bluuebunny/crossref_metadata_2025 huggingface dataset:
Arabidopsisand Maize Terminator Strength is Determined by GC Content, Polyadenylation Motifs and Cleavage Probability
Authors: Gorjifard Sayeh , Jores Tobias , Tonnies Jackson , Mueth Nicholas A , Bubb Kerry , Wrightsman Travis , Buckler Edward S , Fields Stanley , Cuperus Josh T , Queitsch Christine
Published: June 2023

The 3’ end of a gene, often called a terminator, modulates mRNA stability, localization, translation, and polyadenylation. Here, we adapted Plant STARR-seq, a massively parallel reporter assay, to measure the activity of over 50,000 terminators from the plantsArabidopsis thalianaandZea mays. We characterize thousands of plant terminators, including many that outperform bacterial terminators commonly used in plants. Terminator activity is species-specific, differing in tobacco leaf and maize protoplast assays. While recapitulating known biology, our results reveal the relative contributions of polyadenylation motifs to terminator strength. We built a computational model to predict terminator strength and used it to conductin silicoevolution that generated optimized synthetic terminators. Additionally, we discover alternative polyadenylation sites across tens of thousands of terminators; however, the strongest terminators tend to have a dominant cleavage site. Our results establish features of plant terminator function and identify strong naturally occurring and synthetic terminators.
Characterization of novel fungal-algal symbiosis on LDPE plastic surfaces in the Mediterranean Sea
Authors: Itzahri Sheli , Davidov Keren , Oren Matan
Published: June 2023

Plastic debris in the ocean serves as a stable ground for the formation of a complex ecosystem, termed plastisphere, which includes a variety of organisms from different taxonomic groups. Not much is known about the relationships between the organisms of the plastisphere communities. In this study we describe a novel symbiotic relationship between a marine fungus and several species of diatoms on plastic surfaces that were submerged in the water of a Mediterranean Sea marina in Israel. Scanning electron microscope images of the surfaces revealed a network of fungal hyphae with multiple diatom cells attached to them via the side or the tip of their body. Using DNA metabarcoding for the fungal Internal Transcribed Spacer (ITS) barcode locus, we found that the symbiotic fungus belongs to the phylum Ascomycota, and that it is more abundant on low density polyethylene (LDPE) surfaces compared to other plastic polymers and glass. We hypothesize that the observed symbiotic relationship may have mutual benefits for both parties, including surface-anchoring for the diatoms and nutritional benefits for the fungus, that reflects a recent adaptation for life on floating plastic debris.
Cellular Iron Deficiency Disrupts Thyroid Hormone Regulated Gene Expression in Developing Hippocampal Neurons
Authors: Monko Timothy R. , Tripp Emma H. , Burr Sierra E. , Gunderson Karina N. , Lanier Lorene M. , Georgieff Michael K. , Bastian Thomas W.
Published: June 2023

Background

Developing neurons have high thyroid hormone and iron requirements to support their metabolism and growth. Early-life iron and thyroid hormone deficiencies are prevalent, often coexist, and increase the risk of permanently impaired neurobehavioral function in children. Early-life dietary iron deficiency reduces thyroid hormone levels and impairs thyroid hormone-responsive gene expression in the neonatal rat brain.

Objective

This study determined whether neuronal-specific iron deficiency alters thyroid hormone-regulated gene expression in developing neurons.

Methods

Iron deficiency was induced in primary mouse embryonic hippocampal neuron cultures with the iron chelator deferoxamine (DFO) beginning at 3 days in vitro (DIV). At 11DIV and 18DIV, mRNA levels for thyroid hormone-regulated genes indexing thyroid hormone homeostasis (Hr,Crym,Dio2,Slco1c1,Slc16a2) and neurodevelopment (Nrgn,Pvalb,Klf9) were quantified. To assess the effect of iron repletion, DFO was removed at 14DIV from a subset of DFO-treated cultures and gene expression and ATP levels were quantified at 21DIV.

Results

At 11DIV and 18DIV, neuronal iron deficiency decreasedNrgn, Pvalb,andCrym, and by 18DIV,Slc16a2, Slco1c1, Dio2,andHrwere increased; collectively suggesting cellular sensing of a functionally abnormal thyroid hormone state. Dimensionality reduction with Principal Component Analysis (PCA) reveals that thyroid hormone homeostatic genes strongly correlate with and predict iron status (Tfr1mRNA). Iron repletion from 14–21DIV restored neurodevelopmental genes, but not all thyroid hormone homeostatic genes, and ATP concentrations remained significantly altered. PCA clustering suggests that cultures replete with iron maintain a gene expression signature indicative of previous iron deficiency.

