bluuebunny/crossref_metadata_2025 huggingface dataset:
FAIR Data Station for Lightweight Metadata Management & Validation of Omics Studies
Authors: Nijsse Bart , Schaap Peter J. , Koehorst Jasper J.
Published: August 2022

Background

The Life sciences is an interdisciplinary field of research and one of the the biggest suppliers of scientific data. Reusing and connecting this data can uncover hidden insights and lead to new concepts, provided there is machine-actionable metadata available about the scientific experiments conducted with a degree of completeness that reflect the FAIR guiding principles. While stakeholders have embraced the FAIR principles, in practice there are a limited number of easy to adopt practical implementations available that fulfil the needs of data producers.

Findings

We developed the FAIR Data Station, a lightweight application written in Java, that aims to support researchers in managing research metadata according to the FAIR principles. It uses the ISA metadata framework and metadata standards to capture experimental metadata. The FAIR Data Station metadata registration workflow consists of three main modules. Based on the minimal information checklist(s) selected by the user, a web-based “form generation module” creates a standardized metadata template Excel workbook which is used as a familiar environment for offline sample metadata registration. A web-based “validation module” checks the format of the metadata recorded in the workbook. The “resource module” subsequently exports the validated set of recorded metadata into an RDF data file, enabling (cross-project) meta data searches.

Conclusions

Turning FAIR into reality requires the availability of easy to adopt data FAIRification workflows that provide immediate beneficial incentives to the individual researcher. As such the FAIR Data Station provides in addition to the means to correctly FAIRify sequence data, the means to build searchable databases of (local) projects and can assists in ENA metadata submission of sequence data. The FAIR Data Station is available at http://fairbydesign.nl.
Interactions of curcumin’s degradation products with the Aβ42 dimer: A computational study
Authors: Dehabadi Maryam Haji , Caflisch Amedeo , Ilie Ioana M. , Firouzi Rohoullah
Published: August 2022

Amyloid-β (Aβ) dimers are the smallest toxic species along the amyloid aggregation pathway and among the most-populated oligomeric accumulations present in the brain affected by Alzheimer’s disease (AD). A proposed therapeutic strategy to avoid the aggregation of Aβ into higher order structures is to develop molecules that inhibit the early stages of aggregation, i.e. dimerization. Under physiological conditions the Aβ dimer is highly dynamic and does not attain a single well defined structure but is rather characterized by an ensemble of conformations. In a recent work, a highly heterogeneous library of conformers of the Aβ dimer was generated by an efficient sampling method with constraints based on ion mobility mass spectrometry data. Here, we make use of the Aβ dimer library to study the interaction with two curcumin degradation products, ferulic aldehyde and vanillin, by molecular dynamics (MD) simulations. Ensemble docking and MD simulations are used to provide atomistic detail of the interactions between the curcumin degradation products and the Aβ dimer. The simulations show that the aromatic residues of Aβ, and in particular 19FF20 interact with ferulic aldehyde and vanillin through π−π stacking. The binding of these small molecules induces significant changes on the 16KLVFF20 region.
TMAO Destabilizes RNA Secondary Structure via Direct Hydrogen Bond Interactions
Authors: Cho Samuel S. , Green Adam T. , Hyeon Changbong , Thirumalai D.
Published: August 2022

Trimethylamine N-oxide (TMAO) is an osmolyte that accumulates in cells in response to osmotic stress. TMAO stabilizes proteins by the entropic stabilization mechanism, which pictures TMAO as a nano-crowder that predominantly destabilizes the unfolded state. However, the mechanism of action of TMAO on RNA is much less understood. Here, we use all atom molecular dynamics simulations to investigate how TMAO interacts with a 12-nt RNA hairpin with a high melting temperature, and an 8-nt RNA hairpin, which has a relatively fluid native basin in the absence of TMAO. The use of the two hairpins with different free energy of stabilization allows us to probe the origin of the destabilization effect of TMAO on RNA molecules without the possibility of forming tertiary interactions. We generated multiple trajectories using allatom molecular dynamics (MD) simulations in explicit water by employing AMBER and CHARMM force fields, both in the absence and presence of TMAO. We observed qualitatively similar RNA-TMAO interaction profiles from the simulations using the two force fields. TMAO hydrogen bond interactions are largely depleted around the paired RNA bases and ribose sugars. In contrast, we show that the oxygen atom in TMAO, the hydrogen bond acceptor, preferentially interacts with the hydrogen bond donors in the solvent exposed bases, such as those in the stem-loop, the destabilized base stacks in the unfolded state, especially in the marginally stable 8-nt RNA hairpin. The predicted destabilization mechanism through TMAO-RNA hydrogen bond interactions could be tested using two-dimensional IR spectroscopy. Since TMAO does not significantly interact with the hydroxyl group of the ribose sugars, we predict that similar results must also hold for DNA.
Multi-environment Genome Wide Association Studies of Yield Traits in Common Bean (Phaseolus vulgaris L.) × Tepary Bean (P. acutifolius A. Gray) Interspecific Advanced Lines at the Humid and Dry Colombian Caribbean Subregions
Authors: López-Hernández Felipe , Burbano-Erazo Esteban , León-Pacheco Rommel Igor , Cordero-Cordero Carina Cecilia , Villanueva-Mejía Diego F. , Tofiño-Rivera Adriana Patricia , Cortés Andrés J.
Published: August 2022

