bluuebunny/crossref_metadata_2025 huggingface dataset:
Maternal transmission gives way to social transmission during gut microbiota assembly in wild mice
Authors: Wanelik Klara M , Raulo Aura , Troitsky Tanya , Husby Arild , Knowles Sarah CL
Published: August 2022

The mammalian gut microbiota influences a wide array of phenotypes and is considered a key determinant of fitness, yet knowledge about the transmission routes by which gut microbes colonise hosts in natural populations remains limited. Here, we use an intensively studied wild population of wood mice (Apodemus sylvaticus) to examine how vertical (maternal) and horizontal (social) transmission routes influence gut microbiota composition throughout life. We identify independent signals of maternal transmission (sharing of taxa between a mother and her offspring) and social transmission (sharing of taxa predicted by the social network), whose relative magnitudes shift as hosts age. In early life, gut microbiota composition is predicted to a similar extent by both maternal and social relationships, but by adulthood the impact of maternal transmission becomes undetectable, leaving only a signal of social transmission. By exploring which taxa drive the maternal transmission signal, we further identify a candidate maternally-transmitted bacterial family in wood mice, theLactobacillaceae. Overall, our findings suggest a shifting transmission landscape for wild mice, with a mother’s influence on microbiota composition waning as offspring age, while the impact of social contacts remains strong and consistent.
BRCA1/BARD1 intrinsically disordered regions facilitate chromatin recruitment and ubiquitylation
Authors: Witus Samuel R. , Tuttle Lisa M. , Li Wenjing , Zelter Alex , Wang Meiling , Kermoade Klaiten E. , Wilburn Damien B. , Davis Trisha N. , Brzovic Peter S. , Zhao Weixing , Klevit Rachel E.
Published: August 2022

BRCA1/BARD1 is a tumor suppressor E3 ubiquitin (Ub) ligase with roles in DNA damage repair and in transcriptional regulation. BRCA1/BARD1 RING domains interact with nucleosomes to facilitate mono-ubiquitylation of distinct residues on the C-terminal tail of histone H2A. These enzymatic domains constitute a small fraction of the heterodimer, raising the possibility of functional chromatin interactions involving other regions such as the BARD1 C-terminal domains that bind nucleosomes containing the DNA damage signal H2A K15-Ub and H4 K20me0, or portions of the expansive intrinsically disordered regions found in both subunits. Herein, we reveal novel interactions that support robust H2A ubiquitylation activity mediated through a high-affinity, intrinsically disordered DNA-binding region of BARD1. These interactions support BRCA1/BARD1 recruitment to chromatin and sites of DNA damage in cells and contribute to their survival. We also reveal distinct BRCA1/BARD1 complexes that depend on the presence of H2A K15-Ub, including a complex where a single BARD1 subunit spans adjacent nucleosome units. Our findings identify an extensive network of multivalent BARD1- nucleosome interactions that serve as a platform for BRCA1/BARD1-associated functions on chromatin.
Temporal disparity of action potentials triggered in axon initial segments and distal axons in the neocortex
Authors: Rózsa Márton , Tóth Martin , Oláh Gáspár , Baka Judith , Lákovics Rajmund , Barzó Pál , Tamás Gábor
Published: August 2022

Neural population activity determines the timing of synaptic inputs, which arrive to dendrites, cell bodies and axon initial segments (AISs) of cortical neurons. Action potential initiation in the AIS (AIS-APs) is driven by input integration, and the phase preference of AIS-APs during network oscillations is characteristic to cell classes. Distal regions of cortical axons do not receive synaptic inputs, yet experimental induction protocols can trigger retroaxonal action potentials (RA-APs) in axons distal from the soma. We report spontaneously occurring RAAPs in human and rodent cortical interneurons that appear uncorrelated to inputs and population activity. Network linked triggering of AIS-APs versus input independent timing of RA-APs of the same interneurons result in disparate temporal contribution of a single cell to in vivo network operation through perisomatic and distal axonal firing.

One-Sentence Summary

Network linked triggering of AIS-APs versus input independent timing of RA-APs of the same interneurons result in disparate temporal contribution of a single cell to in vivo network operation.
Response of the organellar and nuclear (post)transcriptomes of Arabidopsis to drought stress
Authors: Xu Duorong , Tang Qian , Leister Dario , Kleine Tatjana
Published: August 2022

Plants have evolved sophisticated mechanisms to cope with drought, which involve massive changes in nuclear gene expression. However, little is known about the roles of post-transcriptional processing of nuclear or organellar transcripts and how meaningful these changes are. To address these issues, we used long non-coding RNA-sequencing to monitor (post)transcriptional changes during different times of drought exposure in Arabidopsis Col-0 and a mutant (protein phosphatase 7-like, pp7l), from which we demonstrated that it can survive long periods of drought stress. The changes detected in the pp7l mutant were marginal, while in the wild type chloroplast transcript levels were globally reduced, editing efficiency dropped, but splicing was not affected. Mitochondrial transcripts were slightly elevated, while editing and splicing were unchanged. Also, transcriptional activation of transposable elements played only a minor role. Conversely, alternative splicing (AS) affected nearly 2,000 genes (11% of expressed nuclear genes). Of these, 25% underwent isoform switching, and 15% were regulated solely at the level of AS, representing transcripts that would have gone unnoticed in a microarray-based approach. Our data show that AS enhances proteome diversity to counteract drought stress and represent a valuable resource that will facilitate the development of new strategies to improve plant performance under drought. Moreover, altering the relative contributions of spliced isoforms might enhance drought resistance. For instance, our data imply that accumulation of a non-functional FLM (FLOWERING LOCUS M) isoform – and not the ratio of functional isoforms as suggested for temperature responses - accounts for the early-flowering phenotype under drought conditions.
Inhibition of PI3K p110δ activity reduces IgE production in IL-4 and anti-CD40 stimulated human B cell cultures
Authors: Cutrina-Pons Anna , De Sa Aloka , Fear David J , Gould Hannah J , Ramadani Faruk
Published: August 2022

