bluuebunny/crossref_metadata_2025 huggingface dataset:
Gender, interdisciplinary graduate training, and confidence working in teams
Authors: Lu Lesa Tran , Blake Laura Palucki , Eyler Josh R. , Verduzco Rafael , Biswal Sibani Lisa , Bennett George N. , Silberg Jonathan J.
Published: April 2024

Teamwork is recognized as critical to solving complex societal challenges related to energy, health, and sustainability. With graduate education, students often gain teamwork experience through a problem-focused approach where they are brought into existing collaborations to pursue research that is focused on studying questions that have already been identified. Here, we describe an interdisciplinary educational program where graduate students were tasked with leading team formation, problem identification, and research formulation. This “team-first” training approach used a two-year curriculum to bring together students enrolled in diverse engineering and science graduate programs and provided students with a pedagogical understanding of interdisciplinarity, nurtured the development of student communication skills across disciplines, fostered student-led team formation and idea development, and empowered students to forge new connections between research groups. Assessment of three cohorts immediately following curriculum completion (n = 36) revealed significant gains in confidence in teamwork (p < 0.001) when compared to a control group of academic peers (n = 74). These gains varied across demographic groups, with women in science, technology, engineering, and mathematics presenting the strongest gains. This finding illustrates the importance of exploring how interdisciplinary team curricula in graduate school could support overcoming the gender gap in confidence.

Significance

Pedagogical models for graduate education often neglect the importance of teamwork training. Here, we describe an interdisciplinary training program that was developed to bring together doctoral students from diverse science, technology, engineering, and mathematics disciplines for a two-year curriculum that focused on teamwork training through student-led team formation, problem identification, and research formulation. Following program participation, we measured participant confidence in teamwork relative to a peer group. Our findings reveal gains with confidence in teamwork, with women presenting the strongest increases without negative effects on other groups. This pedagogical approach represents a strategy to close gender gaps in professional role confidence while complementing the benefits of traditional disciplinary training approaches.
Patch-walking: Coordinated multi-pipette patch clamp for efficiently finding synaptic connections
Authors: Yip Mighten C. , Gonzalez Mercedes M. , Lewallen Colby F. , Landry Corey R. , Kolb Ilya , Yang Bo , Stoy William M. , Fong Ming-fai , Rowan Matthew J.M. , Boyden Edward S. , Forest Craig R.
Published: April 2024

Significant technical challenges exist when measuring synaptic connections between neurons in living brain tissue. The patch clamping technique, when used to probe for synaptic connections, is manually laborious and time-consuming. To improve its efficiency, we pursued another approach: instead of retracting all patch clamping electrodes after each recording attempt, we cleaned just one of them and reused it to obtain another recording while maintaining the others. With one new patch clamp recording attempt, many new connections can be probed. By placing one pipette in front of the others in this way, one can “walk” across the tissue, termed “patch-walking.” We performed 136 patch clamp attempts for two pipettes, achieving 71 successful whole cell recordings (52.2%). Of these, we probed 29 pairs (i.e., 58 bidirectional probed connections) averaging 91µm intersomatic distance, finding 3 connections. Patch-walking yields 80-92% more probed connections, for experiments with 10-100 cells than the traditional synaptic connection searching method.

Motivation

Recognizing the manual labor and time-intensive nature of patch clamping when trying to find synaptic connections, we aim to improve its efficiency. We introduce a novel approach, termed “patch-walking,” where one patch clamping electrode is cleaned and reused, enabling the exploration of numerous connections with a single recording attempt and improving the efficiency of identifying synaptic connections.
Can Current Medical Examination Consumption Reduce Long-term Medical Expenses? - Analysis Based on CHARLS Data
Authors: Luo Juan , San Lulu , Han Sunian , Bi Liang , Ren Zhenpeng
Published: April 2024

Background

With the implementation of the healthy China strategy, physical examination, a means of preventing diseases, has gradually been valued by health care department. Can health examination effectively alleviate the pressure on residents’ medical expenses?

Method

Based on the CHARLS2015 and CHARLS2018 databases, establishing an ordered multi-classification logistic regression model. To study the impact of residents’ health examination on the level of long-term medical expenditure.

Results

The results show that adhere to health examination, long-term physical exercise and quit smoking and drinking can reduce residents’ medical expenses. The physical examination behavior of different populations was further discussed based on gender. The study found that the more physical examinations of male residents, the less medical expenses, while the number of physical examinations of women is not significant for reduce medical expenses.

Conclusion

Therefore, China should vigorously improve the enthusiasm of different residents to participate in health check-ups, give full play to health check-ups in disease prevention and to reduce individual’s medical expenses.
Time course metabolomics and13CO2mapping establish BBX31/miP1b mediated metabolic readjustments conferring UV-B tolerance in Arabidopsis
Authors: Lingwan Maneesh , Yadav Arpita , Datta Sourav , Masakapalli Shyam Kumar
Published: April 2024

