of chromosomes. a. Monosomy: one copy of a chromosome, autosomal not seen in human conception, lethal at pre-implantation stage. Monosomy X 1% (turner syndrome) survive, 99% lost in early gestation. b. Turner's Syndrome: ? Mixo-ploidy. XO\XX. X got deleted c. Trisomy: three copies of a chromosome, has been observed for all chr. in human conception. Most cause early embryonic death. 25% of all spontaneous abortion have trisomy. d. Trisomy 16 most common at conception 1%, 16 and 19 not found in live birth. because gene rich e. Full term trisomies: Chrms:13,18,21,13 and 18 lethal within few months because gene poor . f. Aneuploidy for the sex chromosome: No major developmental defects, mean IQ lower. g. Have y (whate ver # of X chr.) male phenotype, male gonadal developmental occurs, but leads to testicular dysfunction and infertility. h. XXY and XXXY Males with testicular dysfunction. XXX normally fertile females.

The Three Chronic Health Conditions that afflict Humanity

1: Cancer 2: Neurodegenerative and neuropsychiatric disorders 3: Cardiovascular Conditions *basis of most costly human expenditure in health because of 3 conditions - we have phenotypes of disease but also genomic basis of disease in post-genomic era helps to develop precision medicine (specific based on genomic understanding of individual and disease with min side effects), better drugs and targeted therapy How do we predict and thus postpone ? Answer to "Health Cost" covid-19- societal rather than a biological issue

'Crispr' Science: Newer Genome Editing Tool Shows Promise in Engineering Human Stem Cells

A powerful "genome editing" technology known as CRISPR has been used by researchers since 2012 to trim, disrupt, replace or add to sequences of an organism's DNA. -microbial immune system and is the way the bacteria chews up phages and viruses when they try to integrate into genome and kill bacteria - small pice of bacteria that tags and kill invader and keeps small piece to use next time - sue tagging mechanism in changing, adding and removing nucelotides "Stem cell technology is quickly advancing, and we think that the days when we can use iPSCs for human therapy aren't that far away," "This is one of the first studies to detail the use of CRISPR in human iPSCs, showcasing its potential in these cells." CRISPR originated from a microbial immune system that contains DNA segments known as clustered regularly interspaced short palindromic repeats. The engineered editing system makes use of an enzyme that nicks together DNA with a piece of small RNA that guides the tool to where researchers want to introduce cuts or other changes in the genome. In July 2019, CRISPR was used to experimentally treat a patient with a genetic disorder. The patient was a 34-year-old woman with sickle cell disease. In March 2020, CRISPR-modified virus was injected into a patient's eye in an attempt to treat Leber congenital amaurosis In the future, CRISPR gene editing could potentially be used to create new species or revive extinct species from closely related ones. CRISPR-based re-evaluations of claims for gene-disease relationships have led to the discovery of potentially important anomalies. Dr He in 2017 altered CCR5 gene in embryos, 2 girls born in 2018 October, the two girls are 2yrs now whats your opinion on what is going on in the crsiper field? - have manipulated embryos - 2 4 year olds in China who have had thei genome changed to prevent AIDS - CCR5 is also in the brain and highly expressed so it has a function which is memory. - everything in genome is linked so you fix one gene and it causes changes in other parts that the gene is expressed in -use gene therapy less because able to biochemically change geneome, particularly CF mutation

MODEL FOR cc RESEARCH

A. The Phenotype of wild-type fission yeast cells; divide rapidly B. Xenopus early development; develop rapidly done most with fast-dividing cells model selection is so important rapid division amendable to chemo

Remember one choice of a cell... a D called Death... an Overview

Apoptosis: A form of cell death in which a programmed sequence of events leads to the elimination of cells without releasing harmful substances into the surrounding area. - p53 controls cell division and mediates cells with lots of dna damage by triggering apoptosis - extrinsic ( P53 stimulates->FAS ligand or death ligand-> FAS-> FADD-> proteolytic enzymes called procaspases 8/10 ( dormant in cell before) or intrinsic ( dna damage by growth factor withdrawal, chemotherapy, X-ray, radiation; BCL2 activate procaspases and stimulate apoptosis). Apoptosis- plays a crucial role in developing and maintaining the health of the body by eliminating old cells, unnecessary cells, and unhealthy cell The coordinated elimination of large populations of cells can provide a means to sculpt tissues without affecting neighboring cells, as shown here for the vertebrate limb & tadpole tail Cellular process: -DNA fragmentation; tagged for death and fragments -Proteolytic cleavage leading to apoptotic bodies- procaspases - Macrophage based engulfing and clean up- recycle parts

Cell Cycle and Circadian Rhythm

Cell Cycle (CC): About 24 hrs: Cell Division and Distribution A circadian rhythm (CR) is any physiological process that displays an oscillation of about 24 hours. These 24-hour rhythms are driven by a circadian clock (hypothalamus brain and neuroendocrine systems and gene regulation of the target genes in the cells of the organs. At the cell level CR and CC cells interact and regulate and cooperate to get CC and CR synchronized . Eg: Preferential S stage in late evenings and night to avoid UV mutations cycle with the sun a cell cycle/replication happens once very 24 hours - happens post sunset and thats why we need to sleep at memory and cellular level - dna replication and repair happening in evening and night - how does body know sunset has happened? certain genes that are cycling based on sunlight available ( circadian genes because rhythmically expressed based on sunlight ) - stimulate downstream porteins - as night time comes these enzymes start a feedback loop to dec amount ( increased during the day) ex; melatonin - interact with cyclin and tumor suppressor gene which then controls cell cycle - gives a feedback loop to start replication at certain times - they are regulated by hypothalamus in endoneurocrine system

Cell DIVISION through Cell CYCLE

Cell Cycle= 4 stages synthesis- DNA duplication/replication Mitotic- synthesize DNA G2- allows for protein synthesis G1- protein synthesis The life cycle of eukaryotic cells can generally be divided into four stages and a typical cell cycle is shown in Figure. When a cell is produced through fertilization or cell division, there is usually a lag before it undergoes DNA synthesis (replication S phase). This lag period is called Gap 1 (G1 ), Ends with the onset of the DNA synthesis (S) phase, during which each chromosome is replicated. Following replication, there may be another lag, called Gap 2 (G2 ), before mitosis (M). Some cells never leave G1 phase, and are said to enter a permanent, non-dividing stage called G0 , Differentiate and Function. Interphase is as term used to include those phases of the cell cycle excluding mitosis and meiosis, they may move from G0 back to G1 cycling when needed some more than others! ? On the other hand, some cells undergo many rounds of DNA synthesis (S) without any mitosis or cell division, leading to endoreduplication ( cell go through synthesis and no mitosis- where chromosomal aberrations may occur and when that cell is fused that particular feature will be spontaneous ). Understanding the control of the cell cycle is an active area of research, particularly because of the relationship between cell division and cancer

CGH: QUANTITATIVE

Comparative genomic hybridization (CGH) is a molecular cytogenetic method for analysing copy number variations (CNVs) relative to ploidy level in the DNA of a test sample compared to a reference sample, without the need for culturing cells. The aim of this technique is to quickly and efficiently compare two genomic DNA samples arising from two sources, which are most often closely related, because it is suspected that they contain differences in terms of either gains or losses of either whole chromosomes or subchromosomal regions (a portion of a whole chromosome). Quantitative evaluation of DNA, no need of metaphase plate, just need DNA. copy number changes - extra pieces or deletion - CGH v SKY which is qualitative - cancer to label in one v normal in other color

SEX CHROMOSOMES AND MEIOSIS

DNA packaged in heterochromatin, such as the Xi, is more condensed than DNA packaged in euchromatin, such as the Xa. The inactive X forms a discrete body within the nucleus called a Barr body. The Barr body is generally located on the periphery of the nucleus is late replicating within the cell cycle, and, as it contains the Xi, contains heterochromatin modifications and the Xist RNA. Barr body: inactive X condensed at nucl.membrane interphase. - late replicating chromosome looks like condensed when stained ( barr body) - barr body has an extra X (inactive and active X) - late replicating X, three X have 2 barr bodies * no barr bodies in males ◼n-1 (n=# of X chromosomes ◼XO Turners and males = 0 ◼XXX= 2 bar bodies ◼XXY Klienfielter =1 Xi: Highly methylated, low level of acetylation • Sex Chromosome in Meiosis: • X (165 Mb and 1000 genes) and Y (60MB, 178 transcribed units) dimorphic Pseudo autosomal region PAR1 and PAR2: X over. Pseudo autosomal regions: a small region of homology between (distal/top and distal bottom region of X and Y) pair in meiosis and crossing over happens here. For proper segregation to occur in meiosis. . In females one X inactivated, early embryonic life, at random ie maternal and paternal. This part of X chromosome ESCAPES INACTIVATION and Y chromosomes which is mostly heterochromatin ie tightly condensed and inactive in other parts but is open and active with euchromatin ie active genes in PARs -light band =active gene Y chromosome has degraded in time. Comparisons between sex chromosomes in many taxa show that once a new sex-determining region has been established on a proto-Y recombination takes place here over millions of years the rest unstable invaded by repetitive elements and deleted. -degradation of repeats but SRY is stable ( loss would loose males) - Y chromosome is degraded and PAR regions are always conserved Both X (5 fold excess of intelligence determining genes, selection peacock tail? in X from mom than dad) and Y have sex determining genes, intelligence and height! - ex; turner syndrome (height) -male peacock has beautiful feather, intelligennce of evolutionary selection happens from female and selects males for reproduction X and Y are dimorphic and during meiosis have to be connected by chaiasma or would be lost - msut split at right time during anaphase - 2 regions in X and Y chromosomal called pseudoautosomal because have expressed gene and inactive X females 1000 genes in X and males 178 transcript units of Y - pseudoautosomal region itself has 24 genes in PAR1 and 4 in PAR2 both in X and Y happens in and beacause ofpseudoautosomal region

