*  ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C...
A chromosome is known to occupy its own territory, and fold into a high-order, non-random structure in a nucleus [1]. The knowledge of the high-order organization of chromosomes is useful for the understanding of genome folding, long-range gene interactions and regulations [2], DNA replication [3], and cellular functions [4, 5]. To gain better insights into the organization of the chromosomes in a cell, a technology called the chromosome conformation capture technique such as 3C [6], 4C [7, 8], 5C [9], and Hi-C [10] has been developed to determine spatial chromosomal interaction within a chromosome region, a chromosome or an entire genome. Particularly, the Hi-C technique [10] is capable of capturing genome-wide chromosomal interactions (or contacts) by cross linking interacting DNA fragments, excising them out, sequencing them, and mapping them to a reference genome. The sequence reads obtained by the Hi-C technique are read pairs that reveal the ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1931-2
*  PLOS Genetics: Heterochromatic Threads Connect Oscillating Chromosomes during Prometaphase I in Drosophila Oocytes
Author Summary Proper chromosome segregation is essential during the production of eggs and sperm. Chromosome missegregation during meiosis results in the lethality of the offspring or in children carrying extra copies of a given chromosome (for example, Down syndrome). Recombination results in homologous chromosomes becoming physically interlocked in a manner that is normally sufficient to ensure proper segregation. Chromosomes that fail to undergo recombination require additional mechanisms to ensure their proper segregation. In Drosophila melanogaster oocytes we show that chromosomes that fail to recombine undergo dynamic movements on the meiotic spindle prior to their proper segregation. Although previous studies had shown that non-recombinant chromosomes move to opposite sides of the developing meiotic spindle, we show that these chromosomes can cross the spindle and re-associate with their homologs to attempt ...
  http://journals.plos.org/plosgenetics/article/comments?id=10.1371/journal.pgen.1000348
*  NewYork-Presbyterian/Queens - Genetics and Cancer - Description of Chromosomes
The usual number of chromosomes inside every cell of your body is 46 total chromosomes, or 23 pairs. You inherit half of your chromosomes (one member of each pair) from your biological mother, and the other half (the matching member of each pair) from your biological father.. Scientists have numbered the chromosome pairs from 1 to 22, with the 23rd pair labeled as X's or Y's, depending on the structure. The first 22 pairs of chromosomes are called "autosomes," which are the body chromosomes. The 23rd pair of chromosomes are known as the "sex chromosomes," because they determine whether someone will be born male or female. Females have two "X" chromosomes, while males have one "X" and one "Y" chromosome. A picture of all 46 chromosomes, in ...
  http://www.nyhq.org/diw/Content.asp?PageID=DIW007176&More=DIW&language=Spanish
*  Education - Chromosomes - History
Original text and figures were provided by N. Kurata). Chromosome number of cultivated rice was reported as 2n=24 by Kuwada in 1910. Until 1930 this number was confirmed by the observation of rice chromosomes at meiosis. However, due to the extreme smallness, the morphology and structure of rice chromosomes remained unclear and no karyotype analysis was reported until the1970s. Only some attempts of morphological identification based on the figures at pachytene stage in meiosis were reported in this period.. In 1978, Kurata and Omura (1978) invented a new method of chromosome preparation technique, with which karyotype analysis on rice chromosomes was first conducted and identification of all twelve chromosomes became realized. Furthermore, all extra chromosomes of 12 trisomics series of rice (2n=24+1) were identified with this method by Kurata et al. (1981) and Iwata et al. (1984) so that the relationship between the ...
