bluuebunny/crossref_metadata_2025 huggingface dataset:
The Characteristics of Organ Function Damage of Hemorrhagic Shock in Hot Environment and the Effect of Hypothermic Fluid Resuscitation
Authors: Zhu Yu , Ma Sheng , Deng Hao-Yue , Wu Yue , Zhang Jie , Xiang Xin-Ming , Peng Xiao-Yong , Liu Liang-Ming , Li Tao
Published: October 2021

Background:

Hemorrhagic shock is the important factor for causing death of trauma and war injuries. However, pathophysiological characteristics and underlying mechanism in hemorrhagic shock with hot environment remain unclear.

Methods:

Hemorrhagic shock in hot environment rat model was used to explore the changes of mitochondrial and vital organ functions, the variation of the internal environment, stress factors, and inflammatory factors; meanwhile, the suitable treatment was further studied.

Results:

Above 36°C hot environment induced the increase of core temperature of rats, and the core temperature was not increased in 34°C hot environment, but the 34°C hot environment aggravated significantly hemorrhagic shock induced mortality. Further study showed that the mitochondrial functions of heart, liver, and kidney were more damaged in hemorrhagic shock rats with 34°C hot environment as compared with room environment. Moreover, the results showed that in hemorrhagic shock rats with hot environment, the blood concentration of Na+, K+, and plasma osmotic pressure, the expression of inflammatory factors tumor necrosis factor-α and interleukin-6 in the serum, as well as the stress factors Adrenocorticotropic Hormone and Glucocorticoid were all notably enhanced; and acidosis was more serous; oxygen supply and oxygen consumption were remarkably decreased. In addition, the present study demonstrated that mild hypothermia (10°C) fluid resuscitation could significantly improve the survival rate in hemorrhagic shock rats with hot environment as compared with normal temperature fluid resuscitation.

Conclusions:

Hot environment accelerated the death of hemorrhagic shock rats, which was related to the disorder of internal environment, the increase of inflammatory and stress factors. Furthermore, moderate hypothermic (10°C) fluid resuscitation was suitable for the treatment of hemorrhagic shock in hot environment.
RUSBoost: A suitable species distribution method for imbalanced records of presence and absence. A case study of twenty-five species of Iberian bats
Authors: Carrasco Jaime , Lisón Fulgencio , Weintraub Andrés
Published: October 2021

Traditional Species Distribution Models (SDMs) may not be appropriate when examples of one class (e.g. absence or pseudo-absences) greatly outnumber examples of the other class (e.g. presences or observations), because they tend to favor the learning of observations more frequently.

We present an ensemble method called Random UnderSampling and Boosting (RUSBoost), which was designed to address the case where the number of presence and absence records are imbalanced, and we opened the “black-box” of the algorithm to interpret its results and applicability in ecology.

We applied our methodology to a case study of twenty-five species of bats from the Iberian Peninsula and we build a RUSBoost model for each species. Furthermore, in order to improve to build tighter models, we optimized their hyperparameters using Bayesian Optimization. In particular, we implemented a objective function that represents the cross-validation loss: , with representing the hyper-parameters Maximum Number of Splits, Number of Learners and Learning Rate.

The models reached average values for Area Under the ROC Curve (AUC), specificity, sensitivity, and overall accuracy of 0.84 ± 0.05%, 79.5 ± 4.87%, 74.9 ± 6.05%, and 78.8 ± 5.0%, respectively. We also obtained values of variable importance and we analyzed the relationships between explanatory variables and bat presence probability.

The results of our study showed that RUSBoost could be a useful tool to develop SDMs with good performance when the presence/absence databases are imbalanced. The application of this algorithm could improve the prediction of SDMs and help in conservation biology and management.
Evolution of a novel female reproductive strategy inDrosophila melanogasterpopulations subjected to long term protein restriction
Authors: Dasgupta Purbasha , Halder Subhasish , Dari Debapriya , Nabeel P. , Vajja Sai Samhitha , Nandy Bodhisatta
Published: October 2021

Reproductive output is often constrained by availability of macronutrients, especially protein. Long term protein restriction, therefore, is expected to select for traits that maximize reproductive output in spite of such nutritional challenge. We subjected four replicate populations ofDrosophila melanogasterto a complete deprivation of live-yeast supplement, thereby mimicking a protein restricted ecology. As yeast supplement is a key source of protein, such an ecology is expected to strongly limit reproductive output, especially in females. Following 24 generations of experimental evolution, compared to their matched controls, females from experimentally evolved populations showed increase in reproductive output early in life, both in presence and absence of yeast supplement. The observed increase in reproductive output was not associated with any accommodating alteration in egg size; and development time, pre-adult survivorship, and body mass at eclosion of the progeny. There was no evidence for evolution of lifespan and lifelong cumulative reproductive output in females. However, females from experiment regime were found to have a significantly faster rate of reproductive senescence, as indicated by a faster rate of age related decline in reproductive output following the attainment of the reproductive peak. Therefore, adaptation to yeast deprivation ecology in our study involved a novel reproductive strategy whereby females attained higher reproductive output early in life followed by faster reproductive aging. To the best of our knowledge, this set of results is one of the most clear demonstration of optimization of fitness by fine tuning of reproductive schedule during adaptation to a prolonged nutritional deprivation.

