Happy 2021! @MBVanElzakker and I are excited to share our new article published in #Immunometabolism: “Pathogens Hijack Host Cell Metabolism: Intracellular Infection as a Driver of the Warburg Effect in Cancer and Other Chronic Inflammatory Conditions”:

2/ In the paper, we detail molecular mechanisms by which #viral, #bacterial, and #parasite intracellular pathogens can induce, or contribute to, a Warburg-like #metabolism in infected host cells in order to meet their own replication and nutritional needs.
3/ We also discuss how host defense towards #infection may impact cellular metabolic changes (including how #mitochondria can participate in the innate immune response towards infection)
4/ We then provide examples of how many of these same intracellular pathogens have been identified in #tumors, atherosclerotic lesions, #granuloma, and other tissues containing cells with a Warburg or altered metabolism.
5/ Last, we examine further trends associated with infection and host cell metabolism, including how #pathogen-driven hijacking of host cell lipid metabolism can support viral, bacterial, and parasite survival and replication.
6/ Overall we argue that, at least in a subset of patients w/ #cancer, #atherosclerosis, #sarcoidosis + related conditions, metabolic changes and inflammatory cascades central to the disease process are driven by intracellular pathogens
7/ We also discuss how pathogen-driven hijacking of cellular metabolism may contribute to #MECFS. ME/CFS is an extremely debilitating #neuroinflammatory condition that often begins with an infection (w/ #herpesvirus or enterovirus involvement already documented in some cases)
8/ A better understanding + acceptance of the trend could result in novel #diagnostics and treatments for patients w/ such conditions (w/ discussion of how a #ketogenic diet might impede pathogen-hijacking of host metabolism)
9/ So many cool people helped make the paper a reality. Special thanks to @lenapernas @Palmer_IMet_lab @dbkell, Dr. Wonder Drake, and @krisfobes for helping us with feedback and on earlier drafts of the manuscript.

More from Science

https://t.co/hXlo8qgkD0
Look like that they got a classical case of PCR Cross-Contamination.
They had 2 fabricated samples (SRX9714436 and SRX9714921) on the same PCR run. Alongside with Lung07. They did not perform metagenomic sequencing on the “feces” and they did not get


A positive oral or anal swab from anywhere in their sampling. Feces came from anus and if these were positive the anal swabs must also be positive. Clearly it got there after the NA have been extracted and were from the very low-level degraded RNA which were mutagenized from

The Taq.
https://t.co/yKXCgiT29w to see SRX9714921 and SRX9714436.
Human+Mouse in the positive SRA, human in both of them. Seeing human+mouse in identical proportions across 3 different sequencers (PRJNA573298, A22, SEX9714436) are pretty straight indication that the originals

Were already contaminated with Human and mouse from the very beginning, and that this contamination is due to dishonesty in the sample handling process which prescribe a spiking of samples in ACE2-HEK293T/A549, VERO E6 and Human lung xenograft mouse.

The “lineages” they claimed to have found aren’t mutational lineages at all—all the mutations they see on these sequences were unique to that specific sequence, and are the result of RNA degradation and from the Taq polymerase errors accumulated from the nested PCR process
1/ Automobiles and Intake Fraction. Since cars are back in the news I thought I would retweet this model result I offered in early April 2020. I focused only on 1 micron particles & accounted for windows completely closed & cracked slightly open.


2/ Related air exchange rates were based on experimental results in literature for mid-sized sedans. Particle deposition to indoor surfaces were accounted for, as the surface to volume ratio in a 3 m3 cab is large. An important outcome was the intake fraction (IF)

3/ Here, IF is the number of particles (or virions in collective particles) inhaled by a receptor DIVIDED BY the number or particles (or virions in collective particles) emitted by an infector.

4/ Integrated over the two hour drive (in this example) the IF for all windows closed & a receptor at rest is 0.08 (8% of what comes out of the infectors respiratory system ends up in the respiratory system of the receptor). 8%! That is a very high intake factor.

5/ With additional ventilation from cracking a window open drops the IF to 0.012 (1.2%) still relatively high. Can get lower by opening more windows.
It was great to talk about reproducible workflows for @riotscienceclub @riotscience_wlv. You can watch the recording below, but if you don't want to listen to me talk for 40 minutes, I thought I would summarise my talk in a thread:


My inspiration was making open science accessible. I wanted to outline the mistakes I've made along the way so people would feel empowered to give it a go. Increased accountability is seen as a barrier to adopting open science practices as an ECR

It also comes across as all or nothing. You are either fully open science or your research won't get anywhere. However, that can be quite intimidating, so I wanted to emphasise this incremental approach to adapting your workflow

There are two sides to why you should work towards reproducibility. The first is communal. It's going to help the field if you or someone else can reproduce your whole pipeline.


There is also the selfish element of it's just going to help you do your work. If you can't remember what your work means after a lunch break, you're not going to remember months or years down the line

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