bluuebunny/crossref_metadata_2025 huggingface dataset:
RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes
Authors: Andrés Penagos-Puig , Sherlyn Claudio-Galeana , Aura Stephenson-Gussinye , Karina Jácome-López , Amaury Aguilar-Lomas , Rosario Pérez-Molina , Mayra Furlan-Magaril
Published: June 2022

Chicken erythrocytes are nucleated cells often referred to as transcriptionally inactive, although the epigenetic changes and chromatin remodeling that mediate transcriptional repression and the extent of gene silencing during avian terminal erythroid differentiation are not fully understood. Here we characterized the changes in gene expression, chromatin accessibility, genome organization, and chromatin nuclear disposition during the terminal stages of erythropoiesis in chicken and found a complex chromatin reorganization at different genomic scales. We identified a robust decrease in transcription in erythrocytes. Nevertheless, a set of genes maintains their expression in erythrocytes, including genes involved in RNA pol II promoter-proximal pausing. Erythrocytes exhibit an inverted nuclear architecture and reposition euchromatin towards the nuclear periphery together with the paused RNA polymerase. In erythrocytes, chromatin domains are partially lost genome-wide except at mini domains retained around paused promoters. Our results suggest that promoter-proximal pausing of the RNA pol II participates in the transcriptional regulation of the erythroid genome and highlight the role of RNA polymerase in the maintenance of local chromatin organization.
Systematic microscopical analysis reveals obligate synergy between extracellular matrix components during Bacillus subtilis colony biofilm development
Authors: Porter Michael , Davidson Fordyce A. , MacPhee Cait E. , Stanley-Wall Nicola R.
Published: June 2022

Single-species bacterial colony biofilms often present recurring morphologies that are thought to be of benefit to the population of cells within and known to be dependent on the self-produced extracellular matrix. However, much remains unknown in terms of the developmental process at the single cell level. Here, we design and implement systematic time-lapse imaging and quantitative analyses of the growth of Bacillus subtilis colony biofilms. We follow development from the initial deposition of founding cells through to the formation of large-scale complex structures. Using the model biofilm strain NCIB 3610, we examine the movement dynamics of the growing biomass and compare with those displayed by a suite of otherwise isogenic matrix-mutant strains. Correspondingly, we assess the impact of an incomplete matrix on biofilm morphologies and sessile growth rate. Our results indicate that radial expansion of colony biofilms results from division of bacteria at the biofilm periphery rather than being driven by swelling due to fluid intake. Moreover, we show that lack of exopolysaccharide production has a negative impact on cell division rate, and the extracellular matrix components act synergistically to give the biomass the structural strength to produce aerial protrusions and agar substrate-deforming ability.
Vitrocam: A simple low cost Vitrobot camera for assessing grid quality
Authors: Chua Eugene Y.D. , Serbynovskyi Viacheslav , Gheorghita Robert , Alink Lambertus M. , Podolsky Daniel , Potter Clinton S. , Carragher Bridget
Published: June 2022

The most widely used sample preparation method for single particle cryo-electron microscopy (cryo-EM) today involves the application of 3-4 μl of sample onto a cryo-EM grid, removing most of the liquid by blotting with filter paper, then rapidly plunging into liquid ethane to vitrify the sample. To determine if the grid has appropriate ice thicknesses and sufficient area for cryo-EM imaging, the grid must be inserted into a transmission electron microscope (TEM) and screened. This process to evaluate grid quality is costly and time consuming. Here, we present our initial attempt to image the sample preparation process in one of the most commonly used plunge freezing devices, the Vitrobot. We do this by building the Vitrocam, a Raspberry Pi high-speed camera, that captures images of grids mid-plunge. Images from the Vitrocam can be correlated to TEM atlases and show promise for providing preliminary feedback on grid quality and ice thickness.
Spatial tuning in nociceptive processing is driven by attention
Authors: Adamczyk Wacław M. , Katra Michał , Szikszay Tibor M. , Peugh James , King Christopher D. , Luedtke Kerstin , Coghill Robert C.
Published: June 2022

When the source of nociception expands across a body area, the experience of pain increases due to the spatial integration of nociceptive information. This well-established effect is called spatial summation of pain (SSp) and has been the subject of multiple investigations. Here, we used cold-induced SSp to investigate the effect of attention on the spatial tuning of nociceptive processing. Forty pain-free volunteers (N=40, 20 females) participated in this experiment. They took part in an SSp paradigm based on three hand immersions into cold water (5°C): Participants either immersed the ulnar segment (“a”), radial segment (“b”) or both hand segments (“a+b”) and provided overall pain ratings. In some trials based on “a+b” immersions, they were also asked to provide divided (i.e., first pain in “a” then in “b”; or reversed) and directed attention ratings (i.e., pain only in “a” or “b”). Results confirmed a clear SSp effect in which reported pain during immersions of “a” or “b” was less intense than pain during immersions of “a+b” (p<0.001). Data also confirmed that spatial tuning was altered. SSp was fully abolished when participants provided two ratings in a divided fashion (p<0.001). Furthermore, pain was significantly lower when attention was directed only to one segment (“a” OR “b”) during “a+b” immersion (p<0.001). We conclude that spatial tuning is dynamically driven by attention as reflected in abolished SSp. Directed attention was sufficient to focus spatial tuning and abolish SSp. Results support the role of cognitive processes such as attention in spatial tuning.

