Still Life With Woodpecker, or, electric piggybacking and 21st-century computing applied to an old method

This site needs to be seen:
  1. Functionalizing graphene by embedded boron clusters
    NASA Astrophysics Data System (ADS)
    Quandt, Alexander; Kunstmann, Jens; Ozdogan, Cem; Fehske, Holger
    We present results from an ab initio study of B7 clusters implanted into graphene [1,2]. Our model system consists of an alternating chain of quasiplanar B7 clusters. We show that graphene easily accepts these alternating B7-C6 chains and that the implanted boron components may dramatically modify the electronic properties. This suggests that our model system might serve as a blueprint for the controlled layout of graphene based nanodevices, where the semiconducting properties are supplemented by parts of the graphene matrix itself, and the basic metallic wiring is provided by alternating chains of implanted boron clusters. [1] A. Quandt, C. "Ozdogan, J. Kunstmann, and H. Fehske, Nanotechnology 19, 335707 (2008). [2] A. Quandt, C. "Ozdogan, J. Kunstmann, and H. Fehske, phys. stat. solidi (b) 245, 2077 (2008).

So this ties together boron and graphene... I still hold that applying boron crystal salts after (or without) oxidizer will peel off rather than help this film.

Can boron get bacteria talking? -- from

about AutoInducer2 : AI2.png

It is used to signal in quorum sensing...

From: Effects of Exogenous Synthetic Autoinducer-2 on Physiological Behaviors and Proteome of Lactic Acid Bacteria, a study on PubMed.
AI-2 appears to upregulate synthesis of sulfur metabolism in the two tested types of bacteria:

There was no significant influence on biofilm formation and individual morphology of cells upon 60 μM AI-2 addition in E. faecium 8-3 and Lactobacillus fermentum 2-1. However, it improved the acid and alkali resistance of E. faecium 8-3. With the addition of AI-2, 15 differentially expressed proteins were identified in E. faecium 8-3, which participate in RNA transport signaling, RNA polymerase, ribosome, oxidative phosphorylation, cysteine and methionine metabolism, pyrimidine metabolism, ATP-binding cassette (ABC) transporters, purine metabolism, biosynthesis of the amino acid pathway, etc. Among them, the expression of 5-methylthioadenosine/S-adenosylhomocysteine nucleosidase, which is known to be involved in AI-2 synthesis and cysteine and amino acid metabolism, was upregulated. These findings will lay the foundation to clarify the mechanism of cell-to-cell communication and bacterial physiological behaviors mediated by AI-2.

What else it signals for I don't know.
4,5-Dihydroxy-2,3-pentanedione (DPD), a product of the LuxS enzyme in the catabolism of S-ribosylhomocysteine, spontaneously cyclizes to form autoinducer 2 (AI-2). AI-2 is proposed to be a universal signal molecule mediating interspecies communication among bacteria. We show that mutualistic and abundant biofilm growth in flowing saliva of two human oral commensal bacteria, Actinomyces naeslundii T14V and Streptococcus oralis 34, is dependent upon production of AI-2 by S. oralis 34. A luxS mutant of S. oralis 34 was constructed which did not produce AI-2. Unlike wild-type dual-species biofilms, A. naeslundii T14V and an S. oralis 34 luxS mutant did not exhibit mutualism and generated only sparse biofilms which contained a 10-fold lower biomass of each species. Restoration of AI-2 levels by genetic or chemical (synthetic AI-2 in the form of DPD) complementation re-established the mutualistic growth and high biomass characteristic for the wild-type dual-species biofilm. Furthermore, an optimal concentration of DPD [Ed: ergo, AI-2] was determined, above and below which biofilm formation was suppressed[Ed.: Suppressed by high concentration]. The optimal concentration was 100-fold lower than the detection limit of the currently accepted AI-2 assay. Thus, AI-2 acts as an interspecies signal and its concentration is critical for mutualism between two species of oral bacteria grown under conditions that are representative of the human oral cavity.
From Autoinducer 2: a concentration-dependent signal for mutualistic bacterial biofilm growth , PubMed article.
Okay, that forum is "swamped", in my estimation, and has little board moderation, following further interactions. I would delete the links to it if I saw the function to do so. Avoid or proceed with caution.

