bluuebunny/crossref_metadata_2025 huggingface dataset:
Computational Analysis of Maize Enhancer Regulatory Elements Using ATAC-STARR-seq
Authors: Marand Alexandre P.
Published: January 2023

The blueprints to development, response to the environment, and cellular function are largely the manifestation of distinct gene expression programs controlled by the spatiotemporal activity ofcis-regulatory elements. Although biochemical methods for identifying accessible chromatin – a hallmark of activecis-regulatory elements – have been developed, approaches capable of measuring and quantifyingcis-regulatory activity are only beginning to be realized. Massively Parallel Reporter Assays coupled to chromatin accessibility profiling present a high-throughput solution for testing the transcription-activating capacity of millions of putatively regulatory DNA sequences in parallel.

However, clear computational pipelines for analyzing these high-throughput sequencing-based reporter assays are lacking. In this protocol, I layout and rationalize a computational framework for the processing and analysis of Assay for Transposase Accessible Chromatin profiling followed by Self-Transcribed Active Regulatory Region sequencing (ATAC-STARR-seq) data from a recent study inZea mays. The approach described herein can be adapted to other sequencing-based reporter assays and is largely agnostic to the model organism with the appropriate input substitutions.
YAP and TAZ couple osteoblast precursor mobilization to angiogenesis and mechanoregulated bone development
Authors: Collins Joseph M. , Lang Annemarie , Parisi Cristian , Moharrer Yasaman , Nijsure Madhura P. , Kim Jong Hyun (Thomas) , Szeto Greg L. , Qin Ling , Gottardi Riccardo L. , Dyment Nathanial A. , Nowlan Niamh C. , Boerckel Joel D.
Published: January 2023

Endochondral ossification requires coordinated mobilization of osteoblast precursors with blood vessels. During adult bone homeostasis, vessel adjacent osteoblast precursors respond to and are maintained by mechanical stimuli; however, the mechanisms by which these cells mobilize and respond to mechanical cues during embryonic development are unknown. Previously, we found that deletion of the mechanoresponsive transcriptional regulators, YAP and TAZ, from Osterix-expressing osteoblast precursors and their progeny caused perinatal lethality. Here, we show that embryonic YAP/TAZ signaling couples vessel-associated osteoblast precursor mobilization to angiogenesis in developing long bones. Osterix-conditional YAP/TAZ deletion impaired endochondral ossification in the primary ossification center but not intramembranous osteogenesis in the bone collar. Single-cell RNA sequencing revealed YAP/TAZ regulation of the angiogenic chemokine, Cxcl12, which was expressed uniquely in vessel-associated osteoblast precursors. YAP/TAZ signaling spatially coupled osteoblast precursors to blood vessels and regulated vascular morphogenesis and vessel barrier function. Further, YAP/TAZ signaling regulated vascular loop morphogenesis at the chondro-osseous junction to control hypertrophic growth plate remodeling. In human cells, mesenchymal stromal cell co-culture promoted 3D vascular network formation, which was impaired by stromal cell YAP/TAZ depletion, but rescued by recombinant CXCL12 treatment. Lastly, YAP and TAZ mediated mechanotransduction for load-induced osteogenesis in embryonic bone.
Microbial methane cycling in a landfill on a decadal time scale
Authors: Grégoire Daniel S. , George Nikhil A. , Hug Laura A.
Published: January 2023

Landfills generate outsized environmental footprints due to microbial degradation of organic matter in municipal solid waste, which produces the potent greenhouse gas methane. With global solid waste production predicted to increase 69% by the year 2050, there is a pressing need to better understand the biogeochemical processes that control microbial methane cycling in landfills. In this study, we had the rare opportunity to characterize the microbial community responsible for methane cycling in landfill waste covering a 39-year timeframe. We coupled long term geochemical analyses to whole-community DNA (i.e., metagenomic) sequencing and identified key features that shape methane cycling communities over the course of a landfill’s lifecycle. Anaerobic methanogenic microbes are more abundant, diverse, and metabolically versatile in newer waste, fueling rapid methane production early in a landfill’s lifecycle. Aerobic methanotrophs were repeatedly found in leachate where low levels of oxygen were present and exhibited adaptations that aid survival under steep redox gradients in landfills. The potential for anaerobic methane oxidation, which has historically been overlooked despite anoxic habitats dominating landfills, was prevalent in a 26-year-old landfill cell which was in a state of slow methanogenesis. Finally, we identified the metabolic potential for methane oxidation in lineages that are widespread in aquatic and terrestrial habitats, whose capacity to metabolize methane remains poorly characterized. Ultimately, this work expands the diversity of methane cycling guilds in landfills and outlines how these communities can curb methane emissions from municipal solid waste.