B-box proteins (BBXs) are transcription factors that act as signal transducers in light signaling pathways. The microprotein BBX31/miP1b is known to play a positive role in promoting photomorphogenesis and stress tolerance under UV-B. However, the BBX31-mediated metabolic reprogramming to confer UV-B tolerance in plants is not well characterised. Here, we integrate metabolomics with kinetic13CO2tracer-based metabolic mapping, morpho-physiological and biochemical analysis to determine the metabolic rewiring in the UV tolerant genotypes. Our results suggest that BBX31 modulates the levels of photosynthetic compounds, reduces TCA cycle intermediates and enhances GS/GOGAT metabolic intermediates and secondary metabolic pathways.13CO2tracing studies established BBX31 modulates phenylpropanoid and GS/GOGAT pathways to divert flux towards the accumulation of UV-B protective metabolites phenylalanine, oxoproline, glutamine, and others. Although metabolomics indicated a higher accumulation of branch chain amino acids (BCAAs) under UV-B, they had negligible 13C incorporation, indicating their biosynthesis from pre-existing intermediates or via protein degradation. Further, we demonstrate that the exogenous application of phenylalanine, identified as one of the marker metabolites, confers tolerance to plants under UV-B. This study sheds light on BBX31-mediated metabolic rewiring under UV-B, which can assist targeted enrichment of metabolites and metabolic engineering to promote UV-B tolerance in plants.

Highlight

BBX31/miP1b modulates the levels of photosynthetic compounds, reduces TCA cycle intermediates and enhances GS/GOGAT metabolic intermediates to confer UV-B tolerance.
Shewanellais a putative producer of polyunsaturated fatty acids in the gut soil of the composting earthwormEisenia fetida
Authors: Wittlinger Jan-Philipp , Castejón Natalia , Hausmann Bela , Berry David , Schnorr Stephanie L.
Published: April 2024

Polyunsaturated fatty acids (PUFAs) play a crucial role in aiding bacteria to adapt to extreme and stressful environments. While there is a well-established understanding of their production, accrual, and transfer within marine ecosystems, knowledge about terrestrial environments remains limited. Investigation of the intestinal microbiome of earthworms has illuminated the presence of PUFAs presumably of microbial origin, which contrasts with the surrounding soil.

To comprehensively study this phenomenon, a multi-faceted approach was employed, combining fatty acid analysis with amplicon sequencing of the PfaA-KS domain of the anaerobic fatty acid synthase gene (pfa), as well as the 16S rRNA and 18S rRNA genes. This methodology was applied to scrutinize the gut microbiome ofEisenia fetida, its compost-based dietary source, and the resultant castings.

This study unveiled a distinct gut soil ecosystem from input compost and output castings in fatty acid profile as well as type and abundance of organisms. 16S sequencing provided insights into the microbial composition, showing increased relative abundance of certain Pseudomonadota, includingShewanellaceae, and Planctomycetota, includingGemmataceaewithin the gut microbiome compared to input bulk soil compost, while Actinomycetota and Bacillota were relatively enriched compared to the casted feces. Sequencing of the PfaA-KS domain revealed ASVs belonging primarily toShewanella. Intriguingly, the 20C PUFAs were identified only in gut-soil samples, though PfaA-KS sequence abundance was highest in output castings, indicating a unique metabolism occurring only in the gut. Overall, the results indicate thatShewanellacan explain PUFA enrichment in the gut environment because ofpfagene presence detected via PfaA-KS sequence data.

Importance

Prior research has demonstrated that earthworm microbiomes can potentially harbor PUFAs that are not found within their residing soil environment. Moreover, distinct indicator species have been pinpointed for various microbial genera in earthworm microbiomes. Nevertheless, none of these studies have integrated metataxonomic and fatty acid analysis to explore the origin of PUFA synthesis in any earthworm species, with the objective of identifying the specific organisms and locations responsible for this production. This study suggests that earthworms accumulate PUFAs produced from bacteria, especiallyShewanella,activated through the gut ecosystem.
An Evidenced-Based Prior for Estimating the Treatment Effect of Phase III Randomized Trials in Oncology
Authors: Sherry Alexander D. , Msaouel Pavlos , Kupferman Gabrielle S. , Lin Timothy A. , Abi Jaoude Joseph , Kouzy Ramez , McCaw Zachary R. , Ludmir Ethan B. , van Zwet Erik
Published: April 2024

Purpose

The primary results of phase III oncology trials may be challenging to interpret, given that such results are generally based on meetingP-value thresholds. The probability of whether a treatment is beneficial, although a more intuitive summary of the results, is not provided by most trials. In this study, we developed and released a user-friendly tool that calculates the probability that a treatment studied in a phase III oncology trial is beneficial using published summary statistics.

Methods

We curated the primary time-to-event outcomes of 415 phase III, superiority design, therapeutic randomized controlled trials of oncologic treatments enrolling 338,600 patients and published between 2004 and 2020. A phase III oncology-specific prior probability distribution for the treatment effect was developed based on an estimated three-component zero-mean mixture distribution of the observed z-scores. Using this prior, we computed the probability of any benefit (hazard ratio < 1) and the probability of clinically meaningful benefit (hazard ratio < 0.8) for each trial. The distribution of signal-to-noise ratios of phase III oncology trials was compared with that of 23,551 randomized trials from the Cochrane Database of Systematic Reviews.

Results

The signal-to-noise ratios of phase III oncology trials tended to be much larger than randomized trials from the Cochrane database. Still, the median power of phase III oncology trials was only 49% (IQR, 14% to 95%), and the power was less than 80% in 65% of trials. Using the developed phase III, oncology-specific prior, only 53% of trials claiming superiority (114 of 216) had a ≥ 90% probability of providing clinically meaningful benefits. Conversely, the probability that the experimental arm was superior to the control arm (HR < 1) exceeded 90% in 17% of trials interpreted as having no benefit (34 of 199).