Perspective

This article presents experimental investigation of spatial tuning in pain and offers mechanistic insights of contiguous spatial summation of pain in healthy volunteers. Depending on how pain is evaluated in terms of attentional derivative (overall pain, directed, divided attention) the pain is reduced and spatial summation abolished.
Subsistence of sib altruism in different mating systems and Haldane’s arithmetic
Authors: Garay József , Csiszár Villő , Móri Tamás F.
Published: June 2022

The moral rule “Risk your life to save your family members” is, at the same time, a biological phenomenon. The prominent population geneticist, J.B.S. Haldane told his friends that he would risk his life to save two drowning brothers, but not one – so the story goes. In biological terms, Haldane’s arithmetic claims that sib altruism is evolutionarily rational, whenever by “self-sacrifice” an altruistic gene “rescues”, on average, more than one copy of itself in its lineage. Here, we derive conditions for evolutionary stability of sib altruism, using population genetic models for three mating systems (monogamy, promiscuity and polygyny) with linear and non-linear group effect on the siblings’ survival rate.

We show that for all considered selection situations, the condition of evolutionary stability is equivalent to Haldane’s arithmetic. The condition for evolutionary stability is formulated in terms of genetic relatedness and the group effect on the survival probability, similarly to the classical Hamilton’s rule. We can set up a “scale of mating systems”, since in pairwise interactions the chance of evolutionary stability of sib altruism decreases in this order: monogamy, polygyny and promiscuity.

Practice of marrying and siblings’ solidarity are moral rules in a secular world and in various religious traditions. These moral rules are not evolutionarily independent, in the sense that the subsistence of sib altruism is more likely in a monogamous population.

Highlights

Haldane’s arithmetic is introduced

Conditions for evolutionary stability of sib altruism are given

Evolutionary stability is equivalent to Haldane’s arithmetic in the studied model

Generalized Hamilton’s rules are formulated
Fitness Functions for RNA Structure Design
Authors: Ward Max , Courtney Eliot , Rivas Elena
Published: June 2022

Abstract

An RNA design algorithm takes a target RNA structure and finds a sequence that folds into that structure. This is fundamentally important for engineering therapeutics using RNA. Computational RNA design algorithms are guided by fitness functions, but not much research has been done on the merits of these functions. We survey current RNA design approaches with a particular focus on the fitness functions used. We experimentally compare the most widely used fitness functions in RNA design algorithms on both synthetic and natural sequences. It has been almost 20 years since the last comparison was published, and we find similar results with a major new result: maximizing probability outperforms minimizing ensemble defect. The probability is the likelihood of a structure at equilibrium and the ensemble defect is the weighted average number of incorrect positions in the ensemble. Also, we observe that many recently published approaches minimize structure distance to the minimum free energy prediction, which we find to be a poor fitness function.
Reduced PDE4D7 expression in prostate cancer correlates with down-regulation of genomic elements within the up-stream PDE4D coding region on chromosome 5
Authors: Gulliver Chloe , Baillie George S , Hoffmann Ralf
Published: June 2022

PDE4D7 expression is diminished during progression of PCa and the phosphodiesterase has been proposed as a prognostic biomarker. RNA sequencing of PCa tissue identified sequences in the PDE4D coding region on Chr5q12 exhibiting similarities in mRNA expression profile to PDE4D7. As previously identified, PART1 had a significantly similar expression pattern to PDE4D7 across samples. However, other genes also matched expression to PDE4D7, including miRNAs and lncRNAs. These novel PDE4D7 associated genes represent putative PCa biomarkers and could have mechanistic roles in PCa progression.
Composite mutations give an extra insight into epistasis
Authors: Zorin Evgenii M. , Erazo Carolina M. , Ivankov Dmitry N.
Published: June 2022

The intricate genotype-phenotype relationship has been a long-standing issue in biology, important both from the fundamental and applied points of view. One of the major irregularities hindering progress in establishing these links is epistasis – the complex and elusive interaction between mutations. Despite the vast accumulated genetic data and progress in this area, epistasis is still far from being completely understood. Epistasis can be studied quantitatively in combinatorially complete datasets, which form hypercubes in protein sequence space, where connected sequences are one mutation away from each other. However, this might be insufficient to portray the full picture of epistatic interactions. To extend the repertoire of the methods for exploring epistasis, we propose here to consider hyperrectangles, where some edges connect sequences being two or more mutations away from each other. The present work formalizes the theoretical knowledge about these novel structures and compares the amount of epistasis identified in hypercubes and hyperrectangles constructed from experimental datasets. A new algorithm, CuboidME, was developed for calculating hyperrectangles, which were then compared to hypercubes. In the experimental datasets, there were four orders of magnitude more hyperrectangles than hypercubes for the same sample size. Subsequently, we showed that for the studied datasets there is an increase in epistasis measured by epistatic coefficients in hyperrectangles compared to hypercubes. For the same datasets, hyperrectangles could find more sign epistasis than using hypercubes alone. We also show that there is a trend for increase in epistasis with increasing number of mutations being considered in a hyperrectangle. The results indicate that hyperrectangles can be used to reveal more information on epistasis in a fitness landscape, especially if it is combinatorially incomplete.
Epithelial protein lost in neoplasm (EPLIN)-β is a novel substrate of ornithine decarboxylase antizyme 1, mediating cellular migration
Authors: Li Dan , Neo Suat Peng , Gunaratne Jayantha , Sabapathy Kanaga
Published: June 2022