Supplementary information

A separate file that includes three figures and six tables.
Preserved motor representations after paralysis
Authors: Guan Charles , Aflalo Tyson , Zhang Carey Y. , Rosario Emily R. , Pouratian Nader , Andersen Richard A.
Published: October 2021

Abstract

Neural plasticity allows us to learn skills and incorporate new experiences. What happens when our lived experiences fundamentally change, such as after a severe injury? To address this question, we analyzed intracortical population activity in a tetraplegic adult as she controlled a virtual hand through a brain-computer interface (BCI). By attempting to move her fingers, she could accurately drive the corresponding virtual fingers. Neural activity during finger movements exhibited robust representational structure and dynamics that matched the representational structure, previously identified in able-bodied individuals. The finger representational structure was consistent during extended use, even though the structure contributed to BCI decoding errors. Our results suggest that motor representations are remarkably stable, even after complete paralysis. BCIs re-engage these preserved representations to restore lost motor functions.
Controlling astrocyte-mediated synaptic pruning signals for schizophrenia drug repurposing with Deep Graph Networks
Authors: Gravina Alessio , Wilson Jennifer L. , Bacciu Davide , Grimes Kevin J. , Priami Corrado
Published: October 2021

Schizophrenia is a debilitating psychiatric disorder, leading to both physical and social morbidity. Worldwide 1% of the population is struggling with the disease, with 100,000 new cases annually only in the United States. Despite its importance, the goal of finding effective treatments for schizophrenia remains a challenging task, and previous work conducted expensive large-scale phenotypic screens. This work investigates the benefits of Machine Learning for graphs to optimize drug phenotypic screens and predict compounds that mitigate abnormal brain reduction induced by excessive glial phagocytic activity in schizophrenia subjects. Given a compound and its concentration as input, we propose a method that predicts a score associated with three possible compound effects, i.e., reduce, increase, or not influence phagocytosis. We leverage a high-throughput screening to prove experimentally that our method achieves good generalization capabilities. The screening involves 2218 compounds at five different concentrations. Then, we analyze the usability of our approach in a practical setting, i.e., prioritizing the selection of compounds in the SWEETLEAD library. We provide a list of 64 compounds from the library that have the most potential clinical utility for glial phagocytosis mitigation. Lastly, we propose a novel approach to computationally validate their utility as possible therapies for schizophrenia.

Author summary

Phagocytosis is a fundamental biological process to protect biological organisms from exogenous infectious particles as well as to preserve equilibrium and efficiency of the host by removing its unwanted cells. A dysregulation of the phagocytic activity can lead to severe consequences for the host. In this study, we focus on a recent theory that relates an excessive phagocytic activity in brain cells, and a consequent abnormal reduction in brain volume, to the development of schizophrenia. Our working hypothesis is that pharmaceutical compounds that can reduce excessive of phagocytic activity might prove effective as a schizophrenia treatment. Rather than attempting to develop ex-novo such a chemical compound, we rely on a more cost-effective and efficient approach that seeks candidate therapies in a set of approved chemical compounds. To achieve this, we train a machine learning model capable of predicting, with good accuracy, the ability of a molecular compound to increase or decrease phagocytosis in the target brain cells. Our approach leverages learning models capable of directly processing the molecular graph of the compound, leading to the identification of 64 candidate drugs of potential clinical utility.
The value of corticospinal excitability and intracortical inhibition in predicting motor skill improvement driven by action observation
Authors: Nuara Arturo , Bazzini Chiara , Cardellicchio Pasquale , Scalona Emilia , De Marco Doriana , Rizzolatti Giacomo , Fabbri-Destro Maddalena , Avanzini Pietro
Published: October 2021

BACKGROUND AND OBJECTIVE

Action observation can sustain motor skill improvement. At the neurophysiological level, action observation affects the excitability of the motor cortices, as measured by transcranial magnetic stimulation. However, whether the cortical modulations induced by action observation may explain the amount of motor improvement driven by action observation training (AOT) remains to be addressed.

METHODS

We conducted a two-phase study involving 40 volunteers. First, we assessed the effect of action observation on corticospinal excitability (amplitude of motor evoked potentials), short-interval intracortical inhibition, and transcallosal inhibition (ipsilateral silent period). Subsequently, a randomized-controlled design was applied, with AOT participants asked to observe and then execute, as quickly as possible, a right-hand dexterity task six consecutive times, whereas controls had to observe a no-action video before performing the same task.

RESULTS

AOT participants showed greater performance improvement relative to controls. The amount of improvement in the AOT group was predicted by the amplitude of corticospinal modulation during action observation and even more by the amount of intracortical inhibition induced by action observation. Importantly, these relations were found specifically for the AOT group and not for the controls.