Conclusions

These novel findings suggest there is an intracellular mechanism coordinating cellular iron/thyroid hormone activities. We speculate this is a part of homeostatic response to match neuronal energy production and growth signaling for these important metabolic regulators. However, iron deficiency may cause permanent deficits in thyroid hormone-dependent neurodevelopmental processes even after recovery from iron deficiency.
THUMPD2 catalyzesN2-methylation on the spliceosome catalytic center of U6 snRNA and regulates pre-mRNA splicing
Authors: Yang Wen-Qing , Ge Jian-Yang , Zhang Xiao-Feng , Lin Lin , Zhu Wen-Yu , Shi Yi-Gong , Xu Bei-Si , Liu Ru-Juan
Published: June 2023

How the relatively evolutionarily conserved spliceosome is able to manage the enormously expanded number of splicing events that occur in humans (∼200,000 vs. ∼400 reported for yeast) is not well understood. Here, we show deposition of one RNA modification-N2-methylguanosine (m2G)-on the G72 nucleoside of U6 snRNA (known to function as the catalytic center of the spliceosome) results in profoundly increased pre-mRNA splicing activity in human cells. This U6 m2G72 modification is conserved among vertebrates. Further, we demonstrate that THUMPD2 is the methyltransferase responsible for U6 m2G72 and show that it interacts with an auxiliary protein (TRMT112) to specifically recognize both sequence and structural elements of U6.THUMPD2KO blocks U6 m2G72 and down-regulates the pre-mRNA splicing activity of major spliceosome, yielding thousands of changed alternative splicing events of endogenous pre-mRNAs. Notably, the aberrantly spliced pre-mRNA population of theTHUMPD2KO cells elicits the nonsense-mediated mRNA decay (NMD) pathway and restricts cell proliferation. Our study thus demonstrates how an RNA epigenetic modification of the major spliceosome differentially regulates global pre-mRNA splicing.
The mitochondrial calcium uniporter transports Ca2+via a ligand-relay mechanism
Authors: Chan Connie , Yuan Chen-Ching , McCoy Jason G. , Ward Patrick S. , Grabarek Zenon
Published: June 2023

The mitochondrial calcium uniporter (mtCU) is a multicomponent Ca2+-specific channel that imparts mitochondria with the capacity to sense the cytosolic calcium signals. The metazoan mtCU comprises the pore-forming subunit MCU and the essential regulator EMRE, arranged in a tetrameric channel complex, and the Ca2+sensing peripheral proteins MICU1-3. The mechanism of mitochondrial Ca2+uptake by mtCU and its regulation is poorly understood. Our analysis of MCU structure and sequence conservation, combined with molecular dynamics simulations, mutagenesis, and functional studies, led us to conclude that the Ca2+conductance of MCU is driven by a ligand-relay mechanism, which depends on stochastic structural fluctuations in the conserved DxxE sequence. In the tetrameric structure of MCU, the four glutamate side chains of DxxE (the E-ring) chelate Ca2+directly in a high-affinity complex (site 1), which blocks the channel. The four glutamates can also switch to a hydrogen bond-mediated interaction with an incoming hydrated Ca2+transiently sequestered within the D-ring of DxxE (site 2), thus releasing the Ca2+bound at site 1. This process depends critically on the structural flexibility of DxxE imparted by the adjacent invariant Pro residue. Our results suggest that the activity of the uniporter can be regulated through the modulation of local structural dynamics.

A preliminary account of this work was presented at the 67thAnnual Meeting of the Biophysical Society in San Diego, CA, February 18-22, 2023
IsEEG is better left alone?
Authors: de Cheveigné Alain
Published: June 2023

A recent article (Delorme, A., 2023, EEG is better left alone.Scientific Reports,13, 2372.https://doi.org/10.1038/s41598-023-27528-0) proposed a metric to determine the benefit of applying pre-processing methods to EEG data. Using that metric, it concluded that most pre-processing methods donotimprove data quality. The question is revisited in this short paper, using a sample of the same data as used by that paper. It is argued that the metric is of limited applicability, and that in some situations pre-processing might be critical to make good use of the data.

Note: This paper was submitted to Scientific Reports as a commentary to the paper cited and rejected without review.
Liquid Transmission Electron Microscopy for Probing Collagen Biomineralization
Authors: DiCecco Liza-Anastasia , Gao Ruixin , Gray Jennifer L. , Kelly Deborah F. , Sone Eli D. , Grandfield Kathryn
Published: June 2023

Collagen biomineralization is foundational to hard tissue assembly. While studied extensively, collagen mineralization processes are not fully understood as the majority of theories are derived from electron microscopy (EM) in static, dehydrated, or frozen conditions, unlike the liquid phase environment where mineralization occurs dynamically. Herein, novel liquid transmission EM (TEM) strategies are presented, where collagen mineralization was explored in liquid conditions for the first time. Custom thin-film enclosures were employed to visualize the mineralization of reconstituted collagen fibrils in a calcium-phosphate and polyaspartic acid solution to promote intrafibrillar mineralization. TEM highlighted that at early time points, precursor mineral particles attached to collagen and progressed to crystalline mineral platelets aligned with fibrils at later time points. This aligns with observations from other techniques and validates this liquid TEM approach. This work provides a new liquid imaging approach for exploring collagen biomineralization, advancing toward understanding disease pathogenesis and remineralization strategies for hard tissues.
WAS IT A MATch I SAW? Approximate palindromes lead to overstated false match rates in benchmarks using reversed sequences
Authors: Glidden-Handgis George , Wheeler Travis J.
Published: June 2023

Background

Software for labeling biological sequences typically produces a theory-based statistic for each match (the E-value) that indicates the likelihood of seeing that match’s score by chance. E-values accurately predict false match rate for comparisons of random (shuffled) sequences, and thus provide a reasoned mechanism for setting score thresholds that enable high sensitivity with low expected false match rate. This threshold-setting strategy is challenged by real biological sequences, which contain regions of local repetition and low sequence complexity that cause excess matches between non-homologous sequences. Knowing this, tool developers often develop benchmarks that use realistic-seeming decoy sequences to explore empirical tradeoffs between sensitivity and false match rate. A recent trend has been to employ reversed biological sequences as realistic decoys, because these preserve the distribution of letters and the existence of local repeats, while disrupting the original sequence’s functional properties. However, we and others have observed that sequences appear to produce high scoring alignments to their reversals with surprising frequency, leading to overstatement of false match risk that may negatively effect downstream analysis.

