bluuebunny/crossref_metadata_2025 huggingface dataset:
Differential Evasion of Delta and Omicron Immunity and Enhanced Fusogenicity of SARS-CoV-2 Omicron BA.4/5 and BA.2.12.1 Subvariants
Authors: Qu Panke , Faraone Julia N. , Evans John P. , Zou Xue , Zheng Yi-Min , Carlin Claire , Bednash Joseph S. , Lozanski Gerard , Mallampalli Rama K. , Saif Linda J. , Oltz Eugene M. , Mohler Peter J. , Gumina Richard J. , Liu Shan-Lu
Published: May 2022

The rising case numbers of the SARS-CoV-2 Omicron BA.4, BA.5, and BA.2.12.1 subvariants has generated serious concern about the course of the pandemic. Here we examine the neutralization resistance, infectivity, processing, and fusogenicity of spike from the BA.4/5 and BA.2.12.1 SARS-CoV-2 variants compared with other Omicron subvariants and Delta. Critically, we found that the new Omicron subvariants BA.4/5 and BA.2.12.1 were more resistant to neutralization by mRNA-vaccinated and boosted health care worker sera and Omicron-BA.1-wave patient sera than were the BA.1 and BA.2 variants. Interestingly, Delta-wave patient sera neutralized more efficiently against not only Delta but also BA.4/5 and BA.2.12.1 variants that also contain substitutions at position L452, similar to Delta. The BA.4/5 and BA.2.12.1 variants also exhibited higher fusogenicity, and increased spike processing, dependent on the L452 substitution. These results highlight the key role of the L452R and L452Q mutations in BA.4/5 and BA.2.12.1 subvariants.
A study of a diauxic growth experiment using an expanded dynamic flux balance framework
Authors: Karlsen Emil , Gylseth Marianne , Schulz Christian , Almaas Eivind
Published: May 2022

Flux balance analysis (FBA) remains one of the most used methods for modeling the entirety of cellular metabolism, and a range of applications and extensions based on the FBA framework have been generated. Dynamic flux balance analysis (dFBA), the expansion of FBA into the time domain, still has issues regarding accessibility limiting its widespread adoption and application, such as a lack of a consistently rigid formalism and tools that can be applied without expert knowledge. Recent work has combined dFBA with enzyme-constrained flux balance analysis (decFBA), which has been shown to greatly improve accuracy in the comparison of computational simulations and experimental data, but such approaches generally do not take into account the fact that altering the enzyme composition of a cell is not an instantaneous process.

Here, we have developed a decFBA method that explicitly takes enzyme change constraints (ecc) into account, decFBAecc. The resulting software is a simple yet flexible framework for using genome-scale metabolic modeling for simulations in the time domain that has full interoperability with COBRA toolbox 3.0. To assess the quality of the computational predictions of decFBAecc, we conducted a diauxic growth fermentation experiment with Escherichia coli BW2523 in glucose minimal M9 medium. The comparison of experimental data with dFBA, decFBA and decFBAecc predictions demonstrates how systematic analyses within a fixed constraint-based framework can aid the study of model parameters.

Finally, in explaining experimentally observed phenotypes, our computational analysis also demonstrates the importance of non-linear dependence of exchange fluxes on medium metabolite concentrations and the non-instantaneous change in enzyme composition, effects of which have not previously been accounted for in constraint-based analysis.
COR27/28 Regulate the Evening Transcriptional Activity of the RVE8-LNK1/2 Circadian Complex
Authors: Sorkin Maria L. , Tzeng Shin-Cheng , Romanowski Andrés , Kahle Nikolai , Bindbeutel Rebecca , Hiltbrunner Andreas , Yanovsky Marcelo J. , Evans Bradley S. , Nusinow Dmitri A.
Published: May 2022

The timing of many molecular and physiological processes in plants occurs at a specific time of day. These daily rhythms are driven by the circadian clock, a master timekeeper that uses daylength and temperature to maintain rhythms of approximately 24 hours in various clock-regulated phenotypes. The circadian MYB-like transcription factor REVEILLE 8 (RVE8) interacts with its transcriptional coactivators NIGHT LIGHT INDUCIBLE AND CLOCK REGULATED 1 (LNK1) and LNK2 to promote the expression of evening-phased clock genes and cold tolerance factors. While genetic approaches have commonly been used to discover new connections within the clock and between other pathways, here we use affinity purification coupled with mass spectrometry to discover time-of-day-specific protein interactors of the RVE8-LNK1/2 complex. Among the interactors of RVE8/LNK1/LNK2 were COLD REGULATED GENE 27 (COR27) and COR28, which were coprecipitated in an evening-specific manner. In addition to COR27/28, we found an enrichment of temperature-related interactors that led us to establish a novel role for LNK1/2 in temperature entrainment of the clock. We established that RVE8, LNK1, and either COR27 or COR28 form a tripartite complex in yeast and that the effect of this interaction in planta serves to antagonize transcriptional activation of RVE8 target genes through mediating RVE8 protein degradation in the evening. Together, these results illustrate how a proteomic approach identified time-of-day-specific protein interactions and a novel RVE8-LNK-COR protein complex that implicates a new regulatory mechanism for circadian and temperature signaling pathways.
A plastidial DEAD box RNA helicase plays a critical role in high light acclimation by modulating ribosome biogenesis inChlamydomonas reinhardtii
Authors: Djouani-Tahri El Batoul , Nellaepalli Sreedhar , Auroy Pascaline , Billon Emmanuelle , Burlacot Adrien , Chaux-Jukic Frédéric , Cuiné Stéphan , Epting Virginie , Huleux Marie , Ghysels Bart , Schulz-Raffelt Miriam , Te Isabelle , Brugière Sabine , Couté Yohann , Takahashi Yuichiro , Li-Beisson Yonghua , Peltier Gilles
Published: May 2022

