Biology subjects

Richards, J.

Publications and source records attributed to Richards, J..

14 recordsLinked to original sources

bioRxiv2026

Genetic mapping of a spontaneous short-grain mutation reveals a novel loss-of-function allele of SRS3 in rice

Spontaneous mutations are a rare but important source of novel genetic variation, yet their detection and characterization within active breeding programs are seldom documented at gene-level resolution. Grain size and shape are key determinants of rice quality, yield, and market classification. Here, we report the discovery and genetic characterization of a spontaneous short-grain (SG) mutation arising in the long-grain wild-type (WT) advanced breeding line RU2002174 from the LSU AgCenter Rice Breeding Program. The SG phenotype was first observed in 2019 and segregated in subsequent generations as a single recessive gene across both indica and japonica genetic backgrounds. Genetic mapping localized the mutation to a 41.6 kb interval on chromosome 5. Whole-genome sequencing identified a single candidate causal variant: a G[->]T transversion in exon 4 of SRS3 (Os05g06280), introducing a premature stop codon and resulting in a truncated protein. This allele was absent from representative U.S. breeding germplasm and the IRRI 3K SNP database, demonstrating that it represents a novel spontaneous loss-of-function allele of a previously characterized grain-size gene. These findings document the real-time emergence of functional genetic variation in elite rice germplasm and highlight the importance of monitoring off-types during seed increase and purification in breeding programs. They also provide additional insight into the role of kinesin-mediated cell elongation in determining rice grain architecture.

genetics↗

bioRxiv2026

Museum specimens reveal evolutionary drivers and functions of oral microbiome in mammals

The microbiomes of wild animals, despite being integral to host survival, remain largely unexplored, particularly beyond the gut. Here, using > 450 museum-preserved dental calculus samples from 34 ecologically and phylogenetically diverse mammalian species, most of them previously unstudied, we determine the main drivers of oral microbiome evolution. We show that, similar to the gut, the oral microbiome is shaped by host ecology, particularly diet, and to a lesser extent host phylogenetic relationships. It may contribute to host adaptation, by synthesising essential micronutrients and degrading potentially harmful compounds. We also find that some oral microorganisms consistently associated with mammals throughout over evolutionary time scales and provide evidence for a likely oral origin of some rumen taxa. Together our findings demonstrate the importance of this mostly overlooked microbial community for mammalian biology.

evolutionary biology↗

bioRxiv2025

Examining the Macroecological Context of Life-History, Niche Regime, and Phylogeny in Serpentine Reptiles and Amphibians

Life history is key to understanding macroecological patterns. Measurable characteristics are particularly critical to the study of ecology. These quantifiable traits can be compared between numerous taxonomic clades to examine how evolutionary forces have shaped biological systems. Although numerous in-depth studies have focused on assessing the life histories of mammalian and avian taxa, few scientific endeavors have addressed the diversity of measurable reproductive characteristics in other vertebrate clades. Here we present the first work examine the macroecology of life history traits in serpentine reptiles and amphibians. Both chosen clades comprise taxa that are limbless, predatory, and primarily restricted to tropical and subtropical latitudes. To test the hypothesis that phylogeny limits the extent to which life-history may overlap, the body mass, lifespan, hatchling size, and clutch size of serpentine amphibians and reptiles will be compared using statistical inference methods (t-tests). The distributions of body mass, lifespan, hatchling size, and clutch size differ among serpentine reptiles and amphibians. Linear models suggest that how hatchling and clutch size vary with body mass also differ between the two. Only the linear model examining how lifespan varies with body mass indicates that broad similarities in life histories exist between serpentine amphibians and reptiles. Our results--that little overlap exists in life-history--suggest that the same macroevolutionary processes that allow serpentine amphibian and reptile ecological niche regimes to converge are not acting on their quantifiable life-history traits.

ecology↗

bioRxiv2025

Predator-prey scaling laws support a suspension-feeding lifestyle in Cambrian lobopodians