Genome Wide Associations Studies GWAS are a powerful strategy for the exploration adaptive genetic variation to drought stress in advanced lines in common bean with interspecific genotypes, yet they still lack behind in the use of arid multi-environments as the subregions of the Colombian Caribbean. In order to bridge this gap, we couple an advanced genotypes panel integrated with Common Bean (Phaseolus vulgaris L.) × Tepary Bean (P. acutifolius A. Gray) interspecific lines with GWAS algorithms to identify novel sources of drought tolerance across the subregions of Colombian Caribbean. One of the most important challenges in agriculture is to achieve food security in environments vulnerable to climate change which worsens with the passing of the years. The common bean, a key product of the food basket of vulnerable regions of the Caribbean is affected by the reduction in yield under drought stress. A total of 87 advanced accessions with interspecific lines were genotyped by sequencing (GBS), leading to the discovery of 15,645 single-nucleotide polymorphism (SNP) markers. Five yield traits were developed for each accession and inputted in GWAS algorithms (i.e. FarmCPU, and BLINK) to identify putative associated loci in drought stress. Best-fit models revealed 47 significantly associated alleles distributed in all 11 common bean chromosomes. Flanking candidate genes were identified using 1-kb genomic windows centered in each associated SNP marker. A pathways enriched analysis was carried out using the mapped output in the GWAS step for each yield traits indices. Some of these genes were directly linked to response mechanisms of drought stress to level morphological, physiological, metabolic, signal transduction, and fatty acid and phospholipid metabolism. This work offers putative associated loci for marker-assisted and genomic selection for drought tolerance in common bean. It also demonstrates that it is feasible to identify genome-wide associations with an interspecific panel of genotypes and modern GWAS algorithms in multiples environments.
Convection and extracellular matrix binding control interstitial transport of extracellular vesicles
Authors: Sariano Peter A. , Mizenko Rachel R. , Shirure Venktesh S. , Brandt Abigail , Nesiri Cem , Shergill Bhupinder , Rocke David M. , Carney Randy P. , George Steven C.
Published: August 2022

Extracellular vesicles (EVs) influence a host of normal and pathophysiological processes in vivo. Compared to soluble mediators, EVs are relatively large (~30-150 nm) and can traffic a wide range of proteins on their surface including extracellular matrix (ECM) binding proteins. We isolated EVs from the MCF10 series – a model human cell line of breast cancer progression – and demonstrated increasing presence of laminin-binding integrins α3β1 and α6β1 on the EVs as the malignant potential of the MCF10 cells increased. Transport of the EVs within a microfluidic device under controlled physiological interstitial flow (0.15-0.75 μm/s) demonstrated that convection was the dominant mechanism of transport. Binding of the EVs to the ECM enhanced the spatial concentration and gradient, which was partially mitigated by blocking integrins α3β1 and α6β1. Our studies demonstrate that convection and ECM binding are the dominant mechanisms controlling EV interstitial transport and should be leveraged in the design of nanotherapeutics.
Actin architecture steers microtubules in active cytoskeletal composite
Authors: Kučera Ondřej , Gaillard Jérémie , Guérin Christophe , Théry Manuel , Blanchoin Laurent
Published: August 2022

Cytoskeletal motility assays use surface-immobilised molecular motors to propel cytoskeletal filaments. These assays have been widely employed to characterise the motor properties and interactions of cytoskeletal elements with themselves or with external factors. Moreover, the motility assays are a promising class of bio-inspired active tools for nanotechnological applications. While effective utilisation of these assays involves controlling the filament direction and speed, either as a sensory readout or a functional feature, designing a subtle control embedded in the assay is an ongoing challenge. Here we investigate the interaction between motor-propelled microtubules and networks of actin filaments. We demonstrate that the microtubules respond to a network of actin filaments and that this response depends on the network’s architecture. Both linear actin filaments and a network of actin branched by the Arp2/3 complex decelerate microtubule gliding; however, an unbranched actin network provides additional guidance and effectively steers the microtubules. This effect, which resembles the recognition of cortical actin architecture by microtubules, is a conceptually new means of controlling the filament gliding in the motility assay with potential application in the design of active materials and cytoskeletal nano-devices.
Intra-peritoneal transplantation for efficient and easy generation of experimental acute myeloid leukemia in mice
Authors: Qian Fenghua , Arner Brooke E. , Nettleford Shaneice K. , Paulson Robert F. , Prabhu K. Sandeep
Published: August 2022

Objective

There is an unmet need for novel therapies to treat acute myeloid leukemia (AML) and the associated relapse that involves leukemia stem cells (LSCs). An experimental AML rodent model to test therapies based on successfully transplanting these cells via retro-orbital injections in recipient mice is fraught with challenges. The aim of this study was to develop an easy, reliable, and consistent method to generate a robust murine model of AML using an intra-peritoneal route.

Methods

Bone marrow cells were transduced with a retrovirus expressing human MLL-AF9 fusion oncoprotein. Efficiency of lineage negative (Lin−) and Lin−Sca-1+c-Kit+ (LSK) populations as donor LSCs in the development of primary AML was tested. We developed a new method to generate AML by intra-peritoneal injection and discuss the pros and cons of intra-peritoneal and retro-orbital injections in serial transplantations.

