RT @aetarke@twitter.com

Can CD4+ T cells cross-recognize different coronaviruses (CoV), offering immune protection from potential future CoV pandemics? We explore this concept in our new study, just posted in pre-print. biorxiv.org/content/10.1101/20
@Alba_Grifoni@twitter.com @SetteLab@twitter.com 1/5

🐦🔗: twitter.com/aetarke/status/161

Targets and cross-reactivity of human T cell recognition of Common Cold Coronaviruses

The Coronavirus (CoV) family includes a variety of viruses able to infect humans. Endemic CoVs that can cause common cold belong to the alphaCoV and betaCoV genera, with the betaCoV genus also containing subgenera with zoonotic and pandemic concern, including sarbecoCoV (SARS-CoV and SARS-CoV-2) and merbecoCoV (MERS-CoV). It is therefore warranted to explore pan-CoV vaccine concepts, to provide adaptive immune protection against new potential CoV outbreaks, particularly in the context of betaCoV sub lineages. To explore the feasibility of eliciting CD4+ T cell responses widely cross-recognizing different CoVs, we utilized samples collected pre-pandemic to systematically analyze T cell reactivity against representative alpha (NL63) and beta (OC43) common cold CoVs (CCC). Similar to previous findings on SARS-CoV-2, the S, N, M, and nsp3 antigens were immunodominant for both viruses while nsp2 and nsp12 were immunodominant for NL63 and OC43, respectively. We next performed a comprehensive T cell epitope screen, identifying 78 OC43 and 87 NL63-specific epitopes. For a selected subset of 18 epitopes, we experimentally assessed the T cell capability to cross-recognize sequences from representative viruses belonging to alphaCoV, sarbecoCoV, and beta-non-sarbecoCoV groups. We found general conservation within the alpha and beta groups, with cross-reactivity experimentally detected in 89% of the instances associated with sequence conservation of >67%. However, despite sequence conservation, limited cross-reactivity was observed in the case of sarbecoCoV (50% of instances), indicating that previous CoV exposure to viruses phylogenetically closer to this subgenera is a contributing factor in determining cross-reactivity. Overall, these results provided critical insights in the development of future pan-CoV vaccines. ### Competing Interest Statement A.S. is a consultant for Gritstone Bio, Flow Pharma, Moderna, AstraZeneca, Qiagen, Fortress, Gilead, Sanofi, Merck, RiverVest, MedaCorp, Turnstone, NA Vaccine Institute, Emervax, Gerson Lehrman Group and Guggenheim. LJI has filed for patent protection for various aspects of T cell epitope and vaccine design work.

biorxiv.org

RT @ejustin46@twitter.com

DOES VACCINATION WORK AGAINST XBB.1 LINEAGES?
In a study to be interpreted with caution because it was carried out on particles, and not in vivo, XBB.1 escapes almost completely from the immunity provided by vaccines, including with a booster!!! 😨
thelancet.com/journals/laninf/

🐦🔗: twitter.com/ejustin46/status/1

🦟 By targeting #bonemarrow, @MattMartiLab's team @UofGlasgow hope to block a deadly parasite’s ability to transmit #malaria – an important step towards developing drugs and #vaccines that could eventually eradicate the disease.

👉 bit.ly/3uS0zRh

@CORDIS_EU #mosquito

🐦🔗: n.respublicae.eu/ERC_Research/

Fission is in the news, but few recognize that a woman physicist was behind the discovery.

Lise Meitner’s brilliance led to the discovery of nuclear fission. But her long time collaborator Otto Hahn, was awarded the Nobel Prize in Chemistry w/o her in 1944, even though she had given the first theoretical explanation.

Albert Einstein called Meitner “our Marie Curie." She also adamantly refused to work on the atomic bomb during WWII. aps.org/publications/apsnews/2 #women #history #science #energy

"In this work, we explored possibility of using drug-sensitivity data together with basal gene expression data on pancreatic cell lines to predict the combinatorial options available for HDACi and developed bioinformatics screening protocol for predictions of synergistic drug combinations in PDAC. "

biorxiv.org/content/10.1101/20

Correlating basal gene expression across chemical sensitivity data to screen for novel synergistic interactors of HDAC inhibitors in pancreatic carcinoma

