bluuebunny/crossref_metadata_2025 huggingface dataset:
ParA and its functions that go beyond chromosome segregation in Caulobacter crescentus
Authors: Menikpurage Inoka P. , Puentes-Rodriguez Stephanie G. , Elaksher Rawan A. , Mera Paola E.
Published: May 2022

Maintaining the integrity of the chromosome after the completion of each cell cycle is paramount for bacterial survival. Mechanistic details remain incomplete for how bacteria manage to retain intact chromosomes in each daughter cell after each cell division. In this study, we examined the partitioning protein ParA and its functions on chromosomal maintenance that go beyond triggering the onset of chromosome segregation. Our data demonstrate that ParA can promote the onset of chromosome replication initiation in Caulobacter crescentus cells with sub-physiological levels of the replication initiator protein DnaA. Increasing the cellular levels of ParA results in over-initiation of chromosome replication in this bacterium. We show that the ability of ParA to impact replication initiation is independent from ParA’s ability to trigger the onset of chromosome segregation. Surprisingly, our work revealed that perturbing the balance of the components of ParA’s nucleotide-dependent cycle can have severe defects in cell cycle coordination and can potentially be lethal to the cell. Increasing the levels of different forms of ParA also impacted cell length independent of their replication initiation frequencies. Our results, together with past observations, suggest a model where ParA can serve as a checkpoint coordinating various cell cycle events involved in maintenance of the chromosome.
The Microbiome and Volatile Organic Compounds Reflect the State of Decomposition in an Indoor Environment
Authors: Cappas Veronica M. , Davenport Emily R. , Sykes Dan G.
Published: May 2022

Because of the variety of factors that can affect the decomposition process, it can be difficult to determine the post-mortem interval (PMI). The process is highly dependent on microbial activity, and volatile organic compounds (VOCs) are a by-product of this activity. Given both have been proposed to assist in PMI determination, a deeper understanding of this relationship is needed. The current study investigates the temporal evolution of the microbiome and VOC profile of a decomposing human analog (swine) in a controlled, indoor environment. Microbial communities and VOCs were sampled at six-time points, up to the active decay phase. Sampling locations included the abdominal area, anus, right ear canal, and right nostril. Bacterial communities were found to significantly change during decomposition (p-value < 0.001), and communities evolved differently based on sampling location. The families Moraxellaceae, Planococcaceae, Lactobacillaceae, and Staphylococcaceae drove these community shifts. From random forest analysis, the nostril sampling location was determined to be the best location to predict stage of decomposition. Individual VOCs exhibited large temporal shifts through decomposition stage in contrast to smaller shifts when evaluated based on functional groups. Finally, pairwise linear regression models between abdominal area bacteria and selected VOCs were assessed; Planococcaceae and Tissierellaceae were significantly correlated to indole. Overall, this study provides an exploratory analysis to support the connection between the microbiome, VOCs, and their relationship throughout decomposition.

Importance

This research provides valuable insight into the complex process of decomposition, which is pertinent to forensic death investigations. The temporal evolution of both the microbiome and volatile organic compounds (VOCs) were characterized as a function of stage of decomposition and evaluated their interdependency upon one another. In turn, this information may assist in determining time since death, and fill a knowledge gap about VOC-bacteria associations during the decay process.
Functional gene analysis and cultivation experiments predict the degradation of diverse extracellular polysaccharides by ubiquitous taxa in pustular microbial mats from Shark Bay, Western Australia
Authors: Cutts Elise , Schauberger Clemens , Skoog Emilie , Bosak Tanja
Published: May 2022

Microbial exopolymeric substances (EPSs) form the organic, polysaccharide-rich matrix of marine microbial mats and can mediate the binding and precipitation of carbonate minerals therein. Here, we investigate the molecular ecology of carbohydrate degradation and production in pustular mats from Shark Bay, Western Australia, by analyzing 84 metagenome-assembled genomes (MAGs) and the composition of microbial communities enriched from a pustular mat on various polysaccharide substrates. The annotation of 4000 genes from hundreds of carbohydrate-active enzyme (CAZyme) families in the MAGs and mapping of polysaccharide-degrading CAZymes to their predicted substrates identify trends in the distribution and localization of degradation-associated CAZymes across different bacterial phyla. The compositions of microbial communities enriched on a range of polysaccharides inoculated with pustular mat material support the predicted trends. The combined metagenomic and experimental analyses reveal a widespread potential for EPS degradation among MAGs from Shark Bay pustular mats and suggest distinct roles for some phyla that are reported at high abundances in mats. Specifically, Bacteroidetes are likely to be primary degraders of polysaccharide EPSs, alongside Planctomycetes and a small subset of Alphaproteobacteria and Gammaproteobacteria. Planctomycetes, some Bacteroidetes, Verrucomicrobia, Myxococcota and Anaerolineae are also predicted to favor degradation of sulfated substrates, which are present in the EPS matrix of pustular mats. Large sets of functionally varied CAZymes without signal peptides tagging them for export implicate Anaerolineae and Verrucomicrobia in degrading the downstream products of primary EPS degradation.

