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Richards, K.

Publications and source records attributed to Richards, K..

13 recordsLinked to original sources

Gravitropism Shapes the Pareto Front of Root System Architecture

The root systems of wild tomatoes (S. Pimpinellifolium) can be understood as biological networks in which the lateral roots branch from a single main root and together balance two competing objectives: minimizing the material cost of building the network (wiring cost) and minimizing the transport time from the root tips to the shoot (conduction delay). Our prior work showed that S. Pimpinellifolium root architectures cluster near the Pareto-optimal front defined by these two objectives, with morphological diversity resolving into four qualitative topologies ((Chandrasekhar and Julkowska, 2022)). That framework assumed lateral roots grow as straight lines - ignoring gradual onset of lateral root gravitropism, the tendency of roots to curve toward the gravity vector. Because curved trajectories are longer than straight lines, gravitropism directly increases both wiring cost and conduction delay, constraining which architectures are physically realizable and thereby reshaping the Pareto front itself. Here we extend the model to explicitly incorporate lateral root gravitropism, producing predicted architectures that align much more closely with observed S. Pimpinellifolium root systems. We present a computational method to infer gravitropic sensitivity directly from anatomical tracing data - without reorientation assays - and apply it to 2423 arbors across different root topologies, growth conditions, and hormone treatments. Incorporating gravitropism reveals variation invisible to the straight-line model:notably, lateral roots show reduced gravitropic sensitivity under salt stress, mirroring a phenomenon previously described only for main roots and overlooked in lateral roots until now.

plant biology↗

Detection of Japanese Encephalitis (JE) Virus in Piggery effluent from an Australian Farm Prior to Outbreaks of JE

Japanese encephalitis virus (JEV), a mosquito-borne orthoflavivirus, raises concerns about its seasonal re-emergence. Pigs are a major amplifying host and JEV infection can manifest as significant reproductive disease and losses, necessitating robust surveillance. This study evaluated effluent surveillance for early JEV detection in piggery effluent from a Victorian farm between December 2024 and March 2025. Effluent samples were tested using JEV-specific real-time reverse transcription (RT)-PCR, with positive detections found on four separate sampling days, despite an absence of clinical signs in livestock through the testing period. Subsequent veterinary investigations for JEV in litters born on 17/05/2025 (suspect cases only) aligned with a positive effluent sample collected during the estimated JEV infection exposure periods of the sows. With the single clinically confirmed JEV case (which farrowed on 1/06/2025) collection of the same positive effluent sample fell just outside, but near, the estimated exposure period for the affected sow. These findings highlight ability of effluent monitoring to detect JEV infection 2 to 4 months before clinical manifestations present, offering potential for a non-invasive, herd-level early warning system. Intermittent detections may suggest limitations in grab sampling and low viral loads in effluent samples. Integrating effluent surveillance with veterinary clinical testing of litters suspected of being exposed to JEV or during high-risk periods could enhance JEV management in Australias enzootic regions, supporting One Health strategies.

molecular biology↗

Cell Type-Specific Changes in Dendritic Spines Across Adolescence Within Mouse Medial Prefrontal Cortex

Across species, cognitive capacities that rely on the frontal cortex do not fully mature until adulthood. Adolescent circuit refinement, including structural remodeling of dendritic spines, is believed to underlie this protracted maturation. Understanding cell type-dependent patterns of structural maturation would provide important insight into frontal cortex development. Here, we leveraged retrograde adeno-associated viruses to quantify dendritic spines on pyramidal tract (PT) vs. intratelencephalic (IT) neuronal populations in parallel within the mouse medial prefrontal cortex (mPFC) across adolescence. IT-type neurons showed opposing changes in mushroom and thin spines that were: 1) consistent with increasing synaptic maturity and 2) largely absent in PT-type neurons. We next probed the function of brain-resident immune cells, microglia, by transiently ablating them within the mPFC at mid-adolescence. This led to cell type-dependent changes in dendritic spines in late adolescence, with thin spine proportion increasing on both cell types but total spine density increasing on IT-type neurons only. Meanwhile, there was no effect on performance in an mPFC-dependent task of cognitive flexibility at either late adolescent or adult time points following microglia ablation. These findings provide evidence that mPFC IT-type neurons undergo greater spine remodeling during adolescence compared to PT-type neurons and implicate microglia as potential mediators.

neuroscience↗

Antimicrobial stewardship in animal health: experience-based co-design framework to capture progress and accelerate improvement

