bluuebunny/crossref_metadata_2025 huggingface dataset:
A high-continuity and annotated tomato reference genome
Authors: Su Xiao , Wang Baoan , Geng Xiaolin , Du Yuefan , Yang Qinqin , Liang Bin , Meng Ge , Gao Qiang , Huang Sanwen , Yang Wencai , Zhu Yingfang , Lin Tao
Published: May 2021

Genetic and functional genomics studies require a high-quality genome assembly. Tomato (Solanum lycopersicum), an important horticultural crop, is an ideal model species for the study of fruit development. Here, we assembled an updated reference genome ofS. lycopersicumcv. Heinz 1706 that was 799.09 Mb in length, containing 34,384 predicted protein-coding genes and 65.66% repetitive sequences. By comparing the genomes ofS. lycopersicumandS. pimpinellifoliumLA2093, we found a large number of genomic fragments probably associated with human selection, which may have had crucial roles in the domestication of tomato. Our results offer opportunities for understanding the evolution of the tomato genome and will facilitate the study of genetic mechanisms in tomato biology. Information for the assembled genome SLT1.0 was deposited both into the Genome Warehouse (GWH) database (https://bigd.big.ac.cn/gwh/) in the BIG Data Center under Accession Number GWHBAUD00000000.
Delta oscillations coordinate intra-cerebellar and cerebello-hippocampal network dynamics during sleep
Authors: Torres-Herraez A , Watson TC , Rondi-Reig L
Published: May 2021

During sleep, the widespread coordination of neuronal oscillations across both cortical and subcortical brain regions is thought to support various physiological functions, including memory consolidation. However, how sleep-related activity within the brain’s largest sensorimotor structure, the cerebellum, is multiplexed with well described sleep-related mechanisms in regions such as the hippocampus remains unknown.

To address this gap in knowledge, we simultaneously recorded from the dorsal hippocampus and three distinct regions of the cerebellum (Crus I, lobule VI and lobules II/III) during natural murine sleep. We found that LFP oscillations are coordinated between the two structures in a sleep-stage specific manner. Particularly during non-REM sleep, prominent delta frequency coherence was observed between lobule VI and hippocampus. We additionally observed that non-REM associated hippocampal sharp wave ripple activity can drive discrete LFP modulation in all the recorded cerebellar regions, with the shortest latency effects observed in lobule VI.

We also describe discrete phasic sharp potentials, synchronized across cerebellar regions, which were strongly phase locked to the peak of ongoing cerebellar delta oscillations and found in greatest numbers during REM. These phasic sharp potentials recorded within the cerebellar cortex were found to be phase-locked to the trough of the hippocampal theta oscillation, further suggesting cross-structural coordination. During REM, cerebellar delta oscillation phase significantly modulated hippocampal theta frequency, and this effect was greatest when phasic sharp potentials were most abundant. Within all three cerebellar regions, prominent LFP oscillations were observed at both low (delta, <4 Hz) and very high frequencies (~ 250 Hz) during non-REM and REM sleep. Intra-cerebellar cross-frequency analysis revealed that delta frequency oscillations strongly modulate those in the very high frequency range.

Together, these results reveal multiple candidate physiological mechanisms to support ‘offline’, bi-directional interaction within distributed cerebello-hippocampal networks. In particular, we describe a prominent cerebellar delta oscillation, which appears to act as a temporal coordinator of cerebellar activity at both local (intra-cerebellar) and distributed (cerebello-hippocampal) network levels.
Inter-laboratory automation of thein vitromicronucleus assay using imaging flow cytometry and deep learning
Authors: Wills John W. , Verma Jatin R. , Rees Benjamin J. , Harte Danielle S. G. , Haxhiraj Qiellor , Barnes Claire M. , Barnes Rachel , Rodrigues Matthew A. , Doan Minh , Filby Andrew , Hewitt Rachel E. , Thornton Catherine A. , Cronin James G. , Kenny Julia D. , Buckley Ruby , Lynch Anthony M. , Carpenter Anne E. , Summers Huw D. , Johnson George , Rees Paul
Published: May 2021

Thein vitromicronucleus assay is a globally significant method for DNA damage quantification used for regulatory compound safety testing in addition to inter-individual monitoring of environmental, lifestyle and occupational factors. However it relies on time-consuming and user-subjective manual scoring. Here we show that imaging flow cytometry and deep learning image classification represents a capable platform for automated, inter-laboratory operation. Images were captured for the cytokinesis-block micronucleus (CBMN) assay across three laboratories using methyl methanesulphonate (1.25 – 5.0 µg/mL) and/or carbendazim (0.8 – 1.6 µg/mL) exposures to TK6 cells. Human-scored image sets were assembled and used to train and test the classification abilities of the “DeepFlow” neural network in both intra- and inter-laboratory contexts. Harnessing image diversity across laboratories yielded a network able to score unseen data from an entirely new laboratory without any user configuration. Image classification accuracies of 98%, 95%, 82% and 85% were achieved for ‘mononucleates’, ‘binucleates’, ‘mononucleates with MN’ and ‘binucleates with MN’, respectively. Successful classifications of ‘trinucleates’ (90%) and ‘tetranucleates’ (88%) in addition to ‘other or unscorable’ phenotypes (96%) were also achieved. Attempts to classify extremely rare, tri- and tetranucleated cells with micronuclei into their own categories were less successful (≤ 57%). Benchmark dose analyses of human or automatically scored micronucleus frequency data yielded quantitation of the same equipotent dose regardless of scoring method. We conclude that this automated approach offers significant potential to broaden the practical utility of the CBMN method across industry, research and clinical domains. We share our strategy using openly-accessible frameworks.
Flexible neural control of motor units
Authors: Marshall Najja J. , Glaser Joshua I. , Trautmann Eric M. , Amematsro Elom A. , Perkins Sean M. , Shadlen Michael N. , Abbott L.F. , Cunningham John P. , Churchland Mark M.
Published: May 2021