CONCLUSIONS

In this study, we identified the neurophysiological signatures associated with, and potentially sustaining, the outcome of AOT. Intracortical inhibition driven by action observation plays a major role. These findings elucidate the cortical mechanisms underlying AOT efficacy and open to predictive assessments for the identification of potential responders to AOT, informing the rehabilitative treatment individualization.
Tracing the invasion of a leaf-mining moth in the Palearctic through DNA barcoding of historical herbaria
Authors: Kirichenko Natalia I. , Zakharov Evgeny V. , Lopez-Vaamonde Carlos
Published: October 2021

Historical herbaria are valuable sources of data in invasion biology. Here we study the invasion history of the lime leaf-miner,Phyllonorycter issikii, by surveying over 15 thousand herbarium specimens of limes (Tiliaspp.) collected in the Palearctic during last 253 years (1764–2016). The majority of herbarium specimens with the pest’s mines (89%) originated from East Asia (1859–2015), whereas remaining 11% of specimens with the mines came from Europe, European Russia and Western Siberia (1987–2015). These results support the hypothesis of a recentPh. issikiiinvasion from Eastern to Western Palearctic.

Single molecule real-time sequencing of the COI barcode region of 93 archival larvae and pupae (7–162 years old) dissected from the mines on historical herbaria allowed to distinguish betweenPh. issikiiandPh. messaniella, a polyphagous species rarely feeding onTilia, which mines were found in herbarium from Europe dated by 1915–1942. We discovered 25 haplotypes ofPh. issikii, of which 16 haplotypes were present solely in East Asia, and revealed wide distribution of the species in China. Six haplotypes shared between Eastern and Western Palearctic suggest the contribution ofPh. issikiipopulations from the Russian Far East, China and Japan to the westward invasion.
Prioritizing Management for Cumulative Impacts
Authors: Singh Gerald G. , Rhodes Jonathan , McDonald-Madden Eve , Possingham Hugh P. , Hammill Edd , Murray Cathryn Clarke , Mach Megan , Martone Rebecca , Halpern Benjamin , Satterfield Terre , Chan Kai M. A.
Published: October 2021

Determining where environmental management is best applied, either through regulating single sectors of human activities or across sectors, is complicated by interactions between human impacts and the environment. In this article, we show how an explicit representation of human-environment interactions can help, via “impact networks” including activities (e.g. shipping), stressors (e.g. ship strikes), species (e.g. humpback whales) or ecosystem services (e.g. marine recreation). Impact networks can enable the identification of “leverage nodes”, which, if present, can direct managers to the activities and stressors crucial for reducing risk to important ecosystem components. Exploring an impact network for a coastal ecosystem in British Columbia, Canada, we seek to identify these leverage nodes using a new approach employing Bayesian Belief Networks of risks to ecosystems. In so doing, we address three key questions: (1) Do leverage nodes exist? (2) Do management plans for species correctly identify leverage nodes? (3) Does the management of leverage nodes for certain species realize benefits for other species and ecosystem services? We show that there are several leverage nodes across all species investigated, and show that preconceptions about the regulation of risk to species can misidentify leverage nodes, potentially leading to ineffective management. Notably, we show that managing fisheries does not reduce overall risk to herring whereas managing diverse cumulative impacts including nutrient runoff, oil spills, and marine debris can reduce risk to herring, additional species, and related ecosystem services. Thus, by targeting leverage nodes, managers can efficiently mitigate risks for whole communities, ecosystems, and ecosystem services.
Genetic patterns in Montipora capitata across an environmental mosaic in Kāne’ohe Bay
Authors: Caruso Carlo , de Souza Mariana Rocha , Ruiz-Jones Lupita , Conetta Dennis , Hancock Joshua , Hobbs Callum , Hobbs Caroline , Kahkejian Valerie , Kitchen Rebecca , Marin Christian , Monismith Stephen , Madin Joshua , Gates Ruth , Drury Crawford
Published: October 2021

Spatial genetic structure (SGS) is important to a population’s ability to adapt to environmental change. For species that reproduce both sexually and asexually, the relative contribution of each reproductive mode has important ecological and evolutionary implications because asexual reproduction can have a strong effect on SGS. Reef building corals reproduce sexually, but many species also propagate asexually under certain conditions. In order to understand SGS and the relative importance of reproductive mode across environmental gradients, we evaluated genetic relatedness in almost 600 colonies of Montipora capitata across 30 environmentally characterized sites in Kāne’ohe Bay, O’ahu, Hawai’i using low-depth restriction digest associated sequencing. Clonal colonies were relatively rare overall but influenced SGS. Clones were located significantly closer to one another spatially than average colonies and were more frequent on sites where wave energy was relatively high, suggesting a strong role of mechanical breakage in their formation. Excluding clones, we found no evidence of isolation by distance within sites or across the bay. Several environmental characteristics were significant predictors of the underlying genetic variation (including degree heating weeks, time spent above 30°C, depth, sedimentation rate and wave height); however, they only explained 5% of this genetic variation. Our results show that colony fragmentation contributes to the ecology of M. capitata at local scales and that genetic diversity is maintained despite strong environmental gradients in a highly impacted ecosystem, suggesting potential for broad adaptation or acclimatization in this population.
Perinatal Outcomes of Fetuses and Infants Diagnosed with Trisomy 13 or Trisomy 18
Authors: Cortezzo DonnaMaria E. , Tolusso Leandra K. , Swarr Daniel T.
Published: October 2021

Objectives

To identify factors associated with adverse prenatal, perinatal and postnatal outcomes, and determine the utilization medical care for fetuses & infants with trisomy 13 (T13) and trisomy (T18).

