Human Papillomavirus

Shown in this electron micrograph from 1986 is a single, negatively stained human papilloma virus (HPV), the primary culprit of skin warts and cervical cancer.

Note how the papillomavirus is non-enveloped, meaning that its outer protein coat, or capsid, is not covered by a lipid bilayer membrane. The HPV capsid looks roughly spherical, but, in fact, it has an icosahedral symmetry with a triangulation number equal to 7. Rather than a structure based on pentamers mixed with hexamers (like that of the soccer ball), the HPV capsid is composed of 72 L1 pentamers of two different types: 60 hexavalent pentamers and 12 pentavalent pentamers.

References: Visual Science / Wikipedia.
Photo Credit
: Laboratory of Tumor Virus Biology / National Cancer Institute.


The Structural Biology of HIV

HIV (human immunodeficiency virus) is composed of two strands of RNA (yellow), 15 types of viral proteins, and a few proteins (purple) from the last host cell it infected, all surrounded by a lipid bilayer membrane. Together, the molecules allow the virus to infect cells of the immune system and force them to build new copies of the virus. Each molecule in HIV plays a role in this process, from the first steps of viral attachment to the final process of budding.

25 years of research on the structural biology of HIV have revealed the atomic details of these proteins. These structures are all publicly available in the Protein Data Bank (PDB) archive. Using these data, researchers have designed new treatments for HIV infection, including effective drug regimens that halt the growth of the virus. The structures also provide new hope for development of a vaccine.

To learn more about the function of each of the viral proteins depicted, check out this interactive Flash activity.

The science behind the painting is described in: BaMBEd 40(5): 291-296.

Caption: courtesy of the RCSB Protein Data Bank.
Image Credit: David S. Goodsell at The Scripps Research Institute (TSRI), La Jolla, California, USA.

The Feminist Wire Associate Editor Joseph Osmundson today in the Los Angeles Review of Books (LARB):

"HIV has been present in my life because HIV has always touched those who live on our margins: gay people, poor people, people of color, people in prison, and these are my people, my family, my life. We know the statistics. We were born into the danger. We know that sex can kill. And yet, we are the newly infected. We see people living with. Living in spite of. Living. We are tired of being afraid of sex, of bodies. All people have affairs. All human bodies know disease. All bodies take risks. It is just that some of us pay more dearly for ours."


This is all the shit i fucking did

bacillus bacteria looks like multiple little nubs things that look like rabit food

Virus is made up of proteins, nucleic acuds, and some lipids that can reporduce only by infecting living cells.

The body of a virus is called capsid.

I group of virues that contrain RNA in their genetic information is the Retrovirus.

Capsid proteins bind to receptor proteins on the host cell to trick the cell into taking in the virus or its genetic material.

In a lytic infection, a virus enters a cell, makes copies of itself, and causes the cell to burst, releasing many copies of the virus.

A prophage is bacteriophage DNA that is embedded in the bacterial host’s DNA.

Viruses usually cause disease by infecting and destroying cells.

Antiboidtics fight against viruses.

Prokaryotes are differnert from other organisms because they lack nuclei. (also they are unicellual)

Prokaryotes that thrive in oxygen-free places are called Anaerobes.

Prokaryotes produce asexual by Binary fission.

Converting nitrogen into a form plants can use is known as nitrogen fixation

Plant cells do not contain chitin

Land plants most likly evloved from green algea

The term is alternation of generations, which refers to the two alternating phases of a plant’s life cycle: the gametophyte, or haploid phase, and the sporophyte, or diploid phase.

under unfavorable conditions Chlamydomonas forms a diploid zygote

the dominate state in moss is gametophyte

water is cared from the roots by xylem

fronds are the leaves of ferns

Tracheids are hollow cells with thick cell walls that make up xylem. Their function is to transport water through a plant.

The evolution of lignin made the cell walls of plants rigid. This enabled plants to grow upright and reach great heights.

gymno-sperms do not have flowers

the male reproductive structures of seed plants are called pollen grains.

Similarities: reproduce without requiring open water, produce seeds; Differences: Gymnosperms produce seeds in cones, the seeds are not encased in fruit, and wind carries pollen. Angiosperms produce seeds in flowers, the seeds are protected within a fruit, and animals play a large role in pollination.

Angiosperms, the mature seed is surrounded by fruit.