  https://shigen.nig.ac.jp/rice/oryzabase/education/chromosomes
*  Section D - Prokaryotic and Eukaryotic Chromosome Structure - ppt video online download
Contents D1 Prokaryotic chromosome structure D2 Chromatin Structure The Escherichia. coli chromosome, DNA domains, Supercoling of the genome, DNA-binding proteins D2 Chromatin Structure Chromatin, Histones, Nucleosomes, The role of H1, Linker DNA, The 30 nm fiber, Highter order structure D3 Eukaryotic Chromosomal Structure The mitotic chromosome, The centromere, Telomeres, Interphase chromosome, Heterochromatin, Euchromatin, DNase Ⅰ hypersensitivity, CpG methylation, Histone variants and modification D4 Genome complexity Noncoding DNA, Reasociation Kinetics, Unique sequence DNA, Tandem gene clusters, Dispersed repetitive DNA, Satellite DNA, Genetic polymorphism D5 The flow of genetic information The central dogma, Prokaryotic gene expression, Eukaryotic gene expression
  http://slideplayer.com/slide/3309361/
*  Structure of eukaryotic chromosomes and chromatin - III. Transcription Introductory remarks | Philosophical Transactions of the...
This discussion meeting is entitled 'Structure of eukaryotic chromosomes and chromatin'. Now, some scientists are interested in the study of structure for its own sake; they are the purists, the Ars gratia artis school, as it were. Others, including myself, are interested in structure mainly because this knowledge may help to elucidate the way in which chromosomes function. By chromosomal function we mean the role of chromosomes in gene expression, mainly the control of transcription. This session is devoted to consideration of the proposition that the transcriptionally active part of chromatin is structurally different from the inactive part. Indeed, there is a good deal of evidence for this. The notion is inferred from morphological studies of chromosomes, notably lampbrush chromosomes in amphibians and giant chromosomes in dipterans. Lampbrush loops have long been suspected and more recently have been ...
  http://rstb.royalsocietypublishing.org/content/283/997/331
*  PLOS Genetics: Mechanisms of Chromosome Number Evolution in Yeast
Author Summary The number of chromosomes in organisms often changes over evolutionary time. To study how the number changes, we compare several related species of yeast that share a common ancestor roughly 150 million years ago and have varying numbers of chromosomes. By inferring ancestral genome structures, we examine the changes in location of centromeres and telomeres, key elements that biologically define chromosomes. Their locations change over time by rearrangements of chromosome segments. By following these rearrangements, we trace an evolutionary path between existing centromeres and telomeres to those in the ancestral genomes, allowing us to identify the specific evolutionary events that caused changes in chromosome number. We show that, in these yeasts, chromosome number has generally decreased over time except for one notable exception: an event in an ancestor of several species where the whole genome was duplicated. Chromosome number reduction ...
  http://journals.plos.org/plosgenetics/article/metrics?id=10.1371/journal.pgen.1002190
*  In vivo dissection of the chromosome condensation machinery | JCB
Two simple models can be envisaged: either cohesins are needed to activate condensin function or, alternatively, cohesins are required to ensure correct chromosome folding by condensins. These models can be distinguished by following the state of the mitotic chromosomes after a loss of cohesin activity. In the first scenario, the chromosomes remain in an interphase state, and thus would condense upon the readdition of cohesin and the subsequent "activation" of condensin. In contrast, the latter scenario predicts that misfolded chromosomes would result from the inappropriate action of condensin, and these would likely prove refractory to refolding. To test this, we asked whether chromosome condensation is reversible in the cohesin mutant mcd1-1. In contrast to both the brn1-9 and ycg1-2 condensin mutants, the condensation defect in the mcd1-1 strain was not reversible (Fig. 7 B). One trivial explanation is that no new functional Mcd1-1p protein is made after ...
  http://jcb.rupress.org/content/156/5/805
*  The Shumways: What's up with those Chromosomes
The sex of a human baby is determined by the composition of its sex chromosomes (a single distinct pair among humans' 23 pairs of chromosomes). Females possess two copies of the same chromosome (referred to as the 'X' chromosome); males have one copy of the X chromosome and one copy of the smaller, hook-shaped Y chromosome.. When fertilization occurs, the new gamete (the initial cell from which a fetus grows) always inherits one of the mother's X chromosomes, and either an X or a Y from the father, depending on which chromosome the fertilizing sperm cell happened to inherit. One could say, then, that the father-or, at least, his sperm-determines the sex of the child. On the other hand, the first sperm to reach the egg isn't necessarily the one that fertilizes it; human eggs are rather choosy about that sort of thing. So, in an indirect way, the maternal parent also has some ...
