bluuebunny/crossref_metadata_2025 huggingface dataset:
Comprehensive Approach to Simulating Large Scale Conformational Changes in Biological Systems Utilizing a Path Collective Variable and New Barrier Restraint
Authors: Kolossváry István , Sherman Woody
Published: March 2023

Conformational sampling of complex biomolecules is an emerging frontier in drug discovery. Advances in lab-based structural biology and related computational approaches like AlphaFold have made great strides in obtaining static protein structures for biologically relevant targets. However, biology is in constant motion and many important biological processes rely on conformationally-driven events. Conventional molecular dynamics (MD) simulations run on standard hardware, are impractical for many drug design projects, where conformationally-driven biological events can take microseconds to milliseconds or longer. An alternative approach is to focus the search on a limited region of conformational space defined by a putative reaction coordinate (i.e. path collective variable). The search space is typically limited by applying restraints, which can be guided by insights about the underlying biological process of interest. The challenge is striking a balance between the degree to which the system is constrained while still allowing for natural motions along the path. A plethora of restraints exist to limit the size of conformational search space, although each has drawbacks when simulating complex biological motions. In this work, we present a three-stage procedure to construct realistic path collective variables (PCV), and introduce a new kind of barrier restraint that is particularly well suited for complex conformationally-driven biological events, such as allosteric modulations and conformational signalling. The PCV presented here is all-atom (as opposed to C-alpha or backbone only) and is derived from all-atom MD trajectory frames. The new restraint relies on a barrier function (specifically, the scaled reciprocal function), which we show is particularly beneficial in the context of molecular dynamics, where near-hard-wall restraints are needed with zero tolerance to restraint violation. We have implemented our PCV and barrier restraint within a hybrid sampling framework that combines well-tempered meta-dynamics and extended-Lagrangian adaptive biasing force (meta-eABF). We use three particular examples of high pharmaceutical interest to demonstrate the value of this approach: (1) sampling the distance from ubiquitin to a protein of interest within the supramolecular Cullin-RING ligase complex, (2) stabilizing the wild-type conformation of the oncogenic mutant JAK2-V617F pseudokinase domain, and (3) inducing an activated state of the stimulator of interferon genes (STING) protein observed upon ligand binding. For (2) and (3), we present statistical analysis of meta-eABF free energy estimates and for each case, code for reproducing this work.
Dev’s Formulae for Diagnostic Test Accuracy Meta-analysis
Authors: Desai Dev
Published: March 2023

Calculating the sensitivity and specificity values from True Positive, True Negative, False Positive, and False Negative is easy. But estimating the True and False values back is not possible. All the formulae present do that need the value of the disease’s prevalence in the population and hospital-based studies are usually biased in the prevalence. We have tried to create formulae and have been successful along with its proof on formulae that uses Sensitivity, Specificity, PPV and Total participants of the study to calculate True and False values.
Prevalence and risk factors of adverse effects after the first COVID-19 booster dose: evidence from Greece
Authors: Galanis Petros , Katsiroumpa Aglaia , Vraka Irene , Chrysagi Vanessa , Siskou Olga , Konstantakopoulou Olympia , Katsoulas Theodoros , Gallos Parisis , Kaitelidou Daphne
Published: March 2023

Background

In general, COVID-19 vaccines are safe and effective, but minor adverse effects are common.

Objective

To estimate the prevalence of adverse effects after the first COVID-19 booster dose, and to identify possible risk factors.

Material and methods

We conducted a cross-sectional study with a convenience sample in Greece during November 2022. We measured several adverse effects after the booster dose, such as pain at the injection site, swelling at the injection site, fatigue, muscle pain, headaches, fever, chills, nausea, etc. We considered gender, age, chronic disease, self-assessment of health status, COVID-19 diagnosis, and self-assessment of COVID-19 course as possible predictors of adverse effects.

Results

In our sample, 96% developed at least one adverse effect. Half of the participants (50.2%) developed one to five adverse effects, 35.9% developed six to ten adverse effects, and 9.5% developed 11 to 16 adverse effects. Mean number of adverse effects was 5.5. The most frequent adverse effects were pain at the injection site (84.3%), fatigue (70.8%), muscle pain (61%), swelling at the injection site (55.2%), headache (49.8%), fever (42.9%), and chills (41%). Females developed more adverse effects than males (p<0.001). Also, we found a positive relationship between severity of COVID-19 symptoms and adverse effects of COVID-19 vaccines (p=0.005). Moreover, younger age was associated with increased adverse effects (p<0.001).

Conclusions

Almost all participants in our study developed minor adverse effects after the booster dose. Female gender, worse clinical course of COVID-19, and decreased age were associated with increased adverse effects.
A single-cell atlas of the miracidium larva of the human blood flukeSchistosoma mansoni: cell types, developmental pathways and tissue architecture
Authors: Attenborough Teresa , Rawlinson Kate A. , Soria Carmen L. Diaz , Ambridge Kirsty , Sankaranarayanan Geetha , Graham Jennie , Cotton James A. , Doyle Stephen R. , Rinaldi Gabriel , Berriman Matthew
Published: March 2023