The early Paleozoic saw a dramatic diversification of shelly epibenthic metazoans adapted to suspension and filter-feeding, but the extent to which these radiations affected the evolution of non-biomineralized suspension-feeding taxa is uncertain because these organisms are not typically well represented in the fossil record. Luolishaniids are a highly derived and disparate clade of (typically) armoured lobopodians widely interpreted as having a suspension-feeding ecology based on the presence of five or six anterior pairs of setulose appendages. Luolishaniids are globally widespread and represent the only Cambrian non-biomineralized free living epibenthic bilaterians regarded as having a suspension feeding mode of life, but their proposed ecology only relies on a qualitative interpretation of their functional morphology. Here we test the hypothesis that the setulose appendages of luolishaniids were adapted for a suspension feeding function. Quantitative morphological comparisons reveal a positive and statistically significant relationship between body length and the mesh spacing of the setulose anterior limbs of luolishaniids. This pattern correlates with suspension-feeding scaling in extant aquatic organisms, and suggests that luolishaniids primarily fed on mesoplanktonic seston. We provide quantitative evidence for suspension-feeding in luolishaniids, which represents the first statistically supported example of modern-like predator-prey scaling patterns observed in Cambrian soft-bodied metazoans.

paleontology↗

bioRxiv2025

A Quantitative Review of Biodiversity Trends during the Great Ordovician Biodiversification Event

The Great Ordovician Biodiversification Event (GOBE) embodies the most dramatic increase of marine biodiversity and escalation of macroecological complexity during the early Phanerozoic. Despite its critical role, the precise timing and duration of the GOBE remain controversial. Numerous palaeobiological studies have attempted to quantify the GOBE based on estimates of species richness through time for various groups of marine organisms. However, these studies use fossil data restricted to specific geographic regions or employ disparate methodologies that preclude direct analytical comparisons. We present a meta-analysis of Ordovician biodiversity that integrates information from multiple temporal, geographic, and ecological scales. We collate 98 datasets from 54 publications to analyze temporally standardized rates of marine species biodiversity accumulation between the latest Cambrian and throughout the entire Ordovician using an effect-size approach. Our results indicate statistically significant high rates of sustained species accumulation that can be traced from the late Cambrian and until the Middle Ordovician, stabilization during the Late Ordovician and then a precipitous decline caused by the Late Ordovician Mass Extinction. Geographic scale (global vs regional) has no significant bearing on rates of biodiversification, with the only exception observed during the Dapingian-Darriwilian transition, supporting the hypothesis of mass dispersal of generalists during the Early Ordovician. Benthic and suspension-feeding organisms show high rates of biodiversity accumulation throughout most of the Ordovician (Tremadocian-Sandbian), whereas the diversification of nektonic, pelagic and predatory/scavenger organisms was mostly restricted to the Early Ordovician.

paleontology↗

bioRxiv2025

Host traits impact the outcome of metagenomic library preparation from dental calculus samples across diverse mammals

Dental calculus metagenomics has emerged as a valuable tool for studying the oral microbiomes of humans and a few select mammals. With increasing interest in wild animal microbiomes, it is important to understand how widely this material can be used across the mammalian tree of life, refine the related protocols and understand the expected outcomes and potential challenges of dental calculus sample processing. In this study we significantly expand the breadth of studied host species, analysing laboratory and bioinformatics metadata of dental calculus samples from 32 ecologically and phylogenetically diverse mammals. While we confirm the presence of an oral microbiome signature in the metagenomes of all studied mammals, the fraction recognised as oral varies between host species, possibly due to both biological differences and methodological biases. The overall success rate of dental calculus processing, from extractions to sequencing, was ~74%. Although input sample weight was positively associated with the number of produced library molecules, we identify a negative impact of enzymatic inhibition on the library preparation protocol. The inhibition was most prevalent in herbivores and frugivores and is likely diet-derived. In contrast, hosts with an animalivore diet posed fewer challenges during laboratory processing, and yielded more DNA relative to sample weight. Our results translate into recommendations for future studies of dental calculus metagenomics from a variety of host species, identifying required sample amounts, and emphasising the utility of dental calculus in exploring the oral microbiome in relation to broader ecological and evolutionary questions.