Results

We demonstrate that an alignment between a sequence S and its (possibly mutated) reversal tends to produce higher scores than alignment between truly unrelated sequences, even when S is a shuffled string with no notable repetitive or low-complexity regions. This phenomenon is due to the unintuitive fact that (even randomly shuffled) sequences contain palin-dromes that are on average longer than the longest common substrings shared between permuted variants of the same sequence. Though the expected palindrome length is only slightly larger than the expected longest common substring, the distribution of alignment scores involving reversed sequences is strongly right-shifted, leading to greatly increased frequency of high-scoring alignments to reversed sequences.

Impact

Overestimates of false match risk can motivate unnecessarily high score thresholds, leading to potentially reduced true match sensitivity. Also, when tool sensitivity is only reported up to the score of the first matched decoy sequence, a large decoy set consisting of reversed sequences can obscure sensitivity differences between tools. As a result of these observations, we advise that reversed biological sequences be used as decoys only when care is taken to remove positive matches in the original (un-reversed) sequences, or when overstatement of false labeling is not a concern. Though the primary focus of the analysis is on sequence annotation, we also demonstrate that the prevalence of internal palindromes may lead to an overstatement of the rate of false labels in protein identification with mass spectrometry.
Particle size distribution shift and diurnal concentration changes of environmental DNA caused by fish spawning behaviour
Authors: Tsuji Satsuki , Shibata Naoki
Published: June 2023

Spawning is one of the most significant aspects of fish life history, so understanding spawning is critical for the conservation and management of species. Recently, an efficient and non-invasive spawning detection method for spawning behaviour has been proposed, utilising the increased environmental DNA (eDNA) concentration and nuclear/mitochondrial eDNA ratio associated with fish spawning. However, little is known about the characteristics and dynamics of sperm-derived eDNA, which is key to detection. This study focused on changes in eDNA particle size distribution (PSD) and concentrations pre-, post-, and during spawning of Ayu,Plecoglossus altivelis. Firstly, PSD changes between pre- and post-spawning were investigated by comparing concentrations and proportions of eDNA obtained from filters with different pore sizes. Secondly, the diurnal changes in eDNA concentration were monitored at the peak of the spawning season by collecting river water every one or three hours. Results showed that eDNA related to sperm-head size increased at post-spawning, and eDNA concentrations had significant diurnal changes with a peak during the spawning time window. These findings suggest that semi-selective recovery of sperm-derived eDNA based on particle size and/or sampling during the spawning time window with increased concentrations can improve the detection sensitivity of eDNA-based spawning surveys. This study provides essential basic information for advancing eDNA-based spawning surveys and contributes to their further development.
Multicenter analysis of COVID-19 hospitalizations and stacking machine learning algorithms for prediction of high-risk patients
Authors: Shaw Reid , Bassily David , Patel Love , O’Connor Timothy , Rafidi Robert , Formanek Perry
Published: June 2023

Objective

To create and validate an ensemble of machine learning algorithms to accurately predict ICU admission or mortality upon initial presentation to the emergency department.

Methods

This is a retrospective cohort study of a multicenter hospital system in the United States. The electronic health record was queried from March 2020 to December 2021 for patients who presented to the emergency department who were subsequently COVID-positive. Associated patient demographics, vitals, and laboratory vitals were obtained. High-risk individuals were defined as those who required ICU admission or died; low-risk individuals did not meet those criteria. The dataset was split into a 3:1 training to testing dataset. A machine learning ensemble stack was built to predict ICU admission and mortality.

Results

Of the 3,142 hospital admissions with a COVID positive test, there were 1,128 (36%) individuals labeled as high-risk, and 2,014 (64%) as low-risk. We obtained 147 unique variables. CRP, LDH, procalcitonin, glucose, anion gap, creatinine, age, oxygen saturation, oxygen device, and obtainment of an ABG were chosen. Six machine learning models were then trained over model-specific hyperparameters, and then assessed on the testing dataset, generating an area under the receiver operator curve of 0.751, with a specificity of 95% in predicting high-risk individuals based on an initial emergency department assessment.

