bluuebunny/crossref_metadata_2025 huggingface dataset:
A heteroskedastic model of Park Grass spring hay yields in response to weather suggests continuing yield decline with climate change in future decades
Authors: Addy John W. G. , Ellis Richard H. , MacLaren Chloe , Macdonald Andy J. , Semenov Mikhail A. , Mead Andrew
Published: August 2022

UK grasslands perform important environmental and economic functions, but their future productivity under climate change is uncertain. Spring hay yields from 1902 to 2016 at one site (the Park Grass Long Term Experiment) in southern England under four different fertilizer regimes were modelled in response to weather (seasonal temperature and rainfall). The modelling approach applied comprised: (1) a Bayesian model comparison to model parametrically the heteroskedasticity in a gamma likelihood function; (2) a Bayesian varying intercept multiple regression model with an autoregressive lag one process (to incorporate the effect of productivity in the previous year) of the response of hay yield to weather from 1902 to 2016. The model confirmed that warmer and drier years, specifically, autumn, winter and spring, in the twentieth and twenty-first centuries reduced yield. The model was applied to forecast future spring hay yields at Park Grass under different climate change scenarios (HadGEM2 and GISS RCP 4.5 and 8.5). This application indicated that yields are forecast to decline further between 2020 and 2080, by as much as 48–50%. These projections are specific to Park Grass, but implied a severe reduction in grassland productivity in southern England with climate change during the twenty-first century.
Distinct decision-making properties underlying the species specificity of group formation of flies
Authors: Shirasaki Riku , Tanaka Ryoya , Takekata Hiroki , Shimada Takashi , Ishikawa Yuki , Kamikouchi Azusa
Published: August 2022

Many animal species form groups. Group characteristics differ between species, suggesting that the decision-making of individuals for grouping varies across species. However, the actual decision-making properties that lead to interspecific differences in group characteristics remain unclear. Here, we compared the group formation processes of two Drosophilinae fly species,
Colocasiomyia alocasiae
and
Drosophila melanogaster
, which form dense and sparse groups, respectively. A high-throughput tracking system revealed that
C. alocasiae
flies formed groups faster than
D. melanogaster
flies, and the probability of
C. alocasiae
remaining in groups was far higher than that of
D. melanogaster
.
C. alocasiae
flies joined groups even when the group size was small, whereas
D. melanogaster
flies joined groups only when the group size was sufficiently large.
C. alocasiae
flies attenuated their walking speed when the inter-individual distance between flies became small, whereas such behavioural properties were not clearly observed in
D. melanogaster
. Furthermore, depriving
C. alocasiae
flies of visual input affected grouping behaviours, resulting in a severe reduction in group formation. These findings show that
C. alocasiae
decision-making regarding grouping, which greatly depends on vision, is significantly different from
D. melanogaster
, leading to species-specific group formation properties.
Exploiting node metadata to predict interactions in bipartite networks using graph embedding and neural networks
Authors: Runghen Rogini , Stouffer Daniel B. , Dalla Riva Giulio V.
Published: August 2022

Networks are increasingly used in various fields to represent systems with the aim of understanding the underlying rules governing observed interactions, and hence predict how the system is likely to behave in the future. Recent developments in network science highlight that accounting for node metadata improves both our understanding of how nodes interact with one another, and the accuracy of link prediction. However, to predict interactions in a network within existing statistical and machine learning frameworks, we need to learn objects that rapidly grow in dimension with the number of nodes. Thus, the task becomes computationally and conceptually challenging for networks. Here, we present a new predictive procedure combining a statistical, low-rank graph embedding method with machine learning techniques which reduces substantially the complexity of the learning task and allows us to efficiently predict interactions from node metadata in bipartite networks. To illustrate its application on real-world data, we apply it to a large dataset of tourist visits across a country. We found that our procedure accurately reconstructs existing interactions and predicts new interactions in the network. Overall, both from a network science and data science perspective, our work offers a flexible and generalizable procedure for link prediction.
A model of spatio-temporal regulation within biomaterials using DNA reaction–diffusion waveguides
Authors: Dorsey Phillip J. , Scalise Dominic , Schulman Rebecca
Published: August 2022

In multi-cellular organisms, cells and tissues coordinate biochemical signal propagation across length scales spanning micrometres to metres. Designing synthetic materials with similar capacities for coordinated signal propagation could allow these systems to adaptively regulate themselves across space and over time. Here, we combine ideas from cell signalling and electronic circuitry to propose a biochemical waveguide that transmits information in the form of a concentration of a DNA species on a directed path. The waveguide could be seamlessly integrated into a soft material because there is virtually no difference between the chemical or physical properties of the waveguide and the material it is embedded within. We propose the design of DNA strand displacement reactions to construct the system and, using reaction–diffusion models, identify kinetic and diffusive parameters that enable super-diffusive transport of DNA species via autocatalysis. Finally, to support experimental waveguide implementation, we propose a sink reaction and spatially inhomogeneous DNA concentrations that could mitigate the spurious amplification of an autocatalyst within the waveguide, allowing for controlled waveguide triggering. Chemical waveguides could facilitate the design of synthetic biomaterials with distributed sensing machinery integrated throughout their structure and enable coordinated self-regulating programmes triggered by changing environmental conditions.
A mammalian messenger RNA sex determination method from humpback whale (
Megaptera novaeangliae
) blubber biopsies
Authors: Linsky Jacob M. J. , Dunlop Rebecca A. , Noad Michael J. , McMichael Lee A.
Published: August 2022