genomics↗

bioRxiv2024

Vaccination against helminth IL-33-modulators permits immune-mediated parasite ejection

The murine intestinal nematode Heligmosomoides polygyrus bakeri powerfully modulates the host immune response. This is achieved in part through the HpARI family (HpARI1/2/3), which act on IL-33, and the HpBARI family (HpBARI and HpBARI_Hom2), which act on ST2. Here, we find that this immunomodulation is evident only in the first week of infection, with abrogation of ST2 detection and systemic suppression of IL-33-dependent responses. Vaccination with individual HpARI or HpBARI family members raised antibody responses which could block these proteins immunomodulatory activities. During infection, vaccination could release the host from immunosuppression: HpARI2 vaccination resulted in much increased ILC2 and Th2 immunity, with heightened serum IL-4 and IL-5 responses, but did not abrogate ST2 suppression. In contrast, a HpBARI+HpBARI_Hom2 vaccination cocktail resulted in abrogation of ST2 suppression, and again increased Th2 immunity and serum cytokine responses. Either of the HpARI2 or the HpBARI cocktail vaccinations provided significant protection against subsequent H. polygyrus bakeri infection. We therefore show a proof of principle that vaccination with immunomodulatory proteins can protect the host against infection, and can be used as a tool for blocking the effects of specific parasite-derived proteins.

immunology↗

bioRxiv2021

Mutations in a barley cytochrome P450 gene enhances pathogen induced programmed cell death and cutin layer instability

Disease lesion mimic mutants (DLMMs) are characterized by spontaneous development of necrotic spots with various phenotypes designated as necrotic (nec) mutants in barley. The nec mutants were traditionally considered to have aberrant regulation of programmed cell death (PCD) pathways, which have roles in plant immunity and development. Most barley nec3 mutants express cream to orange necrotic lesions contrasting them from typical spontaneous DLMMs that develop dark pigmented lesions indicative of serotonin/phenolics deposition. Also, barley nec3 mutants grown under sterile conditions did not exhibit necrotic phenotypes until inoculated with adapted pathogens suggesting that they are not typical DLMMs. The F2 progeny of a cross between nec3-{gamma}1 and variety Quest segregated as a single recessive gene post inoculation with Bipolaris sorokiniana, the causal agent of the disease spot blotch. Nec3 was genetically delimited to 0.14 cM representing 16.5 megabases of physical sequence containing 149 annotated high confidence genes. RNAseq and comparative analysis of wild type and five independent nec3 mutants identified a single candidate cytochrome P450 gene (HORVU.MOREX.r2.6HG0460850) that was validated as nec3 by independent mutations that result in predicted nonfunctional proteins. Histology studies determined that nec3 mutants had an unstable cutin layer that disrupted normal Bipolaris sorokiniana germ tube development. AUTHOR SUMMARYAt the site of pathogen infection, plant defense mechanisms rely on controlled programmed cell death (PCD) to sequester biotrophic pathogens that require living cells to extract nutrient from the host. However, these defense mechanisms are hijacked by necrotrophic plant pathogens that purposefully induce PCD mechanism to feed from the dead cells facilitating further disease development. Thus, understanding PCD responses is important for resistance to both classes of pathogens. We characterized five independent disease lesion mimic mutants of barley designated necrotic 3 (nec3) that show aberrant regulation of PCD responses upon pathogen challenge. A cytochrome P450 gene was identified as Nec3 encoding a Tryptamine 5-Hydroxylase that functions as a terminal serotonin biosynthetic enzyme in the Tryptophan pathway of plants. The nec3 mutants have disrupted serotonin biosynthesis resulting in expansive PCD, necrotrophic pathogen susceptibility and cutin layer instability. The nec3 mutants lacking serotonin deposition in pathogen induced necrotic lesions show expansive PCD and disease susceptibility suggesting a role of serotonin to sequester PCD and suppress pathogen colonization. The identification of Nec3 will facilitate functional analysis to elucidate the role serotonin plays in the elicitation or suppression of PCD immunity responses to diverse pathogens and effects it has on cutin layer biosynthesis.

