Biology subjects

Holland, R.

Publications and source records attributed to Holland, R..

9 recordsLinked to original sources

bioRxiv2025

Evaluation of Aggregate Oral Fluid Sampling for Early Detection of African Swine Fever Virus Infection

African swine fever (ASF) is a highly infectious viral disease that poses significant threat to the United States and global pig industries. Given the lack of effective vaccines, control and prevention of the spread of African swine fever virus (ASFV) is dependent on enhanced surveillance and early disease detection. Commercial swine operations in the US are characterized by comparatively large number of pigs, and sampling individual pigs, which represents the main strategy for current ASF surveillance, is both costly and labor intensive. The major objective of this study was to estimate the diagnostic sensitivity of pen-based aggregate oral fluid testing for ASFV in infected pigs in a pen of 30 animals and evaluate its utility as a tool to support surveillance of ASF in the United States. The study was performed in three phases: (i) Virus (Ghana ASFV24) amplification in a target host species to generate the challenge inoculum, (ii) Titration of the inoculum (10% spleen homogenate) in target host species to determine the minimum dose inducing acute ASF in pigs with survival up to 5 - 6 days post-inoculation (dpi), and (iii) The main study involving 186 pigs consisting of 6 replicates of 30 pigs per pen and one seeder pig inoculated with the Ghana ASFV24 per pen. Daily sampling of aggregate oral fluids, uncoagulated blood, oropharyngeal swabs, fecal and water nipple swabs, and recording of rectal temperatures and clinical observations, was carried out. The seeder pigs were each inoculated intramuscularly with 0.5 ml of the 10% spleen homogenate which induced the desired clinical course of ASF in the pigs with survival of up to 6 dpi. ASFV DNA could be detected in the seeder pigs as early as 1 dpi and 2 dpi in the blood and oropharyngeal swabs, respectively. Transmission of ASFV from the seeder pigs to the contact pig population was detected via positive amplification of ASFV DNA in aggregate oral fluid samples at 3 days post-contact (dpc) in 4 out of 6 pens, and in all 6 pens at 4 dpc. Testing of oropharyngeal swabs and blood samples from individual pigs revealed variable number of ASFV positive pigs between 3 and 5 dpc, with detection of 100% positivity between 6 and 18 dpc, the study endpoint. These findings demonstrate the potential utility of aggregate oral fluid sampling for sensitive and early detection of ASFV incursion into naive swine herds. It also demonstrates that testing of environmental samples from the premises could further enhance overall ASF early detection and surveillance strategy. Author summaryEarly detection of ASFV in swine farms requires robust passive surveillance using sample types and sampling methods that allow sensitive and timely detection. Commercial swine operations in the US or North America are characterized by comparatively large number of pigs, and sampling individual pigs, which represents the current strategy for ASF surveillance, is both costly and labor-intensive. Oral fluid has been shown to be an acceptable sample type for detection of ASFV in individual infected pigs. For the first time on such a scale, we conducted a study enrolling 186 pigs, with daily sampling, in six experimental replicates at 3.2% pen prevalence using a highly virulent ASFV (Ghana ASFV24) to evaluate the utility of aggregate oral fluids for early detection of ASFV. Whole genome sequencing and characterization confirmed grouping of the virus with those in the p72 genotype II cluster. We demonstrate that intramuscular inoculation of the seeder pigs induces acute ASF and transmission to the contact pigs which is detectable in aggregate oral fluids as early as 3 - 4 dpc. We have shown that ASFV DNA detections in aggregate oral fluids correlate with the oropharyngeal swabs of individual pigs. In comparison, ASFV DNA in individual blood samples is detected 1-3 days later. The study demonstrates the potential utility of aggregate oral fluid sampling for enhanced surveillance of ASFV in large commercial swine operations.

microbiology↗

bioRxiv2024

Curative levels of endogenous gene replacement achieved in non-human primate liver using programmable genomic integration

The ability to efficiently place a large piece of DNA in a specific genomic location has been a goal for the gene therapy field since its inception; however, despite significant advances in gene editing technology, this had yet to be achieved. Here we describe two methods of programmable genomic integration (PGI) that overcome some of the limitations of current approaches. Using a combination of clinically validated delivery technologies (LNP, AAV), we demonstrate the ability to specifically integrate large (>2 kb) DNA sequences into endogenous introns in the liver of non-human primates (NHP). PGI was effective across multiple genomic locations and transgenes, and insertion led to expression from the endogenous promoter. PGI was highly efficient, achieving expression in >50% of liver cells after a single course of treatment, which would be curative for most monogenic recessive liver diseases. This is the first report of clinically curative level of gene insertion at endogenous loci in NHP.

