Code & Data for "Viral infection switches the balance between bacterial and eukaryotic recyclers of organic matter during coccolithophore blooms"

Code & Data for "Viral infection switches the balance between bacterial and eukaryotic recyclers of organic matter during coccolithophore blooms"Data also available on Dryad: (https://doi.org/10.5061/dryad.q573n5tfr)Sequences are deposited on NCBI: Bioproject PRJNA694552: 16S data is available under Biosample SAMN17576248 and 18S data is available under Biosample SAMN20295136Flow cam data is deposited on Ecotaxa: "Flowcam Composite Aquacosm_2018_VIMS-Ehux"THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV

Code & Data for: Fundamental metabolic strategies of heterotrophic bacteria

Code & Data for: Fundamental metabolic strategies of heterotrophic bacteria (bioRxiv )THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV

Code & Data for: Environmental heterogeneity can tip the population genetics of range expansions

Code & Data for: Environmental heterogeneity can tip the population genetics of range expansions (Matti Gralka & Oskar Hallatschek), under review at Elife (2019)

MODELING OF THE METAL BINDING SITES IN PROTEINS INVOLVED IN NEURODEGENERATION

Many proteins involved in the neurodegeneration processes are potential metalloproteins. In some of them the metal binding domain is flexible or unstructured (e.g. prion proteins, β-amyloid peptide, α-synuclein) resembling oligo-peptide chains. The regular protein structure usually has a critical impact on the binding ability of metal ion to protein scaffold, while in peptides with random structures the individual binding ability of the particular amino acid residue may decide about the peptide binding to metal ion

Allele surfing promotes microbial adaptation from standing variation.

The coupling of ecology and evolution during range expansions enables mutations to establish at expanding range margins and reach high frequencies. This phenomenon, called allele surfing, is thought to have caused revolutions in the gene pool of many species, most evidently in microbial communities. It has remained unclear, however, under which conditions allele surfing promotes or hinders adaptation. Here, using microbial experiments and simulations, we show that, starting with standing adaptive variation, range expansions generate a larger increase in mean fitness than spatially uniform population expansions. The adaptation gain results from soft' selective sweeps emerging from surfing beneficial mutations. The rate of these surfing events is shown to sensitively depend on the strength of genetic drift, which varies among strains and environmental conditions. More generally, allele surfing promotes the rate of adaptation per biomass produced, which could help developing biofilms and other resource-limited populations to cope with environmental challenges

The complex-formation behaviour of His residues in the fifth Cu2+ binding site of human Prion protein: a close look

Human Prion Protein (hPrPC) is able to bind up to six Cu2+ ions. Four of them can be allocated in the “octarepeat domain”, a region of the unstructured N-terminal domain containing four tandem-repetitions of the sequence PHGGGWGQ. It is widely accepted that the additional binding sites correspond to His-96 and His-111 residues. However, recent literature does not agree on the role and the behavior of these sites in Cu2+ complexation to hPrPC. In order to shed more light on this topic, some peptidic analogues of the PrP92-113 fragment were synthesized: (H96A)PrP92-113, (H111A)PrP92-113, (H96Nτ-Me-His)PrP92-113, (H111Nτ-Me-His)PrP92-113, (H96Nτ-Me-His)PrP92-100, (H111Nτ-Me-His)PrP106-113, where an alanine or a histidine methylated at the τ nitrogen atom of its imidazole ring have been substituted to His-96 or His-111. The first two ligands allowed to confirm that His-111 binding site is stronger than His-96 one: they act as independent sites even at Cu2+-ion substoichiometric levels. Neither multi-histidine binding nor bis-complex formation has been detected at neutral pH. Nτ methylation gave evidence that τ nitrogens of imidazole residues can participate in complex-formation only at acidic pH, where displacement of amidic protons by Cu2+ ions is not allowed. Finally, the length of the fragment does not look to have any significant influence on the behavior of the two His-96 and His-111 binding sites, from the point of view of neither the coordination geometry nor their relative strength