Acute multi-level response to defective de novo chromatin assembly in S-phase.

Long-term perturbation of de novo chromatin assembly during DNA replication has profound effects on epigenome maintenance and cell fate. The early mechanistic origin of these defects is unknown. Here, we combine acute degradation of Chromatin Assembly Factor 1 (CAF-1), a key player in de novo chromatin assembly, with single-cell genomics, quantitative proteomics, and live-microscopy to uncover these initiating mechanisms in human cells. CAF-1 loss immediately slows down DNA replication speed and renders nascent DNA hyperaccessible. A rapid cellular response, distinct from canonical DNA damage signaling, is triggered and lowers histone mRNAs. As a result, histone variants usage and their modifications are altered, limiting transcriptional fidelity and delaying chromatin maturation within a single S-phase. This multi-level response induces a cell-cycle arrest after mitosis. Our work reveals the immediate consequences of defective de novo chromatin assembly during DNA replication, explaining how at later times the epigenome and cell fate can be altered.

Genotype-environment associations reveal genes potentially linked to avian malaria infection in populations of an endemic island bird.

Patterns of pathogen prevalence are, at least partially, the result of coevolutionary host-pathogen interactions. Thus, exploring the distribution of host genetic variation in relation to infection by a pathogen within and across populations can provide important insights into mechanisms of host defence and adaptation. Here, we use a landscape genomics approach (Bayenv) in conjunction with genome-wide data (ddRADseq) to test for associations between avian malaria (Plasmodium) prevalence and host genetic variation across 13 populations of the island endemic Berthelot's pipit (Anthus berthelotii). Considerable and consistent spatial heterogeneity in malaria prevalence was observed among populations over a period of 15 years. The prevalence of malaria infection was also strongly positively correlated with pox (Avipoxvirus) prevalence. Multiple host loci showed significant associations with malaria prevalence after controlling for genome-wide neutral genetic structure. These sites were located near to or within genes linked to metabolism, stress response, transcriptional regulation, complement activity and the inflammatory response, many previously implicated in vertebrate responses to malarial infection. Our findings identify diverse genes - not just limited to the immune system - that may be involved in host protection against malaria and suggest that spatially variable pathogen pressure may be an important evolutionary driver of genetic divergence among wild animal populations, such as Berthelot's pipit. Furthermore, our data indicate that spatio-temporal variation in multiple different pathogens (e.g. malaria and pox in this case) may have to be studied together to develop a more holistic understanding of host pathogen-mediated evolution.

Multiple cancers escape from multiple MAPK pathway inhibitors and use DNA replication stress signaling to tolerate aberrant cell cycles.

Many cancers harbor pro-proliferative mutations of the mitogen-activated protein kinase (MAPK) pathway. In BRAF-driven melanoma cells treated with BRAF inhibitors, subpopulations of cells escape drug-induced quiescence through a nongenetic manner of adaptation and resume slow proliferation. Here, we found that this phenomenon is common to many cancer types driven by EGFR, KRAS, or BRAF mutations in response to multiple, clinically approved MAPK pathway inhibitors. In 2D cultures and 3D spheroid models of various cancer cell lines, a subset of cells escaped drug-induced quiescence within 4 days to resume proliferation. These "escapee" cells exhibited DNA replication deficits, accumulated DNA lesions, and mounted a stress response that depended on the ataxia telangiectasia and RAD3-related (ATR) kinase. We further identified that components of the Fanconi anemia (FA) DNA repair pathway are recruited to sites of mitotic DNA synthesis (MiDAS) in escapee cells, enabling successful completion of cell division. Analysis of patient tumor samples and clinical data correlated disease progression with an increase in DNA replication stress response factors. Our findings suggest that many MAPK pathway-mutant cancers rapidly escape drug action and that suppressing early stress tolerance pathways may achieve more durable clinical responses to MAPK pathway inhibitors.

Cyclin E/CDK2 and feedback from soluble histone protein regulate the S phase burst of histone biosynthesis.

