bluuebunny/crossref_metadata_2025_split huggingface dataset:
PME-mediated pectin modifications promote haustoria initiation and xylem bridge development in the parasitic plantPhtheirospermum japonicum
Authors: Leso Martina , Kokla Anna , Feng Ming , Melnyk Charles W. 
Published: February 2023

SummaryParasitic plants produce cell wall modifying enzymes that are thought to be important for efficient host infection. Here, we investigated the role of pectin methylesterases (PMEs) and their inhibitors (PMEIs) during haustorium development in the facultative parasitic plantPhtheirospermum japonicuminfectingArabidopsis thaliana.We employed immunohistochemistry to characterise tissue-specific changes in pectin methylesterification during haustorium development. We found putativePMEandPMEIgenes inP. japonicumand used genetic and transcriptomic approaches to identify those involved in haustorium development.Our results show tissue-specific changes in pectin methylesterification during haustorium development. De-methylesterified pectin correlated with haustorial intrusive cells whereas highly methylated pectin correlated with vascular tissues. We also found that inhibition of PME activity delayed haustoria development and xylem connectivity. SeveralPjPMEandPjPMEIgenes increased expression specifically during haustorium development but such increases did not occur when haustorium initiation or xylem connections were blocked by chemical treatment.This study describes the importance of pectin modifications in parasitic plants during host infection. Our results suggest a dynamic regulation of PMEs and PMEIs contributes to haustoria initiation and to the establishment of xylem connections between parasite and host.
Pan-Cancer Biomarker miR-151a Regulates p21 Partially Through p53
Authors: Kurata Jessica S. , Lin Ren-Jang 
Published: February 2023

ABSTRACTDysregulation of microRNAs (miRNAs) has been associated with a variety of cancers. We previously identified miR-151a as a potential cell fitness-regulating microRNA using a miRNA-targeted CRISPR-Cas9 genetic screen. In this study, we created mutant cell clones with loss of miR-151a expression and verified miR-151a mutations indeed decreased cell growth. In miR-151a mutant cells, there was an increase in the fraction of cells in the G1-phase of the cell cycle. This increase in G1 cells corresponded to an increase in p53 (TP53) and p21 (CDKN1A) protein levels. Both strands of miR-151a could suppress p53; miR-151a-3p was able to directly suppress p53 expression, but the miR-151a-5p suppression of p53 apparently was indirect. Re-expression of miR-151a-5p in the mutant cells significantly decreased the p53 and p21 protein levels as well as the percentage of cells in G1, while re-expression of miR-151a-3p ironically had a modest effect. These results suggest that both the 5p and 3p strands as well as additional factors are involved in the regulation of p53/p21 and the cell cycle by miR-151a. We also analyzed the TCGA database and discovered that increased miR-151a expression occurs in many tumor types; furthermore, there was an inverse correlation between miR-151a and p21 expression, and high miR-151a expression was often associated with poor overall survival. Taken together, results from this study identify a previously underappreciated role of miR-151a in cancer through regulation of the cell cycle, and they also suggest inhibiting the less abundant 5p may be more important than inhibiting the more abundant 3p of miR-151a for therapeutic considerations.
Exploring the host range for genetic transfer of magnetic organelle biosynthesis
Authors: Dziuba M.V. , Müller F.D. , Pósfai M. , Schüler D. 
Published: February 2023

AbstractMagnetosomes produced by magnetotactic bacteria have great potential for application in biotechnology and medicine due to their unique physicochemical properties and high biocompatibility. Recent studies uncovered the genetic determinants for magnetosome formation and inspired ideas to transfer the pathway into hitherto non-magnetic organisms. However, previous efforts to genetically magnetize other species have been successful in only a few bacterial recipients, revealing significant challenges in this approach. Here, by systematic examination of 25 proteobacterial hosts, we generated 7 novel magnetosome-producing strains. We further characterized the recombinant magnetosomes produced by these strains and delineate a set of auxiliary factors linked to magnetosome formation. Our findings will have significant implications for generation of magnetized life cells and the potential to facilitate the production of biogenic magnetic nanoparticles for a wide range of biomedical applications.
TTBK2mutations associated with spinocerebellar ataxia type 11 disrupt peroxisome dynamics and ciliary localization of SHH signaling proteins
Authors: Muñoz-Estrada Jesús , Nguyen Abraham V. , Goetz Sarah C. 
Published: February 2023