Results

Both Lin− and LSK cells transduced with human MLL-AF9 virus engrafted well in the bone marrow and spleen of recipients, leading to a full-blown AML. Intra-peritoneal injection of donor cells established AML in recipients upon serial transplantation.Infiltration of AML cells was detected in the blood, bone marrow, spleen, and liver of recipients by flow cytometry, qPCR, and histological analyses.

Conclusions

Intra-peritoneal injection is an efficient method of AML induction using serial transplantation of donor cells.

Delayed homing to bone marrow, seen in intra-peritoneal injection that impedes the progression of AML, can be easily overcome by increasing the number of transplanted donor cells.

Increasing the number of transplanted donor cells can also help shorten the duration of onset of AML.

Sorting of LSK population within donor cells is not necessary in the generation of MLL-AF9-induced primary AML given that Lin− population are equally efficient as LSK donor cells in primary transplantation of AML in mice.
A new Critically Endangered cloud forest tree Microcos (Grewiaceae-Malvaceae) from the Rumpi Hills of S.W. Region Cameroon
Authors: Cheek Martin , Edwards Sara , Onana Jean Michel
Published: August 2022

We describe Microcos rumpi (Grewiaceae-Malvaceae) as a new species to science from the Rumpi Hills of SW Region Cameroon, a proposed Tropical Important Plant Area. Confined on current evidence to submontane forest, the species is threatened by expanding habitat clearance for farms and is assessed as Critically Endangered. A massive tree, attaining 35 – 40 m height, and 80 cm trunk diameter at 1.3 m above ground, its biomass is calculated as in the range of 7 – 8 metric tonnes. It is the third tree species of the genus recorded from Cameroon and only the fourth recorded west of D.R. Congo. A key to these four species is presented.

The concept of Microcos in Africa in relation to Grewia is discussed, and three new combinations are made, transferring three species names from Grewia to Microcos: Microcos louisii (Wilczek) Cheek, M. evrardii(Wilczek) Cheek and M.schmitzii (Wilczek) Cheek.
Molecular formula discovery via bottom-up MS/MS interrogation
Authors: Xing Shipei , Shen Sam , Xu Banghua , Huan Tao
Published: August 2022

A substantial fraction of metabolic features remains undetermined in mass spectrometry (MS)-based metabolomics. Here we present bottom-up tandem MS (MS/MS) interrogation to illuminate the unidentified features via accurate molecular formula annotation. Our approach prioritizes MS/MS-explainable formula candidates, implements machine-learned ranking, and offers false discovery rate estimation. Compared to the existing MS1-initiated formula annotation, our approach shrinks the formula candidate space by 42.8% on average. The superior annotation accuracy of our bottom-up interrogation was demonstrated on reference MS/MS libraries and real metabolomics datasets. Applied on 155,321 annotated recurrent unidentified spectra (ARUS), our approach confidently annotated >5,000 novel molecular formulae unarchived in chemical databases. Beyond the level of individual metabolic features, we combined bottom-up MS/MS interrogation with global peak annotation. This approach reveals peak interrelationships, allowing the systematic annotation of 37 fatty acid amide molecules in human fecal data, among other applications. All bioinformatics pipelines are available in a standalone software, BUDDY (https://github.com/HuanLab/BUDDY/).
Early Side Effects after Administration of the 1st Dose of Oxford-AstraZeneca Vaccine
Authors: Singh Pramod , Faisal Abdul Rafae , Shah M. Hassaan , Saeed Ahmad , Younas Hadia , Butt Usamah Saeed , Pudasaini Sudip , Pasha Abdul Rafay , Rehman Umair
Published: August 2022

Vaccines have played a central role in minimizing new infections, the rate of hospitalizations, and the overall burden on the health sector. Fear of side-effects is the biggest and commonest reason for avoiding getting vaccinated. It is, therefore, essential to maintain the clarity and consistency of message, to support and encourage people to get vaccinated. This study aims to contribute in that regard, by registering and quantifying the early side-effects of the Oxford-AstraZeneca COVID-19 vaccine in Pakistan. This study employs a non-random cross-sectional design. Data collected from 477 participants using a structured questionnaire was used to investigate the relationship between socio-demographic characteristics and side effect profiles of the participants. Binomial Logistic Regression was used to analyze the data. Odds Ratio (OR) gives the likelihood of having a side effect versus the reference group. Significance level (α) for the probability value (p-value) is set at 0.05. Fever (30.19%) was the most commonly experienced side effect, followed closely by fatigue (22.01%). 71.11% of those with fever experienced low grade fever (99-100F) while 62.69% of body aches experienced were moderate in intensity (Grades 4-6). In general, younger people are significantly more likely (p=0.023) to experience side effects (OR-1 = 1.023: interpreted as 1.023 times increase per unit decrease in age). Similarly, they are more likely (p= 0.029) to have a headache (OR-1 =1.039). Also, they are more likely (p= 0.007) to have a body ache (OR-1 =1.038). The Oxford-AstraZeneca COVID-19 vaccine side-effects seem to be more prevalent among younger age groups, which points to increased vaccine safety among older individuals that are usually more susceptible to severe COVID-19 infection. In addition, we found a substantially reduced number of side-effects, as compared to the clinical trials, which is an encouraging indicator for vaccine safety.
Neuronal SNAP-23 scales hippocampal synaptic plasticity and memory
Authors: Huang Mengjia , Bin Na-Ryum , Rai Jayant , Ma Ke , Chow Chun Hin , Eide Sarah , Harada Hidekiyo , Xiao Jianbing , Feng Daorong , Sun Hong-Shuo , Feng Zhong-Ping , Gaisano Herbert Y. , Pessin Jeffrey E. , Monnier Philippe P. , Okamoto Kenichi , Zhang Liang , Sugita Shuzo
Published: August 2022

