Biology subjects

Semper, C.

Publications and source records attributed to Semper, C..

7 recordsLinked to original sources

bioRxiv2024

A proposed framework for evaluating meat alternatives

Concerns surrounding the environmental, economic, and ethical consequences of meat production and industrial agriculture have prompted substantial research and capital investment into the production of meat alternatives. Alternative meat production encompasses a variety of technological approaches including plant-based meats, cell-based or cultivated meats, meat alternatives relying on fungal protein sources, and hybrids thereof; each of which offers unique advantages and disadvantages and has been associated with a myriad of claims supporting it as the preferred alternative to animal-derived meats. As part of XPRIZE Foundations Feed the Next Billion competition, we developed a framework for evaluating meat alternatives by measuring their structural, nutritional, and organoleptic properties while also assessing safety and their purported environmental and economic benefits compared to animal-derived meats. The framework is technologically agnostic and can be used to evaluate meat alternatives of all types. The output of the framework enables a data-driven comparison to animal-derived meat and/or other alternative meats, allowing a range of stakeholders (e.g., food startups, investors, government) to assess technological readiness, competitive advantage, and impact potential. This framework can assist this nascent industry as it moves towards standardizing approaches to evaluating the quality, safety and proposed benefits of meat alternatives.

bioengineering↗

bioRxiv2024

Cryo-EM Structure of Salmonella typhimurium ArnC; the Key Enzyme in Lipid-A Modification Conferring Polymyxin Resistance

1Polymyxins are last-resort antimicrobial peptides administered clinically against multi-drug resistant bacteria, including Gram-negative ESKAPE pathogens. However, an increasing number of pathogens employ a defense strategy involving a relay of enzymes encoded by the pmrE(ugd) loci and the arnBCDTEF operon. As a result, an Ara-4N headgroup is added to the lipid-A component of outer membrane (OM) lipopolysaccharides (LPS) rendering polymyxins ineffective. Here, we report the cryo-EM structures of glycosyltransferase ArnC from Salmonella typhimurium resolved in both apo and UDP-bound forms at resolutions 2.75 [A] and 3.8 [A], respectively. The structure of the ArnC protomer comprises of three distinct regions: an N-terminal glycosyltransferase domain, transmembrane region, and the interface helices (IHs). ArnC forms a stable tetramer with C2 symmetry through interactions in the C-terminal region, which is expected to protrude into the cytosol, where the {beta}8 strand inserts into the adjacent protomer. ArnC protomers have two distinct types of interfaces involving multiple hydrogen bonds and salt bridges. The binding of UDP induces conformational changes that stabilizes structurally labile A-loop, spanning residues 201 to 213, and part of the putative catalytic pocket formed by IH1 and IH2. The comparative analysis of ArnC structures with homologs GtrB and DPMS suggests the key residues involved in ArnC catalytic activity.

biochemistry↗

bioRxiv2024

Global survey of secondary metabolism in Aspergillus niger via activation of specific transcription factors

Genomics analysis confirmed the status of the filamentous fungi as a rich source of novel secondary metabolites; however, the discovery of these compounds is hampered by the cryptic nature of their biosynthetic pathways under laboratory conditions. Consequently, despite substantial research effort over the past decades, much of the secondary metabolome remains uncharacterized in fungal organisms. Our manual curation of biosynthetic gene clusters (BGCs) in the Aspergillus niger NRRL3 genome revealed that only 13 of 86 BGCs have had their cognate secondary metabolite products confirmed or reliably inferred. We also identified 60 transcription factors associated with cryptic BGCs. To further characterize A. niger secondary metabolism, we created a collection of strains each overexpressing a single BGC-associated transcription factor. We analyzed the strain collection using a standardized pipeline where we monitored phenotypic changes and compound production using mass spectrometry. Strains showing evidence of secondary metabolism activation were selected for gene expression analysis. Our approach resulted in the production of multiple potentially novel secondary metabolites and linked a specific BGC to tensidol production in A. niger. More broadly, this study found evidence counter to the existing paradigm of BGC expression controlled by co-localized transcription factors, lending credence to the emerging picture of a complex regulatory network governing fungal secondary metabolism. Significance StatementFungi produce an array of chemically diverse compounds that are routinely found to harbour valuable bioactivity. The products of secondary metabolism, these compounds have been a source of antimicrobials, anti-cancer agents, and other biopharmaceutical compounds termed natural products. Despite their demonstrated economic value, much is still unknown about the biosynthesis, regulation, and identities of these compounds. This study adopted a genome-wide approach to improve our understanding of the regulatory mechanisms that control fungal secondary metabolism, improving our ability to investigate the pathways responsible for natural product production.

microbiology↗

bioRxiv2024

Global atlas of predicted functional domains in Legionella pneumophila Dot/Icm translocated effectors

