Publications related to Biotechnology

Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design

Proteins are foundational biomolecules of life playing a crucial role in a myriad of biological processes. Their function often requires interplay with other biomolecules, including proteins themselves. Protein-protein interactions (PPIs) are essential for ...

EPFL2024

Industrial Biotechnology Conservation Processes: Similarities with Natural Long-Term Preservation of Biological Organisms

Philippe Abdel Sayed, Corinne Scaletta, Lee Ann Laurent-Applegate, Nathalie Hirt-Burri, Laurent Alexis Clément Vannay, Alexis Laurent

Cryopreservation and lyophilization processes are widely used for conservation purposes in the pharmaceutical, biotechnological, and food industries or in medical transplantation. Such processes deal with extremely low temperatures (e.g., -196 degrees C) a ...

MDPI2023

Gyrokinetic moment-based simulations of the Dimits shift

Paolo Ricci, Baptiste Jimmy Frei, Antoine Cyril David Hoffmann

We present a convergence study of the gyromoment (GM) approach, which is based on projecting the gyrokinetic distribution function onto a Hermite–Laguerre polynomial basis, focused on the cyclone base case (CBC) (Lin et al., Phys. Rev. Lett., vol. 83, no. ...

Cambridge University Press2023

Biotechnological Frontiers of DNA Nanomaterials Continue to Expand: Bacterial Infection using Virus-Inspired Capsids

Maartje Martina Cornelia Bastings

The elegant geometry of viruses has inspired bio-engineers to synthetically explore the self-assembly of polyhedral capsids employed to protect new cargo or change an enzymatic microenvironment. Recently, Yang and co-workers used DNA nanotechnology to revi ...

Wiley-VCH Verlag GmbH2023

Interplay of the mechanical and structural properties of DNA nanostructures determines their electrostatic interactions with lipid membranes

Maartje Martina Cornelia Bastings, Cem Tekin, Diana Kornelia Morzy, Vincenzo Caroprese

Nucleic acids and lipids function in close proximity in biological processes, as well as in nanoengineered constructs for therapeutic applications. As both molecules carry a rich charge profile, and frequently coexist in complex ionic solutions, the electr ...

ROYAL SOC CHEMISTRY2023

Symbolic kinetic models in python (SKiMpy): intuitive modeling of large-scale biological kinetic models

Vassily Hatzimanikatis, Georgios Fengos, Maria Masid Barcon, Daniel Robert Weilandt, Zhaleh Hosseini, Pierre Guy Rémy Salvy

Motivation: Large-scale kinetic models are an invaluable tool to understand the dynamic and adaptive responses of biological systems. The development and application of these models have been limited by the availability of computational tools to build and ...

OXFORD UNIV PRESS2022

Reviewing Challenges of Predicting Protein Melting Temperature Change Upon Mutation Through the Full Analysis of a Highly Detailed Dataset with High-Resolution Structures

Luciano Andres Abriata

Predicting the effects of mutations on protein stability is a key problem in fundamental and applied biology, still unsolved even for the relatively simple case of small, soluble, globular, monomeric, two-state-folder proteins. Many articles discuss the li ...

2021

A minimalistic cyclic ice-binding peptide from phage display

Harm-Anton Klok, Luciano Andres Abriata, Matthew Gibson, Xudong Kong, Corey Alfred Stevens

Developing molecules that emulate the properties of naturally occurring ice-binding proteins (IBPs) is a daunting challenge. Rather than relying on the (limited) existing structure–property relationships that have been established for IBPs, here we report ...

Nature Research2021

Biotechnology Applications of Nanocarbons in Plant and Algal Systems

Ardemis Anoush Boghossian, Alice Judith Gillen, Alessandra Antonucci

The unique combination of structural, optical, and electronic properties of nanocarbons (NCs) has made these materials particularly attractive for various applications in biotechnology and biomedicine, ranging from sensing, gene-delivery, bioimaging and th ...

Royal Society of Chemistry2021

Synthetic Biology: A Solution for Tackling Nanomaterial Challenges

Ardemis Anoush Boghossian, Alice Judith Gillen, Benjamin Paul Johanès Gabriel Lambert

Bioengineers have mastered practical techniques for tuning a biomaterial’s properties with only limited information on the relationship between the material’s structure and function. These techniques have been quintessential to engineering proteins, which ...

