bluuebunny/crossref_metadata_2025 huggingface dataset:
Growth form matters – crustose lichens are sensitive to forest management on dead wood
Authors: Kantelinen Annina , Purhonen Jenna , Halme Panu , Myllys Leena
Published: April 2022

Lichens have a vital role in forest ecosystems and they are a threatened group in boreal forests. However, the conservation ecology of the total lichen community has very rarely been studied. Here we studied lichen species and communities, including macrolichens (= foliose and fruticose growth forms) and rarely studied crustose lichens, on decaying wood in boreal spruce-dominated forests in Finland. We also studied obligate lignicoles that grow only on dead wood and are mostly crustose in growth form. Species richness and community composition were examined on decaying logs and natural or cut stumps of Picea abies at different decay stages (2–5) in 14 stands, half of which were natural or seminatural and half recently managed. We used thorough search to yield a species list as close to complete as possible. Our study questions were: 1) Are species richness and lichen communities different in natural and managed forests, and if so, are there differences between macrolichens, crustose lichens and obligate lignicoles in how they respond to forest management? 2) How does the decay stage and dead wood type affect the lichens, i.e. are there differences between stumps and logs? We found a total of 127 lichen species. Most (75%) of the recorded lichen species were crustose. With a generalized linear model we found that crustose lichens and obligate lignicoles had a higher species richness in natural than managed forests, but macrolichen richness was not significantly affected by forest management. Utilizing non-metric multidimensional scaling we discovered that site level community composition of macrolichens, crustose lichens and obligate lignicoles was also significantly different between natural and managed forests. We found that on dead wood unit level the decay stage had a significant effect on species richness and community composition, so that the species richness of all studied groups declined during the decay process. The dead wood type (stump vs. log) had a significant effect on species richness of macrolichens and obligate lignicoles, as well as on the communities of crustose lichens.
Evolution of selfish multicellularity collective organisation of individual spatio-temporal regulatory strategies
Authors: Vroomans Renske M.A. , Colizzi Enrico Sandro
Published: April 2022

Background

The unicellular ancestors of modern-day multicellular organisms were remarkably complex. They had an extensive set of regulatory and signalling genes, an intricate life cycle and could change their behaviour in response to environmental changes. At the transition to multicellularity, some of these behaviours were co-opted to organise the development of the nascent multicellular organism. Here, we focus on the transition to multicellularity before the evolution of stable cell differentiation, to reveal how the emergence of clusters affects the evolution of cell behaviour.

Results

We construct a computational model of a population of cells that can evolve the regulation of their behavioural state – either division or migration – in a unicellular or multicellular context. They compete for reproduction and for resources to survive in a seasonally changing environment. We find that the evolution of multicellularity strongly determines the co-evolution of cell behaviour, by altering the competition dynamics between cells. When adhesion cannot evolve, cells compete for survival by rapidly migrating towards resources before dividing. When adhesion evolves, emergent collective migration alleviates the pressure on individual cells to reach resources. This allows cells to selfishly maximise replication. Migrating adhesive clusters display striking patterns of spatio-temporal cell state changes that visually resemble animal development.

Conclusions

Our model demonstrates how emergent selection pressures at the onset of multicellularity can drive the evolution of cellular behaviour to give rise to developmental patterns.
From Specification to Implementation: Assume-Guarantee Contracts for Synthetic Biology
Authors: Pandey Ayush , Incer Inigo , Sangiovanni-Vincentelli Alberto , Murray Richard M.
Published: April 2022

We provide a new perspective on using formal methods to model specifications and synthesize implementations for the design of biological circuits. In synthetic biology, design objectives are rarely described formally. We present an assume-guarantee contract framework to describe biological circuit design objectives as formal specifications. In our approach, these formal specifications are implemented by circuits modeled by ordinary differential equations, yielding a design framework that can be used to design complex synthetic biological circuits at scale. We describe our approach using the design of a biological AND gate as a motivating, running example.
Population-level hypertension control rate in India: A systematic review and meta-analysis of community based non-interventional studies, 2001-2020
Authors: Koya Shaffi Fazaludeen , Pilakkadavath Zarin , Wilson Tom , Chandran Praseeda , Kuriakose Serin , Akbar Suni K , Ali Althaf
Published: April 2022

Background

Hypertension is a significant contributor to mortality in India. Adequate control of hypertension is important to prevent cardiovascular morbidity and mortality.

Methods

We conducted a systematic review and meta-analysis of community-based, non-interventional studies published between 2001 and 2020. We screened records from PubMed, Embase, and Web of Science databases, extracted data, and assessed risk of bias. We conducted random-effects meta-analysis to provide overall summary estimates and subgroup estimates, and mixed-effects meta-regression with sex, region, and study period as covariates. The risk of bias was assessed using modified New Castle-Ottawa scales. This study is registered with PROSPERO, CRD42021267973.

