bluuebunny/crossref_metadata_2025 huggingface dataset:
Independence of 3D chromatin conformation and gene regulation during Drosophila dorsoventral patterning
Authors: Ing-Simmons Elizabeth , Vaid Roshan , Mannervik Mattias , Vaquerizas Juan M.
Published: July 2020

The relationship between the 3D organisation of chromatin inside the nucleus and the regulation of gene expression remains unclear. While disruption of domains and domain boundaries can lead to mis-expression of developmental genes, acute depletion of key regulators of genome organisation, such as CTCF and cohesin, and major reorganisation of genomic regions have relatively small effects on gene expression. Therefore, it is unclear whether changes in gene expression and chromatin state drive chromatin reorganisation, or whether changes in chromatin organisation facilitate cell type-specific activation of genes and their regulatory elements. Here, using the Drosophila melanogaster dorsoventral patterning system as a model, we demonstrate the independence of 3D chromatin organisation and developmental gene regulation. We define tissue-specific enhancers and link them to expression patterns at the single-cell level using single cell RNA-seq. Surprisingly, despite tissue-specific differences in chromatin state and gene expression, 3D chromatin organisation is maintained across tissues. Our results provide strong evidence that tissue-specific chromatin conformation is not required for tissue-specific gene expression, but rather acts as an architectural framework to facilitate proper gene regulation during development.
The evolutionary history of ACE2 usage within the coronavirus subgenusSarbecovirus
Authors: Wells H.L , Letko M , Lasso G , Ssebide B , Nziza J , Byarugaba D.K , Navarrete-Macias I , Liang E , Cranfield M , Han B.A , Tingley M.W , Diuk-Wasser M , Goldstein T , Johnson C.K , Mazet J , Chandran K , Munster V.J , Gilardi K , Anthony S.J
Published: July 2020

SARS-CoV-1 and SARS-CoV-2 are not phylogenetically closely related; however, both use the ACE2 receptor in humans for cell entry. This is not a universal sarbecovirus trait; for example, many known sarbecoviruses related to SARS-CoV-1 have two deletions in the receptor binding domain of the spike protein that render them incapable of using human ACE2. Here, we report three sequences of a novel sarbecovirus from Rwanda and Uganda which are phylogenetically intermediate to SARS-CoV-1 and SARS-CoV-2 and demonstrate via in vitro studies that they are also unable to utilize human ACE2. Furthermore, we show that the observed pattern of ACE2 usage among sarbecoviruses is best explained by recombination not of SARS-CoV-2, but of SARS-CoV-1 and its relatives. We show that the lineage that includes SARS-CoV-2 is most likely the ancestral ACE2-using lineage, and that recombination with at least one virus from this group conferred ACE2 usage to the lineage including SARS-CoV-1 at some time in the past. We argue that alternative scenarios such as convergent evolution are much less parsimonious; we show that biogeography and patterns of host tropism support the plausibility of a recombination scenario; and we propose a competitive release hypothesis to explain how this recombination event could have occurred and why it is evolutionarily advantageous. The findings provide important insights into the natural history of ACE2 usage for both SARS-CoV-1 and SARS-CoV-2, and a greater understanding of the evolutionary mechanisms that shape zoonotic potential of coronaviruses. This study also underscores the need for increased surveillance for sarbecoviruses in southwestern China, where most ACE2-using viruses have been found to date, as well as other regions such as Africa, where these viruses have only recently been discovered.
Adenoviral chromatin organization primes for early gene activation
Authors: Schwartz Uwe , Komatsu Tetsuro , Huber Claudia , Lagadec Floriane , Baumgartl Conradin , Silberhorn Elisabeth , Nuetzel Margit , Rayne Fabienne , Basyuk Eugenia , Bertrand Edouard , Rehli Michael , Wodrich Harald , Laengst Gernot
Published: July 2020

Within the virion, adenovirus DNA associates with the virus-encoded, protamine-like structural protein pVII. Whether this association is organized, and how genome packaging changes during infection and subsequent transcriptional activation is currently unknown. Here, we combined RNA-seq, MNase-seq, ChIP-seq and single genome imaging during early adenovirus infection to unveil the structure- and time-resolved dynamics of viral chromatin changes as well as their correlation with gene transcription. Our MNase mapping data indicates that the viral genome is arranged in precisely positioned nucleoprotein particles (Adenosomes), like nucleosomes. We identified 238 Adenosomes, being positioned by a DNA sequence code and protecting about 60 to 70bp of DNA. The incoming genome is more accessible at early gene loci that undergo additional chromatin de-condensation upon infection. Histone H3.3 containing nucleosomes specifically replace pVII at distinct genomic sites and at the transcription start sites of early genes. Acetylation of H3.3 is predominant at the transcription start sites, preceding transcriptional activation. Based on our results we propose a central role for the viral pVII nucleoprotein-architecture, which is required for the dynamic structural changes during early infection, including the regulation of nucleosome assembly prior to transcription initiation. Our study thus may aid the rational development of recombinant adenoviral vectors exhibiting sustained expression in gene therapy.
Anoxygenic phototrophicChloroflexotamember uses a Type I reaction center
Authors: Tsuji JM , Shaw NA , Nagashima S , Venkiteswaran JJ , Schiff SL , Watanabe T , Fukui M , Hanada S , Tank M , Neufeld JD
Published: July 2020