Here is a better link to hosting of the video archive: Lookoutfa Charlie

Still Life With Woodpecker is a book I recommend for reading, a love story. I apologize.
I have just joined here.
LOFC (lookoutfacharlie) is giving very bad advice with his "protocol". And yes that zero echo nine forum is absolutely a swamp.
I'm pissed. More at myself.
I generally (I thought) had better "discernment".
I just called him out on something..and into defense mode he went.

Can't trust anybody.
I have just joined here.
LOFC (lookoutfacharlie) is giving very bad advice with his "protocol". And yes that zero echo nine forum is absolutely a swamp.
I'm pissed. More at myself.
I generally (I thought) had better "discernment".
I just called him out on something..and into defense mode he went.

Can't trust anybody.
Hi Mountainpainter,

Let me ask you, please -- what do you find to be bad advice about LOFC's protocol?

FWIW, in my experience talking with him, I think he's earnest, and struggling through regular life while trying to document his work. It might just be that it's difficult to get results as intentioned/imagined in the real world, or how to keep the ball rolling to that, or that there there might be something going on he can't let on about, strategically. I don't know.

I thought the forum had a lot of interesting discussion on technological sensor technology, and other things; a lot of people seem earnest. Hard to be discerning, so practice; I dunno where I am when rowing that boat.

Also -- what do you know about boron and graphene? Are they used together to create something with different properties? Any thoughts on the phenomena, or how it's facilitated?
From @Tsidkenu around July 1, 2020 on
"In this report we are going to add the results of a particular research we have done from the data
published on the alleged SARS-CoV-2 and on the protocols endorsed by the WHO for the use of
RT-PCR as well as the data corresponding to the rest of the "human coronaviruses". And the
conclusions are extremely serious: none of the seven "human coronaviruses" have actually been
isolated and all the sequences of the primers of their respective PCRs as well as those of a large
number of fragments of their supposed genomes are found in different areas of the human
genome and in genomes of bacteria and archaea, such as these: Shwanella marina JCM, Dialister
succinatiphilus, Lactobacillus porcine, Lactobacillus manihotivorans, Leptospira sarikeiensis,
Bizionia echini, Sanguibacteroides justesenil, Bacteroides massiliensis, Lacinutrix venerupis,
Moraxella bovis, Leptospira saintgironsiae, Winogradskyella undariae, Acetobacterium puteale,
Chryseobacterium hispanicum, Paenibacillius koleovorans, Tamiana fuccidanivorans, Fontibacillua
panacisegetis, Ru bacter ruber , Skemania piniformis, Chryseobacterium shigense, Caloramator
peoteoclasticus, Cellulosilyticum ruminicola, Nitrosopumilius evryensis and a long list of others."

Lots of other microorganisms share sequence homology with SARS-CoV-2 primers, although this study needs to be vetted better, to put it mildly.

Wed. 15, July 2020

Study available on PubMed PMC: Thorell, Kaisa et al. “Whole-Genome Sequencing Redefines Shewanella Taxonomy.” Frontiers in microbiology vol. 10 1861. 28 Aug. 2019, doi:10.3389/fmicb.2019.01861

The family Shewanellaceae, was formally established by Ivanova et al. (2004) 15 years ago. The type (and only) genus within this family is Shewanella, which had been defined already by MacDonell and Colwell after their taxonomic revision of the family Vibrionaceae (MacDonell and Colwell, 1985) and named after J. M. Shewan in recognition for his work in the microbiology of fish and fishery products (Shewan et al., 1960). Shewanella are Gram negative, facultative anaerobic, rod-shaped bacteria with a single polar flagellum, most of which are able to grow at low temperature. Some species produce polyunsaturated fatty acids. The type species is Shewanella putrefaciens (MacDonell and Colwell, 1985).

