User:Puhlaa/notes

The genus Actinomadura is one of four genera of actinobacteria that belong to the family Thermomonosporaceae. It contains aerobic, Gram-positive, non-acid-fast, non-motile, chemo-organotrophic actinomycetes that produce well-developed, non-fragmenting vegetative mycelia and aerial hyphae that differentiate into surface-ornamented spore chains. These chains are of various lengths and can be straight, hooked or spiral.^[1] The genus currently comprises 37 species with validly published names with standing in nomenclature,^[2] although the species status of some strains remains uncertain, and further comparative studies are needed.^[1]

Members of the genus are characterized chemotaxonomically by type III/B cell walls (meso-diaminopimelic acid and madurose are present) with peptidoglycan structures of the acetyl type. The predominant menaquinone types are MK-9(H4), MK-9(H6) and MK-9(H8). The phospholipid pattern is PI (diphosphatidylglycerol and phosphatidylinositol are present as major phospholipids) and the fatty acid pattern is type 3a (branched saturated and unsaturated fatty acids plus tuberculostearic acid).^[3]

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Streptomyces
Slide culture of a Streptomyces species
Scientific classification
Kingdom:	Bacteria
Phylum:	Actinobacteria
Class:	Actinobacteria
Order:	Actinomycetales
Family:	Streptomycetaceae
Genus:	Streptomyces Waksman & Henrici 1943
Diversity
[[#Selected species|About 550 species]]
Synonyms
Streptoverticillium

Streptomyces is the largest genus of Actinobacteria and the type genus of the family Streptomycetaceae.^[4] Over 500 species of Streptomyces bacteria have been described.^[5] As with the other Actinobacteria, streptomycetes are Gram-positive, and have genomes with high GC content.^[6] Found predominantly in soil and decaying vegetation, most streptomycetes produce spores, and are noted for their distinct "earthy" odor that results from production of a volatile metabolite, geosmin.

Streptomycetes are characterised by a complex secondary metabolism.^[6] They produce over two-thirds of the clinically useful antibiotics of natural origin (e.g., neomycin and chloramphenicol).^[7] The now uncommonly used streptomycin takes its name directly from Streptomyces. Streptomycetes are infrequent pathogens, though infections in humans, such as mycetoma, can be caused by S. somaliensis and S. sudanensis, and in plants can be caused by S. caviscabies, S. acidiscabies, S. turgidiscabies and S. scabies.

is the type genus of the family Streptomycetaceae^[8] and currently covers close to 576 species with the number increasing every year.^[9] Acidiphilic and acid-tolerant strains which were initially classified under this genus have later been moved to Kitasatospora (1997) ^[10] and Streptacidiphilus (2003).^[11] Species nomenclature are usually based on their color of hyphae and spores.

Saccharopolyspora erythraea was formerly placed in the present genus too (as Streptomyces erythraeus).

The genus Streptomyces includes aerobic, Gram-positive, filamentous bacteria which produce well developed vegetative hyphae (between 0.5-2.0 µm in diameter) with branches. They form a complex substrate mycelium that aids in scavenging organic compounds from their substrates.^[12] Although the mycelium and the aerial hyphae that arises from them are amotile, mobility is achieved by dispersion of spores.^[12] Spore surfaces may be hairy, rugose, smooth, spiny or warty.^[13] In some species, aerial hyphae consist of long, straight filaments, which bear 50 or more spores at more or less regular intervals, arranged in whorls (verticils). Each branch of a verticil produces, at its apex, an umbel which carries from two to several chains of spherical to ellipsoidal smooth or rugose spores.^[12] Some strains form short chains of spores on substrate hyphae. Sclerotia-, pycnidia-, sporangia- and synnemata-like structures are produced by some strains.

The complete genome of "S. coelicolor strain A3(2)" was published in 2002.^[14] At the time, the "S. coelicolor" genome was thought to contain the largest number of genes of any bacterium.^[14] The chromosome is 8,667,507 bp long with a GC-content of 72.1%, and is predicted to contain 7,825 protein-encoding genes.^[14] Taxonomically, "S. coelicolor A3(2)" belongs to the species S. violaceoruber, and is not a validly described separate species; "S. coelicolor A3(2)" is not to be mistaken for the actual S. coelicolor (Müller), although it is often referred to as S. coelicolor for convenience.^[15]