Polyamines promote cellular proliferation, and their levels are controlled by ornithine decarboxylase antizyme 1 (Az1), through the proteasome-mediated, ubiquitin-independent degradation of ornithine decarboxylase (ODC), the rate-limiting enzyme of polyamine biosynthesis. Az1-mediated degradation of other substrates such as cyclin D1, DNp73 and Mps1 also regulate cellular migration and centrosome amplification, and collectively, the currently known six Az1-substrates are all linked with tumorigenesis. To understand if Az1-mediated protein degradation might play a key role in regulating cellular process associated with tumorigenesis, we employed quantitative proteomics to identify novel Az1 substrates. In this report, we describe the identification of LIM domain and Actin-binding protein 1 (LIMA1), also known as epithelial protein lost in neoplasm (EPLIN), as a new target of Az1. Interestingly, between the two isoforms of EPLIN (α and β), only EPLIN-β is the substrate of Az1, degraded in a proteasome-dependent and ubiquitination-independent manner. Absence of Az1 led to elevated EPLIN-β levels, which is causal to enhanced cellular migration of Az1-/- cells. Consistently, higher levels of LIMA1 expression correlated with poorer overall survival of colorectal cancer patients. Taken together, this study identifies EPLIN-β as a novel Az1 substrate that regulates cellular migration.
Energy landscapes of Aβ monomers are sculpted in accordance with Ostwald’s rule of stages
Authors: Chakraborty Debayan , Straub John E. , Thirumalai D
Published: June 2022

The transition from a disordered to an assembly-competent and sparsely populated monomeric state (N*) in amyloidogenic sequences is a crucial event in the aggregation cascade. Using a well-calibrated model for Intrinsically Disordered Proteins (IDPs), we show that the N* states, which bear considerable resemblance to distinct polymorphic fibril structures found in experiments, not only appear as excitations on the monomer free energy landscapes of Aβ40 and Aβ42 but also initiate the aggregation cascade. Interestingly, for Aβ42, the transitions to the different N* states are in accord with Ostwald’s rule of stages, with the least stable structures forming ahead of thermodynamically favored structures, which appear only on longer time-scales. Despite having similar topographies, the Aβ40 and Aβ42 monomer landscapes exhibit different extent of ruggedness, particularly in the vicinity of N* states, which we show have profound implications in dictating the intramolecular diffusion rates, and subsequent self-assembly into higher order structures. The network of connected kinetic states, which for Aβ42 is considerably more complex than for Aβ40, shows that the most favored dimerization routes proceed via the N* states. Direct transition between the disordered ground states within the monomer and dimer basins is less likely. The Ostwald’s rule of stages holds widely, qualitatively explaining the unusual features in other fibril forming IDPs, such as Fused in Sarcoma (FUS). Similarly, the N* theory accounts for dimer formation in small disordered polyglutamine peptides, implicated in the Huntington disease.

Graphical TOC Entry
Oligomerisation of a plant helper NLR requires cell-surface and intracellular immune receptor activation
Authors: Feehan Joanna M. , Wang Junli , Sun Xinhua , Choi Jihyeon , Ahn Hee-Kyung , Ngou Bruno Pok Man , Parker Jane E. , Jones Jonathan D. G.
Published: June 2022

Plant disease resistance involves both detection of microbial molecular patterns by cell-surface pattern recognition receptors and detection of pathogen effectors by intracellular NLR immune receptors. NLRs are classified as sensor NLRs, involved in effector detection, or helper NLRs required for sensor NLR signalling. TIR-domain-containing sensor NLRs (TNLs) require helper NLRs NRG1 and ADR1 for resistance, and their activation of defense also requires the lipase-domain proteins EDS1, SAG101 and PAD4. We investigated how the helper NLR NRG1 supports TNL-initiated immunity with EDS1 and SAG101. We find that NRG1 associates with EDS1 and SAG101 at the plasma membrane and in the nucleus, but only self-associates at the plasma membrane. Activation of TNLs is sufficient to trigger NRG1-EDS1-SAG101 interaction, but cell-surface receptor-initiated defense is also required to form an oligomeric Resistosome. The data point to formation of NRG1-EDS1-SAG101 heterotrimers in the nucleus upon intracellular receptor activation alone and indicate formation of NRG1-EDS1-SAG101 Resistosomes at the plasma membrane upon co-activation of intracellular and cell surface-receptor pathways.
Small RNAs target native and cross-kingdom transcripts on both sides of the wheat stripe rust interaction
Authors: Mueth Nicholas A. , Hulbert Scot H.
Published: June 2022