Voluntary movement requires communication from cortex to the spinal cord, where a dedicated pool of motor units (MUs) activates each muscle. The canonical description of MU function rests upon two foundational tenets. First, cortex cannot control MUs independently but supplies each pool with a common drive. Second, MUs are recruited in a rigid fashion that largely accords with Henneman’s size principle. While this paradigm has considerable empirical support, a direct test requires simultaneous observations of many MUs across diverse force profiles. We developed an isometric task that allowed stable MU recordings even during rapidly changing forces. MU activity patterns were surprisingly behavior-dependent. MU activity could not be accurately described as reflecting common drive, but could be captured by assuming multiple drives. Neuropixels probe recordings revealed that, consistent with the requirements of flexible control, the motor cortex population response displays a great many degrees of freedom. Neighboring cortical sites recruited different MUs. Thus, MU activity is flexibly controlled to meet task demands, and cortex may contribute to this ability.
Telomeric 8-Oxoguanine Drives Rapid Premature Senescence In The Absence Of Telomere Shortening
Authors: Barnes Ryan P. , de Rosa Mariarosaria , Thosar Sanjana A. , Detwiler Ariana C. , Roginskaya Vera , Van Houten Bennett , Bruchez Marcel P. , Stewart-Ornstein Jacob , Opresko Patricia L.
Published: May 2021

Oxidative stress is a primary cause of cellular senescence and contributes to the pathogenesis of numerous human diseases. Oxidative damage to telomeric DNA is proposed to trigger premature senescence by accelerating telomere shortening. Here we tested this model directly using a precision tool to produce the common base lesion 8-oxo-guanine (8oxoG) exclusively at telomeres in human fibroblast and epithelial cells. A single induction of telomeric 8oxoG is sufficient to trigger multiple hallmarks of p53-dependent senescence. Telomeric 8oxoG activates ATM and ATR signaling, and enriches for markers of telomere dysfunction in replicating, but not quiescent cells. Acute 8oxoG production fails to shorten telomeres, but rather generates fragile sites and delayed mitotic DNA synthesis at telomeres, indicative of impaired replication. Based on our results we propose that oxidative stress promotes rapid senescence by producing oxidative base lesions which drive replication-dependent telomere fragility and dysfunction in the absence of shortening and shelterin loss.
Genetic determinism of phage-bacteria coevolution in natural populations
Authors: Piel Damien , Bruto Maxime , Labreuche Yannick , Blanquart Francois , Chenivesse Sabine , Lepanse Sophie , James Adèle , Barcia-Cruz Rubén , Dubert Javier , Petton Bruno , Lieberman Erica , Wegner K. Mathias , Hussain Fatima A. , Kauffman Kathryn M. , Polz Martin F. , Bikard David , Gandon Sylvain , Le Roux Frédérique
Published: May 2021

Coevolution between bacteriophage (or phage) and their bacterial host is thought to be key for the coexistence of these antagonists. Recent studies have revealed the major role of mobile genetic elements in the emergence of phage resistant hosts but how phage escape these defenses in the wild remained to be explored. Here we show a striking parallel in phage evolving counter defenses to host defenses in natural population. We established a large collection of phages and their bacterial hosts and we explored the genetic structure of their interaction. We find that clearly delineated genomic clusters of phage are specific for distinct clades within a bacterial species,Vibrio crassostreae, yet while all phages can adsorb, only a subset of hosts are killed due to intracellular defense mechanisms. Host genomes contain multiple mobile defense genes and susceptibility to phage is negatively correlated with genome size. Phages also display extensive gene content variation, but their genome size remains conserved. We show that this gene content variation in hosts and phage is due to rapid turnover of genes involved in defense and escape, and that by exchanging anti-defense genes, phages irreversibly switch host. This could be indicative of co-evolution following the matching-allele-model of specificity and the spatial and temporal variability of phage infectivity further suggests that negative-frequency dependent selection drives phage-vibrio coevolutionary dynamics. We propose a “pan-escape system” that can be shared among phages by homologous recombination within a population that infects a bacterial host.
Behavioral-transcriptomic landscape of engineered T cells targeting human cancer organoids
Authors: Dekkers Johanna F. , Alieva Maria , Cleven Astrid , Keramati Farid , Brazda Peter , Rebel Heggert G. , Wezenaar Amber K.L. , Puschhof Jens , Buchholz Maj-Britt , Román Mario Barrera , Johanna Inez , Meringa Angelo D. , Fasci Domenico , Geurts Maarten H. , Ariese Hendrikus C.R. , van Vliet Esmée J. , van Ineveld Ravian L. , Karaiskaki Effrosyni , Kopper Oded , Bar-Ephraim Yotam E. , Kretzschmar Kai , Eggermont Alexander M.M. , Wehrens Ellen J. , Stunnenberg Henk G. , Clevers Hans , Kuball Jürgen , Sebestyen Zsolt , Rios Anne C.
Published: May 2021