ABSTRACTFrameshift mutations inTau Tubulin Kinase 2(TTBK2) cause spinocerebellar ataxia type 11 (SCA11), which is characterized by the progressive loss of Purkinje cells and cerebellar atrophy. Previous work showed that theseTTBK2variants generate truncated proteins that interfere with primary ciliary trafficking and with Sonic Hedgehog (SHH) signaling in mice. Nevertheless, the molecular mechanisms underlying the dominant interference of mutations remain unknown. Herein, we discover that SCA11-associated variants contain abona fideperoxisomal targeting signal type 1. We find that their expression in RPE1 cells reduces peroxisome numbers within the cell and at the base of the cilia, disrupts peroxisome fission pathways, and impairs trafficking of ciliary SMO upon SHH signaling activation. This work uncovers a neomorphic function of SCA11-causing mutations and identifies requirements for both peroxisomes and cholesterol in trafficking of cilia-localized SHH signaling proteins. In addition, we postulate that molecular mechanisms underlying cellular dysfunction in SCA11 converge on the SHH signaling pathway.SUMMARYMolecular mechanisms underlying spinocerebellar ataxia type 11 are not well understood. In this study, we identified a neomorphic function of the mutated gene (TTBK2) associated with this disease highlighting a functional inter-organelle interaction between peroxisomes and cilia.
A one-stage approach for the spatio-temporal analysis of high-throughput phenotyping data
Authors: Pérez-Valencia Diana M. , Rodríguez-Álvarez María Xosé , Boer Martin P. , van Eeuwijk Fred A. 
Published: February 2023

AbstractThis work is motivated by the need to accurately estimate genetic effects over time when analysing data from high-throughput phenotyping (HTP) experiments. The HTP data we deal with here are characterised by phenotypic traits measured multiple times in the presence of spatial and temporal noise and a hierarchical organisation at three levels (populations, genotypes within populations, and plants within genotypes). We propose a feasible one-stage spatio-temporal P-spline-based hierarchical approach to model the evolution of the genetic signal over time on a given phenotype while accounting for spatio-temporal noise. We provide the user with appealing tools that take advantage of the sparse model matrices structure to reduce computational complexity. We illustrate the performance of our method using spatio-temporal simulated data and data from the PhenoArch greenhouse platform at INRAE Montpellier. In the plant breeding context, we show that information extracted for genomic selection purposes from our fitted genotypic curves is similar to those obtained using a comparable two-stage P-spline-based approach.
Rickettsiales’ deep evolutionary history sheds light on the emergence of intracellular lifestyles
Authors: Moncadas Lucas Serra , Shabarova Tanja , Kavagutti Vinicius Silva , Bulzu Paul-Adrian , Chiriac Maria-Cecilia , Park Soo-Je , Mukherjee Indranil , Ghai Rohit , Andrei Adrian-Stefan 
Published: February 2023

AbstractAncient bacteria largely lived and flourished as free-living cells till the rise of eukaryotes triggered their adaptation to a new habitat: the intracellular milieu. Rickettsiales bacteria are the most prevalent intracellular microorganisms discovered and the culprits behind some of mankind’s worst pestilential diseases. Here, we show that intracellularity is not a defining feature of the group and describe the eco-evolutionary processes that transformed harmless free-living bacteria into obligate intracellular symbionts and parasites. We found that the evolution of free-living lineages towards enhanced cross-feeding interactions with microbial eukaryotes trapped them in a nutritional bind to their trophic partners. We discovered that the oldest Rickettsiales lineages are the closest relatives to modern eukaryotes and are enriched in proteins predicted to have been present in the mitochondrial ancestor. This study not only opens avenues for the detection and surveillance of emerging diseases but also expands our understanding of the origins of complex life.One-Sentence SummaryCross-feeding interactions shaped Rickettsiales genomic architectures along the parasite/free-living spectrum
CRISPR/Cas12a toolbox for genomic manipulation inMethanosarcina acetivorans
Authors: Zhu Ping , Bao Jichen , Scheller Silvan 
Published: February 2023