bioengineering↗

bioRxiv2022

Medullary kappa-opioid receptor neurons inhibit pain and itch through a descending circuit

In perilous and stressful situations, the ability to suppress pain can be critical for survival. The rostral ventromedial medulla (RVM) contains neurons that robustly inhibit nociception at the level of the spinal cord through a top-down modulatory pathway. Although much is known about the role of the RVM in the inhibition of pain, the precise ability to directly manipulate pain-inhibitory neurons in the RVM has never been achieved. We now expose a cellular circuit that inhibits nociception and itch in mice. Through a combination of molecular, tracing, and behavioral approaches, we found that RVM neurons containing the kappa-opioid receptor (KOR) inhibit itch and nociception. With chemogenetic inhibition, we uncovered that these neurons are required for stress-induced analgesia. Using intersectional chemogenetic and pharmacological approaches, we determined that RVMKOR neurons inhibit nociception and itch through a descending circuit. Lastly, we identified a dynorphinergic pathway arising from the periaqueductal gray (PAG) that modulates nociception within the RVM. These discoveries highlight a distinct population of RVM neurons capable of broadly and robustly inhibiting itch and nociception.

neuroscience↗

bioRxiv2021

Cued Naming and the left inferior frontal cortex

Clinical studies have shown that naming can be behaviorally facilitated by priming, e.g., phonemic cues reduce anomia. Rehabilitation of language is argued to rely upon the same processes of priming in healthy speakers. Here we show, in healthy older adults, the immediate facilitatory behavioral and neural priming elicited by phonemic cues presented during an fMRI experiment of overt naming; thus, bridging the gap between lesion and neuroimaging studies. Four types of auditory cues were presented concurrently with an object picture (e.g., cat): (i) word (i.e., the target name (/kat/), (ii) initial phoneme segment (e.g., /ka/), (iii) final phoneme segment (/at/), or (iv) acoustic (noise) control cue. Naming was significantly faster with word, initial and final phonemic cues compared to noise; and word and initial cues compared to final cues, with no difference between word and initial cues. A neural priming effect - a significant decrease in neural activity - was observed in the left inferior frontal cortex (LIFC, pars triangularis, BA45) and the anterior insula bilaterally consistent with theories of primed articulatory encoding and post-lexical selection. The reverse contrast revealed increased activation in left posterior dorsal supramarginal gyrus for word cues that, we argue, may reflect integration of semantic and phonology processing during word rather than phonemic conditions. Taken together, these data from unimpaired speakers identified nodes within the naming network affected by phonemic cues. Activity within these regions may act as a possible biomarker to index anomic individuals responsiveness to phonemically cued anomia treatment.

neuroscience↗

bioRxiv2021

Lesion site and therapy time predict responses to a therapy for anomia after stroke: a prognostic model development study

BACKGROUNDStroke is a leading cause of disability, and language impairments (aphasia) after stroke are both common and particularly feared. Most stroke survivors with aphasia exhibit anomia (difficulties with naming common objects), but while many therapeutic interventions for anomia have been proposed, treatment effects are typically much larger in some patients than others. Here, we asked whether that variation might be more systematic, and even predictable, than previously thought. METHODS18 patients, each at least 6 months after left hemisphere stroke, engaged in a computerised treatment for their anomia over a 6 week period. Using only: (a) the patients initial accuracy when naming (to-be) trained items; (b) the hours of therapy that they devoted to the therapy; and (c) whole-brain lesion location data, derived from structural MRI; we developed Partial Least Squares regression models to predict the patients improvements on treated items, and tested them in cross-validation. RESULTSSomewhat surprisingly, the best model included only lesion location data and the hours of therapy undertaken. In cross-validation, this model significantly out-performed the null model, in which the prediction for each patient was simply the mean treatment effect of the group. This model also made promisingly accurate predictions in absolute terms: the correlation between empirical and predicted treatment response was 0.62 (95%CI: 0.27, 0.95). DISCUSSIONOur results indicate that individuals variation in response to anomia treatment are, at least somewhat, systematic and predictable, from the interaction between where and how much lesion damage they have suffered, and the time they devoted to the therapy.