The large size of free-ranging mysticetes, such as humpback whales (
Megaptera novaeangliae
), make capture and release health assessments unfeasible for conservation research. However, individual energetic condition or reproductive health may be assessed from the gene expression of remotely biopsied tissue. To do this, researchers must reliably extract RNA and interpret gene expression measurements within the context of an individual's sex. Here, we outline an RNA extraction protocol from blubber tissue and describe a novel mammalian RNA sex determination method. Our method consists of a duplex reverse transcription-quantitative (real-time) polymerase chain reaction (RT-qPCR) with primer sets for a control gene (
ACTB
) and the X-chromosome inactivation gene (
XIST
). Products of each RT-qPCR had distinct melting temperature profiles based on the presence (female) or absence (male) of the
XIST
transcript. Using high-resolution melt analysis, reactions were sorted into one of two clusters (male/female) based on their melting profiles. We validated the
XIST
method by comparing results with a standard DNA-based method. With adequate quantities of RNA (minimum of approx. 9 ng µl
−1
), the
XIST
sex determination method shows 100% agreement with traditional DNA sex determination. Using the
XIST
method, future cetacean health studies can interpret gene expression within the context of an individual's sex, all from a single extraction.
Modelling the anomalous shock response of titanium diboride
Authors: Clayton J. D. , Williams C. L.
Published: August 2022

In planar shock compression experiments, polycrystalline titanium diboride (TiB2) often exhibits double-yield phenomena, atypical among non-transforming ceramics, in particle velocity histories. A finite-strain phase-field theory, with order parameters accounting for fracture and dilatation, followed by limited plastic slip and compaction, is specialized to study the uniaxial shock response ofTiB2. The model accurately depicts longitudinal stress up to 120 GPa on the Hugoniot from multiple published sources, as well as shear stress inferred elsewhere from experimental shock data. A novel phase-field analysis enables one-, two- or three-wave structures depending on impact stress. These results are observed in experimental data and have not been successfully captured by prior numerical models. Results support the conjecture that (i) fracture and dilatation, followed by (ii) plastic deformation and compaction, and then (iii) fragmentation to a comminuted, viscous granular medium is a plausible sequence of physical mechanisms as shock stress increases. The first break in the velocity profile always corresponds to micro-cracking in the model, which correlates with the first yield point on the Hugoniot. In the three-wave regime, two plastic waves correlate with two yield points, where the first plastic wave after the precursor is due to fracture and the second dominated by plasticity. When impact is severe enough such that the second plastic wave overtakes the first, a single plastic waveform with multiple kinks emerges in particle velocity histories, consistent with some experimental data. These kinks are well explained by pressure-dependent viscosity in crack kinetics and by small-magnitude plastic deformation, and corresponding stress perturbations need not precisely correspond to particular cusps on the stress–volume Hugoniot.
Divergence in brain size and brain region volumes across wild guppy populations
Authors: Reyes Angie S. , Bittar Amaury , Ávila Laura C. , Botia Catalina , Esmeral Natalia P. , Bloch Natasha I.
Published: August 2022

Complex evolutionary dynamics have produced extensive variation in brain anatomy in the animal world. In guppies,
Poecilia reticulata
, brain size and anatomy have been extensively studied in the laboratory contributing to our understanding of brain evolution and the cognitive advantages that arise with brain anatomical variation. However, it is unclear whether these laboratory results can be translated to natural populations. Here, we study brain neuroanatomy and its relationship with sexual traits across 18 wild guppy populations in diverse environments. We found extensive variation in female and male relative brain size and brain region volumes across populations in different environment types and with varying degrees of predation risk. In contrast with laboratory studies, we found differences in allometric scaling of brain regions, leading to variation in brain region proportions across populations. Finally, we found an association between sexual traits, mainly the area of black patches and tail length, and brain size. Our results suggest differences in ecological conditions and sexual traits are associated with differences in brain size and brain regions volumes in the wild, as well as sexual dimorphisms in the brain's neuroanatomy.
Warming in the land of the midnight sun: breeding birds may suffer greater heat stress at high- versus low-Arctic sites
Authors: O'Connor Ryan S. , Le Pogam Audrey , Young Kevin G. , Love Oliver P. , Cox Christopher J. , Roy Gabrielle , Robitaille Francis , Elliott Kyle H. , Hargreaves Anna L. , Choy Emily S. , Gilchrist H. Grant , Berteaux Dominique , Tam Andrew , Vézina François
Published: August 2022