Phosphoinositide 3-kinase (PI3K) p110δ signalling negatively regulates the production of mouse IgE. However, there are disparities between the mouse and human IgE biology, and the role of PI3K p110δ in the production of human IgE is yet to be determined. To investigate the effect of PI3K p110δ inhibition in the production of human IgE we isolated human B cells from tonsil tissue and stimulated them with IL-4 and anti-CD40 antibody to induce class switching to IgE and IgG1 in the presence or absence of IC87114, a small molecule inhibitor of PI3K p110δ. Using FACS, RT-PCR and ELISA we examined the effect of PI3K p110δ inhibition on IgE production and also determined the mechanisms involved. Unlike in mice, we observed that PI3K p110δ inhibition significantly reduces the number of IgE+ switched cells and the amounts of secreted IgE in IL4 and anti-CD40 cultures. However, the number of IgG1+ cells and secreted IgG1 were largely unaffected by PI3K p110δ inhibition. The expression levels of AID, ε and γ1 germinal transcripts or other factors involved in the regulation of CSR to IgE and IgG1 were also unaffected by IC87114. However, we found that IC87114 significantly decreases the proliferation of tonsil B cells stimulated with IL-4 and anti-CD40, specifically reducing the frequency of cells that had undergone 4 divisions or more. Our data identifies proliferation as the key mechanism through which PI3K p110δ regulates CSR of human B cells to IgE and highlights PI3K p110δ as a pharmacological target for the treatment of allergic disease.
From empirical to data-driven host selection: a broad-host-range expression platform to facilitate chassis screening
Authors: Mol Viviënne , Falkenberg Kristoffer Bach , De Almeida Will Ácil , Pogrebnyakov Ivan , Beck Charlotte , Skøttrup Anna Lyhne , Nielsen Alex Toftgaard , Jensen Sheila Ingemann
Published: August 2022

Nature has provided a vast landscape of organisms through evolution, each with unique phenotypic traits adapted to varying environments. Nevertheless, host selection in biotechnological research is exceedingly dominated by empirical preference, where the endogenous physiology of the selected host is often not suited to the desired application. Considering that large parts of cellular regulation and metabolism remain obscure, empirical selection of a preferred model organism may lead to undue caveats in further engineering attempts, arising from intrinsic metabolism. One reason for the empirical host selection is the lack of engineering tools for screening novel organisms. In this study, we provide a modular, single vector-based expression platform, compatible with a wide range of prokaryotes. It centers around a tight and titratable promoter system, inducible by anhydrotetracyclin within an 84-fold dynamic range. It enables easy screening of recombinant proteins and pathways in both mesophilic and thermophilic Gram-negative and Gram-positive hosts. Overall, this platform enables simple screening of heterologous expression and production in a variety of hosts, including the exploration of previously unconsidered hosts thereby aiding the transition from empirical to data-driven host selection.
Tetracenomycin X sequesters peptidyl-tRNA during translation of QK motifs
Authors: Leroy Elodie C. , Perry Thomas N. , Renault Thibaud T. , Innis C. Axel
Published: August 2022

With antibiotic-resistant bacteria threatening our ability to treat common infections, new lead compounds with distinct target binding sites and limited cross-resistance are urgently needed. Natural products that inhibit the bacterial ribosome – a target for more than half of the antibiotics in use today – are a promising source of such leads and have the potential to be developed into potent drugs through structure-guided design. However, because the mechanisms of action of many of these compounds are not well understood, they are often poor candidates for a structure-based approach. Here, we use inverse toeprinting coupled to next-generation sequencing to show that the aromatic polyketide tetracenomycin X (TcmX) primarily inhibits the formation of a peptide bond between an incoming aminoacyl-tRNA and a terminal Gln-Lys (QK) motif in the nascent polypeptide. Using cryogenic electron microscopy, we reveal that translation inhibition at QK motifs occurs via an unusual mechanism involving sequestration of the 3’ adenosine of peptidyl-tRNALysin the drug-occupied nascent polypeptide exit tunnel of the ribosome. Our study provides mechanistic insights into the mode of action of TcmX on the bacterial ribosome and suggests a path forward for the development of novel antibiotics based on a common aromatic polyketide scaffold.
Quorum-sensing control of matrix protein production drives fractal wrinkling and interfacial localization of Vibrio cholerae pellicles
Authors: Qin Boyang , Bassler Bonnie L.
Published: August 2022