Schistosomes are parasitic flatworms that cause the water-borne disease schistosomiasis, affecting millions of people worldwide. The miracidium larva of schistosomes represents the first post-embryonic stage of development and is critical to transmission. After hatching, a miracidium infects a freshwater snail and transforms into a mother sporocyst, where its stem cells generate daughter sporocysts that give rise to many human-infective cercariae larvae. To understand this important life cycle stage at the cellular and molecular levels, we have used single-cell RNA sequencing,in situhybridisation and image analysis to create a whole-body cell atlas of the miracidium larva ofSchistosoma mansoni. Our atlas shows that each miracidium is composed of ∼365 cells and 19 transcriptionally distinct cell types. We show that 93% of miracidium cells are somatic (57% neural, 19% muscle, 13% epidermal (tegument), 2% parenchyma, 2% protonephridia), and the remaining 7% are stem cells. Cellular diversity within tissue types is revealed, and is highest in neurons. There are two stem cell populations, and they show different activation and potency states. Trajectory analysis indicates that one stem cell population is the origin of the tegument lineage and the other likely contains pluripotent cells. Furthermore, each of these stem populations is transcriptionally distinct based on sex-linked gene expression in male and female larvae. Through single cell transcriptomics andin-situhybridisation we identified every cell in the whole organism revealing the organisation of the miracidium. This single cell atlas provides the foundation to understand the development and interaction of cell types and tissues as they change over a life cycle that is characterised by complex morphological changes.
Cleavage kinetics of human mitochondrial RNase P and contribution of its non-nuclease subunits
Authors: Vilardo Elisa , Toth Ursula , Hazisllari Enxhi , Rossmanith Walter
Published: March 2023

RNase P is the endonuclease responsible for the 5’-end processing of tRNA precursors (pre-tRNAs). Unlike the single-subunit protein-only RNase P (PRORP) found in plants or protists, human mitochondrial RNase P is a multi-enzyme assembly that in addition to the homologous PRORP subunit comprises a methyltransferase (TRMT10C) and a dehydrogenase (SDR5C1) subunit; these proteins, but not their enzymatic activities, are required for efficient pre-tRNA cleavage. Here we report a detailed kinetic analysis of the cleavage reaction by human PRORP and its interplay with TRMT10C-SDR5C1 using a comprehensive set of mitochondrial pre-tRNAs. Surprisingly, we found that PRORP alone binds pre-tRNAs with nanomolar affinity and can even cleave some of them at reduced efficiency without the other subunits. Thus, the ancient binding mode, involving the tRNA elbow and PRORP’s PPR domain, seems retained by human PRORP, and its metallonuclease domain is in principle correctly folded and functional. Our findings support a model according to which the main function of TRMT10C-SDR5C1 is to direct PRORP’s nuclease domain to the cleavage site, thereby increasing the rate and accuracy of cleavage. Human PRORP’s dependence on the extra tRNA binder appears to have evolved to secure specificity in the cleavage of the structurally degenerating mitochondrial tRNAs.
Anticancer efficacy of KRASG12C inhibitors is potentiated by PAK4 inhibitor KPT9274 in preclinical models of KRASG12C mutant pancreatic and lung cancers
Authors: Khan Husain Yar , Nagasaka Misako , Aboukameel Amro , Alkhalili Osama , Uddin Md. Hafiz , Bannoura Sahar , Mzannar Yousef , Azar Ibrahim , Beal Eliza , Tobon Miguel , Kim Steve , Beydoun Rafic , Baloglu Erkan , Senapedis William , El-Rayes Bassel , Philip Philip A. , Mohammad Ramzi M. , Shields Anthony F. , Al-Hallak Mohammed Najeeb , Azmi Asfar S.
Published: March 2023

KRASG12C inhibitors have revolutionized the treatment landscape for cancer patients harboring the G12C mutant isoform of KRAS. With the recent FDA approval of sotorasib and adagrasib, patients now have access to more promising treatment options. However, patients who receive these agents as a monotherapy usually develop drug resistance. Thus, there is a need to develop logical combination strategies that can delay or prevent the onset of resistance and simultaneously enhance the antitumor effectiveness of the treatment regimen. In this study, we aimed at pharmacologically targeting PAK4 by KPT9274 in combination with KRASG12C inhibitors in KRASG12C mutant pancreatic ductal adenocarcinoma (PDAC) and non–small cell lung cancer (NSCLC) preclinical models. PAK4 is a hub molecule that links several major signaling pathways and is known for its tumorigenic role in mutant Ras-driven cancers. We assessed the cytotoxicity of PAK4 and KRASG12C inhibitors combination in KRASG12C mutant 2D and 3D cellular models. KPT9274 synergized with both sotorasib and adagrasib in inhibiting the growth of KRASG12C mutant cancer cells. The combination was able to reduce the clonogenic potential of KRASG12C mutant PDAC cells. We also evaluated the antitumor activity of the combination in a KRASG12C mutant PDAC cell line-derived xenograft (CDX) model. Oral administration of a sub-optimal dose of KPT9274 in combination with sotorasib (at one-fourth of MTD) demonstrated significant inhibition of the tumor burden (p= 0.002). Similarly, potent antitumor efficacy was observed in an NSCLC CDX model where KPT9274, acting as an adjuvant, prevented tumor relapse following the discontinuation of sotorasib treatment (p= 0.0001). KPT9274 and sotorasib combination also resulted in enhanced survival. This is the first study showing that KRASG12C inhibitors can synergize with PAK4 inhibitor KPT9274 bothin vitroandin vivoresulting in remarkably enhanced antitumor activity and survival outcomes.