Rising global temperatures are expected to increase reproductive costs for wildlife as greater thermoregulatory demands interfere with reproductive activities. However, predicting the temperatures at which reproductive performance is negatively impacted remains a significant hurdle. Using a thermoregulatory polygon approach, we derived a reproductive threshold temperature for an Arctic songbird—the snow bunting (Plectrophenax nivalis). We defined this threshold as the temperature at which individuals must reduce activity to suboptimal levels (i.e. less than four-time basal metabolic rate) to sustain nestling provisioning and avoid overheating. We then compared this threshold to operative temperatures recorded at high (82° N) and low (64° N) Arctic sites to estimate how heat constraints translate into site-specific impacts on sustained activity level. We predict buntings would become behaviourally constrained at operative temperatures above 11.7°C, whereupon they must reduce provisioning rates to avoid overheating. Low-Arctic sites had larger fluctuations in solar radiation, consistently producing daily periods when operative temperatures exceeded 11.7°C. However, high-latitude birds faced entire, consecutive days when parents would be unable to sustain required provisioning rates. These data indicate that Arctic warming is probably already disrupting the breeding performance of cold-specialist birds and suggests counterintuitive and severe negative impacts of warming at higher latitude breeding locations.
Clinical nomogram using novel CT based radiomics predicts survival in non-small cell lung cancer patients treated with SBRT
Authors: Somasundaram Eashwar , Wadhwa Raoul R. , Litzler Adam , Barker-Clarke Rowan , Qi Peng , Videtic Gregory , Stephans Kevin , Pennell Nathan A. , Raymond Daniel , Yang Kailin , Kattan Michael W. , Scott Jacob G.
Published: August 2022

Introduction

Improved survival prediction and risk stratification in non-small cell lung cancer (NSCLC) would lead to better prognosis counseling, adjuvant therapy selection, and clinical trial design. We propose the PHOM (persistent homology) score, the radiomic quantification of solid tumor topology, as a solution.

Methods

Patients diagnosed with stage I or II NSCLC primarily treated with stereotactic body radiation therapy (SBRT) were selected (n= 554). The PHOM score was calculated on each patient’s pre-treatment CT scan (10/2008 to 11/2019). PHOM score, age, sex, stage, Karnofsky Performance Status (KPS), Charlson-Comorbidity Index (CCI), and post-SBRT chemotherapy were predictors in the Cox proportional hazards models for overall and cancer-specific survival. Patients were split into high and low PHOM score groups compared using Kaplan-Meier curves for overall survival and cumulative incidence curves for cause specific death. Finally, we generated a validated nomogram to predict overall survival, publicly available athttps://eashwarsoma.shinyapps.io/LungCancerTDATest/.

Results

PHOM score was a significant predictor for overall survival (HR: 1.17, 95% CI: 1.07−1.28) and was the only significant predictor for cancer-specific survival (1.31, 95% CI: 1.11−1.56) in the multivariable Cox model. The median survival for the high PHOM group was 29.2 months (95% CI: 23.6−34.3), which was significantly worse compared to the low PHOM group (45.4 months, 95% CI: 40.1−51.8,p <0.001). The high PHOM group had a significantly greater chance of cancer-specific death at post treatment month 65 (0.244, 95%CI: 0.192−0.296) compared to the low PHOM group (0.171, 95% CI: 0.123−0.218,p= 0.029).

Conclusions

The PHOM score is associated with cancer-specific survival and predictive of overall survival. Our developed nomogram can be used to inform clinical prognosis and assist in making post-SBRT treatment considerations.
A bioluminescence-basedex vivoburn wound model for real-time assessment of novel antibacterial compounds
Authors: De Maesschalck V. , Gutiérrez D. , Paeshuyse J. , Briers Y. , Vande Velde G. , Lavigne R.
Published: August 2022

The silent pandemic of antibiotic resistance is thriving, prompting the urgent need for the development of new antibacterial drugs. However, within the preclinical pipeline,in vitroscreening conditions can differ significantly from the finalin vivosettings. To bridge the gap betweenin vitroandin vivoassays, we developed a pig skin-based bioluminescentex vivoburn wound infection model, enabling real-time assessment of antibacterials in a longitudinal, non-destructive manner. We provide a proof-of-concept forA. baumanniiNCTC13423, a multidrug-resistant clinical isolate, which was equipped with theluxCDABEoperon as a reporter using a Tn7-based tagging system. This bioluminescence model provided a linear correlation between the number of bacteria and a broad dynamic range (104to 109CFU). This longitudinal model was subsequently validated using a fast-acting enzybiotic as an antibacterial. Since this model combines a realistic, clinically relevant yet strictly controlled environment with real-time measurement of bacterial burden, we put forward thisex vivomodel as a valuable tool to assess the preclinical potential of novel antibacterial compounds.

