bluuebunny/crossref_metadata_2025 huggingface dataset:
Mitochondrial phylogeography of grassland caterpillars (Lepidoptera: Lymantriinae:Gynaephora) endemic to the Qinghai-Tibetan Plateau
Authors: Yuan Ming-Long , Bao Ming-Hui , Zhang Qi-Lin , Guo Zhong-Long , Li Min , Wang Juan
Published: March 2023

Grassland caterpillars (Lepidoptera: Lymantriinae:Gynaephora) are the most damaging pests to alpine meadows in the Qinghai-Tibetan Plateau (QTP). Here, we conducted extensive sampling from 39 geographic populations covering almost the entire distribution of the eightGynaephoraspecies in the QTP to investigate phylogeographic patterns and speciation based on two mitochondrial genes (cox1andnad5). A total of 40 haplotypes were detected in the 39 populations, with >70% of haplotypes specific to single population. The monophyletic QTPGynaephoramigrated from non-QTP regions during the Pliocene, corresponding to the uplift of the QTP, suggesting a mode of transport into the QTP. Among the eight QTPGynaephoraspecies described by morphological characteristics, two species (G. alpherakiiandG. menyuanensis) were recovered as monophyletic groups (Clades B and C), while the remaining six species formed two monophyletic clades: Clade A (G. qinghaiensis,G. jiuzhiensis, andG. qumalaiensis) and Clade D (G. aureate,G. rouergensis, andG. minora). These results suggested that the number of the QTPGynaephoraspecies may be overestimated and further studies based on both morphological and nuclear gene data are needed. Genetic differentiation and speciation were driven by intensive uplifts of the QTP and associated climate fluctuations during the Pleistocene, suggesting that isolation and subsequent divergence was the dominant mode of speciation. The Sanjiangyuan region (i.e., Clade A, characterized by high genetic diversity) may have been a glacial refugium of the QTPGynaephora, as supported by analyses of gene flow and biogeography. High levels of genetic diversity were found in QTPGynaephora,without population expansion, which may explain the high-altitude adaptation and outbreaks of grassland caterpillars in alpine meadows of the QTP. This study provides the largest phylogeographic analysis of QTPGynaephoraand improves our understanding of the diversity and speciation of QTP insects.
Combining pairwise structural similarity and deep learning interface contact prediction to estimate protein complex model accuracy in CASP15
Authors: Cheng Jianlin , Roy Raj Shekhor , Liu Jian , Giri Nabin , Guo Zhiye
Published: March 2023

Estimating the accuracy of quaternary structural models of protein complexes and assemblies (EMA) is important for predicting quaternary structures and applying them to studying protein function and interaction. The pairwise similarity between structural models is proven useful for estimating the quality of protein tertiary structural models, but it has been rarely applied to predicting the quality of quaternary structural models. Moreover, the pairwise similarity approach often fails when many structural models are of low quality and similar to each other. To address the gap, we developed a hybrid method (MULTICOM_qa) combining a pairwise similarity score (PSS) and an interface contact probability score (ICPS) based on the deep learning inter-chain contact prediction for estimating protein complex model accuracy. It blindly participated in the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) in 2022 and ranked first out of 24 predictors in estimating the global accuracy of assembly models. The average per-target correlation coefficient between the model quality scores predicted by MULTICOM_qa and the true quality scores of the models of CASP15 assembly targets is 0.66. The average per-target ranking loss in using the predicted quality scores to rank the models is 0.14. It was able to select good models for most targets. Moreover, several key factors (i.e., target difficulty, model sampling difficulty, skewness of model quality, and similarity between good/bad models) for EMA are identified and analayzed. The results demonstrate that combining the multi-model method (PSS) with the complementary single-model method (ICPS) is a promising approach to EMA. The source code of MULTICOM_qa is available at https://github.com/BioinfoMachineLearning/MULTICOM_qa .
Linking folding dynamics and function of SAM/SAH riboswitches at the single molecule level
Authors: Liao Ting-Wei , Huang Lin , Wilson Timothy J. , Ganser Laura R. , Lilley David M. J. , Ha Taekjip
Published: March 2023

Riboswitches are found in the 5’-UTR of many bacterial mRNAs. They function as cisacting regulatory elements that control downstream gene expression through ligand-induced conformational changes. Here, we used single-molecule FRET to map the conformational landscape of the SAM/SAH riboswitch and probe how co-transcriptional ligand-induced conformational changes of this translational switch alter ribosome accessibility. The folding of the riboswitch is highly heterogenous, indicating a complex and rugged conformational landscape that enables sampling of the ligand-bound conformation even in the absence of the ligand. Upon ligand binding, the landscape shifts towards the ligand-bound conformation. Mutations at key stabilizing structures alter the ligand-free folding behavior and decrease ligand responsiveness. We also explored translational regulation through folding kinetics by utilizing short oligonucleotides to probe the accessibility of the Shine-Dalgarno sequence within the riboswitch. Additionally, we employed a helicase-based vectorial folding assay to simulate co-transcriptional folding. We find that a competition between ligand binding and ribosome binding is fined tuned via the kinetics of folding. During transcription, the riboswitch takes minutes before reaching equilibrated conformations, and such slow equilibration decreases the effective ligand affinity. Overall, our data demonstrate the significance of conformational polymorphism in RNA function, emphasizing the utilization of complex folding landscapes for regulating ribosome accessibility through ligand induction. Furthermore, we provide direct evidence on how folding kinetics modulate this regulation process.
Long-term climatic stability drives accumulation and maintenance of divergent freshwater fish lineages in a temperate biodiversity hotspot
Authors: Buckley Sean James , Brauer Chris J. , Unmack Peter J. , Hammer Michael P. , Adams Mark , Beatty Stephen J. , Morgan David L. , Beheregaray Luciano B.
Published: March 2023

