Biology subjects

Sil, A.

Publications and source records attributed to Sil, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Temperature-driven isoform switching reprograms developmental gene expression in a human fungal pathogen

Post-transcriptional regulation is key to development, and yet little is known about how RNA isoform choice contributes to developmental choices in fungi. Here we assemble the first isoform-level transcriptome of Histoplasma, a ubiquitous human fungal pathogen that grows as an infectious environmental form (hyphae) or a pathogenic host form (yeast) in response to temperature. We find extensive morphology-associated longer leader and trailer isoforms, rapid temperature-driven transcription start site remodeling, and inclusion of regulatory elements in longer leaders. We observe isoform-specific patterns of ribosome and polysome association, indicating that isoform switching regulates the proteome. Our results suggest a model in which isoform diversity and rapid isoform switching are central to post-transcriptional regulation during thermal dimorphism, enabling precise and timely translation of factors needed to establish and maintain hyphal and yeast forms. These studies illuminate how eukaryotic systems utilize post- transcriptional regulation to determine developmental states in response to external stimuli.

microbiology↗

bioRxiv2026

Optimization of conidial production in the thermally dimorphic fungal pathogen Histoplasma

Sporulation is an integral process in the lifecycle of many fungal pathogens, including Histoplasma, a primary human pathogen that causes respiratory infections. Histoplasma conidia, or asexual spores, are the primary infectious particle but very little is known about them, in part due to the need for Biosafety Level 3 containment and inconsistency in generating viable conidia under laboratory conditions. Here, we identify media that consistently promote Histoplasma conidiation, yielding both micro- and macroconidia, and conditions that promote high levels of germination. We show that conidiation media and duration affect the proportion of macroconidia produced, and we demonstrate that Histoplasma strains vary in their response to these conidiation parameters. Finally, imaging studies of chitin, exposed chitin, and cell wall mannoproteins show that while micro- and macroconidia have similar cell wall compositions, strain type and conidiation media variation result in qualitative differences in staining. These optimized methods for Histoplasma conidial preparations will enable more detailed investigations into this understudied aspect of the biology of an important human fungal pathogen.

microbiology↗

bioRxiv2025

Macrophage phagocytosis of Coccidioides promotes its differentiation into the parasitic form

Coccidioides is an endemic fungus that is increasing in prevalence and can cause life threatening disease in otherwise immunocompetent people. In the environment the spores (arthroconidia) develop into hyphae, yet when they are inhaled by a mammalian host, they develop into a unique form called the spherule. The transition to spherule can be triggered in vitro with elevated temperatures and high CO2 levels, but the signals and host cells that might trigger Coccidioides spherulation in vivo are not known. We used live imaging to investigate how macrophages affect the fate of Coccidioides arthroconidia. Under tissue culture conditions, arthroconidia quickly developed into hyphae. The addition of macrophages promoted spherule development and delayed hyphal formation, indicating that innate immune cells can influence Coccidioides development into the pathogenic form. Exposure of arthroconidia to macrophage supernatants was not sufficient to stimulate spherulation, which was dependent on phagocytosis of arthroconidia by macrophages. Transcriptomics analysis of Coccidioides co-cultured with macrophages revealed a signature concordant with spherules grown in vitro and allowed the identification of a core set of spherule-specific transcripts. In addition, we identified Coccidioides transcripts with significantly higher abundance in the presence of macrophages compared to in vitro spherules, suggesting these factors may be needed to survive and thrive in the presence of innate immune cells. This work lays a foundation for uncovering host-pathogen signaling as well as Coccidioides factors that are critical for pathogenesis.

microbiology↗

bioRxiv2025

The Rpd3 histone deacetylase is critical for temperature-mediated morphogenesis and virulence in the human fungal pathogen Histoplasma