Significance

KRASG12C inhibitors demonstrate limited durable response in patients with KRASG12C mutations. In this study, combining PAK4 inhibitor KPT9274 with KRASG12C inhibitors has resulted in potent antitumor effects in preclinical cancer models of PDAC and NSCLC. Our results bring forward a novel combination therapy for cancer patients that do not respond or develop resistance to KRASG12C inhibitor treatment.
Small molecule machine learning: All models are wrong, some may not even be useful
Authors: Kretschmer Fleming , Seipp Jan , Ludwig Marcus , Klau Gunnar W. , Böcker Sebastian
Published: March 2023

Small molecule machine learning tries to predict chemical, biochemical or biological properties from the structure of a molecule. Applications include prediction of toxicity, ligand binding or retention time. A recent trend is to develop end-to-end models that avoid the explicit integration of domain knowledge via inductive bias. A central assumption in doing so, is that there is no coverage bias in the training and evaluation data, meaning that these data are a representative subset of the true distribution we want to learn. Usually, the domain of applicability is neither considered nor analyzed for such large-scale end-to-end models.

Here, we investigate how well certain large-scale datasets from the field cover the space of all known biomolecular structures. Investigation of coverage requires a sensible distance measure between molecular structures. We use a well-known distance measure based on solving the Maximum Common Edge Subgraph (MCES) problem, which agrees well with the chemical intuition of similarity between compounds. Unfortunately, this computational problem is provably hard, severely restricting the use of the corresponding distance measure in large-scale studies. We introduce an exact approach that combines Integer Linear Programming and intricate heuristic bounds to ensure efficient computations and dependable results.

We find that several large-scale datasets frequently used in this domain of machine learning are far from a uniform coverage of known biomolecular structures. This severely confines the predictive power of models trained on this data. Next, we propose two further approaches to check if a training dataset differs substantially from the distribution of known biomolecular structures. On the positive side, our methods may allow creators of large-scale datasets to identify regions in molecular structure space where it is advisable to provide additional training data.
Nascent evolution of recombination rate differences as a consequence of chromosomal rearrangements
Authors: Näsvall K. , Boman J. , Höök L. , Vila R. , Wiklund C. , Backström N.
Published: March 2023

Reshuffling of genetic variation occurs both by independent assortment of chromosomes and by homologous recombination. Such reshuffling can generate novel allele combinations and break linkage between advantageous and deleterious variants which increases both the potential and the efficacy of natural selection. Here we used high-density linkage maps to characterize global and regional recombination rate variation in two populations of the wood white butterfly (Leptidea sinapis) with distinct karyotypes. The recombination data were compared to estimates of genetic diversity and measures of selection to assess the relationship between chromosomal rearrangements, crossing over, maintenance of genetic diversity and adaptation. Our data show that the recombination rate is influenced by both chromosome size and number, but that the difference in recombination rate between karyotypes is reduced as a consequence of a higher frequency of double crossovers in larger chromosomes. As expected from effects of selection on linked sites, we observed an overall positive association between recombination rate and genetic diversity in both populations. Our results also revealed a significant effect of chromosomal rearrangements on the rate of intergenic diversity change between populations, but limited effects on polymorphisms in coding sequence. We conclude that chromosomal rearrangements can have considerable effects on the recombination landscape and consequently influence both maintenance of genetic diversity and efficiency of selection in natural populations.

Author summary

Reshuffling genetic variation is fundamental for maintaining genetic diversity and creating novel allelic combinations. The two main processes involved are the independent assortment of chromosomes and homologous recombination. The number and size of chromosomes can influence the amount of pairwise reshuffling and local recombination patterns. However, studying this in natural populations is challenging. In this study, we used the wood white butterfly, which exhibits an extreme within-species karyotype difference. Extensive fusions and fissions have resulted in almost twice as many chromosomes in the southern populations compared to the northeast populations. This unique system allowed us to assess the relationship between karyotype differences, pairwise reshuffling, recombination rate variation and subsequent effects on diversity and linked selection. We found that a higher number of chromosomes result in a higher recombination rate, although the difference was less than expected due to multiple recombination events occuring on longer chromosomes. Both populations showed an association between recombination rate and genome-wide patterns of genetic diversity and efficacy of selection. We provide evidence that chromosomal rearrangements have considerable effects on the recombination landscape and thereby influence the maintenance of genetic diversity in populations.
Flattening the curve - How to get better results with small deep-mutational-scanning datasets
Authors: Wirnsberger Gregor , Pritišanac Iva , Oberdorfer Gustav , Gruber Karl
Published: March 2023

Proteins are utilized in various biotechnological applications, often requiring the optimization of protein properties by introducing specific amino acid exchanges. Deep mutational scanning (DMS) is an effective high-throughput method for evaluating the effects of these exchanges on protein function. DMS data can then inform the training of a neural network to predict the impact of mutations. Most approaches employ some representation of the protein sequence for training and prediction. As proteins are characterized by complex structures and intricate residue interaction networks, directly providing structural information as input reduces the need to learn these features from the data.

We introduce a method for encoding protein structures as stacked 2D contact maps, which capture residue interactions, their evolutionary conservation, and mutation-induced interaction changes. Furthermore, we explored techniques to augment neural network training performance on smaller DMS datasets. To validate our approach, we trained three neural network architectures originally used for image analysis on three DMS datasets, and we compared their performances with networks trained solely on protein sequences. The results confirm the effectiveness of the protein structure encoding in machine learning efforts on DMS data. Using structural representations as direct input to the networks, along with data augmentation and pre-training, significantly reduced demands on training data size and improved prediction performance, especially on smaller datasets, while performance on large datasets was on par with state-of-the-art sequence convolutional neural networks.