Study Design

This population-based retrospective cohort study included all prenatal and postnatal diagnoses of T13 or T18 in the Greater Cincinnati area from 1/1/12-12/31/18. Overall survival, survival to hospital discharge, approach to medical management, and maternal, fetal and neonatal characteristics are analyzed.

Results

124 pregnancies (125 fetuses) were identified, which resulted in 72 liveborn infants. Male fetal sex and hydrops were associated with a higher rate of spontaneous loss. The median length of survival was 7 days (95% CI, 0-18 days) and 29 days (95% CI, 2-115 days), for infants with T13 and T18, respectively. Of the 27 infants who were alive at 1 month of age, 14 (52%) were alive at 1 year of age. Only the trisomy type, chosen goals of care (comfort care), and extremely low birthweight were associated with overall length of survival. A high degree of variability existed in the use of medical services, with 28% of infants undergoing at least one surgical procedure and some children requiring repeated (up to 29) or prolonged hospitalization (> 1 year).

Conclusions

Although many infants with T13 or T18 did not survive past the first week of life, up to 25% of infants lived for more than one year. Length of survival for an individual infant cannot be easily predicted, and surviving infants have high health care utilization throughout their lifespan.
Variability is actively regulated in speech
Authors: Tang Ding-lan , Parrell Benjamin , Niziolek Caroline A.
Published: October 2021

Although movement variability is often attributed to unwanted noise in the motor system, recent work has demonstrated that variability may be actively controlled. To date, research on regulation of motor variability has relied on relatively simple, laboratory-specific reaching tasks. It is not clear how these results translate to complex, well-practiced and real-world tasks. Here, we test how variability is regulated during speech production, a complex, highly over-practiced and natural motor behavior that relies on auditory and somatosensory feedback. Specifically, in a series of four experiments, we assessed the effects of auditory feedback manipulations that modulate perceived speech variability, shifting every production either towards (inward-pushing) or away from (outward-pushing) the center of the distribution for each vowel. Participants exposed to the inward-pushing perturbation (Experiment 1) increased produced variability while the perturbation was applied as well as after it was removed. Unexpectedly, the outward-pushing perturbation (Experiment 2) also increased produced variability during exposure, but variability returned to near baseline levels when the perturbation was removed. Outward-pushing perturbations failed to reduce participants’ produced variability both with larger perturbation magnitude (Experiment 3) or after their variability had increased above baseline levels as a result of the inward-pushing perturbation (Experiment 4). Simulations of the applied perturbations using a state space model of motor behavior suggest that the increases in produced variability in response to the two types of perturbations may arise through distinct mechanisms: an increase in controlled variability in response to the inward-pushing perturbation, and an increase in sensitivity to auditory errors in response to the outward-pushing perturbation. Together, these results suggest that motor variability is actively regulated even in complex and well-practiced behaviors, such as speech.
Kidney pathology alters cell-clustering in single cell RNA sequencing
Authors: Ma Lijun , Murea Mariana , Choi Young A , Hemal Ashok K. , Mikhailov Alexei V. , Snipes James A. , Chou Jeff W. , Langefeld Robert C. , Cui Wei , Miller Lance D. , Hawkins Gregory A. , Palmer Nicholette D. , Langefeld Carl D. , Freedman Barry I.
Published: October 2021

Single cell RNA sequencing (scRNA-Seq) is useful to classify cell-specific gene expression profiles in kidney tissue. As viable cells are required, we report an optimized cell dissociation methodology and the necessity of screening tissue histology prior to scRNA-Seq. We demonstrate that glomerular injury can selectively reduce the appearance of groups of cells during analysis of cell clustering and we confirmed reductions in cell-specific markers among injured cells on kidney sections with fluorescence microscopy. Interpretation of scRNA-Seq results may be refined based upon these considerations.
A Proposed Unified Interphase Nucleus Chromosome Structure: Preliminary Preponderance of Evidence
Authors: Sedat John , McDonald Angus , Cang Hu , Lucas Joseph , Arigovindan Muthuvel , Kam Zvi , Murre Cornelis , Elbaum Michael
Published: October 2021

Cellular cryo-electron tomography (CET) of the cell nucleus using Scanning Transmission Electron Microscopy (STEM) and the use of deconvolution (DC) processing technology has highlighted a large-scale, 100–300 nm interphase chromosome structure (LSS), that is present throughout the nucleus. This chromosome structure appears to coil the nucleosome 11-nm fiber into a defined hollow structure, analogous to a Slinky (S) (1, motif used in 2) helical spring. This S architecture can be used to build chromosome territories, extended to polytene chromosome structure, as well as to the structure of Lampbrush chromosomes.