Faithful DNA replication requires that cells fine-tune their histone pool in coordination with cell-cycle progression. Replication-dependent histone biosynthesis is initiated at a low level upon cell-cycle commitment, followed by a burst at the G1/S transition, but it remains unclear how exactly the cell regulates this burst in histone biosynthesis as DNA replication begins. Here, we use single-cell time-lapse imaging to elucidate the mechanisms by which cells modulate histone production during different phases of the cell cycle. We find that CDK2-mediated phosphorylation of NPAT at the restriction point triggers histone transcription, which results in a burst of histone mRNA precisely at the G1/S phase boundary. Excess soluble histone protein further modulates histone abundance by promoting the degradation of histone mRNA for the duration of S phase. Thus, cells regulate their histone production in strict coordination with cell-cycle progression by two distinct mechanisms acting in concert.

Youth advancing anti-racism in the 2020s.

In this review, we highlight articles on youth anti-racist action undertaken alongside the COVID-19 pandemic. Three contexts for youth anti-racism development are reviewed: educational settings, out-of-school programs, and youth-led participatory action research. The burden and costs of these undertakings are substantial for youth (particularly racially and ethnically marginalized youth), and pandemic-related stressors have exacerbated the costs and toll of this work. Accordingly, the current review centers opportunities to better scaffold and support youth-led anti-racist action with a focus on systemic and programmatic supports including engaging youth in research as a vehicle for racial justice. We conclude with a call to action for adult activists, scholars, and allies committed to partnering with youth to envision and create a more equitable and just future as we collectively emerge from a global pandemic.

Grape Heterogeneity Index: Assessment of Overall Grape Heterogeneity Using an Aggregation of Multiple Indicators.

Uniform grape maturity can be sought by producers to minimise underripe and/or overripe proportions of fruit and limit any undesirable effects on wine quality. Considering that grape heterogeneity is a multifaceted phenomenon, a composite index summarising overall grape heterogeneity was developed to benefit vineyard management and harvest date decisions. A grape heterogeneity index (GHI) was constructed by aggregating the sum of absolute residuals multiplied by the range of values from measurements of total soluble solids, pH, fresh weight, total tannins, absorbance at 520 nm (red colour), 3-isobutyl-2-methoxypyrazine, and malic acid. Management of grape heterogeneity was also studied, using Cabernet Sauvignon grapes grown under four viticultural regimes (normal/low crop load, full/deficit irrigation) during the 2019/2020 and 2020/2021 seasons. Comparisons of GHI scores showed grape variability decreased throughout ripening in both vintages, then significantly increased at the harvest time point in 2020, but plateaued on sample dates nearing the harvest date in 2021. Irrigation and crop load had no effect on grape heterogeneity by the time of harvest in both vintages. Larger vine yield, leaf area index, and pruning weight significantly increased GHI score early in ripening, but no significant relationship was found at the time of harvest. Differences in the Ravaz index, normalised difference vegetation index, and soil electrical conductivity did not significantly change the GHI score.

Cyclin E/CDK2 and feedback from soluble histone protein regulate the S phase burst of histone biosynthesis.

Faithful DNA replication requires that cells fine-tune their histone pool in coordination with cell-cycle progression. Replication-dependent histone biosynthesis is initiated at a low level upon cell-cycle commitment, followed by a burst at the G1/S transition, but it remains unclear how exactly the cell regulates this change in histone biosynthesis as DNA replication begins. Here, we use single-cell timelapse imaging to elucidate the mechanisms by which cells modulate histone production during different phases of the cell cycle. We find that CDK2-mediated phosphorylation of NPAT at the Restriction Point triggers histone transcription, which results in a burst of histone mRNA precisely at the G1/S phase boundary. Excess soluble histone protein further modulates histone abundance by promoting the degradation of histone mRNA for the duration of S phase. Thus, cells regulate their histone production in strict coordination with cell-cycle progression by two distinct mechanisms acting in concert.

Use of Machine Learning with Fused Spectral Data for Prediction of Product Sensory Characteristics: The Case of Grape to Wine.