Results

The systematic review included 37 studies (n=170,631 hypertensive patients). Twelve studies (32%) reported poorer control rates among males than females, four studies (11%) reported poorer control rates among rural patients, while very few studies reported differences across socioeconomic variables. The overall control rate was 33.2% (n=84,485, 95% CI=27.9,38.6) with substantial heterogeneity (I2=99.1%, \chi^2= 3003.91, 95% CI=98.9,99.2; p <0.001). Unadjusted sub-group analysis showed significantly different hypertension control rates across regions (n=12,938, p=0.003) but not across study periods (n= 84,485, p=0.22), or sex (n= 81,197, p=0.22). Meta-regression showed that control rates increased by 14.7% during 2011-2020 compared to 2001-2010 (95%CI=5.8, 23.5, p=0.0021), and was 26.3% higher in the south (95%CI=12.6, 39.9, p=0.0005) and 15.9% higher in the west (95%CI=3.4, 31.4, p=0.0456) compared to the east. The control rates did not differ by sex.

Conclusion

Hypertension is adequately controlled only among one-third of patients in India. The control rate has improved during 2011-2020 compared to 2001-2010, but substantial differences exist across regions. Very few studies examined relevant socioeconomic factors relevant to hypertension control. India needs more studies at the community level to understand the health system and socioeconomic factors that determine uncontrolled hypertension in India.
Inferring microRNA regulation: A proteome perspective
Authors: Ofer Dan , Linial Michal
Published: April 2022

Post-transcriptional regulation in multicellular organisms is mediated by microRNAs. However, the mechanisms that determine if a gene is regulated by miRNAs are poorly understood. Previous works focused mostly on miRNA seed matches and other features of the 3’-UTR of transcripts. These common approaches relied on knowledge of the miRNA families, and computational approaches still yield poor, inconsistent results, with many false positives. In this work, we present a different paradigm for predicting miRNA-regulated genes based on proteins. In a novel, automated machine learning framework, we use sequence as well as diverse functional annotations to train models on multiple organisms using experimentally validated data. We present insights from tens of millions of features extracted and ranked from different modalities. We show high predictive performance per organism and in generalization across species. We provide a list of novel predictions for Danio rerio (zebrafish) and Arabidopsis thaliana (mouse-ear cress). We compare genomic models, and observe that our protein model outperforms genomics, while a unified model improves on both. While most membranous and disease related proteins are regulated by miRNAs, we observe the G-protein coupled receptor (GPCR) family is an exception, being mostly unregulated by miRNAs, and we raise possible explanations for this. We further show that the evolutionary conservation among duplicated genes does not imply a coherence in miRNA regulation. We conclude that duplicated genes diverge in their tendency to be miRNA regulated. However, protein function is informative across species in predicting post-transcriptional miRNA regulation in living cells.
Quantum chemical elucidation of a sevenfold symmetric bacterial antenna complex
Authors: Cupellini Lorenzo , Qian Pu , Nguyen-Phan Cam Tu , Gardiner Alastair T. , Cogdell Richard J.
Published: April 2022

The light-harvesting complex 2 (LH2) of purple bacteria is one of the most studied photosynthetic antenna complexes. Its symmetric structure and ring-like bacteriochlorophyll arrangement make it an ideal system for theoreticians and spectroscopists. LH2 complexes from most bacterial species are thought to have eightfold or ninefold symmetry, but recently a sevenfold symmetric LH2 structure from the bacterium Mch. purpuratum was solved by Cryo-Electron microscopy. This LH2 also possesses unique nearinfrared absorption and circular dichroism (CD) spectral properties. Here we use an atomistic strategy to elucidate the spectral properties of Mch. purpuratum LH2 and understand the differences with the most commonly studied LH2 from Rbl. acidophilus. Our strategy exploits a combination of molecular dynamics simulations, multiscale polarizable quantum mechanics/molecular mechanics calculations, and lineshape simulations. Our calculations reveal that the spectral properties of LH2 complexes are tuned by site energies and exciton couplings, which in turn depend on the structural fluctuations of the bacteriochlorophylls. Our strategy proves effective in reproducing the absorption and CD spectra of the two LH2 complexes, and in uncovering the origin of their differences. This work proves that it is possible to obtain insight into the spectral tuning strategies of purple bacteria by quantitatively simulating the spectral properties of their antenna complexes.
Intrinsically photosensitive retinal ganglion cells evade temporal filtering to encode environmental light intensity
Authors: Sabbah Shai , Papendorp Carin , Behrendt Inbar , Rasras Hala , Cann Jesse , Leyrer Megan L. , Koplas Elizabeth , Beltoja Marjo , Etebari Cameron , Gunesch Ali Noel , Carrete Luis , Kim Min Tae , Manoff Gabrielle , Bhatia-Lin Ananya , Zhao Tiffany , Dowling Henry , Briggman Kevin L. , Berson David M.
Published: April 2022