Birth Defects

DiGeorge Syndrome aka 22q del syndrome. Both linkage and association studies of people with schizophrenia (25%) have implicated several susceptibility genes, of which three are in the 22q11.2 region; catechol‐o‐methyltransferase (COMT) neurotransmitter, proline dehydrogenase (PRODH), and Gnb1L (Gtpase) (energy). In addition, variation in Gnb1L is associated with the presence of psychosis in males with 22q11. - particular phenotype so you see in neonatal will know exactly what it is (high load of schizoprenia) - identify exact region with FISH DiGeorge is good natural model to study Schizophrenia in population - genes involved in neural development and transmission - Gnb1L- brain, NT, menopause, 25% energy - changes in this particular enzyme, not enough deletion syndrome at chromosome 22 ( del 22 q11.2) 11.2 region deleted. - consistant phenotype cytogenetics is a window into common diseases; can identify common causes of diseases that are widely present in population

STRUCTURE of CELL

Dna- nuclear membrane, eukaryotes - nucleoplasm- ribsomes -nuclear pore- where mRNA is sent out centrosomes- in cytoplasm that puts out spindle fibers and attach to centromere chromosomes- where centromere mitochondria- atp generation ribosomes- protein syn thesis ER- proteins syn, rough ER ( ribosomes), smooth ER, golgi ( packaging or post office that modified protein and post translational modifcation and sends to other parts of the cell) lysosome and perioxisomes- encapsulated where long chain FA etc are digested ( recycling for reabsorption)

I S C N (1995) (An International System for Human Cytogenetic Nomenclature)

Editor: Felix Mitelman Recommendations of the International standing committee on Human Cytogenetic Nomenclature Published in collaboration with Cytogenetics and Cell genetics - arrange karyotype from chromosome 1-23, X and Y - size and centrosome position and banding pattern

genetics

Evil spirits to Bacteria and viruses to Antibiotics to disease in the (woman to (WO)MAN in the Disease (Genomic basis of Disease) -in beginning no knowledge of disease or how it starts - at that point we depended on spirits and imagination to come to conclusions - disease that came were caused by evil spirit and later realized it was bacteria and viruses that cause diseases and other microbial agents like antibiotics and drugs that work against infections - we knew a lot of phenotypes (fever, toxicity, failure of organs) of diseases and in 1960-70 realized there is another element which is the genetic part and not just the environment. how we react, genetic or genomic basis of particular interaction of human and environment. why some get sick and others dont or certain species are affected and others arent? (asthma, allergies, cancer, etc) *more to human health that we should know the other side, black box, or genome- something in genome that interacts with environment that makes people more resistant and susceptible-> how genome project started - now in post-genomic era; not just disease in man or women but also the man and woman in disease ( genome of man or woman that are exposed are just as important as the genome of infectious agents)** Three reason of explosive growth 1. Exponential Technology 2. Interactive Technology (visualization and genomic interaction) 3. Cost of Technology decreased drastically (Murphy's Law) we are in a process of learning ( human experienced) and we have a concious and we constantly update our knowledge and info. memory bank that we build in grey matter to record messages over time came from a place of ignorance - evolutionary change of humans from basic ignorance to knowledge and date *ignorance->observation->information - what becomes meaningful; patterns, life experience (knowledge->wisdom) -transcendce knowledge- looking at life from global concious *wisdom and transcedence are philosophical

MEIOSIS OOCYTES FROM YOUNGER AND OLDER WOMEN

Figure illustrating what may be the physical basis of the maternal age effect. The microtubules of the spindle stain green, and the chromosomes stain orange.

omic terms

Genome is the genetic material of an organism. It consists of DNA (or RNA in RNA viruses. The genome includes both the genes and the non-coding sequences of the DNA/RNA Functional genomics is a field of molecular biology that describe gene and protein functions and interactions. Unlike genomics , functional genomics focuses on the dynamic aspects such as gene transcription, translation, regulation of gene expression and protein-protein interactions, as opposed to the static aspects of the genomic information such as DNA sequence or structures -dynamic aspect of interaction of mRNA or proteins that come together in transcription or translation process that regulation of a particular gene -protein protein gene protein interaction -functional genes, how substrates come together to forma. specific function -functional endpoint of all genes to come together to a specific cellular endpoint An epigenome consists of a record of the chemical changes to the DNA and histone (transcription and translation) proteins of an organism * chemical markers; these changes can be passed down to an organism's offspring. Changes to the epigenome can result in changes to the structure of chromatin and changes to the function of the genome.The epigenome is involved in regulating gene expression, development, tissue differentiation, and suppression of transposable elements. Unlike the underlying genome which is largely static within an individual, the epigenome can be dynamically altered by environmental conditions. - epigenome are chemical tags to turn on or off to form particular prtoien; added to DNA or histones - important in development from single cell into multicellular organisms -*easily altered by environmental factors; easily malleable by the environment transcriptomics- common, costly and tissue specific The exome is the part of the genome formed by exons, the sequences which when transcribed remain within the mature RNA after introns are removed by RNA splicing. It consists of all DNA that is transcribed into mature RNA in cells of any type as distinct from the *species specific transcriptome, which is the RNA that has been transcribed only in a specific cell population. The exome (nonspecific to a particular cell type) of the human cell consists of roughly 180,000 exons constituting about 1% of the total genome, or about 30 megabases of DNA *tissue specific. The proteome is the entire set of proteins expressed by a genome, cell, tissue or organism at a certain time. Phenome (vague?) is the set of all phenotypes expressed by a cell, tissue, organ, organism, or species -starts whole organism down to substrates; need to better define this rather than contextual meaning it has now A connectome is a comprehensive map of neural connections in the brain, and may be thought of as its "wiring diagram". More broadly, a connectome would include the mapping of all neural connections within an organism 's nervous system. Research has successfully constructed the full connectome of one animal: the roundworm C. elegans.. (Obama's "Brain project": 2015-2025= 6 billion).The ultimate goal of connectomics is to map the human brain. This effort is pursued by the Human Connectome Project, sponsored by the National Institutes of Health, whose focus is to build a network map of the human brain in healthy, living adults. - hard because of fatty content, so can dissolve fatty and leave skeleton and get a wiring diagram -neuropsych conditions, neuron degenerative and death based diseases -tracts= neural network and what is disturbed in certain conditions An interactome is the whole set of molecular interactions in a particular cell. The term specifically refers to physical interactions among molecules (such as those among proteins, also known as protein-protein interactions but can also describe sets of indirect interactions among genes genetic interactions. Mathematically, interactomes are generally displayed as graphs -mathematical concept of milllions of interactions and chemicals in a cell The kinome of an organism is the set of protein kinases in its genome. Kinases are enzymes that catalyze phosphorylation reactions (of amino acids) and fall into several groups and families, e.g., those that phosphorylate the amino acids serine and threonine, those that phosphorylate tyrosine and some that can phosphorylate both. Kinases are work horse of the cell and maintain "functional status" of the cell. -activate enzyme or proteins - how they interact will give a functional element on how the cell is behaving - in cancer can stop cell evolution and growth - antibiotics are developed based off of understanding of kinome Metagenomics is the study of genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. The lipidome refers to the totality of lipids in cells - biological material in sample, bacteria survive in communities - kill one set others will die Pharmacogenome: The effect of changes on the genome on the basis of pharmacology ie drug reaction to the cell, organ or organism - dosage, or what drugs based on how we metabolize Transcriptome is the set of all messenger RNA molecules in one cell or a population of cells. It differs from the exome in that it includes introns ie the total RNA, it also refers only those RNA molecules found in a specified cell population, and usually includes the amount or concentration of each RNA molecule in addition to the molecular identities.! IMPORTNT IN INDIVIDUALIZED PRECISION MEDICINE - tissue specific, all mRNA in tissue, certain cell populations - important tool in individualized medicine

Over View of Cell Cycle

Growth Phase1: Cellular content grows and doubles, and RNA and Protein for DNA Synthesis Machinery . G1 check point : Checks for DNA Integrity-Mutation Nutrient, Growth factors Cell size S: Synthesis ...DNA Doubles. S check point: Integrity-Mutation and DNA content - hour Growth Phase 2: Grows further and RNA and Protein for Mitosis Cell Division Machinery - 5-6 hours G2 Check point: Checks for DNA integrity duplication is complete, Enters G0. Can renter into CC or differentiate based on stimulus or signals it receives - 3-4 hours each stage has transition that it must go through - for it to happen there are checkpoints to make sure it is ready for next phase ( G1, G2 and pre-Mitosis checkpoints) - restriction point; late G1 checkpoint before synthesis problems with post-mitotic neuronal cell they will die and cause neurodegeneration like alzheimers and parkinsons - lost of regulation of pre-mitotic epithelila cells leads to cancer transition takes place because of a particular event between to players called cyclins and cyclin-dependent kinase ( basis for transitions) - adding and removing ( reversible) phosphorylation are regulated because cause diseases if unregulated - inhibitors, transcription factors brought in by intracellular compartmentalization

Targted therapy example...

