Biology subjects

LaRock, C.

Publications and source records attributed to LaRock, C..

6 recordsLinked to original sources

bioRxiv2026

Impact of cathelicidin cleavage by SpeB on Streptococcus pyogenes CovRS signaling

Cathelicidins are a class of antimicrobial peptides (AMPs) that are part of the first line of defense of the innate immune system. While cathelicidin-derived peptides such as LL-37 can be directly bactericidal, Streptococcus pyogenes (Spy; Group A Streptococcus) is highly resistant to killing. Furthermore, Spy detects LL-37 through the CovRS two-component system to regulate its virulence factors. One effect of this signaling is the repression of expression of the bacterial protease SpeB. Prior work has also shown that SpeB, along with other bacterial proteases can cleave LL-37. However, it is unclear if SpeB cleavage of LL-37 impacts antimicrobial function and CovRS signaling activity. Using a genetic approach, we show that the presence SpeB did not significantly impact the killing of Spy by LL-37 relative to other known resistance factors. Furthermore, while SpeB cleaves LL-37, CovRS maintains sensitivity to LL-37 fragments. These results indicate that SpeB cleavage of LL-37 does not negatively impact virulence factor regulation in Spy.

microbiology↗

bioRxiv2026

A protease-sensing circuit links neutrophil inflammation to virulence regulation in Streptococcus pyogenes

Streptococcus pyogenes (Group A Streptococcus) causes infections with a disproportionately hyperinflammatory response from the host, such as scarlet fever, necrotizing fasciitis, and toxic shock syndrome. Inflammation is specifically driven by S. pyogenes virulence factors, including the protease SpeB, but how inflammation impacts SpeB expression in return during disease is unknown. In this study, we identify a novel interaction between NETosis, a form of inflammatory cell death for neutrophils, and the induction of speB. Specifically, while the cathelicidin peptide LL-37 can repress speB through the two-component regulatory system CovRS, neutrophil proteases released during NETosis relieve repression of speB by degrading another repressor of speB, the bacterial protein Vfr. Furthermore, at high cell densities, SpeB autoregulates its expression through similar degradation of Vfr. Abrogating the formation of NETs or depleting neutrophils resulted in speB repression in vivo, showing the mutual host and pathogen counterattacks collectively lead to the pathological exacerbations characteristic of disease.

microbiology↗

bioRxiv2025

Therapeutic Inhibition of Metalloproteases by Tetracyclines during Infection by Multi-Drug Resistant Pseudomonas

IntroductionBoth host and microbial proteases contribute to the destruction of tissue during Pseudomonas aeruginosa pulmonary infections. We previously reported that beneficial therapeutic effects of metalloprotease inhibitors in Pseudomonas aeruginosa pulmonary infections are not only from targeting the host matrix metalloproteases, the intended target, but also from cross-inhibition of the secreted bacterial metalloprotease LasB. MethodsWe used computation modeling and biochemical assays to investigate whether doxycycline and other structurally-related antibiotics of the tetracycline family inhibit the Pseudomonas protease, LasB. Modeling infection in vitro with human neutrophils and in vivo with a murine model of pulmonary infection, we investigate the effect of on tetracyclines inhibit LasB activity, bacterial survival, and inflammation. ResultsTetracycline, doxycycline, minocycline, and sanocycline all inhibit proteolysis by Pseudomonas LasB. At sub-antimicrobial concentrations, this sensitizes the bacterium killing by neutrophils. During pulmonary infection, tetracyclines significantly reduce pathological inflammation in the lung. ConclusionsOur study shows that tetracycline-family antibiotics, known inhibitors of mammalian matrix metalloproteinases, also inhibit LasB and have beneficial anti-inflammatory activity during infections by extensively drug-resistant P. aeruginosa. By controlling pathological host inflammation, inhibiting bacterial virulence factors, and directly killing bacteria, tetracyclines can have tripartite therapeutic benefits.

