Structure and mechanism of human DNA polymerase η

The variant form of the human syndrome xeroderma pigmentosum (XPV) is caused by a deficiency in DNA polymerase eta (Pol eta), a DNA polymerase that enables replication through ultraviolet-induced pyrimidine dimers. Here we report high-resolution crystal structures of human Pol eta at four consecutive steps during DNA synthesis through cis-syn cyclobutane thymine dimers. Pol eta acts like a 'molecular splint' to stabilize damaged DNA in a normal B-form conformation. An enlarged active site accommodates the thymine dimer with excellent stereochemistry for two-metal ion catalysis. Two residues conserved among Pol eta orthologues form specific hydrogen bonds with the lesion and the incoming nucleotide to assist translesion synthesis. On the basis of the structures, eight Pol eta missense mutations causing XPV can be rationalized as undermining the molecular splint or perturbing the active-site alignment. The structures also provide an insight into the role of Pol eta in replicating through D loop and DNA fragile sites

Crown Plasticity and Competition for Canopy Space: A New Spatially Implicit Model Parameterized for 250 North American Tree Species

BACKGROUND: Canopy structure, which can be defined as the sum of the sizes, shapes and relative placements of the tree crowns in a forest stand, is central to all aspects of forest ecology. But there is no accepted method for deriving canopy structure from the sizes, species and biomechanical properties of the individual trees in a stand. Any such method must capture the fact that trees are highly plastic in their growth, forming tessellating crown shapes that fill all or most of the canopy space. METHODOLOGY/PRINCIPAL FINDINGS: We introduce a new, simple and rapidly-implemented model--the Ideal Tree Distribution, ITD--with tree form (height allometry and crown shape), growth plasticity, and space-filling, at its core. The ITD predicts the canopy status (in or out of canopy), crown depth, and total and exposed crown area of the trees in a stand, given their species, sizes and potential crown shapes. We use maximum likelihood methods, in conjunction with data from over 100,000 trees taken from forests across the coterminous US, to estimate ITD model parameters for 250 North American tree species. With only two free parameters per species--one aggregate parameter to describe crown shape, and one parameter to set the so-called depth bias--the model captures between-species patterns in average canopy status, crown radius, and crown depth, and within-species means of these metrics vs stem diameter. The model also predicts much of the variation in these metrics for a tree of a given species and size, resulting solely from deterministic responses to variation in stand structure. CONCLUSIONS/SIGNIFICANCE: This new model, with parameters for US tree species, opens up new possibilities for understanding and modeling forest dynamics at local and regional scales, and may provide a new way to interpret remote sensing data of forest canopies, including LIDAR and aerial photography

Cosmology intertwined III: fσ8 and S8

The standard Cold Dark Matter cosmological model provides a wonderful fit to current cosmological data, but a few statistically significant tensions and anomalies were found in the latest data analyses. While these anomalies could be due to the presence of systematic errors in the experiments, they could also indicate the need for new physics beyond the standard model. In this Letter of Interest we focus on the tension between Planck data and weak lensing measurements and redshift surveys, in the value of the matter energy density and the amplitude (or the growth rate ) of cosmic structure. We list a few promising models for solving this tension, and discuss the importance of trying to fit multiple cosmological datasets with complete physical models, rather than fitting individual datasets with a few handpicked theoretical parameters

Snowmass2021 - Letter of interest cosmology intertwined IV: the age of the universe and its curvature

A precise measurement of the curvature of the Universe is of prime importance for cosmology since it could not only confirm the paradigm of primordial inflation but also help in discriminating between different early-Universe scenarios. Recent observations, while broadly consistent with a spatially flat standard Cold Dark Matter (CDM) model, show tensions that still allow (and, in some cases, even suggest) a few percent deviations from a flat universe. In particular, the Planck Cosmic Microwave Background power spectra, assuming the nominal likelihood, prefer a closed universe at more than 99% confidence level. While new physics could be at play, this anomaly may be the result of an unresolved systematic error or just a statistical fluctuation. However, since positive curvature allows a larger age of the Universe, an accurate determination of the age of the oldest objects provides a smoking gun in confirming or falsifying the current flat CDM model