Generations of sensors have been developed for predicting food sensory profiles to circumvent the use of a human sensory panel, but a technology that can rapidly predict a suite of sensory attributes from one spectral measurement remains unavailable. Using spectra from grape extracts, this novel study aimed to address this challenge by exploring the use of a machine learning algorithm, extreme gradient boosting (XGBoost), to predict twenty-two wine sensory attribute scores from five sensory stimuli: aroma, colour, taste, flavour, and mouthfeel. Two datasets were obtained from absorbance-transmission and fluorescence excitation-emission matrix (A-TEEM) spectroscopy with different fusion methods: variable-level data fusion of absorbance and fluorescence spectral fingerprints, and feature-level data fusion of A-TEEM and CIELAB datasets. The results for externally validated models showed slightly better performance using only A-TEEM data, predicting five out of twenty-two wine sensory attributes with R2 values above 0.7 and fifteen with R2 values above 0.5. Considering the complex biotransformation involved in processing grapes to wine, the ability to predict sensory properties based on underlying chemical composition in this way suggests that the approach could be more broadly applicable to the agri-food sector and other transformed foodstuffs to predict a product's sensory characteristics from raw material spectral attributes.

Machine learning for classifying and predicting grape maturity indices using absorbance and fluorescence spectra.

Absorbance-transmission and fluorescence excitation-emission matrix (A-TEEM) spectroscopy was investigated as a rapid method for predicting maturity indices using Cabernet Sauvignon grapes produced under four viticulture treatments during two growing seasons. Machine learning models were developed with fused spectral data to predict 3-isobutyl-2-methoxypyrazine (IBMP), pH, total tannins (Tannin), total soluble solids (TSS), and malic and tartaric acids based on the results from traditional analysis methods. Extreme gradient boosting (XGB) regression yielded R2 values of 0.92-0.96 for IBMP, malic acid, pH, and TSS for externally validated (Test) models, with partial least squares regression being superior for TSS prediction (R2 = 0.97). R2 values of 0.64-0.81 were achieved with either approach for tartaric acid and Tannin predictions. Classification of grape maturity, defined by quantile ranges for red colour, IBMP, malic acid, and TSS, was investigated using XGB discriminant analysis, providing an average of 78 % correctly classified samples for the Test model.

Genomic associations with poxvirus across divergent island populations in Berthelot's pipit.

Understanding the mechanisms and genes that enable animal populations to adapt to pathogens is important from an evolutionary, health and conservation perspective. Berthelot's pipit (Anthus berthelotii) experiences extensive and consistent spatial heterogeneity in avian pox infection pressure across its range of island populations, thus providing an excellent system with which to examine how pathogen-mediated selection drives spatial variation in immunogenetic diversity. Here, we test for evidence of genetic variation associated with avian pox at both an individual and population-level. At the individual level, we find no evidence that variation in MHC class I and TLR4 (both known to be important in recognising viral infection) was associated with pox infection within two separate populations. However, using genotype-environment association (Bayenv) in conjunction with genome-wide (ddRAD-seq) data, we detected strong associations between population-level avian pox prevalence and allele frequencies of single nucleotide polymorphisms (SNPs) at a number of sites across the genome. These sites were located within genes involved in cellular stress signalling and immune responses, many of which have previously been associated with responses to viral infection in humans and other animals. Consequently, our analyses indicate that pathogen-mediated selection may play a role in shaping genomic variation among relatively recently colonised island bird populations and highlight the utility of genotype-environment associations for identifying candidate genes potentially involved in host-pathogen interactions.

Engineered Chimeras Unveil Swappable Modular Features of Fatty Acid and Polyketide Synthase Acyl Carrier Proteins.

The strategic redesign of microbial biosynthetic pathways is a compelling route to access molecules of diverse structure and function in a potentially environmentally sustainable fashion. The promise of this approach hinges on an improved understanding of acyl carrier proteins (ACPs), which serve as central hubs in biosynthetic pathways. These small, flexible proteins mediate the transport of molecular building blocks and intermediates to enzymatic partners that extend and tailor the growing natural products. Past combinatorial biosynthesis efforts have failed due to incompatible ACP-enzyme pairings. Herein, we report the design of chimeric ACPs with features of the actinorhodin polyketide synthase ACP (ACT) and of the Escherichia coli fatty acid synthase (FAS) ACP (AcpP). We evaluate the ability of the chimeric ACPs to interact with the E. coli FAS ketosynthase FabF, which represents an interaction essential to building the carbon backbone of the synthase molecular output. Given that AcpP interacts with FabF but ACT does not, we sought to exchange modular features of ACT with AcpP to confer functionality with FabF. The interactions of chimeric ACPs with FabF were interrogated using sedimentation velocity experiments, surface plasmon resonance analyses, mechanism-based cross-linking assays, and molecular dynamics simulations. Results suggest that the residues guiding AcpP-FabF compatibility and ACT-FabF incompatibility may reside in the loop I, α-helix II region. These findings can inform the development of strategic secondary element swaps that expand the enzyme compatibility of ACPs across systems and therefore represent a critical step toward the strategic engineering of "un-natural" natural products.