Soluble NSF Attachment protein REceptor (SNARE)-mediated membrane fusion plays a crucial role not only in presynaptic vesicle exocytosis but also in postsynaptic receptor delivery. The latter is considered particularly important for long-term synaptic plasticity and learning and memory, yet underlying mechanisms including the identity of the key SNARE proteins remain elusive. Here, we investigate the role of neuronal Synaptosomal-Associated Protein-23 (SNAP-23) by analyzing pyramidal-neuron specific SNAP-23 conditional knockout (cKO) mice. SNAP-23 immunostaining in postsynaptic spines was effectively decreased in the SNAP-23 cKO hippocampus. Electrophysiological analysis of SNAP-23 deficient neurons using acute hippocampal slices showed normal basal neurotransmission in CA3-CA1 synapses with unchanged AMPA and NMDA currents. Nevertheless, we found theta-burst stimulation induced long-term potentiation (LTP) was vastly diminished in SNAP-23 cKO. Moreover, unlike syntaxin-4 cKO mice in which both basal neurotransmission and LTP decrease manifested changes in a broad set of behavioral tasks, deficits of SNAP-23 cKO is more limited to spatial memory. Our data reveal that neuronal SNAP-23 is selectively crucial for synaptic plasticity and spatial memory without affecting basal glutamate receptor function.
The hologenome of Osedax frankpressi reveals the genetic interplay for the symbiotic digestion of vertebrate bone
Authors: Moggioli Giacomo , Panossian Balig , Sun Yanan , Thiel Daniel , Martín-Zamora Francisco M. , Tran Martin , Clifford Alexander M. , Goffredi Shana K. , Rimskaya-Korsakova Nadezhda , Jékelly Gáspár , Tresguerres Martin , Qian Pei-Yuan , Qiu Jian-Wen , Rouse Greg W. , Henry Lee M. , Martín-Durán José M.
Published: August 2022

The marine annelid Osedax has evolved a unique heterotrophic symbiosis that allows it to feed exclusively on sunken bones. Yet, the genetic and physiological principles sustaining this symbiosis are poorly understood. Here we show that Osedax frankpressi has a small, AT-rich genome shaped by extensive gene loss. While the Oceanospirillales endosymbiont of Osedax is enriched in genes for carbohydrate and nitrogen metabolism, O. frankpressi has undergone genetic changes to accommodate bone digestion, including the expansion of matrix metalloproteases, and a loss of pathways to synthesize amino acids that are abundant in collagen. Unlike other symbioses, however, innate immunity genes required to acquire and control the endosymbionts are reduced in O. frankpressi. These findings reveal Osedax has evolved an alternative genomic toolkit to bacterial symbiosis where host-symbiont co-dependence has favoured genome simplicity in the host to exploit the nutritionally unbalanced diet of bones.

Teaser

Genome reduction and adaptations for collagen digestion underpin the symbiosis of Osedax worms to exploit decaying bones.
AVP neurons act as the primary circadian pacesetter cells in vivo
Authors: Tsuno Yusuke , Peng Yubo , Horike Shin-ichi , Yamagata Kanato , Sugiyama Mizuki , Nakamura Takahiro J. , Daikoku Takiko , Maejima Takashi , Mieda Michihiro
Published: August 2022

The central circadian clock of the suprachiasmatic nucleus (SCN) is a network consisting of various neurons and glia. Individual cells have the autonomous molecular machinery of a cellular clock, but their intrinsic periods are considerably variable. Here, we show that arginine vasopressin (AVP) neurons set the ensemble period of the SCN network to control circadian behavior rhythm. Artificial lengthening of cellular periods by deleting casein kinase 1 delta (CK1δ) in the whole SCN lengthened the free-running period of behavior rhythm to an extent similar to CK1δ deletion specific to AVP neurons. In SCN slices, PER2::LUC reporter rhythms of these mice did not recapitulate the period lengthening. However, in vivo calcium rhythms of both AVP and vasoactive intestinal peptide (VIP) neurons demonstrated lengthened periods similar to the behavioral rhythm upon AVP neuron-specific CK1δ deletion. These results indicate that AVP neurons act as the primary determinant of the SCN ensemble period.
Detection of YAP1 and AR-V7 mRNA for Prostate Cancer prognosis using an ISFET Lab-On-Chip platform
Authors: Broomfield Joseph , Kalofonou Melpomeni , Pataillot-Meakin Thomas , Powell Sue M. , Moser Nicolas , Bevan Charlotte L. , Georgiou Pantelis
Published: August 2022

