bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of highly ferulate-tolerant Acinetobacter baylyi ADP1 isolates by a rapid reverse-engineering method
Authors: Luo Jin , McIntyre Emily A. , Bedore Stacy R. , Santala Ville , Neidle Ellen L. , Santala Suvi
Published: September 2021

Adaptive laboratory evolution (ALE) is a powerful approach for improving phenotypes of microbial hosts. Evolved strains typically contain numerous mutations that can be revealed by whole-genome sequencing. However, determining the contribution of specific mutations to new phenotypes is typically challenging and laborious. This task is complicated by factors such as the mutation type, the genomic context, and the interplay between different mutations. Here, a novel approach was developed to identify the significance of mutations in strains derived from Acinetobacter baylyi ADP1. This method, termed Rapid Advantageous Mutation ScrEening and Selection (RAMSES), was used to analyze mutants that emerged from stepwise adaptation to, and consumption of, high levels of ferulate, a common lignin-derived aromatic compound. After whole-genome sequence analysis, RAMSES allowed both rapid determination of effective mutations and seamless introduction of the beneficial mutations into the chromosomes of new strains with different genetic backgrounds. This simple approach to reverse-engineering exploits the natural competence and high recombination efficiency of ADP1. The growth advantage of transformants under selective pressure revealed key mutations in genes related to aromatic transport, including hcaE, hcaK, and vanK, and a gene, ACIAD0482, which is associated with lipopolysaccharide synthesis. This study provides insights into enhanced utilization of industrially relevant aromatic substrates and demonstrates the use of A. baylyi ADP1 as a convenient platform for strain development and evolution studies.

Importance

Microbial conversion of lignin-enriched streams is a promising approach for lignin valorization. However, the lignin-derived aromatic compounds are toxic to cells at relevant concentrations. Adaptive laboratory evolution is a powerful approach to develop more tolerant strains, but revealing the underlying mechanisms behind phenotypic improvement typically involves laborious processes. We employed Acinetobacter baylyi ADP1, an aromatic compound degrading strain that may be useful for biotechnology. The natural competence and high recombination efficiency of strain ADP1 can be exploited for critical applications such as the breakdown of lignin and plastics, abundant polymers composed of aromatic subunits. The natural transformability of this bacterium enabled us to develop a novel approach that allows rapid screening of advantageous mutations from ALE-derived aromatic-tolerant ADP1 strains. We clarified the mechanisms and genetic targets for improved tolerance towards common lignin-derived aromatic compounds. This study facilitates metabolic engineering for lignin valorization.
Non-canonical Staphylococcus aureus pathogenicity island repression
Authors: Miguel-Romero Laura , Alqasmi Mohammed , Bacarizo Julio , Tan Jason A. , Cogdell Richard J. , Chen John , Byron Olwyn , Christie Gail E , Marina Alberto , Penadés José R
Published: September 2021

Mobile genetic elements (MGEs) control their life cycles by the expression of a master repressor, whose function must be disabled to allow the spread of these elements in nature. Here we describe an unprecedented repression-derepression mechanism involved in the transfer of the Staphylococcus aureus pathogenicity islands (SaPIs). Contrary to the classical phage and SaPI repressors, which are dimers, the SaPI1 repressor StlSaPI1 presents a unique tetrameric conformation, never seen before. Importantly, not just one but two tetramers are required for SaPI1 repression, which increases the novelty of the system. To derepress SaPI1, the phage-encoded protein Sri binds to and induces a conformational change in the DNA binding domains of StlSaPI1, preventing the binding of the repressor to its cognate StlSaPI1 sites. Finally, our findings demonstrate that this system is not exclusive to SaPI1 but widespread in nature. Overall, our results characterise a novel repression-induction system involved in the transfer of MGE-encoded virulence factors in nature.

Significance

While most repressors controlling the transfer of mobile genetic elements are dimers, we demonstrate here that the Staphylococcal pathogenicity island 1 (SaPI1) is repressed by two tetramers, which have a novel structural fold in their body that has never been seen before in other proteins. Moreover, by solving the structure of the SaPI1 repressor in complex with its inducing protein Sri, we have demonstrated that Sri forces the SaPI1 repressor to adopt a conformation that is incompatible with DNA binding, explaining how SaPI1 is induced. Finally, our results demonstrate that this repression system is not exclusive of the SaPIs but widespread in nature. Our studies provide important insights understanding how SaPIs spread in nature.
Anterior Gradient-2 (AGR2) is overexpressed in colon cancer and is a potential biomarker of microsatellite instability (MSI) tumors
Authors: Fessart Delphine , Mahouche Isabelle , Brouste Veronique , Velasco Valerie , Soubeyran Isabelle , Soubeyran Pierre , Pernot Simon , Chevet Eric , Evrard Serge , Robert Jacques , Delom Frederic
Published: September 2021

Background

Colon cancer is one of the most common leading causes of death worldwide. Prognostic at an early stage is an efficient way to decrease mortality. The Endoplasmic Reticulum (ER)-resident protein anterior gradient-2 (AGR2), a Protein Disulfide Isomerase (PDI) is highly expressed in various tumours and is involved in tumour-associated processes. This study aims at examining the expression of AGR2 protein in colon cancer.