Adaptive responses to environmental stimuli are integral to the survival and virulence of microbial pathogens. The thermally dimorphic human fungal pathogen Histoplasma senses temperature to transition between a mold form in soil and a pathogenic yeast in mammalian hosts. The contributions of chromatin-modifying enzymes to the ability of Histoplasma to appropriately respond to temperature have never been explored. Through chemical inhibition and genetics, we determined that the class I histone deacetylase (HDAC) RPD3 is required for normal Histoplasma yeast morphology at 37 {degrees}C. Rpd3 regulated the expression of key morphology-specific genes, including critical virulence factors and transcription factors (TFs), was required for normal DNA-binding activity of yeast-promoting TFs, and influenced histone acetylation levels at the loci of putative pro-filamentation TFs. Furthermore, Rpd3 was required for virulence in a macrophage model of infection. Taken together, Rpd3 is a critical regulatory component that both activates the pathogenesis program and represses the filamentation program to enable thermal dimorphism in Histoplasma. This work uncovers the crucial role that chromatin regulation plays in temperature response of this ubiquitous pathogen.

microbiology↗

bioRxiv2025

An unusual genetic switch controls Mycobacterium avium pathogenesis, antibiotic resistance and colony morphology

Mycobacterium avium subspecies hominissuis (Mah) is an emerging environmental pathogen highly adapted to a wide range of niches, from treated water systems to mammalian tissues. On solid media, Mah forms two distinct colony morphologies, smooth transparent (SmT) and smooth opaque (SmO). These colony morphologies are representative of broader differential phenotypic states in which SmT cells are virulent and have high resistance to antibiotics while SmO cells are avirulent, antibiotic-sensitive and grow faster than SmT cells in culture. Importantly, Mah interconverts between these two morphotypes but the mechanism of SmT-SmO switching is unknown. Here we show that SmT-SmO switching is governed by a reversible transposition event that regulates expression of a periplasmic lipoprotein, Erp (extracellular repetitive protein). We found that transposition of IS1245, an endogenous insertion sequence, into the erp gene correlated with the SmT-SmO transition, and its precise removal coincided with the switch back to SmT. Genetic analyses showed that erp is required for maintenance of the SmT state and sufficient to drive the switch from SmO to SmT. We also identified a mutation in a periplasmic protease, MarP, that locks Mah in the SmO state and blocks erp-mediated switching to SmT. Our results indicate that Erp and MarP function in a signal transduction pathway that regulates a broad transcriptional response to periplasmic stress. Moreover, identification of components that control Mah colony morphology switching has revealed a potential new strategy for combating the inherent antibiotic resistance of Mycobacterium avium infections.

microbiology↗

bioRxiv2025

Rapid gain and loss of a chromosome drives key morphology and virulence phenotypes in Histoplasma, a fungal pathogen of humans

Heritable phenotypic switches are fundamental to the ability of cells to respond to specific conditions. Such switches are key to the success of environmental pathogens, which encounter disparate conditions as they transition between the environment and host. We determine that the copy number of chromosome seven in the thermally dimorphic fungus Histoplasma dramatically affects the rate of transition. Though Histoplasma is haploid, a second copy of this chromosome is present in natural isolates of multiple Histoplasma species and is gained and lost at a high rate. Cells carrying two copies of this chromosome exhibit aspects of the environmental transcriptome even under host-like conditions and have a competitive advantage in the transition to the environmental form. Conversely, these cells are considerably less virulent than euploid cells and have a competitive disadvantage in the mouse model of infection. Chromosome seven contains a previously unstudied transcription factor that, when overexpressed in euploid Histoplasma, is sufficient to promote some of the key phenotypes of aneuploidy. We hypothesize that rapid gain and loss of this chromosome benefits Histoplasma by increasing phenotypic variation, thus helping populations of cells survive abrupt transitions between environment and host.

genetics↗

bioRxiv2025

A remarkable expansion of secreted cysteine knot proteins reveals novel virulence factors in the human fungal pathogen Histoplasma