Prostate cancer (PCa) is the second most common cause of male cancer-related death worldwide. The gold standard of treatment for advanced PCa is androgen deprivation therapy (ADT). However, eventual failure of ADT is common and leads to lethal metastatic castration resistant PCa (mCRPC). As such, the detection of relevant biomarkers in the blood for drug resistance in mCRPC patients could lead to personalized treatment options. mRNA detection is often limited by the low specificity of qPCR assays which are restricted to specialised laboratories. Here, we present a novel reversetranscription loop-mediated isothermal amplification (RT-LAMP) assay and have demonstrated its capability for sensitive detection of AR-V7 and YAP1 RNA (3×101 RNA copies per reaction). This work presents a foundation for the detection of circulating mRNA in PCa on a non-invasive Lab-on-chip (LoC) device for use at point-of-care. This technique was implemented onto a Lab-on-Chip platform integrating an array of chemical sensors (ion-sensitive field-effect transistors - ISFETs) for real-time detection of RNA. Detection of RNA presence was achieved through the translation of chemical signals into electrical readouts. Validation of this technique was conducted with rapid detection (<15 min) of extracted RNA from prostate cancer cell lines 22Rv1s and DU145s.
In the spotlight, losing IR region: insights from euglenophytes challenge the importance of inverted repeats in the genomes of secondary plastids
Authors: Maciszewski Kacper , Fells Alicja , Karnkowska Anna
Published: August 2022

Plastids, similarly to mitochondria, are organelles of endosymbiotic origin, which retained their vestigial genomes (ptDNA). Their unique architecture, commonly referred to as the quadripartite (four-part) structure, is considered to be strictly conserved; however, the bulk of our knowledge on their variability and evolutionary transformations comes from studies of the primary plastids of green algae and land plants. To broaden our perspective, we obtained seven new ptDNA sequences from freshwater species of photosynthetic euglenids – a group which obtained secondary plastids, known to have dynamically evolving genome structure, via endosymbiosis with a green alga. Our analyses have demonstrated that the evolutionary history of euglenid plastid genome structure is exceptionally convoluted, riddled with losses and multiple subsequent regains of inverted ribosomal operon (rDNA) repeats, as well as independent acquisitions of tandemly repeated rDNA copies. Moreover, we have shown that inverted repeats in euglenid ptDNA do not share their genome stabilizing property documented in chlorophytes. We hypothesize that the degeneration of the quadripartite structure of euglenid plastid genomes is connected to the group II intron expansion. These findings challenge the current global paradigms of plastid genome architecture evolution, and underscore the often-underestimated divergence between the functionality of shared traits in primary and complex plastid organelles.
Detecting Boolean Asymmetric Relationships with a Loop Counting Technique and its Implications for Analyzing Heterogeneity within Gene Expression Datasets
Authors: Zhou Haosheng , Lin Wei , Labra Sergio R. , Lipton Stuart A. , Elman Jeremy A. , Schork Nicholas J. , Rangan Aaditya V.
Published: August 2022

Many traditional methods for analyzing gene-gene relationships focus on positive and negative correlations, both of which are a kind of ‘symmetric’ relationship. Biclustering is one such technique that typically searches for subsets of genes exhibiting correlated expression among a subset of samples. However, genes can also exhibit ‘asymmetric’ relationships, such as ‘if-then’ relationships used in boolean circuits. In this paper we develop a very general method that can be used to detect biclusters within gene-expression data that involve subsets of genes which are enriched for these ‘boolean-asymmetric’ relationships (BARs). These BAR-biclusters can correspond to heterogeneity that is driven by asymmetric gene-gene interactions, e.g., reflecting regulatory effects of one gene on another, rather than more standard symmetric interactions. Unlike typical approaches that search for BARs across the entire population, BAR-biclusters can detect asymmetric interactions that only occur among a subset of samples. We apply our method to a single-cell RNA-sequencing data-set, demonstrating that the statistically-significant BAR-biclusters indeed contain additional information not present within the more traditional ‘boolean-symmetric’-biclusters. For example, the BAR-biclusters involve different subsets of cells, and highlight different gene-pathways within the data-set. Moreover, by combining the boolean-asymmetric- and boolean-symmetric-signals, one can build linear classifiers which outperform those built using only traditional boolean-symmetric signals.
Analysis of companion cell and phloem metabolism using a transcriptome-guided model of Arabidopsis metabolism
Authors: Hunt Hilary , Brueggen Nico , Galle Alexander , Vanderauwera Sandy , Frohberg Claus , Fernie Alisdair R , Sonnewald Uwe , Sweetlove Lee J
Published: August 2022

Companion cells and sieve elements play an essential role in vascular plants and yet the details of the metabolism that underpins their function remain largely unknown. Here we construct a tissue-scale flux balance analysis (FBA) model to describe the metabolism of phloem loading in a mature Arabidopsis leaf. We explore the potential metabolic interactions between mesophyll cells, companion cells, and sieve elements based on current understanding of the physiology of phloem tissue and through the use of cell-type-specific transcriptome data as a weighting in our model. We find that companion cell chloroplasts likely play a very different role to mesophyll chloroplasts. Our model suggests that, rather than carbon capture, the most crucial function of companion cell chloroplasts is to provide photosynthetically-generated ATP to the cytosol. Additionally, our model predicts that the metabolites imported into the companion cell are not necessarily the same metabolites that are exported in phloem sap; phloem loading is more efficient if certain amino acids are synthesised in the phloem tissue. Surprisingly, in our model predictions the H+-PPiase is the more important contributor than the H+ ATPase to the energisation of the companion cell plasma membrane.
Novel adaptation supports enhanced macrophage efferocytosis in limited-oxygen environments
Authors: Wang Ya-Ting , Trzeciak Alissa , Rojas Waleska Saitz , Saavedra Pedro , Chen Yan-Ting , Chirayil Rachel , Etchegaray Jon Iker , Lucas Christopher D. , Puleston Daniel J. , Keshari Kayvan R. , Perry Justin S. A.
Published: August 2022