Shewanella are ubiquitously distributed in marine and freshwater environments, including deep-sea and polar regions, with some species being part of the microbiota of aquatic animals. One species, S. algae, is considered to be an emergent human pathogen (Martín-Rodríguez et al., 2017), with a few additional species being occasionally pathogenic. While human infections are still relatively scarce, the number of case reports is raising quickly, which can be partly due to higher medical awareness and refined identification methods (Martín-Rodríguez et al., 2017). Recent human microbiome studies have reported the presence of Shewanella in association with disease (Flemer et al., 2017; Kalyana Chakravarthy et al., 2018). [Ed.: Add data to MALDI-TOF cross-x library.]
[Ed.: To "Shwanella marina JCM", inccorigibly bad reference from questionable reference cited at the beginning]
Emended Description of Shewanella marina Park et al. (2009)

The description is as before (Park et al., 2009) with the following modification: the G+C content of the type-strain (C4 = JCM 15074 = KCTC 22185) genome is 40.4%, its approximate size is 4.42 Mbp, and its GenBank accession is GCA_000614975.1/ASM61497v1. [Ed.: Shewanella marina, noted for sequence homology by DSALUD article]

----ref:Park S. C., Baik K. S., Kim M. S., Kim D., Seong C. N. (2009). Shewanella marina sp. nov., isolated from seawater. Int. J. Syst. Evol. Microbiol. 59 1888–1894. 10.1099/ijs.0.005470-0 [PubMed] [CrossRef] [Google Scholar]

Other references for overview from Kaisa, et al.:

---ref:Baumann L., Baumann P., Mandel M., Allen R. D. (1972). Taxonomy of aerobic marine eubacteria. J. Bacteriol. 110 402–429. [PMC free article] [PubMed] [Google Scholar]
ref: Bozal N., Montes M. J., Tudela E., Jiménez F., Guinea J. (2002). Shewanella frigidimarina and Shewanella livingstonensis sp. nov. isolated from Antarctic coastal areas. Int. J. Syst. Evol. Microbiol. 52 195–205. 10.1099/00207713-52-1-195 [PubMed] [CrossRef] [Google Scholar]
ref: Ivanova E. P., Flavier S., Christen R. (2004). Phylogenetic relationships among marine Alteromonas-like proteobacteria: emended description of the family alteromonadaceae and proposal of Pseudoalteromonadaceae fam. nov., Colwelliaceae fam. nov., Shewanellaceae fam. nov., Moritellaceae fam. nov., Ferrimonadaceae fam. nov., Idiomarinaceae fam. nov. and Psychromonadaceae fam. nov. Int. J. Syst. Evol. Microbiol. 54 1773–1788. 10.1099/ijs.0.02997-0 [PubMed] [CrossRef] [Google Scholar]
ref: Kim S.-J., Park S.-J., Oh Y.-S., Lee S.-A., Shin K.-S., Roh D.-H., et al. (2012). Shewanella arctica sp. nov., an iron-reducing bacterium isolated from Arctic marine sediment. Int. J. Syst. Evol. Microbiol. 62 1128–1133. 10.1099/ijs.0.031401-0 [PubMed] [CrossRef] [Google Scholar]
ref: Satomi M., Vogel B. F., Gram L., Venkateswaran K. (2006). Shewanella hafniensis [Ed.:See Zhao, et al., below] sp. nov. and Shewanella morhuae sp. nov., isolated from marine fish of the Baltic Sea. Int. J. Syst. Evol. Microbiol. 56 243–249. 10.1099/ijs.0.63931-0 [PubMed] [CrossRef] [Google Scholar]
ref:Simidu U., Kita-Tsukamoto K., Yasumoto T., Yotsu M. (1990). Taxonomy of four marine bacterial strains that produce tetrodotoxin. Int. J. Syst. Bacteriol. 40 331–336. 10.1099/00207713-40-4-331 [PubMed] [CrossRef] [Google Scholar]
Zhao J.-S., Manno D., Leggiadro C., O’Neil D., Hawari J. (2006). Shewanella halifaxensis sp. nov., a novel obligately respiratory and denitrifying psychrophile. [Ed.: See then spp. "marina" from Park (2009) in Korea; Shwanella marina homology with SARS-CoV-2 sequences] Int. J. Syst. Evol. Microbiol. 56 205–212. 10.1099/ijs.0.63829-0 [PubMed]
[CrossRef] [Google Scholar]
ref: MacDonell M. T., Colwell R. R. [Ed.: spp. colwelliana 1989 also, below] (1989). Phylogeny of the vibrionaceae, and recommendation for two new genera, listonella and shewanella. Syst. Appl. Microbiol. 6 171–182. 10.1016/s0723-2020(85)80051-5 [CrossRef] [Google Scholar]