Legionella pneumophila utilizes the Dot/Icm type IVB secretion system to deliver hundreds of effector proteins inside eukaryotic cells to ensure intracellular replication. Our understanding of the molecular functions of this largest pathogenic arsenal known to the bacterial world remains incomplete. By leveraging advancements in 3D protein structure prediction, we provide a comprehensive structural analysis of 368 L. pneumophila effectors, representing a global atlas of predicted functional domains summarized in a database (https://pathogens3d.org/legionella-pneumophila). Our analysis identified 157 types of diverse functional domains in 287 effectors, including 159 effectors with no prior functional annotations. Furthermore, we identified 35 unique domains in 30 effector models that have no similarity with experimentally structurally characterized proteins, thus, hinting at novel functionalities. Using this analysis, we demonstrate the activity of thirteen domains, including three unique folds, predicted in L. pneumophila effectors to cause growth defects in the Saccharomyces cerevisiae model system. This illustrates an emerging strategy of exploring synergies between predictions and targeted experimental approaches in elucidating novel effector activities involved in infection.

microbiology↗

bioRxiv2023

Environmental life cycle assessment of recombinant growth factor production for cultivated meat applications

Growth factors are critical components of current serum-supplemented and serum-free media formulations for cultivated meat production. However, growth factors have been excluded, estimated using proxies, or modeled using proprietary data in existing environmental assessments of cultivated meat products. Cell culture media has been identified as a hotspot in such studies, therefore it is important to accurately quantify the environmental impacts of growth factor supplementation. To address this gap, this study applied life cycle assessment (LCA) methodology to comparatively assess the environmental impacts of recombinant growth factor production for cultivated meat applications. Life cycle inventories were developed for four recombinant growth factors (IGF-1, FGF, TGF-{beta}, and PDGF) produced using a novel bench- scale process. The functional unit of the product output was selected as 1 mg of produced growth factor. The results indicate that recombinant growth factors can have significant environmental impacts within cultivated meat systems, despite being used in very small quantities. For example, the global warming potential of production of 1 mg of IGF-1, FGF, TGF-{beta}, and PDGF was estimated to be 0.1, 0.04, 0.2 and 0.2 kg CO2 eq, respectively. Future research should explore the sustainability of producing these growth factors at scale to meet the needs of the expanding cultivated meat industry or identifying alternatives to these growth factors that have a lower impact on the environment. Nomenclature O_TBL View this table: org.highwire.dtl.DTLVardef@1f0c19org.highwire.dtl.DTLVardef@534179org.highwire.dtl.DTLVardef@1ef86b1org.highwire.dtl.DTLVardef@73fd9eorg.highwire.dtl.DTLVardef@10fb642_HPS_FORMAT_FIGEXP M_TBL C_TBL

ecology↗

bioRxiv2022

Recombinant production of growth factors for application in cell culture

Culturing eukaryotic cells has widespread applications in research and industry, including the emerging field of cell-cultured meat production colloquially referred to as "cellular agriculture". These applications are often restricted by the high cost of growth medium necessary for cell growth. Mitogenic protein growth factors (GFs) are essential components of growth medium and account for upwards of 90% of the total costs. Here, we present a set of expression constructs and a simplified protocol for recombinant production of functionally active GFs, including FGF-2, IGF-1, PDGF-BB and TGF-{beta}1 in Escherichia coli. Using this expression system, we produced soluble GFs from species including bovine, chicken, and fish. Bioactivity analysis revealed orthologs with improved performance compared to commercially available alternatives. We estimated that the production cost of GFs using our methodology will significantly reduce the cost of cell culture medium, facilitating low-cost protocols tailored for cultured meat production and tissue engineering.

cell biology↗

bioRxiv2020

Structural characterization of Nonstructural protein 1 from SARS-CoV-2

Severe acute respiratory syndrome (SARS) coronavirus-2 (SARS-CoV-2) is a single-stranded, enveloped RNA virus and the etiological agent of the current COVID-19 pandemic. Efficient replication of the virus relies on the activity of nonstructural protein 1 (Nsp1), a major virulence factor shown to facilitate suppression of host gene expression through promotion of host mRNA degradation and interaction with the 40S ribosomal subunit. Here, we report the crystal structure of the globular domain of SARS-CoV-2 Nsp1, encompassing residues 13 to 127, at a resolution of 1.65 [A]. Our structure features a six-stranded, capped {beta}-barrel motif similar to Nsp1from SARS-CoV and reveals how variations in amino acid sequence manifest as distinct structural features. Through comparative analysis of structural homologues, we identified a topological signature associated with this protein fold that facilitated modeling of Nsp1 from MERS-CoV. Combining our high-resolution crystal structure with existing data on the C-terminus of Nsp1 from SARS-CoV-2, we propose a model of the full-length protein. Our results provide unparalleled insight into the molecular structure of a major pathogenic determinant of SARS-CoV-2.

microbiology↗