The first complete genome sequence of S. avermitilis was completed in 2003.^[16] Each of these genomes forms a chromosome with a linear structure, unlike most bacterial genomes, which exist in the form of circular chromosomes.^[17] The genome sequence of S. scabies, a member of the genus with the ability to cause potato scab disease, has been determined at the Wellcome Trust Sanger Institute. At 10.1 Mbp long and encoding 9,107 provisional genes, it is the largest known Streptomyces genome sequenced, probably due to the large pathogenicity island.^[17][18]

In recent years, biotechnology researchers have begun using Streptomyces species for heterologous expression of proteins. Traditionally, Escherichia coli was the species of choice to express eukaryotic genes, since it was well understood and easy to work with.^[19][20] Expression of eukaryotic proteins in E. coli may be problematic. Sometimes proteins do not fold properly, which may lead to insolubility, deposition in inclusion bodies, and loss of bioactivity of the product.^[21] Though E. coli have secretion mechanisms, these are of low efficiency and result in secretion into the periplasmic space, whereas secretion by a Gram-positive bacterium such as a Streptomyces sp. results in secretion directly into the extracellular medium. In addition, Streptomyces spp. have more efficient secretion mechanisms than E.coli. The properties of the secretion system is an advantage for industrial production of heterologously expressed protein because it simplifies subsequent purification steps and may increase yield. These properties among others make Streptomyces spp. an attractive alternative to other bacteria such as E. coli and Bacillus subtilis.^[21]

So far ten species of bacteria belonging to this genus have been found to be pathogenic to plants.^[9]

1. S. scabiei,
2. S. acidiscabies,
3. S. europaeiscabiei,
4. S. luridiscabiei,
5. S. niveiscabiei,
6. S. puniciscabiei,
7. S. reticuliscabiei,
8. S. stelliscabiei,
9. S. turgidiscabies (scab disease in potatoes) &
10. S. ipomoeae (soft rot disease in sweet potatoes)

Streptomyces is the largest antibiotic-producing genus, producing antibacterial, antifungal, and antiparasitic drugs, and also a wide range of other bioactive compounds, such as immunosuppressants.^[22] Almost all of the bioactive compounds produced by Streptomyces are initiated during the time coinciding with the aerial hyphal formation from the substrate mycelium.^[12]

Streptomycetes produce numerous antifungal compounds of medicinal importance, including nystatin (from S. noursei), amphotericin B (from S. nodosus), and natamycin (from S. natalensis).

Members of the Streptomyces genus are the source for numerous antibacterial pharmaceutical agents; among the most important of these are:

• Chloramphenicol (from S. venezuelae)^[23]
• Daptomycin (from S. roseosporus)^[24]
• Fosfomycin (from S. fradiae)^[25]
• Lincomycin (from S. lincolnensis)^[26]
• Neomycin (from S. fradiae)^[27]
• Puromycin (from S. alboniger)^[28]
• Streptomycin (from S. griseus)^[29]
• Tetracycline (from S. rimosus and S. aureofaciens^[30]

Clavulanic acid (from S. clavuligerus) is a drug used in combination with some antibiotics (like amoxicillin) to block and/or weaken some bacterial-resistance mechanisms by irreversible beta-lactamase inhibition.

S. avermitilis is responsible for the production of one of the most widely employed drugs against nematode and arthropod infestations, ivermectin.

Less commonly, streptomycetes produce compounds used in other medical treatments: migrastatin (from S. platensis) and bleomycin (from S. verticillus) are antineoplastic (anticancer) drugs.

S. hygroscopicus and S. viridochromeogenes produce the natural herbicide bialaphos.

• Antimycin A - compound produced by this bacterium used in piscicides

• Baumberg S (1991). Genetics and Product Formation in Streptomyces. Kluwer Academic. ISBN 978-0-306-43885-1.
• Gunsalus IC (1986). Bacteria: Antibiotic-producing Streptomyces. Academic Press. ISBN 978-0-12-307209-2.
• Hopwood DA (2007). Streptomyces in Nature and Medicine: The Antibiotic Makers. Oxford University Press. ISBN 978-0-19-515066-7.
• Dyson P, ed. (2011). Streptomyces: Molecular Biology and Biotechnology. Caister Academic Press. ISBN 978-1-904455-77-6.