Apoptotic cell clearance (efferocytosis), a process essential for organismal homeostasis, is performed by phagocytes that inhabit a wide range of environments, including physiologic hypoxia. Here, we find macrophages, the predominant tissue-resident phagocyte, display enhanced efferocytosis under prolonged (chronic) physiological hypoxia, characterized by increased internalization and accelerated degradation of apoptotic cells. Analysis of mRNA and protein programs revealed that chronic physiological hypoxia induces two distinct but complimentary states in macrophages. The first, ‘primed’ state consists of concomitant induction of transcriptional and translational programs broadly associated with metabolism in apoptotic cell-naïve macrophages that persist during efferocytosis. The second, ‘poised’ state consists of transcription, but not translation, of phagocyte function programs in apoptotic cell-naïve macrophages that are subsequently translated during efferocytosis. Importantly, we discovered that both states are necessary for enhanced continual efferocytosis. Mechanistically, we find that one such ‘primed’ state consists of the efficient flux of glucose into a noncanonical pentose phosphate pathway (PPP) loop, whereby PPP-derived intermediates cycle back through the PPP to enhance production of NADPH. Furthermore, we found that PPP-derived NADPH directly supports enhanced continual efferocytosis under chronic physiological hypoxia via its role in phagolysosomal maturation and maintenance of cellular redox homeostasis. Thus, macrophages residing under chronic physiological hypoxia adopt states that both support cell fitness and ensure ability to perform essential homeostatic functions rapidly and safely.

Highlights

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Macrophages residing in chronic physiological hypoxia have enhanced apoptotic cell uptake and degradation

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Chronic physiological hypoxia induces both primed and poised states in macrophages

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Both primed and poised state programs directly support enhanced continual efferocytosis

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A noncanonical PPP loop, a unique primed state, directly supports enhanced efferocytosis and maintains redox homeostasis
Species invasions shift microbial phenology in a two-decade freshwater time series
Authors: Rohwer Robin R. , Hale Riley J. , Vander Zanden M. Jake , Miller Todd R. , McMahon Katherine D.
Published: August 2022

Invasive species impart abrupt changes on ecosystems, but their impacts on microbial communities are often overlooked. We paired a 20-year freshwater microbial community time series with zooplankton and phytoplankton counts, rich environmental data, and a 6-year cyanotoxin time series. We observed strong microbial phenological patterns that were disrupted by the invasions of spiny water flea (Bythotrephes cederströmii) and zebra mussels (Dreissena polymorpha). First, we detected shifts inCyanobacteriaphenology. After the spiny water flea invasion,Cyanobacteriadominance crept earlier into clearwater; and after the zebra mussel invasion,Cyanobacteriaabundance crept even earlier into the diatom-dominated spring. During summer, the spiny water flea invasion sparked a cascade of shifting diversity where zooplankton diversity decreased andCyanobacteriadiversity increased. Second, we detected shifts in cyanotoxin phenology. After the zebra mussel invasion, microcystin increased in early summer and the duration of toxin production increased by over a month. Third, we observed shifts in heterotrophic bacteria phenology. TheBacteroidotaphylum and members of the acINanopelagicaleslineage were differentially more abundant. The proportion of the bacterial community that changed also differed by season; the spring and clearwater bacterial communities changed most following the spiny water flea invasion that lessened clearwater duration and intensity, while the diverse summer bacterial community changed least following the zebra mussel invasion despite the observed shifts in diversity and toxicity during summer. These long-term invasion-mediated shifts in microbial phenology demonstrate the interconnectedness of microbes with the broader food web, and their susceptibility to long-term environmental change.

Significance Statement

Microbial communities are typically studied as part of the microbial loop, separately from the broader food web. Using a two-decade freshwater time series, we explored whether two species invasions that shifted the metazoan food web (spiny water flea and zebra mussels) also impacted the microbial communities. We looked for seasonal responses because the microbial communities had strong seasonal patterns. We discovered thatCyanobacteriaincreased early in the year, andCyanobacteriadiversity increased in the summer. Cyanotoxins also increased, along with the duration of toxin production. In the heterotrophic bacterial community, some organisms changed consistently within lineages and seasons while others diverged. These findings illustrate the importance of seasonal context, and highlight the interconnectedness of bacteria with the broader food web.
Collective polarization dynamics in gonococcal colonies
Authors: Hennes Marc , Bender Niklas , Cronenberg Tom , Welker Anton , Maier Berenike
Published: August 2022