Methods

AGR2 protein expression was determined using immunohistochemistry on tissue samples issued from a cohort of 82 colorectal carcinomas.

Results

AGR2 protein expression was significantly higher in tumours than in adjacent nontumour controls. AGR2 expression subgroup analyses indicated that AGR2 low expression in colon cancer patients was significantly associated with worse overall survival. Mucinous colon cancers exhibited higher AGR2 expression levels than non-mucinous cancers. Additionally, tumours with microsatellite instability (MSI) were characterised by a strong upregulation of AGR2 mRNA and protein expression despite an absence of MLH1/MSH2 mutations.

Conclusions

Our findings indicate that high AGR2 protein expression is correlated with longer patient survival and that AGR2 overexpression is associated with MSI tumours and could represent an MSI biomarker. Overall, AGR2 might serve as a biomarker to stratify colon tumours and to contribute to the prognosis of colon cancer patients.
High-resolution structures of the actomyosin-V complex in three nucleotide states provide insights into the force generation mechanism
Authors: Pospich Sabrina , Sweeney H. Lee , Houdusse Anne , Raunser Stefan
Published: September 2021

The molecular motor myosin undergoes a series of major structural transitions during its force-producing motor cycle. The underlying mechanism and its coupling to ATP hydrolysis and actin binding is only partially understood, mostly due to sparse structural data on actin-bound states of myosin. Here, we report 26 high-resolution cryo-EM structures of the actomyosin-V complex in the strong-ADP, rigor, and a previously unseen post-rigor transition state that binds the ATP analog AppNHp. The structures reveal a high flexibility of myosin in each state and provide valuable insights into the structural transitions of myosin-V upon ADP release and binding of AppNHp, as well as the actomyosin interface. In addition, they show how myosin is able to specifically alter the structure of F-actin. The unprecedented number of high-resolution structures of a single myosin finally enabled us to assemble a nearly complete structural model of the myosin-V motor cycle and describe the molecular principles of force production.
Real age prediction from the transcriptome with RAPToR
Authors: Bulteau Romain , Francesconi Mirko
Published: September 2021

Transcriptomic data is often affected by uncontrolled variation among samples that can obscure and confound the effects of interest. This is frequently due to unintended differences in developmental stages between samples. The transcriptome itself can be used to estimate developmental progression, but existing methods require many samples and do not estimate a real developmental time.

Here we present RAPToR, a simple and precise computational method that estimates the real age of a sample from its transcriptome, exploiting existing time-series data as reference. RAPToR works with whole animal, dissected tissue and single-cell data, for the most common animal models, humans and even for nonmodel organisms lacking reference data. We show RAPToR estimated age improves differential expression analysis by recovering the signal of interest when confounded with age. RAPToR will be especially useful in large scale single organism profiling because it eliminates the need for accurate staging or synchronization before profiling.
Yersinia remodels epigenetic histone modifications in human macrophages
Authors: Bekere Indra , Huang Jiabin , Schnapp Marie , Rudolph Maren , Berneking Laura , Ruckdeschel Klaus , Grundhoff Adam , Günther Thomas , Fischer Nicole , Aepfelbacher Martin
Published: September 2021

Various pathogens systematically reprogram gene expression in macrophages, but the underlying mechanisms are largely unknown. We investigated whether the enteropathogen Yersinia enterocolitica alters chromatin states to reprogram gene expression in primary human macrophages. Genome-wide chromatin immunoprecipitation (ChIP) seq analyses showed that pathogen-associated molecular patterns (PAMPs) induced up- or down-regulation of histone modifications (HMod) at approximately 14500 loci in promoters and enhancers. Effectors of Y. enterocolitica reorganized about half of these dynamic HMod, with the effector YopP being responsible for about half of these modulatory activities. The reorganized HMod were associated with genes involved in immune response and metabolism. Remarkably, the altered HMod also associated with 61 % of all 534 known Rho GTPase pathway genes, revealing a new level in Rho GTPase regulation and a new aspect of bacterial pathogenicity. Changes in HMod were associated to varying degrees with corresponding gene expression, e. g. depending on chromatin localization and cooperation of the HMod. In summary, infection with Y. enterocolitica remodels HMod in human macrophages to modulate key gene expression programs of the innate immune response.

Author Summary

Human pathogenic bacteria can affect epigenetic histone modifications to modulate gene expression in host cells. However, a systems biology analysis of this bacterial virulence mechanism in immune cells has not been performed. Here we analyzed genome-wide epigenetic histone modifications and associated gene expression changes in primary human macrophages infected with enteropathogenic Yersinia enterocolitica. We demonstrate that Yersinia virulence factors extensively modulate histone modifications and associated gene expression triggered by the pathogen-associated molecular patterns (PAMPs) of the bacteria. The epigenetically modulated genes are involved in several key pathways of the macrophage immune response, including the Rho GTPase pathway, revealing a novel level of Rho GTPase regulation by a bacterial pathogen. Overall, our findings provide an in-depth view of epigenetic and gene expression changes during host-pathogen interaction and might have further implications for understanding of the innate immune memory in macrophages.
R-Loops between nascent pri-miRNAs and the encoding loci promote co-transcriptional processing of miRNAs in plants
Authors: Gonzalo Lucia , Tossolini Ileana , Gulanicz Tomasz , Cambiagno Damian A. , Kasprowicz-Maluski Anna , Smolinski Jan Dariusz , Marquardt Sebastian , Szweykowska-Kulinska Zofia , Jarmolowski Artur , Manavella Pablo A.
Published: September 2021

