bluuebunny/crossref_metadata_2025 huggingface dataset:
Direct Nuclear Delivery of Proteins on Living Plant via Partial Enzymatic Cell Wall Digestion
Authors: Gu Qufei , Ming Nathan , Wei Xiaoyang , Aizezi Yalikunjiang , Yuan Yizhong , Esquivel Brian , Wang Zhiyong
Published: September 2024

While many variations of protein delivery methods have been described, it can still be difficult or inefficient to introduce exogenous proteins into plants. A major barrier to progress is the cell wall which is primarily composed of polysaccharides and thus only permeable to small molecules. Here, we report a partial enzymatic cell wall digestion-mediated uptake method that efficiently delivers protein into the nucleus of plant cells. Such a method allowed efficient nuclear delivery of GFP proteins into Arabidopsis root cells throughout all cell layers. This study establishes that a partial enzymatic cell wall degradation could enable a myriad of plant biotechnology applications that rely on functional protein delivery into walled plant cells.
Legume genome structures and histories inferred from Cercis canadensis and Chamaecrista fasciculata genomes
Authors: Lee Hyun-oh , Stai Jacob S , Xu Qiaoji , Hewavithana Thulani , Batra Rabnoor , Liu Alex , Jordan Brandon D , Walstead Rachel , Jenkins Jerry W , Williams Melissa , Webber jenell , Grimwood Jane , Lovell John T , Bruna Tomas , Shu Shengqiang , Keymanesh Keykhosrow , Eichenberger Joanne , Schmutz Jeremy , Goodstein David M , Barry Kerrie W , Sankoff David , Jin Lingling , Leebens-Mack James , Cannon Steven B
Published: September 2024

The legume family originated ca. 70 million years ago and soon diversified into at least six lineages (now extant subfamilies). The signal of whole genome duplications (WGD) is apparent in species sampled from all six subfamilies. The early diversification has posed difficulties for resolving the legume backbone structure and the timing of WGDs. In this study, we report the genome sequences and annotations for Cercis canadensis (Cercidoideae) and Chamaecrista fasciculata (Caesalpinoideae) to help resolve the relative taxonomic placements along the legume backbone, the timings of WGDs relative to subfamily origins, and the ancestral legume karyotype. Analyses of genome assemblies from four subfamilies within Fabaceae show that the last common ancestor of all legumes likely had seven chromosomes, with a genome structure similar to the extant Cercis genome. Our analysis supports an allopolyploid origin of the subfamily Caesalpinoideae, with progenitors involving lineages along the backbone of the legume phylogeny. A probable allopolyploid origin of Caesalpinoideae subfamily provides a partial explanation for the difficulty in resolving the structure of the legume backbone. The retained karyotype structure and lack of a WGD in the last 100+ Mya, underscore the utility of the Cercis genome as an ancestral reference for the legume family.
Selective Agonism of Liver and Gut FXR Prevents Cholestasis and Intestinal Atrophy in Parenterally Fed Neonatal Pigs
Authors: Jiang Yanjun , Fang Zhengfeng , Guthrie Gregory , Stoll Barbara , Chacko Shaji , Lin Sen , Hartmann Bolette , Holst Jens J. , Dawson Harry , Pastor Jose J. , Ipharraguerre Ignacio R. , Burrin Douglas G.
Published: September 2024

BACKGROUND & AIMS

We aimed to investigate the relative efficacy of feeding different bile acids in preventing PNALD in neonatal pigs.

METHODS

Newborn pigs given total parenteral nutrition (TPN) combined with minimal enteral feeding of chenodeoxycholic acid (CDCA), or increasing doses of obeticholic acid (OCA) for 19 days.

RESULTS

Enteral OCA (5 and 15 mg/kg), but not CDCA (30 mg/kg) reduced blood cholestasis markers compared to TPN controls and increased bile acids in the gallbladder and intestine. Major bile acids in the liver and distal intestine were CDCA, HCA, HDCA and OCA, and their relative proportions were increased by the type of bile acid (CDCA or OCA) given enterally. High doses of OCA increased the total NR1H4-agonistic bile acid profile in the liver and intestine above 50% total bile acids. Both CDCA and OCA treatments suppressed hepatic cyp7a1 expression, but only OCA increased hepatobiliary transporters, ABCB11, ABCC$ and ABCB1. Plasma phytosterol levels were reduced and biliary levels were increased by CDCA and OCA and hepatic sterol transporters, abcg5/8, expression were increased by OCA. Both CDCA and OCA increased plasma FGF19 and OCA increased intestinal FGF19, FABP6, and SLC51A. Both CDCA and OCA increased intestinal mucosal growth, whereas CDCA increased the plasma GLP-2, GLP-1 and GIP.