AbstractMethanogenic archaea play an important role in the global carbon cycle and are regarded as promising host organisms for the biotechnological generation of fuels and chemicals from one-carbon substrates.Methanosarcina acetivoransis extensively studied as a model methanogen due to the availability of genetic tools and its versatile substrate range. Although genome editing inM. acetivoransvia CRISPR/Cas9 has already been demonstrated, we now describe a user-friendly CRISPR/Cas12a toolbox that recognizes a T-rich (5′-TTTV) PAM sequence. This new system can manage deletions of 3500 bp (i.e., knockout of the entirefrhADGBoperon) and heterologous gene insertions with 80% efficiency observed in ten PurRtransformants. Our CRISPR/Cas12a system also enables multiplex genome editing at high efficiency, which helps speed up genetic engineering. Deletions of 100 bp generated on two separate sites of the genome yielded 8/8 correctly edited transformants. Simultaneous gene deletion (100 bp) and replacement (100-bp region replaced by the 2400-bpuidAexpression cassette) at a separate site was achieved, with 3/6 of transformants being edited correctly. In combination with the Cas9-based system, our CRISPR/Cas12a toolbox enables targeted genome editing at two sites (guanine-rich and thymine-rich, respectively) and, in so doing, hastens the overall genetic engineering of theMethanosarcinalesspecies.
A role for the V0 sector of the V-ATPase in neuroexocytosis: exogenous V0d blocks complexin and SNARE interactions with V0c
Authors: Leveque Christian , Maulet Yves , Wang Qili , Rame Marion , Mochida Sumiko , Sangiardi Marion , Fahamoe Youssouf , Iborra Cécile , Seagar Michael , Vitale Nicolas , El Far Oussama 
Published: February 2023

AbstractV-ATPase is an important factor in synaptic vesicle acidification and is implicated in synaptic transmission. Rotation of the extra-membranous V1 sector drives proton transfer through the membrane-embedded multi-subunit V0 sector of the V-ATPase. Intra-vesicular protons are then used to drive neurotransmitter uptake by synaptic vesicles. V0a and V0c, two membrane subunits of the V0 sector have been shown to interact with SNARE proteins and their photo-inactivation rapidly impairs synaptic transmission. V0d, a soluble subunit of the V0 sector strongly interacts with its membrane embedded subunits and is crucial for the canonic proton transfer activity of the V-ATPase. Our investigations show that the loop 1.2 of V0c interacts with complexin, a major partner of the SNARE machinery and that V0d1 binding to V0c inhibits this interaction, as well as V0c association with SNARE complex. Injection of recombinant V0d1 in rat superior cervical ganglion neurons rapidly reduced neurotransmission. In chromaffin cells, V0d1 overexpression and V0c silencing modified in a comparable manner several parameters of unitary exocytotic events. Our data suggest that V0c subunit promotes exocytosis via interactions with complexin and SNAREs and that this activity can be antagonized by exogenous V0d.
Microtubule competition and cell growth recenter the nucleus after anaphase in fission yeast
Authors: Bellingham-Johnstun Kimberly , Thorn Annelise , Belmonte Julio , Laplante Caroline 
Published: February 2023

ABSTRACTCells actively position their nucleus based on their activity. In fission yeast, microtubule-dependent nuclear centering is critical for symmetrical cell division. After spindle disassembly at the end of anaphase, the nucleus recenters over a ~90 min period, approximately half of the duration of the cell cycle. Live cell and simulation experiments support the cooperation of two distinct mechanisms in the slow recentering of the nucleus. First, a push-push mechanism acts from spindle disassembly to septation and involves the opposing actions of the mitotic Spindle Pole Body microtubules that push the nucleus away from the ends of the cell while post-anaphase array of microtubules basket the nucleus and limit its migration toward the division plane. Second, a slow-and-grow mechanism finalizes nuclear centering in the newborn cell. In this mechanism, microtubule competition stalls the nucleus while asymmetric cell growth slowly centers it. Our work underlines how intrinsic properties of microtubules differently impact nuclear positioning according to microtubule network organization and cell size.
Scalable neighbour search and alignment with uvaia
Authors: de Oliveira Martins Leonardo , Mather Alison E. , Page Andrew J. 
Published: February 2023