Conclusion

By enabling computation of contextual probabilities for the treatment effect from summary statistics, our robust, highly practical tool, now posted on a user-friendly webpage, can aid the wider oncology community in the interpretation of phase III trials.
Optimal Timing of Organs-at-Risk-Sparing Adaptive Radiation Therapy for Head-and-Neck Cancer under Re-planning Resource Constraints
Authors: Nosrat Fatemeh , Dede Cem , McCullum Lucas B. , Garcia Raul , Mohamed Abdallah S. R. , Scott Jacob G. , Bates James E. , McDonald Brigid A. , Wahid Kareem A. , Naser Mohamed A. , He Renjie , Karagoz Aysenur , Moreno Amy C. , van Dijk Lisanne V. , Brock Kristy K. , Heukelom Jolien , Hosseinian Seyedmohammadhossein , Hemmati Mehdi , Schaefer Andrew J. , Fuller Clifton D.
Published: April 2024

Background and Purpose

Prior work on adaptive organ-at-risk (OAR)-sparing radiation therapy has typically reported outcomes based on fixed-number or fixed-interval re-planning, which represent one-size-fits-all approaches and do not account for the variable progression of individual patients’ toxicities. The purpose of this study was to determine the personalized optimal timing for re-planning in adaptive OAR-sparing radiation therapy, considering limited re-planning resources, for patients with head and neck cancer (HNC).

Materials and Methods

A novel Markov decision process (MDP) model was developed to determine optimal timing of re-planning based on the patient’s expected toxicity, characterized by normal tissue complication probability (NTCP), for four toxicities. The MDP parameters were derived from a dataset comprising 52 HNC patients treated at the University of Texas MD Anderson Cancer Center between 2007 and 2013. Kernel density estimation was used to smooth the sample distributions. Optimal re-planning strategies were obtained when the permissible number of re-plans throughout the treatment was limited to 1, 2, and 3, respectively.

Results

The MDP (optimal) solution recommended re-planning when the difference between planned and actual NTCPs (ΔNTCP) was greater than or equal to 1%, 2%, 2%, and 4% at treatment fractions 10, 15, 20, and 25, respectively, exhibiting a temporally increasing pattern. The ΔNTCP thresholds remained constant across the number of re-planning allowances (1, 2, and 3).

Conclusion

In limited-resource settings that impeded high-frequency adaptations, ΔNTCP thresholds obtained from an MDP model could derive optimal timing of re-planning to minimize the likelihood of treatment toxicities.

Graphical Abstract

Overview of the analysis method. The sub-figures displaying Organs at risk and toxicities are adapted from [1] with permission. Abbreviation: NTCP = Normal tissue complications probability.
Long-read sequencing to detect full-length protein-protein interactions
Authors: Schaefer-Ramadan Stephanie , Guan Yue , Ahmed Ayeda A. , Aleksic Jovana , Elmagarmid Khadija A. , Syed Leena F. , Mohamoud Yasmin A. , Malek Joel A.
Published: April 2024

Given the increased predictions on interactome size and demand for protein function information, methods for detecting protein-protein interactions remain a significant development area. The all-vs.-all sequencing (AVA-Seq) method utilizes a convergent fusion plasmid design to make two-hybrid technology amenable to next-generation sequencing. Here, we further innovate to take advantage of synthetic DNA technologies and Oxford Nanopore Technologies long-read sequencing improvements to allow us to determine full-length protein-protein interactions. Here, using this approach we recovered 159 protein-protein interactions from a set of 57 human proteins using multiple forms of validation. Further, when referencing a human gold standard set of interactions, eight full-length protein-protein interactions were recovered from an expected 28 interaction pairs (28.6%), a typical recovery rate for two-hybrid technologies. The AVA-Seq, in combination with the ease of synthetic DNA production and the MinION platform, offers a low-cost, high-throughput alternative for determining protein-protein interactions, which can be utilized in research labs at all stages.

3

Key Points

First application of long-read sequencing for full-length protein-protein interaction studies.

The recovery rate of the AVA-Seq method using full-length proteins is on par with other leading methods.

Advances in synthetic biology and sequencing technologies make full-length protein interactomes affordable and accessible.

GRAPHICAL ABSTRACT
O Short-branch Microsporidia, Where Art Thou? Identifying diversity hotspots for future sampling
Authors: Gross Megan , Rajter Ľubomír , Mahé Frédéric , Bass David , Berney Cédric , Henry Nicolas , de Vargas Colomban , Dunthorn Micah
Published: April 2024