Pancreatic ductal adenocarcinoma (PDAC) is considered as one of the most aggressive and lethal malignancies. Development of chemoresistance in PDAC is one of the key contributors for the poor survival outcomes of PDAC patients and the major reason for urgent development of novel pharmacological approaches for effective treatment of PDAC. Systematically tailored combination therapy holds the promise for advancing the treatment of PDAC, but number of possible combinations considering all approved drugs and drug candidates is too large to be explored empirically. In respect to the many epigenetic alterations in PDAC, epigenetic drugs including histone deacetylase inhibitors (HDACi) could be seen as a game changers but available data indicates their efficacy only in combined therapy settings. In this work, we explored possibility of using drug-sensitivity data together with basal gene expression data on pancreatic cell lines to predict the combinatorial options available for HDACi and developed bioinformatics screening protocol for predictions of synergistic drug combinations in PDAC. Our results identified sphingolipid signaling pathway with associated downstream effectors as a promising novel target for future development of multi-target therapeutics or combined therapy with HDACi. Through the process of experimental validation of the methodology, we have characterized novel synergism between HDACi and Rho-associated protein kinase (ROCK) inhibitors. ### Competing Interest Statement The authors have declared no competing interest.

www.biorxiv.org

The historic MBL Physiology Course is now accepting applications! If you're interested in learning more about the course and the application process, be sure to join us on Friday, January 13 at 9 AM PT for a virtual open house (berkeley.zoom.us/meeting/regis).

More info about the course is available here: mbl.edu/education/advanced-res

RT @YamanakaNaoki@twitter.com

As the year 2022 comes to an end, we are happy to announce the 6th International Insect Hormone Workshop, which will be hosted by UC Riverside and held at the historic Mission Inn Hotel & Spa in downtown Riverside, California from June 18th (Sun) to June 24th (Sat), 2023! 1/5

🐦🔗: twitter.com/YamanakaNaoki/stat

It's hard to know where to start with references to the correlation vs. causation problem in scientific publication. There's obviously an absolutely massive literature on causal inference that gets at how to draw this distinction.

As for abuses in the published literature, there are a number of metaresearch papers on this as well. In particular, @noahhaber has written extensively on this.

For starters:

pubmed.ncbi.nlm.nih.gov/211967

pubmed.ncbi.nlm.nih.gov/298475

pubmed.ncbi.nlm.nih.gov/359250

Show thread

Some belated #introduction:

I'm a philosopher of science, in particular cognitive (neuro)science, computation and information. Here's my book: mitpress.mit.edu/9780262018869

My second field is #nlp: see LanguageTool (languagetool.org), a style and grammar checker for many natural languages (I have developed the rule set for Polish).

Associate Prof at the Institute of Philosophy and Sociology, Polish Academy of Sciences. I chair the Section for Logic and Cognitive Science.

I've literally taught grad level seminars on selection bias and yet spent a non-trivial amount of time this evening wondering "why are conspiracy theorists so bad at doing their research?"

#introduction Hi All. I am @tisimpson on Twitter, just starting on here.

I'm interested in the application of computational/statistical methods to biomedical areas. Much of our work involves using multi-modal data: #genomic, #clinical, and #molecular to better understand neurological disease of genetic origin.

We develop and use a lot of #network, #dataintegration, #statistics, and #machinelearning approaches in our research.

Exciting to have the next phase of #UCCFutures launched.

UCC Futures: Food, Microbiome & Health builds on our long history of groundbreaking research in food, nutrition, health & microbiome science

Recruiting 14 academic posts!

'But the authors are particularly set off by the habit of referring to the unfolded state as some sort of unique form common to most proteins, whether this unfolding is done by excess heat, lack of heat, pressure changes, chemical means, or whatever.

I can see their point. This is an example of “reification”, the philosophical mistake of “turning something into a thing” when it isn’t actually a separate entity or even a real one.'

cc @pradeu

science.org/content/blog-post/

RT @EricTopol@twitter.com

Just out @NEJM@twitter.com, a "milestone"
The level of neutralizing antibodies induced by Covid vaccines has been established as a correlate of protection, i.e. a surrogate endpoint for predicting clinical outcomes and use for regulatory approvals
nejm.org/doi/full/10.1056/NEJM

🐦🔗: twitter.com/EricTopol/status/1

From Kevin Foster and collaborators

"The order and identity of incoming symbionts is critical for health, but what determines the success of the assembly process remains poorly understood. Here we develop ecological theory to identify factors important for microbial community assembly. Our method maps out all feasible pathways for the assembly of a given microbiome—with analogies to the mutational maps underlying fitness landscapes in evolutionary biology."

journals.plos.org/plosbiology/

Really excited to launch @Dev_journal@twitter.com "Pathway to Independence Programme"

Are you, or do you know, a dev bio or stem cell researcher planning to apply for their 1st PI position in 2023?