Anthropogenic climate change is forecast to drive regional climate disruption and instability across the globe. These impacts are likely to be exacerbated within biodiversity hotspots, both due to the greater potential for species loss but also to the possibility that endemic lineages might not have experienced significant climatic variation in the past, limiting their evolutionary potential to respond to rapid climate change. We assessed the role of climatic stability on the accumulation and persistence of lineages in an obligate freshwater fish group endemic in the southwest Western Australia (SWWA) biodiversity hotspot. Using 19,426 genomic (ddRAD-seq) markers and species distribution modelling, we explored the phylogeographic history of western (Nannoperca vittata) and little (Nannoperca pygmaea) pygmy perches, assessing population divergence and phylogenetic relationships, delimiting species and estimating changes in species distributions from the Pliocene to 2100. We identified two deep phylogroups comprising three divergent clusters, which showed no historical connectivity since the Pliocene. We conservatively suggest these represent three isolated species with additional intraspecific structure within one widespread species. All lineages showed long-term patterns of isolation and persistence owing to climatic stability but with significant range contractions likely under future climate change. Our results highlighted the role of climatic stability in allowing the persistence of isolated lineages in the SWWA. This biodiversity hotspot is under compounding threat from ongoing climate change and habitat modification, which may further threaten previously undetected cryptic diversity across the region.
Fast alignment of mass spectra in large proteomics datasets, capturing dissimilarities arising from multiple complex modifications of peptides
Authors: Prunier Grégoire , Cherkaoui Mehdi , Lysiak Albane , Langella Olivier , Blein-Nicolas Mélisande , Lollier Virginie , Benoist Emile , Jean Géraldine , Fertin Guillaume , Rogniaux Hélène , Tessier Dominique
Published: March 2023

Background

In proteomics, the interpretation of mass spectra representing peptides carrying multiple complex modifications is still challenging, currently limited by the number of potential modifications considered in a single analysis and the need to know them in advance. Further developments must be done in the field to help the scientific community to discover new post-translational modifications that play an essential role in disease and to understand how chemical modifications carried by food proteins could impact our health.

Results

To make progress on this issue, we implemented SpecGlobX (SpecGlob eXTended to eXperimental spectra), a standalone Java application that quickly determines the best spectral alignments of a (possibly very large) list of Peptide-to-Spectrum Matches (PSMs) provided by any open modification search method, or generated by the user. As input, SpecGlobX reads a file containing spectra in MGF or mzML format and a semicolon-delimited spreadsheet describing the PSMs. As output, SpecGlobX returns the best alignment for each PSM, splitting the mass difference between the spectrum and the peptide into one or more shifts while considering the possibility of non-aligned masses (a phenomenon resulting from many situations including neutral losses).

SpecGlobX is fast, able to align one million PSMs in about 1.5 minutes on a standard desktop. Firstly, we remind the foundations of the algorithm and detail how we adapted SpecGlob (the method we previously developed following the same aim, but limited to the interpretation of perfect simulated spectra) to the interpretation of imperfect experimental spectra. Then, we highlight the interest of SpecGlobX as a complementary tool downstream to three open modification search methods on a large simulated spectra dataset. Finally, we show on a smaller dataset that SpecGlobX performs equally well on experimental and simulated spectra.

Conclusions

SpecGlobX is helpful as a decision support tool, providing keys to interpret peptides carrying complex modifications still poorly considered by current open modification search software. Better alignment of PSMs enhances confidence in the identification of spectra provided by open modification search methods and should improve the interpretation rate of spectra.
Effectiveness of heat tolerance rice cultivars in preserving grain appearance quality under high temperatures - A meta-analysis
Authors: Wakatsuki Hitomi , Takimoto Takahiro , Ishigooka Yasushi , Nishimori Motoki , Sakata Mototaka , Saida Naoya , Akagi Kosuke , Makowski David , Hasegawa Toshihiro
Published: March 2023

Background

Climate change, particularly rising temperatures, negatively affects rice grain quality, increasing chalky grain percentage (CG) and hampering rice grade and price. Heat-tolerant cultivars have been bred and released since the 2000s, but the effectiveness of heat tolerance in reducing the occurrence of CG has yet to be quantified.

Objectives

This study aimed to measure the effectiveness of breeding for better heat tolerance in reducing the negative impact of high temperatures on rice quality.

Methods

Through a systematic literature search, we developed a dataset including 1297 field observations covering 48 cultivars from five different heat tolerant ranks (HTRs) at 44 sites across Japan. A linear mixed-effect model (LME) and a random forest model (RF) were fitted to the data to analyze the effect of HTR and climatic factors such as the cumulative mean air temperature above 26 °C (TaHD), mean solar radiation, and mean relative humidity for 20 days after heading on CG.