Tuning the band gap and carrier concentration of titania films grown by spatial atomic layer deposition: a precursor comparison.

Spatial atomic layer deposition retains the advantages of conventional atomic layer deposition: conformal, pinhole-free films and excellent control over thickness. Additionally, it allows higher deposition rates and is well-adapted to depositing metal oxide nanofilms for photovoltaic cells and other devices. This study compares the morphological, electrical and optical properties of titania thin films deposited by spatial atomic layer deposition from titanium isopropoxide (TTIP) and titanium tetrachloride (TiCl4) over the temperature range 100-300 °C, using the oxidant H2O. Amorphous films were deposited at temperatures as low as 100 °C from both precursors: the approach is suitable for applying films to temperature-sensitive devices. An amorphous-to-crystalline transition temperature was observed for both precursors resulting in surface roughening, and agglomerates for TiCl4. Both precursors formed conformal anatase films at 300 °C, with growth rates of 0.233 and 0.153 nm s-1 for TiCl4 and TTIP. A drawback of TiCl4 use is the HCl by-product, which was blamed for agglomeration in the films. Cl contamination was the likely cause of band gap narrowing and higher defect densities compared to TTIP-grown films. The carrier concentration of the nanofilms was found to increase with deposition temperature. The films were tested in hybrid bilayer solar cells to demonstrate their appropriateness for photovoltaic devices.

Replication-dependent histone biosynthesis is coupled to cell-cycle commitment.

The current model of replication-dependent (RD) histone biosynthesis posits that RD histone gene expression is coupled to DNA replication, occurring only in S phase of the cell cycle once DNA synthesis has begun. However, several key factors in the RD histone biosynthesis pathway are up-regulated by E2F or phosphorylated by CDK2, suggesting these processes may instead begin much earlier, at the point of cell-cycle commitment. In this study, we use both fixed- and live-cell imaging of human cells to address this question, revealing a hybrid model in which RD histone biosynthesis is first initiated in G1, followed by a strong increase in histone production in S phase of the cell cycle. This suggests a mechanism by which cells that have committed to the cell cycle build up an initial small pool of RD histones to be available for the start of DNA replication, before producing most of the necessary histones required in S phase. Thus, a clear distinction exists at completion of mitosis between cells that are born with the intention of proceeding through the cell cycle and replicating their DNA and cells that have chosen to exit the cell cycle and have no immediate need for histone synthesis.

Genomic variation, population history and within-archipelago adaptation between island bird populations.

Oceanic island archipelagos provide excellent models to understand evolutionary processes. Colonization events and gene flow can interact with selection to shape genetic variation at different spatial scales. Landscape-scale variation in biotic and abiotic factors may drive fine-scale selection within islands, while long-term evolutionary processes may drive divergence between distantly related populations. Here, we examine patterns of population history and selection between recently diverged populations of the Berthelot's pipit (Anthus berthelotii), a passerine endemic to three North Atlantic archipelagos. First, we use demographic trees and f3 statistics to show that genome-wide divergence across the species range is largely shaped by colonization and bottlenecks, with evidence of very weak gene flow between populations. Then, using a genome scan approach, we identify signatures of divergent selection within archipelagos at single nucleotide polymorphisms (SNPs) in genes potentially associated with craniofacial development and DNA repair. We did not detect within-archipelago selection at the same SNPs as were detected previously at broader spatial scales between archipelagos, but did identify signatures of selection at loci associated with similar biological functions. These findings suggest that similar ecological factors may repeatedly drive selection between recently separated populations, as well as at broad spatial scales across varied landscapes.