The retina encodes environmental light intensity to drive innate physiological responses. The synaptic basis of such coding remains obscure. Intrinsically photosensitive retinal ganglion cells (ipRGCs) are the only retinal output neurons stably encoding intensity. They do so even without their melanopsin photopigment, so specializations in their synaptic drive from bipolar cells (BCs) must also contribute. Here, we shed new light on mechanisms responsible for this unique intensity-coding drive. By ultrastructural reconstruction, we show that specific BC types and unusual ribbon synapses carry photoreceptor signals to ipRGCs. By glutamate imaging and electrophysiology, we show that their light responses are unusually persistent. Still, we find that virtually all BCs encode intensity. Intensity coding becomes restricted to ipRGCs primarily because other RGCs filter out steady-state intensity signals postsynaptically. Thus, neural “pinholes” in global, persistent neural “masking” allow intensity signals to be encoded by ipRGCs and sent to specific centers of the visual brain.
Ecological and evolutionary drivers of phenotypic and genetic variation in the European crabapple (Malus sylvestris (L.) Mill.), a wild relative of the cultivated apple
Authors: Chen X. , Avia K. , Forler A. , Remoué C. , Venon A. , Rousselet A. , Lucas G. , Kwarteng A.O. , Rover R. , Le Guilloux M. , Belcram H. , Combes V. , Corti H. , Vazquez S. , Falque M. , Alins G. , Kirisits T. , Ursu T.M. , Roman A. , Volk G.M. , Bazot Stéphane , Cornille A
Published: April 2022

Characterizing the phenotypic and genetic variation among populations of crop wild relatives help understanding the ecological and evolutionary processes involved in population divergence, and better harness their diversity to mitigate the impact of climate change on crops. We assessed genetic and phenotypic diversity of the European crabapple, Malus sylvestris, a main contributor to the cultivated apple genome (Malus domestica), and investigated for ecological divergence.

We assessed variation in growth rate and traits related to carbon uptake between seedlings measured in a common garden, and related it to the genetic ancestry of the seedlings, assessed using 13 microsatellite loci and Bayesian clustering method. The occurrence of patterns of isolation-by-distance, -by-climate and -by-adaptation that might have caused genetic and phenotypic differentiation among M. sylvestris populations was also tested.

Seedlings belonged to seven M. sylvestris populations in Europe, with 11.6% of seedlings introgressed by M. domestica. Significant trait variation among M. sylvestris populations was observed, which for some was of moderate to high heritability. Lack of association between trait and genetic divergence suggests that this significant phenotypic variation is not adaptive, but strong association between genetic variation and the climate during the last glacial maximum suggests local adaptation of M. sylvestris to past climates.

This study provides an insight into the ecological and evolutionary drivers of phenotypic and genetic differentiation among populations of a wild apple species and relative of cultivated apples, which is a starting point for future breeding programs.

Societal impact Statement

Apple is a major fruit crop worldwide and a model species for understanding the evolutionary processes underlying perennial crop domestication. Several wild species have contributed to the genetic make-up of the cultivated apple, yet phenotypic and genetic diversity data across their natural distribution is lacking. This study revealed phenotypic variation between populations of the European crabapple, and showed that both geography, and surprisingly, past but not current climate, shaped its genetic structure. We provide a starting point for harnessing wild apple diversity for apple breeding programs to mitigate the impact of climate change on this perennial crop.
Integrated Systems-Level Proteomics and Metabolomics Reveals the Diel Molecular Landscape of Diverse Kale Cultivars
Authors: Scandola Sabine , Mehta Devang , Castillo Brigo , Boyce Nicholas , Uhrig R. Glen
Published: April 2022

Kale are a group of diverseBrassicaceaespecies that are nutritious leafy greens consumed for their abundance of vitamins and micronutrients. Typified by their curly, serrated and/or wavy leaves, kale varieties have been primarily defined based on their leaf morphology and geographic origin, despite having complex genetic backgrounds. Kale is a very promising crop for vertical farming due to its high nutritional content; however, being a non-model organism, foundational, systems-level analyses of kale are lacking. Previous studies in kale have shown that time-of-day harvesting can affect its nutritional composition. Therefore, to gain a systems-level diel understanding of kale across its wide-ranging and diverse genetic landscape, we selected nine publicly available and commercially grown kale cultivars for growth under near-sunlight LED light conditions ideal for vertical farming. We then analyzed changes in morphology, growth and nutrition using a combination of phenomics, proteomics and metabolomics. As the diel molecular activities of plants drive their daily growth and development, ultimately determining their productivity as a crop, we harvested kale leaf tissue at both end-of-day (ED) and end-of-night (EN) time-points for all molecular analyses. Our results reveal that diel proteome and metabolome signatures divide the selected kale cultivars into two distinct groups, defined by their amino acid and sugar content, along with significant proteome differences involving carbon and nitrogen metabolism, mRNA splicing, protein translation and light harvesting. Together, our multi-cultivar, multi-omic analysis provides robust quantitative insights into the molecular underpinnings of the diel growth and development landscape of kale, significantly advancing our fundamental understanding of this nutritious leafy green super-food for next-generation horticulture / vertical farming applications.
TIGER: A Web Portal of Tumor Immunotherapy Gene Expression Resource
Authors: Chen Zhihang , Luo Ziwei , Zhang Di , Li Huiqin , Liu Xuefei , Zhu Kaiyu , Zhang Hongwan , Wang Zongping , Zhou Penghui , Ren Jian , Zhao An , Zuo Zhixiang
Published: April 2022

