Victoria Baca-González

Plants are simultaneously exposed to multiple abiotic stresses, yet how opposing epigenetic signals are integrated remains unclear. Here, we investigated the combined effects of heat stress and phosphate deficiency in Arabidopsis thaliana , two conditions with antagonistic impacts on DNA methylation. Using an integrated multi‐omic approach (WGBS, RNA‐seq and small RNA‐seq) in roots and shoots under field‐mimicking conditions, we show that combined stress establishes a distinct, non‐additive epigenomic state characterised by widespread CHH hypomethylation and differential engagement of RdDM and CMT2 pathways. Despite extensive methylation remodelling across transposable elements, genes and intergenic regions, we observe a genome‐wide decoupling between DNA methylation dynamics and transcriptional output. Notably, differentially methylated regions are enriched in transcription factor binding sites, particularly GATA motifs, linking CHH hypomethylation to increased chromatin accessibility and activation of GATA‐associated regulatory networks. In contrast, nuclear mitochondrial DNA insertions represent a notable exception, where CHH hypomethylation is directly coupled to transcriptional activation. Functional analyses reveal distinct contributions of RdDM and CMT2 to basal silencing and stress responsiveness at these loci. Overall, our results support a model that positions DNA methylation as a regulator of regulatory potential rather than a direct determinant of transcription under combined stress.

Root knot nematodes (RKNs) induce galls, containing multinucleated giant cells (GCs) to nourish them. The differentiation of precursor cells to galls/GCs involves extensive cellular reprogramming with multiple layers of regulation. Epigenetic regulation during the early stages of infection indicates that RNA-directed DNA methylation (RdDM) and microRNA-dependent gene silencing contribute to transcriptional and post-transcriptional reprogramming during gall organogenesis. Although later stages of galls/GC development are crucial for nematode life-cycle maintenance, epigenetic reprogramming events remain largely unexplored. An integrative analysis of sRNAs, DNA methylation, and transcriptomic dynamics in galls induced by Meloidogyne javanica revealed that enrichment of 24 nt sRNAs represents a gall hallmark across early and late developmental stages. Fewer gall-distinctive sRNAs were detected at mid-to-late stages than at early stages, alongside a pronounced spatial reorganization of rasiRNA accumulation. At early stages, gall-distinctive rasiRNAs preferentially accumulated in pericentromeric retrotransposon-rich regions, whereas, at mid-to-late stages, they predominantly localized to chromosome arms, matching DNA transposons, promoters, and gene bodies. A decline in the regulatory influence of miRNAs was observed as infection progressed, possibly reflecting a transition toward specialized regulatory states associated with gall maintenance. Moreover, three regulatory modules, miR2111-5p/HOLT, miR172/AP2, and miR156/SPL10, were tightly but oppositely regulated at 3 and 14 days post-infection. Furthermore, miR156/SPL10 showed crucial functions during gall formation and/or maintenance, possibly influenced by hormonal cues involving ARF8 among other ARFs. Our results highlight stage-specific patterns involving sRNA dynamics, DNA methylation, and transcriptomic changes underlying nematode feeding site development and maintenance.

Summary: Phosphate (Pi) is an essential nutrient for plant growth, and understanding how Arabidopsis thaliana root cells respond to Pi deficiency is crucial to decipher whole plant responses. We perform high‐resolution transcriptomic profiling across five distinct root cell types, identifying differentially expressed genes (DEGs) and differential alternative splicing (DAS) events that define cell‐type‐specific Pi‐responsive regulatory layers. We identify over 7000 DEGs and 733 DAS that act largely independently and are cell‐type‐specific, affecting distinct loci and biological pathways. Transcription factors such as LHY , REV7 and MYB88 , linked to circadian rhythms, stomatal regulation and ABA perception, acquire novel functions under Pi starvation. We show that the splicing factor SR45 , previously associated with iron homeostasis, regulates Pi allocation. The sr45‐1 mutant displays increased root‐to‐shoot Pi ratio and reduced biomass. A substantial number of Pi‐responsive DAS transcripts are SR45 bound, indicating that SR45 operates as a regulatory hub for Pi transport and homeostasis. This cell‐type‐resolved dataset provides a detailed molecular map of Pi deficiency responses and highlights the importance of post‐transcriptional regulation in shaping root adaptive strategies. Transcriptional regulation and alternative splicing emerge as coordinated mechanisms orchestrating plant adaptation to Pi starvation.

The deep-sea fauna of the southeastern Pacific remains vastly understudied, particularly along the northern coast of Chile, a transitional zone influenced by both Peruvian and subtropical ecosystems. During the Schmidt Ocean Institute's FKT240425 expedition aboard the R/V Falkor (too), conducted systematic deep-sea ROV surveys between 1816 and 4504 m depth off the Peninsula de Mejillones, Chile. The study reports new in situ records and significant range extensions for about one hundred species. A total of 79 macroinvertebrate samples were collected using the ROV SuBastian. The preliminary analysis of groups such as Arthropoda, Echinodermata, Decapoda, Mollusca, and Porifera indicates the potential presence of at least 35 new species. The preliminary conclusions of the observed and collected material are presented here, with comments about the taxonomic status of each one. Thus, this research cruise has contributed the most up-to-date records to the biodiversity of the Atacama Trench.