Importance

Modern marine microbial mats are rich in exopolymeric substances (EPSs) — complex, high molecular weight polymers secreted by bacteria — that mediate the formation of carbonate minerals and the preservation of microbial textures in mats. However, the organisms involved in EPS cycling in these mats have not been identified and the links between EPS degradation, carbonate precipitation, and microbial ecology in mats remain poorly understood. We define distinct roles in EPS cycling for many major microbial taxa that are both ubiquitous and abundant in pustular microbial mats from Shark Bay, Australia. The large genomic potential of these microbes for the modification and degradation of diverse extracellular organic polymers provides a blueprint for future studies aimed at quantifying and verifying the specific contributions of these microbes to EPS degradation, carbon cycling and carbonate precipitation.
A framework to trace microbial engraftment at the strain level during fecal microbiota transplantation
Authors: Jiang Yiqi , Wang Shuai , Wang Yanfei , Zhang Xianglilan , Li Shuaicheng
Published: May 2022

Background

Fecal microbiota transplantation (FMT) may treat microbiome-associated diseases effectively. However, the mechanism and pattern of the FMT process require expositions. Previous studies indicated the necessity to track the FMT process at the microbial strain level. At this moment, shotgun metagenomic sequencing enables us to study strain variations during the FMT.

Result

We implemented a software package PStrain-tracer to study microbial strain variations during FMT from the shotgun metagenomic sequencing data. The package visualizes the strain alteration and traces the microbial engraftment during the FMT process. We applied the package to two typical FMT datasets: one ulcerative colitis (UC) dataset and one Clostridium difficile infection (CDI) dataset. We observed that when the engrafted species has more than one strain in the source sample, 99.3% of the engrafted species will engraft only a subset of strains. We further confirmed that the all-or-nothing manner unsuited the engraftment of species with multiple strains by heterozygous single-nucleotide polymorphisms (SNPs) count, revealing that strains prefer to engraft independently. Furthermore, we discovered a primary determinant of strain engrafted success is their proportion in species, as the engrafted strains from the donor and the pre-FMT recipient with proportions 33.10 % (p-value = 6e − 06) and 37.08 % (p-value = 9e − 05) significantly higher than ungrafted strains on average, respectively. All the datasets indicated that the diversity of strains bursts after FMT and decreases to one after eight weeks for twelve species. Previous studies neglected strains with their corresponding species showing insignificant differences between different samples. With the package, from the UC dataset, we successfully determined the strain variations of the species Roseburia intestinalis, a beneficial species reducing intestinal inflammation, colonized in the cured UC patient being engrafted from the donor, even if the patient hosted the same species yet before treatment. We found seven strains in donors from the CDI dataset and one strain in pre-FMT recipients from eight species that associated CDI FMT failure.

Conclusion

PStrain-tracer is the first framework that tracks strain alterations in metagenomic sequencing data of FMT. PStrain-tracer implemented several methods specialized for FMT experiment samples, such as visualization of strains abundance alteration in the FMT experiment and determinant strains detection in FMT failure. We applied PStrain-tracer on two published datasets, uncovered novel strains related to FMT failure, and demonstrated the necessity of analyzing the whole-genome shotgun metagenomic data of FMT at the strain level. We also developed an online visualizer of PStrain-tracer for the users to adjust their visualized results online. The package is available at https://github.com/deepomicslab/PStrain-tracer.
The majority of microorganisms in gas hydrate-bearing subseafloor sediments ferment macromolecules
Authors: Zhang Chuwen , Fang Yun-Xin , Yin Xiuran , Lai Hongfei , Kuang Zenggui , Zhang Tianxueyu , Xu Xiang-Po , Wegener Gunter , Wang Jiang-Hai , Dong Xiyang
Published: May 2022

Background

Gas hydrate-bearing subseafloor sediments harbor a large number of microorganisms. Sedimentary organic matter and upward methane fluids represent two important sources of carbon and energy for deep biosphere. However, which metabolism dominates the deep subseafloor of gas hydrate zone is poorly constrained. Here we studied the microbial communities in gas-hydrate rich sediments up to 49 meters below seafloor recovered by drilling in the South China Sea. We focused on distinct geochemical conditions, and performed metagenomic and metatranscriptomic analyses to characterize microbial diversity and their role in carbon mineralization.

Results

Comparative microbial community analysis revealed that samples above and in sulfate-methane interface (SMI) zones clearly distinguish from those below the SMI. Chloroflexota, are most abundant above the SMI, whereas Caldatribacteriota dominate below the SMI. Verrucomicrobiota, Bathyarchaeia and Hadarchaeota were similarly present in both types of sediment. The genomic inventory and transcriptional activity suggest roles in fermentation of macromolecule. By contrast, sulfate reducers and methanogens, organisms that catalyze the consumption or production of commonly observed chemical compounds in sediments are rare. Methanotrophs of the ANME-1 group thrived in or slightly below the current sulfate methane interface. Rare members from Heimdallarchaeia were identified to encode the potential for anaerobic oxidation of short-chain hydrocarbons.