Scientific exploration of phototrophic bacteria over nearly 200 years has revealed large phylogenetic gaps between known phototrophic groups that limit understanding of how phototrophy evolved and diversified. Through Boreal Shield lake water incubations, we cultivated an anoxygenic phototrophic bacterium from a previously unknown order within theChloroflexotaphylum that represents a highly novel transition form in the evolution of photosynthesis. Unlike all other known phototrophs, this bacterium uses a Type I reaction center (RCI) for light energy conversion yet belongs to the same bacterial phylum as organisms that use a Type II reaction center (RCII) for phototrophy. Using physiological, phylogenomic, and environmental metatranscriptomic data, we demonstrate active RCI-utilizing metabolism by the strain alongside usage of chlorosomes and bacteriochlorophylls related to those of RCII-utilizingChloroflexotamembers. Despite using different reaction centers, our phylogenomic data provide strong evidence that RCI- and RCII-utilizingChloroflexiamembers inherited phototrophy from a most recent common phototrophic ancestor that used RCI, RCII, or both reaction center classes, substantially revising our view of the diversity and evolution of phototrophic life. TheChloroflexotaphylum preserves an evolutionary record of interaction between RCI and RCII among anoxygenic phototrophs that gives new context for exploring the origins of phototrophy on Earth.
Noncanonical targeting contributes significantly to miRNA-mediated regulation
Authors: Tan Jennifer Y. , Abdulkarim Baroj , Marques Ana C.
Published: July 2020

Determining which genes are targeted by miRNAs is crucial to elucidate their contributions to diverse biological processes in health and disease. Most miRNA target prediction tools rely on the identification of complementary regions between transcripts and miRNAs. Whereas important for target recognition, the presence of complementary sites is not sufficient to identify transcripts targeted by miRNAs.

Here, we describe an unbiased statistical genomics approach that explores genetically driven changes in gene expression between human individuals. Using this approach, we identified transcripts that respond to physiological changes in miRNA levels. We found that a much smaller fraction of mRNAs expressed in lymphoblastoid cell lines (LCLs) than what is predicted by other tools is targeted by miRNAs. We estimate that each miRNA has a relatively small number of targets. The transcripts we predict to be miRNA targets are enriched in AGO-binding and previously validated miRNAs target interactions, supporting the reliability of our predictions. Consistent with previous analysis, these targets are also enriched among dosage sensitive and highly controlled genes.

Almost a third of genes we predict to be miRNA targets lack sequence complementarity to the miRNA seed region (noncanonical targets). These noncanonical targets have higher complementary with the miRNA 3’ end. The impact of miRNAs on the levels of their canonical or noncanonical targets is identical supporting the relevance of this poorly explored mechanism of targeting.
Alignment of virus-host protein-protein interaction networks by integer linear programming: SARS-CoV-2
Authors: Llabrés Mercè , Valiente Gabriel
Published: July 2020

Beside socio-economic issues, coronavirus pandemic COVID-19, the infectious disease caused by the newly discovered coronavirus SARS-CoV-2, has caused a deep impact in the scientific community, that has considerably increased its effort to discover the infection strategies of the new virus. Among the extensive and crucial research that has been carried out in the last few months, the analysis of the virus-host relationship plays an important role in drug discovery. Virus-host protein-protein interactions are the active agents in virus replication, and the analysis of virus-host protein-protein interaction networks is fundamental to the study of the virus-host relationship. We have adapted and implemented a recent integer linear programming model for protein-protein interaction network alignment to virus-host networks, and obtained a consensus alignment of the SARS-CoV-1 and SARS-CoV-2 virus-host protein-protein interaction networks. Despite the lack of shared human proteins in these virus-host networks and the low number of preserved virus-host interactions, the consensus alignment revealed aligned human proteins that share a function related to viral infection, as well as human proteins of high functional similarity that interact with SARS-CoV-1 and SARS-CoV-2 proteins, whose alignment would preserve these virus-host interactions.
Defining the sediment microbiome of the Indian River Lagoon, FL, USA, an Estuary of National Significance
Authors: Bradshaw David J. , Dickens Nicholas J. , Trefry John H. , McCarthy Peter J.
Published: July 2020

The Indian River Lagoon, located on the east coast of Florida, USA, is an Estuary of National Significance and an important economic and ecological resource. The Indian River Lagoon faces several environmental pressures, including freshwater discharges through the St. Lucie Estuary; accumulation of a anoxic, fine-grained, organic-rich sediment; and metal contamination from agriculture and marinas. Although the Indian River Lagoon has been well-studied, little is known about its microbial communities; thus, a two-year 16S amplicon sequencing study was conducted to assess the spatiotemporal changes of the sediment microbiome. In general, the Indian River Lagoon exhibited a microbiome that was consistent with other estuarine studies. Statistically different microbiomes were found between the Indian River Lagoon and St. Lucie Estuary due to changes in porewater salinity causing microbes that require salts for growth to be higher in the Indian River Lagoon. The St. Lucie Estuary exhibited more obvious microbial seasonality, such as higher Betaproteobacteriales, a freshwater associated organism, in wet season and higher Flavobacteriales in dry season samples. Distance-based linear models revealed these microbiomes were more affected by changes in total organic matter and copper than changes in temperature. Anaerobic organisms, such as Campylobacterales, were more associated with high total organic matter and copper samples while aerobic organisms, such as Nitrosopumilales, were more associated with low total organic matter and copper samples. This initial study fills the knowledge gap on the Indian River Lagoon microbiome and serves as an important baseline for possible future changes due to human impacts or environmental changes.
TheVibrio choleraecytotoxin MakA induces noncanonical autophagy resulting in the spatial inhibition of canonical autophagy
Authors: Corkery Dale P. , Nadeem Aftab , Aung Kyaw Min , Hassan Ahmed , Liu Tao , Cervantes-Rivera Ramón , Lystad Alf Håkon , Wang Hui , Persson Karina , Puhar Andrea , Simonsen Anne , Uhlin Bernt Eric , Wai Sun Nyunt , Wu Yao-Wen
Published: July 2020