Photosynthetic organisms have developed sophisticated strategies to fine-tune light energy conversion to meet the metabolic demand, thereby optimizing growth in fluctuating light environments. Although mechanisms such as energy dissipation, photosynthetic control, or the photosystem II (PSII) damage and repair have been widely studied, little is known about the regulation of protein synthesis capacity during light acclimation. By screening aChlamydomonas reinhardtiiinsertional mutant library using chlorophyll fluorescence imaging, we isolated a high chlorophyll fluorescence mutant (hf0) defected in a gene encoding a putative plastid targeted DEAD-box RNA helicase called CreRH22. CreRH22 is rapidly induced upon illumination and belongs to the GreenCut, a set of proteins specific to photosynthetic organisms. While photosynthesis is slightly affected in the mutant under low light (LL), exposure to high light (HL) induces a marked decrease in both PSII and PSI, and a strong alteration of the light-induced gene expression pattern. These effects are explained by the inability ofhf0to increase plastid ribosome amounts under HL. We conclude that CreRH22, by promoting ribosomal RNA precursor maturation in a light-dependent manner, enables the assembly of extra-ribosomes required to synthesize photosystem subunits at a higher rate, a critical step in the acclimation of algae to HL.
Carbon footprint of South Dakota dairy production system and assessment of mitigation options
Authors: Naranjo Anna M. , Sieverding Heidi , Clay David , Kebreab Ermias
Published: May 2022

Livestock production contributes to greenhouse gas (GHG) emissions. However, there is a considerable variability in the carbon footprint associated with livestock production. Site specific estimates of GHG emissions are needed to accurately focus GHG emission reduction efforts. A holistic approach must be taken to assess the full environmental impact of livestock production using appropriate geographical scale. The objective of this study was to determine baseline GHG emissions from dairy production in South Dakota using a life cycle assessment (LCA) approach. A cradle-to-farm gate LCA was used to estimate the GHG emissions to produce 1 kg of energy-and-protein corrected milk (ECM) in South Dakota. The system boundary was divided into feed production, farm management, enteric methane emissions, and manure management as these activities are the main contributors to the overall GHG emissions. The production of 1 kg ECM in South Dakota dairies was estimated to emit 1.21 kg CO2 equivalents. The major contributors were enteric methane emissions (46.3%) and manure management (32.6%). Feed production and farm management made up 13.9 and 7.2 %, respectively. The estimate was similar to the national average but slightly higher than the California dairy system. The source of corn used in the dairies influences the footprint. For example, South Dakota corn had fewer GHG emissions than grain produced in Iowa. Therefore, locally and more sustainably sourced feed input will contribute to further reducing the environmental impacts. Improvements in efficiency of milk production through better genetics, nutrition animal welfare and feed production are expected to further reduce the carbon footprint of South Dakota dairies. Furthermore, use of feed additives and anaerobic digesters will reduce emissions from enteric and manure sources, respectively.
Second-generation transfer mediates efficient propagation of ICEBs1 in biofilms
Authors: Bourassa Jean-Sébastien , Jeannotte Gabriel , Lebel-Beaucage Sandrine , Beauregard Pascale B.
Published: May 2022

Horizontal gene transfer (HGT) by integrative and conjugative elements (ICEs) is an important mechanism in the spread of antibiotic resistance genes. However, little is known about the spatiotemporal dynamic of ICEs propagation in bacterial biofilms, which are multicellular structures ubiquitous in the natural and clinical environment. Using a fluorescently marked ICEBs1, we report here that its propagation in biofilms is favored in recipient cells expressing the biofilm matrix. Also, conjugation appears restricted to clusters of bacteria in a close neighborhood in which a high level of ICEBs1 transfer occurs. These conjugative clusters are heterogenously distributed in the biofilm, forming close to the air-biofilm interface. Importantly, we established that transconjugant cells are the main contributors to ICEBs1 propagation in biofilms. Our findings provide a novel spatiotemporal understanding of ICEs propagation in biofilms, which should have an important role in our understanding of horizontal gene transfer in relevant settings.

Importance

The transfer of mobile genetic elements between bacteria is the main cause of the spread of antibiotic resistance genes. While biofilms are the predominant bacterial lifestyle both in the environment and in clinical settings, their impact on the propagation of mobile genetic elements is still poorly understood. In this study, we examined the spatiotemporal propagation of the well-characterized integrative and conjugative element (ICE) ICEBs1. Using the Gram-positive B. subtilis, we observed that the main actors of ICEBs1 propagation in biofilms are the newly formed transconjugants that allow rapid transfer of ICEBs1 to new recipients. Our study provides a better understanding of the spatiotemporal dynamic of conjugative transfer in biofilms.
Parallel evolution of mutational fitness effects over 50,000 generations
Authors: Limdi Anurag , Owen Siân V. , Herren Cristina M. , Lenski Richard E. , Baym Michael
Published: May 2022

As evolving populations accumulate mutations, the benefits and costs of subsequent mutations change. As fitness increases, the relative benefit of new mutations typically decreases. However, the question remains whether deleterious mutations tend to have larger or smaller costs as a population adapts; theory and experiments provide support for both conflicting hypotheses. To address this question, we compared the effects of insertion mutations in every gene inEscherichia colibetween ancestral and 12 independently derived strains after 50,000 generations in a uniform environment. We found both increases and decreases in the fitness costs of mutations, leaving the overall distribution of effects largely unchanged. However, at the extreme, more genes became essential over evolution than vice versa. Both changes in fitness effects and essentiality evolved in parallel across the independent populations, and most changes were not explained by structural variation or altered gene expression. Thus, the macroscopic features of the local fitness landscape remained largely unchanged, even as access to particular evolutionary trajectories changed consistently during adaptation to the experimental environment.