• Current research on Streptomyces coelicolor at the Norwich Research Park
• Some current Streptomyces Research & Methods / Protocols / Resources
• S. avermitilis genome homepage (Kitasato Institute for Life Sciences)
• S. coelicolor A3(2) genome homepage (Sanger Institute)
• Streptomyces.org.uk homepage (John Innes Centre)
• StrepDB - the Streptomyces genomes annotation browser
• Streptomyces Genome Projects from Genomes OnLine Database

Chiropractors obtain a first professional degree in the field of chiropractic.^[1] The World Health Organization (WHO) guidelines for chiropractic education suggest three major full-time educational paths culminating in either a DC, DCM, BSc, or MSc degree.^[2] Doctors of chiropractic often argue that their education is as good or better than medical doctors'. A comparative study of the curriculum content of North American chiropractic and medical colleges concluded that with regard to basic and clinical sciences, medical and chiropractic programs are similar, both in the types of subjects offered and in the time allotted to each subject.^[3] However, chiropractic colleges have the least stringent matriculation requirements,^[4] and the clinical internship is considerably less rigorous when compared to a medical/osteopathic internship.^[5]

Accredited chiropractic programs in the U.S. require that applicants have 90 semester hours or three years of undergraduate education with a grade point average of at least 3.0 on a 4.0 scale prior to starting chiropractic college; some programs now also require a bachelor's degree.^[6] Canada requires a minimum three years of undergraduate education for applicants, followed by at least 4200 instructional hours of full-time chiropractic education for matriculation through an accredited chiropractic program.^[7] Since 2005, graduates of the Canadian Memorial Chiropractic College (CMCC) are formally recognized to have at least 7–8 years of university level education.^[8][9] Specialty and graduate training is also available to chiropractors, available through part-time or full-time postgraduate residency programs such as chiropractic orthopedics, chiropractic clinical sciences, sports chiropractic, and radiology.^[10]

There are 18 accredited Doctor of Chiropractic programs in the U.S.,^[11] 2 in Canada,^[12] 6 in Australasia,^[13] and 5 in Europe.^[14] All but one of the chiropractic colleges in the U.S. are privately funded, but in several other countries they are in government-sponsored universities and colleges.^[15] Of the two chiropractic colleges in Canada, one is publicly funded (UQTR) and one is privately funded (CMCC). In 2005, CMCC was granted the privilege of offering a professional health care degree under the Post-secondary Education Choice and Excellence Act, which sets the program within the hierarchy of education in Canada as comparable to that of other primary contact health care professions such as medicine, dentistry and optometry.^[8][9]

In the U.S., chiropractic schools are accredited through the Council on Chiropractic Education (CCE) , in Canada they are accredited through the Canadian Federation of Chiropractic Regulatory and Educational Accrediting Boards (CFCREAB), while the General Chiropractic Council (GCC) is the statutory governmental body responsible for the regulation of chiropractic in the UK.^[16][17][18] It is the job of these councils to determine and to certify the achievement and maintenance of appropriate national standards of education for chiropractors in their respective nations. The accreditation councils in the U.S., Canada, Australia and Europe have also joined to form CCE-International (CCE-I) as a model of accreditation standards with the goal of having credentials standardized internationally.^[19]

Upon graduation, chiropractic students must pass national and/or state/provincial board examinations before being licensed to practice in a particular jurisdiction.^[20][21] Depending on the location, continuing education may be required each year to renew these licenses.^[22][23]

There are an estimated 49,000 chiropractors in the U.S. (2008),^[24] 6,500 in Canada (2010),^[25] 2,500 in Australasia (2000),^[26] and 1,500 in the UK (2000).^[27] A 2008 commentary proposed that the chiropractic profession actively regulate itself to combat abuse, fraud, and quackery, which are more prevalent in chiropractic than in other health care professions, violating the social contract between patients and physicians.^[28] To achieve this, regulatory colleges and chiropractic boards in the U.S., Canada, Mexico, the UK and Australia are responsible for protecting the public, standards of practice, disciplinary issues, quality assurance and maintenance of competency.^[29][30] A study of California disciplinary statistics during 1997–2000 reported 4.5 disciplinary actions per 1000 chiropractors per year, compared to 2.27 for MDs; the incident rate for fraud was 9 times greater among chiropractors (1.99 per 1000 chiropractors per year) than among MDs (0.20).^[31]

[1]

The conclusion of the chiropractic lead violates WP:LEAD

Consistent with WP:NPOV, the body of the chiropractic article (in safety) accurately reviews the unresolved debate in the literature regarding the association between chiropractic manipulation and stroke by discussing:

1. The temporal association: "Collectively, these data suggest that spinal manipulation is associated with frequent, mild and transient adverse effects as well as with serious complications which can lead to permanent disability or death."1
2. The potential for under-reporting: "Retrospective investigations have repeatedly shown that under-reporting is close to 100%."1
3. Deaths that have been associated: "Twenty six fatalities were published in the medical literature and many more might have remained unpublished. The alleged pathology usually was a vascular accident involving the dissection of a vertebral artery."2
4. The lack of definitive evidence for causation: "Yet causal inferences are, of course, problematic. Vascular accidents may happen spontaneously or could have causes other than spinal manipulation. A temporal relationship is insufficient to establish causality, and recall bias can further obscure the truth."1 and "Weak to moderately strong evidence exists to support causation between CMT and VAD and associated stroke. Further research, employing prospective cohort study designs, is indicated to uncover both the benefits and the harms associated with CMT."3
5. Evidence that a stroke may already be in progress when a person visits a chiropractor: "The association between chiropractic visits and VBA stroke is similar to the association between physician visits and VBA stroke. This suggests that, on average, patients who seek chiropractic care for neck pain or headaches, and who then developed a VBA stroke may have actually been in the prodromal phase of a stroke when consulting the chiropractor; that is, the neck pain or headaches, which lead them to seek care were early symptoms of a VBA stroke." and "because this increased risk is also seen in those seeking health care from their primary care physician, this association is likely due to patients with headache and neck pain from VBA dissection seeking care before their stroke."4

Thus, the body of the article accurately presents both sides of an unresolved debate in the literature.

However, the lead of the article is concluded by: "Spinal manipulation is frequently associated with mild to moderate adverse effects, with serious or fatal complications in rare cases. 1 A systematic review determined that the risk of death from manipulations to the neck by far outweighs the benefits. 2"

• As per WP:LEAD: "The lead should be able to stand alone as a concise overview of the article. It should define the topic, establish context, explain why the subject is interesting or notable, and summarize the most important points—including any prominent controversies."

Thus, the lead of the article does not accurately summarize the body of the article, nor does it include any of the prominent controversies. The lead currently violates WP:LEAD and WP:NPOV by not accurately summarizing the body or including any mention at all of the prominent controversies.Puhlaa (talk) 02:12, 15 January 2011 (UTC)

I am somewhat stuck here, but from what Brangifer has suggested I am currently leaning towards one of two possibilities to deal with this issue until better research is available that conform to policy:

1. Remove the specific mention of Ernst-death and just add the Ernst-death citation to the previous sentence. This is definitely the simplest way to go.
2. Alternatively, perhaps we should just the mention of the controversy as (has been done in VAD) "The association between chiropractic neck manipulation and vertebral artery dissection is disputed by proponents of these treatment modalities.(Ernst 2007)"

Thoughts?Puhlaa (talk) 02:12, 15 January 2011 (UTC)

Nice work setting up that LEAD/NPOV issue. I think the framework will be very helpful. I prefer a little more info in the lead, so i like #2 as well as Ernst (with some context). Maybe we can say, in combination of Ernst and Cochrane (and Brangifer), something like:

Current consensus in the medical community is that the benefits of cervical manipulation have not been established, and since there is an association between treatment and VA injury/stroke, with the potential for death, and with the possibility of under-reporting, that the precautionary principle applies and the risk outweighs the benefit, at least for now. Research is not definitive, however, and major reviews of the literature agree that further study is needed to established the scope and causal relationship involved. Anatomical research suggests that healthy vertebral arteries do not experience more stress during manipulation than in many regular activities, and there is evidence that the association between CSM and VAD may be due to pre-existing conditions (patients with a vertebral artery condition seeking Chiropractic care). Many Chiropractors defend their practice, citing flaws in prior studies which depended on case reports and surveys across vastly different time-periods where specific conditions such as VAD had not been formally recognized. They also point generally to the very high number of incident-free treatments about which patients describe a positive response.

I'd like to see something along those lines, so that our reader can know as much as we know. I believe the majority of the above can be sourced with secondary MEDRS studies, and the parts that cannot I believe fall under RS anyway. Ocaasi (talk) 07:05, 15 January 2011 (UTC)