Bacterial cells at fluid interfaces can self-assemble into collective communities with stunning macroscopic morphologies. Within these soft, living materials, called pellicles, constituent cells gain group-level survival advantages including increased antibiotic resistance. However, the regulatory and structural components that drive pellicle self-patterning are not well defined. Here, using Vibrio cholerae as our model system, we report that two sets of matrix proteins and a key quorum-sensing regulator jointly orchestrate the sequential mechanical instabilities underlying pellicle morphogenesis, culminating in fractal patterning. A pair of matrix proteins, RbmC and Bap1, maintain pellicle localization at the interface and prevent self-peeling. A single matrix protein, RbmA, drives a morphogenesis program marked by a cascade of ever finer wrinkles with fractal scaling in wavelength. Artificial expression of rbmA restores fractal wrinkling to a ΔrbmA mutant and enables precise tuning of fractal dimensions. The quorum-sensing regulatory small RNAs Qrr1-4 first activate matrix synthesis to launch pellicle primary wrinkling and ridge instabilities. Subsequently, via a distinct mechanism, Qrr1-4 suppress fractal wrinkling to promote fine modulation of pellicle morphology. Our results connect cell-cell signaling and architectural components to morphogenic patterning and suggest that manipulation of quorum-sensing regulators or synthetic control of rbmA expression could underpin strategies to engineer soft biomaterial morphologies on demand.
Uncovering structural ensembles from single particle cryo-EM data using cryoDRGN
Authors: Kinman Laurel F. , Powell Barrett M. , Zhong Ellen D. , Berger Bonnie , Davis Joseph H.
Published: August 2022

CryoDRGN is a machine learning system for heterogeneous cryo-EM reconstruction of proteins and protein complexes from single particle cryo-EM data. Central to this approach is a deep generative model for heterogeneous cryo-EM density maps, which we empirically find effectively models both discrete and continuous forms of structural variability. Once trained, cryoDRGN is capable of generating an arbitrary number of 3D density maps, and thus interpreting the resulting ensemble is a challenge. Here, we showcase interactive and automated processing approaches for analyzing cryoDRGN results. Specifically, we detail a step-by-step protocol for analysis of the assembling 50S ribosome dataset (Davis et al., EMPIAR-10076), including preparation of inputs, network training, and visualization of the resulting ensemble of density maps. Additionally, we describe and implement methods to comprehensively analyze and interpret the distribution of volumes with the assistance of an associated atomic model. This protocol is appropriate for structural biologists familiar with processing single particle cryo-EM datasets and with moderate experience programming in Python and navigating Jupyter notebooks. It requires 3-4 days to complete.
CCS Predictor 2.0: An Open-Source Jupyter Notebook Tool for Filtering Out False Positives in Metabolomics
Authors: Rainey Markace A. , Watson Chandler A. , Asef Carter K. , Foster Makayla R. , Baker Erin S. , Fernández Facundo M.
Published: August 2022

Metabolite annotation continues to be the widely accepted bottleneck in non-targeted metabolomics workflows. Annotation of metabolites typically relies on a combination of high resolution mass spectrometry (MS) with parent and tandem measurements, isotope cluster evaluations, and Kendrick mass defect (KMD) analysis. Chromatographic retention time matching with standards is often used at the later stages of the process, which can also be followed by metabolite isolation and structure confirmation utilizing nuclear magnetic resonance (NMR) spectroscopy. The measurement of gas phase collision cross section (CCS) values by ion mobility (IM) spectrometry also adds an important dimension to this workflow by generating an additional molecular parameter that can be used for filtering unlikely structures. The millisecond timescale of IM spectrometry allows the rapid measurement of CCS values and allows easy pairing with existing MS workflows. Here, we report on a highly accurate machine learning algorithm (CCSP 2.0) in an open-source Jupyter Notebook format to predict CCS values based on linear support vector regression models. This tool allows customization of the training set to the needs of the user, enabling the production of models for new adducts or previously unexplored molecular classes. CCSP produces predictions with accuracy equal to or greater than existing machine learning approaches such as CCSbase, DeepCCS and AllCCS, while being better aligned with FAIR (Findable, Accessible, Interoperable and Reusable) data principles. Another unique aspect of CCSP 2.0 its inclusion of a large library of 1613 molecular descriptors via the Mordred Python package, further encoding the fine aspects of isomeric molecular structures. CCS prediction accuracy was tested using CCS values in the McLean CCS Compendium with median relative errors of 1.25, 1.73 and 1.87% for the 170 [M-H]-, 155 [M+H]+ and 138 [M+Na]+ adducts tested. For class-matched data sets, CCS predictions via CCSP allowed filtering of 36.1% of incorrect structures while retaining a total of 100% of the correct annotations using a ΔCCS threshold of 2.8% and a mass error of 10 ppm.
Deciphering the Inter-domain Decoupling in the Gram-negative Bacterial Membrane Insertase
Authors: Polasa Adithya , Badiee Shadi A , Moradi Mahmoud
Published: August 2022