One Sentence Summary

Limdi et al. report parallel changes in the cost of mutations in replicate lineages of a decades-longE. colievolution experiment.
Structural disruption of BAF chromatin remodeller impairs neuroblastoma metastasis by reverting an invasiveness epigenomic program
Authors: Jiménez Carlos , Antonelli Roberta , Nadal-Ribelles Mariona , Devis-Jauregui Laura , Latorre Pablo , Solé Carme , Masanas Marc , Molero-Valenzuela Adrià , Soriano Aroa , de Toledo Josep Sánchez , Llobet-Navas David , Roma Josep , Posas Francesc , de Nadal Eulàlia , Gallego Soledad , Moreno Lucas , Segura Miguel F.
Published: May 2022

Background

Epigenetic programming during development is essential for determining cell lineages, and alterations in this programming contribute to the initiation of embryonal tumour development. In neuroblastoma, neural crest progenitors block their course of natural differentiation into sympathoadrenergic cells, leading to the development of aggressive and metastatic paediatric cancer. Research of the epigenetic regulators responsible for oncogenic epigenomic networks is crucial for developing new epigenetic-based therapies against these tumours. Mammalian switch/sucrose non-fermenting (mSWI/SNF) ATP-dependent chromatin remodelling complexes act genome-wide translating epigenetic signals into open chromatin states. The present study aimed to understand the contribution of mSWI/SNF to the oncogenic epigenomes of neuroblastoma and its potential as a therapeutic target.

Methods

Functional characterisation of the mSWI/SNF complexes was performed in neuroblastoma cells using proteomic approaches, loss-of-function experiments, transcriptome and chromatin accessibility analyses, andin vitroandin vivoassays.

Results

Neuroblastoma cells contain three main mSWI/SNF subtypes, but only BRG1-associated factor (BAF) complex disruption through silencing of its key structural subunits, ARID1A and ARID1B, impairs cell proliferation by promoting cell cycle blockade. Genome-wide chromatin remodelling and transcriptomic analyses revealed that BAF disruption results in the epigenetic repression of an extensive invasiveness-related expression program involving integrins, cadherins, and key mesenchymal regulators, thereby reducing adhesion to the extracellular matrix and the subsequent invasionin vitroand drastically inhibiting the initiation and growth of neuroblastoma metastasisin vivo.

Conclusions

We report a novel ATPase-independent role for the BAF complex in maintaining an epigenomic program that allows neuroblastoma invasiveness and metastasis, urging for the development of new BAF pharmacological structural disruptors for therapeutic exploitation in metastatic neuroblastoma.
Homeostatic feedback between lysosomal mTORC1 and mTORC2-AKT signaling controls nutrient uptake in brown adipose tissue
Authors: Liebscher Gudrun , Vujic Nemanja , Schreiber Renate , Heine Markus , Krebiehl Caroline , Duta-Mare Madalina , Lamberti Giorgia , de Smet Cedric H. , Hess Michael W. , Eichmann Thomas O. , Hölzl Sarah , Scheja Ludger , Heeren Joerg , Kratky Dagmar , Huber Lukas A.
Published: May 2022

In brown adipose tissue (iBAT), the balance of lipid/glucose uptake and lipolysis is regulated by insulin signaling. Downstream of the insulin receptor, PDK1 and mTORC2 phosphorylate AKT, which activates glucose uptake and lysosomal mTORC1 signaling. The latter requires the late endosomal/lysosomal adaptor and MAPK and mTOR activator (LAMTOR/Ragulator). Deletion of LAMTOR2 (and thereby loss of the LAMTOR complex) in mouse adipocytes resulted in insulin-independent AKT hyperphosphorylation in iBAT, causing increased glucose and fatty acid uptake as evidenced by massively enlarged lipid droplets. As LAMTOR2 was essential for the upregulation ofde novolipogenesis, LAMTOR2 deficiency triggered exogenous glucose storage as glycogen in iBAT. These effects are cell autonomous, since AKT hyperphosphorylation was reversed by PI3K inhibition or by deletion of the mTORC2 component Rictor in LAMTOR2-deficient mouse embryonic fibroblasts. We identified a homeostatic circuit connecting LAMTOR-mTORC1 signaling with PI3K-mTORC2-AKT signaling downstream of the insulin receptor to maintain iBAT metabolism.
Mammalian D-Cysteine controls insulin secretion in the pancreas
Authors: Roychaudhuri Robin , West Timothy , Bhattacharya Soumyaroop , Saavedra Harry G. , Albacarys Lauren , Gadalla Moataz M. , Amzel Mario , Yang Peixin , Snyder Solomon H.
Published: May 2022