microbiology↗

bioRxiv2024

inSequio: A Programmable 3D CAD Application for Designing DNA Nanostructures

DNA nanotechnology is evolving rapidly, paralleling the historic trajectory of the 1970s electronics industry. However, current DNA nanostructure (DN) design software limits users to either manual design with minimal automation or a constrained range of automated designs. inS[e]quio Design Studio, developed by Parabon(R) NanoLabs, bridges this gap as a programmable 3D computer-aided design (CAD) application, integrating a domain-specific graphical editor with a Python API for versatile DN design. Developed in C++ for Windows(R) and Macintosh(R) systems, inS[e]quio features a user-friendly GUI with extensive CAD tools, capable of managing complex designs and offloading computational tasks to the cloud. It supports various DNA design formats, PDB molecule integration, residue modifications, and includes preloaded designs and thorough documentation. With its combination of features, inS[e]quio enables a code-centric design (CCD) approach, enhancing DN construction with improved precision, scalability, and efficiency. This approach is elucidated through a streptavidin barrel cage designed via Python notebook and a spheroid origami case study. Marking a significant advance in DN design automation, inS[e]quio, the first fully programmable 3D CAD tool for DN design, enables both manual and programmatic 3D editing. This fusion of features establishes inS[e]quio as a transformative tool, poised to significantly enhance designer productivity and expand the scope of possible designs. Extended AbstractAdvances in DNA nanotechnology have positioned the field at a juncture reminiscent of the pivotal growth phase of the electronics industry in the 1970s. The evolution of software for designing DNA nanostructures (DNs) is following a similar historical trajectory and dozens of software packages have been developed for creating them. Existing software options, however, require users to choose between manual design with minimal automation support or selecting from a limited set of designs, typically wireframe, that can be generated from a high-level structural description. Here, we introduce the inS[e]quio Design Studio, a programmable 3D computer-aided design (CAD) application that effectively bridges this gap. By integrating a domain-specific, freeform graphical editor with a Python application programming interface (API), inS[e]quio provides a comprehensive and extensible platform for designing complex nucleic acid (NA) nanostructures. The inS[e]quio desktop application, developed in C++, runs on Windows(R) and Macintosh(R) operating systems. Its graphical user interface (GUI) features multiple synchronized view panels and a diverse set of CAD and NA-specific editing tools. Its optimized graphics pipeline enables editing of designs with >2M nucleotides, and it includes an integrated service infrastructure for offloading heavy computations to cloud servers. The software also supports import and export of various DNA design file formats, integration of arbitrary PDB molecules, and specification of residue modifications. Additionally, it includes preloaded sample designs, scripts, and comprehensive documentation. Parabon has used evolving versions of inS[e]quio for over a decade to design a variety of proprietary DNs and have now transitioned it into a commercially available product. This paper summarizes inS[e]quios features, discusses its strengths and limitations, and outlines planned enhancements. Although freeform 3D design is well supported in inS[e]quio, the integration of its CAD environment with its API facilitates a code-centric design (CCD) approach for DN construction that offers notable productivity advantages over traditional methods, including enhanced precision, scalability, and efficiency. Here we describe CCD, outline its benefits and demonstrate its use through a well-documented Python notebook, included with the product, which generates a sample design within the inS[e]quio application. A spheroid origami created using CCD is also presented. As the first commercial fully programmable 3D CAD application specifically created for DN design, the release of inS[e]quio represents a milestone in the field of DN design automation. It introduces a new dimension to the discipline by enabling both manual and programmatic 3D editing, thereby facilitating an innovative CCD approach. The availability of extensive documentation and technical support enables designers to efficiently adopt and utilize these capabilities. This combination of features establishes inS[e]quio as a noteworthy addition to the tools available for DN design, with the potential to significantly increase designer productivity and broaden the scope of designs that can be developed by practitioners of all skill levels. Windows and Mac versions of the inS[e]quio desktop application are available for download at https://parabon.com/insequio. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC="FIGDIR/small/586810v1_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@16a2714org.highwire.dtl.DTLVardef@2bc610org.highwire.dtl.DTLVardef@1d852e2org.highwire.dtl.DTLVardef@129b3fa_HPS_FORMAT_FIGEXP M_FIG C_FIG An illustration of the inS[e]quio Design Studio desktop application interoperating with a Python Jupyter notebook and molecular dynamics (MD) simulation tools to support an iterative code-centric design (CCD) process. The design cycle includes (a) programmatic and/or manual creation of objects in the inS[e]quio editors; (b) visual inspection and manipulation of objects via user interface; (c) in silico evaluation of designs via MD simulation using native or external tools; repeating a-c as necessary; and (d) procurement of strands and synthesis of DNA nanostructures (DNs).