Results

The LME model explained 63 % of the variation with a 14% RMSE. The RF partial dependence plot revealed that the logit-transformed CG response to climate factors was linear, supporting the assumption of LME. The statistical analysis showed that CG increased as a function of TaHD (P < 0.001), with significant differences among HTRs (P < 0.001). The strongest effect of TaHD was obtained for the lowest HTR and was found to decrease with increasing HTR. CG also increased with higher relative humidity (P < 0.001) and solar radiation (P < 0.01). Based on our modeling, we estimated that as TaHD increased from 20 to 80 °Cd (equivalent to a mean temperature increase from 27 °C to 30 °C), CG increased by 66 % points (difference in CG) for cultivars with the lowest HTR, 45 % points for cultivars with an intermediate HTR, and 19 % points for cultivars with the highest HTR. Raising HTR by just one step (from intermediate to moderately tolerant) is projected to increase the proportion of first-grade rice at a grain-filling temperature of 27 °C, but tolerance levels need to be improved further in case of stronger warming.

Conclusions

The effect of high temperatures on CG was highly dependent on the cultivar’s HTR. Improvements in HTR effectively reduce the negative impacts of high temperatures on rice grain quality.

Significance

Heat-tolerant cultivars are projected to suppress the prevalence of CG more than threefold compared with heat-sensitive cultivars when grain-filling temperature increases from 27 to 30 °C.
Species-specific stomatal ABA responses in juvenile ferns grown from spores
Authors: Wuyun Tana , Niinemets Ülo , Hõrak Hanna
Published: March 2023

Adjustable stomatal pores in leaves control the balance between CO2entry for photosynthesis and water loss via transpiration. The drought and low humidity-induced phytohormone abscisic acid (ABA) is the major regulator of active stomatal closure responses in angiosperms. Whether the ABA signalling pathway for stomatal closure functions similarly in older land plant groups, such as lycophytes and ferns, is still unclear: some studies find no stomatal ABA response in ferns, others find that ABA response is present or triggered by specific environmental conditions. Here we analysed steady-state gas-exchange, stomatal density and stomatal response to exogenously applied ABA in nine fern species grown from spores under controlled growth conditions. We find that ABA responses in ferns are species-specific: stomata in four out of nine species closed in response to ABA. The ABA-sensitive species mostly had slow responses of low magnitude, suggesting reduced ABA-sensitivity of ABA signalling pathway in ferns. Species with larger stomatal conductance tended to close stomata in response to ABA, whereas a relatively strong response of ~35% was also found inCyrtomium falcatum, a fern with low stomatal conductance. Our results show that ferns constitute a diverse group with varying degree of stomatal ABA-sensitivity. Further characterisation of ABA signalling pathway components in diverse fern species is needed to understand the genetic basis for the variable ABA-sensitivity in ferns.
General encoding of canonicalk-mers
Authors: Wittler Roland
Published: March 2023

To index or compare sequences efficiently, oftenk-mers, i.e., substrings of fixed lengthk, are used. For efficient indexing or storage,k-mers are often encoded as integers, e.g., applying some bijective mapping between all possibleσkk-mers and the interval [0,σk−1], whereσis the alphabet size.

In many applications, e.g., when the reading direction of a DNA-sequence is ambiguous,canonical k-mers are considered, i.e., the lexicographically smaller of a givenk-mer and its reverse (or reverse complement) is chosen as a representative. In naive encodings, canonicalk-mers are not evenly distributed within the interval [0,σk−1].

We present a minimal encoding of canonicalk-mers on alphabets of arbitrary size, i.e., a mapping to the interval [0,σk/2−1]. The approach is introduced for canonicalization under reversal and extended to canonicalization under reverse complementation. We further present a space and time efficient bit-based implementation for the DNA alphabet.
Postsynaptic protein assembly in three- and two-dimensions studied by mesoscopic simulations
Authors: Yamada Risa , Takada Shoji
Published: March 2023

Recently, cellular biomolecular condensates formed via phase separation have received considerable attention. While they can be formed either in cytosol (denoted as 3D) or beneath the membrane (2D), the underlying difference between the two has not been well clarified. To compare the phase behaviors in 3D and 2D, postsynaptic density (PSD) serves as a model system. PSD is a protein condensate located under the postsynaptic membrane that influences the localization of glutamate receptors and thus contributes to synaptic plasticity. Recentin vitrostudies have revealed the formation of droplets of various soluble PSD proteins via liquid-liquid phase separation. However, it is unclear how these protein condensates are formed beneath the membrane and how they specifically affect the localization of glutamate receptors in the membrane. In this study, focusing on the mixture of a glutamate receptor complex, AMPAR-TARP, and a ubiquitous scaffolding protein, PSD-95, we constructed a mesoscopic model of protein-domain interactions in PSD and performed comparative molecular simulations. The results showed a sharp contrast in the phase behaviors of protein assemblies in 3D and those under the membrane (2D). A mixture of a soluble variant of the AMPAR-TARP complex and PSD-95 in the 3D system resulted in a phase-separated condensate, which was consistent with the experimental results. However, with identical domain interactions, AMPAR-TARP embedded in the membrane formed clusters with PSD-95, but did not form a stable separated phase. Thus, the cluster formation behaviors of PSD proteins in the 3D and 2D systems were distinct. The current study suggests that, more generally, stable phase separation can be more difficult to achieve in and beneath the membrane than in 3D systems.