Immunotherapy is a promising cancer treatment method, but only a few patients benefit from it. Developing new immunotherapy strategies and effective biomarkers of response and resistance is urgent. Recent high-throughput bulk and single-cell gene expression profiling technologies have generated valuable resources in these regards. However, these resources are not well organized and systematic analysis is difficult. Here, we present TIGER, a tumor immunotherapy gene expression resource, which contains bulk transcriptome data of 1508 tumor samples with immunotherapy clinical outcome and 11,057 tumor/normal samples without immunotherapy clinical outcome, as well as single-cell transcriptome data of 2,116,945 immune cells of 655 samples. TIGER provides many useful modules to analyze the collected data and user-provided data. Using the resource in TIGER, we identified a tumor enriched subset of CD4+ T cells. Melanoma patients with higher signature score of this subset have significantly better response and survival under immunotherapy. We believe that TIGER will be helpful for understanding anti-tumor immunity mechanisms and discovering effective biomarkers. TIGER is freely accessible at http://tiger.canceromics.org/.
Heterogeneity in the size of the apical surface of cortical progenitors
Authors: Badouel Caroline , Audouard Christophe , Davy Alice
Published: April 2022

The apical surface of epithelial cells is highly specialized, it is important for morphogenetic processes that are essential to shape organs and tissues and it plays a role in morphogen and growth factor signaling. Apical progenitors in the mammalian neocortex are pseudoepithelial cells whose apical surface lines the ventricle. Whether changes in their apical surface sizes are important for cortical morphogenesis and/or other aspects of neocortex development after neurulation has not been thoroughly addressed. Here we show that apical progenitors are heterogeneous with respect to their apical surface area. In Efnb1 mutants, the size of the apical surface is modified and this correlates with discrete alterations of tissue organization without impacting proliferation or differentiation. Altogether, our data reveal heterogeneity in apical progenitors AS area in the developing neocortex and shows a role for Ephrin B1 in controlling AS size. Our study also indicates that changes in AS size does not have strong repercussion on apical progenitor behavior.
Saccades are locked to the phase of alpha oscillations during natural reading
Authors: Pan Yali , Popov Tzvetan , Frisson Steven , Jensen Ole
Published: April 2022

We saccade three to five times per second when reading. However, little is known about the neuronal mechanisms coordinating the oculomotor and visual system during such rapid processing. Here we ask if brain oscillations play a role in the temporal coordination of the visuomotor integration. We simultaneously acquired MEG and eye-tracking data while participants read sentences silently. Every sentence was embedded with target words of either high or low lexical frequency. Our key finding demonstrated that saccade onsets were locked to the phase of alpha oscillations (8 – 13 Hz); in particular, for saccades towards low-frequency words. Source modelling demonstrated that the alpha oscillations to which the saccades were locked, were generated in the right-associative visual cortex (BA 19). Our findings suggest that the alpha oscillations serve to time the processing between the oculomotor and visual systems during natural reading, and that this coordination becomes more pronounced for demanding words.

Significance Statement

Reading is an essential skill in modern society that allows us to acquire information from written language. While we effortlessly can acquire the meaning of a text, the task of reading requires precisely timed saccades as our eyes jump from word to word. By using a natural reading task, we demonstrate that the coordination between saccades and visual processing is clocked by ongoing ~10 Hz alpha oscillations in the visual cortex. The clocking of the saccades by brain oscillations became particularly pronounced when the participants made saccades to demanding words.
Peptide-RNA Coacervates as a Cradle for the Evolution of Folded Domains
Authors: Seal Manas , Weil-Ktorza Orit , Despotović Dragana , Tawfik Dan S. , Levy Yaakov , Metanis Norman , Longo Liam M. , Goldfarb Daniella
Published: April 2022

Peptide-RNA coacervates can result in the concentration and compartmentalization of simple biopolymers. Given their primordial relevance, peptide-RNA coacervates may have also been a key site of early protein evolution. However, the extent to which such coacervates might promote or suppress the exploration of novel peptide conformations is fundamentally unknown. To this end, we used electron paramagnetic resonance (EPR) spectroscopy to characterize the structure and dynamics of an ancient and ubiquitous nucleic acid binding element, the helix-hairpin-helix (HhH) motif, alone and in the presence of RNA, with which it forms coacervates. Double electron-electron resonance (DEER) spectroscopy applied to singly labeled peptides containing one HhH motif reveals the presence of dimers, even in the absence of RNA, and transient α-helical character. Moreover, dimer formation is promoted upon RNA binding and was detectable within peptide-RNA coacervates. The distance distributions between spin labels are consistent with the symmetric (HhH)2-Fold, which is generated upon duplication and fusion of a single HhH motif and traditionally associated with dsDNA binding. These results support the hypothesis that coacervates are a unique testing ground for peptide oligomerization and that phase-separating peptides could have been a resource for the construction of complex protein structures via common evolutionary processes, such as duplication and fusion.
WDR47 facilitates ciliogenesis by modulating intraflagellar transport
Authors: Song Chun-Xue , Zeng Xian-Ting , Zeng Wan-Xin , Tong Xia-Jing , Li Qian
Published: April 2022