The wheat stripe rust fungus (Puccinia striiformis f.sp tritici) poses a significant challenge to global wheat production. Plant defense induction against pathogens is partly modulated by small RNA (sRNA) molecules that downregulate complementary protein-coding transcripts. Additionally, the two-way RNA exchange between host and microbe involves cross-kingdom gene silencing that impacts pathogen virulence, yet few examples are known among rust fungi. The purpose of this study was to discover small RNA-target pairs on each side of this interaction. We performed sRNA sequencing and parallel analysis of RNA ends (PARE) in infected and uninfected wheat seedlings and combined these data with gene expression information. Wheat 24 nt heterochromatic siRNA (hc-siRNA) sequences were suppressed upon infection, while specific 35 nt tRNA and rRNA fragments were strongly induced. Target transcripts were identified by the observation of high mRNA slicing frequency at the precise position of sRNA binding sites. Wheat small RNAs showed evidence of cleaving several fungal transcripts including a ribosomal protein-coding gene and a glycosyl hydrolase effector gene. In P. striiformis, we confirmed and expanded previous findings that sRNAs feature microRNA-like sequences and siRNAs originating from long inverted repeats near protein-coding genes. Long inverted repeat regions produced sets of phased sRNAs at 21 nt intervals. Fungal sRNAs were identified that target native transcripts coding for transposons and protein kinases. Cross-kingdom gene targets of pathogen sRNAs included wheat nucleotide-binding domain leucine-rich repeat receptors (NLRs) and multiple families of defense-related transcription factors. The identified target genes shed light on an intricately co-evolved interaction and provide useful prospects for the development of pathogen control biotechnology.
Calcineurin associates with centrosomes and regulates cilia length maintenance
Authors: Tsekitsidou Eirini , Wang Jennifer T. , Wong Cassandra J. , Ulengin-Talkish Idil , Stearns Tim , Gingras Anne-Claude , Cyert Martha S.
Published: June 2022

Calcineurin, or PP2B, the Ca2+ and calmodulin-activated phosphatase and target of immunosuppressants, has many substrates and functions that remain undiscovered. By combining rapid proximity-dependent labeling with cell cycle synchronization, we mapped calcineurin’s spatial distribution in different cell cycle stages. While calcineurin-proximal proteins did not vary significantly between interphase and mitosis, calcineurin consistently associated with multiple centrosomal/ciliary proteins. These include POC5, which binds centrin in a Ca2+-dependent manner and is a component of the luminal scaffold that stabilizes centrioles. We show that POC5 contains a calcineurin substrate motif (PxIxIT-type) that mediates calcineurin binding in vivo and in vitro. Using indirect immunofluorescence and expansion microscopy, we demonstrate that calcineurin co-localizes with POC5 at the centrosome, and further show that calcineurin inhibitors alter POC5 distribution within the centriole lumen. Our discovery that calcineurin directly associates with centrosomal proteins highlights a role for Ca2+ and calcineurin signaling at these organelles. Calcineurin inhibition promotes primary cilia elongation without affecting ciliogenesis. Thus, Ca2+ signaling within cilia includes previously unknown functions for calcineurin in cilia length maintenance, a process frequently disrupted in ciliopathies.

Summary statement

Calcineurin phosphatase participates in centrosome and cilia regulation. Calcineurin localizes to centrosomes, where it interacts with partner POC5, and its inhibition promotes cilia elongation.
Cytokine and phenotypic cell profiles in human cutaneous leishmaniasis caused byLeishmania donovani
Authors: Wijesooriya Hiruni , Samaranayake Nilakshi , Karunaweera Nadira D.
Published: June 2022

Background

The innate immune mediators are likely to influence the clinical phenotype of leishmaniasis by primary responses which limit or facilitate the spread of the parasite, as well as by modulating adaptive immunity. This study investigated the response of key innate immune cells in a focus which regularly reports localised cutaneous leishmaniasis (LCL) caused byLeishmania donovani, a species which typically causes visceral disease.

Methods

Peripheral blood mononuclear cell (PBMC) derived macrophage and dendritic cell responses to solubleLeishmaniaantigen (SLA) were compared between patients with LCL and healthy controls from endemic and non-endemic areas. Inflammatory mediators produced by macrophages (TNF-α, NO, TGF-β and IL-10) and dendritic cells (IL-12p70, IL-10) and cell surface markers of macrophage polarization, activation and maturation were determined at 24h, 48h and 72h by Enzyme-linked immunosorbent assay (ELISA) and flowcytometry.

Results

Patient derived macrophages and dendritic cells produced higher levels of both pro and anti-inflammatory mediators compared to controls (p<0.05) with the best discrimination for active disease observed at 72h. Data demonstrated an early activation of macrophages and a subsequent pro-inflammatory bias, as indicated by temporal profiles of TNF-α/TGF-β and TNF-α/IL-10 ratios and higher proportions of classical (M1) macrophages. Higher TGF-β levels were observed in cells from patients with ulcerated or persistent lesions. Immune responses by cells derived from controls in endemic and non-endemic regions did not differ significantly from each other.

Conclusions

The overall immunophenotypic profile suggests that LCL observed in the country is the result of a balancing immune response between pro-inflammatory and regulatory mediators. The mediators which showed distinct profiles in patients warrant further investigation as potential candidates for immunotherapeutic approaches. A comparison with visceral leishmaniasis caused by the same species, would provide further evidence on the differential role of these mediators in the resulting clinical phenotype.
KLF7 Promotes Preadipocyte Proliferation via Activation of the Akt Signaling Pathway by Cis-regulating CDKN3
Authors: Jia Ziqiu , Jin Zhao , Shao Shuli , Xu Hu , Li Wen , Khan Mahmood , Wang Weiyu , Zhang Weiwei , Sun Yingning
Published: June 2022

