Maturation and persistence of the anti-SARS-CoV-2 memory B cell response

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ERα is an RNA-binding protein sustaining tumor cell survival and drug resistance

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Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs

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Structural Insight into Chromatin Recognition by Multiple Domains of the Tumor Suppressor RBBP1

Retinoblastoma-binding protein 1 (RBBP1) is involved in gene regulation, epigenetic regulation, and disease processes. RBBP1 contains five domains with DNA-binding or histone-binding activities, but how RBBP1 specifically recognizes chromatin is still unknown. An AT-rich interaction domain (ARID) in RBBP1 was proposed to be the key region for DNA-binding and gene suppression. Here, we first determined the solution structure of a tandem PWWP-ARID domain mutant of RBBP1 after deletion of a long flexible acidic loop L12 in the ARID domain. NMR titration results indicated that the ARID domain interacts with DNA with no GC- or AT-rich preference. Surprisingly, we found that the loop L12 binds to the DNA-binding region of the ARID domain as a DNA mimic and inhibits DNA binding. The loop L12 can also bind weakly to the Tudor and chromobarrel domains of RBBP1, but binds more strongly to the DNA-binding region of the histone H2A-H2B heterodimer. Furthermore, both the loop L12 and DNA can enhance the binding of the chromobarrel domain to H3K4me3 and H4K20me3. Based on these results, we propose a model of chromatin recognition by RBBP1, which highlights the unexpected multiple key roles of the disordered acidic loop L12 in the specific binding of RBBP1 to chromatin.     

On the relation between gene flow theory and genetic gain

In conventional gene flow theory the rate of genetic gain is calculated as the summed products of genetic selection differential and asymptotic proportion of genes deriving from sex-age groups. Recent studies have shown that asymptotic proportions of genes predicted from conventional gene flow theory may deviate considerably from true proportions. However, the rate of genetic gain predicted from conventional gene flow theory was accurate. The current note shows that the connection between asymptotic proportions of genes and rate of genetic gain that is embodied in conventional gene flow theory is invalid, even though genetic gain may be predicted correctly from it.     

Tropane alkaloid production by Agrobacterium rhizogenes transformed hairy root cultures of Atropa baetica Willk. (Solanaceae)

Atropa baetica hairy root cultures were induced after infecting stem segments with Agrobacterium rhizogenes strain ATCC 15834. Accumulation of the tropane alkaloids atropine and scopolamine by hairy roots cultured in half- and full-strength Murashige and Skoog (MS) medium was high, although this was not growth associated. These alkaloids were also released into both liquid media. Higher tropane alkaloids present both in hairy roots and liquid medium occurred in half MS medium, showing a clear relationship between slow growth of cultures and higher product accumulation. The pH of both nutrient media varied as culture progressed, and seemed to be associated with the release of scopolamine. GC-MS analyses showed the presence of a new compound, namely tigloylpseudotropine; moreover, 3α-isobutyryloxytropane, formerly found only in plant leaf tissue, was also identified in the hairy roots. Received: 18 August 1997 / Revision received: 30 November 1997 / Accepted: 20 January 1998     

Prey: predator ratio dependence in the functional response of a freshwater amphipod

1. First known for their shredding activity, freshwater amphipods also behave as active predators with consequences for prey population regulation and amphipod coexistence in the context of biological invasions. 2. A way to quantify predation is to determine the average consumption rate per predator, also known as its functional response (FR). 3. Although amphipods are gregarious and can display social interactions that can alter per capita consumption rates, previous studies using the FR approach to investigate amphipod predation ignored such potential mutual interference because they did not consider variations in predator density. 4. We investigated the FR of Echinogammarus berilloni feeding on dipteran larvae with joint variations in prey and predator densities. This bivariate experimental design allowed us to estimate interference and to compare the fits of the three main classes of theoretical FR models, in which the predation rate is a function of prey density alone (prey‐dependent models), of both prey and predator densities (predator‐dependent models) or of the prey‐to‐predator ratio (ratio‐dependent models). 5. The Arditi–Ginzburg ratio‐dependent FR model provided the best representation of the FR of E. berilloni, whose predation rate showed a decelerating rise to a horizontal asymptote as prey abundance increased. 6. Ratio dependence means that mutual interference between amphipods leads to prey sharing. Mutual interference is likely to vary between amphipod species, depending on their level of aggressiveness.