AbstractDespite millions of SARS-CoV-2 genomes being sequenced and shared globally, manipulating such data sets is still challenging, especially selecting sequences for focused phylogenetic analysis. We present a novel method, uvaia, which is based on partial and exact sequence similarity for quickly extracting database sequences similar to query sequences of interest. Many SARS-CoV-2 phylogenetic analyses rely on very low numbers of ambiguous sites as a measure of quality since ambiguous sites do not contribute to single nucleotide polymorphism (SNP) differences, which uvaia alleviates by using measures of sequence similarity that consider partially ambiguous sites. Such fine-grained definition of similarity allows not only for better phylogenetic analyses, but also for improved classification and biogeographical inferences. Uvaia works natively with compressed files, can use multiple cores and efficiently utilises memory, being able to analyse large data sets on a standard desktop.
A modular plasmid toolkit applied in marine Proteobacteria reveals functional insights during bacteria-stimulated metamorphosis
Authors: Alker Amanda T. , Aspiras Alpher E. , Dunbar Tiffany L. , Farrell Morgan V. , Fedoriouk Andriy , Jones Jeffrey E. , Mikhail Sama R. , Salcedo Gabriella Y. , Moore Bradley S. , Shikuma Nicholas J. 
Published: February 2023

ABSTRACTA conspicuous roadblock to studying marine bacteria for fundamental research and biotechnology is a lack of modular synthetic biology tools for their genetic manipulation. Here, we applied, and generated new parts for, a modular plasmid toolkit to study marine bacteria in the context of symbioses and host-microbe interactions. To demonstrate the utility of this plasmid system, we genetically manipulated the marine bacteriumPseudoalteromonas luteoviolacea, which stimulates the metamorphosis of the model tubeworm,Hydroides elegans. Using these tools, we quantified constitutive and native promoter expression, developed reporter strains that enable the imaging of host-bacteria interactions, and used CRISPR interference (CRISPRi) to knock down a secondary metabolite and a host-associated gene. We demonstrate the broader utility of this modular system for rapidly creating and iteratively testing genetic tractability by modifying marine bacteria that are known to be associated with diverse host-microbe symbioses. These efforts enabled the successful transformation of twelve marine strains across two Proteobacteria classes, four orders and ten genera. Altogether, the present study demonstrates how synthetic biology strategies enable the investigation of marine microbes and marine host-microbe symbioses with broader implications for environmental restoration and biotechnology.
GNOM-Dependent Endosomal Recycling Sets the Timing of Founder Cell Specification
Authors: Perez-Garcia Pablo , Perianez-Rodriguez Juan , Sanchez-Corrionero Alvaro , Moreno-Risueno Miguel A. 
Published: February 2023

1.ABSTRACTLateral root growth occurs from primed xylem pole pericycle cells that can be specified as founder cells, but how these cells acquire the pluripotency state to initiate a root organogenesis program is not fully understood. Here, we find that the EMS 204 mutant is unable to specify founder cells due to a point mutation affecting the C-terminal HDS3 domain of the GNOM protein. We used genetics and cell biology to study the trafficking machinery of xylem pole pericycle cells, cells in which GNOM is primarily associated with recycling endosomes. We found that the lack of the HDS3 domain negatively affects the stability of the GNOM protein within the cells of the xylem pole pericycle and, subsequently, the integrity of the trafficking machinery of these cells. We determined that GNOM is responsible for the recycling of AUX1 toward the plasma membrane at the xylem pole pericycle and impairment of this recycling results in premature accumulation of AUX1 in the vacuole. In this work, we describe a cell type-specific cellular mechanism and the role of a particular domain during lateral root development.
Genetic control of mRNA splicing as a potential mechanism for incomplete penetrance of rare coding variants
Authors: Einson Jonah , Glinos Dafni , Boerwinkle Eric , Castaldi Peter , Darbar Dawood , de Andrade Mariza , Ellinor Patrick , Fornage Myriam , Gabriel Stacey , Germer Soren , Gibbs Richard , Hersh Craig P. , Johnsen Jill , Kaplan Robert , Konkle Barbara A. , Kooperberg Charles , Nassir Rami , Loos Ruth J.F. , Meyers Deborah A , Mitchell Braxton D. , Psaty Bruce , Vasan Ramachandran S. , Rich Stephen S. , Rienstra Michael , Rotter Jerome I. , Saferali Aabida , Shoemaker M. Benjamin , Silverman Edwin , Smith Albert Vernon ,   NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Mohammadi Pejman , Castel Stephane E. , Iossifov Ivan , Lappalainen Tuuli 
Published: February 2023