YidC is a membrane protein that plays an important role in inserting newly generated proteins into lipid membranes. The Sec-dependent complex is responsible for inserting proteins into the lipid bilayer, and this process is facilitated by YidC in bacteria. In addition, YidC acts as a chaperone during the folding process of proteins. Multiple investigations have conclusively shown that the gram-positive bacterial YidC has Sec-independent insertion mechanisms. Through the use of microsecond-level all-atom molecular dynamics (MD) simulations, we have carried out the first in-depth investigation of the YidC protein originating from gram-negative bacteria. This research sheds light on the significance of multiple domains of YidC structure at an atomic level by utilizing equilibrium MD simulations. Specifically, in this research, multiple models of YidC embedded in the lipid bilayer were constructed to characterize the critical role of the C2 loop and the periplasmic domain present in gram-negative YidC, which is absent in its gram-positive counterpart. Based on our results, the C2 loop is responsible for the overall stabilization of the protein, most notably in the transmembrane region, and it also has an allosteric influence on the periplasmic domain. We have found critical inter- and intra-domain interactions that contribute to the stability of the protein and its function. Finally, our study provides a hypothetical Sec-independent insertion mechanism for gram-negative bacterial YidC.
Multi-site Performance Evaluation of the cobas 5800 System and Comparison to the cobas 6800/8800 Systems for Quantitative Measurement of HBV, HCV, and HIV-1 Viral Load
Authors: Tschäpe Jakob , Cobernuss-Rahn Anika , Boyle Sean , Parkin Neil , LaBrot Ben , Aslam Shagufta , Young Stephen , Gohl Peter
Published: August 2022

Background

The cobas® 5800 System (“cobas 5800”) is a new low to mid-throughput PCR-based nucleic acid testing system which performs both qualitative and quantitative testing, including viral load (VL) determination. cobas 5800 shares numerous design elements and technical characteristics with the existing cobas 6800/8800 Systems.

Study Design

We compared HBV, HCV, and HIV-1 VL results from cobas 5800 in three different laboratories to those from the same specimens tested on a cobas 6800 system. We also assessed cobas 5800 assay reproducibility by repetitive testing of specimens with VL close to values used as thresholds for patient management or classification.

Results

The correlation between VL measurements generated using cobas 5800 vs 6800 was extremely high, with r2 correlation coefficients between 0.990 and 0.999 for the three targets at the different sites. The slope of the Deming regression line ranged from 0.994 (HBV, site 3) to 1.025 (HIV-1, site 1). The standard deviation values ranged from 0.04 to 0.19 log10 IU/mL for HBV, 0.05 to 0.31 log10 IU/mL for HCV, and 0.05 to 0.31 log10 copies/mL for HIV-1. In general, variability was higher at lower VL. Between 98.6% and 100% of results fell within the allowable total difference zone that defines expected variability on the existing 6800/8800 system.

Conclusions

This multi-site comparison study demonstrates equivalent performance of the new cobas 5800 system compared to cobas 6800. This establishes cobas 5800 as a new option for low to mid-throughout laboratories seeking to optimize efficiency of their viral molecular testing.
ERK2-topoisomerase II regulatory axis is important for gene activation in immediate early genes
Authors: Bunch Heeyoun , Kim Deukyeong , Naganuma Masahiro , Nakagawa Reiko , Cong Anh , Jeong Jaehyeon , Ehara Haruhiko , Vu Hongha , Chang Jeong Ho , Schellenberg Matthew J. , Sekine Shun-ichi
Published: August 2022

The transcription of stress-inducible genes requires synchronized and robust activation, which is critical for organismal survival and homeostasis. The function of the mitogen-activated protein kinase (MAPK) signaling pathway is required for the activation of immediate early genes (IEGs), includingEGR1andFOS, for cell growth and proliferation1–3. In addition, recent studies have identified topoisomerase II (TOP2) as one of the important regulators of the transcriptional activation of IEGs4–6. However, the mechanism underlying transcriptional regulation involving TOP2 in IEG activation has remained unknown. Here, we demonstrate that ERK2, but not ERK1, is important for IEG transcriptional activation and report a critical ELK1 binding sequence for ERK2 function at theEGR1gene. Our data indicate that both ERK1 and ERK2 extensively phosphorylate the C-terminal domain of TOP2B at mutual and distinctive residues. Although both ERK1 and ERK2 enhance the catalytic rate of TOP2B required to relax positive DNA supercoiling, ERK1 can relax the DNA by itself and produces a semi-relaxed DNA, which is apparently resistant to TOP2B catalysis. Inhibition of ERK2 kinase activity or ERK2 knock-down interferes with transcription and deregulates TOP2B in IEGs. Furthermore, we obtained the first cryo-EM structure of the human cell-purified TOP2B and etoposide together with theEGR1transcriptional start site (50 nt; –30 to +20) that has the strongest affinity to TOP2B within –423 to +332. The structure elucidated in our studies showed TOP2B-mediated breakage and dramatic bending of the double-stranded DNA, comparable to previously reported structures of TOP2. Our cell-based analyses showed transcriptional activation by etoposide and transcriptional inhibition by ICRF193 atEGR1andFOS, suggesting that TOP2B-mediated DNA break to favor transcriptional activation. Taken together, this study suggests that activated ERK2 phosphorylates TOP2B to regulate TOP2-DNA interactions and favor transcriptional activation in IEGs. We propose that TOP2B association, catalysis, and dissociation on its substrate DNA are important processes for regulating transcription and that ERK2-mediated TOP2B phosphorylation may be key for the catalysis and dissociation steps.
The evolution of the human DNA replication timing program
Authors: Bracci Alexa N. , Dallmann Anissa , Ding Qiliang , Hubisz Melissa J. , Caballero Madison , Koren Amnon
Published: August 2022