The methods presented here have the potential to provide the same workflow as DMS without the experimental and financial burden of testing thousands of mutants. Additionally, we present an open-source, user-friendly software tool to make these data analysis techniques accessible, particularly to biotechnology and protein engineering researchers who wish to apply them to their mutagenesis data.
A network of CD163+macrophages monitors enhanced permeability at the blood-dorsal root ganglion barrier
Authors: Lund Harald , Hunt Matthew , Kurtovic Zerina , Sandor Katalin , Fereydouni Noah , Julien Anais , Göritz Christian , Han Jinming , Zhu Keying , Harris Robert A. , Lampa Jon , Haglund Lisbet , Yaksh Tony L. , Svensson Camilla I.
Published: March 2023

In dorsal root ganglia (DRG), macrophages reside in close proximity to sensory neurons, and their functions have largely been explored in the context of pain, nerve injury and repair. In this study, however, we discovered that the majority of macrophages in DRGs are in direct contact with the vasculature where they constantly monitor the circulation, efficiently phagocytosing proteins and macromolecules from the blood. Characterization of the DRG endothelium revealed a specialized vascular network spanning the arteriovenous axis, which gradually transformed from a barrier type endothelium in arteries to a highly permeable endothelium in veins. Macrophage phagocytosis spatially aligned with peak endothelial permeability and we identified caveolar transcytosis as a mechanism regulating endothelial permeability. Profiling of the DRG immune landscape revealed two subsets of perivascular macrophages with distinct transcriptome, turnover and function. CD163 expressing macrophages self-maintained locally, specifically participated in vasculature monitoring, displayed distinct responses during peripheral inflammation and were conserved in mouse and Man. Our work provides a molecular explanation for the permeability of the blood-DRG barrier and identifies an unappreciated role of macrophages as integral components of the DRG-neurovascular unit.
Novel RNA m6A methyltransferase METTL16 inhibitors
Authors: Selberg Simona , Ivanova Larisa , Kotli Mihkel , Herodes Koit , Blokhina Daria , Kankuri Esko , Seli Neinar , Ilves Ivar , Teino Indrek , Saarma Mart , Karelson Mati
Published: March 2023

The overexpression of RNA 6-N-methyladenosine (m6A) methyltransferase METTL16 has oncogenic role in the case of several cancer types, including leukemia, but efficient small-molecule inhibitors are not available. Initially identified by high-throughput virtual screening of the ZINC15 databasein vivosubset, but then confirmed by measuring catalytic activity, two nanomolar-active METTL16 inhibitors, compounds1(IC50= 25.82 ± 17.19 nM) and2(IC50= 60.91 ± 2.75 nM) were found. The inhibitory activity of the compounds was measured using the m6A antibody-based ELISA assay. We also present the results on the effect of these inhibitors on the viability of promyeloblast HL-60 and lymphoblast CCRF-CEM leukemia cell lines. In unstressed growth conditions, both identified METTL16 inhibitors reduced the viability of HL-60 cells by up to 40%. The effect on the viability of CCRF-CEM cells was smaller with no dose dependency observed. In parallel, the level of the m6A as compared to unmodified adenosine in the HL-60 cell mRNAs was significantly reduced by the inhibitor1. Collectively, we herein demonstrate novel METTL16 inhibitors that exert tumor cell-lineage-selective antiproliferative effects.
ATP citrate lyase is an essential player of the metabolic rewiring induced by PTEN loss during T-ALL development
Authors: Andrieu Guillaume P. , Hypolite Guillaume , Balducci Estelle , Costa Caroline , Verhoeyen Els , Nemazanyy Ivan , Panasyuk Ganna , Wellen Kathryn , Macintyre Elizabeth , Asnafi Vahid , Tesio Melania
Published: March 2023

Alterations inactivating the tumor suppressor genePTENdrive the development of solid and hematological cancers, such as T-cell acute lymphoblastic leukemia (T-ALL), whereby PTEN loss defines poor-prognosis patients. We investigated the metabolic rewiring induced by PTEN loss in T-ALL, aiming at identifying novel metabolic vulnerabilities. We showed that the enzyme ATP citrate lyase (ACLY) is strictly required for the transformation of thymic immature progenitors and for the growth of human T-ALL, which remain dependent on ACLY activity even upon transformation. Whereas PTEN mutant mice all died within 17 weeks, the concomitant ACLY deletion prevented disease initiation in 70% of the animals, where it prevented the apoptosis of pre-malignant DP thymocytes by up-regulating BCL-2. Transcriptomic and metabolic analysis of primary T-ALL cells next translated our findings to the human pathology, showing that PTEN-altered T-ALL cells selectively activate ACLY and are specifically sensitive to its genetic targeting. ACLY activation thus represents a metabolic vulnerability with therapeutic potential for high-risk T-ALL patients.
Comparative analysis of soybean transcriptional profiles reveals defense mechanisms involved in resistance againstDiaporthe caulivora
Authors: Mena Eilyn , Reboledo Guillermo , Stewart Silvina , Montesano Marcos , de León Inés Ponce
Published: March 2023