Conclusions

These findings indicate that fermentation of macromolecules is the predominant energy source for microorganisms in deep subseafloor sediments that are experiencing upward methane fluxes.
Multi-modal analysis and integration of single-cell morphological data
Authors: Govek Kiya W. , Crawford Jake , Saturnino Artur B. , Zoga Kristi , Hart Michael P. , Camara Pablo G.
Published: May 2022

High-resolution imaging-based single-cell profiling has transformed the study of cells in their spatial context. However, the lack of quantitative methods that can summarize the great diversity of complex cell shapes found in tissues and infer associations with other single-cell data modalities limits current analyses. Here, we report a general computational framework for the multi-modal analysis and integration of single-cell morphological data. We build upon metric geometry to construct cell morphology latent spaces, where distances in these spaces indicate the amount of physical deformation needed to change the morphology of one cell into that of another. Using these spaces, we integrate morphological data across technologies and leverage associated single-cell RNA-seq data to infer relations between morphological and transcriptomic cellular processes. We apply this framework to imaging and multi-modal data of neurons and glia to uncover genes related to neuronal plasticity. Our approach represents a strategy for incorporating cell morphological data into single-cell omics analyses.
Targeting Nup358/RanBP2 by a viral protein disrupts stress granule formation
Authors: Sadasivan Jibin , Vlok Marli , Wang Xinying , Nayak Arabinda , Andino Raul , Jan Eric
Published: May 2022

Viruses have evolved mechanisms to modulate cellular pathways to facilitate infection. One such pathway is the formation of stress granules (SG), which are ribonucleoprotein complexes that assemble during translation inhibition following cellular stress. Inhibition of SG assembly has been observed under numerous virus infections across species, suggesting a conserved fundamental viral strategy. However, the significance of SG modulation during virus infection is not fully understood. The 1A protein encoded by the model dicistrovirus, Cricket Paralysis Virus (CrPV), is a multifunctional protein that can bind to and degrade Ago-2 in an E3 ubiquitin ligase-dependent manner to block the antiviral RNA interference pathway and inhibit SG formation. Moreover, the R146 residue of 1A is necessary for SG inhibition and CrPV infection in both Drosophila S2 cells and adult flies. Here, we uncoupled CrPV-1A’s functions and provide insight into its underlying mechanism for SG inhibition. CrPV-1A mediated inhibition of SGs requires the E3 ubiquitin-ligase binding domain and the R146 residue, but not the Ago-2 binding domain. Wild-type but not mutant CrPV-1A R146A localizes to the nuclear membrane which correlates with nuclear enrichment of poly(A)+ RNA. Transcriptome changes in CrPV-infected cells are dependent on the R146 residue. Finally, Nup358/RanBP2 is targeted and degraded in CrPV-infected cells in an R146-dependent manner and the depletion of Nup358 blocks SG formation. We propose that CrPV utilizes a multiprong strategy whereby the CrPV-1A protein interferes with a nuclear event that contributes to SG inhibition in order to promote infection.

AUTHOR SUMMARY

Viruses often inhibit a cellular stress response that leads to the accumulation of RNA and protein condensates called stress granules. How this occurs and why this would benefit virus infection are not fully understood. Here, we reveal a viral protein that can block stress granules and identify a key amino acid residue in the protein that inactivates this function. We demonstrate that this viral protein has multiple functions to modulate nuclear events including mRNA export and transcription to regulate stress granule formation. We identify a key host protein that is important for viral protein mediate stress granule inhibition, thus providing mechanistic insights. This study reveals a novel viral strategy in modulating stress granule formation to promote virus infection.
Associations between abstract working memory abilities and brain activity underlying long-term recognition of auditory sequences
Authors: Fernández Rubio G. , Carlomagno F. , Vuust P. , Kringelbach M. L. , Bonetti L.
Published: May 2022

Memory is a complex cognitive process comprised by several subsystems, namely short- and long-term memory and working memory (WM). Previous research has shown that adequate interaction between subsystems is crucial for successful memory processes such as encoding, storage and manipulation of information. However, few studies have investigated the relationship between different subsystems at the behavioral and neural levels. Thus, here we assessed the relationship between individual WM abilities and brain activity underlying the recognition of previously memorized auditory sequences.

First, recognition of previously memorized versus novel auditory sequences was associated with a widespread network of brain areas comprising the cingulate gyrus, hippocampus, insula, inferior temporal cortex, frontal operculum, and orbitofrontal cortex.

Second, we observed positive correlations between brain activity underlying auditory sequence recognition and WM. We showed a sustained positive correlation in the medial cingulate gyrus, a brain area which was widely involved in the auditory sequence recognition. Remarkably, we also observed positive correlations in the inferior temporal, temporal-fusiform, and postcentral gyri, brain areas which were not strongly associated to auditory sequence recognition.

In conclusion, we discovered positive correlations between WM abilities and brain activity underlying long-term recognition of auditory sequences, providing new evidence on the relationship between memory subsystems. Furthermore, we showed that high WM performers recruited a larger brain network including areas associated to visual processing (i.e., inferior temporal, temporal-fusiform and postcentral gyri) for successful auditory memory recognition.