Hypothesis of overcoming the resistance to cancer treatment by the inhibition of different signaling pathways involved in non-small cell lung cancer (NSCLC) tumor growth by a multi-drug regimen of targeted therapy drugs. Intracellular signaling pathways activated by VEGFR, EGFR, CXCR4 and E-prostanoid receptors (EP) in tumor cells and in endothelial cells found to be involved in NSCLC tumor growth and maintenance are shown. Crosstalk mechanisms between several of these pathways leading to resistance against singleagent targeted therapies alone or in combination with chemotherapeutics. Multiple inhibition of intracellular connected pathways may overcome the tumor insensitivity for targeted therapies. Targeted therapy drugs such as sunitinib, gefitinib, etoricoxib and plerixafor are clinically evaluated and FDA approved. PGE2, prostaglandin E2; VEGFR, vascular endothelial growth factor receptor; EGFR, epidermal growth factor receptor; COX2, cyclooxygenase 2. genomic basis of understanding disease - how targeted therapy works n cancer - sample sent to companies to sequence genome and physician has a direct prescription that isnt random but based upon signaling changes that is targeted therapy - several drugs and antibodies - different signaling mechanisms and this specific drug works on this mutation and found through transcriptomics - COX2 prostiglandins- inflammation better treatment and longer life expectancy because of study of sigaling mechanism and changes and use of targeted combination therapy personalized cancer therapy- molecular profiling, trancriptomic, diagnositc and predicitive markers, toxic side effects of drugs in the individual - specifically targeting based on individual and molecular changes we want to manipulate to bring to normal

MITOSIS-SOMATIC CELLS

IN NATURE IT IS A CONTINOUS PROCESS • These basic events of mitosis include , nuclear membrane break down chromosome condensation, formation of the mitotic spindle, and attachment of chromosomes to the spindle microtubules. Sister chromatids then separate from each other and move to opposite poles of the spindle, followed by the formation of daughter nuclei and nuclear membrane and cytoplasm divides. • MPF-mitosis promoting factor (a protein kinase (Cdc2/cyclin B). Triggers APF - combination of a cycling protein ( cell cycle) and protein kinase that phosphorylates cyclin B/CdC2 which is called mitosis promotion factor ( these two together are necessary part of mitosis and trigger mitosis and once it is triggered it will trigger downstream factor protein APF) * more active in prophase • APF: anaphase promoting factor a ubiquitin ligase degrades cyclin B promotes cytokinesis - much more active in anaphase - promoting factor must be degraded so tags Ub that degrades cyclin B and anaphase is allowed to occur **cascade of proteins that will be formed, sometimes multimeric proteins, and do job in particular phase and then degrades next protein coming in ( see in cancer and other diseases; those proteins that have to be degraded arent degraded because of mutations or what not) G2- nuclear membrane, sister chromatid, centromere and replicated. DNA after synthesis you have 4C content ( twice amount DNA content of a diploid cell) -spindle fibers appear nucleosome and attach to the centromere and chromosomes condense and aligned with spindle fibers. centromere divided into two sister chromatid and separates in anaphase, alignment metaphase, telophase where nuclear membrane reform and spindle fibers disappear, and cytokinesis where the cytoplasm divided with equal number of organelles one ach ** happens after g2 phase with 4C-> 2C in mitosis

CANCER GENETICS: FISH

INTERPHASE NUCLEI OF A CHILDHOOD HEPATIC CANCER (HEPATOBLASTOMA) WITH A FLUORESCENT DNA PROBE THAT HYBRIDIZES TO CHROMOSOME 20. UNDER ULTRAVIOLET LIGHT EACH NUCLEUS REVEALS THREE BRIGHT YELLOW FLUORESCENT DOTS REPRESENTING THREE COPIES OF CHROMOSOME 20. NORMAL DIPLOID CELLS HAVE TWO FLUORESCENT DOTS copy number changes because cancer genome is unstable -lots of deletions and additions on chromosomal level at genome mutation level - multiple copies of chromosomes -look only at middle of cell - breast cancer- many genes are amplified

Genetics Of Meoisis in Females:

In females meiosis (of the egg/ovule) is initiated in the 3 month old developing fetus and is **arrested at about 9th month of fetal development at the diplotene stage specifically known as dictoyene stage. At puberty meiosis is reinitiated from this arrest and goes through completion of Meiosis 1 shedding the first polar body with 2C. This process is called Folliculogenesis, since the egg goes through meiosis within a nest of surrounding cells called follicular cell. Now the 2C egg is shed from the follicle and is ready for fertilization by the sperm. If fertilization occurs (this happens in the fallopian tube) Meiosis 2 occurs and the 2C egg has now 1C (the second polar body with (haploid) set and gets a complement haploid set of 1C from sperm. The fertilized egg aka zygote (2C) moves from the fallopian tube to the body of uterus to be implanted and for cell divisions and differentiation occur to form a developing fetus. The second polar body most of time divides and thus a total of 3 polar bodies are formed and all of them get degraded. If the egg is not fertilized the egg and follicules are degraded and shed during menstruation.

X Inactivation:

Inactivation: transcribed from In-active X, Xist gene-regulatory RNA, initiates condensation. X inactivation (also called lyonization) is a process by which one of the copies of the X chromosome present in female mammals is inactivated. The inactive X chromosome is silenced by it being packaged in such a way that it has a transcriptionally inactive structure called heterochromatin. As nearly all female mammals have two X chromosomes, X-inactivation prevents them from having twice as many X chromosome gene products as males, who only possess a single copy of the X chromosome (dosage compensation) Molecular Basis: The X-inactive specific transcript (Xist; particular rna from inactive rna which is a non coding non translating rna) gene encodes a large non-coding RNA (17 kb) ie that is responsible for mediating the specific silencing of the X chromosome from which it is transcribed. The inactive Xi chromosome is coated by Xist RNA whereas the active X or Xa is not. X chromosomes that lack the Xist gene cannot be inactivated Prior to inactivation, both X chromosomes weakly express Xist RNA from the Xist gene. During the inactivation process, the future Xa ceases to express Xist, whereas the future Xi dramatically increases Xist RNA production. The silencing of genes along the Xi occurs soon after coating by Xist RNA -Xi amplifies and binds to Xist and condenses chromosome and completely shuts it down The Xist RNA gene lies within the X-Inactivation Centre (XIC), which plays a major role in Xist expression and X inactivation. There are other genes in XIC region such as Tsix an antisense of Xist that play a role in X chromosome inactivation via methylation and hypoacetylation. -curious complex structure and folds inactive X - starts nearby then spread to distant regions The XIC is located on the q arm of the X chromosome (Xq13). Xist RNA has complex structure, 8 conserved repeat sequences and NOT TRANSLATED Three-dimensional spreading model of Xist localization. Xist might use closeproximity sites for its initial spreading (left and middle panels) before accumulating over the whole chromosome. At the final stages of spreading, Xist shows the highest enrichment at gene-rich regions. - starts at inactivation center and spreads out - high enrichment of transcript binding to gene rich regions

An example NEUROGENOMICS:

JOURNEY FROM COGNITION BRAIN TO GENE PERSPECTIVES FROM WILLIAMS SYNDROME EDITED BYURSULA BELLUGI & MARIE ST.GEORGE Using Williams syndrome as a model, leading researchers in neurocognition, neurophysiology, neuroanatomy, and molecular genetics have been building bridges between disciplines to link higher cognitive functions, their underlying neurobiological bases, and their molecular genetic underpinnings. This book presents the work of a team of scientists who have been using just such as multidisciplinary, integrated approach to link genes with human behavior. One of the books many strengths is that the scientists from each discipline studied the same individuals. Williams syndromeis a fascinating disorder because it produces "peaks and valleys" among cognitive domains; severe intellectual deficits but remarkably spared, indeed effusive language; specific impairment in spatial construction but great strength in face processing and sociability. By focusing on these dissociations in higher cognitive functioning, this book provides a model for the study of brain-behavior relationships as well as for the mapping of brain and behavior phenotypes to the genome and beyond understanding cognition,neurophysiology, and anatomy and bringing phenotype and understand molecular genetic basis of disease - prove their is an molecular genetic underpining to these fields. of study and cognition -williams syndrome had opposite to down. syndrome, good cognition of speech but bad cognition of space ; phenotypically have good language, speech, stories, convo but spatial is bad -down syndrome trisomy 21, low IQ and cognition * the model you take in any question is so important - genomically you. have. an extra chromosome and small region of chromosome 7 lost/deletion

Mutation specific treatment eg: CF

Kalydeco a drug is designed to treat cystic fibrosis caused by particular type of mutation of the Cystic Fibrosis Transmembrane Receptor gene. It works on certain mutations that produce faulty CFTR a chloride ion channel. It enhance its activity. Mutations that cause complete loss of CFTR it DOES NOT WORK! - works on specific one type of mutation where Cl channel has a faulty channel ( in specific area of CFTR gene) ; binds to part of sequence mutation and corrects it but doesnt correct other types of mutations molecular surgery- gene specific drugs - treat dna not but cutting and pasting by crispr but by changing the gene expression, transcription by adding chemical that binds to the structural change to allow trancriptoin and protein production to happen different mutations cause different cellular effects to cause CF

Molecular Cytogenetics

Label the target gene with fluoropores green red orange etc And hybridize insitu on chromosome prepared and dropped on glass slide. take portion as dna probe, label and look for other copies - different colors and you can see what part is normal, and where deletions are - threshold much more sensitive and see what part is deleted or duplicated

Physiological Events in ONEBODY different Organs and Systems : how to think the gene network control or system control of physiologically different events:

Late 1800- early 1900 Analog computer, physics, engineering tools and Experimental Physiology: Oxford Mississippi Digital GENOMIC ANNOTATION-2000> had all the networks of organs systems and how they interact with each other to give a homeostatic complex organism - won nobel prize - all feedback mechanisms of different systems circadian rhythm and digestion-> connection between the physiology to underpinning genes

