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  • 1. Gallego-Villarejo, Lucía
    et al.
    Wallin, Cecilia
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Król, Sylwia
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Enrich-Bengoa, Jennifer
    Suades, Albert
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Universitat Autònoma de Barcelona, Spain.
    Aguilella-Arzo, Marcel
    Gomara, María José
    Haro, Isabel
    Wärmlander, Sebastian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Muñoz, Francisco J.
    Gräslund, Astrid
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Perálvarez-Marín, Alex
    Big dynorphin is a neuroprotector scaffold against amyloid β-peptide aggregation and cell toxicity2022Ingår i: Computational and Structural Biotechnology Journal, E-ISSN 2001-0370, Vol. 20, s. 5672-5679Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Amyloid β-peptide (Aβ) misfolding into β-sheet structures triggers neurotoxicity inducing Alzheimer’s disease (AD). Molecules able to reduce or to impair Aβ aggregation are highly relevant as possible AD treatments since they should protect against Aβ neurotoxicity. We have studied the effects of the interaction of dynorphins, a family of opioid neuropeptides, with Aβ40 the most abundant species of Aβ. Biophysical measurements indicate that Aβ40 interacts with Big Dynorphin (BigDyn), lowering the amount of hydrophobic aggregates, and slowing down the aggregation kinetics. As expected, we found that BigDyn protects against Aβ40 aggregates when studied in human neuroblastoma cells by cell survival assays. The cross-interaction between BigDyn and Aβ40 provides insight into the mechanism of amyloid pathophysiology and may open up new therapy possibilities.

  • 2.
    Izabel-Shen, Dandan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Understanding response of microbial communities to saltwater intrusion through microcosms2021Ingår i: Computational and Structural Biotechnology Journal, E-ISSN 2001-0370, Vol. 19, s. 929-933Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A central pursuit of microbial ecology is to accurately describe and explain the shifts in microbial community composition and function that occur in response to environmental changes. This goal requires a thorough understanding of the individual responses of different species and of the processes guiding the assembly of microbial populations similar in their response traits and corresponding functional traits. These research topics are addressed and synthesized in this Highlights, in four studies applying a traitbased framework to assess how environmental change affected the composition and functional performance of bacterioplankton of natural origin in microcosm experiments. The salinity of many aquatic environments is currently changing, due to climate change and anthropogenic activities. The mechanisms by which salinity influences community assembly, functional redundancy and functional genes involved in nitrogen cycle, and how dispersal modifies community outcome are explored in the four studies. Together, the findings of these case studies demonstrate the feasibility of using novel experiments in combination with integrative analyses of 16S rRNA and meta-'omic' data to address ecological questions. This combined approach has the potential to elucidate both the processes contributing to bacterial community assembly and the possible links between the compositional and functional changes that occur under shifting environmental conditions.

  • 3. Loch, Rolf Antonie
    et al.
    Wang, Hongzhi
    Perálvarez-Marín, Alex
    Berger, Philipp
    Nielsen, Henrietta
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Chroni, Angeliki
    Luo, Jinghui
    Cross interactions between Apolipoprotein E and amyloid proteins in neurodegenerative diseases2023Ingår i: Computational and Structural Biotechnology Journal, E-ISSN 2001-0370, Vol. 21, s. 1189-1204Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Three common Apolipoprotein E isoforms, ApoE2, ApoE3, and ApoE4, are key regulators of lipid homeostasis, among other functions. Apolipoprotein E can interact with amyloid proteins. The isoforms differ by one or two residues at positions 112 and 158, and possess distinct structural conformations and functions, leading to isoform-specific roles in amyloid-based neurodegenerative diseases. Over 30 different amyloid proteins have been found to share similar characteristics of structure and toxicity, suggesting a common interactome. The molecular and genetic interactions of ApoE with amyloid proteins have been extensively studied in neurodegenerative diseases, but have not yet been well connected and clarified. Here we summarize essential features of the interactions between ApoE and different amyloid proteins, identify gaps in the understanding of the interactome and propose the general interaction mechanism between ApoE isoforms and amyloid proteins. Perhaps more importantly, this review outlines what we can learn from the interactome of ApoE and amyloid proteins; that is the need to see both ApoE and amyloid proteins as a basis to understand neurodegenerative diseases.