Identifying fungal secreted factors that influence host infection remains a key challenge in microbial pathogenesis. While secreted effectors, particularly small cysteine-rich proteins, are well characterized in plant fungal pathogens, their counterparts in mammalian pathogens remain elusive. We applied criteria from plant fungal effectors to the mammalian fungal pathogen Histoplasma, yielding a set of putative effectors highly enriched for knottins, proteins that adopt a distinctive cysteine knot fold. Using a novel algorithm, we further identified 25 putative knottins in the Histoplasma genome, revealing a significant expansion of knottin genes. Knottin domains are found in diverse molecules but play an unknown role in virulence. Functional studies of individual Histoplasma knottins demonstrated their critical roles in intracellular survival and host cell lysis during macrophage infection as well as virulence in vivo. These findings highlight the importance of knottins in fungal pathogenesis and suggest their broader relevance for discovering conserved mechanisms of host manipulation.

microbiology↗

bioRxiv2025

Genome Dynamics and Chromosome Structural Variations in Histoplasma ohiense, a fungal pathogen of humans

Histoplasma is a clinically important but understudied genus of thermally dimorphic human fungal pathogens. Histoplasma species normally transition between a multicellular sporulating hyphal form in the soil and a unicellular pathogenic yeast form in a mammalian host. Little is known about genome plasticity of Histoplasma, which we address in this study with the ultimate goal of increasing our understanding of its pathogenicity. This study addresses the Histoplasma genome and its plasticity to further our understanding Histoplasmas ability to cause severe disease. Here we present the first telomere-to-telomere genome assemblies for Histoplasma ohiense. To analyze genome alterations between isolates, we develop an analysis tool to identify genome discontinuities relative to a reference genome. We utilize this analysis to interrogate the genome of laboratory strains and natural Histoplasma isolates and discover that the previously published reference genome does not completely match the chromosome structure of the majority of isolates, instead harboring reciprocal chromosome translocations. We identify the telomere-to-telomere Histoplasma ohiense reference genome that is most representative of clinical isolates. Additionally, to determine the rate of Histoplasma genomic changes, we sequence 46 passaged isolates and calculate the mutation rate to be 2.6 x10-10 SNP/base/doubling--the first such measurement to our knowledge within the order Onygenales, which encompasses several critical fungal pathogens. Finally, we sequence populations of cells to assess genome stability over the course of a month under both yeast and hyphal growth conditions. Interestingly, we observe that transposon signal is not static over time and instead increases during growth in both the yeast and hyphal forms as well as through morphologic transitions, suggesting an increase in transposon copy number. Taken together, this work highlights the plasticity of the Histoplasma genome and presents a comprehensive genome assembly that is representative of Histoplasma ohiense natural isolates.

genomics↗

bioRxiv2024

Transcriptomic atlas of the morphologic development of the fungal pathogen Coccidioides reveals key phase-enriched transcripts

Coccidioides spp. are highly understudied but significant dimorphic fungal pathogens that can infect both immunocompetent and immunocompromised people. In the environment, they grow as multicellular filaments (hyphae) that produce vegetative spores called arthroconidia. Upon inhalation by mammals, arthroconidia undergo a process called spherulation. They enlarge and undergo numerous nuclear divisions to form a spherical structure, and then internally segment until the spherule is filled with multiple cells called endospores. Mature spherules rupture and release endospores, each of which can form another spherule, in a process thought to facilitate dissemination. Spherulation is unique to Coccidioides and its molecular determinants remain largely unknown. Here, we report the first high-density transcriptomic analyses of Coccidioides development, defining morphology-dependent transcripts and those whose expression is regulated by Ryp1, a major regulator required for spherulation and virulence. Of approximately 9000 predicted transcripts, we discovered 273 transcripts with consistent spherule-associated expression, 82 of which are RYP1-dependent, a set likely to be critical for Coccidioides virulence. ChIP-Seq revealed 2 distinct regulons of Ryp1, one shared between hyphae and spherules and the other unique to spherules. Spherulation regulation was elaborate, with the majority of 227 predicted transcription factors in Coccidioides displaying spherule-enriched expression. We identified provocative targets, including 20 transcripts whose expression is endospore-enriched and 14 putative secreted effectors whose expression is spherule-enriched, of which 6 are secreted proteases. To highlight the utility of these data, we selected a cluster of RYP1-dependent, arthroconidia-associated transcripts and found that they play a role in arthroconidia cell wall biology, demonstrating the power of this resource in illuminating Coccidioides biology and virulence.