Autophagy plays an essential role in the defence against many microbial pathogens as a regulator of both innate and adaptive immunity. Among some pathogens, sophisticated mechanisms have evolved that promote their ability to evade or subvert host autophagy. Here, we describe a novel mechanism of autophagy subversion mediated by the recently discoveredVibrio choleraecytotoxin, MakA. pH-dependent endocytosis of MakA by host cells resulted in the formation of a cholesterol-rich endolysosomal membrane aggregate in the perinuclear region. Aggregate formation induced the noncanonical autophagy pathway driving unconventional LC3 lipidation on endolysosomal membranes. Subsequent sequestration of the ATG12-ATG5-ATG16L1 E3-like enzyme complex required for LC3 lipidation at the membranous aggregate resulted in an inhibition of both canonical autophagy and autophagy-related processes including the unconventional secretion of IL-1β. These findings identify a novel mechanism of host autophagy subversion and immune modulation employed byV. choleraeduring bacterial infection.
Nonsense-mediated mRNA decay relies on “two-factor authentication” by SMG5-SMG7
Authors: Boehm Volker , Kueckelmann Sabrina , Gerbracht Jennifer V. , Britto-Borges Thiago , Altmüller Janine , Dieterich Christoph , Gehring Niels H.
Published: July 2020

Eukaryotic gene expression is constantly regulated and controlled by the translation-coupled nonsense-mediated mRNA decay (NMD) pathway. Aberrant translation termination leads to NMD activation and robust clearance of NMD targets via two seemingly independent and redundant mRNA degradation branches. Here, we uncover that the loss of the first SMG5-SMG7-dependent pathway also inactivates the second SMG6-dependent branch, indicating an unexpected functional hierarchy of the final NMD steps. Transcriptome-wide analyses of SMG5-SMG7-depleted cells confirm complete NMD inhibition resulting in massive transcriptomic alterations. The NMD activity conferred by SMG5-SMG7 is determined to varying degrees by their interaction with the central NMD factor UPF1, heterodimer formation and the initiation of deadenylation. Surprisingly, we find that SMG5 functionally substitutes SMG7 and vice versa. Our data support an improved model for NMD execution that requires two-factor authentication involving UPF1 phosphorylation and SMG5-SMG7 recruitment to access SMG6 activity.
SARS-CoV-2 Nsp1 binds ribosomal mRNA channel to inhibit translation
Authors: Schubert Katharina , Karousis Evangelos D. , Jomaa Ahmad , Scaiola Alain , Echeverria Blanca , Gurzeler Lukas-Adrian , Leibundgut Marc , Thiel Volker , Mühlemann Oliver , Ban Nenad
Published: July 2020

The non-structural protein 1 (Nsp1), also referred to as the host shutoff factor, is the first viral protein that is synthesized in SARS-CoV-2 infected human cells to suppress host innate immune functions1,2. By combining cryo-electron microscopy and biochemical experiments, we show that SARS-CoV-2 Nsp1 binds to the human 40S subunit in ribosomal complexes including the 43S pre-initiation complex. The protein inserts its C-terminal domain at the entrance to the mRNA channel where it interferes with mRNA binding. We observe potent translation inhibition in the presence of Nsp1 in lysates from human cells. Based on the high-resolution structure of the 40S-Nsp1 complex, we identify residues of Nsp1 crucial for mediating translation inhibition. We further show that the full-length 5’ untranslated region of the genomic viral mRNA stimulates translationin vitro, suggesting that SARS-CoV-2 combines inhibition of translation by Nsp1 with efficient translation of the viral mRNA to achieve expression of viral genes3.
Occipital Intralobar fasciculi and a novel description of three forgotten tracts
Authors: Bugain Maeva , Dimech Yana , Torzhenskaya Natalia , de Schotten Michel Thiebaut , Caspers Svenja , Muscat Richard , Bajada Claude J
Published: July 2020