Meristem tissue is found in the tip of the plant, the steam where a leaf is growing out of and root cap.

tracheids + vessels = Xylem

Pholoem mainly transports functions of photosynthesis

Mature xylem cells have died, leaving behind only their cell walls. Mature phloem cells contain living cells.

most photosythesis from leafs come from palisade and spongy mesophyll

The epidermis and cuticle layers of dermal tissue, which form the outer covering of a leaf, protect tissues and limit water loss.

Stomata open when the air is cool and moist because the transpiration rate is low. In hot, dry air, stomata close to prevent excessive water loss from higher rates of transpiration.

The rise of water in a tall plant depends on capillart action and transportation pull.

Pressure-flow  hypothesis explains water and nutrient movement in phloem

Adehesion is the attraction between wather molecules and other substances.

Phloems main job is to transport sugar

A leaf is flat and thin to maximize its surface area for light absorption. The tough, waxy dermal layer prevents physical damage and water loss. The mesophyll performs photosynthesis to make sugars for the plant’s food. The vascular tissue transports water to the leaf and sugars away from the leaf.

anthers is the part that produces the male gametophyte sperm (for angiosperms)

pollination happens when pollen lands on the stigma

vegetative reporduction is the process in which a single plant produces many offspring identicle

The carpel is a specialized leaf that produces and shelters the female gametophytes and, later, seeds. It is located in the innermost part of the flower.

dormancy is when the embryo is alive but not growing

substances that stimulate cell division and cause dormant seeds to sprout is gibberellins

photoperiod is mesured by day length

Auxins stimulate the initiation of new roots and inhibit the growth of new shoot tips. Cytokinins stimulate the initiation of new shoots and inhibit the growth of new roots.

A tropism is a growth response to a stimulus. Stems show phototropism when they grow toward light. Roots show gravitropism when they grow downward.

Disease causing organismas are known as Pathogens.

Many protists do not fit in the catogory of Animal-like/Plant-like/Fungus-like

Protists can reproduce rapidly through asexual reproduction in a favorable environment. If conditions become unfavorable, protists reproduce sexually, which results in new traits that may help the population survive.

cat turd looking protist moves by cilia

Amoebas do not have a rigid cell membrane

Alternation of generations is the process of alternating between diploid and haploid phases.

Cilia and flagella are the organs of movement in the ciliates and flagellates. The structures are nearly identical, but produce motion differently. In general, cilia are comparatively shorter than flagella. Cilia move somewhat like side oars on a boat. Flagella are located at an end of an organism and move back and forth.

Small photosynthetic organisms near the ocean’s surface are called photoplankton

Slime molds:
Slime molds are found mainly in decaying organic matter

Slime molds produce sporangia and spores when food is scarce for greater mobility and increased genetic diversity. Greater spore mobility increases the organism’s chances of finding another source of food. Greater diversity helps it adapt to changes in environmental conditions.

Not all fungi is unicellular.

Fungi has a symbiotic relationship between green algea or cyanobacterium known as Lichen

Viruses, Vol. 7, Pages 1474-1491: Chondroitin Sulfate N-acetylgalactosaminyltransferase-2 Contributes to the Replication of Infectious Bursal Disease Virus via Interaction with the Capsid Protein VP2

Infectious bursal disease virus (IBDV) is a birnavirus that causes a highly contagious immunosuppressive disease in young chickens. The capsid protein VP2 of IBDV plays multiple roles in its life cycle. To more comprehensively understand the functions of VP2 involved in the communication between virus and host, we used yeast two-hybrid screening to identify the cellular factors that interact with this protein. We found that chondroitin sulfate N-acetylgalactosaminyltransferase-2 (CSGalNAcT2), a typical type II transmembrane protein located in Golgi apparatus, could interact with VP2, and we confirmed this interaction by co-immunoprecipitation and confocal laser scanning microscopy assays. Additionally, up-regulation of CSGalNAcT2 during IBDV infection was observed. Overexpression and #siRNA-mediated knockdown of CSGalNAcT2 assays suggested that CSGalNAcT2 promoted IBDV replication. Moreover, this enhancing effect of CSGalNAcT2 could be inhibited by Brefeldin A, which is a Golgi-disturbing agent. This indicated that the integrity of Golgi apparatus structure was involved in the function of CSGalNAcT2. Taken together, we concluded that CSGalNAcT2, located in the Golgi apparatus, contributed to the replication of IBDV via interaction with VP2. #MDPI

Infectious mononucleosis.

Infectious mononucleosis.