microbiology↗

bioRxiv2024

Inferring the composition of a mixed culture of natural microbial isolates by deep sequencing

Next generation sequencing has unlocked a wealth of genotype information for microbial populations, but phenotyping remains a bottleneck for exploiting this information, particularly for pathogens that are difficult to manipulate. Here, we establish a method for high-throughput phenotyping of mixed cultures, in which the pattern of naturally occurring single-nucleotide polymorphisms in each isolate is used as intrinsic barcodes which can be read out by sequencing. We demonstrate that our method can correctly deconvolute strain proportions in simulated mixed-strain pools. As an experimental test of our method, we perform whole genome sequencing of 66 natural isolates of the thermally dimorphic pathogenic fungus Coccidioides posadasii and infer the strain compositions for large mixed pools of these strains after competition at 37{degrees}C and room temperature. We validate the results of these selection experiments by recapitulating the temperature-specific enrichment results in smaller pools. Additionally, we demonstrate that strain fitness estimated by our method can be used as a quantitative trait for genome-wide association studies. We anticipate that our method will be broadly applicable to natural populations of microbes and allow high-throughput phenotyping to match the rate of genomic data acquisition. Author summaryThe diversity of the gene pool in natural populations encodes a wealth of information about its molecular biology. This is an especially valuable resource for non-model organisms, from humans to many microbial pathogens, lacking traditional genetic approaches. An effective method for reading out this population genetic information is a genome wide association study (GWAS) which searches for genotypes correlated with a phenotype of interest. With the advent of cheap genotyping, high throughput phenotyping is the primary bottleneck for GWAS, particularly for microbes that are difficult to manipulate. Here, we take advantage of the fact that the naturally occurring genetic variation within each individual strain can be used as an intrinsic barcode, which can be used to read out relative abundance of each strain as a quantitative phenotype from a mixed culture. Coccidioides posadasii, the causative agent of Valley Fever, is a fungal pathogen that must be manipulated under biosafety level 3 conditions, precluding many high-throughput phenotyping approaches. We apply our method to pooled competitions of C. posadasii strains at environmental and host temperatures. We identify robustly growing and temperature-sensitive strains, confirm these inferences in validation pooled growth experiments, and successfully demonstrate their use in GWAS.

genetics↗

bioRxiv2024

Optimizing in vitro spherulation cues in the fungal pathogen Coccidioides

Coccidioides spp. are part of a group of thermally dimorphic fungal pathogens, which grow as filamentous cells (hyphae) in the soil and transform to a different morphology upon inhalation into the host. The Coccidioides host form, the spherule, is unique and highly under characterized due to both technical and biocontainment challenges. Each spherule arises from an environmental spore (arthroconidium), matures, and develops hundreds of internal endospores, which are released from the spherule upon rupture. Each endospore can then go on to form another spherule in a cycle called spherulation. One of the foremost technical challenges has been reliably growing spherules in culture without the formation of contaminating hyphae, and consistently inducing endospore release from spherules. Here, we present optimization of in vitro spherule growth and endospore release, by closely controlling starting cell density in the culture, using freshly-harvested arthroconidia, and decreasing the concentration of multiple salts in spherulation media. We developed a minimal media to test spherule growth on various carbon and nitrogen sources. We defined a critical role for the dispersant Tamol in both early spherule formation and prevention of the accumulation of a visible film around spherules. Finally, we examined how the conditions under which arthroconidia are generated influence their transcriptome and subsequent development into spherules, demonstrating that this is an important variable to control when designing spherulation experiments. Together, our data reveal multiple strategies to optimize in vitro spherulation growth, enabling characterization of this virulence-relevant morphology.

microbiology↗

bioRxiv2024

Effects of age and dietary methionine restriction on cognitive and behavioural phenotypes in the rTg4510 model of frontotemporal dementia