Antimicrobial stewardship (AMS) is essential for mitigating antimicrobial resistance (AMR) in animal health but implementing national initiatives is challenging due to diverse influencing factors and the need for context-specific approaches. An Animal AMS Practice Group, comprised of individuals with lived experience overseeing AMS in various animal health contexts was engaged, and through an experience-based co-design approach created a comprehensive AMS Framework that captures progress and supports tangible improvements in AMS practices in each context. The Framework supported a cross-sectoral pilot assessment that helped users identify progress, areas for improvement, and contextualise antimicrobial usage and AMR data, while also motivating further AMS efforts. Despite common barriers to sharing sensitive data, participants willingly shared AMS results for benchmarking and publication. The process demonstrated that co-design coupled with peer learning and expert support are essential to ensuring AMS tools are utilised in practice. Several participants incorporated the Framework into routine practice, with some using it to drive sector-level AMS action. The resulting Framework offers an adaptable, scalable entry point for AMS efforts and a platform for setting meaningful improvement goals. It supports broader opportunities for national-level AMS assessments and strategy development. Impact StatementThis research offers a practical, scalable approach to improving AMS in animal health. By embedding behaviour change into the project through an experience-based co-design process, rather than expecting it to occur afterward, veterinarians, animal managers, and other frontline professionals defined what good AMS looks like in their context and identified achievable actions to improve daily practices that aligned across diverse animal health settings. The resulting AMS Framework provides a clear, accessible starting point for those overseeing daily AMS activities to benchmark practices, set meaningful goals, and track progress, while also informing national-level prioritisation and decision-making. This user-led model demonstrates that when AMS tools are co-developed with those who will use them and users are empowered to shape the projects design and outputs, the resulting tools are more likely to be adopted, shared, and sustained.

microbiology↗

A modular, Galaxy-based immunopeptidogenomic (iPepGen) analysis pipeline for discovery, verification, and prioritization of candidate cancer neoantigen peptides

Characterizing tumor-specific neoantigen peptides, derived from genomic or transcriptomic aberrations and presented to the immune system, is critical for immuno-oncology studies. To this end, the modular iPepGen immunopeptidogenomics pipeline provides these functions: (1) Neoantigen prediction and protein database generation from genomic or transcriptomic sequencing data; (2) Peptide identification (3) Verification from immunopeptidomic mass spectral data; (4) Neoantigen classification and visualization; (5) Candidate prioritization for further study. Easy access via a publicly available, scalable cloud-based gateway coupled with online, interactive training materials streamlines the adoption by cancer researchers who require immunopeptidogenomic analysis tools but lack advanced computational expertise and resources.

bioinformatics↗

Surveillance of Japanese Encephalitis Virus in Piggery Effluent and Environmental Samples: A Complementary Tool for Outbreak Detection

Japanese encephalitis virus (JEV) is an emerging public health and biosecurity concern in Australia, with recent human cases and detections in mosquitoes and pigs across multiple states highlight the risk to susceptible human and animal populations. While traditional surveillance methods such as mosquito trapping, sentinel chicken programs and direct testing of pig specimens remain essential, monitoring effluent offers a valuable complementary approach for detecting infections within animal populations. This study presents the first evidence of JEV in Australian piggery effluents/environmental waters, demonstrating the feasibility of effluent and environmental water surveillance for JEV monitoring. Effluent/environmental samples from multiple piggery sites were analyzed using real-time reverse transcription polymerase chain reaction (RT-PCR), revealing the presence of JEV genetic fragments in solid and liquid fractions of effluents at three farms, with corresponding veterinary cases in some herds. Viral RNA was detected more frequently in solid fraction of effluent samples, aligning with previous findings on the partitioning behaviour of mosquito-borne viruses. The detection of JEV in the borrow pit (i.e., a man-made excavation that holds water) water sample highlights potential transmission pathways via mosquito vectors. These findings demonstrate the value of effluent monitoring as an additional tool for JEV surveillance in piggery settings, supporting potential early warning systems and mitigation strategies. Integrating effluent-based monitoring with traditional surveillance approaches could improve livestock industry related disease detection, risk assessments, and response efforts for human and animal health in endemic and emerging regions. Wastewater/effluent surveillance may have important applications for the management of a wide range of emerging animal diseases. IMPORTANCEThis study presents the first evidence of Japanese encephalitis virus (JEV) detection in Australian piggery effluents, establishing effluent surveillance as a valuable complementary tool for monitoring viral pathogens in animal populations. Our findings support the integration of effluent monitoring with traditional surveillance systems to improve early warning capabilities, enhance biosecurity, and mitigate risks to both animal and human health.

molecular biology↗

Emerging neurodevelopmental mechanisms in patient induced pluripotent stem cells-derived spheroids modelling SCN1A Dravet Syndrome