Krüppel-like transcription factor 7 (KLF7) promotes preadipocyte proliferation; however, its target gene in this process has not yet been identified. Using KLF7 ChIP-seq analysis, we previously showed that a KLF7-binding peak is present upstream of the cyclin-dependent kinase inhibitor 3 gene (CDKN3) in chicken preadipocytes. In the current study, we identified CDKN3 as a target gene of KLF7 that mediates the effects of KLF7 on preadipocyte proliferation. Furthermore, 5′-truncating mutation analysis showed that the minimal promoter was located between CDKN3 nt −160 and nt −7 (relative to the translation initiation codon ATG). KLF7 overexpression increased CDKN3 promoter activity in the DF-1 and immortalized chicken preadipocyte (ICP1) cell lines. Deletion of the putative binding site of KLF7 abolished the promotive effect of KLF7 overexpression on CDKN3 promoter activity. Moreover, CDKN3-knockdown and -overexpression assays revealed that CDKN3 enhanced ICP1 cell proliferation. Flow cytometry analysis showed that CDKN3 accelerated the G1/S transition. Further, we found that KLF7 promoted ICP1 cell proliferation via Akt phosphorylation by regulating CDKN3. Taken together, these results suggest that KLF7 promotes preadipocyte proliferation via activating the Akt signaling pathway by cis-regulating CDKN3, thus driving the G1/S transition.
MIDAS2: Metagenomic Intra-species Diversity Analysis System
Authors: Zhao Chunyu , Dimitrov Boris , Goldman Miriam , Nayfach Stephen , Pollard Katherine S.
Published: June 2022

The Metagenomic Intra-Species Diversity Analysis System (MIDAS) is a scalable metagenomic pipeline that identifies single nucleotide variants (SNVs) and gene copy number variants (CNVs) in microbial populations. Here, we present MIDAS2, which addresses the computational challenges presented by increasingly large reference genome databases, while adding functionality for building custom databases and leveraging paired-end reads to improve SNV accuracy. This fast and scalable reengineering of the MIDAS pipeline enables thousands of metagenomic samples to be efficiently genotyped.

Availability and Implementation

The source code is available at https://github.com/czbiohub/MIDAS2. The documentation is available at https://midas2.readthedocs.io/en/latest/.

Supplementary Information

Supplementary data are available at Bioinformatics online.
The virtualome: a computational framework to evaluate microbiome analyses
Authors: Serrano-Antón Belén , Rodríguez-Ventura Francisco , Colomer-Vidal Pere , Cigliano Riccardo Aiese , Arias Clemente F. , Bertocchini Federica
Published: June 2022

Microbiomes have been the focus of a substantial research effort in the last decades. The composition of microbial populations is normally determined by comparing DNA sequences sampled from those populations with the sequences stored in genomic databases. Therefore, the amount of information available in databanks should be expected to constrain the accuracy of microbiome analyses. Albeit normally ignored in microbiome studies, this constraint could severely compromise the reliability of microbiome data. To test this hypothesis, we generated virtualomes, virtual bacterial populations that exhibit the ecological structure of real-world microbiomes. Confronting the analyses of virtualomes with their original composition revealed critical issues in the current approach to characterizing microbiomes, issues that were empirically confirmed by analyzing the microbiome of Galleria mellonella larvae. To reduce the uncertainty of microbiome data, the effort in the field must be channeled towards significantly increasing the amount of available genomic information.
Mutagenesis and structural modeling implicate RME-8 IWN domains as conformational control points
Authors: Norris Anne , McManus Collin , Wang Simon , Ying Rachel , Grant Barth D.
Published: June 2022

After endocytosis, transmembrane cargo is differentially sorted into degradative or recycling pathways. This process is facilitated by recruitment into physically distinct degradative or recycling microdomains on the limiting membrane of individual endosomes. Endosomal sorting complexes required for transport (ESCRT) mark the degradative microdomain, while the recycling domain is marked by the retromer complex and associated proteins RME-8 and SNX-1. The separation of endosomal microdomains is also controlled by RME-8 and SNX-1, at least in part via removal of degradative component HRS/HGRS-1 from the recycling microdomain. This activity is likely due to recruitment and activation of chaperone Hsc70 to the recycling microdomain by the RME-8 DNAJ domain. To better understand the mechanism of RME-8 function we performed a new phylogenetic analysis of RME-8 and identified new conserved sequence features. In a complementary approach, we performed structure-function analysis that identified the C-terminus as important for microdomain localization and likely substrate binding, while N-terminal sequences beyond the known single N-terminal PH-like domain are important for endosome recruitment. Random mutagenesis identified IWN4, and by analogy IWN3, to be important for the inhibitory DNAJ domain binding. Combining AlphaFold structural predictions with in vivo truncation and point mutation analysis of RME-8, we propose a model whereby SNX-1 and the IWN domains control the conformation of RME-8 and hence the productive exposure of the DNAJ domain. Furthermore, we propose that the activation of RME-8 is cyclical, with SNX-1 acting as an activator and a target of RME-8 uncoating activity.
Inhibition of the TRIM24 bromodomain reactivates latent HIV-1
Authors: Horvath Riley M. , Brumme Zabrina L. , Sadowski Ivan
Published: June 2022

