Here are some discoveries that fascinate me this week.


Structural cells regulate organ-specific immune responses

When we talk about immune response, we often think of gene expression changes that happen in haematopoietic immune cells, which include myeloid cells, such as monocytes and neutrophils that are responsible for innate immunity, and lymphoid cells, such as T cells and B cells that constitute adaptive immunity. But what about other cell types? We know that many of them also contribute to pathogen defence, but how is that achieved? How is expression of immune genes controlled in non-immune cells?

Krausgruber et al. reported in an Nature article their systematic study of regulation of immune genes in three major types of structural cells: epithelium, endothelium, and fibroblasts. They characterized cell types across twelve organs in mice, using cellular phenotyping, transcriptome sequencing, chromatin accessibility profiling, and epigenome mapping. They observed complex immune gene activity and regulation in these structural cells, which are highly organ-specific, and seem to modulate interactions between structural and haematopoietic cells.

The dataset can be used to analyse immune response from structural cells at multiple omics levels. We are not sure yet whether human cells follow the same principles. Another aspect I miss is the multi-omics profiling following perturbation by pathogens or chemical matters that induce immune response. Nevertheless, the dataset is already impressive enough and will for sure inspire further studies in the same direction.

Computational biology

Modelling interactions between the immune system and cancer

This review, Interactions Between the Immune System and Cancer: A Brief Review of Non-spatial Mathematical Models by Eftimie et al. summarizes some commonly used non-spatial mathematical models to study interactions between the immune system and cancer. I discovered it through another paper that I read the other day on integrating mathematical modelling with single-cell omics data, Griffiths et al. (PNAS 2020).

Though the review is almost ten years old and therefore could not anticipate certain types of data, for instance single-cell sequencing, the principles of mathematical modelling are valid, and the approaches may be useful also for other disease indications as well.


  • In a R ShinyApp, changes in ui.R or server.R will cause the server to restart automatically. If other dependencies (say R functions) are changed and a manual restart is necessary, it suffices to run touch restart.txt command in the ShinyApp directory. It will force the ShinyApp to restart.

Other gems

Get the courage to leave familiar tracks

I am reading the book Beschleunigung - Die Veränderung der Zeitstrukturen in der Moderne by Hartmut Rosa (an English version, named Social Acceleration: A New Theory of Modernity, is also available). I find the book a stunningly rich, informative, and comprehensive critique of acceleration. It makes me think how to live.

This week I discovered a talk that Hartmut Rosa gave to first-year students of the Friedrich-Schiller University of Jena in Germany, titled Wächter, wie lange noch die Nacht? Ueber intellektuelle Redlichkeit als Leitprinzip in schwieriger Zeit (in German only). The talk is directed at new students, but I think the lessons are helpful for me, too.

I was reminded of the observation of baseline happiness, namely the grade of happiness for most people remains mostly constant, and reminded of the conclusion that how happy we are is strongly influenced by how we perceive our environment and how we participate in shaping it. In order to actively shape the environment, we can expand our horizon by learning new things, we can bring up our initiative, and we can live and think like people we want to become.

Hartmut Rosa reminded me that we need both enthusiasm and hard work to be successful in our work, but they are not sufficient. Good ideas and inspirations are important. Paradoxically, neuroscience confirms that good ideas and inspirations may not necessarily fall over someone during hard work. Instead, they visit us rather in unexpected time and space, for instance during a walk or in a party, when we are not actively thinking of the problems. Therefore, taking rest and exercising regularly and engaging in hobbies are not only important for a balanced life, but also important for work, especially work where ideas and creativity are important, such as scientific research.

An important concept I learned was scientific honesty (Wissenschaftliche Redlichkeit in German). A key part of it is to take opposite opinions and evidence that arguing against my own opinions seriously, even more seriously than my own opinions. That does not mean I have to change or discard my views and positions. Rather, it urges me not to ignore or deny ‘uncomfortable’ facts. Apparently, the scientific honesty does not only helps to win the respect and understanding of people with a different view from mine, but also helps to make my judgement and world view more informed.

Two other things leave me ponder. One is that when being asked how would she live if she has another chance, the grandmother of Hartmut Rosa, shortly before she passed away, replied that she would live exactly as she did, though without fear. It is a daily challenge to live with trust in oneself, not fear, to deal with the changes in the environment.

The other is the text of lecture Science as a Vocation (Wissenschaft als Beruf) by Max Weber, a German sociologist and political economist. Both German version and English version are available. I was not aware of the text before, and therefore are thankful that Hartmut Rosa introduced this to the students and me.

Blue eyes, brown eyes

I read the story about blue eyes, brown eyes in a German article published on The english version is available at frontline.

The American teacher Jane Elliott divided her class into two groups: blue eyes, and brown eyes, at the end of 1960s. She made up a theory to prefer the blue eyes and to discriminate the brown eyes (in the later phase of the experiment, she switched the groups).

It surprised her to observe that it took only 15 minutes to turn otherwise similar children into two classes. Children who were designated as “inferior” lost self confidence, and performed poorly on tests and other work. In contrast, the “superior” students, who had been sweet and tolerate before the exercise, became mean-spirited and seemed to like discriminating against the “inferior” group.

Screenshot from FRONTLINE's A Class Divided. Source: FRONTLINE
Screenshot from FRONTLINE's A Class Divided. Source: FRONTLINE

“I watched what had been marvelous, cooperative, wonderful, thoughtful children turn into nasty, vicious, discriminating little third-graders in a space of fifteen minutes,” says Elliott. She “created a microcosm of society in a third-grade classroom.”

I think it is a marvelous experiment. Jane Elliott found a simple yet fantastic way to show children and adults alike how discrimination works, and how it affects both discriminating and discriminated people.

Modelling study

Modelling study, from XKCD
Modelling study, from XKCD

Have a nice weekend!