DNA is replicated according to a defined spatiotemporal program that is linked to both gene regulation and genome stability. The evolutionary forces that have shaped replication timing programs in eukaryotic species are largely unknown. Here, we studied the molecular causes and consequences of replication timing evolution across 94 humans, 95 chimpanzees, and 23 rhesus macaques. Replication timing differences recapitulated the species’ phylogenetic tree, suggesting continuous evolution of the DNA replication timing program in primates. Hundreds of genomic regions had significant replication timing variation between humans and chimpanzees, of which 66 showed advances in replication origin firing in humans while 57 were delayed. Genes overlapping these regions displayed correlated changes in expression levels and chromatin structure. Many human-chimpanzee variants also exhibited inter-individual replication timing variation, pointing to ongoing evolution of replication timing at these loci. Association of replication timing variation with genetic variation revealed that DNA sequence evolution can explain replication timing variation between species. Taken together, DNA replication timing shows substantial and ongoing evolution in the human lineage that is driven by sequence alterations and impacts regulatory evolution.
Quorum-sensing- and type VI secretion-mediated spatio-temporal cell death drives genetic diversity in Vibrio cholerae
Authors: Mashruwala Ameya A. , Qin Boyang , Bassler Bonnie L.
Published: August 2022

Bacterial colonies composed of genetically identical individuals can diversify to yield variant cells with distinct genotypes. Variant outgrowth manifests as sectors. Here, we show that Type 6 secretion system (T6SS)-driven cell death in Vibrio cholerae colonies imposes a selective pressure for the emergence of variant strains that can evade T6SS-mediated killing. T6SS-mediated cell death occurs in two distinct spatio-temporal phases, and each phase is driven by a particular T6SS toxin. The first phase is regulated by quorum sensing and drives sectoring. The second phase does not require the T6SS-injection machinery. Variant V. cholerae strains isolated from colony sectors encode mutated quorum-sensing components that confer growth advantages by suppressing T6SS-killing activity while simultaneously boosting T6SS-killing defenses. Our findings show that the T6SS can eliminate sibling cells suggesting a role in intra-specific antagonism. We propose that quorum-sensing-controlled T6SS-driven killing promotes V. cholerae genetic diversity, including in natural habitats and during disease.
Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems
Authors: Ruff S. Emil , Humez Pauline , de Angelis Isabella Hrabe , Nightingale Michael , Diao Muhe , Cho Sara , Connors Liam , Kuloyo Olukayode O. , Seltzer Alan , Bowman Samuel , Wankel Scott D. , McClain Cynthia N. , Mayer Bernhard , Strous Marc
Published: August 2022

Groundwater ecosystems are globally wide-spread yet still poorly understood. We investigated the age, aqueous geochemistry, and microbiology of 138 groundwater samples from 87 monitoring wells (<250m depth) located in 14 aquifers in the Canadian Prairie. Geochemistry and microbial ecology were tightly linked revealing large-scale aerobic and anaerobic hydrogen, methane, nitrogen, and sulfur cycling carried out by diverse microbial communities. Older groundwaters contained on average more cells (up to 1.4×107/mL) than younger ground-waters. Organic carbon-rich strata featured some of the highest abundances, challenging current estimates of global groundwater population sizes. Substantial concentrations of dissolved oxygen (n=57; 0.52±0.12 mg/L [mean±SE]; 0.39 mg/L [median]) in older groundwaters could support aerobic lifestyles in subsurface ecosystems at an unprecedented scale. Metagenomics, oxygen isotope analyses and mixing models indicated that microbial “dark oxygen” contributed to the dissolved oxygen pool in subsurface ecosystems commonly assumed to be anoxic.
Distinct roles of the two SEC scaffold proteins, AFF1 and AFF4, in regulating RNA Pol II transcription elongation
Authors: Che Zhuanzhuan , Liu Xiaoxu , Dai Qian , Fang Ke , Guo Chenghao , Yue Junjie , Fang Haitong , Xie Peng , Luo Zhuojuan , Lin Chengqi
Published: August 2022

The P-TEFb-containing super elongation complex (SEC) plays the essential role in transcriptional elongation control. The AF4/FMR2 family members AFF1 and AFF4 are the central scaffold proteins of SEC, associated with different human diseases. However, their specific roles in transcriptional control remain unclear. Here, we report that AFF1 and AFF4 show distinct genomic distribution patterns around TSS. AFF1 mainly binds upstream of TSS, while AFF4 is enriched downstream of TSS. Pol II occupancies are reduced genome-widely after depletion of AFF1, but not AFF4. Interestingly, in a subset of active genes with strong AFF4 binding signature, AFF4 disruption causes slow elongation and early termination, while AFF1 deletion mirrors the transcriptional defects observed in the fast Pol II mutant. Furthermore, AFF4 knockdown leads to increased AFF1 levels at chromatin, and vice versa. In summary, our data demonstrate that AFF1 and AFF4 function, to some extent, antagonistically to ensure proper Pol II transcription.
Assessing the intrageneric environmental boundaries of the extremophilic cyanobacterium Chroococcidiopsis (Pleurocapsales) and its implications for space exploration
Authors: Cumbers John R. , Rothschild Lynn J.
Published: August 2022