Metabolic disorders such as diabetes and obesity are linked to neurodegenerative diseases, with evidence of decreased brain glucose metabolism and insulin resistance in patients with dementia. Given the rising prevalence of age-related diseases, lifestyle adjustments and nutritional interventions are gaining interest. Dietary methionine restriction (MR) is a nutritional intervention that enhances insulin sensitivity and delays ageing-associated metabolic alterations. Since the potential impact of MR on neurodegenerative diseases like dementia is not fully understood, we here examined the metabolic and behavioural phenotypes of a murine tauopathy model (rTg4510), which overexpresses human P301L mutated tau, and assessed the impact of an 8-week dietary MR. The rTg4510 mice and wild type (WT) littermates were assessed at 6 and 12 months of age. While rTg4510 mice displayed progressive behavioural and motor impairments at 6 and 12 months of age, MR led to significant benefits in the aged 12-month-old cohort, improving motor coordination and learning, short-term memory, and social recognition. These effects were accompanied by increased glycolysis in the hippocampus and higher FGF21 levels in the cortex. These benefits occurred in the absence of alterations in glucose metabolism/adiposity in this model. Overall, our results support the positive impact of MR on rTg4510 mice, suggesting this as a potential therapeutic intervention to delay and/or improve the progression in tau-related disease.

neuroscience↗

bioRxiv2023

Recyclable CRISPR/Cas9 mediated gene disruption and deletions in Histoplasma

Targeted gene disruption is challenging in the dimorphic fungal pathogen Histoplasma due to the low frequency of homologous recombination. Transformed DNA is either integrated ectopically into the genome or maintained extra chromosomally by de novo addition of telomeric sequences. Based on a system developed in Blastomyces, we adapted a CRISPR/Cas9 system to facilitate targeted gene disruption in Histoplasma with high efficiency. We express a codon-optimized version of Cas9 as well as guide RNAs from a single ectopic vector carrying a selectable marker. Once the desired mutation is verified, one can screen for isolates that have lost the Cas9 vector by simply removing the selective pressure. Multiple mutations can then be generated in the same strain by retransforming the Cas9 vector carrying different guides. We used this system to disrupt a number of target genes including RYP2 and SRE1 where loss-of-function mutations could be monitored visually by colony morphology or color, respectively. Interestingly, expression of two guide RNAs targeting the 5 and 3 ends of a gene allowed isolation of deletion mutants where the sequence between the guide RNAs was removed from the genome. Whole-genome sequencing showed that the frequency of off-target mutations associated with the Cas9 nuclease was negligible. Finally, we increased the frequency of gene disruption by using an endogenous Histoplasma regulatory sequence to drive guide RNA expression. These tools transform our ability to generate targeted mutations in Histoplasma. ImportanceHistoplasma is a primary fungal pathogen with the ability to infect otherwise healthy mammalian hosts, causing systemic and sometimes life-threatening disease. Thus far, molecular genetic manipulation of this organism has utilized RNA interference, random insertional mutagenesis, and a homologous recombination protocol that is highly variable and often inefficient. Targeted gene manipulations have been challenging due to poor rates of homologous recombination events in Histoplasma. Interrogation of the virulence strategies of this organism would be highly accelerated by a means of efficiently generating targeted mutations. We have developed a recyclable CRISPR/Cas9 system that can be used to introduce gene disruptions in Histoplasma with high efficiency, thereby allowing disruption of multiple genes.

microbiology↗

bioRxiv2023

Chemical stimuli override a temperature-dependent morphological program by reprogramming the transcriptome of a fungal pathogen.