Meiosis I: Division 1

Meiosis I separates homologous chromosomes, producing two haploid cells (N chromosomes, 23 in humans), so meiosis I is referred to as a reductional division In meiosis II, an equational division similar to mitosis will occur whereby the sister chromatids are finally split, creating a total of 4 haploid cells (23 chromatids, N) per daughter cell from the first division Prophase I (Leptotene, Zygotene, Pachytene , Diplotene (dictyotene), Diakinesis -During prophase I: DNA is exchanged between homologous chromosomes in a process called homologous recombination. This often results in chromosomal crossover. The new combinations of DNA created during crossover are a significant source of genetic variation, and may result in beneficial new combinations of alleles. The paired and replicated chromosomes are called bivalents or tetrads, which have two chromosomes and four chromatids, with one chromosome coming from each parent. At this stage, non-sister chromatids may cross-over at points called chiasmata (plural; singular chiasma) Leptotene- The first stage of prophase I is the leptotene stage, also known as leptonema, from Greek words meaning "thin threads. During this stage, individual chromosomes begin to condense into long strands within the nucleus. However the two sister chromatids are still so tightly bound that they are indistinguishable from one another. Zygotene- The zygotene stage, also known as zygonema, from Greek words meaning "paired threads", occurs as the chromosomes approximately line up with each other into homologous chromosome pairs. This is called the bouquet stage because of the way the telomeres cluster at one end of the nucleus. At this stage, the synapsis (pairing/coming together) of homologous chromosomes takes place. Pachytene stage, also known as pachynema, from Greek words meaning "thick threads" contains the following chromosomal crossover. Nonsister chromatids of homologous chromosomes randomly exchange segments of genetic information over regions of homology. Sex chromosomes in PAR1 and 2 exchange. Exchange takes place at sites where recombination nodules (the chiasmata) have formed. The exchange of information between the non-sister chromatids results in a recombination of information; each chromosome has the complete set of information it had before, and there are no gaps formed as a result of the process Diplotene (ARRESTED HERE IN FEMALE FETUS)- During the diplotene stage, also known as diplonema, from Greek words meaning "two threads", chromosomes separate from one another a little. However, the homologous chromosomes of each bivalent remain tightly bound at chiasmata, the regions where crossingover occurred. The chiasmata remain on the chromosomes until they are severed in Anaphase I. In human fetal oogenesis all developing oocytes develop to this stage and stop before birth. This suspended state is referred to as the dictyotene stage and remains so until puberty. In males, only spermatogonia ( meiosis has NOT started) exist until meiosis begins at puberty. Diakinesis -Chromosomes condense further during the diakinesisstage, from Greek words meaning "moving through". ] This is the first point in meiosis where the four parts of the tetrads are actually visible. Sites of crossing over entangle together, effectively overlapping, making chiasmata clearly visible. Other than this observation, the rest of the stage closely resembles prometaphase of mitosis; the nucleoli disappear, the nuclear membrane disintegrates into vesicles, and the meiotic spindle begins to form. Meiosis division II same as Mitosis Division.

NONDISJUNCTION: TRISOMY

Meiotic nondisjunction: Failure of two members of a chromosome pair to separate from one another during meiosis, causing both chromosomes to go to a single daughter cell - meiosis one or two - meiosis 1 all. off the. gametes are imbalanced ( extra chromosome and then missing one) -- no viable fetus - happens at meiosis 2- 1/2 will not be viable but other help are normal complement • Trisomy mostly arises through meiotic nondysjunction. • Nondysjunction: Failure of two chromosomes (Meiosis I), two chromatids of a chromosome (Meiosis II or Mitosis) to disjoin so that both pass to one daughter cell and the other daughter cell receives neither. • M-I:both members of Chr.21 or lack 21 altogether. • M-II: two copies of one (member) parental chromosome.

Mitosis Vs Meiosis

Mitosis One Divison and no Genetic and Phenotypic difference between the mother and daughter cells Meiosis Two division and has Genetic and Phenotypic difference between mother and daughter cell Meiosis: Male vs Female Male: Testis, starts in puberty till death, 4 viable products sperms, from each Spermatagonia, multiple millions, Hormones- GnRH ( LH, FS in study state) Testicular hormone TESTOSTERONE - not a cycling hormones like females, made more every 74 hours - begins in puberty in males Female: Starts in Embryo ( 3mths- 9mts) dormant and then becomes reactive when menstruation begins, Eggs shed after Puberty 13-15 y/o (Menstrual Cycle) end in Menopause. One product Ovum, Hormones - GnRH ( LH, FS are cycling) Ovarian Hormons (Estrogen and Progesterone are Cycling) * cycling hormones no genetic differences between mother and daughter cells unless in cancer environment - degrading protein issues, sequence, transcription, and function has changed meiosis- complete different between mother and daughter cells

Cell Cycle and Circadian Rhythm ...

Molecular aspects of CELL CYCLE a Fundamental Cellular Event for Multicellular Organism Maintenance and Survival! Physiological Events in ONEBODY different Organs and Systems : how to think the FEED BACK BETWEEN PHYSIOLOGY AND GENETIC NETWORKS Cell to Body Ratio = 1/1000000 fold evolutionary product, starting from single cell with a complex feedback system - cell-> body -> coordinate and cooperate with all cells and that happens through a feedback system - communication between single cells and multicellular organisms - circadian rhythm- cycle will sun causing sleep and waking up - cell cycle division and circadian rhythm are related by cellular networks and how they are related to each other

Mosaicism

Mosaics: individuals with two or more genetically different cell populations are referred mosaics. Mostly seen as sex chromosomal aberrations, but also occurs in autosomal chromosomes . • Post-zygotic-mitotic nondisjunction. - happens after the zygote is formed after the first few division leads to mosaicism ( anaphase lag; one chromosome in spindle is moving very slow) • Anaphase lag: one chromosome is lost during anaphase movement. • Severity based on when it occurred. -- early more severe and later will have less severity ( tiny portion of trisomy 21) - see certain features of down syndrome but not full down syndrome

What about regulation of CDK and Cyclins TUMOR SUPPRESSORS!

P53 GUARDIAN OF THE GENOME directly via P21 or indirectly with P16 via MDM2. - P16 and P21 block CDK as and when necessary RB another key TS also interacts with P53 via MDM2 - tumor suppressant - kept at low transcription and transition level but when need it is divided enough and by phosphorylation blocks specific cyclin dependent kinases -MDM2 binds to P53 to stop from over transcrption and translation Function lost in > 50% of tumors must be regulated too- down regulated - tumor suppressor genes come RB- P53 with mediators scans or hail mary aka apoptosis

Types of Structural Rearrangements

Pericentric: +centromere -inversion involves the centromere paracentric - inversion happens within one arm dicentric- 2 centromeres balanced- no loss of genome and breaks occur robertsonian translocation- acrocentric chromosomes come head to head and come together interstitial deletion- in middle of chromosome and 2 breaks terminal deletion- one break and on end ring- telomere are protected, deletion at telomere and circles to next available gene to stick too isochromosome- 1 arm has duplicated itself and other arm that should be there ; two copies of same arm; 3 copies of p and 1 copy of 1/ trisomy and monosomy

Signal transduction from outside to Cell Nucleus by Growth Factors

Ras in physical touch with Growth Factor Receptors Once GF bind to them they activate Ras - bind to growth factor, ras gets phosphorylated and carries signal with several other proteins that stimulate cyclin D1-> hyperphosporylated Rb-> E2F-> G1 exit * tumor suppresant but also have normal functions too Ras signals to a number of cytoplasmic signaling cascades such as PI3- kinase, Raf and Rho. in their turn, these proteins connect to the nuclear cell cycle machinery to mediate exit from Go into G1 and S phase of the cell cycle * connection between extracellular signals and the cell cycle machinery without apoptosis lead to cancer

SPECTRAL KARYOTYPING: QUALITATIVE

Spectral karyotyping (SKY) is a novel cytogenetic technique, has been developed to unambiguously display and identify all 24 humans chromosomes at one time without a priori knowledge of any abnormalities involved. SKY can discern the aberrations that can't be detected very well by conventional banding technique and Fluorescent in situ hybridization (FISH) - structural changes -label each chromosome with color, fluorescence and chemistry - eyes cant detect it but computer will -completely automated, qualitiative or sturctural changes -cancer monitoring; leukemia Mixture of fluorophores in different combination, computer generated pseudo coloring Monitor Leukemia: The cryptic t[11;19] and 5q- also indicating poor prognosis were found in another research of These reports showed this translocation can be missed by conventional banding analysis. Need Metaphase preparation. QUALITATIVE ABNORMALITIES

Cell Cycle And Circadian Rhythm Metaphor

Temporal order: Load, Fill, Wash, Empty, Fill, Rinse Empty, Spin, Unload Dependent on upstream events Temporal order: •Buffered against external condition •Easily reset - each step is dependent on the previous step circadian gene not easily effected by environment- takes time but will reset whole system

The post genomic "OMIC ERA"

The English-language neologism (incorporation of a new word and disseminated into language new word) omics informally refers to a field of study in biology ending in -omics, such as genomics, proteomics or metabolomics (currently close to 50 accepted "omics" as topic headings). - omics; collective groups of same things under same substances for classification classification based on type of substance studying the name changes or prefix chnages The related suffix -ome is used to address the objects of study of such fields, such as the genome (DNA), proteome (protein) or metabolome (metabolites) respectively. Omics aims at the collective characterization and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms

Future of cytogenetics... micro arrays

The combination of CGH with multicolour FISH or SKY is a powerful combination for characterising complex karyotypes More recently, microarray-based formats using large insert genomic clones, cDNAs or oligonucleotides have replaced metaphase chromosomes as DNA targets providing higher resolution and the ability to directly map the copy number changes to the genome sequence. In other words, chromosomal abnormalities exist as nature's guide to the molecular basis of many unexplained human disorders. Thus, techniques of cytogenetics are bound to continue to be indispensable tools for diagnosing genetic disorders and indicating possible treatment and management especially in prenatal diagnosis and cancer diagnosis

The Emergence of a field of CYTOGENETICS:

The field of human cytogenetics was initiated in 1956, when the number of chromosomes in a diploid human cell was accurately determined to be 46 (Tjio & Levan, 1956).