Clin Transl Immunology. 2015 Feb;4(2):e33

Authors: Balfour HH, Dunmire SK, Hogquist KA

Infectious mononucleosis is a clinical entity characterized by pharyngitis, cervical lymph node enlargement, fatigue and fever, which results most often from a primary Epstein-Barr virus (EBV) infection. EBV, a lymphocrytovirus and a member of the γ-herpesvirus family, infects at least 90% of the population worldwide, the majority of whom have no recognizable illness. The virus is spread by intimate oral contact among adolescents, but how preadolescents acquire the virus is not known. During the incubation period of approximately 6 weeks, viral replication first occurs in the oropharynx followed by viremia as early as 2 weeks before onset of illness. The acute illness is marked by high viral loads in both the oral cavity and blood accompanied by the production of immunoglobulin M antibodies against EBV viral capsid antigen and an extraordinary expansion of CD8(+) T lymphocytes directed against EBV-infected B cells. During convalescence, CD8(+) T cells return to normal levels and antibodies develop against EBV nuclear antigen-1. A typical clinical picture in an adolescent or young adult with a positive heterophile test is usually sufficient to make the diagnosis of infectious mononucleosis, but heterophile antibodies are not specific and do not develop in some patients especially young children. EBV-specific antibody profiles are the best choice for staging EBV infection. In addition to causing acute illness, long-term consequences are linked to infectious mononucleosis, especially Hodgkin lymphoma and multiple sclerosis. There is no licensed vaccine for prevention and no specific approved treatment. Future research goals are development of an EBV vaccine, understanding the risk factors for severity of the acute illness and likelihood of developing cancer or autoimmune diseases, and discovering anti-EBV drugs to treat infectious mononucleosis and other EBV-spurred diseases.

PMID: 25774295 [PubMed]

via pubmed: lymphoma daily
PLOS Computational Biology: Asymmetric Genome Organization in an #RNA Virus Revealed via Graph-Theoretical Analysis of Tomographic Data

@rnomics/bioinfo 200) && (this.width >= this.height) ? 200: true); max-height: 200px; height: expression((this.height > 200) && (this.height >= this.width) ? 200: true); border: none;’/> Author Summary Viruses are responsible for devastating illnesses in humans and cause significant commercial losses in livestock and crops. Their genetic material is transported into their host organisms via protein containers, called viral capsids, that act as Trojan horses: they release their cargo into the cells of their hosts, hijacking their molecular machinery for the production of progeny viruses. Imaging techniques exploiting the symmetric structures of viral capsids have been used to … posted by friends:  (1) @BioinformaticsP: PCB: Asymmetric Genome Organization in an #RNA Virus Revealed via Graph-Theoretical Analysis of Tomographic Dat… 20.03.2015 21.18.22 posted by followers of the list:  (0)

Asymmetric Genome Organization in an #RNA Virus Revealed via Graph-Theoretical Analysis of Tomographic Data

by James A. Geraets, Eric C. Dykeman, Peter G. Stockley, Neil A. Ranson, Reidun Twarock Cryo-electron microscopy permits 3-D structures of viral pathogens to be determined in remarkable detail. In particular, the protein containers encapsulating viral genomes have been determined to high resolution using symmetry averaging techniques that exploit the icosahedral architecture seen in many viruses. By contrast, structure determination of asymmetric components remains a challenge, and novel analysis methods are required to reveal such features and characterize their functional roles during infection. Motivated by the important, cooperative roles of viral genomes in the assembly of single-stranded #RNA viruses, we have developed a new analysis method that reveals the asymmetric structural organization of viral genomes in proximity to the capsid in such viruses. The method uses geometric constraints on genome organization, formulated based on knowledge of icosahedrally-averaged reconstructions and the roles of the #RNA-capsid protein contacts, to analyse cryo-electron tomographic data. We apply this method to the low-resolution tomographic data of a model virus and infer the unique asymmetric organization of its genome in contact with the protein shell of the capsid. This opens unprecedented opportunities to analyse viral genomes, revealing conserved structural features and mechanisms that can be targeted in antiviral drug design. #PLoS


HIV: È un retrovirus del genere lentivirus, caratterizzato cioè dal dare origine a infezioni croniche, che sono scarsamente sensibili alla risposta immunitaria ed evolvono lentamente ma progressivamente e che, se non trattate, possono avere un esito fatale.Il virione di HIV ha una struttura sferica del diametro di circa 100-120 nm, con due membrane esterne (pericapside), formate dal materiale della cellula che lo ha prodotto: le membrane sono un capside di forma conoide e un envelope che ospita le glicoproteine di membrana virali gp120 e gp41: la conoscenza di queste proteine è stata di particolare importanza nella lotta al virus poiché agendo su di esse si può rallentare o frenare il contagio di nuove cellule.