2020

Microfluidic iMITOMI platform to study the architecture of low-affinity transcription factor binding site clusters

Ivan Istomin

Gene regulatory networks (GRNs) determine cellular behaviour, and ultimately the functioning of single- and multicellular organisms. Transcription factors regulate gene expression by binding to DNA or via remodelling chromatin. Recent advances in biotechno ...

EPFL2020

Computational design of anti-CRISPR proteins with improved inhibition potency

Bruno Emanuel Ferreira De Sousa Correia, Sandrine Madeleine Suzanne Georgeon, Andreas Scheck, Wei Sun, Stéphane Rosset, Zander Harteveld, Julius Valten Upmeier Zu Belzen, Yujia Wang

Anti-CRISPR (Acr) proteins are powerful tools to control CRISPR-Cas technologies. However, the available Acr repertoire is limited to naturally occurring variants. Here, we applied structure-based design on AcrIIC1, a broad-spectrum CRISPR-Cas9 inhibitor, ...

NATURE PUBLISHING GROUP2020

A new approach to Cas9-based genome editing in Aspergillus niger that is precise, efficient and selectable

Laure Marie Colette Leynaud-Kieffer Curran

Aspergillus niger and other filamentous fungi are widely used in industry, but efficient genetic engineering of these hosts remains nascent. For example, while molecular genetic tools have been developed, including CRISPR/Cas9, facile genome engineering of ...

2019

Recombinant Proteins for Industrial versus Pharmaceutical Purposes: A Review of Process and Pricing

Florian Maria Wurm

Recombinant proteins have been produced for over 30 years. Applications range from enzymes used in laundry detergents to antigen-detecting antibodies in cancer therapy. Despite similarities in manufacturing, drastic differences in retail pricing between re ...

2019

Gram-type differentiation of bacteria with 2D hollow photonic crystal cavities

Romuald Houdré, Rita Therisod, El Hadji Malick Camara

Fast and label-free techniques to analyze viruses and bacteria are of crucial interest in biological and bio-medical applications. For this purpose, optofluidic systems based on the integration of photonic structures with microfluidic layers were shown to ...

2018

Development and implementation of eco-genomic tools for aquatic ecosystem biomonitoring: the SYNAQUA French-Swiss program

Régis Lionel Vivien

The effectiveness of environmental protection measures is based on the early identification and diagnosis of anthropogenic pressures. Similarly, restoration actions require precise monitoring of changes in the ecological quality of ecosystems, in order to ...

SPRINGER HEIDELBERG2018

Nanoparticle Liposome Interactions

Zekiye Pelin Güven

Protein-mimetic materials are of great interest for biotechnology to grant protein-like properties to artificial systems. Additionally, these materials can be used to shed light on the fundamental properties of proteins in many environments. Nanoparticles, ...

EPFL2018

A synthetic biology approach to engineering living photovoltaics

Ardemis Anoush Boghossian, Nils Schürgers

The ability to electronically interface living cells with electron accepting scaffolds is crucial for the development of next-generation biophotovoltaic technologies. Although recent studies have focused on engineering synthetic interfaces that can maximiz ...

Royal Soc Chemistry2017

Raspberry Pi Driven Flow-Injection System for Electrochemical Continuous Monitoring Platforms

Giovanni De Micheli, Sandro Carrara, Francesca Stradolini, Federico Angiolini, Abuduwaili Tuoheti, Danilo Demarchi, Bruno Donato

Nowadays, there is an immense interest regarding new bio-sensing technologies, highlighting the need for effective validation of their capabilities. This necessity is more crucial when examining the proprieties of a sensor for continuous monitoring of a co ...

IEEE2017

SAS-6 engineering reveals interdependence between cartwheel and microtubules in determining centriole architecture

Pierre Gönczy, Virginie Hamel, Paul Guichard

Centrioles are critical for the formation of centrosomes, cilia and flagella in eukaryotes. They are thought to assemble around a nine-fold symmetric cartwheel structure established by SAS-6 proteins. Here, we have engineered Chlamydomonas reinhardtii SAS- ...

Nature Publishing Group2016