Deep-sea sediments host microbial communities essential to nitrogen, sulfur, and carbon cycling, yet those in the Southern Hemisphere remain understudied. In this work, we analyze sediments from an oceanic trench off northern Chile using metatranscriptomics, aiming to relate community composition with functional activity. Most assayed sites form part of a broadly uniform deep-sea ecosystem fueled by the degradation of marine snow through diverse aerobic and anaerobic pathways. Nitrogen cycling within them is driven by archaeal nitrification and bacterial dissimilatory nitrate reduction. One site, however, appears to be a sulfur-based cold seep inhabited by mats of thiotrophs and vesicomyid clams within darker sediments. In this site, ANME archaea are largely absent despite the presence of dolomite crystals, which are typically associated with anaerobic methane oxidation. Instead, abundant subsurface pyrite and active sulfate reduction point to substantial sulfur cycling. Across the region, heterotrophic communities dependent on marine snow transition to chemosynthetic ones supported by reduced sulfur in a sulfur-driven cold seep with minimal fluid flow.

Microbial resistance is a global health problem that will increase over time. Advances in insect antimicrobial peptides (AMPs) offer a powerful new approach to combat antimicrobial resistance. Invertebrates represent a rich group of animals for the discovery of new antimicrobial agents due to their high diversity and the presence of adaptive immunity or “immune priming”. Here, we report a priming approach for Tenebrio molitor that simulates natural infection via the oral route. This oral administration has the advantage of minimizing the stress caused by conventional priming techniques and could be a viable method for mealworm immunity studies. When using inactivated microorganisms for oral priming, our results showed an increased survival of T. molitor larvae after exposure to various pathogens. This finding was consistent with the induction of antimicrobial activity in the hemolymph of primed larvae. Interestingly, the hemolymph of larvae orally primed with Escherichia coli showed constitutive activity against Staphylococcus aureus and heterologous activity for other Gram-negative bacteria, such as Salmonella enterica. The priming of T. molitor is generally performed via injection of the microorganism. To our knowledge, this is the first report describing the oral administration of heat-inactivated microorganisms for priming mealworms. This technique has the advantage of reducing the stress that occurs with the conventional methods for priming vertebrates.

The immune systems of all vertebrates contain cathelicidins, a family of antimicrobial peptides. Cathelicidins are a type of innate immune effector that have a number of biological functions, including a well-known direct antibacterial action and immunomodulatory function. In search of new templates for antimicrobial peptide discovery, we have identified and characterized the cathelicidin of the small mammal Talpa occidentalis. We describe the heterogeneity of cathelicidin in the order Eulipotyphla in relation to the Iberian mole and predict its antibacterial activity using bioinformatics tools. In an effort to correlate these findings, we derived the putative active peptide and performed in vitro hemolysis and antimicrobial activity assays, confirming that Iberian mole cathelicidins are antimicrobial. Our results showed that the Iberian mole putative peptide, named To-KL37 (KLFGKVGNLLQKGWQKIKNIGRRIKDFFRNIRPMQEA) has antibacterial and antifungal activity. Understanding the antimicrobial defense of insectivores may help scientists prevent the spread of pathogens to humans. We hope that this study can also provide new, effective antibacterial peptides for future drug development.

Bats are unique in their potential to serve as reservoir hosts for intracellular pathogens. Recently, the impact of COVID-19 has relegated bats from biomedical darkness to the frontline of public health as bats are the natural reservoir of many viruses, including SARS-Cov-2. Many bat genomes have been sequenced recently, and sequences coding for antimicrobial peptides are available in the public databases. Here we provide a structural analysis of genome-predicted bat cathelicidins as components of their innate immunity. A total of 32 unique protein sequences were retrieved from the NCBI database. Interestingly, some bat species contained more than one cathelicidin. We examined the conserved cysteines within the cathelin-like domain and the peptide portion of each sequence and revealed phylogenetic relationships and structural dissimilarities. The antibacterial, antifungal, and antiviral activity of peptides was examined using bioinformatic tools. The peptides were modeled and subjected to docking analysis with the region binding domain (RBD) region of the SARS-CoV-2 Spike protein. The appearance of multiple forms of cathelicidins verifies the complex microbial challenges encountered by these species. Learning more about antiviral defenses of bats and how they drive virus evolution will help scientists to investigate the function of antimicrobial peptides in these species.

Antibodies have transformed biomedical research and are now being used for different experimental applications. Generally, the interaction of enzymes with their specific antibodies can lead to a reduction in their enzymatic activity. The effect of the antibody is dependent on its narrow i.e. the regions of the enzyme to which it is directed. The mechanism of this inhibition is rarely a direct combination of the antibodies with the catalytic site, but is rather due to steric hindrance, barring the substrate access to the active site. In several systems, however, the interaction with the antibody induces conformational changes on the enzyme that can either inhibit or enhance its catalytic activity. The extent of enzyme inhibition or enhancement is, therefore, a reflection of the nature and distribution of the various antigenic determinants on the enzyme molecule. Currently, the mode of action of many enzymes has been elucidated at the molecular level. We here review the molecular mechanisms and recent trends by which antibodies inhibit the catalytic activity of enzymes and provide examples of how specific antibodies can be useful for the neutralization of biologically active molecules

In the current worldwide pandemic situation caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and the newest coronavirus disease (COVID-19), therapeutics and prophylactics are urgently needed for a large population. Some of the prophylaxis strategies are based on the development of antibodies targeting viral proteins. IgY antibodies are a type of immunoglobulin present in birds, amphibians, and reptiles. They are usually obtained from egg yolk of hyper-immunized hens and represent a relatively inexpensive source of antibodies. Specific IgY can be produced by immunizing chickens with the target antigen and then purifying from the egg yolk. Chicken IgY has been widely explored as a clinical anti-infective material for prophylaxis, preventive medicine, and therapy of infectious diseases. Administered non-systemically, IgY antibodies are safe and effective drugs. Moreover, passive immunization with avian antibodies could become an effective alternative therapy, as these can be obtained relatively simply, cost-efficiently, and produced on a large scale. Here, we highlight the potential use of polyclonal avian IgY antibodies as an oral prophylactic treatment for respiratory viral diseases, such as COVID-19, for which no vaccine is yet available.