CONCLUSIONS

Enteral OCA prevented cholestasis and phytosterolemia by increased hepatic bile acid and sterol transport via induction of hepatobiliary transporter FXR target genes and not by suppression of bile acid synthesis genes. We also showed an intestinal trophic action of OCA that demonstrates a dual clinical benefit of FXR agonism in the prevention of PNALD in piglets.
Construction of Discrete Element Model of Different Moisture Hygroscopic Fertilizer Particles and Fertilizer Discharging Verification
Authors: Fei Chen Xiong , Yu Sun Ze , Ze Shi Yi , Hua Liu Mu , Jia Yu Jia , An Liu Jun
Published: September 2024

The hygroscopic fertilizer particles were characterized based on discrete element simulation, and its accuracy was verified by the simulation of fertilizer discharge. Firstly, the repose angle of the fertilizer particles served as the key metric for assessment. A mathematical model characterizing the relationship between fertilizer moisture content and the repose angle was established, R2=0.9935; and a mathematical representation of the repose angle for fertilizer moisture content was established, R2=0.9933. Then, the moisture absorbing fertilizer particles was developed utilizing the integrated Hertz Mindlin with JKR model within EDEM system to account for particle adhesion; A robust correlation model between the repose angle of hygroscopic fertilizers and the discrete element method was established, p <0.0001; Finally, a correlation model between moisture content and significant parameters within the discrete element method was established, drawing upon the models for moisture content repose angle and repose angle discrete element parameters. The moisture-absorbing fertilizer particles model at moisture contents of 2% and 6% were resolved, with a relative error of the repose angle not exceeding 1.42% and a single circle fertilizer discharge error below 8.32%. The results show that the moisture content discrete element significant parameter correlation model can reliably and precisely forecast the discrete element parameters of various moisture content hygroscopic fertilizers. The hygroscopic fertilizer particle model can represent surface interaction characteristics of hygroscopic fertilizer granules. which has guiding significance for the design of precision fertilizer discharge technology device.
Tissue-specific and functional loci analysis ofCASP14gene in the sheep horn
Authors: Lu Xiaoning , Zhang Guoqing , Yang Hao , Shan Mingzhu , Zhang Xiaoxu , Wang Yuqin , Bai Junyan , Pan Zhangyuan
Published: September 2024

Under the current context of intensive farming, small-horned animals are more suitable for large-scale breeding. TheCASP14gene, closely associated with skin and keratin formation, may influence horn size due to its link with skin development. This study comprehensively analyzed the tissue-specific expression ofCASP14using RNA-Seq data, identified functional sites through whole-genome sequencing (WGS), and investigated allele-specific expression (ASE) validated by KASP assays. Results showed significantly higherCASP14expression in the scurred group com-pared to the SHE group, with pronounced expression in the skin. Interbreed comparisons also revealed elevatedCASP14levels in the scurred group. Analysis of potential functional sites indicated structural similarities in theCASP14protein among horned mammals. Five ASE events were discovered, and intersecting these with SNPs and high fixation index loci (Fst > 0.05) identified three potential functional sites: 7941628, 7941817, and 7941830. The SNP site 7944295 was selected for T-test analysis and further validated through KASP assays, corroborating the role ofCASP14in sheep horn phenotypes. Our findings suggest thatCASP14plays a significant role in horn development, offering insights into breeding strategies for small-horned animals.
Evaluating Joint Angle Data for Clinical Assessment Using Multidimensional Inverse Kinematics with Average Segment Morphometry
Authors: Taitano Rachel I , Gritsenko Valeriya
Published: September 2024