Cellular immunotherapies are rapidly gaining clinical importance, yet predictive platforms for modeling their mode of action are lacking. Here, we developed a dynamic immuno-organoid 3D imaging-transcriptomics platform; BEHAV3D, to unravel the behavioral and underlying molecular mechanisms of solid tumor targeting. Applied to an emerging cancer metabolome-sensing immunotherapy: TEGs, we first demonstrate targeting of multiple breast cancer subtypes. Live-tracking of over 120,000 TEGs revealed a diverse behavioral landscape and identified a ‘super engager’ cluster with serial killing capability. Inference of single-cell behavior with transcriptomics identified the gene signature of ‘super engager’ killer TEGs, which contained 27 genes with no previously described T cell function. Furthermore, guided by a dynamic type 1 interferon (IFN-I) signaling module induced by high TEG-sensitive organoids, we show that IFN-I can prime resistant organoids for TEG-mediated killing. Thus, BEHAV3D characterizes behavioral-phenotypic heterogeneity of cellular immunotherapies and holds promise for improving solid tumor-targeting in a patient-specific manner.
No evidence that lulworthioid fungi are dark septate endophytes in the roots of the dominant Mediterranean seagrassPosidonia oceanica
Authors: Vohník Martin
Published: May 2021

A previous study from Sicily, Italy indicated that the dominant Mediterranean seagrassPosidonia oceanicaforms a dark septate endophytic (DSE) association with a lulworthioid fungus (“Lulwoanasp.”), which is in conflict with several other studies from the NW Mediterranean Sea that point at the recently described pleosporalean fungusPosidoniomyces atricolor.

I collectedP. oceanicaroots at eight sites around Sicily and checked them for fungal colonization using light microscopy. At three sites, root fungal symbionts (=mycobionts) were isolated into pure cultures and identified using sequencing of the ITS rDNA gene.

Posidoniomyces atricolorrepresented the most frequent mycobiont (56 isolates), closely followed by lulworthioid fungi (51). The obtained mycobiont spectrum also comprisedCladosporium(2),Alternaria(1),Corollospora(1),Fusarium(1),Penicillium(1) andVishniacozyma(1) isolates. The characteristic DSE root colonization similar to those occurring in terrestrial plants but not known from any other seagrass was found in all investigatedP. oceanicaindividuals. The microscopic screening suggests thatP. atricoloris indeed responsible for the observed DSE colonization.

This study extends the known range ofP. atricolorand the DSE association characteristic forP. oceanicafor southern Tyrrhenian Sea/Sicily. While lulworthioid fungi regularly occur inP. oceanicatissues, including terminal fine roots, their significance and functioning are unknown and beg further investigation. However, there are currently no proofs that they belong among dark septate endophytes of this seagrass.

One-sentence summary

This paper corrects an opinion that “Lulwoanasp.” (Lulworthiales) is a dark septate endophyte of the dominant Mediterranean seagrassPosidonia oceanica, because all available evidence suggests that the dark septate endophytic association typical for this seagrass is formed by its specific root mycobiontPosidoniomyces atricolor(Pleosporales).
Ssl2/TFIIH function in Transcription Start Site Scanning by RNA Polymerase II in Saccharomyces cerevisiae
Authors: Zhao Tingting , Vvedenskaya Irina O. , Lai William K.M. , Basu Shrabani , Pugh B. Franklin , Nickels Bryce E. , Kaplan Craig D.
Published: May 2021

In Saccharomyces cerevisiae, RNA Polymerase II (Pol II) selects transcription start sites (TSS) by a unidirectional scanning process. During scanning, a preinitiation complex (PIC) assembled at an upstream core promoter initiates at select positions within a window ∼40-120 basepairs downstream. Several lines of evidence indicate that Ssl2, the yeast homolog of XPB and an essential and conserved subunit of the general transcription factor (GTF) TFIIH, drives scanning through its DNA-dependent ATPase activity, therefore potentially controlling both scanning rate and scanning extent (processivity). To address questions of how Ssl2 functions in promoter scanning and interacts with other initiation activities, we leveraged distinct initiation-sensitive reporters to identify novel ssl2 alleles. These ssl2 alleles, many of which alter residues conserved from yeast to human, confer either upstream or downstream TSS shifts at the model promoter ADH1 and genome-wide. Specifically, tested ssl2 alleles alter TSS selection by increasing or narrowing the distribution of TSSs used at individual promoters. Genetic interactions of ssl2 alleles with other initiation factors are consistent with ssl2 allele classes functioning through increasing or decreasing scanning processivity but not necessarily scanning rate. These alleles underpin a residue interaction network that likely modulates Ssl2 activity and TFIIH function in promoter scanning. We propose that the outcome of promoter scanning is determined by two functional networks, the first being Pol II activity and factors that modulate it to determine initiation efficiency within a scanning window, and the second being Ssl2/TFIIH and factors that modulate scanning processivity to determine the width of the scanning widow.
Activation of Histone 3 Lysine 9 methyl writing and reading capabilities within the G9a-GLP heterodimer
Authors: Sanchez Nicholas A , Kallweit Lena M , Trnka Michael J , Clemmer Charles L , Al-Sady Bassem
Published: May 2021