The continuously developing field of magnetic resonance imaging (MRI) has made a considerable contribution to the knowledge of brain architecture. It has given shape to a desire to construct a complete map of functional and structural connections. In particular, diffusion MRI paired with tractography has facilitated a non-invasive exploration of structural brain anatomy, which has helped build evidence for the existence of many association, projection and commissural fiber tracts. However, there is still a scarcity in research studies related to intralobar association fibers. The Dejerines’ (two of the most notable neurologists of 19thcentury France) gave an in-depth description of the intralobar fibers of the occipital lobe. Unfortunately, their exquisite work has since been sparsely referred to in the modern literature. This work gives the first modern description of many of the occipital intralobar lobe fibers described by the Dejerines. We perform a virtual dissection and reconstruct the tracts using diffusion MRI tractography. The virtual dissection is guided by the Dejerines’ treatise,Anatomie des Centres Nerveux.As an accompaniment to this article, the authors provided a French-to-English translation of the treatise portion concerning intra-occipital fiber bundles. This text provides the original description of five intralober occipital tracts, namely: the stratum calcarinum, the stratum proprium cunei, the vertical occipital fasciculus of Wernicke, the transverse fasciculus of the cuneus (TFC) and the transverse fasciculus of the lingual lobe of Vialet. It was possible to reconstruct all these tracts except for the TFC – possibly because its trajectory intermingles with a large amount of other fiber bundles. For completeness, the recently described sledge runner fasciculus, although not one of the Dejerine tracts, was identified and successfully reconstructed.
Favipiravir antiviral efficacy against SARS-CoV-2 in a hamster model
Authors: Driouich Jean-Sélim , Cochin Maxime , Lingas Guillaume , Moureau Grégory , Touret Franck , Petit Paul Rémi , Piorkowski Géraldine , Barthélémy Karine , Coutard Bruno , Guedj Jérémie , de Lamballerie Xavier , Solas Caroline , Nougairède Antoine
Published: July 2020

Despite no or limited pre-clinical evidence, repurposed drugs are massively evaluated in clinical trials to palliate the lack of antiviral molecules against SARS-CoV-2. Here we used a Syrian hamster model to assess the antiviral efficacy of favipiravir, understand its mechanism of action and determine its pharmacokinetics. When treatment was initiated before or simultaneously to infection, favipiravir had a strong dose effect, leading to dramatic reduction of infectious titers in lungs and clinical alleviation of the disease. Antiviral effect of favipiravir correlated with incorporation of a large number of mutations into viral genomes and decrease of viral infectivity. The antiviral efficacy observed in this study was achieved with plasma drug exposure comparable with those previously found during human clinical trials and was associated with weight losses in animals. Thereby, pharmacokinetic and tolerance studies are required to determine whether similar effects can be safely achieved in humans.
Imaging LexA degradation in cells explains regulatory mechanisms and heterogeneity of the SOS response
Authors: Jones Emma C. , Uphoff Stephan
Published: July 2020

The SOS response functions as the central regulator of DNA repair and mutagenesis in most bacteria and stands as a paradigm of gene networks controlled by a master transcriptional regulator, LexA. We developed a single-molecule imaging approach to directly monitor the LexA repressor inside liveEscherichia colicells, demonstrating key mechanisms by which DNA-binding and degradation of LexA regulates the SOS responsein vivo.Our approach revealed that self-cleavage of LexA occurs frequently during unperturbed growth and causes substantial heterogeneity in LexA abundances across cells. LexA variability underlies SOS gene expression heterogeneity and triggers spontaneous SOS pulses, which enhance bacterial survival in anticipation of stress.
Insights into the genomic evolution of insects from cricket genomes
Authors: Ylla Guillem , Nakamura Taro , Itoh Takehiko , Kajitani Rei , Toyoda Atsushi , Tomonari Sayuri , Bando Tetsuya , Ishimaru Yoshiyasu , Watanabe Takahito , Fuketa Masao , Matsuoka Yuji , Barnett Austen A. , Noji Sumihare , Mito Taro , Extavour Cassandra G.
Published: July 2020

Most of our knowledge of insect genomes comes from Holometabolous species, which undergo the complete metamorphosis and have genomes under 2Gb with little signs of DNA methylation. In contrast, Hemiemetabolous insects undergo the ancestral incomplete metamorphosis and have larger genomes with high levels of DNA methylation. Hemimetabolous species from the Orthopteran order (grasshoppers and crickets) have some of the largest insect genomes. What drives the evolution of these unusual insect genome sizes, remains unknown. Here we report the sequencing, assembly and annotation of the 1.66-Gb genome of the Mediterranean field cricketGryllus bimaculatus, and the annotation of the 1.60-Gb genome of the Hawaiian cricketLaupala kohalensis.We compare these two cricket genomes with those of 14 additional insects, and find evidence that hemimetabolous genomes expanded due to transposable element activity. Based on the ratio of observed to expected CpG sites, we find higher conservation and stronger purifying selection of methylated genes than non-methylated genes. Finally, our analysis suggests an expansion of thepickpocketclass V gene family in crickets, which we speculate might play a role in the evolution of cricket courtship, including their characteristic chirping.
Quantitative benzimidazole resistance and fitness effects of parasitic nematode beta-tubulin alleles
Authors: Dilks Clayton M. , Hahnel Steffen R. , Sheng Qicong , Long Lijiang , McGrath Patrick T. , Andersen Erik C.
Published: July 2020