Conclusion

A novel machine learning model was generated to predict ICU admission and patient mortality from a multicenter hospital system and validated on unseen data.
GATA1-defective immune-megakaryocytes as possible drivers of idiopathic pulmonary fibrosis
Authors: Gobbo Francesca , Zingariello Maria , Verachi Paola , Falchi Mario , Arciprete Francesca , Martelli Fabrizio , Peli Angelo , Mazzarini Maria , Vierstra Jeff , Mead-Harvey Carolyn , Dueck Amylou C. , Sarli Giuseppe , Nava Stefano , Sgalla Giacomo , Richeldi Luca , Migliaccio Anna Rita
Published: June 2023

Idiopathic pulmonary fibrosis (IPF) is a progressive fibrotic lung disorder with limited therapeutic options. Insufficient understanding of driver mutations and poor fidelity of currently available animal models has limited the development of effective therapies. Since GATA1 deficient megakaryocytes sustain myelofibrosis, we hypothesized that they may also induce fibrosis in lungs. We discovered that lungs from IPF patients andGata1lowmice contain numerous GATA1negative immune-poised megakaryocytes that, in mice, have defective RNA-seq profiling and increased TGF-β1, CXCL1 and P-selectin content. With age,Gata1lowmice develop fibrosis in lungs. Development of lung fibrosis in this model is prevented byP-selectindeletion and rescued by P-selectin, TGF-β1 or CXCL1 inhibition. Mechanistically, P-selectin inhibition decreases TGF-β1 and CXCL1 content and increases GATA1positive megakaryocytes while TGF-β1 or CXCL1 inhibition decreased CXCL1 only. In conclusion,Gata1lowmice are a novel genetic-driven model for IPF and provide a link between abnormal immune-megakaryocytes and lung fibrosis.
Sustained polyphasic sleep restriction abolishes human growth hormone release
Authors: Rosenblum Yevgenia , Weber Frederik D. , Rak Michael , Zavecz Zsófia , Kunath Nicolas , Breitenstein Barbara , Rasch Björn , Zeising Marcel , Uhr Manfred , Steiger Axel , Dresler Martin
Published: June 2023

Voluntary sleep restriction is a common phenomenon in industrialized societies aiming to increase time spent awake and thus productivity. We explored how restricting sleep to a radically polyphasic schedule affects neural, cognitive, and endocrine characteristics. Ten young healthy participants were restricted to one 30-min nap opportunity at the end of every 4 hours (i.e., 6 sleep episodes per 24 hours) without any extended core sleep window, which resulted in a cumulative sleep amount of just 2 hours per day (i.e., ∼20 min per bout). All but one participant terminated this schedule during the first three weeks. The remaining participant (a 25-year-old male) succeeded to adhere to a polyphasic schedule for 5 weeks with no apparent impairments in cognitive and psychiatric measures except for psychomotor vigilance. While in-blood cortisol or melatonin release pattern and amounts were unaltered by the polyphasic as compared to monophasic sleep, growth hormone seemed almost entirely abolished (>95% decrease), with the residual release showing a considerably changed polyphasic secretional pattern. While coarse sleep structure appeared intact during polyphasic sleep, REM sleep showed decreased oscillatory and increased aperiodic EEG activity compared to monophasic sleep. Considering the decreased vigilance, abolished growth hormone release, and neurophysiological changes observed, it is doubtful that radically polyphasic sleep schedules can subserve the different functions of sleep to a sufficient degree.
Inactivation of face selective neurons alters eye movements when free viewing faces
Authors: Azadi Reza , Lopez Emily , Taubert Jessica , Patterson Amanda , Afraz Arash
Published: June 2023

During free viewing, faces attract gaze and induce specific fixation patterns corresponding to the facial features. This suggests that neurons encoding the facial features are in the causal chain that steers the eyes. However, there is no physiological evidence to support a mechanistic link between face encoding neurons in high-level visual areas and the oculomotor system. In this study, we targeted the middle face patches of inferior temporal (IT) cortex in two macaque monkeys using an fMRI localizer. We then utilized muscimol microinjection to unilaterally suppress IT neural activity inside and outside the face patches and recorded eye movements while the animals free viewing natural scenes. Inactivation of the face selective neurons altered the pattern of eye movements on faces: the monkeys found faces in the scene but neglected the eye contralateral to the inactivation hemisphere. These findings reveal the causal contribution of the high-level visual cortex in eye movements.

Significance

It has been shown, for more than half a century, that eye movements follow distinctive patterns when free viewing faces. This suggests causal involvement of the face-encoding visual neurons in the eye movements. However, the literature is scant of evidence for this possibility and has focused mostly on the link between low-level image saliency and eye movements. Here, for the first time, we bring causal evidence showing how face-selective neurons in inferior temporal cortex inform and steer eye movements when free viewing faces.
Polyploidy enhances desiccation tolerance in the grassMicrochloa caffra
Authors: Marks Rose A. , Delgado Paula , Makonya Givemore Munashe , Cooper Keren , VanBuren Robert , Farrant Jill M.
Published: June 2023