Unique among metazoan repressive histone methyltransferases, G9a and GLP, which chiefly target histone 3 lysine 9 (H3K9), require dimerization for productive H3K9 mono (me1)- and dimethylation (me2)in vivo. Intriguingly, even though each enzyme can independently methylate H3K9, the predominant active formin vivois a heterodimer of G9a and GLP. How dimerization influences the central H3K9 methyl binding (“reading”) and deposition (“writing”) activity of G9a and GLP, and why heterodimerization is essentialin vivoremains opaque. Here, we examine the H3K9me “reading” and “writing” activities of defined, recombinantly produced homo- and heterodimers of G9a and GLP. We find that both reading and writing are significantly enhanced in the heterodimer. Compared to the homodimers, the heterodimer has higher recognition of H3K9me2, and a striking ∼ 10-fold increased turnover rate for nucleosomal substrates under multiple turnover conditions, which is not evident on histone tail peptide substrates. Crosslinking Mass Spectrometry suggests that differences between the homodimers and the unique activity of the heterodimer may be encoded in altered ground state conformations, as each dimer displays different domain contacts. Our results indicate that heterodimerization may be required to relieve autoinhibition of H3K9me reading and chromatin methylation evident in G9a and GLP homodimers. Relieving this inhibition may be particularly important in early differentiation when large tracts of H3K9me2 are deposited by G9a-GLP, which may require a more active form of the enzyme.
Immune priming can prevent WNV establishment inCulex quinquefasciatusmosquitoes: evidence for immune priming based reversal of WNV-mediated immune suppression
Authors: Blagrove Marcus , Barribeau Seth M
Published: May 2021

Mosquito-borne infectious diseases cause wide-spread loss of life and livelihood often in low-income settings. However, control of mosquito-vectored viral diseases such as West Nile virus (WNV) and Japanese encephalitis virus (JEV) remains challenging. Here we use an existing feature of the insect immune system to effectively vaccinateCulex quinquefasciatusmosquitoes against WNV infection. We find that priming mosquitoes by exposure to inactivated WNV reduces their likelihood of developing transmissible infections of WNV after live infection. We used RNA sequencing to identify gene expression in response to WNV and JEV infection, and the role of prior priming exposure on constitutive and induced expression on infection. Infection with either Flavivirus causes broad suppression of gene expression. WNV and JEV infection resulted in suppression of different suites of genes with notable immune genes, such as antimicrobial peptides, being strongly suppressed on WNV infection. We hypothesise that the increased resistance to WNV infection seen in primed mosquitoes may be the result of priming nullifying the immune suppression found in non-primed WNV-fed mosquitoes, potentially through greater expression of mRNA regulatory genes such as cap-binding proteins in primed mosquitoes.

Author summary

Mosquitoes vector many devastating infectious diseases. Two such vectored viral diseases are West Nile virus (WNV) and Japanese encephalitis virus (JEV). Control of these diseases remains challenging, and no vaccine exists for WNV. Here, we tested whether we could instead vaccinate the mosquitoes against WNV. By injecting mosquitoes with dead WNV we found that we could reduce the number of infected mosquitoes by half. We then used whole-genome RNA sequencing to identify which genes are transcribed, which will help us understand genes that are important for this form of insect immune priming, and for responses to normal WNV and JEV infection. We found that WNV suppresses the expression of many immune genes but these genes are expressed normally in vaccinated mosquitoes. Our findings expand our understanding of mosquito infection with these viruses but also demonstrate how prior exposure to a disease can produce lasting protection.
A Kink in DWORF Helical Structure Controls the Activation of the Sarco-plasmic Reticulum Ca2+-ATPase
Authors: Reddy U. Venkateswara , Weber Daniel K. , Wang Songlin , Larsen Erik K. , Gopinath Tata , De Simone Alfonso , Robia Seth , Veglia Gianluigi
Published: May 2021

The sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) is a P-type ATPase embedded in the sarcoplasmic reticulum. For each enzymatic cycle, SERCA transports 2 Ca2+ions per ATP hydrolyzed in exchange for 2 to 3 H+ions. SERCA is responsible for approximately 70% of Ca2+transport and plays a central role in muscle relaxation. SERCA’s function is regulated by endogenous regulins, single-pass membrane proteins that bind the ATPase within the membrane. While most of the regulins, such as phospholamban and sarcolipin, inhibit SERCA’s activity, a newly discovered protein DWarf Open Reading Frame (DWORF) has a unique activating effect. DWORF is a 3.8 kDa bitopic membrane protein expressed in cardiac muscle. In this work, we determine the structure, topology, and per-residue lipid interactions of DWORF in lipid bilayers using a combination of high-resolution oriented sample solid-state NMR (OS-ssNMR) spectroscopy and refinement by replica-averaged orientationally-restrained molecular dynamics (RAOR-MD). We found that DWORF’s structural topology consists of a dynamic N-terminal domain, an amphipathic juxtamembrane helix that crosses the lipid groups at an angle of 64° and a transmembrane (TM) C-terminal helix with an angle of 32°. A kink induced by Pro15, unique to DWORF, separated the two helical domains. A single Pro15Ala mutant significantly decreases the kink and eliminates DWORF’s activating effect on SERCA. Overall, our findings directly link DWORF’s structural topology to its unique activating effect on SERCA.
Variation in Ubiquitin System Genes Creates Substrate-Specific Effects on Proteasomal Protein Degradation
Authors: Collins Mahlon A. , Mekonnen Gemechu , Albert Frank W.
Published: May 2021

Ubiquitin-proteasome system (UPS) protein degradation regulates protein abundance and eliminates mis-folded and damaged proteins from eukaryotic cells. Variation in UPS activity influences numerous cellular and organismal phenotypes. However, to what extent such variation results from individual genetic differences is almost entirely unknown. Here, we developed a statistically powerful mapping approach to characterize the genetic basis of variation in UPS activity. Using the yeastSaccharomyces cerevisiae, we systematically mapped genetic influences on the N-end rule, a UPS pathway that recognizes N-degrons, degradation-promoting signals in protein N-termini. We identified 149 genomic loci that influence UPS activity across the complete set of N-degrons. Resolving four loci to individual causal nucleotides identified regulatory and missense variants in ubiquitin system genes whose products process (NTA1), recognize (UBR1andDOA10), and ubiquitinate (UBC6) cellular proteins. Each of these genes contained multiple causal variants and several individual variants had substrate-specific effects on UPS activity. Acis-acting promoter variant that modulates UPS activity by alteringUBR1expression also alters the abundance of 36 proteins without affecting levels of the corresponding mRNAs. Our results demonstrate that natural genetic variation shapes the full sequence of molecular events in protein ubiquitination and implicate genetic influences on the UPS as a prominent source of post-translational variation in gene expression.
Multiple causal DNA variants in a single gene affect gene expression intrans
Authors: Lutz Sheila , Van Dyke Krisna , Albert Frank W.
Published: May 2021

Identifying the specific causal DNA differences in a genome that contribute to variation in phenotypic traits is a key goal of genetic research.Trans-acting DNA variants that alter gene expression are important sources of genetic variation. Several genes are known to carry single causal variants that affect the expression of numerous genes intrans. Whether these single variants are representative of the architecture oftrans-acting variation is unknown. Here, we studied the geneIRA2, which carries variants with broad,trans-acting effects on gene expression in two strains of the yeastSaccharomyces cerevisiae. We found thatIRA2contains at least seven causal nonsynonymous variants. The causal variants were located throughout the gene body and included a pair of neighboring variants with opposing effects that largely canceled each other out. The causal variants showed evidence for non-additive epistatic interactions, in particular among variants at the 5’ end of the gene. These results show that the molecular basis oftrans-acting variation can involve considerable complexity even within a single gene.
Nuclear NAD+-biosynthetic enzyme NMNAT1 facilitates survival of developing retinal neurons
Authors: Sokolov David , Sechrest Emily , Wang Yekai , Nevin Connor , Du Jianhai , Kolandaivelu Saravanan
Published: May 2021

Despite mounting evidence that the mammalian retina is exceptionally reliant on proper NAD+homeostasis for health and function, the specific roles of subcellular NAD+pools in retinal development, maintenance, and disease remain obscure. Here, we show that deletion of the nuclear-localized NAD+synthase nicotinamide mononucleotide adenylyltransferase-1 (NMNAT1) in the developing murine retina causes early and severe degeneration of photoreceptors and select inner retinal neurons via multiple distinct cell death pathways. This severe phenotype is associated with disruptions to retinal central carbon metabolism, purine nucleotide synthesis, and amino acid pathways. Furthermore, large-scale transcriptomics reveals dysregulation of a collection of photoreceptor and synapse-specific genes in NMNAT1 knockout retinas prior to detectable morphological or metabolic alterations. Collectively, our study reveals previously unrecognized complexity in NMNAT1-associated retinal degeneration and suggests a yet-undescribed role for NMNAT1 in gene regulation during photoreceptor terminal differentiation.
Ooids formingin situwithin microbial mats (Kiritimati atoll, central Pacific)
Authors: Suarez-Gonzalez Pablo , Reitner Joachim
Published: May 2021