Cilia are conserved organelles found in many cell types in eukaryotes, and their dysfunction causes defects in environmental sensing and signaling transduction; such defects are termed ciliopathies. Distinct cilia have cell-specific morphologies and exert distinct functions. However, the underlying mechanisms of cell-specific ciliogenesis and regulation are unclear. Here we identified a WD40-repeat (WDR) protein, WDR47/NMTN-1, and show that it is specifically required for ciliogenesis of AWB chemosensory neurons in C. elegans. WDR47/NMTN-1 is expressed in the AWB chemosensory neuron pair, and is localized at the basal body (BB) of the AWB cilia. Knockout of wdr47/nmtn-1 causes abnormal AWB neuron cilia morphology, structural integrity, and induces aberrant AWB-mediated aversive behaviors. We further demonstrate that wdr47/nmtn-1 deletion affects movement of intraflagellar transport (IFT) particles and their cargo delivery in AWB neurons. Our results indicate that WDR47/NMTN-1 is essential for AWB neuron ciliary morphology and function, which reveal a novel mechanism for cell-specific ciliogenesis. Since WDR47/NMTN-1 is conserved in mammals, our findings may help understand the process of cell-specific ciliogenesis and provide insights for treating ciliopathies.
Type One Protein Phosphatase Regulates Fixed-Carbon Starvation-Induced Autophagy by Dephosphorylating ATG13a to Facilitate ATG1a-ATG13a Formation in Arabidopsis
Authors: Wang Qiuling , Hou Suiwen
Published: April 2022

Autophagy, a conserved pathway which carries out the bulk degradation of cytoplasmic material in eukaryotic cells, is critical in plant physiology and development. It is tightly regulated by ATG13, a core component of ATG1 kinase complex which initiates autophagy. Although it has been reported that ATG13 is dephosphorylated immediately after nutrient starvation, the phosphatase regulating this process is poorly understood. Here, we demonstrated that the septuple mutant (topp-7m) and octuple mutant (topp-8m) of type one protein phosphatase (TOPP) exhibited significantly reduced tolerance to fixed-carbon (C) starvation due to compromised autophagy activity. Genetic analysis placed TOPP upstream of autophagy. Interestingly, ATG13a was found to be an interactor of TOPP. And TOPP directly dephosphorylated ATG13a in vitro and in vivo. Meanwhile, eighteen phosphorylation sites of ATG13a were identified by LC-MS. Mimic dephosphorylation of ATG13a at these 18 sites significantly promoted autophagy and increased the atg13ab mutant tolerance to fixed-C starvation. Further study showed that the dephosphorylation of ATG13a facilitated ATG1a-ATG13a complex formation. Consistently, the recruitment of ATG13a for ATG1a was markedly inhibited in topp-7m-1. In addition, TOPP-controlled dephosphorylation of ATG13a boosted ATG1a phosphorylation. Taken together, our study reveals the crucial role of TOPP in regulating autophagy by stimulating the formation of ATG1a-ATG13a complex through dephosphorylating ATG13a in Arabidopsis.
MPI region of interest (ROI) analysis and quantification of iron in different volumes
Authors: Sehl Olivia C. , Tiret Brice , Berih Maryam A. , Makela Ashley V. , Goodwill Patrick W. , Foster Paula J.
Published: April 2022

MPI directly detects superparamagnetic iron oxides (SPIONs), which should enable precise, accurate, and linear quantification. However, selecting a region of interest (ROI) has strong effects on MPI quantification results. Ideally, ROI selection should be simple, user-independent, and widely applicable. In this work, we describe and compare four MPI ROI selection methods and assess their performance in vitro and in vivo. To explore the effect of ROI selection, ten ferucarbotran phantoms were imaged, each contained the same amount of iron but varied in volume. Three users tested the accuracy of the ROI methods for quantification of these samples. Lastly, the four ROI methods were applied to quantify ferucarbotran in vivo after intravenous, intramuscular, and subcutaneous injections in mice. We demonstrate that each ROI method has strengths. We conclude there is an important trade-off between ROI size and the accuracy of iron quantification, therefore the choice of ROI selection method for each study must be carefully informed.
Visual Mode Switching: Improved General Compensation to Environmental Color Change Requires Only One Exposure Per Day
Authors: Li Yanjun , Tregillus Katherine EM , Engel Stephen A
Published: April 2022

When the visual environment changes, vision adapts in order to maintain accurate perception. For repeatedly encountered environmental changes, the visual system may learn to adjust immediately, a process called “visual mode switching”. For example, following experience with red glasses, participants report the glasses’ redness fades instantly when they put the glasses on. Here we tested: 1) whether once-daily experience suffices for learning to switch visual modes, and 2) whether effects of mode-switching apply to most stimuli affected by the environmental change. In Experiment 1, twelve participants wore bright red glasses for a single 5-hr period each day, for 5 days; and we tested for changes in the perception of unique yellow, which contains neither red nor green. In Experiment 2, we tested how mode switching affects larger parts of the color space. Thirteen participants donned and removed the glasses multiple times a day, for 5 days; and we used a dissimilarity rating task to measure and track perception of many different colors. Across days, immediately upon donning the glasses, the world appeared less and less reddish (Experiment 1), and colors across the whole color space appeared more and more normal (Experiment 2). These results indicate that mode switching can be learned from a once-daily experience, and it applies to most stimuli in a given environment. These findings may help to predict when and how mode switching occurs outside the laboratory.
Microbial Community Dynamics of a Sequentially Fed Anaerobic Digester Treating Solid Organic Waste
Authors: Lee HyunWoo , Fitamo Temesgen M. , Nesbø Camila L. , Guilford Nigel G. H. , Kanger Kärt , Yang Minqing Ivy , Edwards Elizabeth A.
Published: April 2022