  http://shumwayfam.blogspot.com/2010/10/whats-up-with-those-chromosomes.html?showComment=1288572704428
*  "Mitotic chromosome preparations from mouse cells for karyotyping." by E C. Akeson and M T. Davisson
This unit contains protocols for the preparation of mitotic chromosomes from mouse peripheral blood, Giemsa banding of those chromosomes, and classification into a karyotype, including recognition of some common pitfalls of misidentification and information for determining aberrant chromosomes. The methods described can be used to identify visible chromosomal rearrangements and their precise cytological breakpoints in the living mouse. In conjunction with fluorescent in situ hybridization (FISH), the metaphase spreads can also be used for the linear placement of loci on a chromosome and for determining the insertion site(s) of a foreign transgene.
  http://mouseion.jax.org/stfb2000_2009/876/
*  Chromosome Analysis Protocols by John R. Gosden - RUBBERPIXY.COM Book Archive
Left: a metaphase plate. Scale bar =lO pm. Right: a single chromosome from the same metaphase. Scale bar = 1 pm. been possible to combine in situ hybridization with high-quality morphological preservation. As well as providing alternative approaches to chromosome morphology, the methods using cytocentrifuge preparation and isolated chromosomes have the advantage of using little or no fixation prior to the osmium impregnation procedure. They are, therefore, well suited to the study of chromosomal antigens that might be destroyed or extracted by methanol-acetic acid fixation (Fig. Ethidium Bromtde Technique (Originally Described by Ikeuchi [2U. 1. When mamtammg cells for making chromosomes by this method, the cells are kept m a semiconfluent state and only split when the flask is fully confluent (stationary phase). This will give a very crude but reasonably effective means of synchronizing rapidly growing cells. However, the chromosomes are in a more nearly ...
  http://rubberpixy.com/index.php/kindle/chromosome-analysis-protocols-1-st-edition
*  Hrb27C, Sqd and Otu cooperatively regulate gurken RNA localization and mediate nurse cell chromosome dispersion in Drosophila...
Nurse cell chromosomes that fail to disperse are also observed in certain alleles of ovarian tumor (otu) (King et al., 1981; King and Storto, 1988; Heino, 1989; Mal'ceva and Zhimulev, 1993; Heino, 1994; Mal'ceva et al., 1995). otu produces two protein isoforms, Otu98 and Otu104, by alternative splicing of a 126 bp exon. Genetic and molecular analyses reveal distinct requirements for each isoform during oogenesis (Storto and King, 1988; Steinhauer and Kalfayan, 1992; Sass et al., 1995; Tirronen et al., 1995). In particular, a mutant that specifically disrupts the Otu104 product has persistent polytene nurse cell chromosomes, suggesting that the 98 kDa Otu isoform is not capable of mediating wild-type chromosome dispersion (Steinhauer and Kalfayan, 1992). This phenotype was also described for mutants in half pint (hfp; pUf68 - FlyBase). Hfp encodes a polyU-binding factor and plays an important role in the alternative splicing of otu. In hfp ...
  http://dev.biologists.org/content/131/9/1949
*  Genetics & Dysmorphology | CURRENT Diagnosis & Treatment Pediatrics, 23e | AccessPediatrics | McGraw-Hill Medical
Human chromosomes consist of DNA (the blueprint of genetic material), specific proteins forming the backbone of the chromosome (called histones), and other chromatin structural and interactive proteins. Chromosomes contain most of the genetic information necessary for growth and differentiation. The nuclei of all normal human cells, with the exception of gametes, contain 46 chromosomes, consisting of 23 pairs (Figure 37-1). Of these, 22 pairs are called autosomes. They are numbered according to their size; chromosome 1 is the largest and chromosome 22 the smallest. In addition, there are two sex chromosomes: two X chromosomes in females and one X and one Y chromosome in males. The two members of a chromosome pair are called homologous chromosomes. One homolog of each chromosome pair is maternal in origin ...