Ooids (subspherical particles with a laminated cortex growing around a nucleus) are ubiquitous in the geological record since the Archean and have been widely studied for more than two centuries. However, various questions about them remain open, particularly about the role of microbial communities and organic matter in their formation and development. Although ooids typically occur rolling around in agitated waters, here we describe for the first time aragonite ooids forming statically within microbial mats from hypersaline ponds of Kiritimati (Kiribati, central Pacific). Subspherical particles had been previously observed in these mats and classified as spherulites, but they grow around autochthonous micritic nuclei, and many of them have laminated cortices, with alternating radial fibrous laminae and micritic laminae. Thus, they are compatible with the definition of ‘ooid’ and are in fact identical to many modern and fossil examples. Kiritimati ooids are more abundant and developed in some ponds and in some particular layers of the microbial mats, which has led to the discussion and interpretation of their formation processes as product of mat evolution, through a combination of organic and environmental factors. Radial fibrous laminae are formed during periods of increased supersaturation, either by metabolic or environmental processes. Micritic laminae are formed in closer association with the mat exopolymer (EPS) matrix, probably during periods of lower supersaturation and/or stronger EPS degradation. Therefore, this study represents a step forward in the understanding of ooid development as influenced by microbial communities, providing a useful analogue for explaining similar fossil ooids.
Remus: System for Remote Deep Brain Interventions
Authors: Webb Taylor D. , Wilson Matthew G. , Odéen Henrik , Kubanek Jan
Published: May 2021

Motivation

Transcranial focused ultrasound brings personalized medicine to the human brain. Ultrasound can modulate neural activity or release drugs in specific neural circuits but this personalized approach requires a system that delivers ultrasound into specified targets flexibly and on command.

We developed a remote ultrasound system (Remus) that programmatically targets deep brain regions with high spatiotemporal precision and in a multi-focal manner. We validated these functions by safely modulating two deep brain nuclei—the left and right lateral geniculate nucleus–in a task-performing non-human primate. This flexible system will enable researchers and clinicians to diagnose and treat specific deep brain circuits in a noninvasive yet targeted manner, thus embodying the promise of personalized treatments of brain disorders. Animated graphical abstract:onetarget.us/download/rem.
Beneficial and detrimental genes in the cellular response to replication arrest
Authors: Schons-Fonseca Luciane , Lazova Milena D. , Smith Janet L. , Grossman Alan D.
Published: May 2021

DNA replication is essential for all living organisms, and a variety of events can perturb replication, including DNA damage (e.g., pyrimidine dimers, crosslinking) and replication arrest due to “roadblocks” such as DNA-binding proteins or transcription. Bacteria have several well-characterized mechanisms for repairing damaged DNA and restoring functional replication forks. However, little is known about the repair of stalled or arrested replication forks in the absence of DNA lesions. Using a library of random transposon insertions inBacillus subtilis, we identified 35 genes that affect the ability of cells to survive arrest of replication elongation, in the absence of DNA damage. Genes identified included those involved in iron-sulfur homeostasis, cell envelope biogenesis, and DNA repair and recombination. InB. subtilis, and many bacteria, two nucleases (AddAB and RecJ) are involved in early steps in repairing replication forks arrested by DNA damage. Loss of either one causes increased sensitivity to DNA damage. These single-strand nucleases resect DNA ends, leading to assembly of the recombinase RecA onto the single stranded DNA. Notably, we found that disruption ofrecJincreased survival of cells following replication arrest, indicating that, in the absence of DNA damage, RecJ is detrimental to surviving replication arrest. In contrast, and as expected, disruption ofaddAdecreased survival of cells following replication arrest, indicating that AddA promotes survival. The different phenotypes ofaddAandrecJmutants appeared to be due to differences in assembly of RecA onto DNA. RecJ promoted too much assembly of RecA, and loss of RecA compensated for the detrimental effects of RecJ. Our results indicate that in the absence of DNA lesions, RecA is dispensable for cells to survive replication arrest and the stable RecA nucleofilaments favored by the RecJ pathway may lead to cell death by preventing proper processing of the arrested replication fork.
A Modified Comprehensive Grading System for Murine Knee Osteoarthritis: Scoring the Whole Joint as an Organ
Authors: Grote Caleb W. , Mackay Matthew J. , Liu Xiangliang , Lu Qinghua , Wang Jinxi
Published: May 2021

Objective

This study aimed to develop a comprehensive but easy to apply histologic grading system to score osteoarthritic changes in the whole knee joint for both spontaneous and posttraumatic osteoarthritis (OA) mouse models.

Methods

The new OA grading scheme was developed based on extensive literature review and the authors’ experience in mouse OA models with relatively long periods of observation (up to 24 months of age or 24-week post-surgery). Semi-quantitative assessments of the histopathologic OA changes were applied to all four quadrants of the knee. Grading elements per quadrant were defined as follows: cartilage (0-7) including three new grading elements for early- and late-stage OA, respectively; osteophyte (0-2) covering chondro-osteophytes in both outer and inner joint margins; subchondral bone (0-2) containing subchondral bone thickening and destruction; synovitis (0-2) comprised of both synovial plica and intercondylar notch; and peri-articular tissues (0-2) highlighting ectopic chondrogenesis and ossification in the knee capsule, ligament, and musculature.

Results

Statistical analyses showed that the new grading system had high intra- and inter-observer reproducibility (Pearson’s correlation coefficients r >0.9) for both experienced and novice scorers. Sensitivity and reliability analyses confirmed the ability of the new system to detect minimal OA progression between two timepoints with a two-week interval and to accurately identify tissue-specific OA severity within the knee joint.