Short-branch Microsporidia were previously shown to form a basal grade within the expanded Microsporidia clade and to branch near the classical, long-branch Microsporidia. Although they share simpler versions of some morphological characteristics, they do not show accelerated evolutionary rates, making them ideal candidates to study the evolutionary trajectories that has led to long-branch microsporidians unique characteristics. However, most sequences assigned to the short-branch Microsporidia are undescribed, novel environmental lineages for which the identification requires knowledge of where they can be found. To direct future isolation, we used the EukBank database of the global UniEuk initiative that contains the majority of the publicly available environmental V4 SSU-rRNA gene sequences of protists. The curated OTU table and corresponding metadata were used to evaluate the occurrence of short-branch Microsporidia across freshwater, hypersaline, marine benthic, marine pelagic, and terrestrial environments. Presence-absence analyses infer that short-branch Microsporidia are most abundant in freshwater and terrestrial environments, and alpha- and beta-diversity measures indicate that focusing our sampling effort on these two environments would cover a large part of their overall diversity. These results can be used to coordinate future isolation and sampling campaigns to better understand the mysterious evolution of microsporidians unique characteristics.
Developmental convergence and divergence in human stem cell models of autism spectrum disorder
Authors: Gordon Aaron , Yoon Se-Jin , Bicks Lucy K , Martin Jaqueline M , Pintacuda Greta , Arteaga Stephanie , Wamsley Brie , Guo Qiuyu , Elahi Lubayna , Dolmetsch Ricardo E. , Bernstein Jonathan A , O’Hara Ruth , Hallmayer Joachim F , Lage Kasper , Pasca Sergiu P , Geschwind Daniel H
Published: April 2024

Two decades of genetic studies in autism spectrum disorder (ASD) have identified over a hundred genes harboring rare risk mutations. Despite this substantial heterogeneity, transcriptomic and epigenetic analyses have identified convergent patterns of dysregulation across ASD post-mortem brain tissue. To identify shared and distinct mutational mechanisms, we assembled the largest hiPS cell patient cohort to date, consisting of 70 hiPS cell lines after stringent quality control representing 8 ASD-associated mutations, idiopathic ASD, and 20 lines from non-affected controls. We used these hiPS lines to generate human cortical organoids (hCO), profiling by RNAseq at four distinct timepoints up to 100 days ofin vitrodifferentiation. Early timepoints harbored the largest mutation-specific changes, but different genetic forms converged on shared transcriptional changes as development progressed. We identified a shared RNA and protein interaction network, which was enriched in ASD risk genes and predicted to drive the observed down-stream changes in gene expression. CRISPR-Cas9 screening of these candidate transcriptional regulators in induced human neural progenitors validated their downstream molecular convergent effects. These data illustrate how genetic risk can propagate via transcriptional regulation to impact convergently dysregulated pathways, providing new insight into the convergent impact of ASD genetic risk on human neurodevelopment.
Electric-field induced sleep promotion and lifespan extension in Gaucher’s disease model flies: Association with improving ER stress and autophagy
Authors: Nedachi Takaki , Kawasaki Haruhisa , Inoue Eiji , Suzuki Takahiro , Nakagawa-Yagi Yuzo , Ishida Norio
Published: April 2024

Gaucher’s disease (GD), one kind of genetic disease, is characterized by a mutation in metabolic enzyme, glucocerebrosidase (GBA), leading to accumulation of its substrate, glucosylceramide in tissues. We previously discovered that theminos-inserted mutation of theGBAgene in fruit flies,Drosophila melanogaster, reproduced human GD characteristics and can be used as a promising model for molecular mechanisms study. Recently, we reported that extremely low-frequency electric fields (ELF-EFs) promoted sleep and extended the lifespan of normal flies.

In this study, GD model flies were exposed to ELF-EFs, and sleep parameters, gene expressions, and longevity were evaluated. The amount of sleep and lifespan increased after EF exposure. Simultaneously, the expression of the endoplasmic reticulum (ER) stress-related gene,PERKand the autophagy-related gene,p62was elevated. The data suggest that the healthy effects of EFs on GD flies are associated with improved adaptation to cellular stress.
Competing mechanisms for the buckling of an epithelial monolayer identified using multicellular simulation
Authors: Brown Phillip J. , Green J. Edward F. , Binder Benjamin J. , Osborne James M.
Published: April 2024

A model using the rigid body multi–cellular framework (RBMCF) is implemented to investigate the mechanisms of buckling of an epithelial mono-layer. Specifically, the deformation of a monolayer of epithelial cells which are attached to a basement membrane and the surrounding stromal tissue. The epithelial monolayer, supporting basement membrane and stromal tissue are modelled using two separate vertex dynamics models (one for the epithelial monolayer layer and one for the basement membrane and stromal tissue combined) and interactions between the two are considered using the RBMCF to ensure biologically realistic interactions. Model simulations are used to investigate the effects of cell–stromal attachment and membrane rigidity on buckling behaviour. We demonstrate that there are two competing modes of buckling, stromal deformation and stromal separation.

Highlights

A rigid body multi–cellular framework allows for the simulation of an epithelial monolayer which is connected to a basement membrane and surrounding tissue stroma.

Interaction with basement membrane and tissue stroma allows epithelial cells to migrate forming a confluent monolayer.