SIGNIFICANCE

Synaptic plasticity is a key factor in memory and learning. Upon learning, protein condensates that form beneath the postsynaptic membrane are known to change their nature. Recent studies have suggested that condensate formation is related to liquid-liquid phase separation based onin vitroexperiments of soluble parts. However, the phase behavior can be strongly dependent on physical dimensions. The mechanism by which condensate grows beneath the membrane is not well characterized. Taking advantage of the ease of systematic comparison using computer simulations, we investigated the phase behaviors of postsynaptic protein assemblies in 3D and 2D systems. The results revealed that even when a 3D system exhibited clear phase separation, the corresponding 2D system did not exhibit it stably.
Comparative assessment of mosquito size and receptiveness toP. falciparuminfection of two rearing procedures forAnophelesmosquitoes
Authors: Graumans Wouter , Lanke Kjerstin , van de Vegte-Bolmer Marga , Stoter Rianne , Costa Giulia , Levashina Elena A , Yang Annie S P , Gemert Geert-Jan van , Bousema Teun
Published: March 2023

Malaria is transmitted whenAnophelinemosquitoes ingestPlasmodiumparasites during blood-feeding. Artificial feeding assays allow mosquitoes to take up blood from membrane feeders, and are widely used to study malaria transmission. These assays require large quantities of mosquitoes; insectaries optimize their rearing procedures to generate high yields of permissive, homogeneous mosquito populations. Rearing ofAnopheline stephensimosquitoes was protocolized at the Radboudumc in the 1980s, yet infection outcomes remain heterogeneous. This study explores possible improvements in mosquito rearing to improve homogeneity of the resulting mosquito populations. It compares the current mass-rearing standard with an adapted alternative approach from another institute that optimizes larval density per tray and applies a diet that has previously been reported. Differences between procedures were assessed by measuring mosquito size by proxy of wing-length and imbibed blood meal volume. To assess receptiveness toP. falciparuminfection mosquitoes were fed cultured gametocytes. We observed a slight decrease in mosquito size when applying the alternative rearing procedure, but generated equally parasite-receptiveP. falciparummosquitoes compared to the standard procedure. We conclude that both rearing protocols can be used to generate susceptible mosquitoes for conducting malaria research.
Spatiotemporal changes in secondary metabolites during graft formation in grapevine reveal tissue-specific accumulation of metabolites in necrotic and callus tissues
Authors: Loupit Grégoire , Valls Fonayet Josep , Lorensen Marcus Daniel Brandbjerg Bohn , Franc Céline , Revel Gilles De , Janfelt Christian , Cookson Sarah Jane
Published: March 2023

Grafting is widely used in horticulture, shortly after grafting, callus tissues appear at the graft interface and the vascular tissues of the scion and rootstock connect. The graft interface contains a complex mix of tissues, we hypothesized that each tissue have is own metabolic response to wounding/grafting and accumulate different metabolites at different rates. We made intact and wounded cuttings and grafts of grapevine, and then measured changes in bulk secondary metabolite concentration and used metabolite imaging to study tissue specific responses. We show that some metabolites rapidly accumulate in specific tissues after grafting, e.g. stilbenes accumulate in necrotic tissues surrounding mature xylem vessels and gradually oligomerize over time. We also observe that some metabolites accumulate in the newly formed callus tissue at the graft interface and identify genotype-specific responses. Here we reveal the spatiotemporal dynamics of metabolite changes occurring during graft union formation for the first time. The rapid accumulation of stilbenes in the tissues damaged during the grafting process could be a plant defence mechanism, as stilbenes have antioxidant and anti-fungal capacities. The increasing oligomerization of stilbenes often occurs in response to plant stresses (via unknown mechanisms), but it potentially increases antioxidant activity.

Brief summary

Secondary metabolites accumulate after wounding and grafting in plants yet we have limited knowledge of tissue specific accumulation patterns and temporal dynamics. We show that stilbenes accumulate specifically in necrotic tissues and oligomerize over the time, whereas other compounds accumulate in the newly formed callus tissues. This suggests that these compounds have different roles in wounding healing and grafting.
scDeepInsight: a supervised cell-type identification method for scRNA-seq data with deep learning
Authors: Jia Shangru , Lysenko Artem , Boroevich Keith A , Sharma Alok , Tsunoda Tatsuhiko
Published: March 2023