Significance statement

Memory is a complex cognitive process dependent on the successful interaction between its multiple subsystems. Here, we assessed the relationship between individual WM abilities and brain activity underlying the recognition of previously memorized auditory sequences.

We observed positive correlations between brain activity underlying auditory sequence recognition and WM, especially in the medial cingulate gyrus, inferior temporal, temporal-fusiform and postcentral gyri. In this study, we provided new evidence on the relationship between two memory subsystems: WM and long-term auditory recognition. Moreover, we showed that, to successfully complete memory recognition tasks, high WM performers recruited a larger brain network which comprised brain areas mainly associated to visual processing, such as inferior temporal, temporal-fusiform and postcentral gyri.
Programming the lymph node immune response with Amphiphile-CpG induces potent cellular and humoral immunity following COVID-19 subunit vaccination in mice and non-human primates
Authors: Seenappa Lochana M. , Jakubowski Aniela , Steinbuck Martin P. , Palmer Erica , Haqq Christopher M. , Carter Crystal , Fontenot Jane , Villinger Francois , McNeil Lisa K. , DeMuth Peter C.
Published: May 2022

Despite the success of currently authorized vaccines for the reduction of severe COVID-19 disease risk, rapidly emerging viral variants continue to drive pandemic waves of infection, resulting in numerous global public health challenges. Progress will depend on future advances in prophylactic vaccine activity, including advancement of candidates capable of generating more potent induction of cross-reactive T cells and durable cross-reactive antibody responses. Here we evaluated an Amphiphile (AMP) adjuvant, AMP-CpG, admixed with SARS-CoV-2 Spike receptor binding domain (RBD) immunogen, as a lymph node-targeted protein subunit vaccine (ELI-005) in mice and non-human primates (NHPs). AMP-mediated targeting of CpG DNA to draining lymph nodes resulted in comprehensive local immune activation characterized by extensive transcriptional reprogramming, inflammatory proteomic milieu, and activation of innate immune cells as key orchestrators of antigen-directed adaptive immunity. Prime-boost immunization with AMP-CpG in mice induced potent and durable T cell responses in multiple anatomical sites critical for prophylactic efficacy and prevention of severe disease. Long-lived memory responses were rapidly expanded upon re-exposure to antigen. In parallel, RBD-specific antibodies were long-lived, and exhibited cross-reactive recognition of variant RBD. AMP-CpG-adjuvanted prime-boost immunization in NHPs was safe and well tolerated, while promoting multi-cytokine-producing circulating T cell responses cross-reactive across variants of concern (VOC). Expansion of RBD-specific germinal center (GC) B cells in lymph nodes correlated to rapid seroconversion with variant-specific neutralizing antibody responses exceeding those measured in convalescent human plasma. These results demonstrate the promise of lymph-node adjuvant-targeting to coordinate innate immunity and generate robust adaptive responses critical for vaccine efficacy.
Effects of netarsudil-family Rho kinase inhibitors on human trabecular meshwork cell contractility and actin remodeling using a bioengineered ECM hydrogel
Authors: Bagué Tyler , Singh Ayushi , Ghosh Rajanya , Yoo Hannah , Kelly Curtis , deLong Mitchell A. , Kopczynski Casey C. , Herberg Samuel
Published: May 2022

Interactions between trabecular meshwork (TM) cells and their extracellular matrix (ECM) are critical for normal outflow function in the healthy eye. Multifactorial dysregulation of the TM is the principal cause of elevated intraocular pressure that is strongly associated with glaucomatous vision loss. Key characteristics of the diseased TM are pathologic contraction and actin stress fiber assembly, contributing to overall tissue stiffening. Among first-line glaucoma medications, the Rho-associated kinase inhibitor (ROCKi) netarsudil is known to directly target the stiffened TM to improve outflow function via tissue relaxation involving focal adhesion and actin stress fiber disassembly. Yet, no in vitro studies have explored the effect of netarsudil on human TM (HTM) cell contractility and actin remodeling in a 3D ECM environment. Here, we use our bioengineered HTM cell-encapsulated ECM hydrogel to investigate the efficacy of different netarsudil-family ROCKi compounds on reversing pathologic contraction and actin stress fibers. Netarsudil and all related experimental ROCKi compounds exhibited significant ROCK1/2 inhibitory and focal adhesion disruption activities. Furthermore, all ROCKi compounds displayed potent contraction-reversing effects on HTM hydrogels upon glaucomatous induction in a dose-dependent manner, relatively consistent with their biochemical/cellular inhibitory activities. At their tailored EC50 levels, netarsudil-family ROCKi compounds exhibited distinct effect signatures of reversing pathologic HTM hydrogel contraction and actin stress fibers, independent of the cell strain used. Netarsudil outperformed the experimental ROCKi compounds in support of its clinical status. In contrast, at uniform EC50-levels using netarsudil as reference, all ROCKi compounds performed similarly. Collectively, our data suggest that netarsudil exhibits high potency to rescue HTM cell pathobiology in a tissue-mimetic 3D ECM microenvironment, solidifying the utility of our bioengineered hydrogel model as a viable screening platform to further our understanding of TM pathophysiology in glaucoma.
High Frequency of Dynamic Rearrangements In Crispr loci
Authors: Ou Yaqing , McInerney James O.
Published: May 2022