Soybean stem canker (SSC) caused by the fungal pathogenDiaporthe caulivorais an important disease affecting soybean production. However, limited information related to the molecular mechanisms underlying soybean resistance toDiaporthespecies is available. In the present work, the defense responses toD. caulivorain two contrasting soybean genotypes were analyzed. We showed thatGénesis5601 is more resistant to fungal infection than Williams, evidenced by significantly smaller lesion length, reduced disease severity and pathogen biomass. Transcriptional profiling was performed in untreated plants and inD. caulivora-inoculated and control-treated tissues at 8 and 48 hours post inoculation (hpi). In total, 2.322 and 1.855 genes were differentially expressed in Génesis 5601 and Williams, respectively. Interestingly, Génesis 5601 exhibited a significantly higher number of upregulated genes compared to Williams at 8 hpi, 1.028 versus 434 genes. Resistance toD. caulivorawas associated with defense activation through transcriptional reprogramming mediating perception of the pathogen by receptors, biosynthesis of phenylpropanoids, hormones, small heat shock proteins and pathogenesis related (PR) genes. These findings provide novel insights into soybean defense molecular mechanisms used to controlD. caulivora, and generate a foundation for development of resistant SSC varieties within soybean breeding programs.
Phase Separation and Ageing of Glycine-Rich Protein from Tick Adhesive
Authors: Ganar Ketan A. , Turbina Polina , Nandy Manali , Chen Chang , Suylen Dennis , van der Beelen Stan , Pascoe Emily Louise , Koenraadt Constantianus J.M. , Dijkgraaf Ingrid , Deshpande Siddharth
Published: March 2023

Hard ticks feed on their host for multiple days. To ensure firm attachment, they secrete a protein-rich saliva that eventually forms a solid cement cone. The underlying mechanism of this liquid-to-solid transition is not yet understood. This study focuses on the phase transitions of a disordered glycine-rich protein (GRP) that is prominent in tick saliva. We show that GRP undergoes liquid-liquid phase separation via simple coacervation to form biomolecular condensates in salty environments. Cation-pi and pi-pi interactions near the C-terminus promote coacervation while a negatively charged N-terminus prolongs its onset through electrostatic repulsion. Interestingly, GRP condensates exhibit ageing and undergo liquid-to-gel transition to form viscoelastic networks as well as solid-like condensates. Lastly, we provide evidence for protein-rich condensates in natural tick saliva. Our findings provide a starting point to gain insights into the bioadhesion of ticks, develop novel tick control strategies, and towards biomedical applications such as tissue sealants.
A meta-analysis examining how fish biodiversity varies with marine protected area size and age
Authors: Hollitzer Helene A. L. , May Felix , Blowes Shane A.
Published: March 2023

Marine Protected Areas (MPAs) are a well-established conservation practice worldwide, but their effectiveness in protecting or replenishing fish biodiversity remains uneven. Understanding the patterns of this heterogeneity is central to general guidelines for MPA design and can ultimately provide guidance on how to maximize MPA potential. Here, we examine associations between the degree of protection, duration of protection, and protected area size, with fish biodiversity inside of protected areas relative to that of sites nearby, but outside of protected areas. We quantitatively synthesize 116 published estimates of species richness from 72 marine protected areas, and 38 estimates of Shannon entropy from 21 marine protected areas. We show that species richness is on average 18% (95% confidence intervals: 10% to 29%) higher in protected areas relative to areas open to fishing; and, on average Shannon entropy is 13% (95% confidence intervals: −2% to 31%) higher within protected areas relative to outside. We find no relationship between the degree or duration of protection with the ratio of species richness inside versus outside of protected areas; both fully and partially protected areas contribute to the accumulation of species inside protected areas, and protected areas of all ages contribute similarly on average to biodiversity conservation. In contrast to our expectations, increasing protected area size was associated with a decreased ratio of species richness sampled at sites inside versus outside the protected area, possibly due, for example, to insufficient enforcement and/or low compliance. Finally, we discuss why meta-analyses such as ours that summarize effect sizes of local scale biodiversity responses, that is, those at a single site, can only give a partial answer to the question of whether larger protected areas harbor more species than comparable unprotected areas.
Sensing the rainbow: genetic and physiological responses to light quality in Ostreococcus, an ecologically important photosynthetic picoeukaryote
Authors: Sands Elizabeth , Davies Sian , Puxty Richard John , Bouget François-Yves , Scanlan David John , Carré Isabelle Alice
Published: March 2023

Phytoplankton is exposed to dramatic variations in light quality as it moves up and down the water column or encounters the presence of sediments in the water. We investigated the potential impact onOstreococcus,a key marine photosynthetic picoeukaryote, by analysing changes in its transcriptome, pigment content and photophysiology after acclimation to monochromatic red, green or blue light. The clade B species RCC809, isolated from the deep Atlantic Ocean, responded to blue light by accelerating cell division at the expense of storage reserves, and by increasing the relative level of blue-light absorbing pigments. In contrast, it responded to red and green light by increasing its potential for photoprotection. In contrast, the clade A species OTTH0595, which originates from a shallow water environment, showed no difference in photosynthetic properties and minor differences in carotenoid contents between light qualities. These results demonstrate that light quality can have a major influence on the physiology of eukaryotic phytoplankton, and suggest that different light quality environments can drive selection for diverse patterns of responsiveness and environmental niche partitioning.