Significance Statement

Cryo-preservation of the nuclear interior allows a large scale interphase chromosome structure—present throughout the nucleus—to be seen for the first time. This structure can be proposed to be a defined coiled entity, a Slinky. This structure can be further used to explain polytene chromosome structure, an unknown chromosome architecture as well as for lampbrush chromosomes. In addition, this new structure can be further organized as chromosome territories, using all 46 human interphase chromosomes as an example, easily into a 10 micron diameter nucleus. Thus, interphase chromosomes can be unified into a flexible defined structure.
A perceptual glitch in serial perception generating temporal distortions
Authors: Sierra Franklenin , Muralikrishnan R. , Poeppel David , Tavano Alessandro
Published: October 2021

Precisely estimating event timing is essential for survival, yet temporal distortions are ubiquitous in our daily sensory experience. Here, we tested whether the relative position, relative duration and relative distance in time of two sequentially-organized events —standard S, with constant duration, and comparison C, varying trial-by-trial— are causal factors in generating temporal distortions. We found that temporal distortions emerge when the first event is shorter than the second event. Importantly, a significant interaction suggests that a longer ISI helps counteracting such serial distortion effect only the constant S is in first position, but not if the unpredictable C is in first position. These results suggest the existence of a perceptual bias in perceiving ordered event durations, mechanistically contributing to distortion in time perception. We simulated our behavioral results with a Bayesian model and replicated the finding that participants disproportionately expand first-position dynamic (unpredictable) short events. Our results clarify the mechanics generating time distortions by identifying a hitherto unknown duration-dependent encoding inefficiency in human serial temporal perception, akin to a strong prior that can be overridden for highly predictable sensory events but unfolds for unpredictable ones.
An Anatomically and Hemodynamically Realistic Simulation Framework for 3D Ultrasound Localization Microscopy
Authors: Belgharbi Hatim , Porée Jonathan , Damseh Rafat , Perrot Vincent , Milecki Léo , Delafontaine-Martel Patrick , Lesage Frédéric , Provost Jean
Published: October 2021

The resolution of 3D Ultrasound Localization Microscopy (ULM) is determined by acquisition parameters such as frequency and transducer geometry but also by microbubble (MB) concentration, which is also linked to the total acquisition time needed to sample the vascular tree at different scales. In this study, we introduce a novel 3D anatomically- and physiologically-realistic ULM simulation framework based on two-photon microscopy (2PM) and in-vivo MB perfusion dynamics. As a proof of concept, using metrics such as MB localization error, MB count and network filling, we could quantify the effect of MB concentration and PSF volume by varying probe transmit frequency (3-15 MHz). We find that while low frequencies can achieve sub-wavelength resolution as predicted by theory, they are also associated with prolonged acquisition times to map smaller vessels, thus limiting effective resolution. A linear relationship was found between maximal MB concentration and inverse point spread function (PSF) volume. Since inverse PSF volume roughly scales cubically with frequency, the reconstruction of the equivalent of 10 minutes at 15 MHz would require hours at 3 MHz. We expect that these findings can be leveraged to achieve effective reconstruction and serve as a guide for choosing optimal MB concentrations in ULM.
Covert valuation for information sampling and choice
Authors: Butler James L , Muller Timothy H. , Veselic Sebastijan , Nishantha Malalasekera W. M. , Hunt Laurence T. , Behrens Timothy E.J. , Kennerley Steven W.
Published: October 2021

We use our eyes to assess the value of objects around us and carefully fixate options that we are about to choose. Neurons in the prefrontal cortex reliably encode the value of fixated options, which is essential for decision making. Yet as a decision unfolds, it remains unclear how prefrontal regions determine which option should be fixated next. Here we show that anterior cingulate cortex (ACC) encodes the value of options in the periphery to guide subsequent fixations during economic choice. In an economic decision-making task involving four simultaneously presented cues, we found rhesus macaques evaluated cues using their peripheral vision. This served two distinct purposes: subjects were more likely to fixate valuable peripheral cues, and more likely to choose valuable options whose cues were never even fixated. ACC, orbitofrontal cortex, dorsolateral prefrontal cortex, and ventromedial prefrontal cortex neurons all encoded cue value post-fixation. ACC was unique, however, in also encoding the value of cues before fixation and even cues that were never fixated. This pre-saccadic value encoding by ACC predicted which cue was next fixated during the decision process. ACC therefore conducts simultaneous processing of peripheral information to guide information sampling and choice during decision making.
Development and verification of SSR markers from drought stress-responsive miRNAs in common wild rice
Authors: Chen Yong , Fan Yuan-wei , Yang Wan-ling , Ding Gu-mu , Zhao Min-min , Chen Yan-hong , Xie Jian-kun , Zhang Fan-tao
Published: October 2021

PREMISE

Dongxiang wild rice (Oryza rufipogon Griff., DXWR) is the northernmost common wild rice found in the world, which possesses abundant elite genetic resources. We developed a set of drought stress-responsive microRNA (miRNA)-based single sequence repeat (SSR) markers for DXWR, which will help breed drought stress-resistant rice varieties.

METHODS AND RESULTS

Ninety-nine SSR markers were developed from the drought stress-responsive miRNAs of DXWR. The SSR loci were distributed in all 12 rice chromosomes and most were in chromosomes 2 and 6, with di- and trinucleotides being the most abundant repeat motifs. Nine out of ten synthesized SSR markers were displayed high levels of genetic diversity in the genomes of DXWR and 41 modern rice varieties worldwide. The number of alleles per locus ranged from 2 to 6, and the observed and expected heterozygosity ranged from 0.000 to 0.024 and 0.461 to 0.738, respectively.

