How different intrinsic sequence variation or regulatory modifications of histones regulate nucleosome interactions with transcription remain unclear. By contrast with H3 and H2B variants, H2A variants occupy specific domains of chromatin in Arabidopsis thaliana. Broad domains of chromatin are affected by the loss of remodelers that affect the deposition or the exchange of H2A variants. Notably, the chromatin remodeler DECREASED IN DNA METHYLATION (DDM1) is required to maintain enrichment in all markers of constitutive heterochromatin including DNA methylation, H3K9me1/2 and the variant H2A.W. To test the importance of histone variants in the organization of chromatin we investigated how histone variants and histone modifications assemble in the Arabidopsis thaliana genome and showed that a limited number of chromatin states divide euchromatin and heterochromatin into several subdomains. We found that histone variants are as significant as histone modifications in determining the composition of chromatin states. Particularly strong associations were observed between H2A variants and specific combinations of histone modifications. To study the role of H2A variants in organizing chromatin states we determined the role the chromatin remodeler DECREASED IN DNA METHYLATION (DDM1) in the organization of chromatin states. We showed that the loss of DDM1 prevented the exchange of the histone variant H2A.Z to H2A.W in constitutive heterochromatin, resulting in significant effects on the definition and distribution of chromatin states in and outside of heterochromatin. We thus propose that dynamic exchanges of histone variants control the organization of histone modifications into chromatin states, acting as molecular landmarks. 

Histone variants shape the chromatin states in Arabidopsis

Abstract In recent years, aquaculture has seen tremendous growth worldwide due to technological advancements, leading to research and development of various innovations. Aquaculture farmers prioritise early diagnosis for timely treatment to achieve better productive and economic performance. Aquatic animal health experts still employ traditional diagnostic methods using visual diagnosis, cell culture, media culture, histopathology and serology. However, the developments of technologies in aquamedicine, such as sequencing, biosensors and CRISPR, have enabled rapid disease detection within minutes. Furthermore, integrating sensors, drones, artificial intelligence and the internet in aquaculture farm monitoring has helped farmers take decisive actions to improve production. Advancements in diagnostic techniques have significantly enhanced the efficient detection of bacterial, viral, parasitic and fungal diseases in aquatic animals. Moreover, monitoring water quality, aquatic animal health and animal behaviour on farms has become exceptionally streamlined with cutting‐edge tools like drones, sensors and artificial intelligence. Summarising research and development in aquatic animal health and monitoring aids efficient technology adoption in aquaculture. With these advanced technologies' continued development and adoption in developed countries, the aquaculture industry is experiencing growth and increased efficiency, benefiting farmers and consumers in these regions. However, farmers and educators in developing countries lack information about these technologies. Training of agricultural educators and efficient dissemination of knowledge and technologies through advertising and publication in collaboration with companies is essential. This review delves into emerging technologies capable of replacing the conventional diagnostic and monitoring methods utilised in aquaculture. We also explore their strengths, limitations and potential future applications within aquaculture settings. 

Emerging technologies revolutionising disease diagnosis and monitoring in aquatic animal health

Abstract Nucleosomal acetyltransferase of H4 (NuA4) is an essential transcriptional coactivator in eukaryotes, but remains poorly characterized in plants. Here, we describe Arabidopsis homologs of the NuA4 scaffold proteins Enhancer of Polycomb-Like 1 (AtEPL1) and Esa1-Associated Factor 1 (AtEAF1). Loss of AtEAF1 results in inhibition of growth and chloroplast development. These effects are stronger in the Atepl1 mutant and are further enhanced by loss of Golden2-Like (GLK) transcription factors, suggesting that NuA4 activates nuclear plastid genes alongside GLK. We demonstrate that AtEPL1 is necessary for nucleosomal acetylation of histones H4 and H2A.Z by NuA4 in vitro. These chromatin marks are diminished genome-wide in Atepl1 , while another active chromatin mark, H3K9 acetylation (H3K9ac), is locally enhanced. Expression of many chloroplast-related genes depends on NuA4, as they are downregulated with loss of H4ac and H2A.Zac. Finally, we demonstrate that NuA4 promotes H2A.Z deposition and by doing so prevents spurious activation of stress response genes. 