Abstract

CRISPR-Cas immunization of prokaryotes proceeds by the acquisition of short fragments of invading DNA and integrating them into specific positions within the host genome in a process called adaptation. Adaptation is thought to be polarised, which suggests that CRISPR array spacer order reflects the recentness of the infection. The detailed processes through which CRISPR loci arise, and how they evolve are not completely clear. In this study, we collected 12,461 prokaryotic genomes, and using a combination of four different approaches and a series of conservative filters, we identified CRISPR arrays in 82.7% of Archaea and 40.6% of Bacteria. To understand spacer evolution in these CRISPR loci we firstly tracked point mutations in CRISPR repeats, and secondly, we carried out a comparative analysis of arrays that share multiple similar spacers. Both results indicate that CRISPR arrays are frequently dynamically rearranged. These findings are at odds with a model that suggests that spacer order is likely to reflect the recentness of infection. We conclude that the order of spacers in a CRISPR array, as well as the spacer content of the array, is likely to arise from a combination of events, such as insertion in the middle of the array, recombination within or between arrays, or Horizontal transfer of all or part of an array. We suggest these rearrangements are favoured by natural selection in complex and dynamic environments.
Rdh54 stabilizes Rad51 at displacement loop intermediates to regulate genetic exchange between chromosomes
Authors: Keymakh Margaret , Dau Jennifer , Ferlez Bryan , Lisby Michael , Crickard J. Brooks
Published: May 2022

Homologous recombination (HR) is a double-strand break DNA repair pathway that preserves chromosome structure. To repair the damaged recipient DNA, HR requires an intact donor DNA sequence located elsewhere in the genome. After the double-strand break is repaired, DNA sequence information can be transferred between donor and recipient DNA molecules through different mechanisms, including DNA crossovers that form between homologous chromosomes. Regulating this transfer of information is an important step in effectively completing HR and maintaining genome integrity. For example, mitotic exchange of information between homologous chromosomes can result in loss-of-heterozygosity (LOH) in diploid organisms, and in higher eukaryotes, the development of cancer. The DNA motor protein Rdh54 is a highly conserved DNA translocase that functions during HR but has a limited role in repairing DNA. Instead, several existing phenotypes inrdh54Δstrains suggest that Rdh54 may regulate the flow of information between donor and recipient DNA molecules post DNA repair. In our current study, we used a combination of biochemical and genetic techniques to dissect the role of Rdh54 on the exchange of genetic information after DNA repair. Our data indicates thatRDH54regulates DNA sequence exchange between chromosomes by limiting the disruption of Rad51 at an early HR intermediate called the displacement loop (D-loop). Rdh54 also protects Rad51 filaments, acting in opposition to Rad51 removal by the DNA motor protein Rad54. Furthermore, we find that expression of a catalytically inactivate allele of Rdh54,rdh54K318R, displays a different distribution of information exchange outcomes thanrdh54Δ cells. From these results, we propose a model for how Rdh54 may effectively regulate information transfer during homologous recombination.
Resolution doubling in light-sheet microscopy via oblique plane structured illumination
Authors: Chen Bingying , Chang Bo-Jui , Roudot Philippe , Zhou Felix , Sapoznik Etai , Marlar-Pavey Madeleine , Hayes James B. , Brown Peter T. , Zeng Chih-Wei , Lambert Talley , Friedman Jonathan R. , Zhang Chun-Li , Burnette Dylan T. , Shepherd Douglas P. , Dean Kevin M. , Fiolka Reto P.
Published: May 2022

Structured illumination microscopy (SIM) doubles the spatial resolution of a fluorescence microscope without requiring high laser powers or specialized fluorophores. However, the excitation of out-of-focus fluorescence can accelerate photobleaching and phototoxicity. In contrast, light-sheet fluorescence microscopy (LSFM) largely avoids exciting out-of-focus fluorescence, thereby enabling volumetric imaging with low photo-bleaching and intrinsic optical sectioning. Combining SIM with LSFM would enable gentle 3D imaging at doubled resolution. However, multiple orientations of the illumination pattern, which are needed for isotropic resolution doubling in SIM, are challenging to implement in a light-sheet format. Here we show that multidirectional structured illumination can be implemented in oblique plane microscopy, a LSFM technique that uses a single objective for excitation and detection, in a straightforward manner. We demonstrate isotropic lateral resolution below 150nm, combined with lower photo-toxicity compared to traditional SIM systems and volumetric acquisition speed exceeding 1Hz.
Self-organized canals enable long range directed material transport in bacterial communities
Authors: Li Ye , Liu Shiqi , Zhang Yingdan , Seng Zi Jing , Xu Haoran , Yang Liang , Wu Yilin
Published: May 2022