Buckling of monolayer can occur through separation from or deformation of the basement membrane.
Kinetic model for the desensitization of G protein-coupled receptor
Authors: Kim Won Kyu , Lee Yoonji , Jang Seogjoo J. , Hyeon Changbong
Published: April 2024

GPCR desensitization is a general regulatory mechanism adopted by biological organisms against overstimulation of G protein-coupled receptors. Although the details of mechanism aren extensively studied, it is not easy to gain an overarching understanding of the process constituted by a multitude of molecular events with vastly differing time scales. To offer a semi-quantitative yet predictive understanding of the mechanism, we formulate a kinetic model for the G protein signaling and desensitization by considering essential biochemical steps from ligand binding to receptor internalization. The internalization followed by the receptor depletion from the plasma membrane attenuates the downstream signal. Together with the kinetic model, an approximated form of expression derived for the dose-response clarifies the role played by the individual biochemical processes and allows us to identify three distinct regimes for the downregulation that emerge from the balance between phosphorylation, dephosphorylation and the cellular level ofβ-arrestin.
Photophysics-informed two-photon voltage imaging using FRET-opsin voltage indicators
Authors: Brooks F. Phil , Davis Hunter C. , Park Pojeong , Qi Yitong , Cohen Adam E.
Published: April 2024

Microbial rhodopsin-derived genetically encoded voltage indicators (GEVIs) are powerful tools for mapping bioelectrical dynamics in cell culture and in live animals. Förster resonance energy transfer (FRET)-opsin GEVIs use voltage-dependent changes in opsin absorption to modulate the fluorescence of an atached fluorophore, achieving high brightness, speed, and voltage sensitivity. However, the voltage sensitivity of most FRET-opsin GEVIs has been reported to decrease or vanish under two-photon (2P) excitation. Here we investigated the photophysics of the FRET-opsin GEVIs Voltron1 and 2. We found that the voltage sensitivity came from a photocycle intermediate, not from the opsin ground state. The voltage sensitivities of both GEVIs were nonlinear functions of illumination intensity; for Voltron1, the sensitivity reversed sign under low-intensity illumination. Using photocycle-optimized 2P illumination protocols, we demonstrate 2P voltage imaging with Voltron2 in barrel cortex of a live mouse. These results open the door to high-speed 2P voltage imaging of FRET-opsin GEVIsin vivo.

Teaser

Voltage sensitivity in FRET-opsin indicators comes from a photocycle intermediate, reachable via optimized 2P excitation.
Decoding Missense Variants by Incorporating Phase Separation via Machine Learning
Authors: Feng Mofan , Wei Xiaoxi , Zheng Xi , Liu Liangjie , Lin Lin , Xia Manying , He Guang , Shi Yi , Lu Qing
Published: April 2024

Computational models have made significant progress in predicting the effect of protein variants. However, deciphering numerous variants of unknown significance (VUS) located within intrinsically disordered regions (IDRs) remains challenging. To address this issue, we introduced phase separation (PS), which is tightly linked to IDRs, into the investigation of missense variants. Phase separation is vital for multiple physiological processes. By leveraging missense variants that alter phase separation propensity, we developed a machine learning approach named PSMutPred to predict the impact of missense mutations on phase separation. PSMutPred demonstrated robust performance in predicting missense variants that affect natural phase separation. In vitro experimental findings further underscore its validity. By applying PSMutPred on over 522,000 ClinVar missense variants, it significantly contributes to decoding the pathogenesis of disease variants, especially those in IDRs. Our work provides unique insights into the understanding of a vast number of VUSs in IDRs, thereby expediting clinical interpretation and diagnosis of disease variants.
Reanalysis of Orbitrap Astral DIA data demonstrates the capabilities of MS/MS-free proteomics to reveal new biological insights in disease-related samples
Authors: Ivanov Mark V. , Kopeykina Anna S. , Gorshkov Mikhail V.
Published: April 2024

Data-independent acquisition (DIA) became a method of choice for quantitative proteomics. With the advent of the combination of Orbitrap FTMS and asymmetric track lossless analyzer Astral these DIA capabilities were further extended with the recent demonstration of quantitative proteomic sample analyses at the speed of up to hundreds of samples per day. In particular, the dataset containing brain samples related to the multiple system atrophy was acquired using 7 and 28 min chromatography gradients and the Orbitrap Astral mass spectrometer (Guzman et al., Nat. Biotech.2024). In this work, we reanalysed the Orbitrap Astral DIA data using MS1 spectra without applying to fragmentation information using the recently introduced DirectMS1 approach. The results were compared with previous study of the same sample cohort by traditional long gradient DDA analysis. While the quantitation efficiency of DirectMS1 was comparable, we found additional five proteins of biological significance relevant to the analyzed tissue samples. Among the findings, DirectMS1 was able to detect decreased caspase activity for Vimentin protein in the multiple system atrophy samples which was barely observed from MS/MS-based methods. Our study suggests that DirectMS1 can be an efficient MS1-only addition to the analysis of DIA data in quantitative proteomic studies.
An effective and safe maize seed chipping protocol using clipping pliers with applications in small-scale genotyping and marker-assisted breeding
Authors: Zebosi Brian , Ssengo John , Geadelmann Lander F , Unger-Wallace Erica , Vollbrecht Erik
Published: April 2024

