--- Log opened Sat Mar 04 00:00:49 2017 00:14 -!- CRM114 [~urchin@unaffiliated/urchin] has quit [Ping timeout: 260 seconds] 00:36 -!- vicarion [~net@d49-188-0-106.sun1.vic.optusnet.com.au] has joined ##hplusroadmap 00:40 -!- vicarion [~net@d49-188-0-106.sun1.vic.optusnet.com.au] has quit [Ping timeout: 258 seconds] 00:58 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 260 seconds] 01:11 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 01:22 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 260 seconds] 01:37 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 02:00 -!- Gurkenglas [~Gurkengla@dslb-178-000-179-165.178.000.pools.vodafone-ip.de] has joined ##hplusroadmap 02:09 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 02:53 -!- augur [~augur@2602:304:cdac:e260:2ca0:229d:c806:81f1] has joined ##hplusroadmap 03:00 -!- liead is now known as adlai 03:27 -!- darsie [~darsie@84-113-55-42.cable.dynamic.surfer.at] has joined ##hplusroadmap 03:59 -!- augur [~augur@2602:304:cdac:e260:2ca0:229d:c806:81f1] has quit [Remote host closed the connection] 04:07 < kanzure> hrm. 04:41 -!- C0MPAQ_ [~l0rd@dslb-088-076-213-045.088.076.pools.vodafone-ip.de] has quit [Remote host closed the connection] 04:52 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Remote host closed the connection] 05:31 -!- esmerelda [~mabel@unaffiliated/jacco] has quit [Ping timeout: 258 seconds] 06:08 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 240 seconds] 06:26 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 07:08 -!- Taek42 is now known as Taek 08:04 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 08:15 -!- jtimon [~quassel@70.30.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 08:19 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 258 seconds] 08:38 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 09:10 -!- TC [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has joined ##hplusroadmap 09:10 -!- TC is now known as helleshin 09:14 -!- hehelleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has quit [Ping timeout: 246 seconds] 09:29 < kanzure> http://blogs.plos.org/synbio/2017/03/01/synthetic-biology-to-help-colonize-mars/ 09:39 < kanzure> "Rational design of inducible CRISPR guide RNAs for de novo assembly of transcriptional programs" http://www.nature.com/articles/ncomms14633 https://twitter.com/rosscloney/status/837711703303389185 09:44 < kanzure> "Mutations in DCC cause isolated agenesis of the corpus callosum with incomplete penetrance" http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3794.html https://twitter.com/NatureGenet/status/837714195831533568 09:48 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 264 seconds] 09:55 < kanzure> "A neuropeptide modulates sensory perception in the entomopathogenic nematode Steinernema carpocapsae" http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1006185 09:55 < kanzure> something about brain parasites sensing their environments and hosts. 09:55 < kanzure> ( https://twitter.com/PLOSPathogens/status/837376981528240128 ) 10:05 < kanzure> "Assembly of embryonic and extra-embryonic stem cells to mimic embryogenesis in vitro" http://science.sciencemag.org/content/early/2017/03/01/science.aal1810 https://www.theguardian.com/science/2017/mar/02/cambridge-scientists-create-first-self-developing-embryo-from-stem-cells https://twitter.com/NatureMedicine/status/837681792324878336 10:05 < kanzure> oh maybe it was https://twitter.com/NatureBiotech/status/837680378219495424 10:07 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 10:15 < kanzure> "Long-range allosteric signaling in red light-regulated diguanylyl cyclases" http://advances.sciencemag.org/content/3/3/e1602498 https://phys.org/news/2017-03-red-light-optogenetic-tools.html 10:20 < kanzure> "Specialising the parasite nucleus: Pores, lamins, chromatin, and diversity" http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1006170 10:20 < kanzure> human brain morphometry tool http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005350 http://mindboggle.info/ but this seems to only be looking at brain shape specifically 10:21 < kanzure> ( https://twitter.com/PLOSCompBiol/status/836971798013034497 ) 10:27 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Ping timeout: 258 seconds] 10:28 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 10:46 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Remote host closed the connection] 11:08 -!