The menstrual cycle can be divided into three phases:

The follicular phase - FSH stimulates the development of several follicles in the ovary, usually only one of these follicles matures. This dominant follicle produces estrogen, which causes the endometrium to start to thicken. It also causes the mucus in the cervix to become thinner and more stretchy, allowing sperm to reach the egg more easily. Ovulation -Estrogen levels that have been gradually increasing, peak. The LH levels increase rapidly (day 12 onwards) triggering the release of the egg ( 4C to 2C, first polar body out) from the ripened follicle, which usually occurs 36 hours after the onset of the LH surge. - ripen follicle The luteal phase- The levels of FSH and LH decrease. The ruptured follicle closes (after releasing the egg, FIRST POLAR BODY IS SHED so ) and forms a corpus luteum, which produces progesterone. This prepares the endometrium even further, ensuring it is spongy, thick and full of nutrients so that a fertilised egg can implant into it. If the egg is not fertilised the corpus luteum degenerate and progesterone and estrogen levels fall. The endometrial blood vessels constrict and the endometrium breaks down and is shed as a period (menstruation). If fertilization occurs meiosis (2 C to 1C 2nd Polar body out). Fertilization in fallopian tubes, fertilized egg migrates to body uterus and implants) - if sperm and egg dont meet then corpus luteum is degraded ** each hormone cycle increase to peak and decrease at different times which line up with the key events - 13-50 y/o this occurs 1. follicular phase- FSH stim development of follices in ovary; one becomes dominant follicle that produces estrogen which allows endometrium to thicken 2. ovularion- estrogen has peaked, LSH increased rapidly and releases egg. 4C-> 2C or tetraploid to diploid gene 3. FSH and Lh decrease . prepares egg to be fertilize and zygote to move towards body of uterus. fertilization happens in fallopian tubes because fimbrea push eggs into fallopian tubes. if egg meets sperm then fertilization occurs and 2C-> 1 C 2nd polar body is released. 1 haploid from sperm and 1 in egg to form diploid zygote * 4C to 2C there are 2 polar bodies shed one during menstrual cycle and during development of egg and during ovulation 4C-> 2C. 2C-> 1 C only after fertilization in fallopian tubes releasing 2nd polar body. then migrates down to body of uterus and embeds into the uterus

Meiosis Gonads and EMBRYOLOGY :

The male and female reproductive tracts are derived from the same embryonic/ fetal tissue. The gonads and internal and external genetalia begin as bipotential tissues. They differentiate into male and female reproductive organs from PRIMORDIAL GERM CELLS and migrate to their location in abdomen and are exquisitely regulated to their destiny by hormones - males and female at beginning of initial embryogenesis are the same and later on become male or female The differentiation of male gonad is dependent on the expression of SRY (sex reversal Y) = TDF (testes determining factor). Its expression results in a cascade of events leading to the development of seminiferous tubules (TESTES) The absence of SRY expression results in the differentiation of the presumptive gonad into an ovary. - TDF or SRY gene expression leads to acascade of events for the primordial undifferential germ cells to become male - female has no SRY and TDF; fallback system Development of the internal and external genetalia in the male are dependent on the gonad (testes). Development of female internal and external structures are gonad independent

CC Overview: Tight Regulation or Cancer or ND

The replication cycle or Cell Cycle of a typical eukaryotic somatic cell consists of four phases: G1, S (DNA synthesis), G2, and M (Division or mitosis) and three check points a point progression can be halted until completion of that phase The result of this process is the generation of two daughter cells that are equivalent both in genetic makeup and in size to the original parental cell. Feedback controls operating at checkpoints ensure the faithful replication and segregation of the genetic material. In eukaryotic organisms, a general paradigm has emerged in which a family of cyclins and cyclin-dependent protein kinases (Cdks) regulate cell cycle progression precisely. These mechanisms are REGULATED STRICTLY at the level of reversible phosphorylation, inhibitors, transcription, intracellular compartmentalization, and timely protein degradation cell cycle to create more liver cells but have to differentiate into that specific liver cell - G0; compartment of G1 that can move back and forth

Age Ovum and Meiosis

The tracing (b) identifies these components, and the smooth or wavy lines suggest, respectively, an intact or degenerating spindle apparatus (the ages of the women are indicated). The chromosomes are well organized at the metaphase plate at the equator of the cells in the younger women (the 22-year-old's oocyte, on the upper left, is viewed on a tilt). In contrast, the 44-year-old woman's oocyte has one chromosme, at the top, dislocated from the metaphase plate, and the disposition of the other chromosmes at the equator is not as regular as in the younger women. (the color photographs are from Battaglia, D.E., et al. Influence of maternal age on mitotic spindle assembly in oocytes from naturally cycling women 40 years old many protein issues and degraded, spindle fibers not attached properly and seperate-> because eggs were made when baby and they degrade. the chromosomes arent arranged properly and cause more aneuploidy and fetal issues ( amniocentesis after 34 years to make sure eggs are okay)

Age and Ovum

The tracing (b) identifies these components, and the smooth or wavy lines suggest, respectively, an intact or degenerating spindle apparatus (the ages of the women are indicated). The chromosomes are well organized at the metaphase plate at the equator of the cells in the younger women (the 22-year-old's oocyte, on the upper left, is viewed on a tilt). In contrast, the 44-year-old woman's oocyte has one chromosme, at the top, dislocated from the metaphase plate, and the disposition of the other chromosmes at the equator is not as regular as in the younger women. (the color photographs are from Battaglia, D.E., et al. Influence of maternal age on mitotic spindle assembly in oocytes from naturally cycling women. Hum. Reprod. 1996, 11, 2217-2222) spindle fibers degrade and microtubules fall apart and more likely for chromosomal changes

Meiosis 2:

There is division of centromere as in mitosis and the sister chromatids separate to become 1C from 2C and move into two daughter cells *fertilization. -In essence Meiosis 1 and Meiosis 2 result result in 4 daughter cells with 1C DNA content. - in female 3 will end up to be polar bodies and in males have 4 sperm - 1C set from male and 1C from female - sperm meets egg - once sperm meets arrested diplotin stage meisois 1- 4C to 2C

Human Chromosome complement:

Total 23 pairs; 22 pairs autosomes and one pair of sex chromosomes (XX,XY). Karyotype (ISCN International system of Human cytogenetic Nomenclature))-Systematic nomenclature; ideogram. Giemsa stain banding after trypsin treatment. Arranged according to descending order of size, centromere position and band patterns, dark and light G +ve Dark bands Bands: AT rich, Gene poor, late replicating G -ve Light Bands: GC rich, Gene rich, early replicating

NEUROGENOMICS

Williams Syndrome: The frontal lobes, anterior cingulate, superior temporal gyrus, amygdala, fusiform gyrus and cerebellum were found to be relatively preserved in WS, but parietal and occipital lobes, thalamus and basal ganglia, and midbrain were disproportionally decreased in volume (P < 0.0002) *One of the major areas affected by Down syndrome is the hippocampus, which is largely tasked with spacial skills and memory creation/consolidation. As there are three copies of chromosome 21 with Down syndrome (Trisomy 21), one theory is that it is an over expression of specific genes which causes some of the major cognitive difficulties. did imaging once imaging got better - parietal and occipital lobe is much more affected than frontal in william syndrome patients and hippocampus in down syndrome - 3 layers- parts of brain, gene affected and phenotype cognitive behavior neuro genome is a viable field and can study from gene to phenotype using this technology

Genetic susceptibility to COVID-19 by examining DNA polymorphisms in angiotensin-converting enzyme 2 ACE2 and Transmembrane Protease, Serine 2 TMPRSS2 (two key host factors of SARS-CoV-2) genomes.

clear cut population demaraction within african american population -molecular basis of susceptibility *based on frequency of specifc polymer on 2 genes Unique genetic susceptibility across different populations in ACE2 and TMPRSS2 (transmembrane protease); both in endothelial cells and spike proteins of COVID-19 enter to cells through these 2 proteins and transmembrane protein is dissolved to enter in cell -spike protein tags ACE2 and red TMPRSS2 to enter cell . p.Arg514Gly (polymorphism present more freq in african americans) of ACE2 in the African/African-American population and p.Val160Metin TMPRSS2, offer potential explanations for differential genetic susceptibility to COVID-19 as well as for risk ; 3D structures allow spike proteins to enter in easily and cause those ppl to be much more sick -ACE2 or TMPRSS2 polymorphism could guide effective treatments (i.e., hydroxychloroquine for COVID-19. *how severity disease is effected by genomic polymer 39% (24/61) and 54% (33/61) of deleterious variants in ACE2 occur in African/African-American (AFR) and Non-Finnish European (EUR) populations, Prevalence of deleterious variants among Latino/Admixed American (AMR), East Asian (EAS), Finnish (FIN), and South Asian (SAS) populations is 2-10%, while Amish (AMI) and Ashkenazi Jewish (ASJ) populations do not appear to carry such variants in ACE2 coding regions... BMC Med 18, 216 (July 15, 2020).