D-amino acids are being recognized in mammals as important molecules with function. This is a first identification of endogenous D-cysteine in mammalian pancreas. D-cysteine is synthesized by serine racemase (SR) and SR−/−mice produce 6-10 fold higher levels of insulin in the pancreas and plasma including higher glycogen and ketone bodies in the liver. The excess insulin is stored as amyloid in secretory vesicles and exosomes. In glucose stimulated insulin secretion studies in mouse and human islets, equimolar amount of D-cysteine showed higher inhibition of insulin secretion compared to D-serine, another closely related stereoisomer synthesized by SR. In mouse models of diabetes (STZ and NOD) and human pancreas, the diabetic state showed increased expression of D-cysteine compared to D-serine followed by increased expression of SR. SR−/−mice show decreased cAMP in the pancreas followed by reduced phosphorylation of CREB (S133), lower DNA methyltransferase enzymatic and promoter activities resulting in decreased methylation of theIns1promoter. D-cysteine is efficiently metabolized by D-amino acid oxidase and transported by ASCT2 and Asc1. Dietary supplementation with methyl donors restored the high insulin levels and low DNMT enzymatic activity in SR−/−mice. Our data show that endogenous D-cysteine in the mammalian pancreas is a regulator of insulin secretion.

Highlights

Serine Racemase also functions as a cysteine racemase.

Lack of Serine Racemase results in significantly high levels of insulin in the pancreas, plasma and larger islets.

D-cysteine shows greater inhibition of insulin secretion compared to D-serine.

Endogenous D-cysteine signals via cyclic AMP that mediates downstream CREB-DNMT1 interaction.

CREB-DNMT1 interaction results in hypomethylation ofIns1promoter that can be rescued by high methyl donor dietary supplementation rescuing high insulin levels.
The vestibular calyceal junction is dismantled following subchronic streptomycin in rats and sensory epithelium stress in humans
Authors: Maroto Alberto F. , Borrajo Mireia , Prades Sílvia , Callejo Àngela , Amilibia Emilio , Pérez-Grau Marta , Roca-Ribas Francesc , Castellanos Elisabeth , Barrallo-Gimeno Alejandro , Llorens Jordi
Published: May 2022

Hair cell (HC) loss by epithelial extrusion has been described to occur in the rodent vestibular system during chronic 3,3’-iminodipropionitrile (IDPN) ototoxicity. This is preceded by dismantlement of the calyceal junction in the contact between type I HC (HCI) and calyx afferent terminals. Here, we evaluated whether these phenomena have wider significance. First, we studied rats receiving streptomycin for 3 to 8 weeks. Streptomycin caused loss of vestibular function associated with partial loss of HCI and decreased expression of contactin-associated protein (CASPR1), denoting calyceal junction dismantlement, in the calyces encasing the surviving HCI. Additional molecular and ultrastructural data supported the conclusion that HC-calyx detachment precede HCI loss by extrusion. Animals allowed to survive after the treatment showed functional recuperation and rebuilding of the calyceal junction. Second, we evaluated human sensory epithelia obtained during therapeutic labyrinthectomies and trans-labyrinthine tumour excisions. Some samples showed abnormal CASPR1 label strongly suggestive of calyceal junction dismantlement. Therefore, reversible dismantlement of the vestibular calyceal junction may be a common response triggered by chronic stress, including ototoxic stress, before HCI loss. This may partly explain clinical observations of reversion in function loss after aminoglycoside exposure.
Intracellular Calcium links Milk Stasis to Lysosome Dependent Cell Death by Activating a TGFβ3/TFEB/STAT3 Pathway Early during Mammary Gland Involution
Authors: Jeong Jaekwang , Lee Jongwon , Talaia Gabriel , Kim Wonnam , Song Junho , Hong Juhyeon , Yoo Kwangmin , Gonzalez David G. , Athonvarangkul Diana , Shin Jaehun , Dann Pamela , Haberman Ann M , Kim Lark Kyun , Ferguson Shawn M. , Choi Jungmin , Wysolmerski John
Published: May 2022

Involution of the mammary gland after lactation is a dramatic example of coordinated cell death. Weaning causes distension of the alveolar structures due to the accumulation of milk, which, in turn, activates STAT3 and initiates a caspase- independent but lysosome-dependent cell death (LDCD) pathway. Although the importance of STAT3 and LDCD in early mammary involution is well established, it has not been entirely clear how milk stasis activates STAT3. In this report, we demonstrate that protein levels of the PMCA2 calcium pump are significantly downregulated within 2- 4 hours of experimental milk stasis. Reductions in PMCA2 expression correlate with an increase in cytoplasmic calciumin vivoas measured by multiphoton intravital imaging of GCaMP6f fluorescence. These events occur concomitant with the appearance of nuclear pSTAT3 expression but prior to significant activation of LDCD or its previously implicated mediators such as LIF, IL6 and TGFβ3, all of which appear to be upregulated by increased intracellular calcium. We also observed that milk stasis, loss of PMCA2 expression and increased intracellular calcium levels activate TFEB, an important regulator of lysosome biogenesis. This is the result of increased TGFβ signaling and inhibition of cell cycle progression. Finally, we demonstrate that increased intracellular calcium activates STAT3 by inducing degradation of its negative regulator, SOCS3, a process which also appears to be mediated by TGFβ signaling. In summary, these data suggest that intracellular calcium serves as an important proximal biochemical signal linking milk stasis to STAT3 activation, increased lysosomal biogenesis, and lysosome- mediated cell death.
The Nse5/6-like SIMC1-SLF2 Complex Localizes SMC5/6 to Viral Replication Centers
Authors: Oravcová Martina , Nie Minghua , Zilio Nicola , Maeda Shintaro , Jami-Alahmadi Yasaman , Lazzerini-Denchi Eros , Wohlschlegel James A. , Ulrich Helle D. , Otomo Takanori , Boddy Michael N.
Published: May 2022