The cyanobacterium Chroococcidiopsis contains species found in extreme environments, thus providing the opportunity to study adaptation to a range of environments within the confines of a single genus. Due to its extremophilic nature, it has attracted attention for space settlement as well as a model for life elsewhere. In this study, eight unialgal strains from diverse habitats, isolated in unialgal culture and grown in laboratory conditions, were characterized for their ability to survive a range of extreme environments including UVC (254 nm) radiation, oxidative damage, desiccation, and repeated freeze/thawing. The study revealed two previously uncharacterized saltwater isolates of Chroococcidiopsis that were more radiation resistant than most of the other isolates. Isolate CCMP 1991 from Hawaii survived up to 1750 J·m-2, and isolate CCMP 3184 from Samoa survived up to 1000 J·m-2 (254 nm UVR) compared with 250 J·m-2 for most other isolates tested. These two UV radiation-resistant isolates are closely related phylogenetically, but inhabit different environments. Each was further characterized for its ability to repair DNA damage as assessed by the repair of UV- induced thymine dimers and for oxidative damage tolerance via resistance to H2O2-induced (oxidative) damage. Both isolates repaired thymine dimers faster in the light than in the dark with the Hawaiian isolate repairing faster than the Samoan isolate in the light, suggesting repair by photoreactivation. The Hawaiian isolate was more tolerant to H2O2 exposure than the Samoan isolate, indicating a possible role for antioxidants in the protection of the cell. Both isolates were more tolerant than the other isolates tested to freeze/thawing in liquid nitrogen, which is also known to cause DNA damage. Spectral absorbance scans were performed to detect pigments in each isolate. While all showed peaks likely to be chlorophyll a, carotenoids, phycocyanin, scytonemin and MAAs, the Hawaiian isolate contained a pigment that absorbed at around 325 nm that none of the other isolates contained. Although this pigment is outside the range of UVC absorbance, it is hypothesized that it may play a role in DNA protection as a UV sunscreen or as an antioxidant. The phenotypic similarities in radiation resistance and freeze/thawing resistance among the Hawaiian, Somoan and Negev isolates appear to be the result of environmental adaptation rather than phylogenetic markers as the first of these have been previously shown to be part of a saltwater clade, while the Negev strain falls within a freshwater clade. As pigmentation, and likely resistance to other environmental conditions, can be induced, these data provide a baseline study of strains in an uninduced state. Thus, the true environmental limits to Chroococcidiopsis likely go beyond our current knowledge. The implications of this is discussed in relation to space exploration
Heat inactivation of the Monkeypoxvirus
Authors: Batéjat Christophe , Grassin Quentin , Feher Maxence , Hoinard Damien , Vanhomwegen Jessica , Manuguerra Jean-Claude , Leclercq India
Published: August 2022

Different kinds of media spiked with Monkeypoxvirus (MPXV) were subjected to heat inactivation at different temperatures, for various periods of time. Our results showed that MPXV was inactivated in less than 5 min at 70 °C and in less than 15 min at 60 °C, with no difference between virus from West African and Central African clades. Such indications could help laboratory workers to manipulate the virus in optimal biosafety conditions and improve their protocols.
An optimised transformation protocol forAnthoceros agrestisand three more hornwort species
Authors: Waller Manuel , Frangedakis Eftychios , Marron Alan , Sauret-Gueto Susanna , Rever Jenna , Sabbagh Cyrus Raja Rubenstein , Hibberd Julian M. , Haseloff Jim , Renzaglia Karen , Szövényi Péter
Published: August 2022

Land plants comprise two large monophyletic lineages, the vascular plants and the bryophytes, which diverged from their most recent common ancestor approximately 480 million years ago. Of the three lineages of bryophytes, only the mosses and the liverworts are systematically investigated, while the hornworts are understudied. Despite their importance for understanding fundamental questions of land plant evolution, they only recently became amenable to experimental investigation, withAnthoceros agrestisbeing developed as a hornwort model system. Availability of a high quality genome assembly and a recently developed genetic transformation technique makesA. agrestisan attractive model species for hornworts. Here we describe an updated and optimised transformation protocol forA. agrestiswhich can be successfully used to genetically modify one more strain ofA. agrestisand three more hornwort species,Anthoceros punctatus, Leiosporoceros dussiandPhaeoceros carolinianus.The new transformation method is less laborious, faster and results in the generation of greatly increased numbers of transformants compared to the previous method. We have also developed a new selection marker for transformation. Finally, we report the development of a set of different cellular localisation signal peptides for hornworts providing new tools to better understand hornwort cell biology.
Ruminant-specific retrotransposons shape regulatory evolution of bovine immunity
Authors: Kelly Conor J. , Chitko-McKown Carol G. , Chuong Edward B.
Published: August 2022