In applications such as marker-assisted breeding and positional cloning, tissue sampling and plant tracking are vital steps in the genotyping pipeline. They enable the identification of desirable seedlings, saving time and reducing the cost, space, and handling required for growing adult plants, especially for greenhouses and winter nurseries. Small-scale marker-assisted selection laboratories rely heavily on leaf-based genotyping, which involves over-planting large, segregating populations followed by leaf sampling, genotyping, and backtracking to identify desired individuals, which is costly and laborious. Thus, there is a need to adopt seed-based genotyping to reduce costs and save time. Therefore, we developed a safe and cheap seed-chipping protocol using clipping pliers to chip seeds to genotype before planting. To identify a cost-effective and high throughput DNA extraction method, we tested four extraction methods and assessed the quality of the seed DNA using PCR. For three of the methods, seed-based DNA was of comparable quality to DNA extracted from leaf punches. We also compared seed- and leaf-derived DNA from the same individuals in a segregating population to test for genotyping miscalls that could arise due to the presence of maternally derived pericarp in the seed samples and found zero miscalls of 43 potential instances. Germination rates of chipped and unchipped seeds were the same for the inbreds tested, B73 and Mo17. However, chipped seeds grew slower until ∼14 days after sowing. Overall, seed sampling using clipping pliers provides a simple, reliable, and high-throughput method to identify specific genotypes before planting.

Key Features

Provides a quick, safe, and cheap sampling technique for maize kernels that may also be suitable for other plants with relatively large seeds.

Includes procedures and materials to track and organize samples within and across batches involving hundreds to thousands of seeds.

Seeds can be sampled and genotyped relatively quickly for planting; in one day 384 seeds can be sampled, processed for DNA, and genotyped by PCR.
Chemoproteomic profiling of substrate specificity in gut microbiota-associated bile salt hydrolases
Authors: Han Lin , Pendleton Augustus , Singh Adarsh , Xu Raymond , Scott Samantha A. , Palma Jaymee A. , Diebold Peter , Malarney Kien P. , Brito Ilana L. , Chang Pamela V.
Published: April 2024

The gut microbiome possesses numerous biochemical enzymes that biosynthesize metabolites that impact human health. Bile acids comprise a diverse collection of metabolites that have important roles in metabolism and immunity. The gut microbiota-associated enzyme that is responsible for the gateway reaction in bile acid metabolism is bile salt hydrolase (BSH), which controls the host’s overall bile acid pool. Despite the critical role of these enzymes, the ability to profile their activities and substrate preferences remains challenging due to the complexity of the gut microbiota, whose metaproteome includes an immense diversity of protein classes. Using a systems biochemistry approach employing activity-based probes, we have identified gut microbiota-associated BSHs that exhibit distinct substrate preferences, revealing that different microbes contribute to the diversity of the host bile acid pool. We envision that this chemoproteomic approach will reveal how secondary bile acid metabolism controlled by BSHs contributes to the etiology of various inflammatory diseases.
Metatranscriptomics reveals declines in ice cover influence winter viral community activity
Authors: Denison Elizabeth R , Zepernick Brittany N , McKay Robert M , Wilhelm Steven
Published: April 2024

Freshwater lakes are sentinels of environmental change, and climate change-driven declines in ice cover have been shown to disrupt aquatic communities and jeopardize ecosystem services. Viruses shape microbial communities and regulate biogeochemical cycles by acting as top-down controls, yet there is relatively little known about how declining ice cover will influence viral community activity. Lake Erie is a critical freshwater ecosystem and serves as a model system to assess how ice cover extent will affect winter limnology. We surveyed size selected surface water metatranscriptomes for conserved viral hallmark genes as a proxy for active virus populations and compared activity profiles between ice-covered and ice-free conditions from two contrasting winters. Active virus communities were present in both conditions, spanning diverse phylogenetic clades of bacteriophage (Caudovirales), giant viruses (Nucleocytoviricota), and RNA viruses (Orthornavirae). However, viral activity was significantly shaped by the extent of ice cover. Notably, viral richness and relative transcript abundance in the surface waters were reduced under ice relative to the ice-free conditions. Correlations with microbial community metrics suggest the differences in viral communities are at least in part driven by the decreased winter diatom bloom associated with declines in ice cover. Overall, our data suggest viral community activity is influenced by ice cover extent, and viruses may serve as sentinels of environmental disturbance and ecosystem response(s) to climate change.
Beyond Normalization: Incorporating Scale Uncertainty in Microbiome and Gene Expression Analysis
Authors: Nixon Michelle Pistner , Gloor Gregory B. , Silverman Justin D.
Published: April 2024

Though statistical normalizations are often used in differential abundance or differential expression analysis to address sample-to-sample variation in sequencing depth, we offer a better alternative. These normalizations often make strong, implicit assumptions about the scale of biological systems (e.g., microbial load). Thus, analyses are susceptible to even slight errors in these assumptions, leading to elevated rates of false positives and false negatives. We introduce scale models as a generalization of normalizations so researchers can model potential errors in assumptions about scale. By incorporating scale models into the popular ALDEx2 software, we enhance the reproducibility of analyses while often drastically decreasing false positive and false negative rates. We design scale models that are guaranteed to reduce false positives compared to equivalent normalizations. At least in the context of ALDEx2, we recommend using scale models over normalizations in all practical situations.
Age-dependent regulation of axoglial interactions and behavior by oligodendrocyte AnkyrinG
Authors: Ding Xiaoyun , Wu Yu , Rodriguez Victoria , Ricco Emily , Okoh James T. , Liu Yanhong , Kraushaar Daniel C. , Rasband Matthew N.
Published: April 2024