The human SMC5/6 complex is a conserved guardian of genome stability and an emerging component of antiviral responses. These disparate functions likely require distinct mechanisms of SMC5/6 regulation. In yeast, Smc5/6 is regulated by its Nse5/6 subunits, but such regulatory subunits for human SMC5/6 are poorly defined. Here, we identify a novel SMC5/6 subunit called SIMC1 that contains SUMO interacting motifs (SIMs) and an Nse5-like domain. We isolated SIMC1 from the proteomic environment of SMC5/6 within polyomavirus large T antigen (LT)-induced subnuclear compartments. SIMC1 uses its SIMs and Nse5-like domain to localize SMC5/6 to polyomavirus replication centers (PyVRCs) at SUMO-rich PML nuclear bodies. SIMC1’s Nse5-like domain binds to the putative Nse6 orthologue SLF2 to form an anti-parallel helical dimer resembling the yeast Nse5/6 structure. SIMC1-SLF2 structure-based mutagenesis defines a conserved surface region containing the N-terminus of SIMC1’s helical domain that regulates SMC5/6 localization to PyVRCs. Furthermore, SLF1, which recruits SMC5/6 to DNA lesions, binds SLF2 analogously to SIMC1 and forms a distinct Nse5/6-like complex. Thus, two Nse5/6-like complexes independently regulate human SMC5/6: SIMC1-SLF2 responding to viral challenge and SLF1/2 recognizing DNA damage.
FliL has a conserved function in diverse microbes to negatively modulate motor output via its N-terminal region
Authors: Liu Xiaolin , Roujeinikova Anna , Ottemann Karen M.
Published: May 2022

Bacterial surface sensing is often conferred by flagella. The flagellar motor protein FliL plays a key role in this process, but its exact role has been obscured by varying fliL mutant phenotypes. We reanalyzed results from studies on these fliL alleles and found they inadvertently compared mutants with differing length of the retained native N-terminal region, including the transmembrane helix (TM). We find that TM retention in the mutants that lack the native C-terminal domain results in loss of swimming and swarming motility, while alleles that completely lack the TM retain motility. We suggest FliL negatively regulates motor function via its N-terminal region, an observation that may relate to FliL function in mechanosensing.
Efficient querying of genomic reference databases with gget
Authors: Luebbert Laura , Pachter Lior
Published: May 2022

Motivation

A recurring challenge in interpreting genomic data is the assessment of results in the context of existing reference databases. Currently, there is no tool implementing automated, easy programmatic access to curated reference information stored in a diverse collection of large, public genomic databases.

Results

gget is a free and open-source command-line tool and Python package that enables efficient querying of genomic reference databases, such as Ensembl. gget consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying required for genomic data analysis in a single line of code.

Availability

The manual and source code are available at https://github.com/pachterlab/gget.

Contact

lpachter@caltech.edu
Persistence of phenotypic responses to short-term heat stress in the tabletop coral Acropora hyacinthus
Authors: Walker Nia S. , Cornwell Brendan H. , Nestor Victor , Armstrong Katrina C. , Golbuu Yimnang , Palumbi Stephen R.
Published: May 2022

Widespread mapping of coral thermal resilience is essential for developing effective management strategies and requires replicable and rapid multi-location assays of heat resistance and recovery. One- or two-day short-term heat stress experiments have been previously employed to assess heat resistance, followed by single assays of bleaching condition. We tested the reliability of short-term heat stress resistance, and linked resistance and recovery assays, by monitoring the post short-term heat stress phenotypic response of fragments from 101 Acropora hyacinthus colonies located in Palau (Micronesia). Following short-term heat stress, bleaching and mortality were recorded after 16 hours, daily for seven days, and after months one and two into recovery. To follow corals over time, we utilized a qualitative, non-destructive visual bleaching score metric that correlated with standard symbiont retention assays. The bleaching state of coral nubbins 16 hours post-heat stress was highly indicative of their state over the next 7 days, suggesting that symbiont population sizes within corals may quickly stabilize post-heat stress. Bleaching 16 hours post-heat stress predicted likelihood of mortality over the subsequent 3-5 days, after which there was little additional mortality. Together, bleaching and mortality suggested that rapid assays of the phenotypic response following short-term heat stress were good metrics of the total heat treatment effect. Additionally, our data confirm geographic patterns of intraspecific variation in Palau and show that bleaching severity among colonies was highly correlated with mortality over the first week post-stress. We found high survival (98%) and visible recoverability (100%) two months after heat stress among coral nubbins that survived the first week post-stress. These findings help simplify rapid, widespread surveys of heat sensitivity in Acropora hyacinthus by showing that standardized short-term experiments can be confidently assayed after 16 hours, and that bleaching sensitivity may be linked to subsequent survival using experimental assessments.
Analysis of the Drosophila Ajuba LIM protein defines functions for distinct LIM domains
Authors: Rauskolb Cordelia , Han Ahri , Kirichenko Elmira , Ibar Consuelo , Irvine Kenneth D.
Published: May 2022