Long-range material transport is essential to maintain the physiological functions of multicellular organisms such as animals and plants. By contrast, material transport in bacteria is often short-ranged and limited by diffusion. Here we report a unique form of actively regulated long-range directed material transport in structured bacterial communities. UsingPseudomonas aeruginosacolonies as a model system, we discover that a large-scale and temporally evolving open channel system spontaneously develops in the colony via shear-induced banding. Fluid flows in the open channels support high-speed (up to 450 µm/s) transport of cells and outer membrane vesicles over centimeters, and help to eradicate colonies of a competing speciesStaphylococcus aureus. The open channels are reminiscent of human-made canals for cargo transport, and the channel flows are driven by interfacial tension mediated by cell-secreted biosurfactants. The spatial-temporal dynamics of fluid flows in the open channels are qualitatively described by flow profile measurement and mathematical modeling. Our findings demonstrate that mechanochemical coupling between interfacial force and biosurfactant kinetics can coordinate large-scale material transport in primitive life forms, suggesting a new principle to engineer self-organized microbial communities.
Confident Clustering via PCA Compression Ratio and Its Application to Single-cell RNA-seq Analysis
Authors: Li Yingcong , Mukherjee Chandra Sekhar , Zhang Jiapeng
Published: May 2022

Unsupervised clustering algorithms for vectors has been widely used in the area of machine learning. Many applications, including the biological data we studied in this paper, contain some boundary datapoints which show combination properties of two underlying clusters and could lower the performance of the traditional clustering algorithms. We develop a confident clustering method aiming to diminish the influence of these datapoints and improve the clustering results. Concretely, for a list of datapoints, we give two clustering results. The first-round clustering attempts to classify only pure vectors with high confidence. Based on it, we classify more vectors with less confidence in the second round. We validate our algorithm on single-cell RNA-seq data, which is a powerful and widely used tool in biology area. Our confident clustering shows a high accuracy on our tested datasets. In addition, unlike traditional clustering methods in single-cell analysis, the confident clustering shows high stability under different choices of parameters.
A study of the crystal structures, supramolecular patterns and Hirshfeld surfaces of bromide salts of hypoxanthine and xanthine
Authors: Sathya Udhayasuriyan , Nirmalram Jeyaraman Selvaraj , Gomathi Sundaramoorthy , Dhivya Durairaj , Jegan Jennifer Samson , Abdul Razak Ibrahim
Published: May 2022

Two new crystalline salts, namely, hypoxanthinium bromide monohydrate, C5H5N4O+·Br−·H2O (I) and xanthinium bromide monohydrate, C5H5N4O2
+·Br−·H2O (II), were synthesized and characterized by single-crystal X-ray diffraction technique and Hirshfeld surface analysis. The hypoxanthinium and xanthinium cations in salts I and II are both in the oxo-N(9)–H tautomeric form. The crystal packing of the two salts is governed predominantly by N–H...O, N–H...Br, C–H...Br and O–H...Br interactions described by R
2
3(9) and R
2
2(8) synthons. The crystal packing is also consolidated by carbonyl...π interactions between symmetry-related hypoxanthinium (HX+
) cations in salt I and xanthinium cations (XA+
) in salt II. The combination of all these interactions leads to the formation of wave- and staircase-like architectures in salts I and II, respectively. The largest contributions to the overall Hirshfeld surface are from Br...H/H...Br contacts (22.3% in I and 25.4% in II) .
Shaping health and well-being in a COVID era: the role of design
Authors: Asojo Abimbola , Vo Hoa , Fisher Thomas , Singh Virajita
Published: May 2022

Purpose

In this study, an interdisciplinary research team at a Midwest US University collaborated with a local county to co-envision interior design strategies for five county buildings: three libraries and two government buildings to reduce in-person contact in response to the COVID-19 pandemic.

Design/methodology/approach

The authors' interdisciplinary team used a community-based participatory design process which focused on creating consensus, while seeking out divergent perspectives among stakeholders to serve the needs of diverse users. The design process involved meetings with stakeholders remotely and analyzing survey results from the target occupants collected by the county.

Findings

The county with a population of 550,321 is the second most populous and diverse county in the state. The authors' collaborative efforts resulted in short-and long-term recommendations for the interior space planning to promote health, safety, and well-being for the county's diverse user groups of young children, adults, elderly and vulnerable populations. The short-term recommendations focus on service redesigns that can be implemented as the state shifts out of the stay-at-home order and the community returns to the county's public-facing buildings. The long-term recommendations focus on experiences and design strategies that can be carried forward to future-proof buildings in a post-COVID era and provide models for other counties.

Research limitations/implications

One limitation is the dynamic nature of how rapidly our team responded to a critical need in the community to develop tangible interior design solutions during the initial stages of the COVID-19 pandemic for the county. The solutions we proposed were based on the scientific evidence available earlier on during that phase of the pandemic. The authors hope to conduct further studies in the future and conduct assessments of our rapid design responses.

Practical implications

This paper documents a dynamic experience during a once in a lifetime pandemic and thus contributes to further the body of knowledge about the role of interior design in shaping health and well-being during the COVID-19 pandemic.