A 50 kg-scale high solids anaerobic digestor comprising six sequentially-fed leach beds with a leachate recirculation system and an upflow anaerobic sludge blanket reactor was operated at 37°C for 88 weeks. The feedstock contained a constant fibre fraction (a mix of cardboard, boxboard, newsprint, and fine paper) and varying proportions of food waste. Significantly enhanced co-digestion and methane production from the fibres was observed as the proportion of FW was increased. The most abundant 16S rRNA amplicon sequence variant (ASV), classified as Clostridium butyricum, was correlated with the amount of FW in the system and total methane yield. However, methane yield specifically from the fibre fraction was significantly correlated with organisms classified as Candidatus Roizmanbacteria and Spirochaetaceae. These ASVs together with ASVs classified as Anaerovorax and Methanoculleus correlated strongly to other ASVs in the microbial community, suggesting these are vitally important for ecosystem function and methane production. In addition, tracing the fate of microbes derived from incoming food waste helped to diagnose a poor batch of bulking agent.

Table of Contents (TOC)/ Abstract Art
HiFENS: High-throughput FISH detection of endogenous pre-mRNA splicing isoforms
Authors: Shilo Asaf , Pegoraro Gianluca , Misteli Tom
Published: April 2022

Splicing factors play an essential role in regulation of alternative pre-mRNA splicing. While much progress has been made in delineating the mechanisms of the splicing machinery, the identity of signal transduction pathways and upstream factors that regulate splicing factor activity is less well understood. A major challenge in the discovery of upstream regulatory factors of pre-mRNA splicing is the scarcity of functional genomics screening methods to monitor splicing outcomes of endogenous genes. Here, we have developed HiFENS (High throughputFISH Detection ofENdogenousSplicing Isoforms), a high-throughput imaging assay based on hybridization chain reaction (HCR) and used HiFENS to screen for cellular factors that regulate alternative splicing of endogenous genes. We demonstrate optimized detection with high specificity of endogenous splicing isoforms and multiplexing of probes for accurate detection of splicing outcomes with single cell resolution. As proof-of-principle, we perform an RNAi screen of 702 human kinases and identify potential candidate upstream splicing regulators of theFGFR2gene. HiFENS should be a useful tool for the unbiased delineation of cellular pathways involved in alternative splicing regulation.
The effect of different treatment durations with indole-3-acetic acid (IAA)-producing endophyticBacillusspp. on tomato ‘Aicha’ under saline conditions
Authors: Belaouni Hadj Ahmed , Dif Guendouz , Toumatia Omrane , Meklat Atika , Mathieu Florence , Zitouni Abdelghani
Published: April 2022

This study aimed to investigate the effect of indole-3-acetic acid (IAA)-producing endophytes from saline environments on survival and growth of tomato under salt stress, using different treatment times. Twenty-five endophytic bacteria were isolated from halophytes (Atriplex halimusL.,Tamarix aphyllaL.) issued from saline regions (Algeria). Five strains were selected based on tolerance to NaCl. A polyphasic taxonomic study was conducted. The selected strains were assigned to the Bacillus cereus group. Quantification of IAA production was done by high-performance liquid chromatography (HPLC). Anin vitrotest of growth promotion/protection of tomato ‘Aicha’ was conducted under saline conditions (50 mM, 75 mM, 100 mM, and 125 mM), for different durations of seed biopriming (1h, 3h, and 12h). Endophytes led to a significant amelioration of salt stress in tomato ‘Aicha’ at all salinity levels, depending on treatment times, indicating the necessity of optimizing this crucial factor.
In situ single particle classification reveals distinct 60S maturation intermediates in cells
Authors: Lucas Bronwyn A. , Zhang Kexin , Loerch Sarah , Grigorieff Nikolaus
Published: April 2022

Electron cryo-microscopy (cryo-EM) can generate high-resolution views of cells with faithful preservation of molecular structure. In situ cryo-EM, therefore, has enormous potential to reveal the atomic details of biological processes in their native context. However, in practice, the utility of in situ cryo-EM is limited by the difficulty of reliably locating and confidently identifying molecular targets (particles) and their conformational states in the crowded cellular environment. We recently showed that 2DTM, a fine-grained template-based search applied to cryo-EM micrographs, can localize particles in two-dimensional views of cells with high precision. Here we demonstrate that the signal-to-noise ratio (SNR) observed with 2DTM can be used to differentiate related complexes in focused ion beam (FIB)-milled cell sections. We apply this method in two contexts to locate and classify related intermediate states of 60S ribosome biogenesis in the Saccharomyces cerevisiae cell nucleus. In the first, we separate the nuclear pre-60S population from the cytoplasmic mature 60S population, using the subcellular localization to validate assignment. In the second, we show that relative 2DTM SNRs can be used to separate mixed populations of nuclear pre-60S that are not visually separable. We use a maximum likelihood approach to define the probability of each particle belonging to each class, thereby establishing a statistic to describe the confidence of our classification. Without the need to generate 3D reconstructions, 2DTM can be applied even when only a few target particles exist in a cell.
An interplay between JA and SA modulates rapid systemic ROS signaling during responses to high light stress or wounding
Authors: Myers Ronald J , Fichman Yosef , Mittler Ron
Published: April 2022