bioengineering↗

bioRxiv2020

Role of Inflammasome-independent Activation of IL-1β by the Pseudomonas aeruginosa Protease LasB

Pulmonary damage by Pseudomonas aeruginosa during cystic fibrosis lung infection and ventilator-associated pneumonia is mediated both by pathogen virulence factors and host inflammation. Impaired immune function due to tissue damage and inflammation, coupled with pathogen multidrug resistance, complicates management of these deep-seated infections. Therefore, preservation of lung function and effective immune clearance may be enhanced by selectively controlling inflammation. Pathological inflammation during P. aeruginosa pneumonia is driven by interleukin-1{beta} (IL-1{beta}). This proinflammatory cytokine is canonically regulated by caspase-family inflammasome proteases, but we report that plasticity in IL-1{beta} proteolytic activation allows for its direct maturation by the pseudomonal protease LasB. LasB promotes IL-1{beta} activation, neutrophilic inflammation, and destruction of lung architecture characteristic of severe P. aeruginosa pulmonary infection. Discovery of this IL-1{beta} regulatory mechanism provides a distinct target for anti-inflammatory therapeutics, such that matrix metalloprotease inhibitors blocking LasB limit inflammation and pathology during P. aeruginosa pulmonary infections. HighlightsO_LIIL-1{beta} drives pathology during pulmonary infection by Pseudomonas aeruginosa. C_LIO_LIThe Pseudomonas protease LasB cleaves and activates IL-1{beta} independent of canonical and noncanonical inflammasomes C_LIO_LIMetalloprotease inhibitors active against LasB limit inflammation and bacterial growth C_LI Research in ContextInflammation is highly damaging during lung infections by the opportunistic pathogen Pseudomonas aeruginosa. Sun et al. demonstrate that the Pseudomonas LasB protease directly activates IL-1{beta} in an inflammasome-independent manner. Inhibition of IL-1{beta} conversion by LasB protects against neutrophilic inflammation and destruction of the lung. Adjunctive therapeutics that limit pathological inflammation induced by infection would be beneficial for the treatment of pulmonary infections when used with conventional antibiotics.

microbiology↗

bioRxiv2018

Evidence that recurrent Group A streptococcus tonsillitis is animmunosusceptibility disease involving antibody deficiency and aberrant Tfh cells

One Sentence SummaryRecurrent tonsillitis is a multifactorial disease associated with an aberrant tonsillar germinal center response to Group A Streptococcus.\n\nABSTRACTRecurrent Group A Streptococcus (GAS) tonsillitis (RT) is a common indication for pediatric tonsillectomy. Strep throat is highly prevalent among children; yet, it is unknown why some children develop RT. To gain insights into this classic childhood disease, we performed phenotypic, genotypic, and functional studies on pediatric GAS RT and non-RT tonsils. We observed significantly smaller germinal centers in GAS RT tonsils, and underrepresentation of GAS-specific germinal center follicular helper (GC Tfh) CD4+ T cells. RT children exhibited reduced antibody responses to GAS virulence factor SpeA. Risk and protective HLA Class II alleles for RT were identified. Finally, SpeA induced granzyme B+ GC Tfh cells in RT tonsils that had capacity to kill B cells. Together, these observations suggest that RT susceptibility can occur due to genetic differences that can result in aberrant GC Tfh cells and poor antibody responses to GAS SpeA.

immunology↗