Summary statement

Here, we demonstrate the potential of a bioluminescence-basedex vivomodel for the longitudinal assessment of antibacterials. Moreover, we also provide a proof-of-concept with an engineered lysin.
A genome-scale metabolic model of Drosophila melanogaster for integrative analysis of brain diseases
Authors: Cesur Müberra Fatma , Patil Kiran Raosaheb , Çakır Tunahan
Published: August 2022

High conservation of the disease-associated genes between fly and human facilitates the common use of Drosophila melanogaster to study metabolic disorders under controlled laboratory conditions. However, metabolic modeling studies are highly limited for this organism. We here report a comprehensively curated genome-scale metabolic network model of Drosophila using an orthology-based approach. The gene coverage and metabolic information of the orthology-based draft model were expanded via Drosophila-specific KEGG and MetaCyc databases, with several curation steps to avoid metabolic redundancy and stoichiometric inconsistency. Further, we performed literature-based curations to improve gene-reaction associations, subcellular metabolite locations, and updated various metabolic pathways including cholesterol metabolism. The performance of the resulting Drosophila model, termed iDrosophila1 (8,230 reactions, 6,990 metabolites, and 2,388 genes), was assessed using flux balance analysis in comparison with the other currently available fly models leading to superior or comparable results. We also evaluated transcriptome-based prediction capacity of the iDrosophila1, where differential metabolic pathways during Parkinson’s disease could be successfully elucidated. Overall, iDrosophila1 is promising to investigate systems-level metabolic alterations in response to genetic and environmental perturbations.
In vivo and In vitro Characterization of the ClpC AAA+ ATPase of Chlamydia trachomatis
Authors: Pan Stefan , Jensen Aaron A. , Wood Nicholas A. , Henrichfreise Beate , Brötz-Oesterhelt Heike , Fisher Derek J. , Sass Peter , Ouellette Scot P.
Published: August 2022

Bacterial AAA+ unfoldases are crucial for bacterial physiology by recognizing specific substrates and, typically, unfolding them for degradation by a proteolytic component. The caseinolytic protease (Clp) system is one example where a hexameric unfoldase (e.g., ClpC) interacts with the tetradecameric proteolytic core ClpP. Unfoldases can have both ClpP-dependent and ClpP-independent roles in protein homeostasis, development, virulence, and cell differentiation. ClpC is an unfoldase predominantly found in Gram-positive bacteria and mycobacteria. Intriguingly, the obligate intracellular Gram-negative pathogen Chlamydia, an organism with a highly reduced genome, also encodes a ClpC ortholog, implying an important function for ClpC in chlamydial physiology. Here, we used a combination of in vitro and in vivo approaches to gain insight into the function of chlamydial ClpC. ClpC exhibits intrinsic ATPase and chaperone activities, with a primary role for the Walker B motif in the first nucleotide binding domain (NBD1). Furthermore, ClpC binds ClpP1P2 complexes via ClpP2 to form the functional protease ClpCP2P1 in vitro, which degraded arginine-phosphorylated β-casein. In vivo experiments confirmed that higher order complexes of ClpC are present in chlamydial cells. Importantly, the in vivo data further revealed severe negative effects of both overexpression and depletion of ClpC in Chlamydia as revealed by a significant reduction in chlamydial growth. Here again, NBD1 was critical for ClpC function. Hence, we provide the first mechanistic insight into the molecular and cellular function of chlamydial ClpC, which supports its essentiality in Chlamydia. ClpC is, therefore, a potential novel target for the development of anti-chlamydial agents.

Significance

Chlamydia trachomatis is an obligate intracellular pathogen and the world’s leading cause of preventable infectious blindness and bacterial sexually transmitted infections. Due to the high prevalence of chlamydial infections along with negative effects of current broad-spectrum treatment strategies, new anti-chlamydial agents with novel targets are desperately needed. In this context, bacterial Clp proteases have emerged as promising new antibiotic targets, since they often play central roles in bacterial physiology and, for some bacterial species, are even essential for survival. Here, we report on the chlamydial AAA+ unfoldase ClpC, its functional reconstitution and characterization, individually and as part of the ClpCP2P1 protease, and establish an essential role for ClpC in chlamydial growth and intracellular development, thereby identifying ClpC as a potential target for anti-chlamydial compounds.
Public health interventions successfully mitigated multiple incursions of SARS-CoV-2 Delta variant in the Australian Capital Territory
Authors: Hall Robyn , Jones Ashley , Crean Emma , Marriott Victoria , Pingault Nevada , Marmor Alexandra , Sloan-Gardner Timothy , Kennedy Karina , Coleman Kerryn , Johnston Vanessa , Schwessinger Benjamin
Published: August 2022

The Australian Capital Territory rapidly responded to an incursion of the SARS-CoV-2 Delta (B.1.617.2) variant on 12 August 2021 with several public health interventions, including a territory-wide lockdown and genomic sequencing. Prior to this date, SARS-CoV-2 had been eliminated locally since July 7, 2020. Sequencing of >75% of cases identified at least 13 independent incursions with onwards spread in the community during the study period, between 12 August and 11 November 2021. Two incursions resulted in the majority of community transmission during this period, with persistent transmission in vulnerable sections of the community. Ultimately, both major incursions were successfully mitigated through public health interventions, including COVID-19 vaccines. In this study we explore the demographic factors that contributed to the spread of these incursions. The high rates of SARS-CoV-2 sequencing in the Australian Capital Territory and the relatively small population size facilitated detailed investigations of the patterns of virus transmission. Genomic sequencing was critical to disentangling complex transmission chains to target interventions appropriately.

Despite a strict lockdown and interstate travel restrictions, the Australian Capital Territory experienced at least 13 incursions of SARS-CoV-2 Delta (B.1.617.2) with onwards spread in the community between 12 August and 11 November 2021.