CONCLUSIONS

These SSR markers developed from drought stress-responsive miRNAs in DXWR could be additional tools for elite genes mapping and useful for drought stress-resistant rice breeding.
Plastic biodegradation: do Galleria mellonella larvae - bio-assimilate polyethylene? A spectral histology approach using isotopic labelling and infrared microspectroscopy
Authors: Réjasse Agnès , Waeytens Jehan , Deniset-Besseau Ariane , Crapart Nicolas , Nielsen-Leroux Christina , Sandt Christophe
Published: October 2021

Environmental pollution by non-biodegradable polyethylene (PE) plastics is of major concern, thus, organisms capable of bio-degrading PE are required. The larvae of the Greater Wax Moth, Galleria mellonella (Gm), were identified as a potential candidate to digest PE. In this study, we tested whether PE was metabolized by Gm larvae and could found in their tissues. We examined the implication of the larval gut microbiota by using conventional and axenic reared insects. First, our study showed that neither beeswax nor PE alone favour the growth of young larvae. We then used Fourier-Transform Infrared Microspectroscopy (µFTIR) to detect deuterium in larvae fed with isotopically labelled food. Perdeuterated molecules were found in most tissues of larvae fed with deuterium labelled oil for 72 hours proving that µFTIR can detect metabolization of 1-2 mg of deuterated food. No bio-assimilation was detected in the tissues of larvae fed with 1-5 mg of perdeuterated PED4 for 72 hours and 19-21 days, but micron sized PE particles were found in the larval digestive tract cavities. We evidenced weak bio-degradation of PE films in contact for 24 hours with the dissected gut of conventional larvae; and in the PED4 particles from excreted larval frass. Our study confirms that Gm larvae can bio-degrade PE but can not necessarily metabolize it.
The [PSI+] prion and HSP104 modulate cytochromecoxidase deficiency caused by deletion of COX12
Authors: Saini Pawan Kumar , Dawitz Hannah , Aufschnaiter Andreas , Thomas Jinsu , Amblard Amélie , Stewart James , Thierry-Mieg Nicolas , Ott Martin , Pierrel Fabien
Published: October 2021

Cytochromecoxidase is a pivotal enzyme of the mitochondrial respiratory chain, which sustains bioenergetics of eukaryotic cells. Cox12, a peripheral subunit of cytochromecoxidase, is required for full activity of the enzyme, but its exact function is unknown. Here, experimental evolution of aSaccharomyces cerevisiaeΔcox12strain for ~300 generations allowed to restore the activity of cytochromecoxidase. In one population, the enhanced bioenergetics was caused by a A375V mutation in the AAA+ disaggregase Hsp104. Deletion or overexpression of Hsp104 also increased respiration of the Δcox12ancestor strain. This beneficial effect of Hsp104 was related to the loss of the [PSI+] prion, which forms cytosolic amyloid aggregates of the Sup35 protein. Overall, our data demonstrate that cytosolic aggregation of a prion impairs the mitochondrial metabolism of cells defective for Cox12. These findings identify a new functional connection between cytosolic proteostasis and biogenesis of the mitochondrial respiratory chain.
Developmental neuroanatomy of the Rosy Bitterling Rhodeus ocellatus (Teleostei: Cypriniformes)—A microCT study
Authors: Yi Wenjing , Mueller Thomas , Rücklin Martin , Richardson Michael K.
Published: October 2021

Bitterlings are a group of teleost fish (Cyprinifromes: Acheilanathidae) notable for their brood parasitic lifestyle. Bitterling embryos develop as parasites inside the gill chamber of their freshwater mussel hosts. However, little is known about brain development in this species. Here, we have imaged the development of the brain of the Rosy Bitterling (Rhodeus ocellatus) at four embryonic stages (165, 185, 210, 235 hours post-fertilization) using micro-computed tomography (microCT) with special emphasis on developmental regionalization and brain ventricular organization. We provide a detailed neuroanatomical account of the development of the brain divisions with reference to The Atlas of Early zebrafish Brain Development and the updated prosomeric model. Segmentation and three-dimensional visualization of the ventricular system were performed in order to clarify changes in the longitudinal brain axis as a result of cephalic flexure during development. During early embryonic and larval development, we find that histological differentiation, tissue boundaries, periventricular proliferation zones, and ventricular spaces are all recognizable using microCT. Importantly, our approach is validated by the fact that the profile of CT values displayed here in the bitterling brain are consistent with genoarchitecture identified in previous studies. We also find developmental heterochrony of the inferior lobe in the Rosy Bitterling compared to the zebrafish. Our study provides a foundation for future studies of the brain development in the Rosy Bitterling, a valuable model species for studying the evolutionary adaptations associated with brood parasitism.
Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives
Authors: Sielemann Katharina , Pucker Boas , Schmidt Nicola , Viehöver Prisca , Weisshaar Bernd , Heitkam Tony , Holtgräwe Daniela
Published: October 2021

Background

As the major source of sugar in moderate climates, sugar-producing beets (Beta vulgarissubsp.vulgaris) have a high economic value. However, the low genetic diversity within cultivated beets requires introduction of new traits, for example to increase their tolerance and resistance attributes – traits that often reside in the crop wild relatives. For this, genetic information of wild beet relatives and their phylogenetic placements to each other are crucial. To answer this need, we sequenced and assembled the complete plastome sequences from a broad species spectrum across the beet generaBetaandPatellifolia, both embedded in the Betoideae (order Caryophyllales). This pan-plastome dataset was then used to determine the wild beet phylogeny in high-resolution.