Is your proposal what you would like to see in the lead? or in the body? It seems far too long and inclusive for the lead. For the lead I might suggest taking only the first 2 sentences in your proposal and finessing them and adding references. I have proposed this below. If your proposal is meant for the body, I like very much how you have put it all in context, and it reads very much like I would expect a non-biased review paper to sound. However, I dont see how you would ever get it past the OR arguement with additions like "at least for now" and "however", which have caused me problems in the past. Also, this would be a major overhaul and it might be very difficult to achieve consensus. Lastly, I have tried to include Herzogs research in the article in the past as it provides an additional perspective that all the retrospective and survey stuff that exists does not. That being said, although his most recent article is decribed as a review in the intro, no other editors agreed it was a secondary source and his research on cadavers was considered 'basic' and not appropriate for an article meant to provide medical information. Puhlaa (talk) 15:17, 15 January 2011 (UTC)

Original Safety and Effectiveness section in Lead:

Proposed New Safety and Effectiveness Section in Lead:

To make the first comments to my own proposal :), using pieces of the recommendations from both Rangifer and Ocaasi I have come up with the above. I used only secondary sources (per MEDRS), maintained inclusion and the outcome of Ernst-death, and have minimized the 'minority' view while still accurately framing the debate in the literature.Puhlaa (talk) 21:59, 15 January 2011 (UTC)

I didn't quite intend for my entire paragraph to go in the lead, although I'd like to see something along those lines in the body. Your addition is looking pretty good. It might need some copy-editing, my sentence included. The word 'however' may be called OR. If necessary, just let each sentence stand alone without the normal flourishes of conjunctions. Before you post to Chiro/talk, I think it'd be great to get Brangifer and Digital C to look at this. It might make sense, while we're at it, to ensure the body of the article is properly covered first. That way, we won't have to deal with niggling lead <> body objections. Ocaasi (talk) 05:58, 16 January 2011 (UTC)

I have just added a ref to support the claim that back pain is consistent with the evidence (Spine journal systematic review) because the Ernst reference alone does not support the claim. I also removed a couple redundant words.

Ocaasi, if only minor modifications are necessary then you and Rangifer (and any other reasonable editor) should feel free to make edits to the proposal above, until a collective effort generates something that everyone likes (or can tolerate) and has the potential to appease QG. If anyone thinks a major change is needed then just post a revised proposal.Puhlaa (talk) 06:14, 16 January 2011 (UTC)

I have struck the first sentence, as I don't think it is important enough to be in the lead. Others may disagree and I am not adamant on its removal. DigitalC (talk) 02:43, 17 January 2011 (UTC)

I am concerned about WP:SYN. You are using 2 Ernst references to make one sentence. Combining two references to say one thing that neither reference says is a violation of WP:SYN. Can you post the sentence from each reference that you think would allow this sentence to pass WP:V? Could this sentence stand with only one reference? Do we really have a reference stating what current consensus in the medical community is? DigitalC (talk) 02:57, 17 January 2011 (UTC)

there has been a pattern of behavior from one editor, where they continually choose to discuss other editors instead of edits, content or sources. For example:

1. I suggest some edits are inconsistent with policy here and defend the WHO as a reliable source; in return I get COI accusations here.
2. I make a proposal to try and appease both ‘sides’ here and provide numerous high-quality, reliable sources here to support my perspective; in return I get a non-sourced commentary of chiropractic and more accusations of COI here.
3. I suggest that there was sourced text removed inappropriately here; in return I get accusations of COI here. I take the issue to the reliable sources noticeboard here; I receive more accusations of COI from the same editor at the noticeboard here.
4. I asked an objective editor from the RS noticeboard if I was acting appropriately here [2], or I would take a wikibreak. The response was that “you seem to be editing in the proper spirit” [3]. That same objective editor posted a request here to stop the accusations of tendentious editing, so I struck where I had made an accusation [4], but in return I just get more accusations against me from JzG (Guy) right under the warning.
5. I posted at the talk page that some newer edits from John Snow may have been inappropriate. After some polite discussion, it turns out that 1 of my concerns was unjustified, 1 was remedied; thus, I continued polite discussion about the remaining item that concerned me here. As usual, this polite discussion was again moved by JzG (Guy) to one about me as an editor with this post.
6. Even after an RfC where many uninvolved editors repeatedly suggested that COI was not relevant and asked other editors to stay focused on content and sources - I had commented that some additions to the lead may violate policy here; in return I get more accusations of COI in this comment.

I have repeatedly asked editors to indicate specific behaviors that were concerning, but none have been presented. A review of my edits will reveal that I have always posted with sources and discussion of content or policy. Rather than respond with policy, sources or content, editors have chosen repeatedly to discuss other editors. It is amazing that this has all resulted in me having to justify my behavior here!
Eg of comments from uninvolved editors at the RFC: [5] [6] [7] Comments from editors at the Project medicine talk page: [8]