  • 4. Namias, Alice
    et al.
    Sahlin, Kristoffer
    Stockholms universitet, Naturvetenskapliga fakulteten, Matematiska institutionen. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Makoundou, Patrick
    Bonnici, Iago
    Sicard, Mathieu
    Belkhir, Khalid
    Weill, Mylène
    Nanopore sequencing of PCR products enables multicopy gene family reconstruction2023Ingår i: Computational and Structural Biotechnology Journal, E-ISSN 2001-0370, Vol. 21, s. 3656-3664Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The importance of gene amplifications in evolution is more and more recognized. Yet, tools to study multi-copy gene families are still scarce, and many such families are overlooked using common sequencing methods. Haplotype reconstruction is even harder for polymorphic multi-copy gene families. Here, we show that all variants (or haplotypes) of a multi-copy gene family present in a single genome, can be obtained using Oxford Nanopore Technologies sequencing of PCR products, followed by steps of mapping, SNP calling and haplotyping. As a proof of concept, we acquired the sequences of highly similar variants of the cidA and cidB genes present in the genome of the Wolbachia wPip, a bacterium infecting Culex pipiens mosquitoes. Our method relies on a wide database of cid genes, previously acquired by cloning and Sanger sequencing. We addressed problems commonly faced when using mapping approaches for multi-copy gene families with highly similar variants. In addition, we confirmed that PCR amplification causes frequent chimeras which have to be carefully considered when working on families of recombinant genes. We tested the robustness of the method using a combination of bioinformatics (read simulations) and molecular biology approaches (sequence acquisitions through cloning and Sanger sequencing, specific PCRs and digital droplet PCR). When different haplotypes present within a single genome cannot be reconstructed from short reads sequencing, this pipeline confers a high throughput acquisition, gives reliable results as well as insights of the relative copy numbers of the different variants.

  • 5. Perálvarez-Marín, Alex
    et al.
    Baranowski, Eric
    Bierge, Paula
    Pich, Oscar Q.
    Lebrette, Hugo
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Metal utilization in genome-reduced bacteria: Do human mycoplasmas rely on iron?2021Ingår i: Computational and Structural Biotechnology Journal, E-ISSN 2001-0370, Vol. 19, s. 5752-5761Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    Mycoplasmas are parasitic bacteria with streamlined genomes and complex nutritional requirements. Although iron is vital for almost all organisms, its utilization by mycoplasmas is controversial. Despite its minimalist nature, mycoplasmas can survive and persist within the host, where iron availability is rigorously restricted through nutritional immunity. In this review, we describe the putative iron-enzymes, transporters, and metalloregulators of four relevant human mycoplasmas. This work brings in light critical differences in the mycoplasma-iron interplay. Mycoplasma penetrans, the species with the largest genome (1.36 Mb), shows a more classic repertoire of iron-related proteins, including different enzymes using iron-sulfur clusters as well as iron storage and transport systems. In contrast, the iron requirement is less apparent in the three species with markedly reduced genomes, Mycoplasma genitalium (0.58 Mb), Mycoplasma hominis (0.67 Mb) and Mycoplasma pneumoniae (0.82 Mb), as they exhibit only a few proteins possibly involved in iron homeostasis. The multiple facets of iron metabolism in mycoplasmas illustrate the remarkable evolutive potential of these minimal organisms when facing nutritional immunity and question the dependence of several human-infecting species for iron. Collectively, our data contribute to better understand the unique biology and infective strategies of these successful pathogens.

  • 6. Sheng, Xiang
    et al.
    Himo, Fahmi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Mechanisms of metal-dependent non-redox decarboxylases from quantum chemical calculations2021Ingår i: Computational and Structural Biotechnology Journal, E-ISSN 2001-0370, Vol. 19, s. 3176-3186Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Quantum chemical calculations are today an extremely valuable tool for studying enzymatic reaction mechanisms. In this mini-review, we summarize our recent work on several metal-dependent decarboxylases, where we used the so-called cluster approach to decipher the details of the reaction mechanisms, including elucidation of the identity of the metal cofactors and the origins of substrate specificity. Decarboxylases are of growing potential for biocatalytic applications, as they can be used in the synthesis of novel compounds of, e.g., pharmaceutical interest. They can also be employed in the reverse direction, providing a strategy to synthesize value-added chemicals by CO2 fixation. A number of non-redox metal-dependent decarboxylases from the amidohydrolase superfamily have been demonstrated to have promiscuous carboxylation activities and have attracted great attention in the recent years. The computational mechanistic studies provide insights that are important for the further modification and utilization of these enzymes in industrial processes. The discussed enzymes are: 5-carboxyvanillate decarboxylase, gamma-resorcylate decarboxylase, 2,3-dihydroxybenzoic acid decarboxylase, and iso-orotate decarboxylase.

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