- Regex [~Cara@2601:1c0:8500:5edb:55dc:9021:bcb8:e743] has quit [Read error: Connection reset by peer] 11:08 -!- Regex [~Cara@2601:1c0:8500:5edb:55dc:9021:bcb8:e743] has joined ##hplusroadmap 11:09 -!- jtimon [~quassel@70.30.134.37.dynamic.jazztel.es] has quit [Ping timeout: 268 seconds] 12:37 -!- augur [~augur@2602:304:cdac:e260:2ca0:229d:c806:81f1] has joined ##hplusroadmap 12:52 -!- augur [~augur@2602:304:cdac:e260:2ca0:229d:c806:81f1] has quit [Remote host closed the connection] 13:07 < chris_99> Random question, i've got an airbrush type thing, which is clogged i think, i found acupuncture needles seem to get about as thin as 0.12mm diameter, can anyone think of any other kind of needle that might be that thin or thinner? 13:13 -!- Netsplit *.net <-> *.split quits: TMA, juri_ 13:14 -!- Netsplit *.net <-> *.split quits: sachy, drewbot, justanotheruser, thxffo, Jenda`_ 13:15 -!- Netsplit over, joins: justanotheruser 13:15 < redlegion[m]> Not without getting out a sewing kit and micrometers. 13:17 < chris_99> heh, i think sewing needles are thicker than 0.12mm but i could be wrong. i guess i'll get some acupuncture ones and hope it's thin enough 13:18 -!- drewbot [~cinch@ec2-54-80-105-200.compute-1.amazonaws.com] has joined ##hplusroadmap 13:18 -!- Jenda`_ [~bablbam@dekatron.hrach.eu] has joined ##hplusroadmap 13:18 -!- thxffo [smdikus@ircbouncehouse.com] has joined ##hplusroadmap 13:18 -!- sachy [~sachy@nat.brmlab.cz] has joined ##hplusroadmap 13:23 -!- Jenda`_ [~bablbam@dekatron.hrach.eu] has quit [Ping timeout: 240 seconds] 13:23 -!- Jenda` [~bablbam@dekatron.hrach.eu] has joined ##hplusroadmap 13:23 < redlegion[m]> You're right. Some googling yields the smallest needle diameter is something like 0.35mm. 13:40 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 14:02 < cluckj> insulin needles are pretty tiny 14:02 -!- TMA [tma@twin.jikos.cz] has joined ##hplusroadmap 14:02 -!- juri_ [~juri@205.166.94.194] has joined ##hplusroadmap 14:04 < chris_99> it looks like the thinnest is 32 gauge i think, which is apparently 0.20mm. i guess it makes sense they're thicker than acupuncture needles since you've got to get fluid through 14:05 < streety> usually 28 or 29 gauge so 0.36 mm or 0.33 mm for insulin needle 14:06 < chris_99> ah 14:15 < kanzure> what was that paper about generating content (using neural networks) from inferences? it was called inference somethingsomething. 14:26 < fenn> was it 14:26 < fenn> .title http://www.nature.com/nature/journal/v538/n7626/full/nature20101.html 14:27 < yoleaux> fenn: Sorry, that command (.title) took too long to process. 14:27 < fenn> "Hybrid computing using a neural network with dynamic external memory" alex graves, demis hassabis, 50 other authors 14:30 < fenn> nm i have no idea what this paper is about 14:36 < kanzure> nah, it was something on arxiv, probably in the backlog 15:09 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Leaving] 15:23 -!- yashgaroth [~yashgarot@2602:306:35fa:d500:f5e0:f867:a11d:8d52] has joined ##hplusroadmap 15:36 -!- rk[ghost] [~rak@cpe-66-61-32-99.neo.res.rr.com] has quit [Ping timeout: 252 seconds] 15:37 -!- rk[ghost] [~rak@cpe-66-61-32-99.neo.res.rr.com] has joined ##hplusroadmap 16:15 -!- jtimon [~quassel@70.30.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 16:29 -!- c0rw1n [~c0rw1n@91.181.155.251] has quit [Ping timeout: 240 seconds] 17:20 -!- c0rw1n [~c0rw1n@91.181.155.251] has joined ##hplusroadmap 18:05 -!- Gurkenglas [~Gurkengla@dslb-178-000-179-165.178.000.pools.vodafone-ip.de] has quit [Ping timeout: 240 seconds] 18:21 -!- darsie [~darsie@84-113-55-42.cable.dynamic.surfer.at] has quit [Ping timeout: 260 seconds] 18:50 < kanzure> "Many prominent scientists in the field, including FLI's Scientific Advisory Board Member George Church, responded by calling for a temporary moratorium on using the CRISPR/Cas-9 gene-editing tool in human embryos that would be carried to term." 18:50 < kanzure> from https://futurism.com/for-the-first-time-researchers-can-genetically-modify-human-embryos/ re: "UK has given researchers at the Francis Crick Institute permission to edit the genes of early-stage human embryos" 18:51 < kanzure> we still need that moratorium on moratoriums. 18:51 < nmz787_> I'm pretty sure someone must have already done it 18:51 < nmz787_> implanted one 18:51 < nmz787_> for long term 18:51 < kanzure> sure, maybe not cas9-edited, but yes. 18:51 < nmz787_> why not cas9? 