Biology subjects

Anderson, R. R.

Publications and source records attributed to Anderson, R. R..

7 recordsLinked to original sources

bioRxiv2025

TICKHUNTER: A Targeted Hybridization-Capture Sequencing Approach for the Detection and Characterization of Tick-borne Pathogens and Blood Meals

As weather systems quickly change, vector communities and their pathogens evolve faster than assay panels can be redesigned. Additionally, PCRs narrow target range makes it structurally unable to catch divergent or reassorted agents. We developed a hybrid capture next-generation sequencing enrichment platform that provides comprehensive detection and characterization of tick-borne agents alongside ecological vertebrate host identification with low-pass sequencing. Analytical validation demonstrated performance comparable to qPCR with superior variant tolerance and multiplexing capacity. Field deployment in subtropical, metropolitan New York detected Anaplasma phagocytophilum strains (n=3) linked to human granulocytic anaplasmosis and a Babesia microti-like species in urban raccoon (Procyon lotor) populations. Tick vector screening revealed a putatively novel chimeric Flavi-like virus in invasive Haemaphysalis longicornis ticks combining segmented and unsegmented genomic features, with codon adaptation analysis indicating strong human compatibility. Serology revealed high Flavivirus seropositivity in NYC raccoons, suggesting an unrecognized urban reservoir role. Blood meal analysis simultaneously revealed complex ecological pathogen transmission networks spanning multiple vertebrate hosts. This integrated surveillance system enables comprehensive pathogen discovery, real-time evolutionary monitoring, and ecological risk assessment, transforming our capacity to detect emerging tick-borne threats in rapidly changing environments and prevent spillovers.

microbiology↗

bioRxiv2024

Interstitial infusion of purified collagenase Clostridium histolyticum in the cirrhotic liver causes rapid reduction in fibrosis with minimal liver toxicity

Crude mixtures of matrix-degrading enzymes called collagenase Clostridium histolyticum (CCH) have been used to efficiently breakdown tissue for many years. Recently, direct injection of purified CCH has been successfully developed as a treatment for Dupuytrens contracture (DC), a fibrotic disorder of the hand. Given similar histologic and mechanical features between the fibrous bands in DC and cirrhosis, a similar approach may be feasible for the treatment of cirrhosis. Crude and purified CCH were first compared through composition and substrate specificity. The biodistribution of a macromolecule delivered via interstitial infusion in the liver was mapped and quantified with a fluorescent dextran tracer to design a protocol for efficient delivery throughout the liver with minimal off-target exposure. Safety and efficacy of interstitial CCH infusion in the liver was investigated in cirrhotic mice using serum markers of injury and histological analysis of fibrosis. Purified CCH showed high purity and efficient degradation of type I collagen. Tracer experiments showed that interstitial infusion in one lobe of the liver will reach the entire organ in the mouse. A significant amount of the tracer was also found to enter the bloodstream where it is cleared by the kidneys, but was not found to significantly infiltrate other organs. Mild elevation in liver enzymes AST and ALT were observed 1d after infusion of purified CCH, but this was not significantly different than infusion with saline. No elevation in creatinine was observed. Cirrhotic mice infused with purified CCH showed 38% reduction in collagen proportionate area compared to mice infused with saline. These results show interstitial delivery of purified CCH in the cirrhotic liver rapidly decreases collagen content with minimal liver toxicity. This strategy merits further study as a potential treatment for cirrhosis.

bioengineering↗

bioRxiv2024

Antimicrobial blue light-bathing therapy for wound infection control

The prevalence of antibiotic resistance and tolerance in wound infection management poses a serious and growing health threat, necessitating the exploration of alternative approaches. Antimicrobial blue light therapy offers an appealing, non-pharmacological solution. However, its practical application has been hindered by the requirement for high irradiance levels, which particularly raises safety concerns. Here, we introduce a light-bathing strategy that employs prolonged, continuous exposure to blue light at an irradiance range lower by more than an order of magnitude (5 mW/cm2). This method consistently applies bacteriostatic pressure, keeping wound bioburden low, all while minimizing photothermal risks. Leveraging tailor-made, wearable light-emitting patches, we conducted preclinical trials on rat models of wound infection, demonstrating its safety and efficacy for suppressing infections induced by methicillin- resistant S. aureus and multidrug-resistant P. aeruginosa. Our results pave a new way for the application of blue light therapy in wound care.

bioengineering↗

bioRxiv2023

Increased susceptibility to ischemia causes exacerbated response to microinjuries in the cirrhotic liver