The bipolar disorder (BD) risk geneANK3encodes the scaffolding protein AnkyrinG (AnkG). In neurons, AnkG regulates polarity and ion channel clustering at axon initial segments and nodes of Ranvier. Disruption of neuronal AnkG causes BD-like phenotypes in mice. During development, AnkG is also expressed at comparable levels in oligodendrocytes and facilitates the efficient assembly of paranodal junctions. However, the physiological roles of glial AnkG in the mature nervous system, and its contributions to BD-like phenotypes, remain unexplored. Here, we generated oligodendroglia-specific AnkG conditional knockout mice and observed the destabilization of axoglial interactions in aged but not young adult mice. In addition, these mice exhibited profound histological, electrophysiological, and behavioral pathophysiologies. Unbiased translatomic profiling revealed potential compensatory machineries. These results highlight the critical functions of glial AnkG in maintaining proper axoglial interactions throughout aging and suggests a previously unrecognized contribution of oligodendroglial AnkG to neuropsychiatric disorders.
MATRIN3deficiency triggers autoinflammation via cGAS-STING activation
Authors: Islam Zohirul , Polash Ahsan , Suzawa Masataka , Chim Bryan , Kuhn Skyler , Sultana Sabrina , Cutrona Nicholas , Smith Patrick T. , Kabat Juraj , Ganesan Sundar , Foroushani Amir , Hafner Markus , Muljo Stefan A.
Published: April 2024

Interferon-stimulated genes (ISGs) comprise a program of immune effectors important for host immune defense. When uncontrolled, ISGs play a central role in interferonopathies and other inflammatory diseases. The mechanisms responsible for turning on ISGs are not completely known. By investigating MATRIN3 (MATR3), a nuclear RNA-binding protein mutated in familial ALS, we found that perturbing MATR3 results in elevated expression of ISGs. Using an integrative approach, we elucidate a pathway that leads to activation of cGAS-STING. This outlines a plausible mechanism for pathogenesis in a subset of ALS, and suggests new diagnostic and therapeutic approaches for this fatal disease.

One-Sentence Summary

Mis-splicing ofTudor Domain Containing 3(TDRD3) in the absence of MATR3 unleashes R-loops and interferon-stimulated genes.
Supplier-origin gut microbiomes affect host body weight and select autism-related behaviors
Authors: McAdams Zachary L. , Gustafson Kevin L. , Russell Amber L. , Self Rachel , Petry Amy L. , Lever Teresa E. , Ericsson Aaron C.
Published: April 2024

Autism spectrum disorders (ASD) are complex human neurodiversities increasing in prevalence within the human population. In search of therapeutics to improve quality-of-life for ASD patients, the gut microbiome (GM) has become a promising target as a growing body of work supports roles for the complex community of microorganisms in influencing host behavior via the gut-brain-axis. However, whether naturally-occurring microbial diversity within the host GM affects these behaviors is often overlooked. Here we applied a model of population-level differences in the GM to a classic ASD model – the BTBR T+Itpr3tf/J mouse – to assess how complex GMs affect host behavior. Leveraging the naturally occurring differences between supplier-origin GMs, our data demonstrate that differing, complex GMs selectively effect host ASD-related behavior – especially neonatal ultrasonic communication – and reveal a male-specific effect on behavior not typically observed in this strain. We then identified that the body weight of BTBR mice is influenced by the postnatal GM which was potentially mediated by microbiome-dependent effects on energy harvest in the gut. These data provide insight into how variability within the GM affects host behavior and growth, thereby emphasizing the need to incorporate naturally occurring diversity within the host GM as an experimental factor in biomedical research.
Sex-specific brain effective connectivity patterns associated with negative emotions
Authors: Sultana Tajwar , Ijaz Dua , Khan Fareha Asif , Misaal Maryam , Dhamala Elvisha , Razi Adeel
Published: April 2024

Sex differences in effective brain connectivity in emotional intelligence, emotional regulation, and stimuli-induced negative emotions have been highlighted in previous research. However, to our knowledge, no research has yet investigated the sex-specific effective connectivity related to negative emotions in healthy population during resting-state. The goal of this study is to find the association between sex-specific resting-state effective brain connectivity and basic negative emotions. For this, we have employed the NIH emotion battery of the three self-reported, basic negative emotions — anger-affect, fear-affect, and sadness which we divided into high, moderate, and low emotion scores in each. The dataset comprises 1079 subjects (584 females) from HCP Young Adults. We selected large-scale resting-state brain networks important for emotional processing namely default mode, executive, and salience networks. We employed subject-level analysis using spectral dynamic causal modelling and group-level association analyses using parametric empirical Bayes. We report association of the self-connection of left hippocampus in females in high anger-affect, fear-affect, and sadness, whereas in males we found involvement of dorsal anterior cingulate cortex (dACC) in all three negative emotions - association of right amygdala to dACC in high anger-affect, association of the self-connection of dACC in high fear-affect, and association of dACC to left hippocampus in high sadness. Our findings primarily revealed the effective brain connectivity that is related to the higher levels of negative emotions that may lead to psychiatric disorders if not regulated. Sex-specific therapies and interventions that target psychopathology can be more beneficial when informed by the sex-specific resting-state effective connectivity.
Prioritized adjustments in posture stabilization and adaptive reaching during neuromuscular fatigue of lower-limb muscles
Authors: Nardon Mauro , Sinha Oindrila , Kpankpa John , Albenze Eliza , Bonnet Cédrick , Bertucco Matteo , Singh Tarkeshwar
Published: April 2024