This level of detail was only accessible because of the high rate of SARS-CoV-2 sequencing, with sequencing attempted on 1438/1793 (80%) of cases.

Transmission chains varied in size and duration, with two dominant incursions (ACT.19 and ACT.20) comprising 35% and 53% of all sequenced cases during the study period, respectively.

The ACT.20 outbreak persisted longer, due to specific challenges with implementing public health interventions in the affected populations.

Both major incursions were successfully curbed through stringent public health measures, including the widespread acceptance of COVID-19 vaccines (>95% of the eligible population by the end of the study period).
TheVibrioType III Secretion System 2 is not restricted to theVibrionaceaeand encodes differentially distributed repertoires of effector proteins
Authors: Jerez SA , Plaza N , Bravo V , Urrutia IM , Blondel CJ
Published: August 2022

Vibrio parahaemolyticusis the leading cause of seafood-borne gastroenteritis worldwide. A distinctive feature of the O3:K6 pandemic clone, and its derivatives, is the presence of a second, phylogenetically distinct, Type III Secretion System (T3SS2) encoded within the genomic island VPaI-7. The T3SS2 allows the delivery of effector proteins directly into the cytosol of infected eukaryotic cells to subvert key host cell processes, critical forV. parahaemolyticusto colonize and cause disease. Furthermore, the T3SS2 also increases the environmental fitness ofV. parahaemolyticusin its interaction with bacterivorous protists; hence it has been proposed that it contributed to the global oceanic spread of the pandemic clone. Several reports have identified T3SS2-related genes inVibrioand non-Vibriospecies, suggesting that the T3SS2 gene cluster is not restricted to theVibrionaceaeand can mobilize through horizontal gene transfer events. In this work, we performed a large-scale genomic analysis to determine the phylogenetic distribution of the T3SS2 gene cluster and its repertoire of effector proteins. We identified putative T3SS2 gene clusters in 1130 bacterial genomes from 8 bacterial genera, 5 bacterial families and 47 bacterial species. A hierarchical clustering analysis allowed us to define 6 T3SS2 subgroups (I-VI) with different repertoires of effector proteins, redefining the concepts of T3SS2 core and accessory effector proteins. Finally, we identified a subset of T3SS2 gene clusters (subgroup VI) that lack most T3SS2 effector proteins described to date and provided a list of 10 novel effector candidates for this subgroup through bioinformatic analysis. Collectively, our findings indicate that the T3SS2 extends beyond theVibrionaceaefamily and suggest that different effector protein repertories could have a differential impact on the pathogenic potential and environmental fitness of each bacteria that have acquired theVibrioT3SS2 gene cluster.

DATA SUMMARY

All genome sequences used in this study were downloaded from the National Center for Biotechnology Information (NCBI) RefSeq or GenBank databases (SeeTable S1for accession numbers).

Files for the T3SS2 reconstructed phylogenetic tree (Newick tree and MSA fasta file), hierarchical clustering data analysis file from MORPHEUS,Table S1with genome accession numbers and all the data of the absence/presence of T3SS2-related components, andTable S2with the prediction of novel effector proteins are available as part of the online Supporting Dataset at the Zenodo data repository (https://doi.org/10.5281/zenodo.7016552). The T3SS2 phylogenetic tree can be interactively visualized inhttps://itol.embl.de/tree/19016190125374711626959067#
CasDinG is an ATP-dependent 5’-3’ DNA helicase with accessory domains essential for type IV CRISPR immunity
Authors: Domgaard Hannah , Cahoon Christian , Armbrust Matthew J. , Redman Olive , Thomas Aaron , Jackson Ryan N.
Published: August 2022

CRISPR-associated DinG protein (CasDinG) is essential to type IV-A CRISPR function. However, the enzymatic activities of CasDinG are unknown. Here we demonstrate that CasDinG from Pseudomonas aeruginosa strain 83 is an ATP- and metal-dependent 5’-3’ DNA helicase. The crystal structure of CasDinG reveals a helicase core of two RecA-like domains with three accessory domains (N-terminal, arch, and vestigial FeS). To examine the in vivo function of these CasDinG domains, we first identified the preferred PAM sequence (5’-GNAWN-3’ on the 5’-side of the target) with a plasmid library containing all combinations of the five nucleotides upstream of the target sequence. Plasmid clearance assays (using a 5’-GGAAA-3’ PAM) with CasDinG domain mutants demonstrated the vFeS and arch accessory domains are both essential for type IV immunity. These results provide a needed structural and biochemical framework for understanding the type IV-A CRISPR system.
Optimizing E. coli as a formatotrophic platform for bioproduction via the reductive glycine pathway
Authors: Kim Seohyoung , Giraldo Néstor David , Rainaldi Vittorio , Machens Fabian , Collas Florent , Kubis Armin , Kensy Frank , Bar-Even Arren , Lindner Steffen N.
Published: August 2022