Annotation of cell-types is a critical step in the analysis of single-cell RNA sequencing (scRNA-seq) data that allows the study of heterogeneity across multiple cell populations. Currently this is most commonly done using unsupervised clustering algorithms, which project single-cell expression data into a lower dimensional space and then cluster cells based on their distances from each other. However, as these methods do not use reference datasets, they can only achieve a rough classification of cell-types, and it is difficult to improve the recognition accuracy further. To effectively solve this issue we propose a novel supervised annotation method, scDeepInsight. The scDeepInsight method is capable of performing manifold assignments. It is competent in executing data integration through batch normalization, performing supervised training on the reference dataset, doing outlier detection and annotating cell-types on query datasets. Moreover, it can help identify active genes or marker genes related to cell-types. The training of the scDeepInsight model is performed in a unique way. Tabular scRNA-seq data are first converted to corresponding images through the DeepInsight methodology. DeepInsight can create a trainable image transformer to convert non-image RNA data to images by comprehensively comparing interrelationships among multiple genes. Subsequently, the converted images are fed into convolutional neural networks (CNNs) such as EfficientNet-b3. This enables automatic feature extraction to identify the cell-types of scRNA-seq samples. We benchmarked scDeepInsight with six other mainstream cell annotation methods. The average accuracy rate of scDeepInsight reached 87.5%, which is more than 7% higher compared with the state-of-the-art methods.
ZygosityPredictor
Authors: Rheinnecker Marco , Fröhlich Martina , Rübsam Marc , Paramasivam Nagarajan , Heilig Christoph E. , Fröhling Stefan , Schlenk Richard F. , Hutter Barbara , Hübschmann Daniel
Published: March 2023

ZygosityPredictor provides functionality to evaluate how many copies of a gene are affected by mutations in next generation sequencing data. In cancer samples, the tool processes both somatic and germline mutations. In particular, ZygosityPredictor computes the number of affected copies for single nucleotide variants and small insertions and deletions (Indels). In addition, the tool integrates information at gene level via phasing of several variants and subsequent logic to derive how strongly a gene is affected by mutations and provides a measure of confidence. This information is of particular interest in precision oncology, e.g. when assessing whether unmutated copies of tumor-suppressor genes remain.

Availability and implementation

ZygosityPredictor was implemented as an R-package and is available via Bioconductor athttps://bioconductor.org/packages/ZygosityPredictor. Detailed documentation is provided in the vignette including application to an example genome.
Conservation genetics of the white-bellied pangolin in West Africa: a story of lineage admixture, declining demography and wide sourcing by urban bushmeat markets
Authors: Gossé Koffi Jules , Gonedelé-Bi Sery , Dufour Sylvain , Danquah Emmanuel , Gaubert Philippe
Published: March 2023

During the last 40 years, the volumes of African pangolins feeding the illegal wildlife trade have dramatically increased. We conducted a conservation genetics survey of the most traded African species, the white bellied pangolin (WBP;Phataginus tricuspis), across three West African countries including Guinea, Côte d’Ivoire and Ghana. Our study combining mitochondrial DNA (mtDNA) sequencing and microsatellites genotyping is the first to reveal a global pattern of admixture between two of the six mitochondrial lineages as previously delimited within WBP. We found a signature of isolation-by-distance and a lack of population genetic structuring, supporting the idea that WBP may have underestimated dispersal abilities. Levels of genetic diversity were low compared to central African lineages, reinforcing the picture of genetic pauperization shared by West African WBP. We observed a 85-98% decline in the effective population size of WBP occurring c. 3200 to 400 ya, with current numbers (520–590) at the lower end of the conservative thresholds for minimum viable population size. The microsatellites markers were powerful enough to differentiate between individuals and identify replicated samples, confirming the utility of this approach in tracing the pangolin trade. Genetic diversity estimates confirmed that Yopougon, the main bushmeat market from Abidjan (Côte d’Ivoire), was fed by a large trade network as confirmed by vendors reporting 10 different sources situated 62-459 km away from the market. We conclude that WBP distributed in the Upper Guinean Block should be considered a single management unit of high conservation concern, as impacted by genetic diversity erosion, drastic decline in effective population size and wide range sourcing for feeding urban bushmeat markets. Given the genetic admixture pattern detected within WBP from West Africa, we advocate for a multi-locus strategy to trace the international trade of the species.
Facilitating Electrochemical Lateral Flow Assay using NFC-Enabled Potentiostat and Nitrocellulose-based Metal Electrodes
Authors: Gonzalez-Macia Laura , Li Yunpeng , Zhang Kaijia , Nunez-Bajo Estefania , Barandun Giandrin , Cotur Yasin , Asfour Tarek , Olenik Selin , Coatsworth Philip , Herrington Jack , Güder Firat
Published: March 2023

Rapid detection of pathogens at the point-of-need is crucial for preventing the spread of human, animal and plant diseases which can have devastating consequences both on the lives and livelihood of billions of people. Colorimetric, lateral flow assays consisting of a nitrocellulose membrane, are the preferred format today for low-cost on-site detection of pathogens. This assay format has, however, historically suffered from poor analytical performance and is not compatible with digital technologies. In this work, we report the development of a new class of digital diagnostics platform for precision point-of-need testing. This new versatile platform consists of two important innovations: i) A wireless and batteryless, microcontroller-based, low-cost Near Field Communication (NFC)-enabled potentiostat that brings high performance electroanalytical techniques (cyclic voltammetry, chronoamperometry, square wave voltammetry) to the field. The NFC-potentiostat can be operated with a mobile app by minimally trained users; ii) A new approach for producing nitrocellulose membranes with integrated electrodes that facilitate high performance electrochemical detection at the point-of-need. We produced an integrated system housed in a 3D-printed phone case and demonstrated its used for the detection of Maize Mosaic Virus (MMV), a plant pathogen, as a proof-of-concept application.
Patterns of unwanted biological and technical expression variation across 49 human tissues
Authors: Nieuwenhuis Tim O. , Giles Hunter H. , McCall Matthew N. , Halushka Marc K.
Published: March 2023