Cattle are an important livestock species, and mapping the genomic architecture of agriculturally relevant traits such as disease susceptibility is a major challenge in the bovine research community. Lineage-specific transposable elements (TEs) are increasingly recognized to contribute to gene regulatory evolution and variation, but this possibility has been largely unexplored in ruminant genomes. We conducted epigenomic profiling of the type II interferon (IFN) response in bovine cells and found thousands of ruminant-specific TEs including MER41_BT and Bov-A2 elements predicted to act as IFN-inducible enhancer elements. CRISPR knockout experiments in bovine cells established that critical immune factors including IFNAR2 and IL2RB are transcriptionally regulated by TE-derived enhancers. Finally, population genomic analysis of 38 individuals revealed that a subset of polymorphic TE insertions may function as enhancers in modern cattle. Our study reveals that lineage-specific TEs have shaped the evolution of ruminant IFN responses and potentially continue to contribute to immune gene regulatory differences across modern breeds and individuals. Together with previous work in human cells, our findings demonstrate that lineage-specific TEs have been independently co-opted to regulate IFN-inducible gene expression in multiple species, supporting TE co-option as a recurrent mechanism driving the evolution of IFN-inducible transcriptional networks.
Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids
Authors: Zhao Cheng , Biondic Savana , Vandal Katherine , Björklund Åsa K. , Hagemann-Jensen Michael , Sommer Theresa Maria , Canizo Jesica , Clark Stephen , Raymond Pascal , Zenklusen Daniel R. , Rivron Nicolas , Reik Wolf , Petropoulos Sophie
Published: August 2022

The preconceptual, intrauterine, and early life environments can have a profound and long-lasting impact on the developmental trajectories and health outcomes of the offspring. Given the relatively low success rates of assisted reproductive technologies (ART; ∼25%), additives and adjuvants, such as glucocorticoids, are used to improve the success rate. Considering the dynamic developmental events that occur during this window, these exposures may alter blastocyst formation at a molecular level, and as such, affect not only the viability of the embryo and the ability of the blastocyst to implant, but also the developmental trajectory of the first three cell lineages, ultimately influencing the physiology of the embryo. In this study, we present a comprehensive single-cell transcriptome, methylome, and small RNA atlas in the day 7 human embryo. We show that, despite no change in morphology and developmental features, preimplantation glucocorticoid exposure reprograms the molecular profile of the trophectoderm (TE) lineage, and these changes are associated with an altered metabolic and inflammatory response. Our data also suggest that glucocorticoids can precociously mature the TE sublineages, supported by the presence of extravillous trophoblast markers in the polar sublineage and presence of X Chromosome dosage compensation. Further, we have elucidated that epigenetic regulation—DNA methylation and microRNAs (miRNAs)—likely underlies the transcriptional changes observed. This study suggests that exposures to exogenous compounds during preimplantation may unintentionally reprogram the human embryo, possibly leading to suboptimal development and longer-term health outcomes.
The degree of responsiveness of fiscal and monetary policy in Sierra Leone
Authors: Turay Alhassan , Seraj Mehdi , Özdeşer Hüseyin
Published: August 2022

Purpose

The degree of responsiveness of fiscal and monetary policy mechanisms that promote growth and development in Sierra Leone is the subject of this article.

Design/methodology/approach

This article uses both the Auto Regressive Distributed Lag (ARDL) model presented by Hashem and Yongcheol (1998) and the Non-Linear Auto Regressive Distributed Lag (NARDL) model by Shin et al. (2014) to analyze annual time-series data in evaluating the asymmetric effect of real gross domestic product (RGDP), inflation, government expenditure and money supply using annual time-series data for 40 observations over the period 1980–2019.

Findings

The augmented Dickey–Fuller unit root test shows that money supply, government spending and consumer price index are integrated at first difference I (1), while RGDP is stationary at level I (0). The results of the NARDL cointegration test indicate that the variables are cointegrated. The study shows that government expenditure is a positive function of both positive and negative changes. Hence, both positive and negative cumulative sum government expenditures improve economic growth but show a relative weak asymmetric effect with the regressand. This study also reveals that inflation is a negative function of both positive and negative changes with asymmetric effect with the dependent variable. This study shows that the positive change of money supply is statistically insignificant in boosting economic growth, while the negative change positively improves economic growth. Conclusively, this article shows that fiscal policy has a greater and more responsive than monetary policy in promoting growth and development in Sierra Leone. The result of the error correction term of the NARDL model shows a high spend of adjustment of 135% from any disequilibrium of GDP imbalance in the economy.

Originality/value

To address the problem of fiscal dominance in Sierra Leone, this study recommends that fiscal and monetary policies should be coordinated simultaneously and to an appropriate extent to achieve the desired outcome in growth and development.
Evaluating approaches using the Grey-TOPSIS for sustainable supply chain collaboration under risk and uncertainty
Authors: Prakash Surya , Kumar Sameer , Soni Gunjan , Jain Vipul , Dev Saty , Chandra Charu
Published: August 2022

Purpose

Collaboration methods are unique strategies that can help organizations hedge against external and internal supply chain risks without stressing their relationships with supply chain partners. However, selecting the most appropriate collaboration method from a given set of strategies is a multifaceted challenge. This paper aims to address this issue.

Design/methodology/approach

The decision maker's dilemma of fighting data uncertainty in input parameters to check the efficacy of a given collaboration or mitigation approach is tackled by the integration of Grey theory with the technique for order of preference by similarity to ideal solution (TOPSIS) method. The proposed technique is applied and tested for an Indian diesel generator-set manufacturer to identify the most apposite set of sustainable collaboration strategies.