Microbial C1 fixation has a vast potential to support a sustainable circular economy. Hence, several biotechnologically important microorganisms have been recently engineered for fixing C1 substrates. However, reports about C1-based bioproduction with these organisms are scarce. Here, we describe the optimization of a previously engineered formatotrophic Escherichia coli strain. Short-term adaptive laboratory evolution enhanced biomass yield and accelerated growth of formatotrophic E. coli to 3.3 g-CDW/mol-formate and 6 hours doubling time, respectively. Genome sequence analysis revealed that manipulation of acetate metabolism is the reason for better growth performance, verified by subsequent reverse engineering of the parental E. coli strain. Moreover, the improved strain is capable of growing to an OD600 of 22 in bioreactor fed-batch experiments, highlighting its potential use for industrial bioprocesses. Finally, demonstrating the strain’s potential to support a sustainable, formate-based bioeconomy, lactate production from formate and CO2 was engineered. The optimized strain generated 1.2 mM lactate—10 % of the theoretical maximum—providing the first proof-of-concept application of the reductive glycine pathway for bioproduction.
Landscape configurations determining the genetic structure of the Yellow-Spotted Amazon River Turtle (Podocnemis unifilis) in Brazilian Amazonia
Authors: Agostini Maria Augusta Paes , Machado Arielli Fabrício , Ritter Camila Duarte , das Neves da Silva Viana Maria , dos Santos Monjeló Luiz Alberto , Andrade Paulo César Machado , Pantoja-Lima Jackson , Pezzuti Juarez C. B. , Félix-Silva Daniely , de Oliveira Waldesse Piragé , Vogt Richard C. , Hrbek Tomas , Farias Izeni Pires
Published: August 2022

Context

Waterfalls and rapids of Amazon basin have been suggested as causing the speciation and genetic structure of many freshwater species, including turtles. The species behavior affects the way waterfalls and rapids limit gene flow. The Yellow-spotted River Turtle (Podocnemis unifilis), a widely distributed and endangered Amazonian turtle, does not show the habit to migrate long distances for breeding or eating, but has a complex geographic pattern of genetic variation.

Objectives

Here, we investigate isolation by distance and by resistance of P. unifilis. We analyzed if the species ecological niche and waterfalls explain the genetic distance in Brazilian Amazonia.

Methods

We evaluated the P. unifilis spatial distribution of genetic variability and diversity using the control region of mitochondrial DNA. We tested the hypotheses of isolation either by distance and resistance through an integrative approach using genetic, geographic, and ecological data. We created a resistance matrix using species niche modeling. We compared the explanation power of geographical distance (both linear and in-water distance) and resistance distance on genetic distance (ΦST fixation index) using multiple regressions and Mantel tests.

Results

We found a high genetic diversity and pattern of genetic structure proved to be geographically complex. The population structure followed some watersheds but also showed structuring within different rivers. We found that landscape resistance better explains genetic distance than linear and in-water distance.

Conclusions

The resistance of the landscape influences the displacement of individuals by aquatic, vegetational, biological, and geomorphological variables, and efforts to species conservation need to be applied throughout its distribution considering landscape genetics.
MyD88-Dependent Signaling Drives Toll-Like Receptor-Induced Trained Immunity in Macrophages
Authors: Owen Allison M. , Luan Liming , Burelbach Katherine R. , McBride Margaret A. , Stothers Cody L. , Boykin Olivia A. , Sivanesam Kalkena , Schaedel Jessica F. , Patil Tazeen K , Wang Jingbin , Hernandez Antonio , Patil Naeem K. , Sherwood Edward R. , Bohannon Julia K.
Published: August 2022

Immunocompromised populations are highly vulnerable to developing life-threatening infections. Strategies to protect patients with weak immune responses are urgently needed. Employing trained immunity, whereby innate leukocytes undergo reprogramming upon exposure to a microbial product and respond more robustly to subsequent infection, is a promising approach. Previously, we demonstrated that the TLR4 agonist monophosphoryl lipid A (MPLA) induces trained immunity and confers broad resistance to infection. TLR4 signals through both MyD88- and TRIF-dependent cascades, but the relative contribution of each pathway to induction of trained immunity is unknown. Here, we show that MPLA-induced resistance toStaphylococcus aureusinfection is lost in MyD88-KO, but not TRIF-KO, mice. The MyD88-activating agonist CpG (TLR9 agonist), but not TRIF-activating Poly I:C (TLR3 agonist), protects against infection in a macrophage-dependent manner. MPLA- and CpG-induced augmentation of macrophage metabolism and antimicrobial functions is blunted in MyD88-, but not TRIF-KO, macrophages. Augmentation of antimicrobial functions occurs in parallel to metabolic reprogramming and is dependent, in part, on mTOR activation. Splenic macrophages from CpG-treated mice confirmed that TLR/MyD88-induced reprogramming occurs in vivo. TLR/MyD88-triggered metabolic and functional reprogramming was reproduced in human monocyte-derived macrophages. These data show that MyD88-dependent signaling is critical in TLR-mediated trained immunity.
Functional hierarchy among different Rab27 effectors involved in secretory granule exocytosis
Authors: Zhao Kunli , Matsunaga Kohichi , Mizuno Kouichi , Wang Hao , Okunishi Katsuhide , Izumi Tetsuro
Published: August 2022

