Friday, 7 September 2012

Lynn Margulis - endosymbiosis - hybridogenesis

It appears that Lynn Margulis championed a few ideas on how some insects began inhabiting other insects and plants... leading to changes in growth patterns.  I first read about her theories recently in Nick Lane's Power, Sex, Suicide: Mitochondria and the meaning of life, in a discussion about the endosymbiosis of mitochondria into the eukaryote...

Just now I remembered a theory that I'd read somewhere a few years back.. that the caterpillar and the butterfly were once two separate insects, and somehow the two genomes mixed... (by virus? or microRNA? or endosymbiosis? or mimicry?)  I had a quick search and discovered this blog article from BugTracks:
"modern metamorphosing insects arose when velvet worms (phylum Onychophora) somehow hybridized with primitive arthropods"
"she somehow intuited that I would one day become obsessed with gall-making insects, and she showed me a chapter in a book she had edited in which it was hypothesized that fleshy fruits arose when gall-making insects happened to induce galls in the reproductive tissues of plants, so that the genetic coding for gallmaking was incorporated into the plant’s heritable genome."
read more:  http://bugtracks.wordpress.com/2011/11/22/lynn-margulis/
and this paper: Caterpillars evolved from onychophorans by hybridogenesis
and this response: Caterpillars did not evolve from onychophorans by hybridogenesis

Lynn Margulis died of a stroke, 22 November, 2011.

Other interesting effects are Mimicry, Mimetism, Camouflage etc... changes forced through environmental pressures. ...

[Parthenogenesis - Hybridogenesis]

Thursday, 8 December 2011

Sick Building Syndrome - due to fungi?

News coming from the World Allergy Organization XXII World Allergy Congress this week... suggests that fungi might be responsible for Sick Building Syndrome (SBS).  SBS has a range of symptoms, such as cough, nose or throat irritation, headache, fatigue, and concentration difficulty.  I was alerted to this via the Medscape Newsletter... But I have traced it back to the source at the World Allergy Congress:


http://www.medscape.com/viewarticle/754933

http://www.worldallergy.org/wac2011/

http://wao.confex.com/wao/2011wac/webprogram/Paper4067.html


Boechat, J. L., Rios, J. L., et al (2011) "Sick Building Syndrome (SBS) Among Workers of Two Buildings and Exposure to Indoor Fungal Allergens in Rio De Janeiro, Brazil"



Friday, 22 October 2010

Candida and Yeast Genome Databases and OrthologID

The full Candida Genome Database can be found here:  http://www.candidagenome.org/

Search the genome and view/download sequences.  Read the tutorials on Gene Ontology - which describes the complete biology of individual gene products in any organism...

Other strains also available:

  • Candida albicans WO-1
  • Candida dubliniensis CD36
  • Candida glabrata CBS138
  • Candida guilliermondii ATCC 6260
  • Candida lusitaniae ATCC 42720
  • Candida parapsilosis CDC 317
  • Candida tropicalis MYA-3404
  • Debaryomyces hansenii CBS767
  • Lodderomyces elongisporus NRLL YB-4239


The Saccharomyces Genome Database can be found here:  http://www.yeastgenome.org/

What I am interested in, is Orthologs... between different species.  Orthologs between the microbe and its host... .. and resources that enable one to compare two or more genomes... Genome Orthology?  I am still in Year 2 level biology (at the age of 40 and after 20+ years interest)... but I see potential in comparing the ontologies of genes in different genomes...

Isolation and characterization of human orthologs of yeast CCR4–NOT complex subunits
http://nar.oxfordjournals.org/content/28/3/809.full

Orthology between genomes of Brachypodium, wheat and rice
http://www.biomedcentral.com/1756-0500/2/93

OrthologID: automation of genome-scale ortholog identification within a parsimony framework

Tuesday, 5 October 2010

Synchytrium endobioticum: Potato Wart disease or Black Scab

By USDA-APHIS-PPQ [public domain]
Synchytridium endobioticum

Synchytrium endobioticum is a chytrid fungus (chytridiomycota - other species of which are known for their part in amphibian decline, esp. toads; and also maize- and alfalfa-attacking species...)

It affects potatoes and other uncultivated plants of the Solanum genus.

The zoospores of Synchytrium infect suitable epidermal cells on the host.  The infected cells produce more zoospores, swell up, divide and surround the dividing zoospores... producing the characteristic wart.

Synchytrium endobioticum was added to the US Federal for agricultural plant pathogens: Public Health Security and Bioterrorism Preparedness and Response Act (June 12, 2002).

Tuesday, 30 March 2010

Oak Galls: Cynipidae gall flies


Oak Galls produced by the gallfly of the family Cynipidae.  Can be found all over UK... young Oaks appear to be more susceptible than older.  The acorn has been infected by a larvae which alters the normal growth of the acorn.  The flesh of the gall is less tough than an acorn would be and is larger and more rounded.