Significance

Microbes are major contributors to methane emissions from solid waste however the temporal dynamics of methane cycling communities in landfills remain poorly understood. We addressed this gap by using whole-community DNA (i.e., metagenomic) approaches to characterize microbial methane cycling in waste covering a 39-year timeframe. We show that methane-producing microbes are more abundant, diverse, and metabolically versatile in new waste compared to old waste. We highlight that methane oxidation in the absence of oxygen is overlooked in landfill biogeochemical models and that novel lineages can potentially contribute to methane sinks across a broad range of habitats. These findings can strengthen predictive models for methane cycling in landfills and inform sustainable waste management strategies to curb methane emissions from solid waste.
Dasatinib Resensitizes MAPK Inhibitor Efficacy in Standard-of-Care Relapsed Melanomas
Authors: Rebecca Vito W. , Xiao Min , Kossenkov Andrew , Godok Tetiana , Brown Gregory Schuyler , Fingerman Dylan , Alicea Gretchen M. , Wei Meihan , Ji Hongkai , Bravo Jeremy , Chen Yeqing , Fane Mitchell E. , Villanueva Jessie , Nathanson Katherine , Liu Qin , Gopal Y. N. Vashisht , Davies Michael A. , Herlyn Meenhard
Published: January 2023

Resistance to combination BRAF/MEK inhibitor (BRAFi/MEKi) therapy arises in nearly every patient withBRAFV600E/Kmelanoma, despite promising initial responses. Achieving cures in this expanding BRAFi/MEKi-resistant cohort represents one of the greatest challenges to the field; few experience additional durable benefit from immunotherapy and no alternative therapies exist. To better personalize therapy in cancer patients to address therapy relapse, umbrella trials have been initiated whereby genomic sequencing of a panel of potentially actionable targets guide therapy selection for patients; however, the superior efficacy of such approaches remains to be seen. We here test the robustness of the umbrella trial rationale by analyzing relationships between genomic status of a gene and the downstream consequences at the protein level of related pathway, which find poor relationships between mutations, copy number amplification, and protein level. To profile candidate therapeutic strategies that may offer clinical benefit in the context of acquired BRAFi/MEKi resistance, we established a repository ofpatient-derivedxenograft models from heavily pretreated patients with resistance to BRAFi/MEKi and/or immunotherapy (R-PDX). With these R-PDXs, we executedin vivocompound repurposing screens using 11 FDA-approved agents from an NCI-portfolio with pan-RTK, non-RTK and/or PI3K-mTOR specificity. We identify dasatinib as capable of restoring BRAFi/MEKi antitumor efficacy in ∼70% of R-PDX tested. A systems-biology analysis indicates elevated baseline protein expression of canonical drivers of therapy resistance (e.g., AXL, YAP, HSP70, phospho-AKT) as predictive of MAPKi/dasatinib sensitivity. We therefore propose that dasatinib-based MAPKi therapy may restore antitumor efficacy in patients that have relapsed to standard-of-care therapy by broadly targeting proteins critical in melanoma therapy escape. Further, we submit that this experimental PDX paradigm could potentially improve preclinical evaluation of therapeutic modalities and augment our ability to identify biomarker-defined patient subsets that may respond to a given clinical trial.

SINGLE SENTENCE SUMMARY

Broad target inhibition effective as a salvage strategy in BRAF/MEK inhibitor-acquired resistance PDX
The impact of selected abiotic factors on zooplankton hatching process through real-time, in-situ observation
Authors: Dey Preyojon , Bradley Terence M. , Boymelgreen Alicia
Published: January 2023

Current studies on abiotic impacts on marine microorganisms often focus on endpoint analysis (e.g., hatching rates, survival). Here, we demonstrate that a mechanistic understanding can be obtained through real-time measurement of respiration and morphology in controlled microenvironments over extended time periods. As a demonstration, temperature and salinity are chosen to represent critical abiotic parameters that are also threatened by climate change and a target species ofArtemia, a prominent zooplankton whose reproduction can affect the marine food pyramid. Different temperatures (20, 35, and 30ºC) and salinities (0, 25, 50, and 75 ppt) are shown to significantly alter the duration of hatching stages, metabolic rates, and hatchability. Higher temperatures and moderate salinity boosted metabolic reactivation of latent cysts, while higher temperatures alone sped up the process. Hatchability is inversely related to the duration of the differentiation stage of hatching, which persisted longer at lower temperatures and salinities. Initial oxygen availability affects respiration but not hatchability owing to temperature and salinity interactions.

Graphical abstract
mini-MEndR: A 96-well mixed species culture assay to co-evaluate human and mouse Pax7+cell-mediated skeletal muscle repair
Authors: Gulati Nitya , Davoudi Sadegh , Xu Bin , Rjaibi Saifedine T. , Jacques Erik , Pham Justin , Fard Amir , McGuigan Alison P. , Gilbert Penney M.
Published: January 2023

Functional evaluation of molecules that are predicted to promote stem cell mediated endogenous repair often requiresin vivotransplant studies that are low throughput and hinder the rate of discovery. Here, we offer a strategy to rapidly test and prioritize molecules for functional validation studies. We miniaturized, simplified and expanded the functionality of a previously developed muscle endogenous repair (MEndR)in vitroassay that was shown to capture significant events of the first week of thein vivomuscle endogenous repair process. The new “mini-MEndR assay” consists of miniaturized cellulose scaffolds designed to fit in 96-well plates. The scaffold pores are infiltrated with myoblasts encapsulated in a fibrin-based hydrogel to form thin, engineered skeletal muscle tissues. By evaluating multiple commercially available human primary myoblast lines in 2D and 3D culture, we establish quality assurance metrics for cell line selection that standardize myotube template quality. Pre-adsorbing thrombin to the cellulose scaffolds facilitatesin situtissue polymerization, a critical modification that enables users proficient in myoblast culture to rapidly acquire myotube template fabrication expertise. Following the generation of the 3D myotube template, muscle stem cells (MuSCs), enriched from digested mouse skeletal muscle tissue using an improved magnetic-activated cell sorting protocol, are engrafted onto the engineered human muscle template. A regenerative milieu is then introduced by injuring the muscle tissue with a myotoxin. Addition of a known modulator of MuSC mediated repair recapitulates thein vivooutcomes (enhanced muscle production and Pax7+cell expansion), but only in the presence of both the stem cells and the regenerative milieu. By fluorescently labeling the mouse MuSCs, we demonstrate the feasibility of co-evaluating human and mouse Pax7+cell responses to drug treatment, thereby expanding the utility of the assay. Importantly, phenotypic data is collected with a high-content imaging system and is analyzed using CellProfiler-based image analysis pipelines. The miniaturized predictive assay offers a simple, scaled platform with which to co-investigate human and mouse skeletal muscle endogenous repair molecular modulators, and thus is a promising strategy to accelerate the muscle endogenous repair discovery pipeline.
A new Karyopherin-β2 binding PY-NLS epitope of HNRNPH2 is linked to neurodevelopmental disorders
Authors: Gonzalez Abner , Kim Hong Joo , Freibaum Brian D. , Joyce Fung Ho Yee , Brautigam Chad A. , Taylor J. Paul , Chook Yuh Min
Published: January 2023