Plants can send long distance cell-to-cell signals from a single tissue subjected to stress to the entire plant. This ability is termed ‘systemic signaling’ and is essential for plant acclimation to stress and/or defense against pathogens. Several signaling mechanisms are associated with systemic signaling, including the reactive oxygen species (ROS) wave, calcium wave, hydraulic wave, and electric signals. The ROS wave coordinates multiple physiological, molecular, and metabolic responses among different parts of the plant, and is essential for systemic acquired acclimation (SAA) to stress. In addition, it is linked with several plants hormones, including jasmonic acid (JA), salicylic acid (SA), and abscisic acid (ABA). However, how these plant hormones modulate the ROS wave and whether they are required for SAA is not clear. Here we report that SA and JA play antagonistic roles in modulating the ROS wave. While SA augments the ROS wave, JA suppresses it, during responses to a local wounding or high light (HL) stress treatments. We further show that ethylene and ABA are essential for the regulation of the ROS wave during systemic responses to a local wounding treatment. Interestingly, we found that the redox-response protein NONEXPRESSOR OF PATHOGENESIS RELATED PROTEIN 1 (NPR1) is required for systemic ROS accumulation in response to wounding or HL stress, as well as for SAA to HL stress. Taken together, our findings suggests that an interplay between JA and SA could regulate systemic signaling and SAA during responses of plants to abiotic stress or wounding.

One sentence summary

An antagonistic interaction between SA and JA attenuates the accumulation of ROS in local and systemic tissues during responses of plants to light stress or wounding.
Correlation between two- and three-dimensional crystallographic lattices for epitaxial analysis. II. Experimental results
Authors: Simbrunner Josef , Domke Jari , Sojka Falko , Jeindl Andreas , Otto Felix , Gruenewald Marco , Hofmann Oliver T. , Fritz Torsten , Resel Roland , Forker Roman
Published: April 2022

While the crystal structure of the polymorph phase can be studied in three dimensions conveniently by X-ray methods like grazing-incidence X-ray diffraction (GIXD), the first monolayer is only accessible by surface-sensitive methods that allow the determination of a two-dimensional lattice. Here, GIXD measurements with sample rotation are compared with distortion-corrected low-energy electron diffraction (LEED) experiments on conjugated molecules: 3,4;9,10-perylenetetracarboxylic dianhydride (PTCDA), 6,13-pentacenequinone (P2O), 1,2;8,9-dibenzopentacene (trans-DBPen) and dicyanovinyl-quaterthiophene (DCV4T-Et2) grown by physical vapor deposition on Ag(111) and Cu(111) single crystals. For these molecular crystals, which exhibit different crystallographic lattices and crystal orientations as well as epitaxial properties, the geometric parameters of the three-dimensional lattice are compared with the corresponding geometry of the first monolayer. A comparison of the monolayer lattice from LEED investigations with the multilayer lattices determined by rotated GIXD experiments reveals a correlation between the first monolayer and the epitaxial growth of three-dimensional crystals together with lattice distortions and re-alignment of molecules. The selected examples show three possible scenarios of crystal growth on top of an ordered monolayer: (i) growth of a single polymorph, (ii) growth of three different polymorphs; in both cases the first monolayer serves as template. In the third case (iii) strong lattice distortion and distinct molecular re-alignments from the monolayer to epitaxially grown crystals are observed. This is the second part of our work concerning the correlation between two- and three-dimensional crystallographic lattices for epitaxial analysis. In the first part, the theoretical basis has been derived which provides a mathematical relationship between the six lattice parameters of the three-dimensional case and the three parameters obtained for the two-dimensional surface unit cell, together with their orientation to the single-crystalline substrate. In this work, a combined experimental approach of GIXD and LEED is introduced which can be used to investigate the effect of the epitaxial monolayer on the structural properties of molecular crystals grown on top.
Finite element analysis of pitting corrosion on mechanical behavior of E690 steel panel
Authors: Liu Ming
Published: April 2022

Purpose

The purpose of this study is to analysis the pitting corrosion on the mechanical behavior of E690 high-strength steel sandwich panel. The pitting corrosion depth and degree of pitting (DOP) damage were used to evaluate the mechanical behaviors such as peak load and specific energy absorption of E690 panel.

Design/methodology/approach

The mechanical behavior of quasi-static compression, low-speed impact and three-point bending of E690 panel after pitting corrosion was simulated by ABAQUS nonlinear finite element method.

Findings

The quasi-static compression and low-speed impact mechanical properties can be greatly reduced by the pitting corrosion of the panel core, the pitting corrosion of the outer panel shows no obvious effect. The mechanical properties decrease with the increase of the pitting corrosion depth and DOP, and the influence of DOP is greater than that of pitting corrosion depth. The DOP of outer panel has less effect on mechanical properties of three-point bending compared with that of the core. Therefore, the pitting corrosion in the core of panel should be strictly controlled to prevent adverse effects on the mechanical properties of the structure.