Desiccation tolerance evolved recurrently across diverse plant lineages to enable survival in water limited conditions. Many resurrection plants are polyploid and several groups have hypothesized that polyploidy enabled the evolution of desiccation tolerance. However, due to the vast evolutionary divergence between resurrection plant lineages, the rarity of desiccation tolerance, and the prevalence of polyploidy in plants, this hypothesis has been difficult to test. Here, we surveyed variation in morphological, reproductive, and desiccation tolerance traits across natural populations of a single species that has differing ploidies and tested for links between polyploidy and resilience. We sampled multiple populations of the resurrection grassMicrochloa caffraacross an environmental gradient ranging from mesic to xeric in South Africa. We describe two distinct ecotypes ofM. caffrathat occupy different ends of the environmental gradient and exhibit consistent differences in ploidy, morphological, reproductive, and desiccation tolerance traits in both field and common growth conditions. Interestingly, plants with more polyploid genomes were consistently more desiccation tolerant, less reproductive, and larger than plants with smaller genomes and lower ploidy. These data suggest that polyploidy enhances desiccation tolerance and that stronger selective pressures in increasingly xeric sites may play a role in maintaining and increasing desiccation tolerance.
QuantUMS: uncertainty minimisation enables confident quantification in proteomics
Authors: Kistner Franziska , Grossmann Justus L. , Sinn Ludwig R. , Demichev Vadim
Published: June 2023

Mass spectrometry-based proteomics has been rapidly gaining traction as a powerful analytical method both in basic research and translation. While the problem of error control in peptide and protein identification has been addressed extensively, the quality of the resulting quantities remains challenging to evaluate. Here we introduce QuantUMS (Quantification using anUncertaintyMinimisingSolution), a machine learning-based method which minimises errors and eliminates bias in peptide and protein quantification by integrating multiple sources of quantitative information. In combination with data-independent acquisition proteomics, QuantUMS boosts accuracy and precision of quantities, as well as reports an uncertainty metric, enabling effective filtering of data for downstream analysis. The algorithm has linear complexity with respect to the number of mass spectrometry acquisitions in the experiment and is thus scalable to infinitely large proteomic experiments. For an easy implementation in a proteomics laboratory, we integrate QuantUMS in our automated DIA-NN software suite.
The landscape of microRNA interactions annotation: analysis of three rare disorders as case study
Authors: Simona Panni , Panneerselvam Kalpana , Porras Pablo , Duesbury Margaret , Perfetto Livia , Licata Luana , Hermjakob Henning , Orchard Sandra
Published: June 2023

In recent years, a huge amount of data on ncRNA interactions has been described in scientific papers and databases. Although considerable effort has been made to annotate the available knowledge in public repositories, there are still significant discrepancies in how different resources capture and interpret data on ncRNAs functional and physical associations.

In the present paper, we have focused on microRNAs which regulate genes associated with rare diseases, as a case study to investigate data availability.

The list of protein-coding genes with a known role in specific rare diseases was retrieved from the Genome England PanelApp, and associated microRNA-mRNA interactions were annotated in the IntAct database, and compared with other datasets. The annotation follows recognised standard criteria approved by the IMEX consortium. RNAcentral identifiers were used for unambiguous, stable identification of ncRNAs. The information about the interaction was enhanced by a detailed description of the cell types and experimental conditions, providing a computer-interpretable summary of the published data, integrated with the huge amount of protein interactions already gathered in the database. Furthermore, for each interaction, the binding sites of the microRNA are precisely mapped on a well-defined mRNA transcript of the target gene. This information is crucial to conceive and design optimal microRNA mimics or inhibitors, to interfere in vivo with a deregulated process. As these approaches become more feasible, high-quality, reliable networks of microRNA interactions are needed to help, for instance, in the selection of the best target to be inhibited and to predict potential secondary off-target effects.
Cathepsin B abundance, activity and microglial localisation in Alzheimer’s disease – Down syndrome and early onset Alzheimer’s disease; the role of elevated cystatin B
Authors: Wu Yixing , Mumford Paige , Noy Suzanna , Cleverley Karen , Mrzyglod Alicja , Luo Dinghao , van Dalen Floris , Verdoes Martijn , Fisher Elizabeth M.C. , Wiseman Frances K.
Published: June 2023

Cathepsin B is a cysteine protease that is implicated in multiple aspects of Alzheimer’s disease pathogenesis. The endogenous inhibitor of this enzyme, cystatin B (CSTB)is encoded on chromosome 21. Thus, individuals who have Down syndrome, a genetic condition caused by having an additional copy of chromosome 21, have an extra copy of an endogenous inhibitor of the enzyme. Individuals who have Down syndrome are also at significantly increased risk of developing early-onset Alzheimer’s disease (EOAD). The impact of the additional copy of cystatin B (CSTB)on Alzheimer’s disease development in people who have Down syndrome is not well understood. Here we compared the biology of cathepsin B and cystatin B (CSTB) in individuals who had Down syndrome and Alzheimer’s disease, with disomic individuals who had Alzheimer’s disease or were ageing healthily. We find that the activity of cathepsin B enzyme is decreased in the brain of people who had Down syndrome and Alzheimer’s disease compared with disomic individuals who had Alzheimer’s disease. This change occurs independently of an alteration in the abundance of the mature enzyme or the number of cathepsin B+cells. We find that the abundance of cystatin B (CSTB) is significantly increased in the brains of individuals who have Down syndrome and Alzheimer’s disease compared to disomic individuals both with and without Alzheimer’s disease and we go on to investigate how this impacts enzyme activity in mouse and human cellular preclinical models of Down syndrome.
Chance favors the prepared genomes: horizontal transfer shapes the emergence of antibiotic resistance mutations in core genes
Authors: Coluzzi Charles , Guillemet Martin , Mazzamurro Fanny , Touchon Marie , Godfroid Maxime , Achaz Guillaume , Glaser Philippe , Rocha Eduardo PC
Published: June 2023