In most organisms, the maturation of nascent RNAs is coupled to transcription, undergoing many processing steps co-transcriptionally. Unlike in animals, the RNA polymerase II (RNAPII) transcribes microRNAs (miRNAs) as long and structurally variable pri-miRNAs in plants. Current evidence suggests that the miRNA biogenesis complex assembly initiates early during the transcription of pri-miRNAs in plants. However, it is unknown whether miRNA processing occurs co-transcriptionally. Here, we show that plant miRNA biogenesis is coupled to transcription in a process that relies on the formation of DNA:RNA hybrids (R-loops) between the nascent transcript and the encoding loci. We used native elongating transcript sequencing data and imaging techniques to demonstrate that plant miRNA biogenesis occurs co-transcriptionally. We found that the entire biogenesis occurs coupled to transcription for pri-miRNAs processed from the loop but requires a second nucleoplasmic step for those processed from the base of the hairpin. Furthermore, we found that co- and post-transcriptional miRNA processing mechanisms co-exist for most miRNAs in a dynamic balance. Notably, we discovered that R-loops between the 5’-end single-stranded arm of the pri-miRNAs and the encoding loci anchor the transcript, promoting co-transcriptional processing. Our data demonstrate the coupling of transcription and miRNA processing in plants and discovered an unexpected function for R-loops promoting RNA processing. Furthermore, our results suggest the neo-functionalization of co-transcriptionally processed miRNAs, boosting countless regulatory scenarios.
Simultaneous expression of UV and violet SWS1 opsins expands the visual palette in a group of freshwater snakes
Authors: Hauzman Einat , Pierotti Michele E.R. , Bhattacharyya Nihar , Tashiro Juliana H. , Yovanovich Carola A.M. , Campos Pollyanna F. , Ventura Dora F. , Chang Belinda S.W.
Published: September 2021

Snakes are known to express a rod visual opsin and two cone opsins, only (SWS1, LWS), a reduced palette resulting from their supposedly fossorial origins. Dipsadid snakes in the genusHelicopsare highly visual predators that successfully invaded freshwater habitats from ancestral terrestrial-only habitats. Here we report the first case of multiple SWS1 visual pigments in a vertebrate, simultaneously expressed in different photoreceptors and conferring both UV and violet sensitivity toHelicopssnakes. Molecular analysis andin vitroexpression confirmed the presence of two functional SWS1 opsins, likely the result of recent gene duplication. Evolutionary analyses indicate that eachsws1variant has undergone different evolutionary paths, with strong purifying selection acting on the UV-sensitive copy and dN/dS∼1 on the violet-sensitive copy. Site-directed mutagenesis points to the functional role of a single amino acid substitution, Phe86Val, in the large spectral shift between UV and violet opsins. In addition, higher densities of photoreceptors and SWS1 cones in the ventral retina suggest improved acuity in the upper visual field possibly correlated with visually-guided behaviors. The expanded visual opsin repertoire and specialized retinal architecture are likely to improve photon uptake in underwater and terrestrial environments, and provide the neural substrate for a gain in chromatic discrimination, potentially conferring unique color vision in the UV-violet range. Our findings highlight the innovative solutions undertaken by a highly specialized lineage to tackle the challenges imposed by the invasion of novel photic environments and the extraordinary diversity of evolutionary trajectories taken by visual opsin-based perception in vertebrates.
Characterization of Histone Lysine β-hydroxybutyrylation in bovine tissues, cells, and cumulus-oocyte complexes
Authors: Sangalli Juliano Rodrigues , Nociti Ricardo Perecin , del Collado Maite , Sampaio Rafael Vilar , da Silveira Juliano Coelho , Perecin Felipe , Smith Lawrence Charles , Ross Pablo Juan , Meirelles Flávio Vieira
Published: September 2021

Besides their canonical roles as energy sources, short-chain fatty acids act as metabolic regulators of gene expression through the histone post-translational modifications. The ketone body β-hydroxybutyrate (BHB) was shown to cause a novel type of epigenetic modification, Histone Lysine β-hydroxybutyrylation (Kbhb), associated with genes upregulated in starvation-responsive metabolic pathways. Dairy cows increase BHB in early lactation and its effects on cellular epigenome are largely unknown. To unravel these effects, we sought and identified that Kbhb is present in bovine tissues in vivo and further confirmed that this epigenetic mark is responsive to BHB in bovine and human fibroblasts cultured in vitro in a dose-dependent manner. We also demonstrated that the maturation of cumulus-oocyte complexes with high concentrations of BHB did not affect the competence to complete meiotic maturation neither to develop until blastocyst stage. BHB treatment strongly induced H3K9bhb in cumulus cells, but this modification was only faintly detected in oocytes. Profiling the transcriptome in cumulus cells indicated that BHB treatment altered the expression of 345 genes. The down-regulated genes are mainly involved in glycolysis and ribosome assembly pathways, while the up-regulated genes are involved in mitochondrial metabolism and oocyte development. The specific genes and pathways altered by BHB treatment will provide entry points to carry out functional experiments aiming to mitigate problems and improve fertility in cattle suffering metabolic disorders. A key goal for future work will be to understand mechanistically how BHB transmits signals from the environment to affect cellular functions and the bovine epigenome.