Conclusions

The comprehensive histologic grading system presented here covers all-stage osteoarthritic changes in all major knee joint tissues of mice, which enable us to score OA severity for the whole joint reproducibly and accurately without software-assisted time-consuming measurements.
Covalent Flexible Peptide Docking in Rosetta
Authors: Tivon Barr , Gabizon Ronen , Somsen Bente A. , Cossar Peter J. , Ottmann Christian , London Nir
Published: May 2021

Electrophilic peptides that form an irreversible covalent bond with their target have great potential for binding targets that have been previously considered undruggable. However, the discovery of such peptides remains a challenge. Here, we present CovPepDock, a computational pipeline for peptide docking that incorporates covalent binding between the peptide and a receptor cysteine. We applied CovPepDock retrospectively to a dataset of 115 disulfide-bound peptides and a dataset of 54 electrophilic peptides, for which it produced a top-five scoring, near-native model, in 89% and 100% of the cases, respectively. In addition, we developed a protocol for designing electrophilic peptide binders based on known non-covalent binders or protein-protein interfaces. We identified 7,154 peptide candidates in the PDB for application of this protocol. As a proof-of-concept we validated the protocol on the non-covalent complex of 14-3-3σ and YAP1 phosphopeptide. The protocol identified seven highly potent and selective irreversible peptide binders. The predicted binding mode of one of the peptides was validated using X-ray crystallography. This case-study demonstrates the utility and impact of CovPepDock. It suggests that many new electrophilic peptide binders can be rapidly discovered, with significant potential as therapeutic molecules and chemical probes.
Spatial and ecological drivers of population structure inAlkanna tinctoria(Boraginaceae), a polyploid medicinal herb
Authors: Ahmad Muhammad , Leroy Thibault , Krigas Nikos , Temsch Eva M. , Weiss-Schneeweiss Hanna , Lexer Christian , Sehr Eva Maria , Paun Ovidiu
Published: May 2021

Background and Aims

Quantifying genetic variation is fundamental to understand a species’ demographic trajectory and its ability to adapt to future changes. In comparison to diploids, however, genetic variation and factors fostering genetic divergence remains poorly studied in polyploids due to analytical challenges. Here, by employing a ploidy-aware framework, we investigated the genetic structure and its determinants in polyploidAlkanna tinctoria(Boraginaceae), an ancient medicinal herb that is the source of bioactive compounds known as alkannin and shikonin (A/S). From a practical perspective, such investigation can inform biodiversity management strategies.

Methods

We collected 14 populations ofA. tinctoriawithin its main distribution range in Greece and genotyped them using restriction site-associated DNA sequencing (RAD-seq). As an outgroup, we included two populations ofA. sieberi. By using a ploidy-aware genotype calling based on likelihoods, we generated a dataset of 16,107 high quality SNPs. Classical and model-based analysis was done to characterize the genetic structure within and between the sampled populations. Finally, to reveal the drivers of genetic structure, we searched for associations between allele frequencies and spatial and climatic variables.

Key Results

We found support for a marked regional structure inA. tinctoriaalong a latitudinal gradient in line with phytogeographic divisions. Several analyses identified interspecific admixture affecting both mainland and island populations. Modelling of spatial and climatic variables further demonstrated a larger contribution of neutral processes and a lesser albeit significant role of selection in shaping the observed genetic structure inA. tinctoria.

Conclusions

Current findings provide evidence of strong genetic structure inA. tinctoriamainly driven by neutral processes. The revealed natural genomic variation in GreekAlkannacan be used to further predict variation in A/S production, whereas our bioinformatics approach should prove useful for the study of other non-model polyploid species.
Development of a Cell Surface Display System inChlamydomonas reinhardtii
Authors: Molino João Vitor Dutra , Carpine Roberta , Gademann Karl , Mayfield Stephen , Sieber Simon
Published: May 2021

Cell-surface display systems are biotechnological techniques used to express heterologous proteins on the cell surface. Their application depends directly on the cell system used, as well as on the anchoring point for the surface displayed protein. To meet most application demands an inexpensive, safe, and scalable production platform, that reduces the economic barriers for large scale use is needed. Towards this goal, we screened three possible cell surface anchoring points in the green algae Chlamydomonas by fusing mVenus to prospective anchors moieties. The vectors harboring mVenus:anchor were screened for mVenus fluorescence and tested for cellular localization by confocal laser scanning microscopy. This strategy allowed the identification of two functional anchors, one for the cytoplasmic membrane using the MAW8 GPI-anchor signal, and one for the cell wall using the GP1 protein. We also exploited GP1 chemical and biological traits to release the fused proteins efficiently during cell wall shedding. Our work provides a foundation for surface engineering ofC reinhardtiisupporting both cell biology studies and biotechnology applications.
Maternal iron deficiency impacts the placental arterial network
Authors: Kalisch-Smith Jacinta I. , Morris Emily C. , Strevens Mary A.A. , Redpath Andia N. , Klaourakis Kostantinos , Szumska Dorota , Outhwaite Jennifer E. , Vieira Joaquim Miguel , Smart Nicola , De Val Sarah , Riley Paul R. , Sparrow Duncan B.
Published: May 2021