Infections by parasitic nematodes inflict a huge burden on the health of humans and livestock throughout the world. Anthelmintic drugs are the first line of defense against these infections. Unfortunately, resistance to these drugs is rampant and continues to spread. To improve treatment strategies, we must understand the genetics and molecular mechanisms that underlie resistance. Studies of the fungusAspergillus nidulansand the free-living nematodeCaenorhabditis elegansdiscovered that a beta-tubulin gene is mutated in benzimidazole (BZ) resistant strains. In parasitic nematode populations, three canonical beta-tubulin alleles, F200Y, E198A, and F167Y, have long been correlated with resistance. Additionally, improvements in sequencing technologies have identified new alleles - E198V, E198L, E198K, E198I, and E198Stop - also correlated with BZ resistance. However, none of these alleles have been proven to cause resistance. To empirically demonstrate this point, we independently introduced the three canonical alleles as well as two of the newly identified alleles, E198V and E198L, into the BZ susceptibleC. elegansN2 genetic background. These genome-edited strains were exposed to both albendazole and fenbendazole to quantitatively measure animal responses to BZs. We used a range of doses for each BZ compound to define response curves and found that all five of the alleles conferred resistance to BZ compounds equal to a loss of the entire beta-tubulin gene. These results prove that the parasite beta-tubulin alleles cause resistance. The E198V allele is found at low frequencies in natural parasite populations, suggesting that it could affect fitness. We performed competitive fitness assays and demonstrated that the E198V allele reduces animal health, supporting the hypothesis that this allele is less fit in field populations. Overall, we present a powerful platform to quantitatively assess anthelmintic resistance and effects of specific resistance alleles on organismal fitness in the presence or absence of the drug.

Highlights

All three canonical parasitic nematode beta-tubulin alleles (F167Y, E198A, F200Y) and two newly identified alleles (E198V, E198L) confer equal levels of benzimidazole resistance in a defined genetic background using single-generation, high-replication drug response assays.

Beta-tubulin variants are strongly selected in albendazole conditions in multigenerational competitive fitness assays, but these alleles confer different levels of benzimidazole resistance over time.

Only the E198V allele confers a fitness cost in control (non-benzimidazole) conditions as compared to all other tested beta-tubulin alleles, suggesting that this intermediate allele might only be found in field populations at low frequency because it causes reduced fitness.

Graphical Abstract
Repeated loss of variation in insect ovary morphology highlights the role of developmental constraint in life-history evolution
Authors: Church Samuel H. , de Medeiros Bruno A. S. , Donoughe Seth , Márquez Reyes Nicole L. , Extavour Cassandra G.
Published: July 2020

The number of offspring an organism can produce is a key component of its evolutionary fitness and life-history. Here we perform a test of the hypothesized trade off between the number and size of offspring using thousands of descriptions of the number of egg-producing compartments in the insect ovary (ovarioles), a common proxy for potential offspring number in insects. We find evidence of a negative relationship between egg size and ovariole number when accounting for adult body size. However in contrast to prior claims, we note that this relationship is not generalizable across all insect clades, and we highlight several factors that may have contributed to this size-number trade off being stated as a general rule in previous studies. We reconstruct the evolutionary history of the nurse cell arrangement within the ovariole, and show that the diversification of ovariole number and egg size have both been largely independent of nurse cell presence or position within the ovariole. Instead we show that ovariole number evolution has been shaped by a series of transitions between variable and invariant states, with multiple independent lineages evolving to have almost no variation in ovariole number. We highlight the implications of these invariant lineages on our understanding of the specification of ovariole number during development, as well as the importance of considering developmental processes in theories of life-history evolution.
ATP-Citrate lyase fuels axonal transport across species
Authors: Even Aviel , Morelli Giovanni , Le Bail Romain , Shilian Michal , Turchetto Silvia , Broix Loïc , Brandis Alexander , Inbar Shani , Chariot Alain , Saudou Frédéric , Dietrich Paula , Dragatsis Ioannis , Brone Bert , Rigo Jean-Michel , Weil Miguel , Nguyen Laurent
Published: July 2020

Microtubule (MT)-based transport is an evolutionary conserved processed finely tuned by posttranslational modifications. Among them, α-tubulin acetylation, which is catalyzed by the α-tubulin N-acetyltransferase 1, Atat1, promotes the recruitment and processivity of molecular motors along MT tracks. However, the mechanisms that controls Atat1 activity remains poorly understood. Here, we show that a pool of vesicular ATP-citrate lyase Acly acts as a rate limiting enzyme to modulate Atat1 activity by controlling availability of Acetyl-Coenzyme-A (Acetyl-CoA). In addition, we showed that Acly expression is reduced upon loss of Elongator activity, further connecting Elongator to Atat1 in the pathway regulatingα-tubulin acetylation and MT-dependent transport in projection neurons, across species. Remarkably, comparable defects occur in fibroblasts from Familial Dysautonomia (FD) patients bearing an autosomal recessive mutation in the gene coding for the Elongator subunit ELP1. Our data may thus shine new light on the pathophysiological mechanisms underlying FD.
Survival of the salient: Emotion rescues otherwise forgettable memories via neural reactivation and post-encoding hippocampal connectivity
Authors: Clewett David , Dunsmoor Joseph , Bachman Shelby , Phelps Elizabeth , Davachi Lila
Published: July 2020