Summary sentence

Beta-hydroxybutyrate induces Histone Lysine β-hydroxybutyrylation in fibroblasts and cumulus-oocyte complexes, it alters the transcriptome in cumulus cells, but does not affect oocyte’s competence to resume meiosis and develop until blastocyst stage.
Micro-dissection and integration of long and short reads to create a robust catalog of kidney compartment-specific isoforms
Authors: Eksi Ridvan , Yi Daiyao , Li Hongyang , Godfrey Bradley , Mathew Lisa R. , O’Connor Christopher L. , Bitzer Markus , Kretzler Matthias , Menon Rajasree , Guan Yuanfang
Published: September 2021

Studying isoform expression at the microscopic level has always been a challenging task. A classical example is kidney, where glomerular and tubulo-insterstitial compartments carry out drastically different physiological functions and thus presumably their isoform expression also differs. We aim at developing an experimental and computational pipeline for identifying isoforms at microscopic structure-level. We microdissed glomerular and tubulo-interstitial compartments from healthy human kidney tissues from two cohorts. The two compartments were separately sequenced with the PacBio RS II platform. These transcripts were then validated using transcripts of the same samples by the traditional Illumina RNA-Seq protocol, distinct Illumina RNA-Seq short reads from European Renal cDNA Bank (ERCB) samples, and annotated GENCODE transcript list, thus identifying novel transcripts. We identified 14,739 and 14,259 annotated transcripts, and 17,268 and 13,118 potentially novel transcripts in the glomerular and tubulo-interstitial compartments, respectively. Of note, relying solely on either short or long reads would have resulted in many erroneous identifications. We identified distinct pathways involved in glomerular and tubulointerstitial compartments at the isoform level.We demonstrated the possibility of micro-dissecting a tissue, incorporating both long- and short-read sequencing to identify isoforms for each compartment.
Functional characterization of 5’ UTR cis-acting sequence elements that modulate translational efficiency in P. falciparum and humans
Authors: Garcia Valentina E. , Dial Rebekah , DeRisi Joseph L.
Published: September 2021

Background

The eukaryotic parasite Plasmodium falciparum causes millions of malarial infections annually while drug resistance to common antimalarials is further confounding eradication efforts. Translation is an attractive therapeutic target that will benefit from a deeper mechanistic understanding. As the rate limiting step of translation, initiation is a primary driver of translational efficiency. It is a complex process regulated by both cis and trans acting factors, providing numerous potential targets. Relative to model organisms and humans, P. falciparum mRNAs feature unusual 5’ untranslated regions suggesting cis-acting sequence complexity in this parasite may act to tune levels of protein synthesis through their effects on translational efficiency.

Methods

Here, we deployed in vitro translation to compare the role of cis-acting regulatory sequences in P. falciparum and humans. Using parasite mRNAs with high or low translational efficiency, the presence, position, and termination status of upstream “AUG”s, in addition to the base composition of the 5’ untranslated regions, were characterized.

Results

The density of upstream “AUG”s differed significantly among the most and least efficiently translated genes in P. falciparum, as did the average “GC” content of the 5’ untranslated regions. Using exemplars from highly translated and poorly translated mRNAs, multiple putative upstream elements were interrogated for impact on translational efficiency. Upstream “AUG”s were found to repress translation to varying degrees, depending on their position and context, while combinations of upstream “AUG”s had nonadditive effects. The base composition of the 5’ untranslated regions also impacted translation, but to a lesser degree. Surprisingly, the effects of cis-acting sequences were remarkably conserved between P. falciparum and humans.

Conclusion

While translational regulation is inherently complex, this work contributes toward a more comprehensive understanding of parasite and human translational regulation by examining the impact of discrete cis-acting features, acting alone or in context.
A generalized cortical activity pattern at internally-generated mental context boundaries during unguided narrative recall
Authors: Lee Hongmi , Chen Janice
Published: September 2021

Current theory and empirical studies suggest that humans segment continuous experiences into events based on the mismatch between predicted and actual sensory inputs; detection of these “event boundaries” evokes transient neural responses. However, boundaries can also occur at transitions between internal mental states, without relevant external input changes. To what extent do such “internal boundaries” share neural response properties with externally-driven boundaries? We conducted an fMRI experiment where subjects watched a series of short movies and then verbally recalled the movies, unprompted, in the order of their choosing. During recall, transitions between movies thus constituted major boundaries between internal mental contexts, generated purely by subjects’ unguided thoughts. Following the offset of each recalled movie, we observed stereotyped spatial activation patterns in the default mode network, especially the posterior medial cortex, consistent across different movie contents and even across the different tasks of movie watching and recall. Surprisingly, the between-movie boundary patterns did not resemble patterns at boundaries between events within a movie. Thus, major transitions between mental contexts elicit neural phenomena shared across internal and external modes and distinct from within-context event boundary detection, potentially reflecting a cognitive state related to the flushing and reconfiguration of situation models.
The response of three-dimensional pancreatic alpha and beta cell co-cultures to oxidative stress
Authors: Sthijns Mireille M.J.P.E. , Rademakers Timo , Oosterveer Jolien , Geuens Thomas , van Blitterswijk Clemens A. , LaPointe Vanessa L.S.
Published: September 2021