Expression of the HIV-1 genome by RNA Polymerase II is regulated at multiple steps, as are most cellular genes, including recruitment of general transcription factors and control of transcriptional elongation from the core promoter. We recently discovered that tripartite motif protein TRIM24 is recruited to the HIV-1 Long Terminal Repeat (LTR) by interaction with TFII-I and causes transcriptional elongation by stimulating association of PTEF-b/ CDK9. Because TRIM24 is required for stimulation of transcription from the HIV-1 LTR, we were surprised to find that IACS-9571, a specific inhibitor of the TRIM24 C-terminal bromodomain, induces HIV-1 provirus expression in otherwise untreated cells. IACS-9571 reactivates HIV-1 in T cell lines bearing multiple different provirus models of HIV-1 latency. Additionally, treatment with this TRIM24 bromodomain inhibitor encourages productive HIV-1 expression in newly infected cells and inhibits formation of immediate latent transcriptionally repressed provirus. IACS-9571 synergizes with PMA, ionomycin, TNF-α and PEP005 to activate HIV-1 expression. Furthermore, co-treatment of CD4+ T cells from individuals with HIV-1 on antiretroviral therapy (ART) with PEP005 and IACS-9571 caused robust provirus expression. Notably, IACS-9571 did not cause global activation of T cells; rather, it inhibited induction of IL2 and CD69 expression in human PBMCs and Jurkat T cells treated with PEP005 or PMA. These observations indicate the TRIM24 bromodomain inhibitor IACS-9571 represents a novel HIV-1 latency reversing agent (LRA), and unlike other compounds with this activity, causes partial suppression of T cell activation while inducing expression of latent provirus.
Sequential antibiotic therapy in the lab and in the patient
Authors: Nyhoegen Christin , Uecker Hildegard
Published: June 2022

Laboratory experiments suggest that rapid cycling of antibiotics during the course of treatment could successfully counter resistance evolution. Drugs involving collateral sensitivity could be particularly suitable for such therapies. However, the environmental conditionsin-vivodiffer from thosein-vitro. One key difference is that drugs can be switched abruptly in the lab, while in the patient, pharmacokinetic processes lead to changing antibiotic concentrations including periods of dose overlaps from consecutive administrations. During such overlap phases, drug-drug interactions may affect the evolutionary dynamics. To address the gap between the lab and potential clinical applications, we set up two models for comparison - a ‘lab model’ and a pharmacokinetic-pharmacodynamic ‘patient model’. The analysis shows that in the lab, the most rapid cycling suppresses the bacterial population always at least as well as other regimens. For patient treatment, however, a little slower cycling can sometimes be preferable if the pharmacodynamic curve is steep or if drugs interact antagonistically. When resistance is absent prior to treatment, collateral sensitivity brings no substantial benefit unless the cell division rate is low and drug cycling slow. By contrast, drug-drug interactions strongly influence the treatment efficiency of rapid regimens, demonstrating their importance for the optimal choice of drug pairs.
The Prmt5-Vasa module is essential for dichotomous spermatogenesis in Bombyx mori
Authors: Yang Xu , Chen Dongbin , Zheng Shirui , Yi Meiyan , Liu Yongjian , Huang Yongping
Published: June 2022

Spermatogenesis is a key process for the sexual reproduction species. In lepidopteran insects, dichotomous spermatogenesis is a notable feature, which produces eupyrene (nucleate) and apyrene (anucleate) spermatozoa. Both sperm morphs are essential for fertilization, as eupyrene sperm fertilizes the egg, while apyrene sperm is necessary for eupyrene sperm migration. In Drosophila, Prmt5 acts as a type II arginine methyltransferase to catalyze the symmetrical dimethylation of arginine residues (sDMA) in Vasa. However, Prmt5 is involved in regulating spermatogenesis, but Vasa is not. To date, the functional genetic study on dichotomous spermatogenesis in the lepidopteran model Bombyx mori has been limited, thus the underlying mechanism remains largely unknown. In this study, we report that both BmPrmt5 and BmVasa act as essential components in the regulation of dichotomous spermatogenesis in Bombyx mori. The loss-of-function mutants of BmPrmt5 (ΔBmPrmt5) and BmVasa (ΔBmVasa) derived from CRISPR/Cas9-based gene editing show similar male and female-sterile phenotypes. Through immunofluorescence staining analysis, we found that the morphs of both ΔBmPrmt5 and ΔBmVasa sperm show severe defects, indicating an essential role for both BmPrmt5 and BmVasa in the regulation of dichotomous spermatogenesis. RNA-seq analyses indicate that the defects in dichotomous spermatogenesis observed for ΔBmPrmt5 and ΔBmVasa mutants could be attributed to the reduced expression of the spermatogenesis-related genes including Sex-lethal (BmSxl), implying that BmSxl may act downstream of Prmt5 and Vasa in regulating apyrene sperm development. These findings suggest that BmPrmt5 and BmVasa constitute an integral regulatory module essential for dichotomous spermatogenesis in Bombyx mori, in which BmPrmt5 may promote BmVasa activity through sDMA modification.