[Photos by Oliver (cc)]

Wednesday, 13 August 2008

Saccharomyces cerevisiae: Human and Yeast Eukaryote RNA Polymerase Subunits

Species: cerevisiae (and toy) (from latin, 'of beer')
Genus: Saccharomyces (from latin, 'sugar mold')
Family: Saccharomycetaceae
Order: Saccharomycetales
Class: Saccharomycetes
Subphylum: Saccharomycotina
Phylum: Ascomycota

Also known as Brewer's Yeast, Ale Yeast, Baker's Yeast, Budding Yeast
This species is the main source of nutritional yeast and yeast extract.
It is estimated that yeast shares 23% of its genome with that of humans.

Saccharomycetes is the most studied of the yeasts due to its availability and its being around for thousands of years...

Six Human RNA Polymerase Subunits Functionally Substitute for Their Yeast Counterparts
(view PDF at American Society of Microbiology)

McKune, Keith; Moore, Paul A.; Hull, Melissa W.; Woychik, Nancy A.
MOLECULAR AND CELLULAR BIOLOGY, Dec. 1995, p. 6895–6900

This study looks at Saccharomyces cerevisiae pol II

"Immunoprecipitation of the cell extracts from yeast cells containing either of the human subunits that function in place of their yeast counterparts in vivo suggested that they assemble with the complete set of yeast RNA polymerase II subunits. Overall, a total of six of the seven human subunits tested previously or in this study are able to substitute for their yeast counterparts in vivo, underscoring the remarkable similarities between the transcriptional machineries of lower and higher eukaryotes."

Tuesday, 12 August 2008

Candida albicans: and Psoriasis

A study in 2001 by A. Waldman et al at Rappaport Institute, Haifa, Israel printed in Mycoses (2001, May;44(3-4):77-81) looked into the correlation between C.Albicans and other Candida species in the saliva and faeces of Psoriatic patients. A predominance of C.albicans and C.rugosa were found.
"Our results reinforce the hypothesis that C. albicans is one of the triggers to both exacerbation and persistence of psoriasis."
Waldman, A., A. Gilhar, L. Duek, and I. Berdicevsky. 2001. Incidence of Candida in psoriasis—a study on the fungal flora of psoriatic patients. Mycoses 44:77–81.

This does not mean that C.albicans is the cause of Psoriasis. Psoriasis appears to have several causal agents and quite possibly two patients with psoriasis do not share the same causal agent. Other agents are trauma to the skin, streptococcal infections, and even lithium, antimalarial agents, NSAIDs and angiotensin-converting enzyme inhibitors can exacerbate or possibly induce psoriasis...

C.albicans has only been hinted at as existing more in Psoriatic patients than those with dermatitis or normal but it is not a hugely significant difference and thus has been declared irrelevant by one later study in 2007
[Leibovici et al, 2007. Prevalence of Candida on the tongue and intertriginous areas of psoriatic and atopic dermatitis patients. Mycoses 51:63-66]

Taphrina pruni: Pocket Plum galls


The photo here is from Hainault Forest's website which shows many other examples of galls caused by various agents including fungi, insects etc.

Genus: Taphrina
Family: Taphrinaceae
Order: Taphrinales

Taphrina pruni transforms the ovaries of plums into hollow galls without a stone - hence the name 'Pocket Plum'.

Taphrina deformans: Peach Leaf Curl


[photos from The Fifth Kingdom Chapter 4b and Backyard Nature]

Genus: Taphrina
Family: Taphrinaceae
Order: Taphrinales

In Peach Leaf Curl the leaves become thickened, distorted and turn yellow or reddish in colour, later causing the leaves to turn brown, dusty with ascospores and to fall. Taphrina deformans also affects the flowers and peach fruits, causing them either to drop early or become crooked at the stem or develop reddish to purple, wart-like deformities on the fruit surface.

Peach Leaf Curl (Kearnseyville Tree Fruit Research and Education Centre, West Virginia University)


"the lifecycle begins with an ascospore. The ascospore itself produces smaller spores by budding. On the leaf surface these spores produce more spores by budding, and when conditions are just right the spores sprout mycelium -- maybe after two spores fuse together. The full story isn't yet known."
"The mycelium enters the leaf and works its way among the leaf's cells. At this time, while a lot of complex genetic stuff is going on inside the mycelium cells, something causes the leaf's cells to elongate, causing twisting and blistering of the leaf. Eventually certain cells of the mycelium begin enlarging, growing to such an extent that they cause the leaf's cuticle, or "skin," to burst. Now these special, enlarged mycelium cells work themselves onto the leaf's surface and form a very thin surface called the hymenium consisting of stacked-together, clublike asci. The asci rupture, releasing ascospores, and now the life cycle starts over."
[from Backyard Nature]

Candida albicans: Escaping the host's immune response

Genus: Candida
Family: Saccharomycetaceae
Order: Saccharomycetales
Class: Saccharomycetes
Subphylum: Saccharomycotina
Phylum: Ascomycota

So... the question that I would like to ask is ... If C.albicans is eluding the immune system, then isn't the immune system compromised? Does the immune system have to be compromised already for infection by C.albicans to occur? The following are quotes from a paper investigating the effect of the yeast and hyphal forms of C.albicans on differentiating monocytes in the human immune system.