The pancreatic islets of Langerhans have low endogenous antioxidant levels and are thus especially sensitive to oxidative stress, which is known to influence cell survival and behaviour. As bioengineered islets are gaining interest for therapeutic purposes, it is important to understand how their composition can be optimized to diminish oxidative stress. We investigated how the ratio of the two main islet cell types (alpha and beta cells) and their culture in three-dimensional aggregates could protect against oxidative stress. Monolayer and aggregate cultures were established by seeding the alphaTC1 (alpha) and INS1E (beta) cell lines in varying ratios, and hydrogen peroxide was applied to induce oxidative stress. Viability, oxidative stress, and the level of the antioxidant glutathione were measured. Both aggregation and an increasing prevalence of INS1E cells in the co-cultures conferred greater resistance to cell death induced by oxidative stress. Increasing the prevalence of INS1E cells also decreased the number of alphaTC1 cells experiencing oxidative stress in the monolayer culture. In 3D aggregates, culturing the alphaTC1 and INS1E cells in a ratio of 50:50 prevented oxidative stress in both cell types. Together, the results of this study lead to new insight into how modulating the composition and dimensionality of a co-culture can influence the oxidative stress levels experienced by the cells.
High Temporal Resolution Measurements of Movement Reveal Novel Early-Life Physiological Decline in C. elegans
Authors: Sinha Drew B. , Pincus Zachary S.
Published: September 2021

Age-related physiological changes are most notable and best-studied late in life, while the nature of aging in early- or middle-aged individuals has not been explored as thoroughly. In C. elegans, studies of movement vs. age generally delineate three distinct phases: sustained, youthful movement; a discrete onset of rapidly progressing impairment; and gross immobility. We investigated whether this first period of early-life adult movement is simply a sustained “healthy” level of high function followed by a discrete “movement catastrophe” — or whether there are early-life changes in movement that precede future physiological declines. To determine how movement varies during early adult life, we followed isolated individuals throughout life with a previously unachieved combination of duration and temporal resolution. By tracking individuals across the first six days of adulthood, we observed declines in movement starting as early as the first two days of adult life, as well as high interindividual variability in total daily movement. These findings suggest that movement is a highly dynamic behavior early in life, and that factors driving movement decline may begin acting as early as the first day of adulthood. Using simulation studies based on acquired data, we suggest that too infrequent sampling in common movement assays limits observation of early-adult changes in motility, and we propose feasible alternate strategies and a framework for designing assays with increased sensitivity for early movement declines.
External drivers of BOLD signal’s non-stationarity
Authors: Ashourvan Arian , Pequito Sérgio , Bertolero Maxwell , Kim Jason Z. , Bassett Danielle S. , Litt Brian
Published: September 2021

A fundamental challenge in neuroscience is to uncover the principles governing how the brain interacts with the external environment. However, assumptions about external stimuli fundamentally constrain current computational models. We show in silico that unknown external stimulation can produce error in the estimated linear time-invariant dynamical system. To address these limitations, we propose an approach to retrieve the external (unknown) input parameters and demonstrate that the estimated system parameters during external input quiescence uncover spatiotemporal profiles of external inputs over external stimulation periods more accurately. Finally, we unveil the expected (and unexpected) sensory and task-related extra-cortical input profiles using functional magnetic resonance imaging data acquired from 96 subjects (Human Connectome Project) during the resting-state and task scans. Together, we provide evidence that this embodied brain activity model offers information about the structure and dimensionality of the BOLD signal’s external drivers and shines light on likely external sources contributing to the BOLD signal’s non-stationarity.
Declining RNA integrity in control autopsy brain tissue is robustly and asymmetrically associated with selective neuronal mRNA signal loss
Authors: Johnson Eleanor S. , Stenzel Kendra E. , Lee Sangderk , Blalock Eric M.
Published: September 2021

RNA integrity numbers (RINs) are a standardized method for semi-quantification of RNA degradation, and are used in quality control prior to transcriptional profiling analysis. Recent work has demonstrated that RINs are associated with downstream transcriptional profiling, and correction procedures are typically employed in bioinformatic analysis pipelines to attempt to control for RIN’s influence on gene expression. However, relatively little work has been done to determine whether RIN’s influence is random, or is specifically targeted to a subset of mRNAs. We tested the hypothesis that RIN would be associated with a robust transcriptional profile seen across multiple studies.