Emotion’s selective effects on memory go beyond the simple enhancement of threatening or rewarding stimuli. They can also rescue otherwise forgettable memories that share overlapping features. Here, we use functional magnetic resonance imaging (fMRI) to examine the brain mechanisms that support this retrograde memory enhancement. In a two-phase incidental encoding paradigm, participants first view images of neutral tools and animals. During Phase 1, these images are intermixed with neutral scenes, which provides a unique ‘context tag’ for this specific phase of encoding. A few minutes later, during Phase 2, new pictures from one category are paired with a mild shock (fear-conditioned stimulus; CS+), while pictures from the other category are not shocked. fMRI analyses reveal that, across participants, retroactive memory benefits for Phase 1 CS+ items are associated with greater phasic reinstatement of the prior mental context during Phase 2 CS+ items. We also see that greater VTA/SN activation during Phase 2 CS+ items relates to this retroactive memory enhancement, suggesting that emotion promotes both the encoding and ongoing consolidation of overlapping representations. Additionally, we find that emotional experience-dependent changes in post-encoding hippocampal functional coupling with CS+ category-selective cortex relate to the magnitude of the retroactive memory effect. These hippocampal connectivity patterns also mediate the relationship between dopaminergic emotional encoding effects and across-participant variability in the retroactive memory benefit. Collectively, our findings suggest that an interplay between online and offline brain mechanisms may enable emotion to preserve seemingly mundane memories that become significant in the future.
Reversible auto-inhibitory regulation ofEscherichia colimetallopeptidase BepA for selective β-barrel protein degradation
Authors: Daimon Yasushi , Narita Shin-ichiro , Miyazaki Ryoji , Hizukuri Yohei , Mori Hiroyuki , Tanaka Yoshiki , Tsukazaki Tomoya , Akiyama Yoshinori
Published: July 2020

Escherichia coliperiplasmic zinc-metallopeptidase BepA normally functions by promoting maturation of LptD, a β-barrel outer membrane protein involved in biogenesis of lipopolysaccharides, but degrades it when its membrane assembly is hampered. These processes should be properly regulated to ensure normal biogenesis of LptD, but the underlying mechanism of regulation, however, remains to be elucidated. A recently solved BepA structure has revealed unique features, in particular the active site is buried in the protease domain and conceivably inaccessible for substrate degradation. Additionally, the His-246 residue in the loop region containing helix α9 (α9/H246 loop), which has a potential flexibility and covers the active site, coordinates the zinc ion as the fourth ligand to exclude a catalytic water molecule, thereby suggesting that the crystal structure of BepA represents a latent form. To examine the roles of the α9/H246 loop in the regulation of the BepA activity, we constructed BepA mutants with a His-246 mutation or a deletion of the α9/H246 loop and analyzed their activitiesin vivoandin vitro. These mutants exhibited an elevated protease activity and, unlike the wild-type BepA, degraded LptD that is in the normal assembly pathway. In contrast, tethering of the α9/H246 loop repressed the LptD degradation, which suggests that the flexibility of this loop is important to the exhibition of the protease activity. Based on these results, we propose that the α9/H246 loop undergoes a reversible structural change that enables His-246-mediated switching (histidine switch) of its protease activity, which is important for regulated degradation of stalled/misassembled LptD.
Rapid degradation of GRASP55 and GRASP65 reveals their immediate impact on the Golgi structure
Authors: Zhang Yijun , Seemann Joachim
Published: July 2020

GRASP65 and GRASP55 have been implicated in stacking of Golgi cisternae and lateral linking of stacks within the Golgi ribbon. However, loss of gene function approaches by RNAi or gene knockout to dissect their respective roles often resulted in conflicting conclusions. Here, we gene-edited GRASP55 and/or GRASP65 with a degron tag in human fibroblasts, allowing for the induced rapid degradation by the proteasome. We show that acute depletion of either GRASP55 or GRASP65 does not affect the Golgi ribbon, while chronic degradation of GRASP55 disrupts lateral connectivity of the Golgi ribbon. Acute double depletion of both GRASPs coincides with the loss of the vesicle tethering proteins GM130, p115 and Golgin-45 from the Golgi and compromises ribbon linking. Furthermore, neither GRASP55 and/or GRASP65 are required for maintaining stacks orde novoassembly of stacked cisternae at the end of mitosis. These results demonstrate that both GRASPs are dispensable for Golgi stacking, but are involved in maintaining the integrity of Golgi ribbon together with GM130 and Golgin-45.
Development of a growth coupled dynamic regulation network balancing malonyl-CoA node to enhance (2S)-naringenin synthesis inE. coli
Authors: Zhou Shenghu , Yuan Shuo-Fu , Nair Priya H , Alper Hal S , Deng Yu , Zhou Jingwen
Published: July 2020

Generally, high- and low-performance nongenetic variants and young and aged cells co-existed in culture at all growth phases. In this regard, individually and dynamically regulating the metabolic flux of single cells based on their cellular state is highly useful for improving the performance of populations. However, balancing the trade-offs between biomass formation and compound over-production requires sophisticated dynamic regulation networks (DRNs) which can be challenging. Here, we developed a growth coupled NCOMB (Naringenin-Coumaric acid-Malonyl-CoA-Balanced) DRN with systematic optimization of (2S)-naringenin andp-coumaric acid-responsive regulation pathways for real-time control of intracellular supply of malonyl-CoA. In doing so, the acyl carrier protein was used as a new critical node for fine-tuning malonyl-CoA consumption instead of fatty acid synthase. Following directed evolution of the NCOMB DRN, we obtained a strain with cumulative 8.4-fold improvement in (2S)-naringenin production with balanced cell growth, demonstrating the high efficiency of this system for improving pathway production.
Effectiveness of Ivermectin as add-on Therapy in COVID-19 Management (Pilot Trial)
Authors: Gorial Faiq I , Mashhadani Sabeeh , Sayaly Hend M , Dakhil Basim Dhawi , AlMashhadani Marwan M. , Aljabory Adnan M , Abbas Hassan M , Ghanim Mohammed , Rasheed Jawad I
Published: July 2020

Background

To date no effective therapy has been demonstrated for COVID-19. In vitro, studies indicated that ivermectin (IVM) has antiviral effect.