/pdf/nua4-and-h2a-z-control-environmental-responses-and-2fy4827b.pdf

NuA4 and H2A.Z control environmental responses and autotrophic growth in Arabidopsis

Winter dormancy – a period of low metabolic activity and no visible growth – appears as an adaptation to harsh winter conditions and can be divided into different phases. It is tightly controlled by environmental cues, with ambient temperature playing a major role. During endodormancy, a cultivar-specific amount of cold needs to be perceived, and during ecodormancy, heat hours accumulate before bud burst and anthesis in spring. Expression analysis, performed in several key fruit tree species, proved to be very useful in elucidating the molecular control of onset and release of dormancy. However, the time resolution of these experiments has been limited. Therefore, in this study, dense time-series expression analysis was conducted for 40 candidate genes involved in dormancy control, under the cool-temperate climate conditions in Dresden. Samples were taken from the cultivars ‘Pinova’ and ‘Gala,’ which differ in flowering time. The set of candidate genes included well-established dormancy genes such as DAM genes, MdFLC-like, MdICE1, MdPRE 1, and MdPIF4. Furthermore, we tested genes from dormancy-associated pathways including the brassinosteroid, gibberellic acid, abscisic acid (ABA), cytokinin response, and respiratory stress pathways. The expression patterns of well-established dormancy genes were confirmed and could be associated with specific dormancy phases. In addition, less well-known transcription factors and genes of the ABA signaling pathway showed associations with dormancy progression. The three ABA signaling genes HAB1_chr15, HAI3, and ABF2 showed a local minimum of gene expression in proximity of the endodormancy to ecodormancy transition. The number of sampling points allowed us to correlate expression values with temperature data, which revealed significant correlations of ambient temperature with the expression of the Malus domestica genes MdICE1, MdPIF4, MdFLC-like, HAB1chr15, and the type-B cytokinin response regulator BRR9. Interestingly, the slope of the linear correlation of temperature with the expression of MdPIF4 differed between cultivars. Whether the strength of inducibility of MdPIF4 expression by low temperature differs between the ‘Pinova’ and ‘Gala’ alleles needs to be tested further.

/pdf/time-resolved-analysis-of-candidate-gene-expression-and-v4t5by87.pdf

Time-Resolved Analysis of Candidate Gene Expression and Ambient Temperature During Bud Dormancy in Apple

Shrimp aquaculture has been growing rapidly over the last three decades. However, high-density aquaculture together with environmental degradation has led to increased incidence of shrimp infections. Thus, devising and implementing effective strategies to predict, diagnose and control the spread of infections of shrimps are crucial, also to ensure biosecurity and sustainability of the food industry. With the recent advancements in biotechnology, more attention has been given to develop novel promising therapeutic tools with potential to prevent disease occurrence and better manage shrimp health. Furthermore, owing to the advent of the next-generation sequencing (NGS) platforms, it has become possible to analyze the genetic basis of susceptibility or resistance of different stocks of shrimps to infections and how sustainable aquaculture could be made free of shrimp diseases. 

Microbes and pathogens associated with shrimps - implications and review of possible control strategies

Author Correction: PHYTOCHROME-INTERACTING FACTORs trigger environmentally responsive chromatin dynamics in plants

/pdf/correction-temporal-proteomic-profiling-reveals-insight-into-28vvap9q.pdf

Correction: Temporal proteomic profiling reveals insight into critical developmental processes and temperature-influenced physiological response differences in a bivalve mollusc

/pdf/author-correction-protein-interaction-network-of-1unqqtz8.pdf

Author Correction: Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism

https://www.nature.com/articles/s41592-023-01768-4.pdf

Author Correction: CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping

The Pacific white shrimp (Penaeus vannamei) is one of the most valuable aquaculture species in the world but has suffered major economic losses from outbreaks of White Spot Syndrome Virus and Taura Syndrome Virus. Rapid detection of these viruses can improve aquaculture practices by enabling more timely action to be taken to combat disease outbreaks. ABSTRACT Timely detection of persistent and emerging pathogens is critical to controlling disease spread, particularly in high-density populations with increased contact between individuals and limited-to-no ability to quarantine. Standard molecular diagnostic tests for surveying pathogenic microbes have provided the sensitivity needed for early detection, but lag in time-to-result leading to delayed action. On-site diagnostics alleviate this lag, but current technologies are less sensitive and adaptable than lab-based molecular methods. Towards the development of improved on-site diagnostics, we demonstrated the adaptability of a loop-mediated isothermal amplification-CRISPR coupled technology for detecting DNA and RNA viruses that have greatly impacted shrimp populations worldwide; White Spot Syndrome Virus and Taura Syndrome Virus. Both CRISPR-based fluorescent assays we developed showed similar sensitivity and accuracy for viral detection and load quantification to real-time PCR. Additionally, both assays specifically targeted their respective virus with no false positives detected in animals infected with other common pathogens or in certified specific pathogen-free animals. IMPORTANCE The Pacific white shrimp (Penaeus vannamei) is one of the most valuable aquaculture species in the world but has suffered major economic losses from outbreaks of White Spot Syndrome Virus and Taura Syndrome Virus. Rapid detection of these viruses can improve aquaculture practices by enabling more timely action to be taken to combat disease outbreaks. Highly sensitive, specific, and robust CRISPR-based diagnostic assays such as those developed here have the potential to revolutionize disease management in agriculture and aquaculture helping to promote global food security.

Rapid Detection of DNA and RNA Shrimp Viruses Using CRISPR-Based Diagnostics

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