Valuing high-seas ecosystem conservation.

The high seas provide a variety of ecosystem services that benefit society. There have, however, been few attempts to quantify the human welfare impacts of changes to the delivery of these benefits. We assessed the values of several key ecosystem service benefits derived from protecting ecosystems in the high seas of the Flemish Cap through choice experiments conducted in Canada, Norway, and Scotland. Rather than solely eliciting public willingness to pay, we also explored the determinants of variance in the estimates of willingness to pay. We aimed to determine how much respondents were willing to pay for high-seas ecosystems conservation, which factors influence individuals' willingness to pay, and whether individuals in Canada had a higher willingness to pay relative to those living in Norway and Scotland. This latter point captures distance-decay effects. On average, the public placed positive value on conserving high-seas ecosystems and on developing economic activities related to the exploitation and exploration of marine resources, despite a lack of awareness and familiarity with these environments. Distance-decay effects on willingness to pay were not clear. Scots had the highest willingness to pay and the Norwegians the lowest willingness to pay for all attributes, with the only exception being willingness to pay for a large increase in new jobs, in which case Canadians' willingness to pay was higher than Scots'. The public's willingness to pay was influenced by sociodemographic characteristics and their perceptions of high-seas ecosystems. Our results provide evidence of the impacts of high-seas governance on human welfare and that improved governance could increase the value people place on high-seas ecosystems and the services they produce.

La alta mar proporciona una variedad de servicios ambientales que benefician a la sociedad. Sin embargo, ha habido pocos intentos por cuantificar los impactos al bienestar humano ocasionados por los cambios en la entrega de estos beneficios. Analizamos los valores de varios beneficios importantes de los servicios ambientales derivados de la protección al ecosistema en la alta mar del Cabo Flamenco por medio de experimentos de elección realizados en Canadá, Noruega y Escocia. En lugar de sólo suscitar la voluntad pública para pagar, también exploramos las determinantes de la varianza en las estimaciones de la voluntad para pagar. Nuestro objetivo fue determinar cuánto están dispuestos a pagar los respondientes por la conservación de los ecosistemas de alta mar, cuáles factores influyen sobre la voluntad para pagar de cada individuo y si los individuos en Canadá tenían una mayor voluntad para pagar que aquellos individuos que viven en Noruega y en Escocia. Este último punto captura los efectos de la descomposición por distancia. En promedio, el público le colocó un valor positivo a la conservación de los ecosistemas de alta mar y al desarrollo de actividades económicas relacionadas con la explotación y la exploración de los recursos marinos, a pesar de la falta de conocimiento y familiaridad con estos ambientes. Los efectos de la descomposición por distancia sobre la voluntad para pagar no estuvieron claros. Los escoceses tuvieron la mayor voluntad para pagar y los noruegos la menor voluntad para pagar por todos los atributos, siendo la única excepción la voluntad para pagar por un incremento de trabajos nuevos, en cuyo caso, la voluntad de los canadienses fue más alta que la de los escoceses. La voluntad del público para pagar estuvo influenciada por las características sociodemográficas y su percepción de los ecosistemas de alta mar. Nuestros resultados proporcionan una evidencia de los impactos que tiene la gestión de alta mar sobre el bienestar humano y que la gestión mejorada podría incrementar el valor que las personas le ponen a los ecosistemas de alta mar y a los servicios que producen.

Have environmental preferences and willingness to pay remained stable before and during the global Covid-19 shock?

This study tests the stability of environmental preferences and willingness to pay (WTP) values using a discrete choice experiment (DCE) across three countries pre and post the peak of the first wave of the Covid-19 pandemic. A DCE examining the public's preferences for alternative environmental management plans on the high seas, in the area of the Flemish Cap, was carried out in Canada, Scotland and Norway in late 2019 and was rerun in early May 2020 shortly after the Covid-19 pandemic had officially peaked in the three countries. The same choice set sequence is tested across the two periods, using different but nationally representative samples in each case. Entropy balancing, a multivariate reweighting method, is used to achieve covariate balance between the pre and post Covid samples in the analysis. The results suggest that both preferences and WTP remain relatively stable in the face of a major public health crisis and economic upheaval.