Objectives

To assess the effectiveness of ivermectin (IVM) as add-on therapy to hydroxychloroquine (HCQ) and azithromycin (AZT) in treatment of COVID-19.

Methods

This Pilot clinical trial conducted on hospitalized adult patients with mild to moderate COVID-19 diagnosed according to WHO interim guidance. Sixteen Patients received a single dose of IVM 200Mcg /kg on admission day as add on therapy to hydroxychloroquine (HCQ)and Azithromycin (AZT) and were compared with 71 controls received HCQ and AZT matched in age, gender, clinical features, and comorbidities.

The primary outcome was percentage of cured patients, defined as symptoms free to be discharged from the hospital and 2 consecutive negative PCR test from nasopharyngeal swabs at least 24 hours apart. The secondary outcomes were time to cure in both groups and evaluated by measuring time from admission of the patient to the hospital till discharge.

Results

Of 87 patients included in the study,t he mean age ± SD (range) of patients in the IVM group was similar to controls [44.87 ± 10.64 (28-60) vs 45.23 ± 18.47 (8-80) years, p=0.78] Majority of patients in both groups were male but statistically not significant [11(69%) versus 52 (73%), with male: female ratio 2.21 versus 2.7-, p=0.72)

All the patients of IVM group were cured compared with the controls [16 (100 %) vs 69 (97.2 %)]. Two patients died in the controls. The mean time to stay in the hospital was significantly lower in IVM group compared with the controls (7.62 ± 2.75 versus 13.22 ±5.90 days, p=0.00005, effect size= 0.82). No adverse events were observed

Conclusions

Add-on use of IVM to HCQ and AZT had better effectiveness, shorter hospital stay, and relatively safe compared with controls. however, a larger prospective study with longer follow up may be needed to validate these results.
Loss of PRC2 subunits primes lineage choice during exit of pluripotency
Authors: Loh Chet H , Perino Matteo , Bark Magnus R , Veenstra Gert Jan C
Published: July 2020

Polycomb Repressive Complex 2 (PRC2) is crucial for the coordinated expression of genes during early embryonic development, catalyzing histone H3 lysine 27 trimethylation. There are two distinct PRC2 complexes, PRC2.1 and PRC2.2, which contain respectively MTF2 and JARID2 in ES cells. Very little is known about the roles of these auxiliary PRC2 subunits during the exit of pluripotency. In this study, we explored their roles in lineage specification and commitment, using single-cell transcriptomics and mouse embryoid bodies derived fromMtf2andJarid2null embryonic stem cells (ESCs). We observed that the loss ofMtf2resulted in enhanced and faster differentiation towards cell fates from all germ layers, while theJarid2null cells were predominantly directed towards early differentiating precursors and neuro-ectodermal fates. Interestingly, we found that these effects are caused by derepression of developmental regulators that were poised for activation in pluripotent cells and gained H3K4me3 at their promoters in the absence of PRC2 repression. Upon lineage commitment, the differentiation trajectories were relatively similar to those of wild type cells. Together, our results uncovered a major role for MTF2-containing PRC2.1 in balancing poised lineage-specific gene activation, providing a threshold for lineage choice during the exit of pluripotency.

Highlights

Enhanced and faster differentiation into all three germ layers inMtf2null embryoid bodies

Jarid2null cells enriched for early differentiating precursors and neuro-ectodermal cell fates

MTF2 is critical for the balance of activation and repression of key developmental regulators

PRC2 coordinates lineage choice and execution of the lineage-specific program by thresholding of lineage-priming
Pulse-to-pulse wavefront sensing at free-electron lasers using ptychography
Authors: Sala Simone , Daurer Benedikt J. , Odstrcil Michal , Capotondi Flavio , Pedersoli Emanuele , Hantke Max F. , Manfredda Michele , Loh N. Duane , Thibault Pierre , Maia Filipe R. N. C.
Published: July 2020

The pressing need for knowledge of the detailed wavefront properties of ultra-bright and ultra-short pulses produced by free-electron lasers has spurred the development of several complementary characterization approaches. Here a method based on ptychography is presented that can retrieve high-resolution complex-valued wavefunctions of individual pulses without strong constraints on the illumination or sample object used. The technique is demonstrated within experimental conditions suited for diffraction experiments and exploiting Kirkpatrick–Baez focusing optics. This lensless technique, applicable to many other short-pulse instruments, can achieve diffraction-limited resolution.
Crystal structure and characterization of magnesium carbonate chloride heptahydrate
Authors: Rincke Christine , Schmidt Horst , Buth Gernot , Voigt Wolfgang
Published: July 2020