BackgroundFractional laser ablation is a technique developed in dermatology to induce remodeling of skin scars by creating a dense pattern of microinjuries. Despite remarkable clinical results, this technique has yet to be tested for scars in other tissues. As a first step towards determining the suitability of this technique, we aimed to (1) characterize the response to microinjuries in the healthy and cirrhotic liver, and (2) determine the underlying cause for any differences in response. MethodsHealthy and cirrhotic rats were treated with a fractional laser then euthanized from 0hr up to 14d after treatment. Differential expression was assessed using RNAseq with a difference-in-differences model. Spatial maps of tissue oxygenation were acquired with hyperspectral imaging and disruptions in blood supply were assessed with tomato lectin perfusion. ResultsHealthy rats showed little damage beyond the initial microinjury and healed completely by 7d without scarring. In cirrhotic rats, hepatocytes surrounding microinjury sites died 4-6hr after ablation, resulting in enlarged and heterogeneous zones of cell death. Hepatocytes near blood vessels were spared, particularly near the highly vascularized septa. Gene sets related to ischemia and angiogenesis were enriched at 4hr. Laser-treated regions had reduced oxygen saturation and broadly disrupted perfusion of nodule microvasculature, which matched the zones of cell death. ConclusionsThe cirrhotic liver has an exacerbated response to microinjuries and increased susceptibility to ischemia from microvascular damage, likely related to the vascular derangements that occur during cirrhosis development. Modifications to the fractional laser tool, such as using a femtosecond laser or reducing the spot size, may be able to prevent large disruptions of perfusion and enable further development of a laser-induced microinjury treatment for cirrhosis.

bioengineering↗

bioRxiv2023

Analysis of culture and RNA isolation methods for precision-cut liver slices from cirrhotic rats

Precision-cut liver slices (PCLS) are increasingly used as a model to investigate anti-fibrotic therapies. However, many studies use PCLS from healthy animals treated with pro-fibrotic stimuli in culture, which reflects only the early stages of fibrosis. The performance of PCLS from cirrhotic animals has not been well characterized and there is no consensus on optimal culture conditions. In this study, we report a method for the collection and culture of cirrhotic PCLS and compare the effect of common culture conditions on viability, function, and gene expression. Additionally, we compared three methods of RNA isolation and identified a protocol with high yield and purity. We observed significantly increased albumin production when cultured with insulin and dexamethasone, and when incubated on a rocking platform. Culturing with insulin and dexamethasone maintained gene expression closer to the levels in fresh slices. However, despite stable viability and function up to 4 days, we found significant changes in expression by day 2. Due to the influence of matrix stiffness on fibrosis and hepatocellular function, it is important to evaluate prospective anti-fibrotic therapies in a platform that preserves tissue biomechanics. PCLS from cirrhotic animals represent a promising tool for the development of treatments for chronic liver disease.

bioengineering↗

bioRxiv2023

Isolation of Actinomyces cricetomyis sp. nov from orocervicofacial abscesses of African giant pouched rats (Cricetomys ansorgei)

African giant pouched rats are of interest for their unique sense of smell and can be trained for a variety of applications including detection of explosives and infectious diseases. A colony housed at a university animal care facility developed abscesses associated with the jaw and eye in multiple animals. The predominant bacterial species in each case was a catalase-positive Actinomyces-like Gram-positive bacillus. The isolates from different sites and animals matched each other genetically but had sequences and biochemical profiles inconsistent with previously described species of this group. Based on whole genome sequence, biochemical characterization, and fatty acid profile, a novel species of the genus Actinomyces is proposed, namely Actinomyces cricetomyis (type strain 186855T). The type strain is deposited at ATCC (TSD-310) and BCCM/LMG (LMG 32803).

microbiology↗

bioRxiv2020

DNA extraction and host depletion methods significantly impact and potentially bias bacterial detection in a biological fluid

Untargeted sequencing of nucleic acids present in food can inform the detection of food safety and origin, as well as product tampering and mislabeling issues. The application of such technologies to food analysis could reveal valuable insights that are simply unobtainable by targeted testing, leading to the efforts of applying such technologies in the food industry. However, before these approaches can be applied, it is imperative to verify that the most appropriate methods are used at every step of the process: gathering primary material, laboratory methods, data analysis, and interpretation. The focus of this study is in gathering the primary material, in this case, DNA. We used bovine milk as a model to 1) evaluate commercially available kits for their ability to extract nucleic acids from inoculated bovine milk; 2) evaluate host DNA depletion methods for use with milk, and 3) develop and evaluate a selective lysis-PMA based protocol for host DNA depletion in milk. Our results suggest that magnetic-based nucleic acid extraction methods are best for nucleic acid isolation of bovine milk. Removal of host DNA remains a challenge for untargeted sequencing of milk, highlighting that the individual matrix characteristics should always be considered in food testing. Some reported methods introduce bias against specific types of microbes, which may be particularly problematic in food safety where the detection of Gram-negative pathogens and indicators is essential. Continuous efforts are needed to develop and validate new approaches for untargeted metagenomics in samples with large amounts of DNA from a single host. ImportanceTracking the bacterial communities present in our food has the potential to inform food safety and product origin. To do so, the entire genetic material present in a sample is extracted using chemical methods or commercially available kits and sequenced using next-generation platforms to provide a snapshot of what the relative composition looks like. Because the genetic material of higher organisms present in food (e.g., cow in milk or beef, wheat in flour) is around one thousand times larger than the bacterial content, challenges exist in gathering the information of interest. Additionally, specific bacterial characteristics can make them easier or harder to detect, adding another layer of complexity to this issue. In this study, we demonstrate the impact of using different methods in the ability of detecting specific bacteria and highlight the need to ensure that the most appropriate methods are being used for each particular sample.

molecular biology↗