SCN1A encodes Na1.1, a voltage-gated sodium channel preferentially expressed in GABAergic interneurons, and it is the major cause of Dravet Syndrome (DS), a rare condition of developmental and epileptic encephalopathy (DEE). Among over 1000 DS mutations reported to date, almost all cause SCN1A loss-of function (LoF). A reduction in NaV1.1 function in inhibitory neurons would subsequently cause an over-excitation of glutamatergic neurons resulting in seizures, which are exacerbated by the use of sodium channel blocking common anti-seizure medications (ASM). In this study we generated and assessed 3D spheroids enriched with GABAergic neurons from SCN1A DS patient to establish a 3D human-derived DS model. To investigate developmental disruptions in DS pathophysiology we profiled the transcriptome of patient-derived spheroids and subsequently, tested the capability of this 3D in vitro model to reveal the cellular mechanisms of DS and predict drug response. In summary, our patient iPSC-derived neuronal model of SCN1A DS revealed a profound dysregulation of developmental processes which correlated with functional disruption in GABAergic neurons and predicted response to fenfluramine, an ASM increasingly used for the treatment of DS.

neuroscience↗

Mutational impact of APOBEC3B and APOBEC3A in a human cell line

A prominent source of mutation in cancer is single-stranded DNA cytosine deamination by cellular APOBEC3 enzymes, which results in signature C-to-T and C-to-G mutations in TCA and TCT motifs. Although multiple enzymes have been implicated, reports conflict and it is unclear which protein(s) are responsible. Here we report the development of a selectable system to quantify genome mutation and demonstrate its utility by comparing the mutagenic activities of three leading candidates - APOBEC3A, APOBEC3B, and APOBEC3H. The human cell line, HAP1, is engineered to express the thymidine kinase (TK) gene of HSV-1, which confers sensitivity to ganciclovir. Expression of APOBEC3A and APOBEC3B, but not catalytic mutant controls or APOBEC3H, triggers increased frequencies of TK mutation and nearly indistinguishable TC-biased cytosine mutation profiles in the selectable TK reporter gene. Whole genome sequences from TK mutant clones enabled an analysis of thousands of single base substitution mutations and extraction of local sequence preferences with APOBEC3A preferring YTCW motifs over 70% of the time and APOBEC3B just under 50% of the time (Y=C/T; W=A/T). Signature comparisons with breast tumor whole genome sequences indicate that most malignancies manifest intermediate percentages of APOBEC3 signature mutations in YTCW motifs, mostly between 50 and 70%, suggesting that both enzymes are contributing in a combinatorial manner to the overall mutation landscape. Although the vast majority of APOBEC3A- and APOBEC3B-induced single base substitution mutations occur outside of predicted chromosomal DNA hairpin structures, whole genome sequence analyses and supporting biochemical studies also indicate that both enzymes are capable of deaminating the single-stranded loop regions of DNA hairpins at elevated rates relative to control conditions. These studies combine to help resolve a long-standing etiologic debate on the source of APOBEC3 signature mutations in cancer and indicate that future diagnostic and therapeutic efforts should focus on both APOBEC3A and APOBEC3B.

cancer biology↗

Antisense oligonucleotide therapy for KCNT1 encephalopathy

Developmental and epileptic encephalopathies (DEE) are characterized by pharmacoresistant seizures with concomitant intellectual disability. Epilepsy of infancy with migrating focal seizures (EIMFS) is one of the most severe of these syndromes. De novo mutations in ion channels, including gain-of-function variants in KCNT1, have been found to play a major role in the etiology of EIMFS. Here, we test a potential precision therapeutic approach in KCNT1-associated DEE using a gene silencing antisense oligonucleotide (ASO) approach. The homozygous p.P924L (L/L) mouse model recapitulates the frequent, debilitating seizures and developmental compromise that are seen in patients. After a single intracerebroventricular bolus injection of a Kcnt1 gapmer ASO in symptomatic mice at postnatal day 40, seizure frequency was significantly reduced, behavioral abnormalities improved, and overall survival was extended compared to mice treated with a control ASO (non-hybridizing sequence). ASO administration at neonatal age was also well-tolerated and effective in controlling seizures and extending the lifespan of treated animals. The data presented here provides a proof of concept for ASO-based gene silencing as a promising therapeutic approach in KCNT1-associated epilepsies.

neuroscience↗

The effect of heat on SARS-CoV-2 viability and RNA integrity as determined by plaque assay, virus culture and real-time RT-PCR

The effect of heat on SARS-CoV-2/England/2/2020 viability was assessed by plaque assay and virus culture. Heating to 56{degrees}C and 60{degrees}C for 15, 30 and 60 minutes led to a reduction in titre of between 2.1 and 4.9 log10 pfu/ml but complete inactivation was not observed. At 80{degrees}C plaques were observed after 15 and 30 minutes of heating, however after 60 minutes viable virus was only detected following virus culture. Heating to 80{degrees}C for 90 minutes and 95{degrees}C for 1 and 5 minutes resulted in no viable virus being detected. At 56{degrees}C and 60{degrees}C significant variability between replicates was observed and the titre often increased with heat-treatment time. Nucleic acids were extracted and tested by RT-PCR. Sensitivity of the RT-PCR was not compromised by heating to 56{degrees}C and 60{degrees}C. Heating to 80{degrees}C for 30 minutes or more and 95{degrees}C for 1 or 5 minutes however, resulted in an increase of at least three Ct values. This increase remained constant when different dilutions of virus underwent heat treatment. This indicates that high temperature heat inactivation of clinical samples prior to nucleic acid extraction could significantly affect the ability to detect virus in clinical samples from patients with lower viral loads by RT-PCR.