The Ajuba LIM protein Jub mediates regulation of Hippo signaling by cytoskeletal tension through interaction with the kinase Warts, and also participates in feedback regulation of junctional tension through regulation of the cytohesin Steppke. To investigate how Jub interacts with and regulates its distinct partners, we investigated the ability of Jub proteins missing different combinations of its three LIM domains to rescue jub phenotypes and to interact with α-catenin, Warts and Steppke. Multiple regions of Jub contribute to its ability to bind α-catenin and to localize to adherens junctions in Drosophila wing imaginal discs. Co-immunoprecipitation experiments in cultured cells identified a specific requirement for LIM2 for binding to Warts. However, in vivo, both LIM1 and LIM2, but not LIM3, were required for regulation of wing growth, Yorkie activity, and Warts localization. Conversely, LIM2 and LIM3, but not LIM1, were required for regulation of cell shape and Steppke localization in vivo, and for maximal Steppke binding in co-immunoprecipitation experiments. These observations identify distinct functions for the different LIM domains of Jub.
ER translocation of suboptimal targeting sequences depends on Sec61β/Sbh1 and its phosphorylation
Authors: Barbieri Guido , Simon Julien , Lupusella Cristina R. , Pereira Fabio , Elia Francesco , Meyer Hadar , Schuldiner Maya , Hanes Steven D. , Nguyen Duy , Helms Volkhard , Römisch Karin
Published: May 2022

The endoplasmic reticulum (ER) protein translocation channel subunit Sec61β/Sbh1 is non-essential, but contains multiple phosphorylation sites suggesting a regulatory role in ER protein import. We show here that mutating two N-terminal, proline-flanked, phosphorylation sites in the Sbh1 cytosolic domain phenocopies the temperature-sensitivity of a yeast strain lacking SBH1/SBH2, and results in reduced translocation into the ER of an Sbh1-dependent substrate, Gls1. In a microscopic screen we show that about 12% of GFP-tagged secretory proteins depend on Sbh1 for translocation. Sbh1-dependent proteins have targeting sequences with less pronounced hydrophobicity and often no or an inverse charge bias. A subset of these proteins was dependent on N-terminal phosphorylation of Sbh1 and on the phospho-S/T-specific proline isomerase Ess1 (PIN1 in mammals) for ER import. We conclude that Sbh1 promotes ER translocation of substrates with suboptimal targeting sequences and that its activity is regulated by a conformational change induced by N-terminal phosphorylation.
On the intrinsic curvature of animal whiskers
Authors: Luo Yifu , Hartmann Mitra J.Z.
Published: May 2022

Facial vibrissae (whiskers) are thin, tapered, and flexible hair-like structures that are an important source of tactile sensory information for many species of animals. In contrast to insect antennae, whiskers have no sensors along their lengths. Instead, when a whisker touches an object, the resulting deformation is transmitted to mechanoreceptors in a follicle at the whisker base. Previous work has shown that the mechanical signals transmitted along the whisker will depend strongly on the whisker’s geometric parameters, in particular on its taper (how diameter varies with arc length) and on its intrinsic curvature. Although previous studies have largely agreed on how to define taper, multiple approaches have been used to quantify intrinsic curvature. The present work, compares and contrasts different mathematical methods to quantify intrinsic curvature, including polynomial, fractional exponent, elliptical, and Cesàro. Comparisons are performed across ten species of whiskered animals, ranging from rodents to pinnipeds. The fractional exponent model is shown to be a particularly promising approach for distinguishing between whiskers of different species. We conclude with a discussion of the advantages and disadvantages of using the different models for different modeling situations.
The Indirect Pathway of the Basal Ganglia Promotes Negative Reinforcement, But Not Motor Suppression
Authors: Isett Brian R. , Nguyen Katrina P. , Schwenk Jenna C. , Snyder Christen N. , Adegbesan Kendra A. , Ziausyte Ugne , Gittis Aryn H.
Published: May 2022

Optogenetic stimulation of Adora2a receptor expressing spiny projection neurons (A2A-SPN) in the striatum drives locomotor suppression and negative reinforcement, results attributed to activation of the indirect pathway. The sole long-range projection target of A2A-SPNs is the external globus pallidus (GPe). Unexpectedly, we found that inhibition of the GPe did not suppress movement, but did drive robust negative reinforcement in a real-time place preference assay. Within the striatum, A2A-SPNs inhibit other SPNs through a short-range inhibitory collateral network, and we found that optogenetic stimuli that drove motor suppression shared a common mechanism of recruiting this inhibitory collateral network. Our results suggest that the indirect pathway plays a more prominent role in negative reinforcement than in motor control and challenges the assumption that activity of A2A-SPNs is synonymous with indirect pathway activity.
Molecular cloning and recombinant protein expression of 9-Lipoxygenase gene from Solanum tuberosum in Pichia pastoris yeast cells
Authors: Olengo Alex , Nanteza Ann , Perino Elvio Henrique Benatto , Garbe Leif-Alexander , Marillonnet Sylvestre , Grützner Ramona , Saimo-Kahwa Margaret , Schultz Fabien , Koch Matthias
Published: May 2022