Highlight

We characterise the effects of light quality on the transcriptome and photophysiology ofOstreococcus, a photosynthetic picoeukaryote, and show that responses are distinct between two ecotypes originating from different environments.
FLASH-RT does not affect chromosome translocations and junction structures beyond that of CONV-RT dose-rates
Authors: Barghouth Paul G. , Melemenidis Stavros , Montay-Gruel Pierre , Ollivier Jonathan , Viswanathan Vignesh , Jorge Patrik G. , Soto Luis A. , Lau Brianna C. , Sadeghi Cheyenne , Edlabadkar Anushka , Manjappa Rakesh , Wang Jinghui , Bouteiller Marie Le , Surucu Murat , Yu Amy , Bush Karl , Skinner Lawrie , Maxim Peter G. , Loo Billy W. , Limoli Charles L. , Vozenin Marie-Catherine , Frock Richard L.
Published: March 2023

The molecular and cellular mechanisms driving the enhanced therapeutic ratio of ultra-high dose-rate radiotherapy (FLASH-RT) over slower conventional (CONV-RT) radiotherapy dose-rate remain to be elucidated. However, attenuated DNA damage and transient oxygen depletion are among several proposed models. Here, we tested whether FLASH-RT under physioxic (4% O2) and hypoxic conditions (≤2% O2) reduces genome-wide translocations relative to CONV-RT and whether any differences identified revert under normoxic (21% O2) conditions. We employed high-throughput rejoin and genome-wide translocation sequencing (HTGTS-JoinT-seq), usingS. aureusandS. pyogenesCas9 “bait” DNA double strand breaks (DSBs), to measure differences in bait-proximal repair and their genome-wide translocations to “prey” DSBs generated by electron beam CONV-RT (0.08-0.13Gy/s) and FLASH-RT (1×102-5×106Gy/s), under varying ionizing radiation (IR) doses and oxygen tensions. Normoxic and physioxic irradiation of HEK293T cells increased translocations at the cost of decreasing bait-proximal repair but were indistinguishable between CONV-RT and FLASH-RT. Although no apparent increase in chromosome translocations was observed with hypoxia-induced apoptosis, the combined decrease in oxygen tension with IR dose-rate modulation did not reveal significant differences in the level of translocations nor in their junction structures. Thus, Irrespective of oxygen tension, FLASH-RT produces translocations and junction structures at levels and proportions that are indistinguishable from CONV-RT.
Potassium transporter OsHAK18 mediates shoot-to-root circulation of potassium and sodium and source-to-sink translocation of soluble sugar in rice
Authors: Peng Lirun , Xiao Huojun , Li Ran , Zeng Yang , Gu Mian , Moran Nava , Yu Ling , Xu Guohua
Published: March 2023

High-affinity potassium (K+) transporters HAK/KUP/KT have been identified in all genome-sequenced terrestrial plants. They play important role in K+acquisition, translocation and enhancing salt tolerance. Here we report that the plasma-membrane-located OsHAK18 functions in K+and sodium (Na+) circulation and sugar translocation in rice. OsHAK18 is expressed mainly, though not exclusively, in vascular tissues and particularly in the phloem. Knockout (KO) ofOsHAK18reduced K+concentration in phloem sap and in the root but increased K+accumulation in the shoot of both Nipponbare and Zhonghua11 cultivars, while overexpression (OX) ofOsHAK18driven by its endogenous promoter increased K+concentration in phloem sap and in roots, and promoted Na+retrieval from shoot to root under salt stress. Split-root experimental analysis of rubidium (Rb+) uptake and circulation indicated thatOsHAK18-OX promoted Rb+translocation from shoot to root. In addition,OsHAK18-KO increased whileOsHAK18-OX reduced soluble sugar content in the shoot and affected oppositely the sugar concentration in the phloem and its content in the root. Moreover,OsHAK18-OX increased dramatically grain yield and physiological K+utilization efficiency. Taken together, our results suggest that – unlike other OsHAKs analyzed heretofore – OsHAK18 is critical to K+and Na+re-circulation from shoot to root and enhances the source-to-sink translocation of a photo-assimilate.

One sentence summary

Rice potassium transporter OsHAK18 mediates shoot-to-root circulation of potassium and sodium and source-to-sink translocation of soluble sugar which improves potassium use efficiency and grain yield.
Shaping and interpretation of Dpp morphogen gradient by endocytic trafficking
Authors: Rasouliha Sheida Hadji , Aguilar Gustavo , Reinger Cindy , Matsuda Shinya
Published: March 2023

Dpp/BMP is a morphogen that controls patterning and growth in the Drosophila wing disc. Endocytic trafficking has been proposed to control extracellular Dpp spreading or removal, and Dpp signaling. However, how Dpp morphogen gradient is shaped and interpreted by endocytic trafficking remains unclear due to the lack of tools to visualize Dpp distribution at the physiological level. Here we generate functional fluorescent protein taggeddppalleles to visualize both extracellular and intracellular Dpp distribution. Using these alleles, we found that, while Dynamin-mediated internalization of Dpp is required for Dpp signal activation, Rab5-mediated trafficking is not required for Dpp spreading or signaling as proposed before but for shutting off Dpp signaling through downregulating activated receptors. We provide evidence that Dpp signaling is terminated at Multivesicular body (MVB) likely through sorting activated receptors into intraluminal vesicles (ILVs) rather than Rab7-mediated lysosomal degradation. We further found that blocking MVB formation expanded Dpp signaling gradient without affecting extracellular Dpp gradient, thus compromising extracellular Dpp gradient interpretation. These results indicate that extracellular Dpp gradient is shaped by Dynamin-mediated internalization of Dpp and interpreted by duration of Dpp signaling.
Risk Assessment and Monitoring of Certain Pollutants in Natural Honeys Imported from Different Countries and Marketing in KSA
Authors: Osman Khaled A. , Elsayed Mohamed Hala H. , Salama Maher S.
Published: March 2023

