Biology subjects

Merino, N.

Publications and source records attributed to Merino, N..

3 recordsLinked to original sources

bioRxiv2026

MagicLamp: a web server and software toolkit for targeted gene annotation of microbial functions

Genome and metagenome annotation tools designed for large databases are ill-suited to the discovery of specialized, ecologically relevant microbial functions. MagicLamp (https://github.com/Arkadiy-Garber/MagicLamp) is a modular command-line software toolkit that performs targeted functional gene annotation searches using curated collections of hidden Markov models (HMMs), each representing discrete microbial metabolic processes. MagicLamp is also available as a web server: https://midauthorbio.com/#magiclamp. This targeted approach enables sensitive and specific annotation of genes involved in defined microbial processes, allowing MagicLamp to serve as a dedicated repository for the annotation of specialized microbial functions currently overlooked in other databases and software. The server accepts unannotated genome assemblies or GenBank-formatted annotations to perform HMM-based searches against curated model sets with reproducible, model-specific bit-score thresholds. Automated results are returned as tabular summaries and interactive HTML reports containing cross-genome/metagenome comparisons.

bioinformatics↗

bioRxiv2019

Structure of the processive human Pol δ holoenzyme

In eukaryotes, DNA polymerase {delta} (Pol {delta}) bound to the proliferating cell nuclear antigen (PCNA) replicates the lagging strand and cooperates with flap endonuclease 1 (FEN1) to process the Okazaki fragments for their ligation. We present the high-resolution cryo-EM structure of the human processive Pol {delta}-DNA-PCNA complex in the absence and presence of FEN1. Pol {delta} is anchored to one of the three PCNA monomers through the C-terminal domain of the catalytic subunit. The catalytic core sits on top of PCNA in an open configuration while the regulatory subunits project laterally. This arrangement allows PCNA to thread and stabilize the DNA exiting the catalytic cleft and recruit FEN1 to one unoccupied monomer in a toolbelt fashion. Alternative holoenzyme conformations reveal important functional interactions that maintain PCNA orientation during synthesis. This work sheds light on the structural basis of Pol {delta}s activity in replicating the human genome.

biochemistry↗

bioRxiv2019

FeGenie: a comprehensive tool for the identification of iron genes and iron gene neighborhoods in genomes and metagenome assemblies

Iron is a micronutrient for nearly all life on Earth. It can be used as an electron donor and electron acceptor by iron-oxidizing and iron-reducing microorganisms, and is used in a variety of biological processes, including photosynthesis and respiration. While it is the fourth most abundant metal in the Earths crust, iron is often limiting for growth in oxic environments because it is readily oxidized and precipitated. Much of our understanding of how microorganisms compete for and utilize iron is based on laboratory experiments. However, the advent of next-generation sequencing and the associated surge in publicly-available sequence data has now made it possible to probe the structure and function of microbial communities in the environment. To bridge the gap between our understanding of iron acquisition and utilization in model microorganisms and the plethora of sequence data available from environmental studies, we have created a comprehensive database of hidden Markov models (HMMs) that is based on genes related to iron acquisition, storage, and reduction/oxidation. Along with this database, we present FeGenie, a bioinformatics tool that accepts genome and metagenome assemblies as input and uses our comprehensive HMM database to annotate the provided datasets with respect to iron-related genes and gene clusters. An important contribution of this tool is the efficient identification of genes involved in iron oxidation and dissimilatory iron reduction, which have been largely overlooked by standard annotation pipelines. While this tool will not replace the reliability of culture-dependent analyses of microbial physiology, it provides reliable predictions derived from the most up-to-date genetic markers. FeGenies database will be maintained and continually-updated as new genetic markers are discovered. FeGenie is freely available: https://github.com/Arkadiy-Garber/FeGenie.

bioinformatics↗