The normally nuclear HNRNPH2 is mutated inHNRNPH2-related X-linked neurodevelopmental disorder causing the protein to accumulate in the cytoplasm. Interactions of HNRNPH2 with its importin Karyopherin–β2 (Transportin-1) had not been studied. We present a structure that shows Karyopherin-β2 binding HNRNPH2 residues 204-215, a proline-tyrosine nuclear localization signal or PY-NLS that contains a typical R-X2-4-P-Y motif,206RPGPY210, followed a new Karyopherin-β2 binding epitope at211DRP213that make many interactions with Karyopherin-β2 W373. Mutations at each of these sites decrease Karyopherin-β2 binding affinities by 70-100 fold, explaining aberrant accumulation in cells and emphasizing the role of nuclear import defects in the disease. Sequence/structure analysis suggests that the new epitope C-terminal of the PY-motif, which binds Karyopherin-β2 W373, is rare and thus far limited to close paralogs HNRNPH2, HNRNPH1 and HNRNPF. Karyopherin-β2 W373, a HNRNPH2-binding hotspot, corresponds to W370 of close paralog Transportin-2, a site of pathological variants in patients with neurodevelopmental abnormalities, suggesting that Transportin-2-HNRNPH2/H1/F interactions may be compromised in the abnormalities.

HNRNPH2 variants inHNRNPH2-related X-linked neurodevelopmental disorder aberrantly accumulate in the cytoplasm. A structure of Karyopherin-β2•HNRNPH2 explains nuclear import defects of the variants, reveals a new NLS epitope that suggests mechanistic changes in pathological variants of Karyopherin-β2 paralog Transportin-2.
Sex and estrous cycle stage shape left-right asymmetry in chronic hippocampal seizures in mice
Authors: Cutia Cathryn A. , Leverton Leanna K. , Christian-Hinman Catherine A.
Published: January 2023

Lateralization of hippocampal function is indicated by varied outcomes of patients with neurological disorders that selectively affect one hemisphere of this structure, such as temporal lobe epilepsy (TLE). The intrahippocampal kainic acid (IHKA) injection model of TLE allows for targeted damage to the left or right hippocampus, enabling systematic comparison of effects of left-right asymmetry on seizure and non-seizure outcomes. Although varying non-seizure phenotypic outcomes based on injection side in dorsal hippocampus were recently evaluated in this model, differences in chronic seizure patterns in left- (IHKA-L) vs. right-injected (IHKA-R) IHKA animals have yet to be evaluated. Here, we evaluated hippocampal seizure incidence in male and female IHKA-L and IHKA-R mice. Females displayed increased electrographic seizure activity compared to males at both 2 months and 4 months post-injection (mpi). In addition, IHKA-L females showed higher seizure frequency than IHKA-R on diestrus and estrus at 2 mpi, but seizure duration and time in seizures were only higher in IHKA-L females on diestrus. These cycle stage-associated changes, however, did not persist to 4 mpi. Furthermore, this lateralized difference in seizure burden was not observed in males. These results indicate for the first time that the side of IHKA injection can shape chronic electrographic seizure burden. Overall, these results demonstrate a female-specific left-right asymmetry in hippocampal function can interact with estrous cycle stage to shape chronic seizures in mice with epilepsy, with implications for neural activity and behavior in both normal and disease states.
Threat and reward imminence processing in the human brain
Authors: Murty Dinavahi V. P. S. , Song Songtao , Surampudi Srinivas Govinda , Pessoa Luiz
Published: January 2023

In the human brain, aversive and appetitive processing have been studied with controlled stimuli in rather static settings. In addition, the extent to which aversive- and appetitive-related processing engage distinct or overlapping circuits remains poorly understood. Here, we sought to investigate the dynamics of aversive and appetitive processing while male and female participants engaged in comparable trials involving threat-avoidance or reward-seeking. A central goal was to characterize the temporal evolution of responses during periods ofthreat or reward imminence. For example, in the aversive domain, we predicted that the bed nucleus of the stria terminalis (BST), but not the amygdala, would exhibit anticipatory responses given the role of the former in anxious apprehension. We also predicted that the periaqueductal gray (PAG) would exhibit threat-proximity responses based on its involvement in proximal-threat processes, and that the ventral striatum would exhibit threat-imminence responses given its role in threat escape in rodents. Overall, we uncovered imminence-related temporally increasing (“ramping”) responses in multiple brain regions, including the BST, PAG, and ventral striatum, subcortically, and dorsal anterior insula and anterior midcingulate, cortically. Whereas the ventral striatum generated anticipatory responses in the proximity of reward as expected, it also exhibited threat-related imminence responses. In fact, across multiple brain regions, we observed a main effect of arousal. In other words, we uncovered extensive temporally-evolving, imminence-related processing in both the aversive and appetitive domain, suggesting that distributed brain circuits are dynamically engaged during the processing of biologically relevant information irrespective of valence, findings further supported by network analysis.