Synthetic fungicides have effectively controlled plant pathogenic fungi but their continued use has been detrimental to natural biological systems, and sometimes resulted into development of fungal resistance. They also have undesirable effects on non-target organisms and foster environmental and human health concerns thus new biodegradable alternatives have to be investigated. Lipoxygenases (LOX) are ubiquitous non-heme Iron containing dioxygenases that catalyze the addition of molecular oxygen to Polyunsaturated Fatty Acids (PUFAs) such as Linoleic acid to form Oxylipins that possess anti-microbial activity.The aim of this study was to generate a recombinant 9-Lipoxygenase protein for chemo enzymatic synthesis of Oxylipin based biodegradable fungicides. Golden gate assembly, a molecular cloning method that allows assembly of many DNA fragments into a complete piece using Type II s restriction enzymes and T4 DNA ligase was used to clone the complete 9-LOX gene into the expression plasmid vector pPICZαB. Protein expression in Pichia pastoris yeast cells was induced by addition of absolute methanol every after 24h for up to four days. Analysis of protein expression from cell lysates was achieved by SDS-PAGE and Western blotting probed with anti-histidine antibody which showed putative protein bands of 97kDa representing recombinant 9-LOX protein. It is recommended that optimization studies on the yeast kex2 convertase and the α- secretion factor can be done to enable secretion of recombinant Solanum tuberosum 9-LOX protein since the protein in this study was recovered from cell lysates.
The COMIX polarimeter: a compact device for XUV polarization analysis
Authors: Pancaldi Matteo , Strüber Christian , Friedrich Bertram , Pedersoli Emanuele , De Angelis Dario , Nikolov Ivaylo P. , Manfredda Michele , Foglia Laura , Yulin Sergiy , Spezzani Carlo , Sacchi Maurizio , Eisebitt Stefan , von Korff Schmising Clemens , Capotondi Flavio
Published: May 2022

We report on the characterization of a novel extreme-ultraviolet polarimeter based on conical mirrors to simultaneously detect all the components of the electric field vector for extreme-ultraviolet radiation in the 45–90 eV energy range. The device has been characterized using a variable polarization source at the Elettra synchrotron, showing good performance in the ability to determine the radiation polarization. Furthermore, as a possible application of the device, Faraday spectroscopy and time-resolved experiments have been performed at the Fe M
2,3-edge on an FeGd ferrimagnetic thin film using the FERMI free-electron laser source. The instrument is shown to be able to detect the small angular variation induced by an optical external stimulus on the polarization state of the light after interaction with magnetic thin film, making the device an appealing tool for magnetization dynamics research.
Stock market reactions to COVID-19 shocks: do financial market interventions walk the talk?
Authors: Marobhe Mutaju Isaack , Kansheba Jonathan Mukiza Peter
Published: May 2022

Purpose

Following the COVID-19 outbreak, various economies imposed different financial interventions as part of initiatives to cushion their stock markets from deteriorating performance. Our article examines the effectiveness of these interventions in protecting stock markets during the pandemic.

Design/methodology/approach

The authors employ Panel Vector Autoregression to model the magnitude and timing of shocks from COVID-19 to stock markets. The fixed effects regression is then utilized to assess the role of financial interventions in protecting stock markets during COVID-19. The study uses daily stock index returns as well COVID-19 containment measures stringency index data from 39 countries ranging from 2nd January 2020 to 30th September 2021.

Findings

Our findings firstly reveal a significant positive stock market reaction to country-level containment measures stringency but only during the first wave of COVID-19. We secondly show that stock market functioning interventions that include short selling bans and circuit breakers amplify the positive effects of COVID-19 containment measures stringency on stock market performance.

Research limitations/implications

The authors stress the need for policymakers and regulators to timely intervene in protecting economies and stock markets during crises such as COVID-19 in order to reduce panic among investors. Moreover, investors should adjust their portfolios by investing in stocks from countries that have proper financial market interventions in place.

Originality/value

Despite growing body of literature on COVID-19 and stock market performance, there is limited evidence on the role of financial sector interventions to cushion stock markets during tumultuous conditions caused by the pandemic.
Entrepreneurial orientation, sustainability practices and performance of small and medium enterprises: evidence from an emerging economy
Authors: Akomea Samuel Yaw , Agyapong Ahmed , Ampah Godwin , Osei Hannah Vivian
Published: May 2022

Purpose

Despite the growing scholarly interest in examining entrepreneurial orientation (EO)-performance link, the results have been inconsistent. However, studies have not explored firm-level and external factors that may serve as mechanisms or boundary conditions to explain this relationship. Therefore, the purpose of the study is to examine how and when EO influences performance by incorporating sustainability practices as a mechanism and competitive intensity as an important contingent factor.

Design/methodology/approach

Using primary data obtained from 323 chief executive officers/entrepreneurs, the authors analyzed the data using structural equation modeling in LISREL and Hayes PROCESS in SPSS.

Findings

The authors found that sustainability practices serve as a mechanism through which EO influences small and medium enterprises' (SMEs) performance. The study further revealed that the relationship between EO and sustainability practices is weakened at high levels of competitive intensity. Still, the relationship between EO and performance through sustainability practices remains strengthened when competitive intensity is present at high levels.