Originality/value

To make up for the deficiency of the research on the corrosion behavior of high-strength steel sandwich panel structure, this paper chose E690 high-strength steel panel as the research object, and nonlinear finite element method was adopted to simulate the influence of pitting corrosion coverage area and pitting depth on its mechanical property degradation. The quasi-static compression, low-speed impact and three-point bending mechanical properties of panel with various DOPs and pitting depths were systematic studied.
Experimental and numerical analysis of humpback whale inspired tubercles on swept wings
Authors: Joseph Jeena , A. Sathyabhama , Sridhar Surya
Published: April 2022

Purpose

With aims to increase the aerodynamic efficiency of aerodynamic surfaces, study on flow control over these surfaces has gained importance. With the addition of flow control devices such as synthetic jets and vortex generators, the flow characteristics can be modified over the surface and, at the same time, enhance the performance of the body. One such flow control device is the tubercle. Inspired by the humpback whale’s flippers, these leading-edge serrations have improved the aerodynamic efficiency and the lift characteristics of airfoils and wings. This paper aims to discusses in detail the flow physics associated with tubercles and their effect on swept wings.

Design/methodology/approach

This study involves a series of experimental and numerical analyses that have been performed on four different wing configurations, with four different sweep angles corresponding to 0°, 10°, 20° and 30° at a low Reynolds number corresponding to Rec=100,000.

Findings

Results indicate that the effect of tubercles diminishes with an increase in wing sweep. A significant performance enhancement was observed in the stall and post-stall regions. The addition of tubercles led to a smooth post-stall lift characteristic compared to the sudden loss in the lift with regular wings. Among the four different wings under observation, it was found that tubercles were most effective on the 0° configuration (no sweep), showing a 10.8% increment in maximum lift and a 38.5% increase in the average lift generated in the post-stall region. Tubercles were least effective on 30° configuration. Furthermore, with an increase in wing sweep, co-rotating vortices were distinctly observed rather than counter-rotating vortices.

Originality/value

While extensive numerical and experimental studies have been performed on straight wings with tubercles, studies on the tubercle effect on swept wings at low Reynolds number are minimal and mainly experimental in nature. This study uses numerical methods to explore the complex flow physics associated with tubercles and their implementation on swept wings. This study can be used as an introductory study to implement passive flow control devices in the low Reynolds number regime.
Can corporate–nonprofit partnerships buffer socially irresponsible corporations from stakeholder backlash?
Authors: Wang Rong , O'Connor Amy
Published: April 2022

Purpose

This study aims to investigate the complex relationship between corporate–nonprofit partnership characteristics (type, duration and source of communication); attitude toward the corporation (pretest and posttest); partnership evaluation; and stakeholders' willingness to engage in anti-corporate behaviors when a corporation behaves irresponsibly and negatively impacts an individual's community. The three partnership characteristics are evaluated, individually and collectively, to discern which, if any, characteristics protect or buffer a corporation from stakeholders' engagement in negative communication behaviors when controlling for how stakeholders evaluate the partnership and the corporation.

Design/methodology/approach

The study used an online experiment with 970 participants who were randomly assigned to a 2 × 2 × 3 × 2 factorial design.

Findings

Contrary to some previous research findings, this study found that individuals who evaluate either the corporation or the partnership favorably are more likely to engage in anti-corporate behaviors. Neither the partnership type nor communication source provides a buffering effect. The only partnership characteristic to generate a buffering effect was duration and that only occurred if the partnership lasted three years. This study concludes that when corporate social responsibility (CSR) and corporate social irresponsibility (CSI) co-occur, an amplification rather than mollifies stakeholders' willingness to enact anti-corporate communication behaviors in instances of CSI.

Originality/value

This study advances scholarly understanding of CSR and CSI as in-tandem concepts and practices. The findings challenge previous claims that corporate–nonprofit partnerships can buffer corporations from negative events. In contrast, we find that partnerships are limited in their ability to reduce stakeholders' willingness to engage in anti-corporate behaviors in instances of CSR. It also answers calls that CSR research should use non-fictitious companies to increase ecological validity of the study design.
Multiobjective optimization based on polynomial chaos expansions in the design of inductive power transfer systems
Authors: Pei Yao , Pichon Lionel , Bensetti Mohamed , Le Bihan Yann
Published: April 2022

Purpose

The purpose of this study is to decrease the computation time that the large number of simulations involved in a parametric sweep when the model is in a three-dimensional environment.

Design/methodology/approach

In this paper, a new methodology combining the PCE and a controlled, elitist genetic algorithm is proposed to design IPT systems. The relationship between the quantities of interest (mutual inductance and ferrite volume) and structural parameters (ferrite dimensions) is expressed by a PCE metamodel. Then, two objective functions corresponding to mutual inductance and ferrite volume are defined. These are combined together to obtain optimal parameters with a trade-off between these outputs.

Findings

According to the number of individuals and the generations defined in the optimization algorithm in this paper, it needs to calculate 20,000 times in a 3D environment, which is quite time-consuming. But for PCE metamodel of mutual inductance M, it requires at least 100 times of calculations. Afterward, the evaluation of M based on the PCE metamodel requires 1 or 2 s. So compared to a conventional optimization based on the 3D model, it is easier to get optimized results with this approach and it saves a lot of computation time.

Originality/value

The multiobjective optimization based on PCEs could be helpful to perform the optimization when considering the system in a realistic 3D environment involving many parameters with low computation time.