Movement analysis is a critical tool in understanding and addressing various disabilities associated with movement deficits. By analyzing movement patterns, healthcare professionals can identify the root causes of these alterations, which is essential for preventing, diagnosing, and rehabilitating a broad spectrum of medical conditions, disabilities, and injuries. With the advent of affordable motion capture technologies, quantitative data on patient movement is more accessible to clinicians, enhancing the quality of care. Nonetheless, it is crucial that these technologies undergo rigorous validation to ensure their accuracy in collecting and monitoring patient movements, particularly for remote healthcare services where direct patient observation is not possible. In this study, motion capture technology was used to track upper extremity movements during a reaching task presented in virtual reality. Kinematic data was then calculated for each participant using a scaled dynamic inertial model. The goal was to evaluate the accuracy of joint angle calculations using inverse kinematics from motion capture relative to the typical movement redundancy. Shoulder, elbow, radioulnar, and wrist joint angles were calculated with models scaled using either direct measurements of each individual’s arm segment lengths or those lengths were calculated from individual height using published average proportions. The errors in joint angle trajectories calculated using the two methods of model scaling were compared to the inter-trial variability of those trajectories. The variance of this error was primarily within the normal range of variability between repetitions of the same movements. This suggests that arm joint angles can be inferred with good enough accuracy from motion capture data and individual height to be useful for the clinical assessment of motor deficits.
AxonFinder: Automated segmentation of tumor innervating neuronal fibers
Authors: Ait-Ahmad Kaoutar , Ak Cigdem , Thibault Guillaume , Chang Young Hwan , Eksi Sebnem Ece
Published: September 2024

Neurosignaling is increasingly recognized as a critical factor in cancer progression, where neuronal innervation of primary tumors contributes to the disease’s advancement. This study focuses on segmenting individual axons within the prostate tumor microenvironment, which have been challenging to detect and analyze due to their irregular morphologies. We present a novel deep learning-based approach for the automated segmentation of axons, AxonFinder, leveraging a U-Net model with a ResNet-101 encoder, based on a multiplexed imaging approach. Utilizing a dataset of whole-slide images from low-, intermediate-, and high-risk prostate cancer patients, we manually annotated axons to train our model, achieving significant accuracy in detecting axonal structures that were previously hard to segment. Our analysis includes a comprehensive assessment of axon density and morphological features across different CAPRA-S prostate cancer risk categories, providing insights into the correlation between tumor innervation and cancer progression. Our paper suggests the potential utility of neuronal markers in the prognostic assessment of prostate cancer in aiding the pathologist’s assessment of tumor sections and advancing our understanding of neurosignaling in the tumor microenvironment.
A Digital Microfluidic Platform for the Microscale Production of Functional Immune Cell Therapies
Authors: Little Samuel R. , Rahbari Niloufar , Hajiaghayi Mehri , Gholizadeh Fatemeh , Cloarec-Ung Fanny-Mei , Phillips Joel , Sinha Hugo , Hirukawa Alison , Knapp David J.H.F. , Darlington Peter J. , Shih Steve C.C.
Published: September 2024

Genetically engineering human immune cells has been shown to be an effective approach for developing novel cellular therapies to treat a wide range of diseases. To expand the scope of these cellular therapies while solving persistent challenges, extensive research and development is still required. Electroporation has recently emerged as one of the most popular techniques for inserting biological payloads into human immune cells to perform genetic engineering. However, several recent studies have reported that electroporation can negatively impact cell functionality. Additionally, the requirement to use large amounts of cells and expensive payloads to achieve efficient delivery can drive up the costs of development efforts. Here we use a digital microfluidic enabled electroporation system (referred to as triDrop) and compare them against two state-of-the-art commercially available systems for the engineering of human T cells. We describe the ability to use triDrop for highly viable, highly efficient transfection while using substantially fewer cells and payload. Subsequently, we perform transcriptomic analysis on cells engineered with each of the three systems and show that electroporation with triDrop lead to less dysregulation of several functionally relevant pathways. Finally, in a direct comparison of immunotherapeutic functionality, we show that T cells engineered with triDrop have an improved ability to mount an immune response when presented with tumor cells. These results show that the triDrop platform is uniquely suited to produce functionally engineered immune cells while also reducing the costs of cell engineering compared to other commercially available systems.
Immunity against Mycobacterium avium induced by DAR-901 and BCG
Authors: Abate Getahun , Meza Krystal , Colbert Chase , Eickhoff Christopher
Published: September 2024