microbiology↗

Antisense oligonucleotide therapy for SCN2A gain-of-function epilepsy

The clinical spectrum associated with SCN2A de novo mutations (DNMs) continues to expand and includes autism spectrum disorder with or without seizures, in addition to early and late seizure onset developmental and epileptic encephalopathies (DEEs). Recent biophysical studies on SCN2A variants suggest that the majority of early seizure onset DEE DNMs cause gain of function. Gain of function in SCN2A, the principal sodium channel of excitatory pyramidal neurons, would result in heightened neuronal activity and is likely to underlie the pathology seen in early seizure onset DEE patients. Supratherapeutic dosing of the non-selective sodium channel blocker phenytoin, is effective in controlling seizures in these patients but does not impact neurodevelopment, raising the idea that more profound and specific reduction in SCN2A function could significantly improve clinical outcome. To test the potential therapeutic benefit of reducing SCN2A in early seizure onset DEE we centrally administered an antisense oligonucleotide (ASO) targeting mouse Scn2a (Scn2a ASO) to a mouse model of human SCN2A early seizure onset DEE. Mice were genetically engineered to harbour the human equivalent SCN2A p.R1882Q mutation (Q/+), one of the most recurrent mutations in early seizure onset DEE. Q/+ mice presented with spontaneous seizures at postnatal day (P) 1 and did not survive beyond P30. Intracerebroventricular Scn2a ASO administration into Q/+ mice between P1-2 (that reduced Scn2a mRNA levels by 50%) significantly extended lifespan and markedly reduced spontaneous seizures occurrence. Across a range of cognitive and motor behavioural tests, Scn2a ASO treated Q/+ mice were largely indistinguishable from wildtype (+/+) mice. Further improvements in survival and behaviour were seen by adjustment of dosing regimens during development. Scn2a ASO efficacy was also evident at the cellular level. Whole cell patch clamp recording showed that Scn2a ASO administration reversed changes in neuronal excitability in layer 2/3 pyramidal neurons of Q/+ mice to levels seen in +/+ mice. Safety was assessed in +/+ mice and showed a developmental stage dependent tolerability and a favourable therapeutic index. This study suggests that a human SCN2A gapmer ASO could profoundly and safely impact early seizure onset DEE patients and heralds a new era of precision therapy in neurodevelopmental disorders.

neuroscience↗

Reptile-like physiology in Early Jurassic stem-mammals

There is uncertainty regarding the timing and fossil species in which mammalian endothermy arose, with few studies of stem-mammals on key aspects of endothermy such as basal or maximum metabolic rates, or placing them in the context of living vertebrate metabolic ranges. Synchrotron X-ray imaging of incremental tooth cementum shows two Early Jurassic stem-mammals, Morganucodon and Kuehneotherium, had lifespans (a basal metabolic rate proxy) considerably longer than comparably sized living mammals, but similar to reptiles, and that Morganucodon had femoral blood flow rates (a maximum metabolic rate proxy) intermediate between living mammals and reptiles. This shows maximum metabolic rates increased evolutionarily before basal rates, and that contrary to previous suggestions of a Triassic origin, Early Jurassic stem-mammals lacked the endothermic metabolism of living mammals.One Sentence Summary Surprisingly long lifespans and low femoral blood flow suggest reptile-like physiology in key Early Jurassic stem-mammals.View Full Text

paleontology↗

Abnormal cell sorting underlies the unique X-linked inheritance of PCDH19 Epilepsy

X-linked diseases typically exhibit more severe phenotypes in males than females. In contrast, Protocadherin 19 (PCDH19) mutations cause epilepsy in heterozygous females but spare hemizygous males. The cellular mechanism responsible for this unique pattern of X-linked inheritance is unknown. We show that PCDH19 contributes to highly specific combinatorial adhesion codes such that mosaic expression of Pcdh19 in heterozygous female mice leads to striking sorting between WT PCDH19- and null PCDH19-expressing cells in the developing cortex, correlating with altered network activity. Complete deletion of PCDH19 in heterozygous mice abolishes abnormal cell sorting and restores normal network activity. Furthermore, we identify variable cortical malformations in PCDH19 epilepsy patients. Our results highlight the role of PCDH19 in determining specific adhesion codes during cortical development and how disruption of these codes is associated with the unique X-linked inheritance of PCDH19 epilepsy.

developmental biology↗