Originality/value

This study contributes to the literature by examining how SMEs who are less endowed with resources can engage in sustainability practices that can match large firms with stronger EO to achieve increased performance. Additionally, the study contributes to the literature by examining the mediating effect of sustainability practices in the EO-performance relationship. Finally, the study contributes to the body of literature by testing how competitive intensity presents as a boundary condition to leverage the relationship between EO and performance.
Drum-Buffer-Rope in an engineering-to-order productive system: a case study in a Brazilian aerospace company
Authors: Telles Eduardo Santos , Lacerda Daniel Pacheco , Morandi Maria Isabel Wolf , Ellwanger Rodrigo , de Souza Fernando Bernardi , Piran Fabio Sartori
Published: May 2022

Purpose

Drum-Buffer-Rope (DBR) is a method to adjust production flows, synchronize the release of materials and enable a process of focused improvement in production systems. Literature on DBR applications in engineer-to-order (ETO) production systems, where customers participate in product design decisions and, consequently, in the way production is planned and executed, is rare. However, the interest in improving production management in ETO systems has received attention from the scientific and business communities. The goal of this research was to evaluate the implementation of DBR in an ETO productive system, critically analyzing the necessary adaptations for its use.

Design/methodology/approach

This research was conducted through a case study in a company that manufactures electronic equipment, known as avionics, in the aerospace sector.

Findings

In this context, the contribution of this study consists of evaluation of the implementation of DBR in an ETO productive system, describing the implementation and the necessary adaptations of the DBR to the ETO productive system explored, comparing it with the DBR theoretical proposals and Simplified Drum-Buffer-Rope (S-DBR) methods.

Originality/value

The study contributes to knowledge by expanding the field of the DBR application to make it more precise, and by applying the theory of constraints, in a general manner, to this type of productive environment.
Fostering resilience through the culture of excellence (CoE) practices: explorative insights from a talent management SME
Authors: Joseph Nidheesh , Totawar Abhishek K. , Sam Oliver
Published: May 2022

Purpose

Organisational researchers have always highlighted the role of leadership during crisis. However, anecdotal evidence shows that leadership often fails when the culture does not back them during a crisis. Hence, actively initiating and developing a culture of excellence (CoE) become all the more relevant during a crisis. This paper aims to understand the role of CoE in building a resilient organisation. Furthermore, it aims to contribute to the understanding of building CoE practices in small businesses.

Design/methodology/approach

The paper reviews relevant literature and gathers evidence from VDart Inc, a digital talent management and services firm based in Atlanta, Georgia, USA. A case study design based on retrospective and real-time data collection is performed to investigate CoE practices before and during the Covid-19 crisis.

Findings

The findings argue that, most often, the culture and not just the leadership determines the fate of an organisation undergoing crisis. From the case evidence, the authors identify reinforce the culture, invest in cultural custodians, seek order, keep them close and industry thought-leadership (“RISK-It”) CoE practices for fostering resilience in small- and medium-sized enterprises/businesses (SMEs) for managing crises.

Originality/value

The authors contribute to knowledge in fostering proactive resilience in small businesses, showing how SMEs should invest in building a CoE when their organisations are stable instead of searching for strong leaders and unique strategies during a crisis. Later, during the crisis, just by reinforcing their CoE using RISK-It CoE practices, leaders and managers would be able to leverage any turbulence to the advantage of their organisations.
The mediating role of organizational silence in the relationship between organizational justice and organizational creativity
Authors: Ölçer Ferit , Coşkun Ömer Faruk
Published: May 2022

Purpose

The purpose of this study is to determine the relationships between organizational justice, organizational silence and organizational creativity and to examine the mediating role of organizational silence in the effect of organizational justice on organizational creativity.

Design/methodology/approach

Research data were collected using a face-to-face survey method applied to employees in the automotive industry in Turkey. The research model and hypotheses were tested by structural equation modeling.

Findings

Research results indicate that organizational justice positively affects organizational silence, organizational creativity is positively affected by organizational justice and organizational silence positively affects organizational creativity. Besides, according to the results, organizational silence has a partial mediating role in the effect of organizational justice on organizational creativity.

Originality/value

Although the relationships between organizational justice, organizational silence and organizational creativity were examined in previous studies in the literature, the role of organizational silence in the relationship between organizational justice and organizational creativity was not investigated. Besides, although previous studies examined the mediating role of variables that are thought to have a positive effect on the organization between organizational justice and organizational creativity, they did not study the role of a variable of organizational silence, which is considered negative. For these reasons, this study is predicted to differentiate the perspective in the literature and fills a gap in the literature.
Turning crises into opportunities in the service sector: how to build antifragility in small and medium service enterprises
Authors: Corvello Vincenzo , Verteramo Saverino , Giglio Carlo
Published: May 2022

Purpose

This work aims at investigating the variables that foster antifragility in the context of small and medium-sized service companies (service SMEs).

Design/methodology/approach

This work adopts an exploratory approach in order to deepen five examples of service SMEs that were able to change their own business models and to reinforce their strategic position while facing the COVID-19 pandemic.

Findings

The ingredients of antifragility ability include: entrepreneurial orientation, context insightfulness and operational dexterity. This article singles out the resources and capacities backing the blossoming of antifragility abilities in service SMEs. Slack financial resources, many and diverse research-and-innovation partners, operational dexterity, fastness and creativity are included among such resources and capabilities.

Practical implications

Crises may occur frequently in many ways; thus, this work provides some guidance geared to services SMEs in order to increase their level of preparedness for future crises and to nurture their ability to transform them into opportunities.

Originality/value

Despite many concepts associated with antifragility have been dealt with in literature such as resilience or agility, antifragility is hitherto underexplored. This article is among the first ones to explore factors fostering antifragility in service SMEs.