Significance Statement

In the human brain, aversive and appetitive processing have been studied with controlled stimuli in rather static settings. Here, we sought to investigate the dynamics of aversive/appetitive processing while participants engaged in trials involving threat-avoidance or reward-seeking. A central goal was to characterize the temporal evolution of responses during periods ofthreat or reward imminence. We uncovered imminence-related temporally increasing (“ramping”) responses in multiple brain regions, including the bed nucleus of the stria terminalis, periaqueductal gray, and ventral striatum, subcortically, and dorsal anterior insula and anterior midcingulate, cortically. Overall, we uncovered extensive temporally-evolving, imminence-related processing in both the aversive and appetitive domain, suggesting that distributed brain circuits are dynamically engaged during the processing of biologically relevant information irrespective of valence.
Genome-wide association analysis of plasma lipidome identifies 495 genetic associations
Authors: Ottensmann Linda , Tabassum Rubina , Ruotsalainen Sanni E. , Gerl Mathias J. , Klose Christian , Widén Elisabeth , FinnGen  , Simons Kai , Ripatti Samuli , Pirinen Matti
Published: January 2023

Human plasma lipidome captures risk for cardio-metabolic diseases. To discover new lipid-associated variants and understand link between lipid species and cardiometabolic disorders, we performed univariate and multivariate genome-wide analyses of 179 lipid species in 7,174 Finnish individuals. We further fine-mapped the associated loci, prioritized genes, and examined their disease links in 377,277 FinnGen participants. We identified 495 genome-trait associations in 56 genetic loci including 9 novel loci, with a considerable boost provided by multivariate analysis. For 26 loci, fine-mapping identified variants with a high causal probability, including 14 coding variants indicating likely causal genes. Phenome-wide analysis across 953 disease endpoints in FinnGen revealed disease associations for 40 lipid loci. For 11 known coronary artery disease risk variants, we detected strong associations with lipid species. Our study demonstrates the power of multivariate genetic analysis in correlated lipidomics data and reveals genetic links between diseases and detailed lipid measures beyond standard lipids.
Increased AGE-RAGE axis stress in methamphetamine (MA) abuse and MA-induced psychosis: associations with oxidative stress and increased atherogenicity
Authors: Al-Hakeim Hussein Kadhem , Altufaili Mazin Fadhil , Alhaideri Amer Fadhil , Almulla Abbas F. , Moustafa Shatha Rouf , Maes Michael
Published: January 2023

Background and aims

Methamphetamine (MA)-induced psychosis (MIP) is associated with increased oxidative toxicity (especially lipid peroxidation) and lowered antioxidant defenses. Advanced glycation end products (AGEs) cause oxidative stress upon ligand binding to AGE receptors (RAGE). There are no data on whether MA use may cause AGE-RAGE stress, and whether the latter is associated with MIP.

Methods

This case-control study recruited 60 patients with MA use disorder and 30 normal controls and measured serum levels of oxidative stress toxicity (OSTOX, lipid peroxidation), antioxidant defenses (ANTIOX), magnesium, copper, atherogenicity, and AGE, soluble RAGE (sRAGE), and computed a composite reflecting AGE-RAGE axis activity.

Findings

MA dependence and use were accompanied by increased AGE, sRAGE, AGE-RAGE, OSTOX/ANTIOX, Castelli risk index 1 and atherogenic index of plasma, indicating that MA causes AGE-RAGE axis stress, oxidative damage, and atherogenicity. The severity of dependence and MA dose were strongly correlated with increased sRAGE concentrations. Increased AGE-RAGE stress was strongly associated with OSTOX, OSTOX/ANTIOX, and MA-induced intoxication symptoms, psychosis, hostility, excitation, and formal thought disorders. We found that 54.8% of the variance in MIP symptoms was explained by the regression on AGE-RAGE, the OSTOX/ANTIOX ratio, lowered magnesium, and increased copper, and that these biomarkers mediated the effects of increasing MA doses on MIP symptoms. We found that 36.0% of the variance in the atherogenicity indices was explained by OSTOX/ANTIOX, AGE-RAGE, and lowered magnesium.