AbstractExonic variants present some of the strongest links between genotype and phenotype. However, these variants can have significant inter-individual pathogenicity differences, known as variable penetrance. In this study, we propose a model where genetically controlled mRNA splicing modulates the pathogenicity of exonic variants. By first cataloging exonic inclusion from RNA-seq data in GTEx v8, we find that pathogenic alleles are depleted on highly included exons. Using a large-scale phased WGS data from the TOPMed consortium, we observe that this effect may be driven by common splice-regulatory genetic variants, and that natural selection acts on haplotype configurations that reduce the transcript inclusion of putatively pathogenic variants, especially when limiting to haploinsufficient genes. Finally, we test if this effect may be relevant for autism risk using families from the Simons Simplex Collection, but find that splicing of pathogenic alleles has a penetrance reducing effect here as well. Overall, our results indicate that common splice-regulatory variants may play a role in reducing the damaging effects of rare exonic variants.
Internationalisation of firms in the digital economy. Analysis of tenants of Polish technology parks
Authors: Błaszczyk Mateusz , Olszewska Karolina Maria , Wróblewski Marek 
Published: February 2023

PurposeThis paper aims to discuss the relationship between the digital economy and the model of internationalisation followed by companies resident in technology parks – institutions designed within the framework of regional and national innovation systems – to promote the country’s digital development. The authors selected Poland as the case study. It is one of the biggest European Union members that joined the EU after 2004. In the second decade of the 21st century, the Polish Government has oriented its economic strategy towards building a competitive digital economy. One of its fundamentals is to support the internationalisation of innovative firms.Design/methodology/approachThe analysis interrogates the forms and determinants of internationalisation undertaken by tenants of technology parks. The study sample consisted of 300 of the total 1,584 enterprises resident at the 36 technology parks in Poland and was a stratified random sample, with particular strata classified by location at a specific park. The research applied an interview questionnaire designed to cover such issues as innovativeness, research and development, public aid and the support offered by technology parks.FindingsThe results show that around half of the investigated enterprises undertake international activities. The key factors determining the chances of a firm’s internationalisation in the digital economy are whether it conducts research and development projects and receives public aid support. Many tenants of technology parks in Poland enter foreign markets at an early stage of their development, using diverse forms of foreign expansion. The findings also show that the internationalisation of tenants of Polish technology parks usually occurs in six relatively independent modes (types).Originality/valueThis study contributes to a better understanding of the internationalisation patterns of firms facing digital development challenges. Technology parks have a crucial role in building a digital economy, facilitating a technological “leapfrog”. The final recommendations can guide the technology parks’ managers to adopt more relevant support services for the internationalisation of their tenants. It is a critical point for small- and mid-size young innovative enterprises.
Performance appraisal justice and work attitudes of health-care workers in Ghana
Authors: Brefo-Manuh Adwoa Benewaa , Anlesinya Alex 
Published: February 2023

Purpose
While the extant literature has mainly examined either organisational justice or performance appraisal on employee attitudes, studies assessing the effect of performance appraisal justice (PAJ) on employee work attitudes are very limited. Hence, this study aims to investigate the effects of PAJ on employee work attitudes (job satisfaction and employee commitment) using empirical insights from health-care workers in Ghana.

Design/methodology/approach
The study collected data from 302 workers in six selected health-care institutions and used multiple regression and bootstrapping mediation methods for the analyses.

Findings
This study found that interpersonal and procedural PAJ has significant positive effects on job satisfaction, but distributive PAJ showed an insignificant positive outcome. Then, while distributive and procedural PAJ has significant positive effects on employee commitment, interpersonal PAJ was insignificant. Moreover, job satisfaction significantly mediated the relationship between employee commitment and the three dimensions of PAJ.

Practical implications
This implies that PAJ can trigger positive employee work attitudes such as job satisfaction and commitment to facilitate the realisation of positive health-care outcomes if fairness and justice are effectively integrated into performance appraisal practices in health-care institutions.

Originality/value
The study contributes to extending organisation and human resource theories in the context of health-care services by applying the organisational justice theory to understand the job attitudes of workers in the health-care sector and institutions: a highly under-research context with respect to the topic.