18:51 < kanzure> i know of at least one family that claims to have done some genetic work, and this was prior to the popularity of cas9 18:51 < nmz787_> if I did it, I wouldn't tell if there were people shouting about moronatoriums 18:52 < nmz787_> well I mean someone is pregnant i.e. now 18:52 < nmz787_> crispin if it's a boy, cassandra if it's a girl 18:53 < kanzure> ace nuclease if it's a boy. 19:35 -!- jtimon [~quassel@70.30.134.37.dynamic.jazztel.es] has quit [Ping timeout: 258 seconds] 19:36 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 19:49 < nmz787_> crispin if it's a boy, cassandra if it's a girl 19:49 < nmz787_> whoops 19:50 < nmz787_> ace reminds me of some cartoon character 19:50 < nmz787_> I like it 19:53 -!- abetusk [~abe@68.175.143.22] has quit [Ping timeout: 264 seconds] 19:55 < nmz787_> raccoons seem pretty smart, I wonder if that holds up statistically vs other animals as far as starting platforms for engineering 20:03 < kanzure> maybe it's the hands. 20:03 < cluckj> did you see that documentary with the genetically modified raccoon in it? 20:04 < cluckj> http://cdn0.dailydot.com/cache/d2/0c/d20c29bf089e1da0e9cd6cdf38b3b83c.jpg 20:14 -!- abetusk [~abe@68.175.143.22] has joined ##hplusroadmap 20:15 -!- abetusk is now known as Guest18863 20:28 -!- Guest18863 is now known as abetusk 20:34 < kanzure> intracellular gold nanoparticles for mouse hippocampus brain stimulation stuff http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0091360 20:36 < kanzure> toxoplasma gondii mouse brain study http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1005447 20:36 < kanzure> "Our understanding of which cells of the brain interact with and are infected by Toxoplasma primarily comes from work in tissue culture, which cannot re-capitulate the complexity of a living animal. Here, we overcome this barrier by studying brain-Toxoplasma interactions using a novel mouse model that allows us to permanently mark and track brain cells that have interacted with parasites. Cont... 20:36 < kanzure> ...rary to what has been shown in cell culture, we find that throughout acute and chronic brain infection Toxoplasma almost exclusively interacts with neurons, and rarely interacts with astrocytes. This neuronal predilection persists even in highly manipulated circumstances such as the introduction of parasites directly into the brain. This work is the first to show that Toxoplasma primarily inte... 20:36 < kanzure> ...racts with neurons in vivo, which suggests that to understand Toxoplasma's ability to persistently infect the brain, we must understand the neuron-Toxoplasma interaction." 20:38 < kanzure> "We overcame this barrier by generating Toxoplasma strains that inject Cre recombinase into host cells [22]. Using these Toxoplasma-Cre strains to infect mice that express GFP in a Cre-dependent manner [23] enables the identification and tracking of host cells that directly interact with parasites. Importantly, this system causes a parasite-triggered permanent genetic change in host cells but ... 20:38 < kanzure> ...does not require active infection. Therefore, host cells are permanently marked even in situations in which the host cell is injected with parasite proteins but is not invaded or in which the parasite invades and is subsequently killed by the host cell [24,25]." 20:39 < kanzure> "... Finally, imaging whole infected neurons in situ reveals that cysts are predominantly found in the extensive network of neuronal processes, not the neuron cell bodies. Collectively, these data highly suggest that Toxoplasma's persistence in neurons is driven by a strong in vivo predilection for interacting almost exclusively with neurons and that physical properties such as the extensive... 20:39 < kanzure> ... size and breadth of neuronal processes may play a role in determining this in vivo preference." 20:46 < kanzure> cool, so they were using an intracellular parasite to deliver gene editing 20:48 < cluckj> that is pretty sweet 20:48 < kanzure> in toxoplasma infection, extracellular glutamate concentration goes up and dendritic spines are reduced http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1005643 21:04 < kanzure> "... this analysis revealed that cysts are most often found in neuronal processes (Fig 5d, 21/28 II-Cre cysts and 23/26 II-Cre cysts) and are commonly far from the cell body, with mean cyst-to-cell-body distance of 56 ?9 ?m for II-Cre cysts and 75 ?10 ?m for III-Cre cysts (Fig 5e). Given that cysts are predominantly found in neuronal processes and are often a significant distance from the ... 