"A special feature of C. albicans that is likely to play an important role in evasion of the immune response is the morphological transition from a unicellular yeast (Y) form to an elongated, multinucleate hyphal or mycelial form through the critical stage of germ tube (GT) formation. Conversion from the Y form to the GT form is strictly associated with virulence, as demonstrated by the fact that several mutants with the hypha-specific genes deleted, as well as wild-type strains unable to grow into the mycelial form, invariably have low systemic pathogenicity"

"The different modulatory effects exerted by Y and GT forms of C. albicans on differentiating monocytes may be a key phenomenon that contributes to an explanation of the intriguing paradox that distinguishes this fungus, as represented by its persistence in some body compartments as a commensal yeast or as pathogen hyphae despite the presence of vigorous cellular and humoral systemic immune responses."

"Thus, the differentiation of human monocytes into DCs appears to be tunable and exploitable by C. albicans to elude immune surveillance."

Candida albicans Yeast and Germ Tube Forms Interfere Differently with Human Monocyte Differentiation into Dendritic Cells: a Novel Dimorphism-Dependent Mechanism To Escape the Host's Immune Response
Antonella Torosantucci, Giulia Romagnoli, Paola Chiani, Annarita Stringaro, Pasqualina Crateri, Sabrina Mariotti, Raffaela Teloni, Giuseppe Arancia, Antonio Cassone, and Roberto Nisini

Infect Immun. 2004 February; 72(2): 833–843. doi: 10.1128/IAI.72.2.833-843.2004.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=321580

Taphrina betulina - Witches Broom


[photo by James Lindsey@Wikimedia Commons]

Genus: Taphrina
Family: Taphrinaceae
Order: Taphrinales

Birch Witches' Brooms are masses of densely branched small twigs that resemble a witch's broom stuck in the tree's canopy. Witches' Brooms can be induced by various parasites including Taphrina betulina Rostrup. (Current thinking believes gall inducing phytoplasma may be responsible for some witches' brooms.)

Witches' Broom on Wikipedia

Birch Leaf Curl is induced by a Taphrina betulae (Fckl.) Johans. infection.

It has been found that Taphrina betulina infections in White Birch (Betula pubescens) trees cause reduced growth (by an average of 25%) and vigour, and 'Witches' Broom' growths (pictured here), the number and sizes of which correlate to the DBH (diameter at breast height), but not to the reductions in height and vigour [1].

1. (from Abstract) The effects of Taphrina betulina infection on growth of Betula pubescens, Y. A. Simmons and S. Woodward, European Journal of Forest Pathology, 2007 - Vol 24, Issue 5, p.277-286

Ascomycetes: Taphrina

[from Wikipedia - highlighting is not]

Genus: Taphrina
Family: Taphrinaceae
Order: Taphrinales
Class: Taphrinomycetes
Subphylum: Taphromycotina
Phylum: Ascomycota

Taphrina is fungal genus within the Ascomycota that causes leaf and catkin curl diseases and witch's brooms of certain flowering plants. One of the more commonly observed species causes peach leaf curl.

Taphrina typically grow as yeasts during one phase of their life-cycles, then infect plant tissues in which typical hyphae are formed, and ultimately they form a naked layer of asci on the deformed, often brightly pigmented surfaces of their hosts.

No discrete fruitbody is formed outside of the gall-like or blister-like tissues of the hosts. The asci form a layer lacking paraphyses, and they lack croziers. The acospores frequently bud into multiple yeast cells within the asci.

Phylogenetically, Taphrina is a member of a basal group within the Ascomycota, and type genus for the subphylum Taphrinomycotina, the class Taphrinomycetes, and order Taphrinales.

Some common Taphrina species:

  • Taphrina betulina Rostrup - Birch Witches' Broom
  • Taphrina pruni Tul. - Pocket Plums (gall affecting fruit on Blackthorn)
  • Taphrina carpini - on Hornbeam
  • Taphrina deformans - Peach Leaf Curl
  • Taphrina caerulescens - Oak Leaf Blister
  • Taphrina sacchari - Maple leaf blister
  • Taphrina populina - Poplar