The endoplasmic reticulum (ER) comprises an array of structurally distinct subdomains, each with characteristic functions. While altered ER-associated processes are linked to age-onset pathogenesis, whether shifts in ER morphology underlie these functional changes is unclear. We report that ER remodeling is a conserved feature of the aging process in models ranging from yeast to C. elegans and mammals. Focusing on C. elegans as an exemplar of metazoan aging, we find that as animals age, ER mass declines in virtually all tissues and ER morphology shifts from rough sheets to tubular ER. The accompanying large-scale shifts in proteomic composition correspond to the ER turning from protein synthesis to lipid metabolism. To drive this substantial remodeling, ER-phagy is activated early in adulthood, promoting turnover of rough ER in response to rises in luminal protein-folding burden and reduced global protein synthesis. Surprisingly, ER remodeling is a pro-active and protective response du

A slow decline in the autophagy-lysosomal pathway is a hallmark of the normal aging brain. Yet, an acceleration of this cellular function may propel neurodegenerative events. In fact, mutations in genes associated with the autophagy-lysosomal pathway can lead to Parkinson’s disease. Also, amyloidogenic protein deposition is observed in lysosomal storage disorders, which are caused by genetic mutations representing risk factors for Parkinson’s disease. For example, Gaucher’s disease GBA1 mutations leading to defects in lysosomal sphingolipid metabolism cause alpha-synuclein accumulation. We observed that increased lysosomal Tau accumulation is found in human dermal fibroblasts engineered for inducible Tau expression. Inhibition of the GBA1 product GCase augmented Tau-dependent lysosomal stress and Tau accumulation. Here, we show increased Tau seed-induced Tau accumulation in Gaucher’s fibroblasts carrying GBA1 mutations when compared to normal fibroblasts. Pharmacological enhancement of

Expansion of carbapenemase-producing Klebsiella pneumoniae (CP- Kp ) is driven by nosocomial dissemination, and effective infection control depends on timely and reliable typing data. Here, we evaluated our previously developed Fourier-transform infrared spectroscopy (FT-IR) with attenuated total reflectance (ATR) workflow for real-time typing of Kp capsular (KL)-types and lineages to support infection control. FT-IR spectra were acquired from Columbia agar with 5% sheep blood cultures of all CP- Kp infection isolates (n=136) from hospitalized patients at a northern Portugal hospital (April 2022 – March 2023), and analyzed using automated machine-learning (ML) classification models. Typing results were confirmed by wzi sequencing, MLST and/or WGS. FT-IR typing on Columbia agar plates showed 73% sensitivity, 79% specificity and 74% accuracy. Our method correctly typed 94% of typeable isolates (78/83), from which 87% were comunicated in <24h. Sixty percent of non-typeable isolates were c

Candida haemulonii comprises a group of pathogenic fungi known for their resistance to primary antifungal treatments. Infections caused by these pathogens present substantial challenges due to the difficulties in accurate identification. Extracellular vesicles (EVs) released by these fungi play a critical role in the pathogen-host interaction, potentially influencing antifungal resistance and virulence. Previous research by our group indicates that EVs contain immunogenic particles capable of impacting the host’s immune response. Understanding the composition of these EVs is crucial for elucidating the mechanisms underlying resistance and virulence in C. haemulonii var. vulnera. This study aims to investigate the contents of EVs from C. haemulonii var. vulnera using proteomic and microRNA sequencing tools, providing insights into their role in adaptation, survival, and the progression of infections. Our findings reveal key proteins transported by EVs, including BMH1, TEF1, CDC19, and P

Understanding gene regulation in organism development is crucial in biology. Techniques like whole-mount in situ hybridization can reveal spatial gene expression in organs and tissues. However, capturing time-lapse images of gene expression dynamics in embryos developing in utero, such as mice, remains technically challenging beyond the early stages. To address this, we present a method to integrate static snapshots of gene expression patterns across limb developmental stages, creating a continuous 2D reconstruction of gene expression patterns over time. This method interpolates small tissue regions over time to create smooth temporal trajectories of gene expression. We successfully applied it to a number of key genes in limb development, including Sox9, Hand2, and Bmp2. This approach enables a detailed spatio-temporal mapping of gene expression, providing insights into developmental mechanisms. By estimating Gene Expression Patterns at previously unobserved time points, it facilitates