Originality/value

The article presents a timely interdisciplinary response to the COVID-19 pandemic to promote community safety inside public buildings at the county. The interior design solutions reflected intensive literature reviews, critical space planning, innovative use of lighting, and thoughtful furniture/material selections.
Effect of AIS on planning process effectiveness: a case of SMEs in a less developed nation
Authors: Al-Hattami Hamood Mohammed , Abdullah Abdulwahid Abdullah Ahmed Hashed , Kabra Jawahar D. , Alsoufi Maged A.Z. , Gaber Mohammed M.A. , Shuraim Abdullah M.A.
Published: May 2022

Purpose

This paper aims to examine the influence of accounting information system (AIS) success on planning process effectiveness (PPE) in small- and medium-sized enterprises (SMEs) of Yemen, a less developed nation (LDN).

Design/methodology/approach

This study developed a theoretical model based on IS success model (DMISS2003). The model’s components were tested using structural equation modeling via SmartPLS on a sample of 325 SMEs.

Findings

The empirical results imply that AIS success positively affects PPE if SMEs focus on AIS information quality, system quality, user satisfaction and usage.

Research limitations/implications

This study focused on SMEs in Yemen. Thus, it can be expanded to include different other countries.

Practical implications

The results of this study could be considered by owners and managers of SMEs, policymakers and AIS designers/vendors. This study could provide them insight into the role of AIS success in promoting PPE in SMEs. This study could assist policymakers in analyzing the work of SMEs and assessing their success, referring to AIS. Moreover, knowing the most critical determinants of AIS success could direct designers’/vendors’ efforts toward upgrading and improving the present AIS.

Social implications

Government policymakers in LDNs considering how to motivate SME development in their nation should be aware of the significance of AIS success and implementation among SMEs and its role in the nation’s economic development.

Originality/value

This research is one of the first that investigates the impact of AIS success on PPE in SMEs. Current literature largely lacks the investigation of such an impact, especially among SMEs in LDNs such as Yemen. Most AIS’s prior research focused on SMEs in developed nations, which may not fully apply to LDNs such as Yemen. Indeed, no existing literature is available where AIS success impacts PPE in SMEs of LDNs. In this respect, this study claims its uniqueness.
Wells Fargo: a corporate recovery model to bank on
Authors: Welch James
Published: May 2022

Purpose

This paper aims to center on the analysis of corporate recovery from internal ethical failure with the examination of Wells Fargo and Company. To move beyond self-inflicted reputational damage and regain sales traction, successful turnaround companies have embarked on a four-step corporate recovery process centered on four key words: Replace, Restructure, Redevelop and Re-brand. Wells Fargo is one recent addition to these recovery stories.

Design/methodology/approach

This paper uses Wells Fargo and Company as a case model to examine corporate recovery. Wells Fargo is just one example of multinational companies that found themselves victims of internal impropriety, poor leadership supervision and unethical strategic decision-making resulting in significant financial losses, drastic declines in stock price and damaged reputation. Using Wells Fargo as an example from the banking industry, the case study approach is an effective way of assessing the viability of the corporate recovery model in various industries.

Findings

The corporate recovery model has served Wells Fargo well over the past few years as the stock price climbed nearly 60% in 2021. In addition, increasingly less public discussion about the account fraud scandal has allowed the reputation of the bank to recover as well. By the last quarter of 2021, the bank saw a 15% increase in revenue and an 86% increase in net income over the previous year. It appears that CEO Scharf is well on his way to turning around the prospects for Wells Fargo and the recovery model has proven again that there is a way through self-inflicted corporate damage.

Originality/value

The recovery story of Wells Fargo and Company adds to the litany of successful corporate recoveries where companies have achieved unprecedented turnarounds by following the model of replacing the leadership, restructuring the organization, redeveloping the strategy and re-branding the product. Implementing this four-pronged recovery strategy can help a company not only survive their specific scandal but also move away from reputational harm and get back on a growth trajectory.
Does earnings quality impact firms’ performance? The case of Portuguese SMEs from the mold sector
Authors: Duarte Ana Filipa , Lisboa Inês , Carreira Pedro
Published: May 2022

Purpose

This study aims to study the impact of earnings quality on firms’ financial performance.

Design/methodology/approach

An unbalanced panel data of 237 small- and medium-sized Portuguese companies from the mold industry, using 2010–2018 yearly data was analyzed. While most studies focus only on earnings management when assessing earnings quality, in this study six proxies for earnings quality are used, namely, accruals quality (a proxy for earnings management), earnings persistence, earnings predictability, earnings smoothness, earnings timeliness and earnings conservatism. Moreover, two proxies of financial performance are considered, the return on assets and the economic value added. An econometric model was estimated using either a fixed-effects or a random-effects specification to account for the individual firm-specific effects and ensure heteroscedasticity corrected estimates.

Findings

The results show that managers must be concerned with the quality of reported earnings, as it can affect positively firms’ financial performance, especially regarding accruals quality. Persistence, predictability, smoothness, timeliness and conservatism are shown not to exert significant influence on financial performance in the sample.

