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Metabarcoding to monitor the crustacean zooplankton of a lake improves when using a reference DNA library from local samples

Authors

National Research Council, Water Research Institute (CNR-IRSA), Verbania Pallanza, Italy.

Biodiversity surveys through morphology provide invaluable data to inform biological monitoring efforts, involving specialised taxonomic skills that are not always available. The revolution brought by the advent of metabarcoding associated to massive sequencing is currently seen as a potential advance, even if different approaches may often provide different results. Here we test if reliable results from metabarcoding can be obtained by i) basing the analyses on a detailed knowledge of the local diversity from morphology, ii) applying tools from DNA taxonomy to create a local reference library, ii) developing custom primers, taking as example the crustacean zooplankton of a subalpine lake in Northern Italy, Lake Maggiore. We support the idea that occurrences from metabarcoding can be reliable, especially with targeted primers, but we confirm that read numbers from massive sequencing could not be related to abundance of individuals in our analyses. Data from metabarcoding can thus be used to reliably monitor species occurrence in the lake, but not changes in abundance.

Arfè A, Quatto P, Zambon A, MacIsaac HJ, Manca M, 2019. Long-term changes in the zooplankton community of Lake Maggiore in response to multiple stressors: A functional prin

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Template-Based Protein Structure Modeling

Abstract

Functional characterization of a protein is often facilitated by its 3D structure. However, the fraction of experimentally known 3D models is currently less than 1% due to the inherently time-consuming and complicated nature of structure determination techniques. Computational approaches are employed to bridge the gap between the number of known sequences and that of 3D models. Template-based protein structure modeling techniques rely on the study of principles that dictate the 3D structure of natural proteins from the theory of evolution viewpoint. Strategies for template-based structure modeling will be discussed with a focus on comparative modeling, by reviewing techniques available for all the major steps involved in the comparative modeling pipeline.

Keywords: Homology modeling, Comparative protein structure modeling, Template-based modeling, Loop modeling, Side chain modeling, Sequence-to-structure alignment

1. Introduction

The class of methods referred to as template-based modeling includes both the threading techniques that return a full 3D description for the target and comparative modeling (1). This class of protein structure modeling relies on detectable similarity spanning most of the modeled sequence and at least one known structure. Comparative modeling refers to those template-based modeling cases where not only the fold is determined from a possible set of available templates, but a full atom model is also built (2). In practice, it means that if the structure of at least one protein in the family has been determined by experimentation, the other members of the family can be modeled based on their alignment to the known structure. It is possible because a small change in the protein sequence usually results in a small change in its 3D structure (3). It is also facilitated by the fact that 3D structure of proteins from the same family is more conserved than their amino-acid sequences (4). Th