Disintegration of organelle membranes induces various cellular responses and has pathological consequences, including autoinflammatory diseases and neurodegeneration. Establishing methods to induce membrane rupture of organelles of interest is essential to analyze the downstream effects of membrane rupture; however, the spatiotemporal induction of rupture of specific membranes remains challenging. Here, we develop a series of optogenetic tools to induce organelle membrane rupture by using engineered Bcl-2-associated X protein (BAX), whose primary function is to form membrane pores in the outer mitochondrial membrane (OMM) during apoptosis. When BAX is forced to target mitochondria, lysosomes, or the endoplasmic reticulum (ER) by replacing its C-terminal transmembrane domain (TMD) with organelle-targeting sequences, the BAX mutants rupture their target membranes. To regulate the activity of organelle-targeted BAX, the photosensitive light-oxygen-voltage-sensing 2 (LOV2) domain is fused

Cotton fiber development entails complex genome-wide gene regulatory networks (GRN) that remain mostly unexplored. Here we present integrative analyses of fiber GRNs using public RNA-seq datasets, integrated with multi-omics genomic, transcriptomic, and cistromic data. We detail the fiber coexpression dynamics and regulatory connections, validating findings with external datasets and transcription factor (TF) binding site data. We elucidate previously uncharacterized TFs that regulate genes involved in fiber-related functions and cellulose synthesis, and identify the regulatory role of two homoeologous G2-like transcription factors on fiber length. Analysis of duplicated gene expression and network relationships in allopolyploid cotton, which has two co-resident genomes (A, D), revealed novel aspects of asymmetric subgenomic developmental contributions. Whereas D-based homoeolog pairs drive higher overall gene expression from the D subgenome, TFs from the A subgenome play a preferentia

Living and fossilized organisms represent only a tiny fraction of Earth’s evolutionary history, motivating “ancestral state reconstruction” techniques that aim to infer the unobserved phenotypes of evolving lineages based on measurements of their relatives. Stochastic character mapping (“simmapping”) methods perform ancestral state reconstruction by randomly sampling maps (“simmaps”) of probable phenotypic evolutionary histories along phylogenies, allowing researchers to conveniently and flexibly analyze macroevolutionary patterns and processes while accounting for the inherent uncertainty of ancestral state estimates. Here, we introduce a flexible and efficient algorithm for simmapping continuous phenotypes evolving under Brownian Motion models, which we term continuous simmaps or “contsimmaps”, thereby generalizing existing simmapping methods which only work with discrete phenotypes. To demonstrate potential applications of contsimmaps, we develop a pipeline that uses contsimmaps to

Ectotherms are essential components of all ecosystems and rely on external heat to regulate their body temperature. For most terrestrial ectotherms the primary sources of heat are ambient temperature and solar radiation. Many insects can use movement to respond to changes in temperature and solar radiation in order to manage their body temperature and optimise life history traits. However, we lack the understanding of the relative importance of temperature and shade that we need to predict how the combined effects of changes in air temperature and cloud cover will impact terrestrial insect populations. We reared developing nymphs of the field cricket (Gryllus campestris) at high and low air temperature sites with partially shaded and unshaded treatments at each site. Given the broad altitudinal range of this species, we tested the possibility of local adaptation to these climate variables by rearing nymphs from high and low altitude genetic lineages in all treatment combinations. We fo

Surveillance and monitoring of zoonotic pathogens is key to identifying and mitigating emerging public health threats. Surveillance is often designed to be taxonomically targeted or systematically dispersed across geography, however, those approaches may not represent the breadth of environments inhabited by a host, vector, or pathogen, leaving significant gaps in our understanding of pathogen dynamics in their natural reservoirs and environments. As a case study on the design of pathogen surveillance programs, we assess how well 20 years of small mammal surveys in Panama have sampled available environments and propose a multistep approach to selecting survey localities in the future. We use >8,000 georeferenced mammal specimen records, collected as part of a long-term hantavirus surveillance program, to test the completeness of country-wide environmental sampling. Despite 20 years of surveillance, our analyses identified a few key environmental sampling gaps. To refine surveillance st