Author Summary

Dichotomous spermatogenesis is a notable feature in Lepidoptera insects, in which a single male produces nucleated and anucleated dimorphic sperm. Both sperm morphs are essential for fertilization, as the eupyrene sperm fertilizes the egg, while the apyrene sperm assists in transporting the eupyrene sperm to the female sperm storage organs. To date, the mechanism of dichotomous spermatogenesis is still unclear, as very limited components participating in this process have been reported. Here we defined the function of BmPrmt5 (Protein arginine methyltransferase 5) and its substrate BmVasa in dichotomous spermatogenesis in the lepidopteran insect Bombyx mori. Our genetic analyses revealed that both BmPrmt5 and BmVasa are essential for dichotomous spermatogenesis. Moreover, RNA-seq analyses, in conjunction with the genetic and immunofluorescence staining analyses, suggest a potential regulatory pathway consisting of the BmPrmt5–BmVasa module in dichotomous spermatogenesis in Bombyx mori. This study expands the knowledge of reproduction biology in insects, and may provide potential gene targets for pest control.
MmCMS: Mouse models’ Consensus Molecular Subtypes of colorectal cancer
Authors: Amirkhah Raheleh , Gilroy Kathryn , Malla Sudhir B , Lannagan Tamsin RM , Byrne Ryan M , Fisher Natalie C , Corry Shania M , Naderi-Meshkin Hojjat , Ahmaderaghi Baharak , Murray Richard , Mills Megan , Campbell Andrew D. ,   ACRCelerate consortium, Llergo Antoni Berenguer , Sanz-Pamplona Rebeca , Villanueva Alberto , Batlle Eduard , Salazar Ramon , Lawler Mark , Sansom Owen J. , Dunne Philip D.
Published: June 2022

BACKGROUND

Colorectal cancer (CRC) primary tumours are molecularly classified into four consensus molecular subtypes (CMS1-4). Genetically engineered mouse models aim to faithfully mimic the complexity of human cancers and, when appropriately aligned, represent ideal pre-clinical systems to test new drug treatments. Despite its importance, dual-species classification has been limited by the lack of a reliable approach. Here we utilise, develop and test a set of options for human-to-mouse CMS classifications of CRC tissue.

METHODS

Using transcriptional data from established collections of CRC tumours, including human (TCGA cohort; n=577) and mouse (n=57 across n=8 genotypes) tumours with combinations of random forest and nearest template prediction algorithms, alongside gene ontology collections, we comprehensively assess the performance of a suite of new dual-species classifiers.

RESULTS

We developed three approaches: MmCMS-A; a gene-level classifier, MmCMS-B; an ontology-level approach and MmCMS-C; a combined pathway system encompassing multiple biological and histological signalling cascades. Although all options could identify tumours associated with stromal-rich CMS4-like biology, MmCMS-A was unable to accurately classify the biology underpinning epithelial-like subtypes (CMS2/3) in mouse tumours.

CONCLUSIONS

When applying human-based transcriptional classifiers to mouse tumour data, a pathway-level classifier, rather than an individual gene-level system, is optimal. Our R package with three options helps researchers select suitable mouse models of human CRC subtype for their experimental testing.
Multidimensional color codes for chair tilings
Authors: Ben-Abraham Shelomo Izhaq , Flom Dvir
Published: June 2022

Ordered aperiodic structures have been of interest to the crystallographic community for several decades, and study of them has in turn led to the study of lattice substitution systems, model sets and chair tilings. In this work a color code for chair tilings in arbitrary dimensions is presented. In two and three dimensions, it is expedient to translate the digital codes into colors. An explicit example of a three-dimensional color coding covering one octant is constructed. The tiling is then extended to the whole three-dimensional space and an indication is given of how to do this in arbitrary dimensions. Illustrations of some four-dimensional objects are also shown. The principle of color coding can be applied to other complex tilings such as brick tiling.
Aerodynamic analysis of a logistics UAV wing with compound ducted rotor
Authors: Guan Ying-Jie , Li Yong-Ping , Zeng Peng
Published: June 2022

Purpose

To solve the problems of short battery life and low transportation safety of logistics drones, this paper aims to propose a design of logistics unmanned aerial vehicles (UAV) wing with a composite ducted rotor, which combines fixed wing and rotary-wing.

Design/methodology/approach

This UAV adopts tiltable ducted rotor combined with fixed wing, which has the characteristics of fast flight speed, large carrying capacity and long endurance. At the same time, it has the hovering and vertical take-off and landing capabilities of the rotary-wing UAV. In addition, aerodynamic simulation analysis of the composite model with a fixed wing and a ducted rotor was carried out, and the aerodynamic influence of the composite model on the UAV was analyzed under different speeds, fixed wing angles of attack and ducted rotor speeds.

Findings

The results were as follows: when the speed of the ducted rotor is 2,500 rpm, CL and K both reach maximum values. But when the speed exceeds 3,000 rpm, the lift will decrease; when the angle of attack of the fixed wing is 10° and the rotational speed of the ducted rotor is about 3,000 rpm, the aerodynamic characteristics of the wing are better.

Originality/value

The novelty of this work comes from a composite wing design of a fixed wing combined with a tiltable ducted rotor applied to the logistics UAVs, and the aerodynamic characteristics of the design wing are analyzed.
Evaluating uncertainties to deliver enhanced service performance in education PPPs: a hierarchical reliability framework
Authors: Geng Linna , Herath Nilupa , Hui Felix Kin Peng , Liu Xuemei , Duffield Colin , Zhang Lihai
Published: June 2022

Purpose

This study aims to develop a hierarchical reliability framework to evaluate the service delivery performance of education public–private partnerships (PPPs) effectively and efficiently during long-term operations.