Placental vascular gene networks in mammals have been largely unexplored due to a lack of well validated molecular markers to identify them. This is required to study how they form in development, and how they are impacted by embryonic or maternal defects, which in-turn adversely affects the forming heart and vasculature. Such defects are known to be a consequence of maternal iron deficiency (ID), the most common nutrient deficiency world-wide. Here we employed marker analysis to characterise the arterial/arteriole and venous/venule endothelial cells (ECs) during normal placental development, and in the context of maternal ID. We reveal for the first time that placental ECs are unique compared with their embryonic counterparts. In the developing embryo, arterial ECs expressNeuropilin1(Nrp1),Delta-like ligand 4(Dll4) andNotch1, while developing venous ECs expressNeuropilin2(Nrp2),Apj (Aplnr)andEphrinb4 (Ephb4). However, in the E15.5 placenta,Nrp1andNotch1were restricted to arteries, but not continuing arteriole ECs. The arterial tree exclusively expressedDll4. Nrp2showed pan-EC expression at E15.5, whileEphb4was not present at this stage. However, we found the placental venous vascular tree could be distinguished from the arterial tree by high versus low Endomucin (EMCN) andApj (Aplnr)expression respectively. Using EMCN, we reveal that the placental arterial, but not venous, vascular tree is adversely impacted by maternal ID, with reduced area, total length and number of junctions of all vessels without affecting the EMCN high vessels. Defects to the embryonic cardiovascular system can therefore have a significant impact on blood flow delivery and expansion of the placental arterial tree.
The relationship between restrictive human resource practices and salary among working professionals
Authors: Baglione Stephen , Tucci Louis , Smith William , Snead Joanne
Published: May 2021

Purpose

This study forces respondents to tradeoff between invasive human resource practices and salary.

Design/methodology/approach

Respondents evaluated 16 calibration profiles to estimate a conjoint model among four categories: pre-employment, employment at the office, employment outside the office, and salary. Each profile included one level from the four categories.

Findings

In a study of mostly full-time employees, conditions at work were paramount. Salary was second followed closely by pre-employment monitoring. Monitoring outside of the office was a distance last.

Practical implications

In a tight employment market, salary may not be the deciding selection factor for employment.

Originality/value

Employee monitoring is advancing dramatically and making human resource activities commonplace and invasive. This study forces respondents to confront these practices and determine whether salary can compensate for their acceptance.
Effect of information sharing in supply chains: understanding the roles of supply chain visibility, agility, collaboration on supply chain performance
Authors: Baah Charles , Opoku Agyeman Douglas , Acquah Innocent Senyo Kwasi , Agyabeng-Mensah Yaw , Afum Ebenezer , Issau Kassimu , Ofori Daniel , Faibil Daniel
Published: May 2021

Purpose

Exploring ways to acquire, sustain and improve competitive positions in supply chains through information sharing, supply chain visibility, collaboration and agility have been essential for scholars and practitioners. Basing on the relational view, resource based view and the extended resource based view, this study assesses the critical role of information sharing in supply chains through emphasizing its effect on supply chain visibility, collaboration, agility and supply chain performance. Particularly, the study proposes that information sharing, supply chain visibility, collaboration and agility collectively have crucial direct and indirect influences on supply chain performance which lead to superior gains, competitiveness and flexibility.

Design/methodology/approach

The study adopted a survey research design, a quantitative approach and partial least square structural equation modeling (PLS-SEM) in making data analysis and interpretations due to its suitability for predictive research models.

Findings

The results indicate information sharing positively and significantly influenced supply chain visibility, collaboration, agility and performance. Supply chain visibility presented significant effects on collaboration, agility and performance, while supply chain collaboration and agility had significant impact on supply chain performance. The study findings connote that information sharing is key to enhancing competitive gains and superior supply chain performance.

Originality/value

The study is among the few to probe on how information sharing as a variable interacts with supply chain visibility, collaboration, agility and performance. Although, information sharing has received a lot of attention in supply chains, this study is among the first to capture the study variables in a single model and thus, exposes the vital need for information sharing in improving supply chain performance seeing that it ensured significant and robust impacts on the study variables.
The Covid-19 pandemic: towards a societally engaged IB perspective
Authors: Dörrenbächer Christoph , Sinkovics Rudolf R. , Becker-Ritterspach Florian , Boussebaa Mehdi , Curran Louise , de Jonge Alice , Khan Zaheer
Published: May 2021

Purpose

This viewpoint takes up the Covid-19 pandemic as a trigger for a research agenda around societally engaged international business (IB) research.

Design/methodology/approach

The paper is organized as a viewpoint. First, it provides an overview of Covid-19 research in business and management and IB in particular. Second, it introduces a societally engaged IB perspective, around poverty and human rights as well as trade.

Findings

The paper offers an annotated introduction to the paper contributions of the special issue with three clusters, “re-reading the crisis”, “crisis protectionism” and “firm strategies during the pandemic”.

Research limitations/implications

The paper points to future research opportunities in terms of crisis management and societally engaged IB research.

Practical implications

The Covid-19 crisis poses new questions for research on international business and its related disciplines. In particular, the political, economic and societal disruption which the pandemic has caused highlights the importance of addressing broader societal issues such as climate change, poverty and inequality through a purposeful and forward-looking research agenda.

Originality/value

The paper and the special issue are some of the first combined research outputs on the Covid-19 pandemic in international business.