Research limitations/implications

This work contributes not only as a literature review on these thematic but also to firms’ managers and stakeholders, who have information that helps them select strategies that guarantee earnings quality and improve firms’ financial performance.

Originality/value

This study proposed an econometric model that studies the relationship between earnings quality (using several proxies for it) and financial performance that can be applied to all companies.
Additive manufacturing value chain adoption
Authors: Luomaranta Toni , Martinsuo Miia
Published: May 2022

Purpose

Adopting additive manufacturing (AM) on a large-scale requires an adoption in company value chains. This may happen through product innovation and require interorganizational cooperation, but the value-adding potential of cooperation and application recognition is still poorly understood. This study aims to investigate the progress of AM adoption in innovation projects featuring AM application recognition and interorganizational cooperation in the value chain.

Design/methodology/approach

A multiple-case study was implemented in successful metallic AM adoption examples to increase the understanding of AM adoption in value chains. Primary data were collected through interviews and documents in three AM projects, and the data were analyzed qualitatively.

Findings

All three AM projects showed evidence of successful AM value chain adoption. Identifying the right application and the added value of AM within it were crucial starting points for finding new value chains. Interorganizational collaboration facilitated both value-based designs and experimentation with new supply chains. Thereby, the focal manufacturing company did not need to invest in AM machines. The key activities of the new value chain actors are mapped in the process of AM adoption.

Research limitations/implications

The cases are set in a business-to-business context, which narrows the transferability of the results. As a theoretical contribution, this paper introduces the concept of AM value chain adoption. The value-adding potential of AM is identified, and the required value-adding activities in collaborative innovation are reported. As a practical implication, the study reveals how companies can learn of AM and adopt AM value chains without investing in AM machines. They can instead leverage relationships with other companies that have the AM knowledge and infrastructure.

Originality/value

This paper introduces AM value chain adoption as a novel, highly interactive phase in the industry-wide adoption of metallic AM. AM value chain adoption is characterized in multi-company collaboration settings, which complements the single-company view dominant in previous research. Theory elaboration is offered through merging technology adoption with external integration from the information processing view, emphasizing the necessity of interorganizational cooperation in AM value chain adoption. Companies can benefit each other during AM adoption, starting with identifying the value-creating opportunities and applications for AM.
Formal institutions, type of diversification and the diversification – performance relationship: a meta-analysis
Authors: Tashman Peter , Spadafora Ettore , Wagner Dominik Pascal Manfred
Published: May 2022

Purpose

The authors meta-analyze research on the diversification–performance relationship to empirically establish the impact of home-country formal institutional quality on this relationship. Prior research assumes that a country’s formal institutional quality negatively affects the diversification–performance relationship, especially when it involves unrelated diversification. However, empirical evidence for these propositions is inconclusive because existing studies consider blocks of countries with limited institutional heterogeneity. To provide more clarity, this study aims to consider the diversification–performance relationship across developed, emerging and developing countries.

Design/methodology/approach

The meta-analysis relies on a sample of 293 effect sizes of the diversification–performance relationship from 76 primary studies across 15 countries between 1988 and 2019. The sample excludes effects sizes from papers that consider both product and international diversification to control for complex interactions between the strategies, as well as papers that did not consider both related and unrelated diversification.

Findings

The results confirm that stronger home-country formal institutions weaken the diversification–performance relationship by decreasing the relative efficiency of internal markets versus external ones. Further, the effect is less negative for related diversification because this strategy can better exploit market frictions in countries with stronger formal institutions and more efficient external markets than its unrelated counterpart.

Originality/value

The study contributes to the literatures on the diversification–performance relationship and home-country governance by providing robust evidence for how formal institutional quality impacts the efficacy of related and unrelated diversification.
The influence of financial literacy on financial resilience – New evidence from Europe during the COVID-19 crisis
Authors: Erdem Diba , Rojahn Joachim
Published: May 2022

Purpose

This study examines the importance of financial literacy in explaining financial resilience in four continental European countries during the coronavirus disease 2019 (COVID-19) crisis while controlling for a wide set of additional determinants.

Design/methodology/approach

Variable importance may vary with the technique applied. Therefore, different classification techniques, such as logistic regression, partial proportional odds regression, and conditional random forest, have been employed. The analysis relies on the Survey of Health, Ageing and Retirement in Europe in the context of COVID-19, collecting 4,781 observations from France, Germany, Italy, and Spain.

Findings

In line with previous studies, financial resilience is found to increase with financial literacy that consistently ranks in the midfield in terms of variable importance among all explanatory variables.

Practical implications

The findings reveal the most important features that improve financial resilience. Financial literacy is one of the few determinants of financial resilience that can be actively shaped. To increase preparedness for future crises, a policy mix of financial education, regulation, and nudging may help increase financial literacy and, subsequently, financial resilience.

Originality/value

The better the financial literacy, the more protected individuals are from macroeconomic shocks. However, most previous studies do not rely on data samples that cover such crises. Moreover, most of the previous studies rely on single classification techniques, while this study applied traditional and data-mining techniques to assess feature importance.