The human fungal pathogen Histoplasma changes its morphology in response to temperature. At 37{degrees}C it grows as a budding yeast whereas at room temperature it transitions to hyphal growth. Prior work has demonstrated that 15-20% of transcripts are temperature-regulated, and that transcription factors Ryp1-4 are necessary to establish yeast growth. However, little is known about transcriptional regulators of the hyphal program. To identify TFs that regulate filamentation, we utilize chemical inducers of hyphal growth. We show that addition of cAMP analogs or an inhibitor of cAMP breakdown overrides yeast morphology, yielding inappropriate hyphal growth at 37{degrees}C. Additionally, butyrate supplementation triggers hyphal growth at 37{degrees}C. Transcriptional profiling of cultures filamenting in response to cAMP or butyrate reveals that a limited set of genes respond to cAMP while butyrate dysregulates a larger set. Comparison of these profiles to previous temperature- or morphology-regulated gene sets identifies a small set of morphology-specific transcripts. This set contains 9 TFs of which we characterized three, STU1, FBC1, and PAC2, whose orthologs regulate development in other fungi. We found that each of these TFs is individually dispensable for room-temperature (RT) induced filamentation but each is required for other aspects of RT development. FBC1 and PAC2, but not STU1, are necessary for filamentation in response to cAMP at 37{degrees}C. Ectopic expression of each of these TFs is sufficient to induce filamentation at 37{degrees}C. Finally, PAC2 induction of filamentation at 37{degrees}C is dependent on STU1, suggesting these TFs form a regulatory circuit that, when activated at RT, promotes the hyphal program. ImportanceFungal illnesses pose a significant disease burden. However, the regulatory circuits that govern the development and virulence of fungi remain largely unknown. This study utilizes chemicals that can override the normal growth morphology of the human pathogen Histoplasma. Using transcriptomic approaches, we identify novel regulators of hyphal morphology and refine our understanding of the transcriptional circuits governing morphology in Histoplasma.

microbiology↗

bioRxiv2023

How stra(i)nge are your controls? A comparative analysis of metabolic phenotypes in commonly used C57 substrains

In recent years, the use of insufficiently characterised control subjects has been a contributing factor to increasing irreproducibility in different areas of biomedical research including neuroscience and metabolism. There is now a growing awareness of phenotypic differences between the metabolic profiles of C57BL/6 substrains which are commonly used as control animals. We here investigated baseline metabolic characteristics such as glucose regulation, fasted serum insulin levels and hepatic insulin signalling in five different C57BL/6 sub-strains (N, J, JOla, JRcc) of both sexes, obtained from two commercial vendors Charles River Laboratories (Crl) and Envigo (Env). Our results indicated systematic and tissue-specific differences between substrains, modulated by both vendor and sex in all parameters investigated, not necessarily mediated by the presence of the Nnt mutation. Not only were there differences between 6J and 6N as expected, all three 6J sub-strains exhibited different profiles, even from the same breeder. Two distinct metabolic profiles were identified, one in which low insulin levels resulted in impaired glucose clearance (6JCrl; both sexes) and the other, where sustained elevations in fasted basal insulin levels led to glucose intolerance (male 6JRccEnv). Further, 6JRccEnv displayed sex differences in both glucose clearance and hepatic insulin signalling markers. In comparison, the two 6N substrains of either sex, irrespective of vendor, did not exhibit considerable differences, with 6NCrl animals presenting a good choice as a healthy baseline control for many types of experiments. Overall, our data emphasise the importance of selecting and characterising control subjects regarding background, sex, and supplier to ensure proper experimental outcomes in biomedical research.

physiology↗

bioRxiv2023

Incorporating fire-smartness into agricultural policies minimises suppression costs and ecosystem services damages from wildfires