Coyne V. E., Pillidge C. J., Sledjeski D. D., Hori H., Ortiz-Conde B. A., Muir D. G., et al. (1989). Reclassification of Alteromonas colwelliana to the genus shewanella by DNA-DNA hybridization, serology and 5S ribosomal RNA sequence data. Syst. Appl. Microbiol. 12 275–279.

[From Thorell, et al., 2019]
The genus Shewanella is renowned for a series of outstanding physiological and metabolic features, including an array of anaerobic respiration pathways and extracellular electron transfer mechanisms (Hau and Gralnick, 2007). Nevertheless, the genomic diversity of the genus remains obscure. One reason is the few genome sequences available in comparison to other bacterial genera (only 147 were deposited in the GenBank as per April 30th, 2019). Another reason is the rapid growth of the genus Shewanella, which has expanded from less than 20 species in 2003 to 67 species at present as per the List of Species with Standing Nomenclature (Parte, 2018), which still needs to be updated with some recent descriptions. Some of these recently described species are based on a single isolate meeting the classic ‘gold standards’ for species definition (Moore et al., 1987; Stackebrandt et al., 2002), namely 16S rRNA sequence relatedness of ≤98.8% (Meier-Kolthoff et al., 2013b) and experimental DNA-DNA hybridization (DDH) values ≤70% as thresholds (Fournier et al., 2015; Fang et al., 2017), being otherwise metabolically and phenotypically similar to previously described species (Kim et al., 2007, 2011). [Ed.: A.k.a., Shewanella putrafasciens, ca. 1931-1975-1989...]
Zhao J.-S., Manno D., Beaulieu C., Paquet L., Hawari J. (2005). Shewanella sediminis sp. nov., a novel Na+-requiring and hexahydro-1,3,5-trinitro-1,3,5-triazine-degrading bacterium from marine sediment. Int. J. Syst. Evol. Microbiol. 55 1511–1520. 10.1099/ijs.0.63604-0 [PubMed] [CrossRef] [Google Scholar]
Zhao J.-S., Manno D., Leggiadro C., O’Neil D., Hawari J. (2006). Shewanella halifaxensis sp. nov., a novel obligately respiratory and denitrifying psychrophile. Int. J. Syst. Evol. Microbiol. 56 205–212. 10.1099/ijs.0.63829-0 [PubMed] [CrossRef] [Google Scholar]
Zhao J.-S., Manno D., Thiboutot S., Ampleman G., Hawari J. (2007). Shewanella canadensis sp. nov. and Shewanella atlantica sp. nov., manganese dioxide- and hexahydro-1,3,5-trinitro-1,3,5-triazine-reducing, psychrophilic marine bacteria. Int. J. Syst. Evol. Microbiol. 57 2155–2262. [PubMed] [Google Scholar]
[Ed.: Everything else, bit-by-bit , is genetic tinkering, and seems to be patentable; like Covid modifications. Here with Shewanella they're also guilty of serial eponymization. Once S. putrefaciens could be picked apart and seen as a cold-tolerant, facultative anaerobe, that can respire metals and use diverse carbon sources, the possibilities for genetic engineering such a thing open up.]
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