Diakinesis Dictoytene

crossover- exchange genetic info between sister chromatids - 4C - RNA synthesis stops and chromatids become visible -crossover is chiasma -homologous chromosomes linked as chiasma in sperms- spermatogenesis - before each cycle there a replication of DNA synthesis in the spermatogia and oogonia that why you have 4C content ( before the meiosis 1 takes place there is a replication that makes it from 4n to allow for 2 different divisions) males: spermatogia (2C)-> primary spermatoocyte (4C)-> 2secondary spermatocytes (2C)-> 4 spermatids -> differentiate into sperms (1C) females: oogonium (2N)-> 4N-> primary oocyte (4N) and release of first polar body-> secondary oocyte ( 2N) and release of second polar body-> matured oocyte (N)-> fertilization with sperm

Genetics of Race and Ethnicity

difference in population is slightly more than those in same population -lots of overlap between population no specific sequnece between different races, no biological basis, 6-7 features that vary for racial construct - genomic level from diff population arent too different from those in. same population - no clear cut differences between races because too much overlap to classify at genomic level - classify based on 4-5 phenotypes

Downs and William Syndrome

different genomes have different phenotypes - no orientation when drawing house but can tell a story; opposite to down syndrome first to tag a specific genomic region and correlate a genetic connection. between cognition and the genes behavior using a simple example

structure inside nucleus

dna in nucleus, naked dna that is extracted is roughly 2 nm 1) Package tight and faithfully transfer between parent to daughter 2) Chromatin is chemical name (DNA and Protein +8 histones and several non histones) in interphase cells is in "open configuration" to function: Access - histones- 4 types present twice so 8 in total. "beads on a string" 3) Chromosome in mitotic cells "closed configuration" much condensed version of chromatin : No Accesss *nucleosome and histones important in regulation; chemical modification on histones you have access or no access to genes that will be transcribed and can become condensed so no access and not transcribed (genes turned on/off) 4) Chromatid is structural ie 2 sister chromatids attached by centromere makes a chromatid chromosome - combo of DNA and histone proteins - 1400 nm thick *Chromatin remodeling : Current information and its importance!

CRISPR Gene Therapy....post and PRE-NATAL: DMD- Molecular Surgery via RNAi oligonucleotides: Manipulating the Open Reading Frame, iPSC cells and back.

ehtical part of life and human experience dystropy- no wheelchair and die soon, simple wheelchair would inc life span and stem cells/treatments but very expensive millions of dollars to give a better quality fo life -the end of spectrum of this disease in africa dont have even basic support modern science and precision medicine will cost more health disparity - or even genetic enhancement will further inc this lucky to live here because of support we have here

post genome era medicine

genotype analyzed through hapmap (snip bit to associate diseases with haploid types) phenotype measured by arrays: DNA, RNA proteins -> individualized medicine and bioinformatics and bioimaging to understand interaction with genotype before come pheonotype with genomic interaction with environment and analyze through these techniques to develop individualized medicine

aCGH @ cancer: (Array CGH)

gleobastoma -chromosome 8 amplification amplification- array technology at the dna level

Anaphase lag

is a consequence of an event during cell division where sister chromatids do not properly separate from each other because of improper spindle formation The chromosome or chromatid does not properly migrate during anaphase and the daughter cells will lose some genetic information. It is one of many causes of aneuploidy. This event can occur during both meiosis and mitosis with unique repercussions. In either case, anaphase lag will cause one daughter cell to receive a complete set of chromosomes while the other lacks one chromosome causing a monosomy. Whether the cell survives depends on the background genomic state of the cell. The passage of abnormal numbers of chromosomes will have unique consequences with regards to mosaicism and development as well as the progression and heterogeneity of cancers Small chromosomes more chances, Y in aging cells and causes aneuplody in cancer increases genomic instability doesnt move to plane and get seperated and moves with other chromosome creating a diploid in gamete and when fertilized have a triploid more than double the age of conception

Cytogenetics

is the branch of genetics that studies the structure of DNA within the cell nucleus. This DNA is condensed during cell division and form chromosomes. The cytogenetic studies the number and morphology of chromosomes. - at metaphase state - used to be one of the most important diagnostic tool but overtime has become less used - cancers, leukemia and lymphoma very useful - prenatal diagnostics - everything is become more whole genome and RNA sequencing - automation- technology moved forward, robotics, cheap have found ways to use small amount for whole genome --Artificial intelligence- look at large amounts of data and look at correlations to the phenotype Using chromosome banding techniques (classical cytogenetics) or hybridization fluorescently labeled probes (molecular cytogenetics) -1960-80; probes or dna pieces that track part of genome that looking for changes in copy number . The number and morphology of chromosomes in a cell of a particular species are always constant, in most cells of the body (with the exception of reproductive cells and others such as the liver). Or in disease state such as cancer and sometimes during aging. - any deviation from chromosomes you can tell something is wrong - brain and liver cells have abnormalities (normal)/ cytogenetic changes This is a characteristic of each species, in humans such as the number of chromosomes is 46

exam questions

meiosis issues from mom lead to chromosomal changes in fetus leading to spontaneous abortion (25%0 - 7-5% mutations from male * meiosis in females is a life long process and as you get older ( perfect age 13 years) more errors occur - body is changing rapidly and evolution changes slowly= mismatch that can be addressed by ethics more mutations in female and meiosis mutation in males -F; because sperms continuously proceed, billions at atime and produced in a short period of time - viable sperm; selection for viable sperm and not mutated ones, healthiest ones win the most - egg is much bigger and stationary and sperm is mobile and dynamic ; nature did this because of wanting a good selection process and pegged towards energy consumption and reproduction - every birth, hundreds are part of fetal wastage *read question properly 10 point question- what do you think about crisper and how to manage the future of crispr - preten it will work for age outcomes but actually work on aging or health to specific population to give an advantage to the population 10-12 sentences in essay - subjective 3-5 sentences - bonus- 3 sentences

WHY IS IMPORTANT TO STUDY CHROMOSOMES? Chromosomal abonormalities in human: estimated frequency

percent of abnormalities; • sperm............................8% - more diseases due to point mutations or inherited disease due to sperm because constantly produced • oocytes.......................25% - spindle fibers are made and degraded over time, some arent as strong during aging process - chromosomal errors come from female • miscarriages(1st trimester)...................50% - because of chromosomal errors • miscarriages(2nd trimester)..................15% • Stillbirths..................7% • Livebirths....................0.5% • The enormous load of cytogenetic abnormalities at conception is unique to humans among studied mammals. • Most such conception are lethal in embryonic or fetal life. • Important in cancer initiation and in diagnosis. most conceptions is lost at early age - human genome and meiosis itself makes a lot fo mistakes

GLOBAL VIEW

resistance v susceptibility -continum from health to disease (4 dimensional) 1.genotype- some get disease and some dont (probability) 2. environment ( oil rigs, contamination inc risk) 3. time (age, how you are continuous being bombarded with different environmental agents; cancer, alzheimers) *measure by epigenetics; epigenetics change over time; keep element of developmental switches 4. geography or exposure- temperate climates, NA, skin color/melanin, food you eat ( Japan mismatch of food habits after WWI movement to US) Genotype+ Environment +Time (Age) +Exposure (Geography)= PHENOTYPE in TIME **overtime phenotype changes GENETICS and EPIGENETICS: STUDIES VIA SNPS AND HAPLOTYPES Gene Expression ARRAYS AND MECHANISM BASED GENETIC STUDIES ENVIRONMENT: STUDIES VIA CHEMISTRY &TOXICOLOGY AND EXPOSURE QUANTIFICATION OVER A "DYNAMIC TIME" OF PRE AND POST EMBRYONIC DEVELOPMENT ALLOWS US TO BE A POINT IN THE CONTINIUM OF HEALTH THROUGH DISEASE AND BACK AND sometimes Back ...Mitigation: Therapy, Epigenetics, Crisper, Stem cells , Ethics

Cytokinesis

s is the part of the cell division process during which the cytoplasm of a single eukaryotic cell divides into two daughter cells. Cytoplasmic division begins during or after the late (anaphase) stages of nuclear division in mitosis and meiosis. The process can be divided to the following distinct steps : 1) anaphase spindle reorganization, 2) division plane specification, (3d body architecture) * that structure is informative, specification of the body structure is based upon the plan of division of the organization of spindle fibers 3) actin-myosin ring assembly and contraction, 4) and abscission (cut). Faithful partitioning of the genome to emerging daughter cells is ensured through the tight temporal coordination of the above individual events by molecular signaling pathways. final stage of cell division - cytoplasm divides, cell pinches in half and the pinch is called a cleavage. furrow

Main features of 5 steps in

stepwise but continuous process - meiosis happens it is important to produce variation, without variation organisms wont survive because they allow them to adapt - the most sophisticated animal is the most fittest for the given environment; humans are not. darwin's definition could be anything - more genetic variation the better you can adapt - COVID- most successful oragnism because able to reproduce and metabolize -Meiosis 1 AKA Reduction Division: -Prophase I: is long with 5 steps. To produce VARIATION homologous chromosome exchange genetic material in the 3rd step (Pachytene) via chromosome non sister chromatid crossover and exchange in a region called "Synaptonemal complex (SC)" assembled in 2nd step called (Zygotene). The site of exchange is called chiasma. In sex chromosomes exchange happens only in two pseudo autosomal regions called PAR1 and PAR 2 present in both X and Y chromosome *based upon structure of DNA seen under microscope; greek words 1) Leptotene: Sister chromatids become visible "thin threads" 2) Zygotene: Homologous begin to pair "paired thread". Chromosome appear as a "bouquet". Synaptonemal complex assembled. 3) Pachytene Stage: Genetic exchange takes place in chiasma within SC region "thick threads".; packaging stage; variation, structural change within homologous chromosomes of mom and dad ( sister chromatin) in synaptonemal complex and degrades after exchange. site of exchange is chias,a 4) Diplotene: SC degrades and homologous chromosome separate "two threads". Arrested in human fetus and called dictyotene stage. 5) Diakenesis: Chromosome condense, chiasma visible "moving through". Leads to Prometaphase of Meiosis I sex chromosome exchange info form Y and X chromosome and only happens 2 particular regions caused pseudoautosomal regions; function in active and inactive X and Y