Design/methodology/approach

The research design included development and test phases. In the development phase, three performance layers, i.e. indicator, component and system, in the education service delivery system were identified. Then, service component reliability was computed through first order reliability method (FORM). Finally, the reliability of the service system was obtained using dynamic component weightings. A PPP school example in Australia was set up in the test phase, where performance indicators were collected from relevant contract documents and performance data were simulated under three assumptive scenarios.

Findings

The example in the test phase yielded good results for the developed framework in evaluating uncertainties of service delivery performance for education PPPs. Potentially underperforming services from the component to the system level at dynamic timepoints were identified, and effective preventative maintenance strategies were developed.

Research limitations/implications

This research enriches reliability theory and performance evaluation research on education PPPs. First, a series of performance evaluation indicators are constructed for assessing the performance of the service delivery of the education PPP operations. Then, a reliability-based framework for service components and system is developed to predict service performance of the PPP school operations with consideration of a range of uncertainties during project delivery.

Practical implications

The developed framework was illustrated with a real-world case study. It demonstrates that the developed reliability-based framework could potentially provide the practitioners of the public sector with a basis for developing effective preventative maintenance strategies with the aim of prolonging the service life of the PPP schools.

Originality/value

Evaluating education PPPs is challenging as it involves long-term measurement of various service components under uncertainty. The developed reliability-based framework is a valuable tool to ensure that reliability is maintained throughout the service life of education PPPs in the presence of uncertainty.
A meta-network-based management framework for megaproject social responsibility behaviour in China
Authors: Xie Linlin , Ju Tianhao , Han Ting , Hou Lei
Published: June 2022

Purpose

As megaprojects bear extensive and profound social responsibilities throughout the project life cycle, formulating effective measures for improving construction enterprise social responsibility is key to project success. Given the current research is relatively lack of these measures, this study aims to formulate a meta-network framework to improve the megaproject social responsibility behaviour (MSRB) for construction enterprises.

Design/methodology/approach

First, this study implements literature review, expert interview and field investigation to identify the construction enterprise MSRB and its influencing factors. Second, this study evaluates the MSRB implementation level of the selected construction enterprises and proposes the above mentioned meta-network framework. Next, this meta-network is configured to reflect the impact of MSRB strategic adjustment. Last but not least, a real-world case study is carried out to validate this framework.

Findings

The best MSRB performance is always witnessed from the contractor group, followed by the project client group and the site supervisor group. The outcomes of implementing certain managerial strategies indicate that (1) social responsibility cognition is a critical factor for all the groups; (2) communication mechanism and normative pressure are the critical factors for clients; (3) coercive pressure is a critical factor for supervisors and (4) cultural cognitive pressure is a critical factor for clients and contractors.

Originality/value

The use of the framework in proactive assessment and management of MSRB can lead to effective strategies for construction enterprises to increase the efficiency and quality of projects.
Fostering product and process innovation through transformational leadership and knowledge management capability: the moderating role of innovation culture
Authors: Gui Linnan , Lei Hui , Le Phong Ba
Published: June 2022

Purpose

Due to the vital role of innovation for firms to respond effectively to the rapid changes of business environment, the purpose of this study is to explore the influence of transformational leadership (TL) on innovation capability of firms via mediating role of knowledge management capability (KMC). It attempts to deepen insight on the moderating mechanism of innovation culture (IC) in enhancing the effects of KMC on two specific aspects of innovation capability namely product and process innovation.

Design/methodology/approach

The paper utilized structural equation modeling (SEM) and cross-sectional design to test hypotheses in the proposed research model using data collected from 339 participants in 75 manufacturing and service firms in China.

Findings

The findings indicate that TL directly or indirectly affect firm's innovation via mediating role of KMC. The findings highlight that influences of KMC on aspects of innovation capability are different and depended on the degree of innovative climate in an organization.

Research limitations/implications

Future research should examine the mediating mechanisms of knowledge acquisition, knowledge sharing and knowledge application to provide deeper insight on specific roles of knowledge management's constituents in linking TL and innovation capability.

Originality/value

This study contributes to bridging research gaps in the literature and advancing the insights of how TL directly and indirectly fosters product and process innovation via mediating roles of KMC. By investigating moderating role of IC, this study has provided the valuable initiatives and integration view of a new mechanism to foster specific dimensions of innovation capability of firms in developing and emerging market.
Unraveling hybrid exchange: virtual tipping on live-streaming platforms
Authors: Sun John Peikang , Fernandez Karen V. , Frethey-Bentham Catherine
Published: June 2022

Purpose

The purpose of this research is to explore the nature of virtual tipping in live game streaming from the perspective of tippers.

Design/methodology/approach

This qualitative research involved six naturalistic group interviews with 27 young adult game streaming tippers in China.

Findings

The research revealed a typology of four virtual tipping exchanges – perfunctory exchange, transactional (commodity) exchange, relational (gift) exchange and hybrid exchange. The most notable finding is hybrid exchange, a synergistic hybrid of transaction and gift-giving.

Practical implications

The authors recommend that both streamers and streaming platforms acknowledge and accommodate both transactional and relational tipping motivations. The authors also recommend platforms to recruit skillful streamers with high emotional intelligence to better convert perfunctory tippers into tippers who tip more generously.

Originality/value

The result of hybrid exchange suggests going beyond the traditional commodity vs gift dichotomy to examine the potential market-gift complementary in a single exchange in the sharing economy.