The physicochemical and antimicrobial properties, as well as metals and pesticide residue contents in honeys imported from different countries and marketing in KSA were investigated. The results indicated that the chemical composition of some of these honeys violated the most national and international guidelines. Also, honey samples showed greater antimicrobial activities against all the osmophilic microorganisms especiallyAspergillus flavus. Pb and Cd were not detected in all the tested samples, while Cu levels were below the guideline value of 5 mg/kg. However, Zn, Fe, and Ni levels in most the tested samples did not comply with the legislation values of 5, 15, and 0.01-1.00 mg/kg, respectively, and may pose a health risk to consumers. Also, Mn was found in higher levels which can be attributed either to the production stages of honey or the region from where the honey has been taken. Regarding the pesticide residues, some residues were detected in honeys imported from Germany, Australia, and Turkey; however, the hazardous indices for all the detected residues were less than one, indicating that these residues could not pose a health risk. It can be concluded that natural honeys should be free of any objectionable metals and pesticides.
A systematic review of ambient heat and sleep in a warming climate
Authors: Chevance Guillaume , Minor Kelton , Vielma Constanza , Campi Emmanuel , O’Callaghan-Gordo Cristina , Basagaña Xavier , Ballester Joan , Bernard Paquito
Published: March 2023

Background

Earlier reviews documented the effects of a broad range of climate change outcomes on sleep but have not yet evaluated the effect of ambient temperature. This systematic review aims to identify and summarize the literature on ambient temperature and sleep outcomes in a warming world.

Methods

For this systematic review, we searched online databases (PubMed, Scopus, JSTOR, GreenFILE, GeoRef and PsycARTICLES) together with relevant journals for studies published before February 2023. We included articles reporting associations between objective indicators of ambient temperature and valid sleep outcomes measured in real-life environments. We included studies conducted among adults, adolescents, and children. A narrative synthesis of the literature was then performed.

Findings

The present systematic review shows that higher outdoor or indoor ambient temperatures, expressed either as daily mean or night-time temperature, are negatively associated with sleep quality and quantity worldwide. The negative effect of higher ambient temperatures on sleep is stronger in the warmest months of the year, among vulnerable populations and in the warmest areas of the world. This result appears consistent across several sleep indicators and measures.

Interpretation

Although this work identified several methodological limitations of the extant literature, a strong body of evidence from both this systematic review and previous experimental studies converge on the negative impact of elevated temperatures on sleep quality and quantity. In absence of solid evidence on fast adaptation to the effects of heat on sleep, rising temperatures induced by climate change pose a planetary threat to human sleep and therefore human health, performance and wellbeing.
Validation of an open-source smartphone step counting algorithm in clinical and non-clinical settings
Authors: Straczkiewicz Marcin , Keating Nancy L. , Thompson Embree , Matulonis Ursula A. , Campos Susana M. , Wright Alexi A. , Onnela Jukka-Pekka
Published: March 2023

Background

Step counts are increasingly used in public health and clinical research to assess wellbeing, lifestyle, and health status. However, estimating step counts using commercial activity trackers has several limitations, including a lack of reproducibility, generalizability, and scalability. Smartphones are a potentially promising alternative, but their step-counting algorithms require robust validation that accounts for temporal sensor body location, individual gait characteristics, and heterogeneous health states.

Objective

Our goal was to evaluate an open-source step-counting method for smartphones under various measurement conditions against step counts estimated from data collected simultaneously from different body locations (“internal” validation), manually ascertained ground truth (“manual” validation), and step counts from a commercial activity tracker (Fitbit Charge 2) in patients with advanced cancer (“wearable” validation).

Methods

We used eight independent datasets collected in controlled, semi-controlled, and free-living environments with different devices (primarily Android smartphones and wearable accelerometers) carried at typical body locations. Five datasets (N=103) were used for internal validation, two datasets (N=107) for manual validation, and one dataset (N=45) used for wearable validation. In each scenario, step counts were estimated using a previously published step-counting method for smartphones that uses raw sub-second level accelerometer data. We calculated mean bias and limits of agreement (LoA) between step count estimates and validation criteria using Bland-Altman analysis.

Results

In the internal validation datasets, participants performed 751.7±581.2 (mean±SD) steps, and the mean bias was -7.2 steps (LoA -47.6, 33.3) or -0.5%. In the manual validation datasets, the ground truth step count was 367.4±359.4 steps while the mean bias was -0.4 steps (LoA -75.2, 74.3) or 0.1 %. In the wearable validation dataset, Fitbit devices indicated mean step counts of 1931.2±2338.4, while the calculated bias was equal to -67.1 steps (LoA -603.8, 469.7) or a difference of 0.3 %.