R point critical to Cellular Homeostasis

stop tumor suppresors-P16, p21 p53, RB go- tumor promorters; cyclin D< E2F, CDK3 4 and 6 wait- P53 for DNA repair- guardian of the genomes Activation: cyclins binding CDKs to activate them pushes CC progression. E2F : a transcription factor needed for CC Progression Rb binding to E2F inhibits transcriptional activity of E2 F and stops CC progress - RB bound to dormant cell to transcription factor or E2F and bound here because if it is released it will go and bind to nucleus and stimulate a lot of proteins and enzymes necessary for cell division - cyclin dependent kinase activated and phosphorylated it needs another CDK and cyclin and RB is double phosphorylated (hyperphosphorylation) caused 3D structure to change, transcription released, and go to nucleus creating a cascade of elements causing cell division * how do we stop? MDM2 degraded, P53 released and translated, P16 and P21 stop CDK that activates transcription aceylations, methylations-> all put together a multicellular organims works Protein modification (such as the phosphorylation of Rb by CDKs resulting in its inability to bind and repress E2F. E2F release allows transcription of DNA polymerases and other substrates needed for and CC progression . P53= quality control: using other signaling molecules including DNA repair Enzymes monitors the genome for Mutation and cellular integrity . All else fails triggers APOPTOSIS CONTROLS ON CELL CYCLE PROGRESSION AND GENOMIC INTEGRITY MEDIATED BY THE RB1, TP53 AND CDKs P53 ALSO HAS OTHER ACTIVITIES.

The general experimental procedure

take mRNA and cut into small fragments by sonicatin or enzymatic means-> add EST at end-> form library or amplify it-> use chem that sequences gene ( bioinformatic; reading frame by software arranges it and spits out sequence, mutation profiles, genetic changes or drugs to use)

PERSONALIZED MEDICINE- GENOMIC BASIS OF MEDICINE: ITS TIME FOR THE (W0)MAN IN THE DISEASE NOT THE DISEASE IN THE MAN!

targeted therapy coorelate genetics, snips, epigentic changes, etc to cancer or disease phenotype, gene changes in genetic pathways or gene signaling to cause a subgroup of lung cancer

origin or eukaryotic cells

we are a product of aerobic prokaryotic cell and archaea cells. - fused together and archea cells had some type of nuclear structure that formed into primative eukaryote mitochondria photosynthetic bacteria-> plants - archaea and photosynthetic bacteria aniamls - aerobic bacteria and archaea

Meiosis male

• After pubertyonly. • Human males produce 200,000,000 sperm per day. • In males, meiosis occurs in precursor cells known as spermatogonia that divide twice to become sperm. These cells continuously divide without arrest in the seminiferous tubules of the testicles. Sperm is produced at a steady pace. The process of meiosis in males occurs during spermatogenesis. • Reabsorbed and cycled. The amount of DNA within a cell changes following each of the following events: fertilization, DNA synthesis, mitosis, and meiosis (Fig) I use "c" to represent the DNA content in a cell, and "n" to represent the number of complete sets of chromosomes. In a gamete (i.e. sperm or egg), the amount of DNA is 1c, and the number of chromosomes is 1n. Upon fertilization, both the DNA content and the number of chromosomes doubles to 2c and 2n, respectively. Following DNA replication, the DNA content doubles again to 4c, but each pair of sister chromatids is still counted as a single chromosome (a replicated chromosome), so the number of chromosomes remains unchanged at 2n. If the cell undergoes mitosis, each daughter cell will return to 2c and 2n, because it will receive half of the DNA, and one of each pair of sister chromatids. In contrast, the 4 cells that come from meiosis of a 2n, 4c cell are each 1c and 1n, since each pair homologous chromosomes separate, and sister chromatids divides during meiosis 1N1C-> 2N2C-> 2N2C-> 2N4C-> 2N4C-> 2N2C (MITOSIS) 1N2C (1 MEIOSIS) 1N MEANS CHROMOSOMES-> 1N1C (MEIOSIS 2); 1N MEANS CHROMATIDS HERE

New Technology

• All towards automation of Karyotyping

CELLULAR HOMEOSTASIS

• Any cell at any time has FOUR CHOICES : DDDD * four endpoints Duplicate , Differentiate, Die (apoptosis), and Dormant cells select one of these options in response to internal and external signals. Environmental Signals, growth factors, receptors, oncogenes and tumor suppressor genes play key roles in generating and interpreting these signals. - UV light, etc - not linerar but complex with so many feedback loops There is myriad amount of feed back loops through rate limiting factors and cross talk between genes and pathways FUN AND CHALLENGE!

CELL CYCLE MOLECULAR GENETICS

• BIOLOGICAL START POINT: CELL CYCLE • SYNTHESIS: Multiply double the content • MITOSIS-MEIOSIS: Division

CELL CYCLE SENESCENCE AND APOPTOSIS

• CELL DEATH NOMENCLATURE: • A: NECROSIS: yes INFLAMMATION • B: APOTOSIS : No INFLAMMATION & A Biological Program. • C: SENESCENCE: A Biological Program? b- Galactosidase is UP regulated : Telomere Shortening: from about 20KB to 10KB - these cells are resistant to chemotherapy - more in older people apoptosis- normal physiologcal thing- no inflammation

Mitosis and Meiosis

• Chromosomes separate in Meiosis I • Chromatids divide in Meiosis II cell division meiosis- reduction division have a haploid genome, -prophase 1; variation/fittness mitosis- daughter cell or diploid genes chromosomal aberration- during conception or meiosis itself, during fertilization. miscarriage due to chromosomal aberration/mistakes *meisosis 2 centromere is divided and only genetic exchange in meiosis 1

Molecular GENETICS

• Cyclins are important core cell cycle regulators. Cyclins are a group of related proteins specific to each phase and partner with specific cyclin dependent kinases CDKs at specific phase. * each transition there is a different cyclin and cyclin dependent kinase that comes into play; and Ub disruption of cyclin and CDK by Ub at each phase - degraded over time • CDKs phosphorylate the Cyclins and also execute transitions • Eg: MPF that helps in transition from G2 to Mitosis is a CDC2 kinase + Cyclin A/B • Ubiquitin Ligase tags of ubiquitin allows proteasome to destroy Cylins TIMELY! • Patterns of cyclin-cdk activity during the mammalian cell cycle. The expression patterns of the specific mammalian cyclins is superimposed upon the cell cycle, along with their respective cdk partners. • The approximate position of the R point late G2 phase is shown. G1; cyclin D and CDK4/5- degraded-> cyclin E CDK2 in S-> cyclin A CDK2-> cyclin B/A CDC2 degraded by specifically tagging them with particular protein called Ubiquition by and an enzyme called Ub ligase - once it is tagged it is marked for degradation by proteosome mitotic dependent factor - tags on Ub liagse and degrades it so it can go into G1 phase

G0 Phase

• Differentiated cells - special compartment of G1 • Active-cell function eg: secretion, motility • Do not divide except under specific stimuli, move to G1 phase. • Tight control.... Cancer!!! - recruited and made to replace cells that are low, etc Restriction point: (G1 checkpoint) a point in the animal cell cycle at which the cell becomes "committed" to the cell cycle, which is determined by external factors and signals. ENERGY, SIZE, DNA DAMAGE - once crosses go through cell cycle and if there is a mistake will be sent for apoptosis - each checkpoint have a specific job; growth of cell , check for dna damage after replication stage - several protein and enzymes to check size of cell and then moves to next phase •The G2 checkpoint ensures all of the chromosomes have been replicated and that the replicated DNA is not damaged before cell enters mitosis . •Same as G1 , DNA damage & duplication important •The M or Spindle checkpoint determines whether all the sister chromatids are correctly attached to the spindle microtubules and kinetochores before the cell enters the irreversible anaphase stage. Prevents separation of the duplicated chromosomes until each chromosome is properly attached to the spindle apparatus •A checkpoint is one of several points in the eukaryotic cell cycle at which the progression of a cell to the next stage in the cycle can be halted until conditions are favorable. •Damage to DNA and other external factors are evaluated at the G1 checkpoint; if conditions are inadequate, the cell will not be allowed to continue to the S phase of interphase •Transitions from phases pushed by specific cyclins and cyclin dependent kinases (CDKs checkpoint is where they stop before each transition so that cell has everything it needs before it moves on

STEM CELL AND CELL CYCLE

• Embryonic stem (ES) cells have atypical cell cycle features including very short gap phases and short generation times. Long S phase . • Certain proteins like pRb are constantly phosphorylated and inactivated. • Because in many embryonic systems differentiation and proliferation are often closely correlated, the unusual properties of the ES cell cycle may be associated with the ability to preserve the undifferentiated state quite different than somatic cell cycle - huge synthesis stage - producing differentiated cells from undifferentaed spaces - gap phases are much shorter - different due to different timing of compartments cancer- stem cells are origin of cancer cells - no easily amendable to chemo because not fast dividing

S PHASE

• Faithful copy of the genome-DNA replication • S-phase control: many origins, late replication • DNA replication-future discussion

Genes are not equally distributed Gene rich-Gene poor Chromosomes.