Genetic diversity and shedding profiles for Cryptosporidium parvum in adult cattle and their calves.

Cryptosporidiosis is an important disease in neonatal calves, causing watery diarrhoea, loss of appetite, and production losses. Dehydration from diarrhoea often results in the calf requiring rehydration or veterinary treatment to prevent calf mortality. Transmission of Cryptosporidium to calves still has some major knowledge gaps, such as the initial source of oocysts ingested by calves and how these oocysts can persist between calving periods. Some studies have examined the role of adult cattle in the transmission of Cryptosporidium oocysts, although these have yielded inconclusive results. In this study, highly sensitive oocyst extraction from faeces and detection techniques, sensitive to 5 oocysts per gram using a 50 g sample, were used to genotype faecal samples from adult cattle and their calves to determine if adult cattle could be a source of Cryptosporidium infection for their calves. On a dairy farm, faecal samples from adult cattle were collected twice per week for 0-3 weeks before calving and from their calves three times per week until they reached 3 weeks of age followed by twice per week until they reached 6 weeks of age. On a beef farm, samples were collected from both adults and calves at a single time point. Faecal samples were examined to compare species and multilocus genotypes of Cryptosporidium parvum. Results show that C. parvum was the most prevalent species on both the dairy and beef farms. The calves within each herd appear to have one predominant single multilocus genotype, whereas adult cattle have multiple distinct genotypes. Adult cattle on the dairy farm, tested before calving, in the majority of cases had a multilocus genotype that is different from that detected in their calves. On the beef farm, where samples were taken at the same time, the majority of adult cattle matched the multilocus genotype of their calves. This study shows that adult cattle display a higher diversity of C. parvum genotypes on both farms compared to the calves. The data also represent a detailed longitudinal prevalence study of the shedding profiles and genotype of Cryptosporidium parasites detected in dairy calves from birth to 6 weeks of age.

Attuning to a changing ocean.

The ocean is a lifeline for human existence, but current practices risk severely undermining ocean sustainability. Present and future social-ecological challenges necessitate the maintenance and development of knowledge and action by stimulating collaboration among scientists and between science, policy, and practice. Here we explore not only how such collaborations have developed in the Nordic countries and adjacent seas but also how knowledge from these regions contributes to an understanding of how to obtain a sustainable ocean. Our collective experience may be summarized in three points: 1) In the absence of long-term observations, decision-making is subject to high risk arising from natural variability; 2) in the absence of established scientific organizations, advice to stakeholders often relies on a few advisors, making them prone to biased perceptions; and 3) in the absence of trust between policy makers and the science community, attuning to a changing ocean will be subject to arbitrary decision-making with unforeseen and negative ramifications. Underpinning these observations, we show that collaboration across scientific disciplines and stakeholders and between nations is a necessary condition for appropriate actions.

Adaptive landscape genetics and malaria across divergent island bird populations.

Environmental conditions play a major role in shaping the spatial distributions of pathogens, which in turn can drive local adaptation and divergence in host genetic diversity. Haemosporidians, such as Plasmodium (malaria), are a strong selective force, impacting survival and fitness of hosts, with geographic distributions largely determined by habitat suitability for their insect vectors. Here, we have tested whether patterns of fine-scale local adaptation to malaria are replicated across discrete, ecologically differing island populations of Berthelot's pipits Anthus berthelotii. We sequenced TLR4, an innate immunity gene that is potentially under positive selection in Berthelot's pipits, and two SNPs previously identified as being associated with malaria infection in a genome-wide association study (GWAS) in Berthelot's pipits in the Canary Islands. We determined the environmental predictors of malaria infection, using these to estimate variation in malaria risk on Porto Santo, and found some congruence with previously identified environmental risk factors on Tenerife. We also found a negative association between malaria infection and a TLR4 variant in Tenerife. In contrast, one of the GWAS SNPs showed an association with malaria risk in Porto Santo, but in the opposite direction to that found in the Canary Islands GWAS. Together, these findings suggest that disease-driven local adaptation may be an important factor in shaping variation among island populations.