Conclusions

This study demonstrates that our open-source step counting method for smartphone data provides reliable step counts across sensor locations, measurement scenarios, and populations, including healthy adults and patients with cancer.
Gradual evolution of hydrogen-bonding patterns with the carbamoylcyanonitrosomethanide anion in a series of aliphatic diammonium salts
Authors: Domasevitch Kostiantyn V. , Senchyk Ganna A. , Lysenko Andrey B. , Rusanov Eduard B.
Published: March 2023

Developing the structures of organic materials that rely on the hydrogen bonding of multifunctional substrates is often complicated due to a competition between various possible motifs. In this context, the illustrative case of the carbamoylcyanonitrosomethanide anion, [ONC(CN)–C(O)NH2]−, suggests sufficient control over the crystal lattice with a set of supramolecular synthons, which are specific to all the present nitroso, carbamoyl and cyano groups. The structures of the carbamoylcyanonitrosomethanide salts of ethane-1,2-diammonium, C2H10N2
2+·2C3H2N3O2
−, (1), piperazine-1,4-diium, C4H12N2
2+·2C3H2N3O2
−, (2), butane-1,4-diammonium, C4H14N2
2+·2C3H2N3O2
−, (3), and hexane-1,6-diammonium, C6H18N2
2+·2C3H2N3O2
−, (4), reveal two- and three-dimensional hydrogen-bonded frameworks governed by a set of site-selective interactions. The strongest N—H...O hydrogen bonds [N...O = 2.6842 (17)–2.8718 (17) Å, mean 2.776 (2) Å] are associated with the polarized ammonium N—H donors and nitroso O-atom acceptors, which sustain invariant motifs in the form of nitroso/ammonium dimers. Subtle structural changes within this series of compounds concern the rupture of some weaker interactions, i.e. mutual hydrogen bonds of the carbamoyl groups in (1)–(3) [N...O = 2.910 (2)–2.9909 (18) Å; mean 2.950 (2) Å] and carbamoyl/nitrile hydrogen bonds in (1), (2) and (4) [N...N = 2.936 (2)–3.003 (3) Å, mean 2.977 (2) Å], providing a gradual evolution of the hydrogen-bonding pattern. A hierarchy of the synthons involving three different groups could be applicable to supramolecular synthesis with polyfunctional methanide species, suggesting also a degree of control over layered and interpenetrated hydrogen-bonded networks.
Crystal structures of (12E)-12-(4-benzylidene)-7,7,16-trimethyl-3-(4-methylphenyl)-1-oxa-16-azatetracyclo[11.2.1.02,11.04,9]hexadeca-2(11),4(9)-dien-5-one and (12E)-12-(4-bromobenzylidene)-73-(4-bromophenyl)-,7,16-trimethyl-10-oxa-16-azatetracyclo[11.2.1.02,11.04,9]hexadeca-2(11),4(9)-dien-5-one
Authors: Meenatchi C. Selva , Vishnupriya R. , Suresh J. , Rubina S. Raja , Selvanayagam S. , Bhandari S. R.
Published: March 2023

The title compounds, C32H35NO2, (I), and C30H29Br2NO2, (II), differ by the presence of a bromine atom instead of a methyl atom in the para position of two benzene rings of compound (II). The two compounds have a structural overlap r.m.s. deviation of 0.27 Å. The pyran and seven-membered cycloheptene rings in both structures adopt boat and boat-sofa conformations, respectively. Intra- and intermolecular C—H...O hydrogen bonds are responsible for the consolidation of the crystal packing of both molecules. In addition to this, weak C—H...π interactions are also observed. The intermolecular interactions were quantified and analysed using Hirshfeld surface analysis.
Synthesis, crystal structure and Hirshfeld surface analysis of the hybrid salt bis(2-methylimidazo[1,5-a]pyridin-2-ium) tetrachloridomanganate(II)
Authors: Vassilyeva Olga Yu. , Buvaylo Elena A. , Kokozay Vladimir N. , Skelton Brian W.
Published: March 2023

The 0-D hybrid salt bis(2-methylimidazo[1,5-a]pyridin-2-ium) tetrachloridomanganate(II), (C8H9N2)2[MnCl4] or [L]2[MnCl4], consists of discrete L
+ cations and tetrachloridomanganate(II) anions. The fused heterocyclic rings in the two crystallographically non-equivalent monovalent organic cations are almost coplanar; the bond lengths are as expected. The tetrahedral MnCl4
2– dianion is slightly distorted with the Mn—Cl bond lengths varying from 2.3577 (7) to 2.3777 (7) Å and the Cl—Mn—Cl angles falling in the range 105.81 (3)–115.23 (3)°. In the crystal, the compound demonstrates a pseudo-layered arrangement of separate organic and inorganic sheets alternating parallel to the bc plane. In the organic layer, pairs of centrosymmetrically related trans-oriented L
+ cations are π-stacked. Neighboring MnCl4
2– dianions in the inorganic sheet show no connectivity, with the minimal Mn...Mn distance exceeding 7 Å. The Hirshfeld surface analysis revealed the prevalence of the non-conventional C—H...Cl—Mn hydrogen bonding in the crystal packing.
5-([(Z)-Methoxyimino]{2-[(2-methylphenoxy)methyl]phenyl}methyl)-1,3,4-oxadiazole-2(3H)-thione dimethyl sulfoxide monosolvate
Authors: Shripanavar Chetan Shrimandhar , Balerao Rishik , Butcher Ray J.
Published: March 2023

The title compound, C18H17N3O3S·C2H6OS, crystallizes in the monoclinic space group P21
/c. In the crystal, C
1
1(9) chains of C—H...O interactions are formed, propogating in the c-axis direction. The N—H hydrogen atom forms a strong hydrogen bond with the oxygen atom of a DMSO solvate molecule.