plant biology↗

bioRxiv2020

Genome-wide association studies reveal the complex genetic architecture of DMI fungicide resistance in Cercospora beticola

Cercospora leaf spot is the most important disease of sugar beet worldwide. The disease is caused by the fungus Cercospora beticola and is managed principally by timely application of fungicides including those of the sterol demethylation inhibitor (DMI) class. However, reliance on DMIs has caused an increase in resistance to this class of fungicides in multiple C. beticola populations. To better understand the genetic and evolutionary basis for resistance in C. beticola, a genome-wide association study (GWAS) and selective sweep analysis were conducted for the first time in this fungal plant pathogen. We performed whole genome resequencing of 190 C. beticola isolates predominantly from North Dakota and Minnesota that were phenotyped for sensitivity to tetraconazole, the most widely used DMI fungicide in this region. GWAS identified mutations in genes associated with DMI fungicide resistance including a Regulator of G-protein Signaling (RGS) protein, an ATP-binding cassette (ABC) pleiotropic drug resistance transporter, a dual-specificity tyrosine phosphorylation-regulated kinase (DYRK), and a gene annotated as a hypothetical protein. A SNP upstream of CbCYP51, the gene encoding the target of DMI fungicides, was also identified via GWAS. Haplotype analysis of CbCYP51 identified a synonymous mutation (E170) in high linkage disequilibrium with the upstream SNP, and multiple non-synonymous mutations (L144F, I387M and Y464S) associated with DMI resistance. Additionally, a putative codon bias effect for the L144F substitution was identified that generated different resistance potentials. We also identified a CbCYP51 paralog in C. beticola, CbCYP51-like, with high protein homology to CYP51C found uniquely in Fusarium species but CbCYP51-like does not appear to influence DMI sensitivity. Genome-wide scans of selection showed that several of the GWAS mutations for fungicide resistance resided in regions that have recently undergone a selective sweep. Using radial plate growth on selected media as a fitness proxy, we did not find a trade-off associated with DMI fungicide resistance suggesting that resistance mutations can persist in C. beticola populations. Taken together, we show that population genomic data from a crop pathogen can allow the identification of mutations conferring fungicide resistance and inform about their origins in the pathogen population.

evolutionary biology↗

bioRxiv2020

A truncated form of HpARI stabilises IL-33, amplifying responses to the cytokine.

1The murine intestinal nematode Heligmosomoides polygyrus releases the H. polygyrus Alarmin Release Inhibitor (HpARI) - a protein which binds to IL-33 and to DNA, effectively tethering the cytokine in the nucleus of necrotic cells. Previous work showed that a non-natural truncation consisting of the first 2 domains of HpARI (HpARI_CCP1/2) retains binding to both DNA and IL-33, and inhibited IL-33 release in vivo. Here, we show that the affinity of HpARI_CCP1/2 for IL-33 is significantly lower than that of the full-length protein, and that HpARI_CCP1/2 lacks the ability to prevent interaction of IL-33 with its receptor. When HpARI_CCP1/2 was applied in vivo it potently amplified IL-33-dependent immune responses to Alternaria alternata allergen, Nippostrongylus brasiliensis infection and recombinant IL-33 injection. Mechanistically, we found that HpARI_CCP1/2 is able to bind to and stabilise IL-33, preventing its degradation and maintaining the cytokine in its active form. This study highlights the importance of IL-33 inactivation, the potential for IL-33 stabilisation in vivo, and describes a new tool for IL-33 research.