• Gene-rich regions of the human karyotype. The bands in red hybridize to genomic DNA abundant in CpG islands . • Note the absence or near absence of gene-rich regions in the three "viable trisomies" autosomes, numbers 13, 18, and 21. - viable fetuses even with absence • Chromosome 19, gene rich by contrast, is well colored-in. No viable birth! - if not present will die/ spontaneous abortion post genomic era- all chromosomes are not equal - genes are not equally distributed around genome - chromosome 19- very gene rich with lots of red, 13 few genes and many are repeat sequences

HAPLOTYPE MAP

• Genotypes: AA,AG,GG • SNPS: A and G • Allele = SNPs Haplotype: Several associated SNPS across a region of chromosome - formed by looking at dna sequences that represent a specific region of chromosome - group of snps brought together - differences in nucleotides, need one particular marker in the whole group as a map to represent the rest of the genome - able to analyze large amounts of data with specific dna markers 12 mil snps • International HapMap Project is expected to be a key resource for researchers to use to find genes affecting health, disease, responses to drugs, common diseases, such as diabetes, cancer, stroke, heart disease, depression, and asthma. Although any two unrelated people are the same at about 99.9% of their DNA sequences, the remaining 0.1% is important because it contains the genetic variants that influence how people differ in their risk of disease or their response to drugs. Discovering the DNA sequence variants that contribute to common disease risk offers one of the best opportunities for understanding the complex causes of disease in humans environmental factor. • 10 million SNPS, each allele should be AT LEAST 1% . • Japan,US,UK,Nigeria,Canada + Private Companies

IDEOGRAM

• IDEOGRAM: Schematic representation. Quality? • Band-a part of Chromosome clearly distinguished from adjacent parts by virtue of its lighter or darker intensity . • It's a landmark------def. region. • Region: area between two adjacent land marks. • Eg:1q24 ( chromsome 1 band 2 and 4 deleted)

IN FEMALES

• In females, meiosis occurs in precursor cells known as oogonia. Each oogonia that initiates meiosis will divide twice to form a single oocyte and three polar bodies. However, before these divisions occur, these cells stop at the diplotene stage of meiosis I and lay dormant within a protective shell of somatic cells called the follicle. Follicles begin growth at a steady pace in a process known as folliculogenesis, and a small number enter the menstrual cycle. Menstruated oocytes continue meiosis I and arrest at meiosis II until fertilization. The process of meiosis in females occurs during oogenesis, and differs from the typical meiosis in that it features a long period of meiotic arrest known as the Dictyate stage and lacks the assistance of centrosomes - first polar body after meiosis 1 , 2 and 3rd after fertilization and egg is released from follicle

Diverging Monozygotic Twins: Epigenetics

• Life style changes • Gene Expression Changes • Epigenetic Changes • Phenotypic Change • Time >>> • TRIM28 gene: Bimodal expression. • Transcriptional control with TF interaction and Chromatin remodelling as they grow they diverge -divergence isnt because of genomic but epigenic changes which are markers of aging - trimm 28 gene produces a protein that have a bimodal expression, it is expressed in certain ages and causes different things in each twin epigenetically different but dna same ** trim 28 bimodal expression causing diverging monozygotic twins (obesity) -controlled by epigentics trimm 22- unimodal like the regular gene expression, looks same but has slight changes, different function -immune response - not controlled by epigentics * same family of gene epigenically can be modified differently and expressed in different ways

Meiosis In Females Overview

• Meiosis-Prenatal (3mts) • 7 to 9 mts: diplotenedictyotene • Nuclear memb/nucleolusresting stage • 99% oocytes degeneratepuberty onset • First half cycle-Pit.LH Stimulates-meiosis-1 st polar body; If fertilized (fallopian tube) 2nd polar • Nucl mem M & P-Pronucleus fuse----first cleavage - meiosis once a month -development of zygote happens after embedded into uterus The menstrual cycle is the process controlled by hormones, during which an egg develops and is released from the ovaries and the lining of the uterus (endometrium) thickens in preparation for a possible pregnancy. A female is born with thousands of egg cells (follicles) which lie dormant (dictyotene stage early meiosis 1 has 4C ) in the ovaries until puberty when rising hormones lead to the maturation of several follicles a month. One follicle matures and produces mature egg completing meiosis 1. - meisosis stops during embryonic development, 3 month old fetus meiosis starts and stops at 9 month. meisosi becomes dormant (dictyotene) with 4C content (amount of DNA) $x the amount the sperm has. 2 divisions to give out, applied geneome that egg and sperm have that form zygote with applied genome -meiosis starts at 3 months in fetus and continues until end of menstrual cycle ( 50-55 years old) - many dormant eggs - one that produces the most estrogen is the dominant one The menstrual cycle is under the control of three sets of hormones: • Gonadotrophin releasing hormones (GnRH). Hypothalamas • Gonadotrophins - luteinising hormone (LH) and follicle stimulating hormone (FSH) from the pituitary gland and regulate ovarian hormones • Ovarian hormones - estrogen and progesterone * 3 layers of hormones in females the reproductive hormones cycle but the men their reproductive hormones dont cycle.

Mosaicism- Post Zygotic

• Mosaics: Individuals with two or more genetically different cell populations are referred mosaics. Mostly seen as sex chromosomal aberrations, but also occurs in autosomal chromosomes. 1. Post-zygotic-mitotic nondisjunction. - some daughter cells will have chromosomal aberrants and other normal (mosaicism) -> down syndrome - not a proper seperation of chromosmes between daughter cells 2. Anaphase lag: one chromosome is lost during anaphase movement. - chromosomes lag behind ( trisomy and monosomy in complement cell) • Severity based on when it occurred; early -> down syndrome, later stage-> some features of down syndrome because have lots of normal cells (brain cells)

MALE AND FEMALE MEIOSIS PRODUCT BY #'s. Swimmers vs Keepers

• Of the 7 million potential oocytes that form during the 5th month of pregnancy. • 2 million at birth, vast majority will be eliminated prior to being ovulated and these are resorbed by the body. - many die but very few eggs are used Typical female # of meitic products: • 45 yrs x 12 cycles/yr = 540 eggs. men- • A 74 hour cycle occurs with several hundred million sperm cells being produced daily with no similar selection process involving polar bodies or daughter cells. *starts at puberty • Meiosis in males is a lifetime endeavor and while sperm production decreases after reaching a peak in the mid 20's and the percentage of sperm that swim erratically increases with age, a healthy human male will continue manufacturing sperm from puberty until death. *both are available for fertilization after puberty

STRUCTURAL CHROMOSOMAL CHANGES

• Structural rearrangements are defined as BALANCED if the chromosomal set has the normal complement of genetic information or UNBALANCED if there is additional or missing information. - balances rearrangement of 23 pairs but no loss or gain of genome - unbalanced- phenotypic cost, loss or gain of genome • Rearrangements are STABLE and passed on (unaltered) if thay have a single functional centromere and the two telomeres, UNSTABLE, either missing - as long has centromere and 2 telomere, that piece of dna will be stably transmitted • Translocation: two non-homologos chromosome exchange genetic material . • At least one break occurs on each of the two chromosome for them to break and stick to each other - anything that isnt the same complement . • Reciprocal translocation are balanced exchanges between two chromosomes in which no genetic material is lost. • The chromosomes carrying the translocation are referred to as derivative (der) chromosome. • Normal individuals spontaneous abortions. •Offsprings may express genetic defects if they do not receive a normal complement genetic material. - balanced translocation- fetal wastage because transfer bad pair rather than normal complement leading to instability of genome

Chromosome Morphology:

• Study of Stru+Func. of Chromosomes-Light microscopy, 5Mb genetic material. Giemsa Stained trypson G-banding ( Gelsma); black bands and white bands, trypson digestes certain parts of chromosome and leaves other parts. dissolved parts are white and others that are staying back ar darker stain - light stains= gene rich -dark rands= resistant to trypsin digestion • Structure-Centromere, G+,G-, p and q arm centromere, ends telomere. • Heteromorphic regions: light and dark bands after trypsin. Heterochromatin ( dark staining blocks of late replicating -repeat seqgene poor) and Euchromatin (gene rich light staining ) variations in heterochromatin, no phenotypic difference - changes in heterochromatin no phenotype . • Molecular-cytogenetics: 1990's • FISH-Fluorescence In-situ Hybridization: Resolution to single genes i.e. about 20kb. --smaller than cytogenetics ordered based on size ( high to low ) and centromere position - centromere in each chromosome and south of centromere is q arm and north is p arm ; typically q i s longer or equal size cytogenetics- changes in genome, light microscope ( h mb (million base pairs) or above) end of each chromosome is the telomere - heteromorphic- light and dark, 2 types of morphisms and 2 chromatins

ENVIRONMENTAL GENOME PROJECT-U.S. POPULATION DIVERSITY

• To better understand how individuals differ in their susceptibility to environmental agents and how these susceptibilities change over time, the National Institute of Environmental Health Sciences (NIEHS) developed EGP in 1997. ***The goal of environmental genome project is to characterize how specific human genetic variations, or polymorphisms, contribute to environmentally induced disease susceptibility. • Primarily DNA repair genes and Cell Cycle and Oxidatve - Phosphorylation genes (600 geness) environmental susceptibility - reactive genes and sequence in diff ethnic groups - platform around the globe so all ethnic groups are recorded so see how they each react to different reactivites - helps reduce health disparity