Global climate warming is expected to increase wildfire hazard in many regions of the world. In southern Europe, land abandonment and an unbalanced investment toward fire suppression instead of prevention has gradually increased wildfire risk, which calls for a paradigm change in fire management policies. Here we combined scenario analysis, fire landscape modelling, and economic tools to identify which land-use policies would minimise the expected wildfire-related losses in a representative mountainous area of the northwestern Iberian Peninsula (the Transboundary Biosphere Reserve Geres-Xures, between Spain and Portugal). To do so, we applied the least-cost-plus-net-value-change approach and estimated net changes in wildfire damages based on their implications for the ecosystem services that affect financial returns to landowners in the study area (i.e. agriculture, pasture, and timber) and the wider economic benefits (i.e. recreation and climate regulation) for the 2010-2050 period. Four land-use scenarios were considered: (1) Business as Usual (BAU); (2) fire-smart, fostering more fire-resistant (less flammable) and/or fire-resilient landscapes (fire-smart); (3) High Nature Value farmlands (HNVf), wherein the abandonment of extensive agriculture is reversed; and (4) a combination of HNVf and fire-smart. We found the highest net value change (i.e. the difference between damages and avoided damages) in BAU for timber and pasture provision, and in fire-smart for recreation and climate regulation. HNVf was the best for suppression cost savings, but it generated the lowest expected present value for climate regulation. In fact, the best scenarios related to fire suppression are HNVf and HNVf combined with fire-smart, which also generate the lowest net value change plus net suppression costs in the entire study area (i.e. considering all ecosystem services damages and suppression costs). Therefore, reverting land abandonment through recultivation and promoting fire-resistant tree species is the most efficient way to reduce wildfire hazard. In this sense, payments for ecosystem services should reward farmers for their role in wildfire prevention. This study improves the understanding of the financial and societal benefits derived from reducing fire suppression spending and ecosystem services damage by undertaking fire-smart land-use strategies, which can be essential to enhance local stakeholders support for wildfire prevention policies. HighlightsO_LILand-use changes impact wildfire ecosystem services (ES) damages and suppression costs C_LIO_LIPromoting agriculture generates significant suppression cost savings C_LIO_LIAgriculture + fire-resistant forests is the best to reduce wildfire ES damages C_LIO_LILand-use policies should balance trade-offs between climate and wildfire regulation C_LIO_LIPayments for ES should reward farmers for their role in wildfire prevention C_LI

ecology↗

bioRxiv2022

NF-κB inhibitor alpha has a cross-variant role during SARS-CoV-2 infection in ACE2-overexpressing human airway organoids

As SARS-CoV-2 continues to spread worldwide, tractable primary airway cell models that accurately recapitulate the cell-intrinsic response to arising viral variants are needed. Here we describe an adult stem cell-derived human airway organoid model overexpressing the ACE2 receptor that supports robust viral replication while maintaining 3D architecture and cellular diversity of the airway epithelium. ACE2-OE organoids were infected with SARS-CoV-2 variants and subjected to single-cell RNA-sequencing. NF-{kappa}B inhibitor alpha was consistently upregulated in infected epithelial cells, and its mRNA expression positively correlated with infection levels. Confocal microscopy showed more I{kappa}B expression in infected than bystander cells, but found concurrent nuclear translocation of NF-{kappa}B that I{kappa}B usually prevents. Overexpressing a nondegradable I{kappa}B mutant reduced NF-{kappa}B translocation and increased viral infection. These data demonstrate the functionality of ACE2-OE organoids in SARS-CoV-2 research and identify an incomplete NF-{kappa}B feedback loop as a rheostat of viral infection that may promote inflammation and severe disease.

microbiology↗

bioRxiv2022

Orphan genes are clustered with allorecognition loci and may be involved in incompatibility and speciation in Neurospora

Lineage-specific genes (LSGs) have long been postulated to play roles in the establishment of genetic barriers to intercrossing and speciation. However, there is a lack of working hypotheses as to how they might play that role. In the genome of Neurospora crassa, most of the 670 Neurospora LSGs that are aggregated adjacent to the telomeres are clustered with 61% of the HET-domain genes, which regulate self-recognition and define vegetative incompatibility groups. Among the 342 LSGs that are dynamically expressed during both asexual and sexual phases, 64% were detectable on unusual carbon sources such as furfural and HMF--wildfire-produced chemicals that are a strong inducer of sexual development. Expression of a significant portion of the LSGs was sensitive to light and temperature, factors that regulate the switch from asexual to sexual reproduction. Furthermore, expression of the LSGs was significantly affected in the knockouts of adv-1 and pp-1 that regulate hyphal communication, and expression of more than one quarter of the LSGs was affected by perturbation of the mating locus. Accordingly, we propose a gene-by-environment interaction model encouraging further investigation of the roles of LSGs and HET-domain genes in speciation in Neurospora. This gene-by-environment interaction model emphasizes the roles of the LSGs in response to genetic and environmental factors, leading to the regulation of the switch from the asexual growth and fusion, such that vegetative incompatibility governed by allorecognition promotes allelic homogeneity, sexual reproduction, and outbreeding, whereas VI repression and meiotic recombination promotes allelic polymorphism.

evolutionary biology↗