  http://accesspediatrics.mhmedical.com/content.aspx?bookid=1795§ionid=125747809
*  First 3D Pictures Of Chromosome Structure Revealed - Redorbit
Biotechnology and Biological Sciences Research Council. A new method for visualizing chromosomes is painting a truer picture of their shape, which is rarely like the X-shaped blob of DNA most of us are familiar with.. Scientists at the BBSRC-funded Babraham Institute, working with the University of Cambridge and the Weizmann Institute, have produced beautiful 3D models that more accurately show their complex shape and the way DNA within them folds up.. The X-shape, often used to describe chromosomes, is only a snapshot of their complexity.. Dr Peter Fraser of the Babraham Institute explains: "The image of a chromosome, an X-shaped blob of DNA, is familiar to many but this microscopic portrait of a chromosome actually shows a structure that occurs only transiently in cells - at a point when they are just about to divide.". "The vast majority of cells in an organism have finished dividing and their chromosomes don't look anything like the X-shape. ...
  http://www.redorbit.com/news/science/1112957737/first-3d-pictures-chromosome-structure-revealed-092513/
*  Chromosome arm legal definition of chromosome arm
Definition of chromosome arm in the Legal Dictionary - by Free online English dictionary and encyclopedia. What is chromosome arm? Meaning of chromosome arm as a legal term. What does chromosome arm mean in law?
  https://legal-dictionary.thefreedictionary.com/chromosome+arm
*  Chromosome Names in genome are incompatible with annotations
Dear community,. while creating an index for the bovine genome with STAR, the process fails because the chromosome names in the annotation file (Bos_taurus.UMD3.1.87.gtf) are incompatible with the ones in the reference file (UMD3.1_chromosomes.fa) (e.g. for chromosome "10" vs "gnl,UMD3.1,GK000010.2 Chromosome 10 AC_000167.1", both should be "10").. Apparently, the solution is to change the names in the reference file. Could you suggest a tool that does this for me or a "one liner" that can transform the names into the chromosome number?. And also, would this affect downstream processing of my results?. I have searched through other threads and couldn't find a better answer than the one given here: Renaming Entries In A Fasta File But it renames chromosomes names in the reference file based on the order they appear.. Cheers!. ...
  https://www.biostars.org/p/242850/
*  Patent US3833796 - Method and apparatus for chromosome digitizing - Google Patents
A chromatizer including an apparatus for and method of effecting the analysis of chromosomes including means for establishing an image of at least one chromosome, means for digitizing the distance each arm of the chromosome is from a preselected reference point, and means for automatically computing a number of quantitative measurements of the chromosome, including the length of each arm and the centromere index. The digitizing means includes means for identifying and recording the location of a plurality of points along each arm of the chromosome relative to the reference point. The establishing means includes means for superimposing the identifying means onto the image of the chromosome. The computing means includes means for displaying the computed quantitative measurements.
  http://www.google.com/patents/US3833796?dq=6,360,693
*  Human Female Chromosome Spread Next to Cells. Brightfield Photographic Print by Michael Abbey at AllPosters.com
Human Female Chromosome Spread Next to Cells. Brightfield Photographic Print by Michael Abbey - at AllPosters.com. Choose from over 500,000 Posters & Art Prints. Value Framing, Fast Delivery, 100% Satisfaction Guarantee.
  http://www.allposters.com/-sp/Human-Female-Chromosome-Spread-Next-to-Cells-Brightfield-Posters_i6014350_.htm
*  Scientist compiling karyotype of human chromosomes - Stock Image G210/0330 - Science Photo Library
MODEL RELEASED. Cytogeneticist analysing a karyotype of human chromosomes for diagnostic purposes. The paired chromosomes facilitate detection of abnormalities of number or structure, which may give rise to defects in the individual (such as Down's Syndrome and some leukaemias). A karyotype is a document of the full complement of chromosomes in a cell, arranged in numbered homologous pairs. The chromosomes are stained and photographed through a light microscope during the metaphase stage of cell division. Each member of a homologous pair (apart from the sex chromosomes in the male) is similar in length & banding pattern. - Stock Image G210/0330
  http://www.sciencephoto.com/media/210916/view
*  The external mechanics of the chromosomes I-The scope of enquiry | Proceedings of the Royal Society of London B: Biological...