The Rab27 effectors play versatile roles in regulated exocytosis. In pancreatic beta cells, exophilin-8 anchors granules in the peripheral actin cortex, whereas granuphilin and melanophilin mediate granule fusion with and without stable docking to the plasma membrane, respectively. However, it is unknown whether these coexisting effectors function in parallel or in sequence to support the whole insulin secretory process. Here, we investigate their functional relationship by comparing the exocytic phenotypes in beta cells simultaneously lacking two effectors with those lacking one of them. Analyses of prefusion profiles by total internal reflection fluorescence microscopy indicate that melanophilin exclusively functions downstream of exophilin-8 to mobilize granules for fusion from the actin network to the plasma membrane after stimulation. The two effectors are physically linked via the exocyst complex. Downregulation of the exocyst component affects granule exocytosis only in the presence of exophilin-8. Exophilin-8 also promotes fusion of granules stably docked to the plasma membrane mediated by granuphilin, although it is dispensable for granule residence beneath the plasma membrane. The current study presents the first diagram for multiple intracellular paths of granule exocytosis and for functional hierarchy among different Rab27 effectors in the same cell.
Oat chromosome and genome evolution defined by widespread terminal intergenomic translocations in polyploids
Authors: Tomaszewska Paulina , Schwarzacher Trude , Heslop-Harrison Pat (J.S)
Published: August 2022

Structural chromosome rearrangements involving translocations, fusions and fissions lead to evolutionary variation between species and potentially reproductive isolation and variation in gene expression. While the wheats (Triticeae, Poaceae) and oats (Aveneae) all maintain a basic chromosome number of x=7, genomes of oats show frequent intergenomic translocations, in contrast to wheats where these translocations are relatively rare. We aimed to show genome structural diversity and genome relationships in tetraploid, hexaploid and octoploid Avena species and amphiploids, establishing patterns of intergenomic translocations across different oat taxa using fluorescence in situ hybridization (FISH) with four well-characterized repetitive DNA sequences: pAs120, AF226603, Ast-R171 and Ast-T116. In A. agadiriana (2n=4x=28), the selected probes hybridized to all chromosomes indicating that this species originated from one (autotetraploid) or closely related ancestors with the same genomes. Hexaploid amphiploids were confirmed as having the genomic composition AACCDD, while octoploid amphiploids showed three different genome compositions: AACCCCDD, AAAACCDD or AABBCCDD. The A, B, C, and D genomes of oats differ significantly in their involvement in non-centromeric, intercalary translocations. There was a predominance of distal intergenomic translocations from the C-into the D-genome chromosomes. Translocations from A- to C-, or D- to C-genome chromosomes were less frequent, proving that at least some of the translocations in oat polyploids are non-reciprocal. Rare translocations from A- to D-, D- to A- and C- to B-genome chromosomes were also visualized. The fundamental research has implications for exploiting genomic biodiversity in oat breeding to through introgression from wild species potentially with contrasting chromosomal structures and hence deleterious segmental duplications or large deletions in amphiploid parental lines.
Optimization of cryo-electron microscopy for quantitative analysis of lipid bilayers
Authors: Heberle Frederick A. , Welsch Doug , Scott Haden L. , Waxham M. Neal
Published: August 2022

Cryogenic electron microscopy (cryo-EM) is among the most powerful tools available for interrogating nanoscale structure of biological structures. We recently showed that cryo-EM can be used to measure the bilayer thickness of lipid vesicles and biological membranes with sub-angstrom precision, resulting in the direct visualization of nanoscopic domains of different thickness in multicomponent lipid mixtures and giant plasma membrane vesicles. Despite the great potential of cryo-EM for revealing the lateral organization of biomembranes, a large parameter space of experimental conditions remains to be optimized. Here, we systematically investigate the influence of instrument parameters and image post-processing steps on the ability to accurately measure bilayer thickness and discriminate regions of different thickness within unilamellar liposomes. We also demonstrate a spatial autocorrelation analysis to extract additional information about lateral heterogeneity.

Significance

Raft domains in unstimulated cells have proven difficult to directly visualize owing to their nanoscopic size and fleeting existence. The few techniques capable of nanoscopic spatial resolution typically rely on interpretation of indirect spectroscopic or scattering signals or require stabilizing the membrane on a solid support. In contrast, cryo-EM yields direct images of nanoscale domains in probe-free, unsupported membranes. Here, we systematically optimize key steps in the experimental and analysis workflow for this new and specialized application. Our findings represent an important step toward developing cryo-EM into a robust method for investigating phase behavior of membranes at length scales relevant to lipid rafts.
Digitization of imaging plates from Guinier powder X-ray diffraction cameras
Authors: Nasir Jamal , Steinbrück Nils , Xu Ke , Engelen Bernward , Schmedt auf der Günne Jörn
Published: August 2022