All tissue-based gene expression studies are impacted by biological and technical sources of variation. Numerous methods are used to normalize and batch correct these datasets. A more accurate understanding of all causes of variation could further optimize these approaches. We used 17,282 samples from 49 tissues in the Genotype Tissue Expression (GTEx) dataset (v8) to investigate patterns and causes of expression variation. Transcript expression was normalized to Z-scores and only the most variable 2% of transcripts were evaluated and clustered based on co-expression patterns. Clustered gene sets were solved to different biological or technical causes related to metadata elements and histologic images. We identified 522 variable transcript clusters (median 11 per tissue) across the samples. Of these, 64% were confidently explained, 15% were likely explained, 7% were low confidence explanations and 14% had no clear cause. Common causes included sex, sequencing contamination, immunoglobulin diversity, and compositional tissue differences. Less common biological causes included death interval (Hardy score), muscle atrophy, diabetes status, and menopause. Technical causes included brain pH and harvesting differences. Many of the causes of variation in bulk tissue expression were identifiable in the Tabula Sapiens dataset of single cell expression. This is the largest exploration of the underlying sources of tissue expression variation. It uncovered expected and unexpected causes of variable gene expression. These identified sources of variation will inform which metadata to acquire with tissue harvesting and can be used to improve normalization, batch correction, and analysis of both bulk and single cell RNA-seq data.
Arabidopsis MEB3 functions as a vacuolar transporter to regulate iron accumulation in roots
Authors: Endo Kaichiro , Basak Arpan Kumar , Wilkens Alwine , Mirzaei Mohamadreza , Kopriva Stanislav , Yamada Kenji
Published: March 2023

Iron is an essential nutrient for plant photosynthesis and development, but excess iron leads to stress. After absorption from the soil, plants store iron in roots and distribute it to shoots via long-distance transport. Vacuole serves as the iron storage organ in root cells, maintaining cellular iron homeostasis, and vacuolar iron transporter (VIT) family proteins have been identified as plant vacuolar iron transporters. However, the contribution of vacuolar iron transporters to the overall iron homeostasis of plants is not fully understood. Here, we show that MEMBRANE PROTEIN OF ER BODY 3 (MEB3), a VIT family member, is a vacuolar iron transporter involved in root–shoot iron distribution inArabidopsis thaliana. Heterologous expression of ArabidopsisMEB3in yeast restored the iron resistance phenotype of the vacuolar iron transporter deficient mutantccc1, indicating that MEB3 regulates iron transport. In Arabidopsis,MEB3was expressed in almost all tissues, albeit to higher levels in roots and seedlings, and the MEB3 protein localized to the tonoplast. At low iron concentration,meb3knockout mutants accumulated less iron in shoots, suggesting that MEB3 promotes iron accumulation in shoots. Consistently,meb3mutants exhibited reduced growth compared with the wild type upon transfer to iron-deficient medium. However, at high iron concentration,meb3mutants accumulated more iron in shoots and less iron in roots than the wild type, indicating the impairment of proper iron distribution inmeb3mutants. These findings demonstrate that MEB3 is a vacuolar iron transporter involved in root-to-shoot iron distribution.
Biological Factors and Statistical Limitations Prevent Detection of Most Noncanonical Proteins by Mass Spectrometry
Authors: Wacholder Aaron , Carvunis Anne-Ruxandra
Published: March 2023

Ribosome profiling experiments indicate pervasive translation of short open reading frames (ORFs) outside of annotated protein-coding genes. However, shotgun mass spectrometry experiments typically detect only a small fraction of the predicted protein products of this noncanonical translation. The rarity of detection could indicate that most predicted noncanonical proteins are rapidly degraded and not present in the cell; alternatively, it could reflect technical limitations. Here we leveraged recent advances in ribosome profiling and mass spectrometry to investigate the factors limiting detection of noncanonical proteins in yeast. We show that the low detection rate of noncanonical ORF products can largely be explained by small size and low translation levels and does not indicate that they are unstable or biologically insignificant. In particular, proteins encoded by evolutionarily young genes, including those with well-characterized biological roles, are too short and too lowly-expressed to be detected by shotgun mass spectrometry at current detection sensitivities. Additionally, we find that decoy biases can give misleading estimates of noncanonical protein false discovery rates, potentially leading to false detections. After accounting for these issues, we found strong evidence for four noncanonical proteins in mass spectrometry data, which were also supported by evolution and translation data. These results illustrate the power of mass spectrometry to validate unannotated genes predicted by ribosome profiling, but also its substantial limitations in finding many biologically relevant lowly-expressed proteins.
T-CLEARE: A Pilot Community-Driven Tissue-Clearing Protocol Repository
Authors: Weiss Kurt , Huisken Jan , Bakalov Vesselina , Engle Michelle , Gridley Lauren , Krzyzanowski Michelle C. , Madden Tom , Maiese Deborah , Waterfield Justin , Williams David , Wu Xin , Hamilton Carol M. , Huggins Wayne
Published: March 2023