The prevalence of pulmonary nontuberculous mycobacteria (NTM) is increasing in Europe and North America. Most pulmonary NTM are caused byMycobacterium aviumcomplex (MAC). The treatment of pulmonary MAC is suboptimal with failure rates ranging from 30% to 40% and there is a need to develop new vaccines. In this study, we tested the ability of two whole cell vaccines, DAR-901 (heat killedM. obuense) and BCG (live attenuatedM. bovis), to induce MAC cross-reactive immunity by first immunizing BALB/c mice and then performing IFN-γ ELISPOT assay after overnight stimulation of splenocytes with live MAC. To study the ability of these vaccines to protect against MAC infection, BALB/c mice were vaccinated with DAR-901 (intradermal) or BCG (subcutaneous or intranasal) and challenged with aerosolized MAC 4 weeks later. Some mice vaccinated with BCG were treated with clarithromycin via gavage. Lung CFU in immunized mice and unvaccinated controls were quantified 4 weeks after infection. Our results showed that i) DAR-901 induced cross-reactive immunity to MAC and the level of MAC cross-reactive immunity was similar to the level of immunity induced by BCG, ii) DAR-901 and BCG protect against aerosol MAC, iii) mucosal BCG vaccination provided the best protection against MAC challenge, and iv) BCG vaccination did not interfere with anti-MAC activities of clarithromycin.
Nebulized and intravenous enzyme replacement therapy in mice with mucopolysaccharidosis type II
Authors: Shamoun Alex J. , Reis Gisienne , Ashley Malaica , Labilloy Anatalia , Ferreira Leonardo F.
Published: September 2024

Mucopolysaccharidosis Type II is a hereditary lysosomal storage disease characterized by deficiency in the enzyme iduronate 2-sulfatase (IDS). IDS is critical in the breakdown of sulfated glycosaminoglycans and its deficiency leads to an accumulation of these compounds across various tissue types resulting in multisystemic dysfunction. Intravenous administration of recombinant IDS (idursulfase) substantially improves patients’ quality and length of life. However, recombinant IDS delivered intravenously is sequestered in the liver and respiratory failure remains as the leading cause of death for patients independent of idursulfase treatment, which suggests insufficient delivery to the lungs. This study aimed to assess a novel method of idursulfase administration using a nebulizer in combination with intravenous treatment and determine if this combination may improve lung delivery of idursulfase and overall pathology. Whole body IDS knockout mice underwent twelve weeks of intravenous, combination treatment, or vehicle injection and we harvested liver and lungs seven days after the last treatment for assessment of IDS activity, histological markers, and global proteomics for comparison with wild-type mice. Combination treatment increased IDS enzyme activity in the liver but not lungs Proteomics data demonstrated attenuation of key features of the disease in liver (metabolic pathways) and lungs (glycosaminoglycan pathways) with both treatments. Overall, adding nebulized administration of IDS did not lead to sustained increase in enzyme activity in the lungs but caused persistent modifications in glycosaminoglycan degradation pathway suggesting additional benefits to intravenous administration alone.
Non-linear stress-softening of the bacterial cell wall confers cell shape homeostasis
Authors: Bardetti Paola , Barber Felix , Rojas Enrique R.
Published: September 2024

The bacillus - or rod - is a pervasive cellular morphology among bacteria. Rod-shaped cells elongate without widening by reinforcing their cell wall anisotropically to prevent turgor pressure from inflating cell width. Here, we demonstrate that a constrictive force is also essential for avoiding pressure-driven widening in Gram-positive bacteria. Specifically, super-resolution measurements of the nonlinear mechanical properties of the cell wall revealed that across a range of turgor pressure cell elongation directly causes width constriction, similar to a “finger trap” toy. As predicted by theory, this property depends on cell-wall anisotropy and is precisely correlated with the cell’s ability to maintain a rod shape. Furthermore, the acute non-linearities in the dependence between cell length and width deformation result in a negative-feedback mechanism that confers cell-width homeostasis. That is, the Gram-positive cell wall is a “smart material” whose exotic mechanical properties are exquisitely adapted to execute cellular morphogenesis.
Stimulus repetition induces a two-stage learning process in primary visual cortex
Authors: Cui Lihan , Bo Ke , Xiong Changhao , Keil Andreas , Ding Mingzhou
Published: September 2024