Bacterial lineages vary in the frequency with which they acquire novel traits, like antibiotic resistance or virulence. While previous studies have highlighted the impact of the genetic background on the successful acquisition of novel traits through horizontal gene transfer, the impact of the latter on the subsequent evolution of bacterial genomes by point mutations remains poorly understood. Here, we studied the evolution of resistance to quinolones in thousands ofEscherichia coligenomes. Resistance-conferring point mutations in the core genes are frequent and accumulate very quickly. We searched for gene gains and losses significantly associated with the subsequent acquisition of these resistance mutations. This revealed 60 groups of genes in genetic linkage whose gain or loss induced a change in the probability of subsequently becoming resistant to quinolones by point mutations ingyrAandparC. Although some of these chronologies may reflect epidemiological trends, most of these groups encoded functions that were previously associated with antibiotic resistance, tolerance, or persistence, often specifically under quinolone treatment. A lot of the largest groups were found in prophages or plasmids, and they usually increased the likelihood of subsequent resistance mutations. Conversely groups of lost genes were typically small and chromosomal. Quinolone resistance was among the first resistances acquired in the extant lineages ofE. coliand its acquisition was associated with an increased likelihood of acquiring other types of resistances, including to aminoglycosides and beta-lactams. Our findings suggest that gene flow shapes the subsequent fixation rate of adaptive mutations in core genes. Given the substantial gene flow within bacterial genomes, interactions between horizontal transfer and point mutations in core genes may be key to the success of adaptation processes.
Use of Recommended Real-World Methods for Electronic Health Record Data Analysis Has Not Improved Over 10 Years
Authors: Li Chenyu , Alsheikh Abdulrahman M. , Robinson Karen A. , Lehmann Harold P.
Published: June 2023

Background and Purpose

To document the use of recommended Real-World Methods (RWM) in Electronic Health Record (EHR)-based analysis in biomedical research over 10 years.

Methods

Sampled-article scoping review of methods used in EHR-based biomedical research. We developed a search strategy to identify reports of biomedical research based on EHR data and systematically sampled articles from different ranges of years (epochs) between 2010 and 2019 to establish a trajectory of use of recommended RWM. Methods were classified by 3 phases of research: pre-analytic (missing data), analytic (specific methods), and post-analytic (sensitivity analysis). The primary outcome was the proportion of studies using recommended RWM within each epoch. Meta-regressions were performed to examine trends.

Data Synthesis

Five epochs were defined between 2010 and 2019 with 35 studies selected per epoch as pre-defined by a sample size calculation. Of the 175 articles reviewed, 70 (40.%) reported recommended RWM in any of the 3 phases of research. The breakdown for the most recent year in the dataset, 2019, was 14.% (95% confidence interval 2.7%, 26.%), 14.% (2.7%, 26.%), and 11.% (0.89%, 22.%), for assessing missing data, using specific methods, and performing sensitivity analysis, respectively. Only 3.4 % of studies used appropriate methods for each phase of research. Meta-regression slopes for each of the three phases were statistically 0.

Limitation and Conclusions

The underuse of recommended Real-World Methods (RWM) in EHR-based biomedical research remains a concern, with less than 50% of reports using these methods in any phase of research over the last decade. This lack of use indicates a continued risk of bias in the EHR-based literature.
Intrinsically disordered regions in the transcription factor MYC:MAX modulate DNA binding via intramolecular interactions
Authors: Schütz Stefan , Bergsdorf Christian , Hänni-Holzinger Sandra , Lingel Andreas , Renatus Martin , Gossert Alvar D. , Jahnke Wolfgang
Published: June 2023

The basic helix-loop-helix leucine zipper (bHLH-LZ) transcription factor (TF) MYC is in large parts an intrinsically disordered oncoprotein. In complex with its obligate heterodimerization partner MAX, MYC preferentially binds E-Box DNA sequences (CANNTG). At promotors containing these sequence motifs, MYC controls fundamental cellular processes such as cell cycle progression, metabolism, and apoptosis. A vast network of proteins controls MYC function via intermolecular interactions. In this work, we establish another layer of MYC regulation by intramolecular interactions. We use Nuclear Magnetic Resonance (NMR) spectroscopy to identify and map multiple binding sites for the C-terminal MYC:MAX DNA binding domain (DBD) on the intrinsically disordered regions (IDRs) in the MYC N-terminus. We find that these binding events intransare driven by electrostatic attraction, that they have distinct affinities, and that they are competitive with DNA binding. Thereby, we observe the strongest effects for the N-terminal MYC box 0 (Mb0), a conserved motif involved in MYC transactivation and target gene induction. We prepared recombinant full-length MYC:MAX complex and demonstrate that the interactions identified in this work are also relevant incis, i.e. as intramolecular interactions. These findings are supported by Surface Plasmon Resonance (SPR) experiments, which revealed that intramolecular IDR:DBD interactions in MYC decelerate the association of MYC:MAX complexes to DNA. Our work offers new insights how bHLH-LZ TFs are regulated by intramolecular interactions, which opens up new possibilities for drug discovery.
The widespread influence of ZSWIM8 on microRNAs during mouse embryonic development
Authors: Shi Charlie Y. , Elcavage Lara E. , Chivukula Raghu R. , Stefano Joanna , Kleaveland Benjamin , Bartel David P.
Published: June 2023