Findings

The results showed that when a firm is bidding for different horizontal collaboration strategies across its supply chain system technology and resource-sharing-centered collaboration strategies are the prominent option. In the case of the company's vertical collaboration deployment, the focus should be kept on information sharing to achieve impactful collaboration. The outcome of the analysis helped the Indian manufacturer to adopt transparent order and production information sharing with its regional distributors and core suppliers within its supply chain.

Originality/value

This study demonstrates from a methodological perspective the successful application of the Grey-TOPSIS approach that effectively captures data uncertainty. It also integrates sustainability parameters in collaboration strategy criteria selections.
The expectations of employability skills in the Fourth Industrial Revolution of the communication and media industry in Malaysia
Authors: Ahmad Tajuddin Siti Nor Amalina , Bahari Khairul Azam , Al Majdhoub Fatima M. , Balraj Baboo Shanthi , Samson Harlina
Published: August 2022

Purpose

The purpose of this paper is to examine the industry's expectations on the key employability skills of fresh graduates in the communication and media industry. The Fourth Industrial Revolution has raised the question of whether the university should produce work-ready graduates with employability skills. Driven by the theory of human capital, society expects higher education to produce graduates with skills that are useful in their workplace.

Design/methodology/approach

The data were gathered primarily through a quantitative survey, which was later extended to include qualitative interviews. Quantitatively, questionnaires were completed by 313 employers from the middle and top-level management from the communication and media industry. This study also expands on qualitative data through in-depth interviews with nine respondents who were among key decision-makers of recruiting graduates to garner their insights on required employability skills.

Findings

The findings revealed the following employability skills required by the industry in the Fourth Industrial Revolution: communication, ICT or digital, leadership, interpersonal, and personal qualities skills.

Research limitations/implications

These findings are beneficial to education providers as well as media and communication industries in preparing students and developing their skills to adapt to the changes in the workplace.

Originality/value

The authors provide an empirical understanding of industry expectations towards employability skills in the Fourth Industrial Revolution of the communication and media industry within the Malaysian context.
A systematic and bibliometric review of the financial well-being: advancements in the current status and future research agenda
Authors: Singh Dharmendra , Malik Garima
Published: August 2022

Purpose

Achieving financial well-being is essential for individuals, families and countries as it leads to life satisfaction and happiness. This study synthesizes and identifies financial well-being’s key areas and dimensions using a blended systematic literature review and bibliometric analysis approach.

Design/methodology/approach

The authors systematically study a sample of 467 articles from the Scopus database to identify the research trend regarding financial well-being during the last 25 years (1997–2021). Various graphs and networks are presented to understand the publication trends, influential papers, conceptual and intellectual structures and research collaboration status.

Findings

Four clusters in the field of financial well-being were found: conceptualization and antecedents of financial well-being, financial well-being of young adults, the relationship between financial literacy and financial well-being and consequences of financial well-being. Further, emerging themes in financial well-being were identified with a content analysis of the papers published during the last five years.

Practical implications

This study will help financial planners, regulatory bodies and academic researchers in getting a better understanding of financial well-being and in identifying potential areas for future research.

Originality/value

Prior to this study, no such comprehensive bibliometric analysis on financial well-being has been carried out to the best of the authors' knowledge. This gap motivated the authors to combine quantitative and qualitative methods to review the published research and do a content analysis, to identify prominent authors and publications.
Assessment of susceptibility of buildings with different façade finishes to microbial decay in the hot-humid tropical environment of Enugu, southeast Nigeria
Authors: Uzuegbunam Francis O. , Isiofia Lawrence A. , Ibem Eziyi O.
Published: August 2022

Purpose

Buildings respond differently to microbial invasion depending on the design, type of construction materials and finishes used and extent of exposure to climatic factors. However, in the hot-humid tropical environment of Nigeria, much is not known about how buildings with different types of façade finishes or claddings are liable to microbial decay. The purpose of this research is to investigate the susceptibility of buildings with different types of façade finishes to microbial decay in Enugu metropolis, southeast Nigeria.

Design/methodology/approach

A survey involving physical observation of purposively selected 383 buildings and questionnaire administration to their owners was carried out in the study area. The data were subjected to descriptive and logistic regression analyses.

Findings

Most of the 383 buildings sampled were less than 41 year and 47% of them had painted façade finishes followed by 25.1% with cementitious finishes. Around 63.4% of the buildings had their façade finishes or claddings colonised by microbes. Older buildings of 15 years and above and those with cementitious materials and paints as their predominant façade finishes were more likely to experience microbial decay than newer ones and those having refractory bricks, ceramic tiles, aluminium composite materials and plastics/polymers as their predominant façade finishes or claddings.

Practical implications

The study identifies the categories of buildings that are likely to be more susceptible to microbial decay; and thus contributes to research on how to slow down the rate of biodeterioration of building façade finishes or claddings in the hot-humid tropical environments.

Originality/value

This is the first study on the susceptibility of buildings with different types of façade finishes or claddings to microbial decay in the hot-humid tropical environment of Enugu metropolis, southeast Nigeria. It also provides a clue on the age at which buildings become more vulnerable to microbial decay in the study area.