Membrane potential in bacterial systems has been shown to be dynamic and tightly related to survivability at the single cell level. However, little is known about spatio-temporal patterns of membrane potential in bacterial colonies and biofilms. Here, we discovered a switch from uncorrelated to collective dynamics within colonies formed by the human pathogen Neisseria gonorrhoeae. In freshly assembled colonies, polarization is heterogeneous with instances of transient and uncorrelated hyper- or depolarization of individual cells. As colonies reach a critical size, the polarization behaviour switches to collective dynamics: A hyperpolarized shell forms at the centre, travels radially outward, and halts several micrometres from the colony periphery. Once the shell has passed, we detect an influx of potassium correlated with depolarisation. Transient hyperpolarization also demarks the transition from volume to surface growth. By combining simulations and the use of an alternative electron acceptor for the respiratory chain, we provide strong evidence that local oxygen gradients shape the collective polarization dynamics. Finally, we show that within the hyperpolarized shell, tolerance against aminoglycoside antibiotics but not against β-lactam antibiotics is increased, suggesting that depolarization instantaneously protects cells, while the protective effect of growth arrest does not set in immediately. These findings highlight that the polarization pattern can demark the differentiation into distinct subpopulations with different growth rates and antibiotic tolerance.

Significance statement

At the level of single bacteria, membrane potential is surprisingly dynamic and transient hyperpolarization has been associated with increased death rate. Yet, little is known about the spatiotemporal dynamics of membrane polarization during biofilm development. Here, we reveal a discrete transition from uncorrelated to collective polarization dynamics within spherical colonies. Suddenly, a shell of hyperpolarized cells forms at the colony centre and hyperpolarization travels radially outward. In the wake of this shell, bacteria depolarize, reduce their growth rate, and become tolerant against antibiotics, indicating the onset of habitat diversity. Single cell live imaging and modelling link hyperpolarization to an oxygen gradient formed within the colonies. We anticipate that dynamical polarization patterns are tightly connected to biofilm differentiation in various bacterial species.
Robust genetic analysis of the X-linked anophthalmic (Ie) mouse
Authors: Hernandez-Moran Brianda Areli , Papanastasiou Andrew S , Parry Dave , Meynert Alison , Gautier Phillipe , Grimes Graeme , Adams Ian R , Trejo-Reveles Violeta , Bengani Hemant , Keighren Margaret , Jackson Ian J , Adams David J , FitzPatrick David R , Rainger Joe
Published: August 2022

Anophthalmia (missing eye) describes a failure of early embryonic ocular development. Mutations in a relatively small set of genes account for 75% of bilateral anophthalmia cases, yet 25% of families currently are left without a molecular diagnosis. Here we report our experimental work that aimed to uncover the developmental and genetic basis of the anophthalmia characterising the X-linked Ie (eye-ear reduction) X-ray induced allele in mouse that was first identified in 1947. Histological analysis of the embryonic phenotype showed failure of normal eye development after the optic vesicle stage with particularly severe malformation of the ventral retina. Linkage analysis mapped this mutation to a ∼ 6Mb region on the X chromosome. Short and long read whole-genome sequencing (WGS) of affected and unaffected male littermates confirmed the Ie linkage but identified no plausible causative variants or structural rearrangements. These analyses did reduce the critical candidate interval and revealed evidence of multiple variants within the ancestral DNA, although none were found that altered coding sequences or that were unique to Ie. To investigate early embryonic events at a genetic level, we then generated mouse ES cells derived from male Ie embryos and wild type littermates. RNA-seq and accessible chromatin sequencing (ATAC-seq) data generated from cultured optic vesicle organoids did not reveal any large differences in gene expression or accessibility of putative cis-regulatory elements between Ie and wild type. However, an unbiased TF-footprinting analysis of accessible chromatin regions did provide evidence of a genome-wide reduction in binding of transcription factors associated with ventral eye development in Ie, and evidence of an increase in binding of the Zic-family of transcription factors, including Zic3, which is located within the Ie-refined critical interval. We conclude that the refined Ie critical region at chrX: 56,145,000-58,385,000 contains multiple genetic variants that may be linked to altered cis regulation but does not contain a convincing causative mutation. Changes in the binding of key transcription factors to chromatin causing altered gene expression during development, possibly through a subtle mis-regulation of Zic3, presents a plausible cause for the anophthalmia phenotype observed in Ie, but further work is required to determine the precise causative allele and its genetic mechanism.
Transfer learning identifies sequence determinants of regulatory element accessibility
Authors: Salvatore Marco , Horlacher Marc , Marsico Annalisa , Winther Ole , Andersson Robin
Published: August 2022

Dysfunction of regulatory elements through genetic variants is a central mechanism in the pathogenesis of disease. To better understand disease etiology, there is consequently a need to understand how DNA encodes regulatory activity. Deep learning methods show great promise for modeling of biomolecular data from DNA sequence but are limited to large input data for training. Here, we develop ChromTransfer, a transfer learning method that uses a pre-trained, cell-type agnostic model of open chromatin regions as a basis for fine-tuning on regulatory sequences. We demonstrate superior performances with ChromTransfer for learning cell-type specific chromatin accessibility from sequence compared to models not informed by a pre-trained model. Importantly, ChromTransfer enables fine-tuning on small input data with minimal decrease in accuracy. We show that ChromTransfer uses sequence features matching binding site sequences of key transcription factors for prediction. Together, these results demonstrate ChromTransfer as a promising tool for learning the regulatory code.
Naturalistic language comprehension is supported by alpha and beta oscillations linked to domain-general inhibition and reactivation
Authors: Zioga Ioanna , Weissbart Hugo , Lewis Ashley G. , Haegens Saskia , Martin Andrea E.
Published: August 2022