Conclusions

MA use causes intertwined increases in AGE-RAGE axis stress and oxidative damage, which together predict the severity of MIP symptoms and increased atherogenicity.
Development and qualification of a high-yield recombinant human Erythropoietin biosimilar
Authors: Nag Kakon , Islam Md. Jikrul , Rahman Khan Md. Maksudur , Rahman Chowdhury Md. Mashfiqur , Haq Sarker Md. Enamul , Kumar Samir , Khan Habiba , Chakraborty Sourav , Roy Rony , Roy Raton , Kaunain Oli Md. Shamsul , Barman Uttam , Hasan Bappi Md. Emrul , Biswas Bipul Kumar , Mohiuddin Mohammad , Sultana Naznin
Published: January 2023

Recombinant human erythropoietin (rhEPO) has been saving millions of lives worldwide as a potent and safe treatment for the lack of erythrocyte, which is caused by chronic kidney disease (CKD) and other issues. Several biosimilars of rhEPO have been approved since the expiry of the relevant patents to provide cost-effective options but the price of rhEPO is still high for the affordability of global community. Therefore, development of biosimilar of rhEPO at a lower price is highly necessary. Here we report the development and characterization of a biosimilar of rhEPO with high-yield satisfying regulatory requirements. The hEPO-expressing cDNA was stably expressed in CHO cells with successive transfection. The master cell bank (MCB) and working cell bank (WCB) were established from the best selected clone and characterized for 50 passages. The rhEPO was expressed from the WCB in single-use suspension culture system with a high-titer (1.24±0.16 g/L). To the best of our knowledge this is the highest reported rhEPO titer to date. The rhEPO was purified using a series of validated chromatography unit processes including virus inactivation and filtration. The purified EPO was formulated in serum-free buffer, sterile filtered, and analyzed as the biosimilar of reference product Eprex®. Physicochemical analysis strongly suggested similarities between the developed rhEPO (GBPD002) and the reference. Thein vitroandin vivofunctional assays confirmed the similar biofunctionality of the GBPD002 and Eprex®. GBPD002 could provide a less-expensive solution to the needful communities as an effective and safe biosimilar where rhEPO treatment is necessary.
Sensitized piRNA reporter identifies multiple RNA processing factors involved in piRNA-mediated gene silencing
Authors: Brown Jordan , Zhang Donglei , Chen Wenjun , Lee Heng-Chi
Published: January 2023

Metazoans guard their germlines against transposons and other foreign transcripts with PIWI-interacting RNAs (piRNAs). Due to the robust heritability of the silencing initiated by piRNAs inC.elegans, previous screens usingCaenorhabditis eleganswere strongly biased to uncover members of this pathway in the maintenance process but not in the initiation process. To identify novel piRNA pathway members, we have utilized a sensitized reporter strain which detects defects in initiation, amplification, or regulation of piRNA silencing. Using our reporter, we have identified Integrator complex subunits, nuclear pore components, protein import components, and pre-mRNA splicing factors as essential for piRNA-mediated gene silencing. We found the snRNA processing cellular machine termed the Integrator complex is required for both type I and type II piRNA production. Notably, we identified a role for nuclear pore and nucleolar components in promoting the perinuclear localization of anti-silencing CSR-1 Argonaute, as well as a role for Importin factor IMA-3 in nuclear localization of silencing Argonaute HRDE-1. Together, we have shown that piRNA silencing is dependent on evolutionarily ancient RNA processing machinery that has been co-opted to function in the piRNA mediated genome surveillance pathway.
RawHash: Enabling Fast and Accurate Real-Time Analysis of Raw Nanopore Signals for Large Genomes
Authors: Firtina Can , Ghiasi Nika Mansouri , Lindegger Joel , Singh Gagandeep , Cavlak Meryem Banu , Mao Haiyu , Mutlu Onur
Published: January 2023

Nanopore sequencers generate electrical raw signals in real-time while sequencing long genomic strands. These raw signals can be analyzed as they are generated, providing an opportunity for real-time genome analysis. An important feature of nanopore sequencing, Read Until, can eject strands from sequencers without fully sequencing them, which provides opportunities to computationally reduce the sequencing time and cost. However, existing works utilizing Read Until either 1) require powerful computational resources that may not be available for portable sequencers or 2) lack scalability for large genomes, rendering them inaccurate or ineffective.

We propose RawHash, the first mechanism that can accurately and efficiently perform real-time analysis of nanopore raw signals for large genomes using a hash-based similarity search. To enable this, RawHash ensures the signals corresponding to the same DNA content lead to the same hash value, regardless of the slight variations in these signals. RawHash achieves an accurate hash-based similarity search via an effective quantization of the raw signals such that signals corresponding to the same DNA content have the same quantized value and, subsequently, the same hash value.

We evaluate RawHash on three applications: 1) read mapping, 2) relative abundance estimation, and 3) contamination analysis. Our evaluations show that RawHash is the only tool that can provide high accuracy and high throughput for analyzing large genomes in real-time. When compared to the state-of-the-art techniques, UNCALLED and Sigmap, RawHash provides 1) 25.8× and 3.4× better average throughput and 2) significantly better accuracy for large genomes, respectively. Source code is available athttps://github.com/CMU-SAFARI/RawHash.
TheMedicago truncatulanodule-specific cysteine-rich peptides, NCR343 and NCR-new35 are required for the maintenance of rhizobia in nitrogen-fixing nodules
Authors: Horváth Beatrix , Güngör Berivan , Tóth Mónika , Domonkos Ágota , Ayaydin Ferhan , Saifi Farheen , Chen Yuhui , Biró János Barnabás , Bourge Mickael , Szabó Zoltán , Tóth Zoltán , Chen Rujin , Kaló Péter
Published: January 2023

In the nodules of Inverted Repeat-Lacking Clade legumes, includingM. truncatula, nitrogen-fixing rhizobia undergo terminal differentiation resulting in elongated and endoreduplicated bacteroids specialised for nitrogen fixation. This irreversible transition of rhizobia is mediated by host produced nodule-specific cysteine-rich (NCR) peptides, of which about 700 are encoded in theM. truncatulagenome. Some of these NCR peptides, NCR169, NCR211 and NCR247, are essential for nitrogen-fixing symbiosis.