Then this scheme is for you. See how to apply:

journals.biologists.com/dev/ar

Pathway to Independence programme: helping postdocs navigate the transition to independence

Making the leap from postdoc to principal investigator is tough. As one of our ‘Transitions in Development’ interviewees, Margot Kossman Williams, told us ‘applying to get a new job is a full-time job!’ (Eve, 2022). From articulating a research vision and putting together budgets to what to expect during the application and interview process, entering the academic job market throws up many new challenges. Although some institutes provide comprehensive training and mentorship to their postdocs, many do not, and access to good advice and support can make all the difference. Another of our interviewees, Aman Husbands, told us that – as a postdoc about to go on the job market – discussions with an Assistant Professor in his department were hugely instructive: he ‘helped me think about the process, put my chalk talk together, and figure out what questions I wanted to ask’ (Grewal, 2022). From speaking to postdocs applying for independent positions and to the community more broadly it's apparent that many people would appreciate a little more support as they navigate the job market and start their first independent position. This got us thinking about what we at Development could do to help. As part of the not-for-profit charitable organisation The Company of Biologists, one of our core aims is to support the biological community – not only through our publishing activities, but also through our grants, meetings and fellowships. As discussed in this recent editorial, over recent years we've been particularly focussed on how we can better support early career researchers (ECRs) (Briscoe and Grewal, 2021). Now, we're delighted to announce a new scheme, Development's ‘Pathway to Independence (PI)’ programme, aimed at researchers about to go on the job market for their first independent position.What does this programme involve? For this first pilot scheme, we invite any developmental biology or stem cell researcher planning to apply for their first principal investigator position in 2023 to apply to become one of our ‘PI fellows’. This will be a competitive scheme: given our limited resources, we will only be able to support a small number of people. These individuals will receive a tailored mentorship session with one of our editors – which might, for example, help the fellow refine their research proposal or conduct a mock job interview. We will give feedback on a job talk and we will also offer to host a recording of a talk on the Node as a showcase of their work. Through features in the journal and on the Node, we will help raise the fellows’ profiles, thus benefitting them as they apply for positions. Although details are still being developed (and will be designed in consultation with the first cohort of fellows), we also plan to provide some financial support for training to help make the transition to an independent position.So if you are a postdoc about to go on the job market and think this scheme could be useful to you, please do apply! The application procedure is straightforward – you can find more details on our website (https://journals.biologists.com/dev/pages/pi-programme) or apply directly via our grants portal (https://cob.smartsimpleuk.com/). Applications must be received by 31 January 2023, and we aim to announce our first group of PI fellows in March 2023. All applications will be reviewed by our team of academic and professional editors, and the successful applicants will be selected based on their research record and future plans, as well as on the extent to which they are likely to benefit from such a scheme. We hope to receive applications from across the world, and we aim to support researchers from a diverse range of backgrounds.We recognise that we're only able to offer this scheme to a small number of individuals compared with how many postdocs in our field go on the job market each year. For this reason, we are looking at ways we might be able to support more of the applicants who do not go on to become PI fellows. When you apply, you will have the option to tell us whether you'd like to be considered to give a talk as part of our ‘Development presents’ webinar series; from this, we aim to put together a set of topic-focussed webinars. We also plan to run one or two seminars for applicants to the scheme focussing on, for example, navigating the publishing process as a new principal investigator.Importantly, we hope that this programme will create a growing network of the next generation of leaders in the developmental biology and stem cell field – we aim to facilitate peer-to-peer mentorship and provide opportunities for our PI fellows to interact with each other and (in subsequent years) with previous cohorts. We anticipate that this network will not just be about the job search but extend to those first important years of running a research group. As we've heard in our ‘Transitions in Development’ interviews with junior group leaders (https://journals.biologists.com/dev/collection/8029/Transitions-in-development), running a lab means moving away from the bench and developing administrative and managerial skills, figuring out how to get funding, how to buy equipment, recruit new team members and set up collaborations. Peer-to-peer support can be invaluable for exchanging information and sharing problems in what can be an isolating experience.Overall, we hope that Development's ‘Pathway to Independence’ programme will provide a valuable set of benefits to our PI fellows and will help to nurture the future leaders of our field. If you have any other ideas of how we can support postdocs as they transition to independence, please do get in touch.

journals.biologists.com
Show older
Qoto Mastodon

QOTO: Question Others to Teach Ourselves
An inclusive, Academic Freedom, instance
All cultures welcome.
Hate speech and harassment strictly forbidden.