immunology↗

bioRxiv2019

Local adaptation drives the diversification of effectors in the fungal wheat pathogen Parastagonospora nodorum in the United States

Filamentous fungi rapidly evolve in response to environmental selection pressures, exemplified by their genomic plasticity. Parastagonospora nodorum, a fungal pathogen of wheat and causal agent of septoria nodorum blotch, responds to selection pressure exerted by its host, influencing the gain, loss, or functional diversification of putative effector genes. Whole genome resequencing of 197 P. nodorum isolates collected from spring, durum, and winter wheat production regions of the United States enabled the examination of effector diversity and genomic regions under selection specific to geographically discrete populations. A total of 1,026,859 quality SNPs/InDels were identified within the natural population. Implementation of GWAS identified novel loci, as well as SnToxA and SnTox3 as major factors in disease. Genes displaying presence/absence variation and predicted effector genes, as well as genes localized on an accessory chromosome, had significantly higher pN/pS ratios, indicating a greater level of diversifying selection. Population structure analyses indicated two major P. nodorum populations corresponding to the Upper Midwest (Population 1) and Southern/Eastern United States (Population 2). Prevalence of SnToxA varied greatly between the two populations which correlated with presence of the host sensitivity gene Tsn1. Additionally, 12 and 5 candidate effector genes were observed to be diversifying among isolates from Population 1 and Population 2, respectively, but under purifying or neutral selection in the opposite population. Selective sweep analysis revealed 10 and 19 regions of positive selection from Population 1 and Population 2, respectively, with 92 genes underlying population-specific selective sweeps. Also, genes exhibiting presence/absence variation were significantly closer to transposable elements. Taken together, these results indicate that P. nodorum is rapidly adapting to distinct selection pressures unique to spring and winter wheat production regions by various routes of genomic diversification, potentially facilitated through transposable element activity.\n\nAuthor SummaryParastagonospora nodorum is an economically important pathogen of wheat, employing proteinaceous effector molecules to cause disease. Recognition of effectors by host susceptibility genes often leads to the elicitation of programmed cell death. However, little is known on the correlation between effector diversity and the spatial distribution of host resistance/susceptibility or the genomic mechanisms of diversification. This research presents the genome resequencing of 197 P. nodorum isolates collected from spring, winter, and durum wheat production regions of the United States, enabling the investigation of genome dynamics and evolution. Results illustrate local adaptation to host resistance or susceptibility, as evidenced by population-specific evolution of predicted effector genes and positively selected selective sweeps. Predicted effector genes, genes exhibiting presence/absence variation, and genes residing on an accessory chromosome, were found to be diversifying more rapidly. Additionally, transposable elements were predicted to play a role in the maintenance or elimination of genes. A GWAS approach identified the previously reported SnToxA and SnTox3 as well as novel virulence candidates, as major elicitors of disease on winter wheat. These results highlight the flexibility of the P. nodorum genome in response to population-specific selection pressures and illustrates the utility of whole genome resequencing for the identification of putative virulence mechanisms.

evolutionary biology↗

bioRxiv2019

In silico identification of novel peptides with antibacterial activity against multidrug resistant Staphylococcus aureus