The analysis of bacteroid and symbiotic host cell differentiation revealed that the symbiotic phenotype ofM. truncatulamutants,Mtsym19,Mtsym20and NF-FN9363, were defective likewise in the formerly studiedncrmutants,Mtdnf4-1andMtdnf7-2. The incomplete differentiation of bacteroids triggered premature senescence of rhizobia in the nitrogen fixation zones of mutant nodules.

Mtsym19andMtsym20mutants are defective in the same peptide NCR-new35 and the lack ofNCR343is responsible for the ineffective symbiosis of NF-FN9363.

The activity ofNCR-new35is significantly lower and limited to the transition zone of the nodule compared with other crucialNCRs. The fluorescent protein-tagged version of NCR343 and NCR-new35 localize to the symbiotic compartment. Our discovery added two additional members to the group ofNCRgenes essential for nitrogen–fixing symbiosis inM. truncatula.
Cognitive and neural bases of salience-driven incidental learning
Authors: Sun Sai , Yu Hongbo , Wang Shuo , Yu Rongjun
Published: January 2023

Humans incidentally adjust their behavioral strategies along feedback dimensions even without explicit reasons to do so. How it occurs may depend on stable individual preferences and contextual factors, such as visual salience. We here examined how task-irrelevant visual salience exerts influence on attention and valuation systems that further drives incidental learning. We first established the baseline behavior with no salience emphasis in Exp.1. We then highlighted either the utility or performance dimension of the chosen outcome usingcolorsin Exp.2. We demonstrated that the difference in switching frequency increased along the salient dimension, confirming a strong salience effect. Moreover, the salience effect was abolished when directional information of feedback was removed in Exp.3, suggesting that the observed salience effect is specific to directional feedback. We then generalized our findings usingtextemphasis in Exp.4 and replicated the non-specific salience effects in Exp.5 with simultaneous eye-tracking. The fixation difference between chosen and unchosen values was enhanced along the feedback-specific salient dimension (Exp.4) but kept unchanged when removing directional information (Exp.5). Moreover, behavioral switching correlates with fixation difference, confirming that salience guides attention and further drives incidental learning. Lastly, our neuroimaging study (Exp.6) showed that the striatum subregions encoded salience-based outcome evaluation, while the vmPFC encoded salience-based behavioral adjustments. The connectivity of the vmPFC-ventral striatum accounted for individual differences in utility-driven, whereas the vmPFC-dmPFC for performance-driven behavioral adjustments. Our results provide a neurocognitive account of how task-irrelevant visual salience drives incidental learning by involving attention and the frontal-striatal valuation systems.
4-methylumbelliferone enhances neuroplasticity in the central nervous system: potential oral treatment for SCI
Authors: Irvine Sîan F. , Gigout Sylvain , Štěpánková Kateřina , Varea Noelia Martinez , Urdzíková Lucia Machová , Jendelová Pavla , Kwok Jessica C. F.
Published: January 2023

Perineuronal nets (PNNs) are specialised extracellular matrix (ECM) structures that act as key plasticity regulators to the central nervous system. Removal of PNNs using chondroitinase ABC injections restores plasticity, however, there are limitations to its application to due to its enzymatic nature. Here, we explore the use of a small molecule 4-methylumbelliferone (4-MU) as an alternative non-invasive strategy to reversibly remove PNNs and enhance plasticity. Oral administration of 4-MU for 10 days successfully and dynamically removed PNNsin vitro. While 4-MU, preferentially downregulated hyaluronan in the spinal cord, a down-regulation of chondroitin sulphate proteoglycans is also observed in the cortex. Long term administration for 8-weeks administration revealed a partial removal of PNNs, and that injury-induced mechanisms promoting cortical structural plasticity are linked to endogenous modulation of ECM molecules. 4-MU is a new tool to unravel the limits of normal and pathological PNN-mediated plasticity.
Heterologous expression of genes from a heterocystous cyanobacterial endosymbiont highlights organic carbon exchange with its diatom host
Authors: Nieves-Morión Mercedes , Camargo Sergio , Bardi Sepehr , Ruiz María Teresa , Flores Enrique , Foster Rachel A.
Published: January 2023

A few genera of diatoms are widespread and thrive in low nutrient waters of the open ocean due to their close association with N2-fixing, filamentous heterocyst-forming cyanobacteria. In one of these symbioses, the symbiont,Richelia euintracellularis, has penetrated the cell envelope of the host,Hemiaulus hauckii, and lives inside the host cytoplasm. How the partners interact, including how the symbiont sustains high rates of N2fixation is unstudied. SinceR. euintracellularishas evaded isolation, heterologous expression of genes in model laboratory organisms was performed to identify the function of proteins from the endosymbiont. Gene complementation of a cyanobacterial invertase mutant and expression of the protein inEscherichia colishowed thatR. euintracellularisHH01 possesses a neutral invertase that splits sucrose producing glucose and fructose. Several solute binding proteins (SBPs) of ABC transporters encoded in the genome ofR. euintracellularisHH01 were expressed inE. coliand their substrates were characterized. The selected SBPs directly linked the host as the source of several substrates, e.g., sugars (sucrose, galactose), amino acids (glutamate, phenylalanine) and a polyamine (spermidine), to support the cyanobacterial symbiont. Finally, transcripts of genes encoding the invertase and SBPs were consistently detected in wild populations ofH. hauckiicollected from multiple stations and depths in the western tropical North Atlantic. Our results support the idea that the diatom host provides the endosymbiotic cyanobacterium with organic carbon to fuel N2fixation. This knowledge is key to understand the physiology of the globally significantH. hauckii-R. euintracellularissymbiosis.