Neuromuscular fatigue (NMF) induces temporary reductions in muscle force production capacity, affecting various aspects of motor function. While studies have extensively explored NMF’s impact on muscle activation patterns and postural stability, its influence on motor adaptation processes remains less understood. This paper investigates the effects of localized NMF on motor adaptation during upright stance, focusing on reaching tasks. Utilizing a force field perturbation paradigm, participants performed reaching movements while standing upright before and after inducing NMF in the ankle dorsiflexor muscles. Results revealed that despite maintained postural stability, participants in the NMF group exhibited larger movement errors during reaching tasks, suggesting impaired motor adaptation. This was evident in both initial and terminal phases of adaptation, indicating a disruption in learning processes rather than a decreased adaptation rate. Analysis of electromyography activation patterns highlighted distinct strategies between groups, with the NMF group showing altered activation of both fatigued and non-fatigued muscles. Additionally, differences in co-activation patterns suggested compensatory mechanisms to prioritize postural stability despite NMF-induced disruptions. These findings underscore the complex interplay between NMF, motor adaptation, and postural control, suggesting a potential role for central nervous system mechanisms in mediating adaptation processes. Understanding these mechanisms has implications for sports performance, rehabilitation, and motor skill acquisition, where NMF may impact the learning and retention of motor tasks. Further research is warranted to elucidate the transient or long-term effects of NMF on motor adaptation and its implications for motor rehabilitation interventions.

New & Noteworthy

We assessed motor adaptation during force field reaching following exercise-induced neuromuscular fatigue (NMF) on postural muscles. NMF impaired adaptation in performance. Similarly, diverging activation strategies were observed in the muscles. No effects were seen on measures of postural control. These results suggest the remodulation of motor commands to the muscles in presence of NMF, which may be relevant in settings where participants could be exposed to NMF while learning, such as sports and rehabilitation.
Large-
N
Principal Chiral Model in Arbitrary External Fields
Authors: Kazakov Vladimir , Sobko Evgeny , Zarembo Konstantin
Published: April 2024

We report the explicit solution for the vacuum state of the two-dimensional SU(N) principal chiral model at large N for an arbitrary set of chemical potentials and any interaction strength, a unique result of such kind for an asymptotically free quantum field theory. The solution matches one-loop perturbative calculation at weak coupling, and in the opposite strong-coupling regime exhibits an emergent spacial dimension from the continuum limit of the SU(N) Dynkin diagram.

Published by the American Physical Society
2024
Vibrational and thermal properties of amorphous alumina from first principles
Authors: Harper Angela F. , Iwanowski Kamil , Witt William C. , Payne Mike C. , Simoncelli Michele
Published: April 2024

Amorphous alumina is employed ubiquitously as a high-dielectric-constant material in electronics, and its thermal-transport properties are of key relevance for heat management in electronic chips and devices. Experiments show that the thermal conductivity of alumina depends significantly on the synthesis process, indicating the need for a theoretical study to elucidate the atomistic origin of these variations. Here we employ first-principles simulations to characterize the atomistic structure, vibrational properties, and thermal conductivity of alumina at densities ranging from 2.28 to 3.49 g/cm3. Moreover, using a machine-learned interatomic potential trained on first-principles data, we investigate how system size affects predictions of the thermal conductivity, showing that simulations containing 120 atoms can already reproduce the bulk limit of the conductivity. Finally, relying on the recently developed Wigner formulation of thermal transport, we shed light on the interplay between atomistic topological disorder and anharmonicity in the context of heat conduction, showing that the former dominates over the latter in determining the conductivity of alumina.

Published by the American Physical Society
2024
Analysis of aero engine plume potential core infrared signature
Authors: Bhatt Ashish , Mahulikar Shripad P.
Published: April 2024

Purpose

Aero-engine exhaust plume length can be more than the aircraft length, making it easier to detect and track by infrared seeker. Aim of this study is to analyze the effect of free stream Mach number (M∞) on length of potential core of plume. Also, change in infrared (IR) signature of plume and aircraft surface with variation in elevation angle (θ) is examined.

Design/methodology/approach

Convergent divergent (CD) nozzle is located outside the rear fuselage of the aircraft. A two dimensional axisymmetric computational fluid dynamics (CFD) study was carried out to study effect of M∞ on potential core. The CFD data with aircraft and plume was then used for IR signature analysis. The sensor position is changed with respect to aircraft from directly bottom towards frontal section of aircraft. The IR signature is studied in mid wave IR (MWIR) and long wave IR (LWIR) band.

Findings

The potential plume core length and width increases as M∞ increases. At higher altitudes, the potential core length increases for a fixed M∞. The plume emits radiation in the MWIR band, whereas the aerodynamically heated aircraft surface emits IR in the LWIR band. The IR signature in the MWIR band continuously decreases as the sensor position changes from directly bottom towards frontal. In the LWIR band the IR signature initially decreases as the sensor moves from the directly bottom to the frontal, as the sensor begins to see the wing leading edges and nose cone, the IR signature in the LWIR band slightly increases.

Originality/value

The novelty of this study comes from the data reported on the effect of free stream Mach number on the potential plume core and variation of the overall IR signature of aircraft with change in elevation angle from directly below towards frontal section of aircraft.