neuroscience↗

bioRxiv2020

Life-long telomere attrition predicts health and lifespan in a large mammal

Telomere length measured in blood cells is predictive of subsequent adult health and survival across a range of vertebrate species. However, we currently do not know whether such associations result from among-individual differences in telomere length determined genetically or by environmental factors early in life, or from differences in the rate of telomere attrition over the course of life. Here, we measured relative leukocyte telomere length (RLTL) multiple times across the entire lifespan of dairy cattle in a research population that is closely monitored for health and milk production and where individuals are only culled in response to health issues and less due to poor milk production than on purely commercial farms. Our results clearly show that the average amount of telomere attrition over an individuals life, not their average or early life telomere length predicted when an individual was culled. Within-individual telomere length attrition could reflect environmental or physiological insults which may accumulate to predict individual health-span. We also show that animals with more telomere attrition in their first year of life were culled at a younger age, indicating that early life stressors may have a prolonged effect on adult life.

evolutionary biology↗

bioRxiv2020

Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Extraction

Convenient, repeatable, large-scale molecular testing for SARS-CoV-2 would be a key weapon to help control the COVID-19 pandemic. Unfortunately, standard SARS-CoV-2 testing protocols are invasive and rely on numerous items that can be subject to supply chain bottlenecks, and as such are not suitable for frequent repeat testing. Specifically, personal protective equipment (PPE), nasopharyngeal (NP) swabs, the associated viral transport media (VTM), and kits for RNA isolation and purification have all been in short supply at various times during the COVID-19 pandemic. Moreover, SARS-CoV-2 is spread through droplets and aerosols transmitted through person-to-person contact, and thus saliva may be a relevant medium for diagnosing SARS-CoV-2 infection status. Here we describe a saliva-based testing method that bypasses the need for RNA isolation/purification. In experiments with inactivated SARS-CoV-2 virus spiked into saliva, this method has a limit of detection of 500-1000 viral particles per mL, rivalling the standard NP swab method, and initial studies also show excellent performance with 100 clinical samples. This saliva-based process is operationally simple, utilizes readily available materials, and can be easily implemented by existing testing sites, thus allowing for high-throughput, rapid, and repeat testing of large populations. Graphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

microbiology↗

bioRxiv2019

Increased genetic marker density reveals high levels of admixture between red deer and introduced sika in Kintyre, Scotland

Hybridization is a natural process at species range boundaries, but increasing numbers of species are hybridizing due to direct or indirect human activities. In such cases of anthropogenic hybridization, subsequent introgression can threaten the survival of native species. To date many such systems have been studied with too few genetic markers to assess the level of threat resulting from advanced backcrossing. Here we use 44,999 single nucleotide polymorphisms and the ADMIXTURE program to study two areas of Scotland where a panel of 22 diagnostic microsatellites previously identified introgression between native red deer (Cervus elaphus) and introduced Japanese sika (Cervus nippon). In Kintyre we reclassify 26% of deer from the pure species categories to the hybrid category whereas in the NW Highlands we only reclassify 2%. As expected, the reclassified individuals are mostly advanced backcrosses. We also investigate the ability of marker panels selected on different posterior allele frequency criteria to find hybrids assigned by the full marker set, and show that in our data, ancestry informative markers (i.e. those that are highly differentiated between the species, but not fixed) are better than diagnostic markers (those markers that are fixed between the species) because they are more evenly distributed in the genome. Diagnostic loci are concentrated on the X chromosome to the detriment of autosomal coverage.

evolutionary biology↗

bioRxiv2019

Left anterior temporal lobe is necessary for efficient lateralised processing of spoken word identity

In the healthy human brain, the processing of spoken words is strongly left-lateralised, while the processing of complex non-linguistic sounds recruits brain regions bilaterally. Here we asked whether the left anterior temporal lobe, strongly implicated in semantic processing, is critical to this special treatment of linguistic stimuli. Nine patients with semantic dementia (SD) and fourteen age-matched controls underwent magnetoencephalography and structural MRI. Voxel based morphometry demonstrated the stereotypical pattern of SD: severe grey matter loss restricted to the left anterior temporal lobe. During magnetoencephalography, participants listened to word sets in which identity and meaning were ambiguous until utterance completion, for example played vs plate. Whereas left-hemispheric responses were similar across groups, patients demonstrated increased right hemisphere activity 174-294ms after stimulus disambiguation. Source reconstructions confirmed recruitment of right-sided analogues of language regions in SD: atrophy of left anterior temporal lobe was associated with increased activity in right temporal pole, middle temporal gyrus, inferior frontal gyrus and supramarginal gyrus. Moreover only healthy controls had differential responses to words versus non-words in right auditory cortex and planum temporale. Overall, the results indicate that anterior temporal lobe is necessary for normal and efficient processing of word identity in the rest of the language network.

neuroscience↗