Brain oscillations are prevalent in all species and are involved in numerous perceptual operations. Alpha oscillations are thought to facilitate processing through the inhibition of task-irrelevant networks, while beta oscillations are linked to the reactivation of content representations. Can the proposed functional role of alpha and beta oscillations be generalized from low-level operations to higher-level cognitive processes? Here we address this question focusing on naturalistic spoken language processing. Twenty-two (18 female) Dutch native speakers listened to stories in spoken Dutch and French while magnetoencephalography (MEG) was recorded. We used dependency parsing to identify three dependency states at each word, as the number of (1) newly opened dependencies, (2) dependencies that remained open, and (3) resolved dependencies. We then constructed linear forward models to predict alpha and beta power from the dependency features. Results showed that dependency features predict alpha and beta power in language-related regions beyond low-level linguistic features. Left temporal, fundamental language regions are involved in language comprehension in the alpha band, while frontal and parietal, higher-order language regions, and motor regions are mostly involved in the beta band. Critically, alpha and beta band dynamics seem to subserve language comprehension tapping into syntactic structure building and semantic composition by providing low-level mechanistic operations for inhibition and reactivation processes. Overall, this study sheds light on the role of alpha and beta oscillations during naturalistic language processing, providing evidence for the generalizability of these dynamics from perceptual to complex linguistic processes.

Significance Statement

Prior research identified the functional role of alpha and beta oscillations in basic perceptual and motor functions. However, it remains unclear whether their proposed role can be generalized to higher-level processes during language comprehension. Here, we found that high-level syntactic features predict alpha and beta power in language-related regions beyond low-level linguistic features when listening to comprehensible naturalistic speech. Our work contributes to the debate about whether the functional roles of brain oscillations are domain-general or depend on the task at hand. We offer experimental findings that integrate a neuroscientific framework on the role of brain oscillations as “building blocks” with language comprehension as a compositional process, and novel evidence regarding the encoding of higher-level syntactic operations in the brain. This supports the view of a domain-general role of cortical oscillations across the hierarchy of cognitive functions, from low-level sensory operations to complex linguistic processes.
Genomic local adaptation of a generalist plant species to pollinator communities and abiotic factors
Authors: Frachon L. , Arrigo L. , Rusman Q. , Poveda L. , Qi W. , Scopece G. , Schiestl F.P.
Published: August 2022

The reproductive success of generalist flowering plants is influenced by a complex ecological network that includes interactions with a diverse pollinator community and abiotic factors. However, knowledge about of the adaptative potential of plants to complex ecological networks and the underlying genetic mechanisms is still limited. Based on a pool-sequencing approach of 21 natural populations of Brassica incana in Southern Italy, we combined a genome-environmental association analysis with a genome scan for signature of selection to discover genetic variants associated with ecological variation. We demonstrated that B. incana is locally adapted both to the identity of functional categories and overall pollinator interactions. Interestingly, we observed only few shared candidate genes associated with long-tongue bees, soil texture, and temperature variation. Our results highlight the genomic architecture of generalist flowering plant adaptation to complex biotic interactions, and the importance of considering multiple environmental factors to describe the adaptive landscape of plant populations.
SARS-CoV-2 entry route impacts a range of downstream viral and cellular processes
Authors: Qu Bingqian , Miskey Csaba , Gömer André , Potmus Dylan , Nocke Maximillian , Kleinert Robin D.V. , Itotia Tabitha K. , Valder Lara , Brückmann Janice , Höck Sebastian , Hastert Florian D. , von Rhein Christine , Schürmann Christoph , Ebenig Aileen , Widera Marek , Ciesek Sandra , Pfaender Stephanie , Ivics Zoltán , Schnierle Barbara S. , Tarr Alexander W. , Goffinet Christine , Mühlebach Michael D. , Todt Daniel , Brown Richard J.P.
Published: August 2022

SARS-CoV-2 entry is promoted by both cell-surface TMPRSS2 and endolysosomal cathepsins. To investigate the impact of differentially routed virions on host and viral processes, lung epithelial cells expressing distinct combinations of entry factors were infected with authentic viruses. Entry route determined early rates of viral replication and transcription, egress and inhibitor sensitivity, with differences observed between virus strains. Transcriptional profiling revealed that induction of innate immunity was correlated to viral genome and transcript abundance in infected cells. Surface entry triggered early activation of antiviral responses, reducing cumulative virion production, while endolysosomal entry delayed antiviral responses and prolonged virus shedding due to extended cell viability. The likely molecular footprints of escape from antiviral effector targeting were also recorded in viral genomes and correlated with entry route-dependent immune status of cells. TMPRSS2 orthologues from diverse mammals, but not zebra fish, facilitated infection enhancement, which was more pronounced for ancestral strains. Leveraging RNA-seq and scRNA-seq datasets from SARS-CoV-2 infected hamsters, we validate aspects of our model in vivo. In summary, we demonstrate that distinct cellular and viral processes are linked to viral entry route, collectively modulating virus shedding, cell-death rates and viral genome evolution.