To test this, we downloaded subsets of raw transcriptional data from six published studies. We only included control, non-pathological post-mortem human brain tissue (n = 383 samples) in which independent subjects’ RIN values were also reported. A robust set of mRNAs consistently and significantly correlated with RIN across multiple studies, appearing to be selectively degraded as RIN declines. Many of the affected gene expression pathways are related to neurons (e.g., vesicle, mRNA transport, synapse, and mitochondria), suggesting that neuronal synaptic mRNA may be particularly vulnerable to degradation. Subsequent analysis of the relationship between RIN and vulnerable mRNA expression revealed most of the decay occurred over a relatively narrow RIN range of 7.2-8.6, with RIN values > 8.6 showing a ceiling effect, and those < 7.2 showing a floor effect on gene expression. Our data suggests that the RIN effect is pathway selective and non-linear, which may be an important consideration for current bioinformatic RIN correcting procedures, particularly in datasets in which declining RIN is confounded with a pathology under study (e.g., in Alzheimer’s disease).
Gene Set Analysis for time-to-event outcome with the Generalized Berk–Jones statistic
Authors: Villain Laura , Ferté Thomas , Thiébaut Rodolphe , Hejblum Boris P.
Published: September 2021

Gene Set analysis allows to evaluate the impact of groups of genes on an outcome of interest, such as the occurrence of a disease. Through the definition of the gene sets, gene set analysis takes into account biological knowledge and makes it easier to interpret the results, while improving the statistical power compared to a gene-wise analysis. In the time-to-event context, few methods exist, but most of them do not take into account the correlation that occurs inside a gene set, which can be strong. As the Generalized Berk-Jones statistics showed great consistency and includes the correlation inside the test statistic, we adapted this method to the time-to-event context by using a Cox model. We compared our approach to other methods based on the Cox model, and showed that the Generalize Berk-Jones statistic offers great adaptability, meaning that it can be used in all kinds of data structures. We applied the different methods to two different contexts: Gliomas and Breast cancer. In terms of statistical power, we did offer similar results to the other Cox model methods, but with greater accuracy. In the breast cancer framework, we showed better statistical power than methods based on Kernel Machine score.
A unique sulfotransferase-involving strigolactone biosynthetic route in Sorghum
Authors: Wu Sheng , Li Yanran
Published: September 2021

LOW GERMINATION STIMULANT 1 (LGS1) plays an important role in strigolactones (SLs) biosynthesis and Striga resistance in sorghum but the catalytic function remains unclear. Using the recently developed SL-producing microbial consortia, we examined the activities of sorghum MAX1 analogs and LGS1. Surprisingly, SbMAX1d (accession # XP_002458367) synthesized 18-hydroxy-carlactonoic acid (18-hydroxy-CLA) directly from carlactone (CL) through four-step oxidations, and addition of LGS1 led to the synthesis of both 5-deoxystrigol (5DS) and 4-deoxyorobanchol (4DO). Further biochemical characterization found that LGS1 functions after SbMAX1d by converting 18-hydroxy-CLA to 18-sulphate-CLA to provide an easier leaving group to afford a spontaneous formation of 5DS and 4DO. The unique functions of SbMAX1 and LGS1 imply a previously unknown synthetic route towards strigolactones.

Abstract Figure
Transcriptional regulation of HSCs in Aging and MDS reveals DDIT3 as a Potential Driver of Dyserythropoiesis
Authors: Berastegui Nerea , Ainciburu Marina , Romero Juan P. , Alfonso-Pierola Ana , Philippe Céline , Vilas Amaia , Martin Patxi San , Ordoñez Raquel , Alignani Diego , Sarvide Sarai , Castro Laura , Lamo-Espinosa José M. , San-Julian Mikel , Jimenez Tamara , López Félix , Muntion Sandra , Sanchez-Guijo Fermin , Molero Antonieta , Montoro Julia , Tazón Bárbara , Serrano Guillermo , Diaz-Mazkiaran Aintzane , Hernaez Mikel , Huerga Sofía , Copley Findlay , Rio-Machin Ana , Maurano Matthew T. , Díez-Campelo María , Valcarcel David , Rouault-Pierre Kevin , Lara-Astiaso David , Ezponda Teresa , Prosper Felipe
Published: September 2021

Myelodysplastic syndromes (MDS) are hematopoietic stem cell (HSC) malignancies characterized by ineffective hematopoiesis, with increased incidence in elderly individuals. In this work, we analyzed the transcriptome of human HSCs purified from young and elderly healthy donors, as well as MDS patients, identifying transcriptional alterations following eight different patterns of expression. While aging-associated lesions seemed to predispose HSCs to myeloid transformation, disease-specific alterations may trigger MDS development. Among MDS-specific lesions, we detected the upregulation of the transcription factor DDIT3. Overexpression of DDIT3 in human healthy HSCs induced an MDS-like transcriptional state, and a delay in erythropoiesis. Such effect was associated with downregulation of transcription factors required for normal erythropoiesis, and with a failure in the activation of their transcriptional programs. Moreover, DDIT3 knockdown in CD34+ cells from MDS patients with anemia was able to restore erythropoiesis. These results identify DDIT3 as a driver of dyserythropoiesis, and a potential therapeutic target to restore the inefficient erythropoiesis characterizing MDS patients.