SIGNIFICANCE

Diatom diazotroph associations (DDAs) between diatoms and N2-fixing bacteria (diazotrophs) have a relevant impact on N2fixation-based production, but the mechanisms underlying their integrated N2and CO2fixation remain unstudied. In the association between the diatomHemiaulus hauckii(host) and the N2-fixing, heterocyst-forming cyanobacteriumRichelia euintracellularis(endosymbiont), the cyanobacterium is uncultivable. Here we used heterologous expression of genes from the endosymbiont to identify the function of proteins involved in the utilization of organic carbon from the host. The importance of these proteins was also confirmed by estimating gene expression in environmental samples. Our results show that the metabolisms of the symbiotic partners are integrated allowing the host to sustain the physiology of the endosymbiont for an important ecological role.
A bacterial tungsten-containing aldehyde oxidoreductase forms an enzymatic decorated protein nanowire
Authors: Winiarska Agnieszka , Ramírez-Amador Fidel , Hege Dominik , Gemmecker Yvonne , Prinz Simone , Hochberg Georg , Heider Johann , Szaleniec Maciej , Schuller Jan Michael
Published: January 2023

Aldehyde oxidoreductases (AOR) are tungsten enzymes catalysing the oxidation of many different aldehydes to the corresponding carboxylic acids. In contrast to other known AORs, the enzyme from the denitrifying betaproteobacteriumAromatoleum aromaticum(AORAa) consists of three different subunits (AorABC) and utilizes NAD as electron acceptor. Here we reveal that the enzyme forms filaments of repeating AorAB protomers which are capped by a single NAD-binding AorC subunit, based on solving its structure via cryo-electron microscopy. The polyferredoxin-like subunit AorA oligomerizes to an electron-conducting nanowire that is decorated with enzymatically active and W-cofactor (W-co) containing AorB subunits. Our structure further reveals the binding mode of the native substrate benzoate in the AorB active site. This, together with QM:MM-based modelling for the coordination of the W-co, enables formulation of catalytic mechanism hypothesis that paves the way for further engineering of AOR for applications in synthetic biology and biotechnology.
Epigenetic signature of human immune aging: the GESTALT study
Authors: Roy Roshni , Kuo Pei-Lun , Candia Julián , Sarantopoulou Dimitra , Ubaida-Mohien Ceereena , Hernandez Dena , Kaileh Mary , Arepalli Sampath , Singh Amit , Bektas Arsun , Kim Jaekwan , Moore Ann Zenobia , Tanaka Toshiko , McKelvey Julia , Zukley Linda , Nguyen Cuong , Wallace Tonya , Dunn Christopher , Wood William , Piao Yulan , Coletta Christopher , De Supriyo , Sen Jyoti Misra , Weng Nan-ping , Sen Ranjan , Ferrucci Luigi
Published: January 2023

Age-associated DNA methylation in blood cells convey information on health status. However, the mechanisms that drive these changes in circulating cells and their relationships to gene regulation are unknown. We identified age-associated DNA methylation sites in six purified blood borne immune cell types (naïve B, naïve CD4+and CD8+T cells, granulocytes, monocytes and NK cells) collected from healthy individuals interspersed over a wide age range. Of the thousand of age-associated sites, only 350 sites were differentially methylated in the same direction in all cell types and validated in an independent longitudinal cohort. Genes close to age-associated hypomethylated sites were enriched for collagen biosynthesis and complement cascade pathways, while genes close to hypermethylated sites mapped to neuronal pathways. In-silico analyses showed that in most cell types, the age-associated hypo- and hypermethylated sites were enriched for ARNT (HIF1β) and REST transcription factor motifs respectively, which are both master regulators of hypoxia response. To conclude, despite spatial heterogeneity, there is a commonality in the putative regulatory role with respect to transcription factor motifs and histone modifications at and around these sites. These features suggest that DNA methylation changes in healthy aging may be adaptive responses to fluctuations of oxygen availability.
Obstacle avoidance in aerial pursuit
Authors: Brighton Caroline H. , Kempton James A. , France Lydia A. , KleinHeerenbrink Marco , Miñano Sofia , Taylor Graham K.
Published: January 2023