MicroRNAs (miRNAs) pair to sites in mRNAs to direct the degradation of these RNA transcripts. Conversely, certain RNA transcripts can direct the degradation of particular miRNAs. This target-directed miRNA degradation (TDMD) requires the ZSWIM8 E3 ubiquitin ligase. Here, we report the function of ZSWIM8 in the mouse embryo.Zswim8−/−embryos were smaller than their littermates and died near the time of birth. This highly penetrant perinatal lethality was apparently caused by a lung sacculation defect attributed to failed maturation of alveolar epithelial cells. Some mutant individuals also had heart ventricular septal defects. These developmental abnormalities were accompanied by aberrant accumulation of >50 miRNAs observed across 12 tissues, which often led to enhanced repression of their mRNA targets. These ZSWIM8-sensitive miRNAs were preferentially produced from genomic miRNA clusters, and in some cases, ZSWIM8 caused a switch in the dominant strand that accumulated from a miRNA hairpin—observations suggesting that TDMD provides a mechanism to uncouple co-produced miRNAs from each other. Overall, our findings indicate that the regulatory influence of TDMD in mammalian biology is widespread and posit the existence of many yet-unidentified transcripts that trigger miRNA degradation.
Revisiting annotation ofSchistosoma mansoniMicro-Exon Gene (MEG) family
Authors: Nedvedova Stepanka , De Stefano Davide , Walker Olivier , Hologne Maggy , Miele Adriana Erica
Published: June 2023

Genome sequencing of the human parasiteSchistosoma mansonirevealed an interesting gene superfamily calledmicro-exon gene(MEG) that encodes MEG secreted proteins. The genes are composed of short exons (3-81 base pairs) with symmetrically inserted long introns (up to 5 kbp). This article recollects 35S. mansonispecificmeggenes that are distributed over 7 autosomes and one pair of sex chromosomes and that code for at least 87 verified MEG proteins. We used various bioinformatics tools to produce an optimal alignment, propose a phylogenetic analysis and highlight intriguing conserved patterns/motifs in the sequences of these MEG proteins. Based on the analyses, we were able to classify the MEG proteins into two subfamilies and to hypothesize their duplication and colonization of all the chromosomes. Together with motif identification, we also proposed to revisit MEGs’ common names and annotation in order to avoid duplication, to help reproducibility of research results and to avoid possible misunderstandings.

Author Abstract

Schistosoma mansoniis a parasitic worm, the etiological agent of schistosomiasis or bilharzia, a chronic tropical disease. It is a vector-borne parasite with a complex life cycle and an equally complex genome, assembled in 7 autosomes and a pair of sexual chromosomes. Within the gene products, one superfamily is particularly interesting, since it is specific toSchistosomatidae, highly variable and redundant: the micro-exon gene (MEG) family. As the name implies, these genes are made by short coding exons (3 to 81 base pairs), symmetrically interspersed by long introns (from 0.2 to 5 kbp). There are 35megsallover the chromosomes, which code for at least 87 MEG proteins. We have aligned all of them, constructed a phylogenetic tree and proposed a theory for their duplication and genome colonization. Based on that, we propose a rational nomenclature to help the community to study MEG’s elusive role. We also propose to help WormBaseParaSite to adopt this new nomenclature to avoid giving the same acronym to different protein sequences.
Kinetics of zoospores approaching a root using a microfluidic device
Authors: Cohen C , Gauci FX , Noblin X , Galiana E , Attard A , Thomen P
Published: June 2023

Phytophthoraspecies are plant pathogens that cause considerable damage to agrosystems and ecosystems, and have a major impact on the economy. Infection occurs when their biflagellate zoospores move and reach a root on which they aggregate. However, the communication between the plant and the zoospores and how this communication modifies the behavior of the swimming zoospores is not yet well characterized. Here we show that using a microfluidic device comprising a growingArabidopsis thalianaroot, we are able to study the kinetics ofPhytophthora parasiticazoospores approaching the root and aggregating on a specific area, in real time. We show that the kinetics of zoospores is modified only below a distance of about 300μm from the center of aggregation, with a decrease in the speed coupled with an increase in the number of turns made. In addition, we show that the rate of aggregation is constant throughout the experiment, approximately one hour, and depends on the density of zoospores. The rate is consistent with a random encounter of zoospores with the root, indicating that no long range signal is evidenced in our set-up.
The Limits of Haplotype-Based Approaches: Exploring the Applicability of the Li and Stephens Haplotype-Copying Model to Ancient Samples
Authors: Cort Isabel Díaz-Pinés , Rubin Joshua Daniel , Sackett Peter Wad , Renaud Gabriel
Published: June 2023