Results

We sequenced the plastomes of 18 closely related accessions representing 11 species of the Betoideae subfamily and provided high-quality plastome assemblies which represent an important resource for further studies of beet wild relatives and the diverse plant order Caryophyllales. Their assembly sizes range from 149,723 bp (Beta vulgarissubsp.vulgaris) to 152,816 bp (Beta nana), with most variability in the intergenic sequences. Combining plastome-derived phylogenies with read-based treatments based on mitochondrial information, we were able to suggest a unified and highly confident phylogenetic placement of the investigated Betoideae species.

Our results show that the genusBetacan be divided into the two clearly separated sectionsBetaandCorollinae. Our analysis confirms the affiliation ofB. nanawith the otherCorollinaespecies, and we argue against a separate placement in theNanaesection. Within thePatellifoliagenus, the two diploid speciesPatellifolia procumbensandPatellifolia webbianaare, regarding the plastome sequences, genetically more similar to each other than to the tetraploidPatellifolia patellaris. Nevertheless, all threePatellifoliaspecies are clearly separated.

Conclusion

In conclusion, our wild beet plastome assemblies represent a new resource to understand the molecular base of the beet germplasm. Despite large differences on the phenotypic level, our pan-plastome dataset is highly conserved. For the first time in beets, our whole plastome sequences overcome the low sequence variation in individual genes and provide the molecular backbone for highly resolved beet phylogenomics. Hence, our plastome sequencing strategy can also guide genomic approaches to unravel other closely related taxa.
Membrane Contact Sites Between Chloroplasts and Pathogen Interface Underpin Plant Focal Immune Responses
Authors: Yuen Enoch Lok Him , Savage Zachary , Adamkova Vanda , Vuolo Cristina , Zhou Yuanyang , Tumtas Yasin , Erickson Jessica Lee , Prautsch Jennifer , Balmez Andrada I. , Stuttmann Johannes , Duggan Cian , Rivetti Francesco , Molinari Camilla , Schattat Martin , Bozkurt Tolga O.
Published: October 2021

Communication between cellular organelles is essential for mounting effective innate immune responses to eliminate pathogens. In plants, the transport of cellular organelles to pathogen penetration sites and their assembly around the host membrane delineating plant-pathogen interface are well-documented. However, whether organelles associate with these specialized plant-pathogen membrane interfaces and the extent to which this process contributes to immunity remain unknown. Here, we discovered defense-related membrane contact sites (MCS) comprising a membrane tethering complex between chloroplasts and the extrahaustorial membrane (EHM) surrounding the pathogen haustorium. The assembly of this membrane tethering complex relies on the association between the chloroplast outer envelope protein CHLOROPLAST UNUSUAL POSITIONING 1 (CHUP1), and its plasma membrane-associated partner, KINESIN-LIKE PROTEIN FOR ACTIN-BASED CHLOROPLAST MOVEMENT 1 (KAC1). Our biochemical assays revealed that CHUP1 and KAC1 interact, while infection cell biology demonstrated their co-accumulation in foci where chloroplasts contact the EHM. Genetic depletion of CHUP1 or KAC1 reduces the deposition of callose—a cell wall material typically deployed to fortify pathogen penetration resistance—around the haustorium, without affecting other core immune processes. Our findings suggest that the chloroplast-EHM attachment complex positively regulates plant focal immunity, revealing the key components and their potential roles in the targeted deposition of defense components at the pathogen interface. These results advance our understanding of organelle-mediated immune responses and highlight the significance of MCS in plant-pathogen interactions.
Connexins evolved after early chordates lost innexin diversity
Authors: Welzel Georg , Schuster Stefan
Published: October 2021

Gap junction channels are formed by two unrelated protein families. Non-chordates use the primordial innexins, while chordates use connexins that superseded the gap junction function of innexins. Chordates retained innexin-homologs, but N-glycosylation prevents them from forming gap junctions. It is puzzling why chordates seem to exclusively use the new gap junction protein and why no chordates should exist that use non-glycosylated innexins to form gap junctions. Here, we identified glycosylation sites of 2270 innexins from 152 non-chordate and 274 chordate species. Among all chordates, we found not a single innexin without glycosylation sites. Surprisingly, the glycosylation motif is also widespread among non-chordate innexins indicating that glycosylated innexins are not a novelty of chordates. In addition, we discovered a loss of innexin diversity during the early chordate evolution. Most importantly, the most basal living chordates, which lack connexins, exclusively possess innexins with glycosylation sites. A bottleneck effect might thus explain why connexins have become the only protein used to form chordate gap junctions.
Peroxisome-derived hydrogen peroxide can modulate the sulfenylation profiles of key redox signaling proteins
Authors: Lismont Celien , Revenco Iulia , Li Hongli , Costa Cláudio F. , Lenaerts Lisa , Hussein Mohamed A. F. , De Bie Jonas , Knoops Bernard , Van Veldhoven Paul P. , Derua Rita , Fransen Marc
Published: October 2021