STATEMENT OF SIGNIFICANCE

This study defines how human aging and MDS development are characterized by transcriptional alterations in HSCs that follow different patterns, some of which may contribute to myeloid transformation. Among them, we demonstrate how MDS-specific upregulation of DDIT3 in HSCs induces dyserythropoiesis, while its knockdown in HSPCs from MDS patients restores proper erythroid differentiation.
α-/γ-Taxilin are required for centriolar subdistal appendage assembly and microtubule organization
Authors: Ma Dandan , Wang Rongyi , Wang Fulin , Chen Zhiquan , Huang Ning , Xia Yuqing , Teng Junlin , Chen Jianguo
Published: September 2021

The centrosome, composed of a pair of centrioles (mother and daughter centrioles) and pericentriolar material, is mainly responsible for microtubule nucleation and anchorage in animal cells. The subdistal appendage (SDA) is a centriolar structure located at the subdistal region on the mother centriole, and it functions in microtubule anchorage. However, the molecular composition and detailed structure of SDA remain largely unknown. Here, we identified a-taxilin and r-taxilin as new SDA components, which form a complex via their coiled-coil domains and serve as a new subgroup during SDA hierarchical assembly. Their SDA localization is dependent on ODF2, and α-taxilin recruits CEP170 to the SDA. Functional analyses suggest that α-taxilin and γ-taxilin are responsible for centrosomal microtubule anchorage during interphase, as well as for proper spindle orientation during metaphase. Altogether, our results shed light on the molecular components and functional understanding of the SDA hierarchical assembly and microtubule organization.
Copper selects for siderophore-mediated virulence in Pseudomonas aeruginosa
Authors: Lear Luke , Hesse Elze , Buckling Angus , Vos Michiel
Published: September 2021

Iron is essential for almost all bacterial pathogens and consequently it is actively withheld by their hosts. However, the production of extracellular siderophores enables iron sequestration by pathogens, increasing their virulence. Another function of siderophores is extracellular detoxification of non-ferrous metals. Here, we experimentally link the detoxification and virulence roles of siderophores by testing whether the opportunistic pathogen Pseudomonas aeruginosa displays greater virulence after exposure to copper. To do this, we incubated P. aeruginosa under different environmentally relevant copper regimes for either two or twelve days. Subsequent growth in a copper-free environment removed phenotypic effects, before we quantified pyoverdine production (the primary siderophore produced by P. aeruginosa), and virulence using the Galleria mellonella infection model. Copper selected for increased pyoverdine production, which was positively correlated with virulence. This effect increased with time, such that populations incubated with high copper for twelve days were the most virulent. Replication of the experiment with a non-pyoverdine producing strain of P. aeruginosa demonstrated that pyoverdine production was largely responsible for the change in virulence. Therefore we here show a direct link between metal stress and bacterial virulence, highlighting another dimension of the detrimental effects of metal pollution on human health.
High-resolution single-particle cryo-EM of samples vitrified in boiling nitrogen
Authors: Engstrom Tyler , Clinger Jonathan A. , Spoth Katherine A. , Clarke Oliver B. , Closs David S. , Jayne Richard , Apker Benjamin A. , Thorne Robert E.
Published: September 2021

Based on work by Dubochet and others in the 1980s and 1990s, samples for single-particle cryo-electron microscopy (cryo-EM) have been vitrified using ethane, propane or ethane/propane mixtures. These liquid cryogens have a large difference between their melting and boiling temperatures and so can absorb substantial heat without formation of an insulating vapor layer adjacent to a cooling sample. However, ethane and propane are flammable, they must be liquified in liquid nitrogen immediately before cryo-EM sample preparation, and cryocooled samples must be transferred to liquid nitrogen for storage, complicating workflows and increasing the chance of sample damage during handling. Experiments over the last 15 years have shown that cooling rates required to vitrify pure water are only ∼250 000 K s−1, at the low end of earlier estimates, and that the dominant factor that has limited cooling rates of small samples in liquid nitrogen is sample precooling in cold gas present above the liquid cryogen surface, not the Leidenfrost effect. Using an automated cryocooling instrument developed for cryocrystallography that combines high plunge speeds with efficient removal of cold gas, we show that single-particle cryo-EM samples on commercial grids can be routinely vitrified using only boiling nitrogen and obtain apoferritin datasets and refined structures with 2.65 Å resolution. The use of liquid nitrogen as the primary coolant may allow manual and automated workflows to be simplified and may reduce sample stresses that contribute to beam-induced motion.
Finite element study on residual internal pressure strength of corroded oil pipes and prediction method for remaining life
Authors: Yuan Yue , Deng Kuanhai , Zhang Jiangjiang , Zeng Wenguang , Kong Xiangwei , Lin Yuanhua
Published: September 2021

Purpose

This study aims to provide a theoretical basis to evaluate the suitability and integrity of corrosion pipes.

Design/methodology/approach

The three-dimensional models of the P110S oil pipe with local corrosion damage, general corrosion damage, pitting corrosion damage are established based on the API 579 standard using the nonlinear finite element analysis method for parametric research.

Findings

The reliability of the model is verified based on the experimental data from the existing literature. The effects of the oil pipe’s size and the corrosion damage’s type on the residual internal pressure strength are simulated and obtained. What’s more, a basic method for predicting the remaining life of corrosion damaged pipes is proposed.