MgCO3·MgCl2·7H2O is the only known neutral magnesium carbonate containing chloride ions at ambient conditions. According to the literature, only small and twinned crystals of this double salt could be synthesised in a concentrated solution of MgCl2. For the crystal structure solution, single-crystal diffraction was carried out at a synchrotron radiation source. The monoclinic crystal structure (space group Cc) exhibits double chains of MgO octahedra linked by corners, connected by carbonate units and water molecules. The chloride ions are positioned between these double chains parallel to the (100) plane. Dry MgCO3·MgCl2·7H2O decomposes in the air to chlorartinite, Mg2(OH)Cl(CO3)·nH2O (n = 2 or 3). This work includes an extensive characterization of the title compound by powder X-ray diffraction, thermal analysis, SEM and vibrational spectroscopy.
Gendered institutions and female entrepreneurship: a fuzzy-set QCA approach
Authors: Li Yaokuang , Wu Juan , Zhang Daru , Ling Li
Published: July 2020

Purpose

This paper aims to examine the contextual embeddedness of female entrepreneurship through a focus on gendered institutions. Specifically, it draws upon Scott’s (1995) institutional categories and explores how the three dimensions of gendered institutions combine to explain both a high level of female Total Early-stage Entrepreneurship Activity (TEA) rates and female/male TEA ratios.

Design/methodology/approach

Collecting data from the Global Entrepreneurship Research Association, the World Economic Forum and the World Bank for 63 countries, this study uses the fuzzy-set qualitative comparative analysis (fsQCA) method to explore causal complexity between the regulative, normative and cognitive dimensions of gendered institutions (conditions) and the female TEA rates and the female/male TEA ratios (outcomes).

Findings

First, this study confirms the complex interactions occurring among institutional components. Second, the results highlight the key role that gender equality in entrepreneurial cognitions plays in achieving high female entrepreneurship. Third, configurations for the high female TEA rates and the female/male TEA ratios share a high similarity.

Practical implications

The study provides policymakers with a holistic viewpoint and alternate solutions with the aim of promoting female entrepreneurship in their respective countries.

Originality/value

The study highlights gendered institutions beyond general institutions, enriching the literature on the gender and institutional determinants of female entrepreneurship. Furthermore, the application of the fsQCA method in the study helps to enhance the understanding of how institutional components complexly interact to shape female entrepreneurship.
The supply side of product differentiation in the Italian mortgage market
Authors: Del Prete Silvia , Demma Cristina , Rossi Paola
Published: July 2020

Purpose

This paper aims to propose a new indicator of product differentiation in the mortgage market and use it to examine how the double crisis, local market competition and bank-specific characteristics have influenced the supply of non-conventional mortgages in Italy.

Design/methodology/approach

This paper uses a special Bank of Italy’s survey on 400 Italian banks over the period 2006–2013, to compute a new indicator for product differentiation in the mortgage market. This paper considers mortgage with non-conventional characteristics: loan-to-value ratio greater than 80%; duration longer than 30 years or with a flexible maturity. This paper estimates probit and ordinary least squares (OLS) models using panel data at bank-time level.

Findings

The findings suggest that during the double crisis that hit the Italian economy between 2008 and 2013, the diversification process in the Italian household mortgage market slowed down. Controlling for banks’ and local markets’ this study finds that larger, less risky banks and those that have adopted scoring systems are more likely to offer non-conventional mortgages; moreover, banks operating in more competitive markets and in markets where other banks offer non-conventional loans tend to diversify their supply more. Most of these indications are confirmed by analyzing the quantities actually granted. These results suggest that the structure of the local markets does matter, and that there could be a non-price competition effect among banks in providing differentiated mortgage contracts.

Originality/value

The indicator, computed using data at bank level drawn from a special Bank of Italy’s survey, goes beyond the standard approach on product differentiation followed in the empirical literature, mainly base on the dichotomy between fixed and variable lending rates. Furthermore, to best of the authors’ knowledge, so far there is no empirical evidence on the supply-side factors that influenced the diversification of mortgages’ contractual terms during the crisis; particularly, there is no evidence on the role of local market competition and bank-specific features. This paper contributes to fill this gap in the literature.
Measuring social housing dimensions: a case study of urban areas in Algeria
Authors: Djafri Riadh , Mohamed Osman Mariana
Published: July 2020

Purpose

The purpose of this study is to develop a measurement model and measure the dimensions of Residential Quality and Housing Adequacy (RQHA), Social Housing Provision (SHP) and Residents’ Quality of Life (RQOL) by social housing residents in Batna city, Algeria.

Design/methodology/approach

This study used a quantitative approach through the distribution of a self-administered questionnaire. A total of 373 useable questionnaires were collected from social housing residents in Batna city and used for the analysis. The data were analysed using descriptive statistics, exploratory factor analysis with principal component analysis through SPSS and confirmatory factor analysis using AMOS.

Findings

The measurement model revealed good fit of indices indicating that RQHA is presented by three sub-constructs, namely satisfaction with housing adequacy, satisfaction with current neighbourhood and satisfaction with housing design. In addition, the constructs of SHP and RQOL were measured by seven items each. The measurement model provides empirical evidence of the correlation between RQHA, SHP and RQOL constructs.

Practical implications

The findings of this study contribute significantly to government, housing stakeholders, architects, project managers and urban planners in the context of social housing policymakers, design, planning and construction. The finding would be helpful to ameliorate housing quality, adequacy, provision and RQOL in terms of social housing scheme.

Originality/value

This study identifies the correlation between constructs (RQHA, SHP and RQOL) and their dimensions in the context of social housing in Batna city by validating a measurement model using CFA.