Selecting and implementing a tissue-clearing protocol is challenging. Established more than 100 years ago, tissue clearing is still a rapidly evolving field of research. There are currently many published protocols to choose from, and each performs better or worse across a range of key evaluation factors (e.g., speed, cost, tissue stability, fluorescence quenching). Additionally, tissue-clearing protocols are often optimized for specific experimental contexts, and applying an existing protocol to a new problem can require a lengthy period of adaptation by trial and error. Although the primary literature and review articles provide a useful starting point for optimization, there is growing recognition that many articles do not provide sufficient detail to replicate or reproduce experimental results. To help address this issue, we have developed a novel, freely available repository of tissue-clearing protocols named T-CLEARE (Tissue CLEAring protocol REpository;https://doryworkspace.org/doryviz). T-CLEARE incorporates community responses to an open survey designed to capture details not commonly found in the scientific literature, including modifications to published protocols required for specific use cases and instances when tissue-clearing protocols did not perform well (negative results). The goal of T-CLEARE is to provide a forum for the community to share evaluations and modifications of tissue-clearing protocols for various tissue types and potentially identify best-in-class methods for a given application.
Spatial and temporal representation of marine fish occurrences available online
Authors: Pizarro Vanessa , Castillo Andrea , Piñones Andrea , Samaniego Horacio
Published: March 2023

Despite the 243,000 species of marine species described by 2022, our knowledge about the biodiversity in the oceans is still incomplete. This may have dreaded and detrimental effect for the conservation of marine ecosystems under the current anthropization of our biota and the fast pacing climate and global change scenario.

However, a large number of online repositories cataloging, storing and distributing biodiversity information hosting taxonomic information and species occurrence data have emerged recently. FishBase, the Global Biodiversity Information Facility (GBIF) and the Ocean Biodiversity Information System (OBIS) are part of these publicly available repositories representing a variety of sources that have exploded in number. However, despite the incredible accumulation of biodiversity records, not all the information is really useful, nor does it represent any new knowledge regarding global species richness patterns.

In this study we evaluated the spatial and temporal representativeness of the records of marine fishes (order Actinopterygii) available in the GBIF and OBIS global repositories. We provide a methodological framework based on a set of non-parametric estimators to calculate species richness from incidence data, using hexagonal grids as sampling units overlapped on the marine bioregions worldwide.

Using standard ecological and spatial analysis tools, we identify regions that are adequately represented in terms of available records and therefore have more reliable data, as well as regions with few records that do not represent current species richness. We overlap these results with the location of marine protected areas and fishing exploitation zones to understand the anthropogenic effect on marine ichthyofauna. We additionally evaluate hypotheses regarding the taxonomic, geographic, and temporal distribution of information biases to deepen our current understanding of public records of species occurrences worldwide.

Considering that more than 40 years of information was analyzed, the results showed that on a global scale, the primary data on marine fish available on GBIF and OBIS platforms are still far from being representative and complete. Only 1.14% of the records were useful for our analyses. In addition, we found that the information seems to be biased towards coastal areas, regions close to developed countries and areas where there is a large fishing activity. Finally, the best represented species and families are those with a small body size, which use shallow habitats and have commercial cultural value.
Right Ventricular Sarcomere Contractile Depression and the Role of Thick Filament Activation in Human Heart Failure with Pulmonary Hypertension
Authors: Jani Vivek , Aslam M. Imran , Fenwick Axel J. , Ma Weikang , Gong Henry , Milburn Gregory , Nissen Devin , Salazar Ilton Cubero , Hanselman Olivia , Mukherjee Monica , Halushka Marc K. , Margulies Kenneth B. , Campbell Kenneth , Irving Thomas C. , Kass David A. , Hsu Steven
Published: March 2023

Rationale

Right ventricular (RV) contractile dysfunction commonly occurs and worsens outcomes in heart failure patients with reduced ejection fraction and pulmonary hypertension (HFrEF-PH). However, such dysfunction often goes undetected by standard clinical RV indices, raising concerns that they may not reflect aspects of underlying myocyte dysfunction.

Objective

To determine components of myocyte contractile depression in HFrEF-PH, identify those reflected by clinical RV indices, and elucidate their underlying biophysical mechanisms.

Methods and Results

Resting, calcium- and load-dependent mechanics were measured in permeabilized RV cardiomyocytes isolated from explanted hearts from 23 HFrEF-PH patients undergoing cardiac transplantation and 9 organ-donor controls. Unsupervised machine learning using myocyte mechanical data with the highest variance yielded two HFrEF-PH subgroups that in turn mapped to patients with depressed (RVd) or compensated (RVc) clinical RV function. This correspondence was driven by reduced calcium-activated isometric tension in RVd, while surprisingly, many other major myocyte contractile measures including peak power, maximum unloaded shortening velocity, and myocyte active stiffness were similarly depressed in both groups. Similar results were obtained when subgroups were first defined by clinical indices, and then myocyte mechanical properties in each group compared. To test the role of thick-filament defects, myofibrillar structure was assessed by X-ray diffraction of muscle fibers. This revealed more myosin heads associated with the thick filament backbone in RVd but not RVc, as compared to controls. This corresponded to reduced myosin ATP turnover in RVd myocytes, indicating less myosin in a cross-bridge ready disordered-relaxed (DRX) state. Altering DRX proportion (%DRX) affected peak calcium-activated tension in the patient groups differently, depending on their basal %DRX, highlighting potential roles for precision-guided therapeutics. Lastly, increasing myocyte preload (sarcomere length) increased %DRX 1.5-fold in controls but only 1.2-fold in both HFrEF-PH groups, revealing a novel mechanism for reduced myocyte active stiffness and by extension Frank-Starling reserve in human HF.