Originality/value

The authors evaluated the residual strength of various corroded tubing, compared the tubing with different corrosion types and proposed a basic method for predicting the remaining life of the corroded tubing from the corrosion depth.
Dependence of hydrogen embrittlement on annealing time in medium-Mn steels
Authors: Xu Juanping , Li Jinxu , Wang Zheng , Fu Hao , Wu Ming
Published: September 2021

Purpose

The purpose of this paper is to investigate the effect of the soft annealing time on the microstructure and hydrogen embrittlement (HE) of Fe-0.22C-11.54Mn-2.05Al steels.

Design/methodology/approach

Steels A and B with different morphologies were prepared by cold rolling after warm rolling, long/short softening annealing and finally annealing at 700 °C for 30 min. Uncharged and charged samples were subjected to tensile, and HE behavior was studied by electron backscattered diffraction, scanning electron microscopy and X-ray diffraction.

Findings

The two samples exhibited similar tensile strengths. The homogeneous equiaxed microstructure of steel B was found to be more conducive to relieve its HE sensitivity. Steel A exhibited bimodal-grained microstructures – blocky and lath. The formation of crack in the blocky grains of steel A resulted in a significant reduction in its plasticity and tensile strength.

Originality/value

The high HE susceptibility of steel A is mainly connected with the inhomogeneity of martensite transformation.
An investigation on cutting of the cold work steel X153CrMoV12 by WEDM
Authors: Ceritbinmez Ferhat
Published: September 2021

Purpose

Wire electric discharge machining (WEDM) is a non-conventional machining process, which is used for cutting parts of civil and military aircraft, rotorcraft, satellites and spacecraft. The cold work steel X153CrMoV12 is used in molds that are needed to produce plastic and metal parts used in these areas. It is only possible to produce parts with precise dimensions and quality with the use of mold steels with sensitive surfaces. The purpose of this study is to analyze X153CrMoV12 material by cutting it with WEDM method in precise dimensions.

Design/methodology/approach

The effects of varying cutting parameters on the size of the finished product, surface roughness (SR) and surface hardness were determined by making rough in one pass and precision cuts in different passes. Nikon SMZ745T, Mitutoyo micrometer, Mitutoyo SJ-210 and Insize ISHL-P100 were used for macro-analysis, dimensional control, SR and surface hardness, respectively, to determine the cut qualities.

Findings

According to the hardness measurement results obtained from the steel surface before cutting and from the cut surfaces after cutting, there was no significant change in the surface hardness owing to the use of heat-treated steel. Increasing the wire tension as a result of the increase in the number of cutting passes and the decrease in the amount of rough stock left for the final cut increased the cut quality. Cutting precision has increased by preventing vibration of the wire with zero upper and lower water pressure required for slag cleaning.

Originality/value

There are many studies on WEDM in the literature, but there is no similar study emphasizing the importance of the processing parameters such as the number of cutting passes and rough stock amount. In this study, cold work steel with a hardness of 56–60 HRC was machined as rough cut in one pass, rough and fine cut in double pass, double fine cut after one roughing in three passes. As a result of the cuts, 3 µm measurement precision and 0.998 Ra SR were obtained as well as there was no hardness change in the cut surfaces.
A review of experimental techniques to predict aircraft spin and recovery characteristics
Authors: Malik Bilal , Masud Jehanzeb , Akhtar Suhail
Published: September 2021

Purpose

This paper aims to provide a detailed review of the experimental research on the prediction of aircraft spin and recovery characteristics using dynamically scaled aircraft models.

Design/methodology/approach

The paper organizes experimental techniques to predict aircraft spin and recovery characteristics into three broad categories: dynamic free-flight tests, dynamic force tests and a relatively novel technique called wind tunnel based virtual flight testing.

Findings

After a thorough review, usefulness, limitations and open problems in the presented techniques are highlighted to provide a useful reference to researchers. The area of application of each technique within the research scope of aircraft spin is also presented.

Originality/value

Previous reviews on the prediction of aircraft spin and recovery characteristics were published many years ago and also have confined scope as they address particular spin technologies. This paper attempts to provide a comprehensive review on the subject and fill the information void regarding the state of the art aircraft spin technologies.
Impacts of inflation on gold price and exchange rate in Vietnam: time-varying vs fixed coefficient cointegrations
Authors: Long Pham Dinh , Hien Bui Quang , Ngoc Pham Thi Bich
Published: September 2021

Purpose

The paper aims to shed light on the effects of inflation on gold price and exchange rate in Vietnam by using time-varying cointegration.

Design/methodology/approach

Using cointegration techniques with fixed coefficient and time-varying coefficient, the study exams the impacts of inflation in models and compares the results through coefficient estimates.

Findings

A significant inflation impacts are found with the time-varying cointegration but not with the fixed coefficient cointegration models. Moreover, monetary policy affects exchange rate not only directly via its instruments as money supply and interest rate but indirectly via inflation. Also, interest rate is one of the determinants of gold price.

Originality/value

To the best of our knowledge, this paper is the first to use time-varying cointegration to analyze the impact of inflation on the gold price and exchange rate in Vietnam. Gold price and exchange rate fluctuations are always the essential and striking issues, which have been emphasized by economists and policymakers. In macroeconometric researches, cointegration models are often used to analyze the long-term relations between variables. Attentionally, applied models show a limitation when estimating coefficients are fixed. This characteristic might not really match with the data properties and the variation of the economy. Currently, time-varying cointegration models are emerging method to solve the above issue.