A Guinier camera equipped with an imaging plate is used to investigate and eliminate the sources of instrumental errors affecting the quality of the obtained scanned Guinier data. A program with a graphical user interface is presented which converts the data of the scanned images into different standard file formats for powder X-ray patterns containing intensities, their standard deviations and the diffraction angles. The program also allows for manual and automatic correction of the 2θ scale against a known reference material. It is shown using LaB6 that the exported X-ray diffraction patterns provide a 2θ scale reproducible enough to allow for averaging diffractograms obtained from different exposures of the imaging plate for the same sample. As shown on a mixture of NaCl and sodalite, the quality of the produced data is sufficient for Rietveld refinement. The software including source code is made available under a free software license.
Radial spin echo small-angle neutron scattering method: concept and performance
Authors: Kadletz Elisabeth , Bouwman Wim G. , Pappas Catherine
Published: August 2022

A novel spin echo small-angle neutron scattering (SESANS) concept based on a rotationally symmetric magnetic field geometry is introduced. The proposed method is similar to the conventional linear SESANS technique but uses longitudinal precession fields and field gradients in a radial direction, as typically found in neutron spin echo (NSE) spectrometers. Radial SESANS could thus be implemented as an add-on to NSE setups. The neutron trajectory through the instrument is encoded with the help of radial gradients generated by radial shifters, which are coils placed in the beam area similar to Fresnel coils. The present work introduces the setup of the instrument and explores its performance and the relationship between the encoded momentum transfer and the precession angle. The results indicate that radial SESANS is only sensitive to scattering along the radial direction and thus measures the projected correlation function along this direction as a function of the spin echo length, defined similarly to linear SESANS. For an evaluation of the performance of the setup, the case of scattering from solid spheres is considered and the results calculated for the radial and linear SESANS cases are compared. Also discussed is the implementation of the radial magnetic field geometry in spin echo modulated small-angle neutron scattering.
diffpy.mpdf: open-source software for magnetic pair distribution function analysis
Authors: Frandsen Benjamin A. , Hamilton Parker K. , Christensen Jacob A. , Stubben Eric , Billinge Simon J. L.
Published: August 2022

The open-source Python package diffpy.mpdf, part of the DiffPy suite for diffraction and pair distribution function analysis, provides a user-friendly approach for performing magnetic pair distribution function (mPDF) analysis. The package builds on existing libraries in the DiffPy suite to allow users to create models of magnetic structures and calculate corresponding one- and three-dimensional mPDF patterns. diffpy.mpdf can be used to perform fits to mPDF data either in isolation or in combination with atomic pair distribution function data for joint refinement of the atomic and magnetic structure. Examples are given using MnO and MnTe as representative antiferromagnetic compounds and MnSb as a representative ferromagnet.
Prison break from financialization: the case of the PRI reporting and assessment framework
Authors: Arjaliès Diane-Laure , Laurel-Fois Daniela , Mottis Nicolas
Published: August 2022

Purpose

This article seeks to unravel the mechanisms through which financial actors agreed upon a sustainability accounting standard without financializing social and environmental issues, i.e. assigning a monetary value to sustainability.

Design/methodology/approach

The article examines the Reporting and Assessment Framework created by the United Nations Principles for Responsible Investment (UN-PRI), the leading reporting sustainability framework in the asset management industry. It relies on a longitudinal case study that draws upon interviews, participant observation, and archival data.

Findings

The article demonstrates that the conception of the framework was a funnelling process of sustainability valuation comprising two co-constituted mechanisms: a process of valorization – judging what is deemed of value – and a process of evaluation – agreeing on how to assess value. This valuation process was unfolded by creating the framework, thanks to two enabling conditions: the creation of non-prescriptive evaluative criteria that avoided financialization and the valuation support of an enabling organization.

Originality/value

The article helps understand how an industry can encompass the diversity of motives and practices associated with the adoption of sustainability by its economic actors while suggesting a common framework to report on and assess those practices. It uncovers alternatives to the financialization process of sustainability accounting standards. The article also offers insights into the advantages and inconveniences of such a framework. The article enriches the literature in the sociology of valuation, financialization, and sustainability accounting.
Consumer adoption of digital grocery shopping: what is the impact of consumer’s prior-to-use knowledge?
Authors: Zolfaghari Alireza , Thomas-Francois Kimberly , Somogyi Simon
Published: August 2022

Purpose

Smart retail technology adoption models are largely focused on consumer perceptions of the technology and the characteristics of digital technologies. However, the impact of the prior-to-use knowledge of consumers on the adoption of the technologies has been understudied. This research examined to what extent social acceptance and consumer learning can facilitate consumer adoption of digital grocery shopping (DGS).

Design/methodology/approach

This paper builds on the innovation–decision model to develop a framework to examine the impact of social acceptance and consumer learning on DGS. The research tested a structural model based on data collected from 611 North American participants.

Findings

This study found that the social acceptance of DGS directly and consumer learning indirectly affects the appeal of grocery shopping to consumers and consequently increases their intention to adopt this new shopping method. Furthermore, the results indicated that both hypothesised directions are parallelly mediated by digital convenience, the consumer’s digital readiness and digital trust.

Originality/value

This study extends the understanding of consumer adoption of DGS by highlighting the influence of consumer knowledge about DGS on their behavioural intention. Several important theoretical and practical implications are provided to help retail managers to develop service strategies.