Conclusions

While there are multiple RV myocyte contractile deficits In HFrEF-PH, clinical indices primarily detect reduced isometric calcium-stimulated force related to deficits in basal and recruitable %DRX myosin. Our results support use of therapies to increase %DRX and enhance length-dependent recruitment of DRX myosin heads in such patients.
CO-ADMINISTRATION OF RESVERATROL RESCUED LEAD-INDUCED TOXICITY INDROSOPHILA MELANOGASTER
Authors: Abdulazeez R. , Highab S. M. , Onyawole U.F. , Jeje M.T. , Musa H. , Shehu D. M. , Ndams I. S.
Published: March 2023

Lead toxicity poses a significant environmental concern linked to diverse health issues, including cognitive impairments, behavioral abnormalities, reproductive defects, and oxidative stress at the cellular level. This study explores the potential mitigating effects of resveratrol on lead-induced toxicity inDrosophila melanogaster. AdultD. melanogasterof the Harwich strain, aged three days, were orally exposed to lead (60 mg/L), Succimer (10 mg/kg), and varying doses of resveratrol (50, 100, and 150 mg/kg). The investigation encompassed the assessment of selected biological parameters, biochemical markers (ALP, AST, TB, CB, Na, Ca, Ur, Cr), oxidative stress indicators (MDA), and antioxidant enzymes (SOD and CAT). Resveratrol exhibited a dose-dependent enhancement of egg-laying, eclosion rate, filial generation output, locomotor activity, and life span inD. melanogaster, significantly to 150 mg/kg of diet. Most of the investigated biochemical parameters showed significant rescue in lead-exposed fruit flies when co-treated with resveratrol (p < 0.05). However, oxidative stress, as indicated by MDA levels, remained unaffected by resveratrol in this study. The findings suggest that resveratrol effectively protects against lead toxicity inDrosophila melanogasterand may hold therapeutic potential as an agent for managing lead poisoning in humans.
Assessing the implementation of user-centred design standards on assistive technology for persons with visual impairments: A systematic review
Authors: Ortiz-Escobar Luisa María , Chavarria Mario Andres , Schönenberger Klaus , Hurst-Majno Samia , Stein Michael Ashley , Mugeere Anthony , Rivas-Velarde Minerva
Published: March 2023

Despite scientific and technological advances in the field of assistive technology (AT) for people with visual impairment (VI), technological designs are frequently based on a poor understanding of the physical and social context of use, resulting in devices that are less than optimal for their intended beneficiaries. To resolve this situation, user-centred approaches in the development process of AT have been widely adopted in recent years. However, there is a lack of systematization on the application of this approach. This systematic review registered in PROSPERO (CRD42022307466), assesses the application of the ISO 9241-210 human-centred design principles in allegedly “user-centred designed” AT developments for persons with VI (see S1 PROSPERO Protocol). The results point to a wide variation of the depth of understanding of user needs, a poor characterization of the application of the User Centred Design (UCD) approach in the initial design phases or in the early prototyping, and a vague description of user feedback and device iteration. Among the principles set out in ISO 9241-210, the application of 5.6: “the design team includes multidisciplinary skills and perspectives” is the one for which the least evidence is found. The results show there is not enough evidence to fully assess the impact of UCD in 1. promoting innovation regarding AT products and practices, and 2. Judging if AT produced following such standards is leading to better user access, wellbeing outcomes and satisfaction. To address this gap it is necessary to, first, generate better implementation of UCD in AT development and second, to strengthen evidence regarding the implementation and outcomes of using UCD for AT. To better engage with the realities of persons with VI, we propose capacity building across development teams regarding UCD, its principles and components; better planning for UCD implementation; and cross-fertilization across engineering disciplines and social and clinical science.
NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A rapid, PCR-free method for whole genome sequencing of pathogens in clinical samples
Authors: Terrazos Miani Miguel A. , Borcard Loïc , Gempeler Sonja , Baumann Christian , Bittel Pascal , Leib Stephen L , Neuenschwander Stefan , Ramette Alban
Published: March 2023

Whole-genome sequencing (WGS) represents the main technology for SARS-CoV-2 lineage characterization in diagnostic laboratories worldwide. The rapid, near-full-length sequencing of the viral genome is commonly enabled by high-throughput sequencing of PCR amplicons derived from cDNA molecules. Here, we present a new approach, called NASCarD (Nanopore adaptive sampling with carrier DNA), which allows low amount of nucleic acids to be sequenced while selectively enriching for sequences of interest, hence limiting the production of non-target sequences. Using clinical samples positive for SARS-CoV-2 during the Omicron wave, we demonstrate how the method leads to up to >100x coverage of the full genome sequences of the target organism as compared to standard shotgun metatranscriptomics approach. It provides complete and accurate genome sequence reconstruction within seven hours at a competitive cost. The new approach may have applications beyond SARS-CoV-2 sequencing for other DNA or RNA pathogens in clinical samples.