Collision avoidance [1–4] and target pursuit [5–8] are challenging flight behaviors for any animal or autonomous vehicle, but their interaction is even more so [9–11]. For predators adapted to hunting in clutter, the demands of these two tasks may conflict, requiring effective reconciliation to avoid a hazardous collision or loss of target. Technical approaches to obstacle avoidance rely mainly on path-planning algorithms [12], but these are unlikely to be effective during closed-loop pursuit of a maneuvering target, so collision avoidance must instead be implemented reactively during prey pursuit. For example, the pursuit-avoidance behavior of predatory flies has been successfully modelled by combining feedback on target motion with feedback on obstacle looming [13]. It is unclear, however, whether this mechanism will generalize to complex environments with many looming obstacles, and it remains unknown how aerial predators reconcile the conflict between obstacle avoidance and prey pursuit in clutter. Here we use high-speed motion capture data to show how Harris’ hawksParabuteo unicinctusavoid collisions by making open-loop steering corrections during closed-loop pursuit. We find that hawks combine continuous feedback on target motion with a discrete feedforward steering correction aimed at clearing an upcoming obstacle as closely as possible at maximum span. By biasing the hawk’s flight direction, this guidance law provides an effective means of prioritizing obstacle avoidance whilst remaining locked-on to the target. We anticipate that a similar mechanism may be used in terrestrial and aquatic pursuit. The same biased guidance law could be used for obstacle avoidance in drones designed to intercept other drones in clutter, or in drones using closed-loop guidance to navigate between fixed waypoints in urban environments.
Hierarchical clinical decision support for breast cancer care empowered with Bayesian networks
Authors: Alomran Omran , Qiu Robin , Yang Hui
Published: January 2023

Purpose

Breast cancer is a global public health dilemma and the most prevalent cancer in the world. Effective treatment plans improve patient survival rates and well-being. The five-year survival rate is often used to develop treatment selection and survival prediction models. However, unlike other types of cancer, breast cancer patients can have long survival rates. Therefore, the authors propose a novel two-level framework to provide clinical decision support for treatment selection contingent on survival prediction.

Design/methodology/approach

The first level classifies patients into different survival periods using machine learning algorithms. The second level has two models with different survival rates (five-year and ten-year). Thus, based on the classification results of the first level, the authors employed Bayesian networks (BNs) to infer the effect of treatment on survival in the second level.

Findings

The authors validated the proposed approach with electronic health record data from the TriNetX Research Network. For the first level, the authors obtained 85% accuracy in survival classification. For the second level, the authors found that the topology of BNs using Causal Minimum Message Length had the highest accuracy and area under the ROC curve for both models. Notably, treatment selection substantially impacted survival rates, implying the two-level approach better aided clinical decision support on treatment selection.

Originality/value

The authors have developed a reference tool for medical practitioners that supports treatment decisions and patient education to identify patient treatment preferences and to enhance patient healthcare.
I can’t always get what I want: low power, service customer (dis)engagement and wellbeing
Authors: Abboud Liliane , Bruce Helen L. , Burton Jamie
Published: January 2023

Purpose

This paper aims to examine experiences of low customer power in service interactions and the impact of those experiences on customers’ engagement and disengagement towards a firm. It subsequently identifies how such experiences may affect customers’ wellbeing.

Design/methodology/approach

The authors conducted visual elicitation interviews with 30 customers of a range of services. Data were analysed thematically using abductive reasoning.

Findings

Low customer power is influenced by several factors perceived by customers as associated with the firm and/or the context of the customer–firm relationship. Results show that low power drives negative customer engagement and may result in behavioural disengagement. Low customer power, negative engagement and disengagement can have negative implications for customers’ eudaimonic (physical and financial) and hedonic wellbeing.

Research limitations/implications

Future studies might explore specific service contexts and power dynamics across service ecosystems and should further analyse the implications of these relationships on firms’ strategic organisational responses.

Practical implications

Firms should monitor customer power and explore means of enhancing the wellbeing of their customers through strategies designed to increase customer power, thus, reducing negative customer engagement and avoiding detrimental impact on customer wellbeing.

Originality/value

This study reframes discussions on low customer power in relation to firms and its impact on firms and customers. It identifies low customer power as a key variable in the study of customer engagement, disengagement and wellbeing.
How attractive are internship advertisements to prospective applicants? A mixed-method examination through the lens of employer branding
Authors: Plakhotnik Maria S. , Shmaytser Kristina S. , Feofilov Kirill A.
Published: January 2023

Purpose

The purpose of this study was to investigate attractiveness of internship advertisements to the prospective applicants through the lens of employer branding. By giving attention to internship attractiveness, universities and companies expand current collaborations around internship provision to enhance student internship experiences, satisfaction and employment prospects and to foster long-term sustainability of internship programs.

Design/methodology/approach

The study used a mixed-methods design employing a concurrent triangulation strategy. The authors conducted a content analysis of 94 internship listings published in the largest Russian job portal, HeadHunter, and collected surveys from 274 prospective interns.

Findings

The study shows a mismatch between employer branding strategies and prospective interns' perceptions of employer attractiveness. Companies emphasize economic value and visual identity as well as functional attributes, while prospective interns prioritize development value and symbolic attributes. The findings suggest internship advertisements do not appeal to potential applicants.

Research limitations/implications

The results are limited to business students from specific universities in Russia, so further research is needed to include students with different majors and from other countries. The study is also limited to advertisements available via a large online job portal. A comparative analysis of effectiveness of various communication channels for internship promotion could yield useful results.

Practical implications

Career center advisors, academic program directors and internship coordinators should work with company leaders, human resources and marketing decision-makers, and recruitment specialists to better understand interns' drivers of attraction and audit the internship advertisements. Employers could use the study results to strengthen recruiting messages and, hence, attractiveness of the employer brand to potential interns.

Originality/value

The study contributes by applying the employer branding theory to an understudied population of interns, hence providing new insights into internships as collaboration between universities and companies. By focusing on internship positions, which differ from full-time permanent positions across many aspects, including the positions' duration, pay, supervision and purpose, the study assists in understanding the distinct drivers of attraction of interns, which are missing from published research on the topic.