The movement of chromosomes may be regarded in two kinds of relationships according as it involves changes of shape and changes of position. The first are due to movements within the chromosomes, and may be used to infer their internal mechanics. The second are due to movements between chromosomes, and may be used to infer their external mechanic. Many experiments have been devoted to elucidating the principles of the external mechanics, and they have been successful in showing certain essential properties of the cell outside the nucleus, particularly of the spindle and the spindle-determining bodies or centrosomes. But, when applied to the chromosomes, artificial treatment has the drawback that in making one primary change it sets up a series of secondary changes whose importance cannot be accurately assessed; comparison is therefore vitiated. The cytoplasm and, in the resting nucleus, a semi-permeable nuclear membrane separates and ...
  http://rspb.royalsocietypublishing.org/content/121/823/264
*  Chromosome structure - Nollmann Lab
The use of super-resolution microscopy and 3C methods to study chromosome architecture (Cattoni et al. A matter of scale: how emerging technologies are redefining our view of chromosome architecture. Trends Genet. 2015 ﻽[PDF]﻽). ...
  http://marcnol.weebly.com/chromosome-structure.html
*  GENES AND CHROMOSOMES. - ppt video online download
The Chromosome Theory of Heredity Traits are determined by pairs of genes (alleles) A pair of genes are located on a pair of chromosomes, one gene for each trait on each chromosome of a pair. In meiosis, the chromosomes and therefore the genes, segregate independently - one of each pair to a gamete In fertilization, gametes unite resulting in a fertilized egg that has two genes for each trait carried on pairs of chromosomes.
  http://slideplayer.com/slide/3461975/
*  Science and Religion: A View from an Evolutionary Creationist: August 2011
Ross argues that the chromosomal evidence that humans and the higher apes have a different number of chromosomes is invalid or misunderstood. In the early 1990s, it was discovered that human chromosome two is an end-to-end-fusion of two ape chromosomes. A close examination of chromosome two revealed that, while the other twenty-two chromosomes have one centromere, or central segment, human chromosome two has an extra non-functional centromere. Furthermore, while every chromosome has end segments known as telomeres, human chromosome two has inactive adjacent telomere segments in the middle of the chromosome. It is argued that, sometime in our early past, there was a translocation of two chromosomes to form Chromosome two. Ross argues that such a translocation could not possibly have happened because this would be "catastrophic for the organism" and would result in death ...
  https://scienceandcreation.blogspot.com/2011/08/
*  Update: Chromosomes Are Shaped Less Like X's, More Like O's
Posted on 09/27/2013 8:44:00 PM PDT by BenLurkin. The images reveal chromosomes that are not at all X-shaped. In fact, they're pretty much the opposite: They're spheroid. Their DNA strands seem to arrange themselves, most of the time, into loose little blobs of genetic material. So why the X-shape that has become so familiar? Because chromosomes do take that form -- during cell division. As Peter Fraser, one of the project's researchers, explains it, 'This microscopic portrait of a chromosome actually shows a structure that occurs only transiently in cells at a point when they are just about to divide.' So it's not that the X-based images of the chromosomes have been wrong; it's that they've been incomplete. Sometimes, it's X's; most often, however, it's O's. In life's grand game of tic-tac-toe, the O's have totally won ...
  http://www.freerepublic.com/focus/f-chat/3072217/posts?page=15
*  Reproduction and Chromosome Transmission - To prepare human chromosomes for viewing Figure 32a
View Notes - Reproduction and Chromosome Transmission from BIO 325 at University of Texas. To prepare human chromosomes for viewing (Figure 3.2a): Somatic cells are obtained from the blood. The cells
  https://www.coursehero.com/file/6260198/To-prepare-human-chromosomes-for-viewing-Figure-32a-Somatic/