Herein we report the identification and characterisation of two linear antimicrobial peptides (AMPs), HG2 and HG4, with activity against a wide range of multidrug resistant (MDR) bacteria, especially methicillin resistant Staphylococcus aureus (MRSA) strains, a highly problematic group of Gram-positive bacteria in the hospital and community environment. To identify the novel AMPs presented here, we employed the classifier model design, a feature extraction method using molecular descriptors for amino acids for the analysis, visualization, and interpretation of AMP activities from a rumen metagenomic dataset. This allowed for the in silico discrimination of active and inactive peptides in order to define a small number of promising novel lead AMP test candidates for chemical synthesis and experimental evaluation. In vitro data suggest that the chosen AMPs are fast acting, show strong biofilm inhibition and dispersal activity and are efficacious in an in vivo model of MRSA USA300 infection, whilst showing little toxicity to human erythrocytes and human primary cell lines ex vivo. Observations from biophysical AMP-lipid-interactions and electron microscopy suggest that the newly identified peptides interact with the cell membrane and may be involved in the inhibition of other cellular processes. Amphiphilic conformations associated with membrane disruption are also observed in 3D molecular modelling of the peptides. HG2 and HG4 both preferentially bind to MRSA total lipids rather than with human cell lipids indicating that HG4 may form superior templates for safer therapeutic candidates for MDR bacterial infections.\n\nAuthor SummaryWe are losing our ability to treat multidrug resistant (MDR) bacteria, otherwise known as superbugs. This poses a serious global threat to human health as bacteria are increasingly acquiring resistance to antibiotics. There is therefore urgent need to intensify our efforts to develop new safer alternative drug candidates. We emphasise the usefulness of complementing wet-lab and in silico techniques for the rapid identification of new drug candidates from environmental samples, especially antimicrobial peptides (AMPs). HG2 and HG4, the AMPs identified in our study show promise as effective therapies for the treatment of methicillin resistant Staphylococcus aureus infections both in vitro and in vivo whilst having little cytotoxicity against human primary cells, a step forward in the fight against MDR infections.

microbiology↗

bioRxiv2018

Genome wide association study of body weight, body mass index, adiposity, and fasting glucose in 3,173 outbred rats

Objective Obesity is influenced by genetic and environmental factors. Despite success of human genome wide association studies (GWAS), the specific genes that confer obesity remain largely unknown. The objective of this study was to use outbred rats to identify genetic loci underlying obesity and related morphometric and metabolic traits.Methods We measured obesity-relevant traits including body weight, body length, body mass index, fasting glucose, and retroperitoneal, epididymal, and parametrial fat pad weight in 3,173 male and female adult N/NIH heterogeneous stock (HS) rats across three institutions, providing data for the largest rat GWAS to date. Genetic loci were identified using a linear mixed model that accounted for the complex family relationships of the HS and covariate to account for differences among the three phenotyping centers.Results We identified 32 independent loci, several of which contained only a single gene (e.g. Epha5, Nrg1 and Klhl14) or obvious candidate genes (Adcy3, Prlhr). There were strong phenotypic and genetic correlations among obesity-related traits, and extensive pleiotropy at individual loci.Conclusions These studies demonstrate utility of HS rats for investigating the genetics of obesity related traits across institutions and identify several candidate genes for future functional testing.Competing Interest StatementThe authors have declared no competing interest.View Full Text

genetics↗

bioRxiv2017

The rumen microbiome: an underexplored resource for novel antimicrobial discovery

Antimicrobial peptides (AMPs) are promising drug candidates to target multi-drug resistant bacteria. The rumen microbiome presents an underexplored resource for the discovery of novel microbial enzymes and metabolites, including AMPs. Using functional screening and computational approaches, we identified 181 potentially novel AMPs from a rumen bacterial metagenome. Here, we show that three of the selected AMPs (Lynronne-1, 2 and 3) were effective against numerous bacterial pathogens, including methicillin resistant Staphylococcus aureus (MRSA). No decrease in MRSA susceptibility was observed after 25 days of sub-lethal exposure to these AMPs. The AMPs bound preferentially to bacterial membrane lipids and induced membrane permeability leading to cytoplasmic leakage. Topical administration of Lynronne-1 (10% w/v) to a mouse model of MRSA wound infection elicited a significant reduction in bacterial counts, which was comparable to treatment with 2% mupirocin ointment. Our findings indicate that the rumen microbiome may provide viable alternative antimicrobials for future therapeutic application.

microbiology↗