Ever since the first characterization of peroxisomes, a central theme has been their involvement in cellular hydrogen peroxide (H2O2) metabolism. While the reputation of H2O2 drastically changed from an exclusively toxic molecule to a signaling messenger, the regulatory role of peroxisomes in these signaling events is still largely underappreciated. This is mainly because the number of known protein targets of peroxisome-derived H2O2 is rather limited and testing of specific targets is predominantly based on knowledge previously gathered in related fields of research. To gain a broader and more systematic insight into the role of peroxisomes in redox signaling, an unbiased approach is urgently needed. To accomplish this goal, we have combined a previously developed cell system in which peroxisomal H2O2 production can be modulated with a yeast AP-1-like-based sulfenome mining strategy to inventory protein thiol targets of peroxisome-derived H2O2 in different subcellular compartments. Using this unbiased approach, we were able to identify specific and common targets of peroxisome-derived and exogenous H2O2 in peroxisomes, the cytosol, and mitochondria. We also observed that the sulfenylation kinetics profiles of key targets belonging to different protein families can vary considerably. In addition, we obtained compelling but indirect evidence that peroxisome-derived H2O2 may oxidize at least some of its targets through a redox relay mechanism. In conclusion, given that sulfenic acids function as key intermediates in H2O2 signaling, the findings presented in this study provide initial but critical insight into how peroxisomes may be integrated in the cellular H2O2 signaling network.

Highlights

YAP1C-trapping is a robust tool to assess the peroxisomal H2O2-dependent sulfenome

Exogenous and peroxisome-derived H2O2 have both common and distinct targets

ANXA2, PRDX1, and SKP1 are major targets of peroxisome-derived H2O2

The sulfenylation kinetics profiles of key redox-active proteins vary considerably

Production of H2O2 inside peroxisomes directly impacts the mitochondrial sulfenome
Longitudinal dynamics of human B-cell response at single-cell level in response to Tdap vaccination
Authors: Khatri Indu , Diks Annieck M. , van den Akker Erik B. , Oosten Liesbeth E.M. , Zwaginga Jaap Jan , Reinders Marcel J.T. , van Dongen Jacques J.M. , Berkowska Magdalena A.
Published: October 2021

Adaptation of the immune system to mount an adequate immune response against pathogens is a crucial function of the adaptive immune system. To better characterize a successful vaccination response, we performed longitudinal (days 0, 5, 7, 10, and 14 after Boostrix vaccination) analysis of the single cell transcriptome as well as the B-cell receptor (BCR) repertoire (scBCR-rep) in plasma cells of an immunized donor and compared it with baseline B cell characteristics as well as flow cytometry findings.

Based on the flow cytometry knowledge and literature findings, we discriminated individual B cell subsets in the transcriptomics data and traced over-time maturation of plasmablasts/plasma cells (PB/PCs) and identified the pathways associated with the plasma cell maturation. We observed that the repertoire in PB/PCs differed from the baseline B cell repertoire e.g. regarding expansion of unique clones in post-vaccination visits, high usage of IGHG1 in expanded clones, increased class switching events post-vaccination represented by clonotypes spanning multiple IGHC classes and positive selection of CDR3 sequences over time. Importantly, the Variable gene family-based clustering of BCRs represented a similar measure as the gene-based clustering, however, certainly improved the clustering of BCRs, as BCRs from duplicated Variable gene families could be clustered together. Finally, we developed a query tool to dissect the immune response to the components of Boostrix vaccine. Using this tool, we could identify the BCRs related to anti-tetanus and anti-pertussis toxoid.

Collectively, we developed a workflow which allows description of key features of an ongoing immune response, such as activation of PB/PCs, Ig class switching, somatic hypermutation, and clonal expansion, all of which are hallmarks of antigen exposure.
A sense-antisense RNA interaction promotes breast cancer metastasis via regulation of NQO1 expression
Authors: Culbertson Bruce , Garcia Kristle , Markett Daniel , Asgharian Hosseinali , Chen Li , Fish Lisa , Navickas Albertas , Yu Johnny , Woo Brian , Nanda Scott , Rabinowitz Joshua , Goodarzi Hani
Published: October 2021

Antisense RNAs are ubiquitous in human cells, yet the role that they play in healthy and diseased states remains largely unexplored. Here, we developed a computational framework to catalog and profile antisense RNAs and applied it to poorly and highly metastatic breast cancer cell lines. We identified one antisense RNA that plays a functional role in driving breast cancer progression by upregulating the redox enzyme NQO1, and hence named NQO1-antisense RNA or NQO1-AS. This upregulation occurs via a stabilizing interaction between NQO1-AS and its complementary region in the 3’UTR of NQO1 mRNA. By increasing expression of NQO1 protein, breast cancer cells are able to tolerate higher levels of oxidative stress, enabling them to colonize the lung. During this process the cancer cells become dependent on NQO1 to protect them from ferroptosis. We have shown that this dependence can be exploited therapeutically in xenograft models of metastasis. Together, our findings establish a previously unknown role for NQO1-AS in the progression of breast cancer by serving as a post-transcriptional regulator of RNA processing and decay for its sense mRNA.