21:04 < kanzure> ...cell body, these data suggest that neuronal size could also play a role in driving Toxoplasma's predilection for neurons." 21:06 < kanzure> .g "recombinant parasite" 21:06 < yoleaux> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC295649/ 21:07 < kanzure> .title 21:07 < yoleaux> Molecular cloning and characterization of recombinant parasite antigens for immunodiagnosis of onchocerciasis. 21:08 < kanzure> .title https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3521960/ 21:08 < yoleaux> Flow cytometry-assisted rapid isolation of recombinant Plasmodium berghei parasites exemplified by functional analysis of aquaglyceroporin 21:09 < kanzure> hehehe "We suggest that flow-cytometric isolation of isogenic parasites overcomes the major roadblock towards a genome-scale repository of mutant and transgenic malaria parasite lines." 21:09 < kanzure> .title http://jeb.biologists.org/content/216/1/113 21:09 < yoleaux> Toxoplasma gondii infection and behaviour - location, location, location? | Journal of Experimental Biology 21:09 < kanzure> "One factor that could contribute to the specific changes is increased dopamine production by T. gondii. Recently, it was found that cells encysted with parasites in the brains of experimentally infected rodents have high levels of dopamine and that the parasite encodes a tyrosine hydroxylase, the rate-limiting enzyme in the synthesis of this neurotransmitter. A mechanism is proposed that coul... 21:10 < kanzure> ...d explain the behaviour changes due to parasite regulation of dopamine. This could have important implications for T. gondii infections in humans." 21:10 < kanzure> .wik tyrosine hydroxylase 21:10 < yoleaux> "Tyrosine hydroxylase or tyrosine 3-monooxygenase is the enzyme responsible for catalyzing the conversion of the amino acid L-tyrosine to L-3,4-dihydroxyphenylalanine (L-DOPA). It does so using molecular oxygen (O2), as well as iron (Fe2+) and tetrahydrobiopterin as cofactors." -- https://en.wikipedia.org/wiki/Tyrosine_hydroxylase 21:12 < kanzure> ".. Parasite tissue cysts are found in all brain areas with some, but not all, prior studies reporting higher numbers located in the amygdala and frontal cortex." 21:13 < kanzure> really you just have to express mRNA i think, you don't need to actually build the enzymes inside the parasite 21:23 < kanzure> "The physiological implications are impressive as tissue cysts in vivo contain a hundredfold more parasites than in vitro cysts and, hence, infected neurones could potentially release several hundred times more dopamine than uninfected dopaminergic neurones. Through this mechanism, T. gondii could discreetly alter dopamine levels from specific (i.e. infected) neurones.The physiological implica... 21:24 < kanzure> ...tions are impressive as tissue cysts in vivo contain a hundredfold more parasites than in vitro cysts and, hence, infected neurones could potentially release several hundred times more dopamine than uninfected dopaminergic neurones. Through this mechanism, T. gondii could discreetly alter dopamine levels from specific (i.e. infected) neurones." 21:24 < kanzure> http://www.toxodb.org/ 21:26 < kanzure> "This tyrosine hydroxylase appears to contain a signal peptide and is localized to the parasite periphery in intracellular parasites within parasitophorous vacuoles (Gaskell et al., 2009; Prandovszky et al., 2011). Hence, the enzyme may be secreted out of the parasite and into the cyst for catalytic function adjacent to the host cytosol, although this has yet to be tested." 22:31 < nmz787_> cluckj: yeah I saw that one... I think the FDA had him destroyed or something 22:49 -!- juri_ [~juri@205.166.94.194] has quit [Ping timeout: 260 seconds] 22:57 -!- yashgaroth [~yashgarot@2602:306:35fa:d500:f5e0:f867:a11d:8d52] has quit [Quit: Leaving] 23:38 -!- drewbot [~cinch@ec2-54-80-105-200.compute-1.amazonaws.com] has quit [Remote host closed the connection] 23:38 -!- drewbot [~cinch@ec2-54-221-71-218.compute-1.amazonaws.com] has joined ##hplusroadmap 23:48 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap --- Log closed Sun Mar 05 00:00:22 2017