The Li and Stephens (LS) haplotype-copying model is a seminal framework that represents a target haplotype as an imperfect mosaic of a set of reference haplotypes. Using a hidden Markov model, it can switch from different source haplotypes to model recombinations. This model has been used in several applications in modern populations including phasing and inference of ancestry. However, recent publications have looked at the applicability of the model to using ancient individuals as targets and modern reference panels as source data. Previous research exploring the impact of time separation between the modern references and the ancient target on the model’s behavior relied on coalescent simulation to generate genetic variation data, which could lead to an underestimation of the ancient population’s genetic diversity. Further, these simulations were restricted to a relatively short time period of anatomically modern human history. To overcome these limitations, our study evaluates the robustness of the LS model using forward-simulated data enabling us to sample haplotypes that do not have direct descendants among the modern population. Additionally, we evaluate the model under the simple demographic scenario of a constant-sized continuous population starting 1.5M years ago to isolate the effect of time separation. Results indicate good performance for target haplotypes up to 900,000 years old, suggesting potential applicability to ancient DNA (aDNA) from anatomically modern humans. Although more complex demographic scenarios should be considered for a definitive answer, this research serves as a starting point for evaluating the haplotype-copying framework in aDNA data analysis.
Major patterns in the introgression history ofHeliconiusbutterflies
Authors: Thawornwattana Yuttapong , Seixas Fernando A. , Yang Ziheng , Mallet James
Published: June 2023

Abstract

Gene flow between species is an important evolutionary process that can facilitate adaptation and lead to species diversification. It also makes reconstruction of species relationships difficult. Here, we use the full-likelihood multispecies coalescent (MSC) approach to estimate species phylogeny and major introgression events inHeliconiusbutterflies from whole-genome sequence data. We obtain a robust estimate of species branching order among major clades in the genus, including the “melpomene-silvaniform” group, which shows extensive historical and on-going gene flow. We obtain chromosome-level estimates of key parameters in the species phylogeny, including species divergence times, present-day and ancestral population sizes as well as the direction, timing, and intensity of gene flow. Our analysis leads to a phylogeny with introgression events that differ from those obtained in previous studies. We find thatH. aoedemost likely represents the earliest-branching lineage of the genus and that “silvaniform” species are paraphyletic within the melpomene-silvaniform group. Our phylogeny provides new, parsimonious histories for the origins of key traits inHeliconius, including pollen feeding and an inversion involved in wing pattern mimicry. Our results demonstrate the power and feasibility of the full-likelihood MSC approach for estimating species phylogeny and key population parameters despite extensive gene flow. The methods used here should be useful for analysis of other difficult species groups with high rates of introgression.
UVA hyperspectral light-sheet microscopy for volumetric metabolic imaging: application to pre-implantation embryo development
Authors: Morizet J. , Chow D. , Wijesinghe P. , Schartner E. , Dwapanyin G. , Dubost N. , Bruce G. D. , Anckaert E. , Dunning K. , Dholakia K.
Published: June 2023

Cellular metabolism is a key regulator of energetics, cell growth, regeneration and homeostasis. Spatially mapping the heterogeneity of cellular metabolic activity is of great importance for unraveling the overall cell and tissue health. In this regard, imaging the endogenous metabolic co-factors NAD(P)H and FAD with sub-cellular resolution and in a non-invasive manner would be useful to determine tissue and cell viability in a clinical environment, but practical use is limited by current imaging techniques. In this article, we demonstrate the use of phasor-based hyperspectral light-sheet (HS-LS) microscopy using a single UVA excitation wavelength as a route to mapping metabolism in three dimensions. We show that excitation solely at a UVA wavelength of 375 nm can simultaneously excite NAD(P)H and FAD autofluorescence, while their relative contributions can be readily quantified using a hardware-based spectral phasor analysis. We demonstrate the potential of our HS-LS system by capturing dynamic changes in metabolic activity during pre-implantation embryo development. To validate our approach, we delineate metabolic changes during pre-implantation embryo development from volumetric maps of metabolic activity. Importantly, our approach overcomes the need for multiple excitation wavelengths, two-photon imaging or significant post-processing of data, paving the way towards clinical translation, such as in situ, non-invasive assessment of embryo viability.
The impact of within-host coinfection interactions on between-host parasite transmission dynamics varies with spatial scale
Authors: Keegan Shaun P. , Pedersen Amy B. , Fenton Andy
Published: June 2023

Within-host interactions among coinfecting parasites can have major consequences for individual infection risk and disease severity. However, the impact of these within-host interactions on between-host parasite transmission, and the spatial scales over which they occur, remain unknown. We developed and apply a novel spatially-explicit analysis to parasite infection data from a wild wood mouse (Apodemus sylvaticus) population. We previously demonstrated a strong negative interaction within individual hosts gastrointestinal parasites, the nematodeHeligmosomoides polygyrusand the coccidiaEimeria hungaryensis, using drug-treatment experiments. Here, we find that this negative within-host interaction can significantly alter the between-host transmission dynamics ofE. hungaryensis, but only within spatially-restricted neighbourhoods around each host. However, for the closely-related speciesE. apionodes, which experiments show does not interact strongly withH. polygyrus, we did not find any effect on transmission over any spatial scale. Our results demonstrate that the effects of within-host coinfection interactions can ripple out beyond each host to alter the transmission dynamics of the parasites, but only over local scales that likely reflect the spatial dimension of transmission. Hence there may be knock-on consequences of drug treatments impacting the transmission of non-target parasites, altering infection risks even for non-treated individuals in the wider neighbourhood.