Repeated stimulus exposure alters the brain’s response to the stimulus. We investigated the underlying neural mechanisms by recording functional MRI data from human observers passively viewing 120 presentations of two Gabor patches (each Gabor repeating 60 times). We evaluated support for two prominent models of stimulus repetition, the fatigue model and the sharpening model. Our results uncovered a two-stage learning process in the primary visual cortex. In Stage 1, univariate BOLD activation in V1 decreased over the first twelve repetitions of the stimuli, replicating the well-known effect of repetition suppression. Applying MVPA decoding along with a moving window approach, we found that (1) the decoding accuracy between the two Gabors decreased from above-chance level (∼60% to ∼70%) at the beginning of the stage to chance level at the end of the stage (∼50%). This result, together with the accompanying weight map analysis, suggested that the learning dynamics in Stage 1 were consistent with the predictions of the fatigue model. In Stage 2, univariate BOLD activation for the remaining 48 repetitions of the two stimuli exhibited significant fluctuations but no systematic trend. The MVPA decoding accuracy between the two Gabor patches was at chance level initially and became progressively higher as stimulus repetition continued, rising above and staying above chance level starting at the ∼35th repetition. Thus, results from the second stage supported the notion that sustained and prolonged stimulus repetition prompts sharpened representations. Additional analyses addressed (1) whether the neural patterns within each learning stage remained stable and (2) whether new neural patterns were evoked in Stage 2 relative to Stage 1.
Enformation Theory: A Blueprint for Evaluating Deep Learning Models in Genomics
Authors: Robson Eyes S , Ioannidis Nilah M.
Published: September 2024

The nascent field of genomic AI is rapidly expanding with new models, benchmarks, and findings. As the field diversifies, there is an increased need for a common set of measurement tools and perspectives to standardize model evaluation. Here, we present a statistically grounded framework for performance evaluation, visualization, and interpretation using the prominent sequence-based deep learning models Enformer and Borzoi as case studies. The Enformer model has been used for applications ranging from understanding regulatory mechanisms to variant effect prediction, but what makes it better or worse than precedent models? Does its follow-up, Borzoi, offer improved performance and more informative embeddings as well as finer resolution? Our goal is to propose a general blueprint for answering such questions and evaluating new models. We start by contrasting the few-shot performance of Enformer and Borzoi to precedent models on the GUANinE benchmark, which emphasizes complex genome interpretation tasks. We then examine Enformer and Borzoi intermediate embeddings in model subjective principal component space, where we identify limiting aspects that affect model generalization. Finally, we present an interpretable decomposition of Enformer and Borzoi, which allows for global model interpretability and partial 'backtracking' to explanatory causal features. Through this case study, we illustrate a new protocol, Enformation Theory, for analyzing and interpreting deep learning models in genomics.
Bacterial transcriptional repressor NrdR – a flexible multifactorial nucleotide sensor
Authors: Rozman Grinberg Inna , Bimaï Ornella , Shahid Saher , Philipp Lena , Martínez-Carranza Markel , Banerjee Ipsita , Lundin Daniel , Stenmark Pål , Sjöberg Britt-Marie , Logan Derek T.
Published: September 2024

NrdR is a bacterial transcriptional repressor consisting of a Zn-ribbon domain followed by an ATP-cone domain. Understanding its mechanism of action could aid the design of novel antibacterials. NrdR binds specifically to two “NrdR boxes” upstream of ribonucleotide reductase operons, of whichEscherichia colihas three: nrdHIEF, nrdDG and nrdAB, where we identified a new box. We show thatE. coliNrdR (EcoNrdR) has similar binding strength to all three sites when loaded with ATP plus dATP or equivalent diphosphate combinations. No other combination of nucleotides promotes binding to DNA. We present crystal structures of EcoNrdR-ATP-dATP and EcoNrdR-ADP-dATP, which are the first high-resolution crystal structures of an NrdR. We have also determined cryo-EM structures of DNA-bound EcoNrdR-ATP-dATP and novel filaments of EcoNrdR-ATP. Tetrameric forms of EcoNrdR involve alternating interactions between pairs of Zn-ribbon domains and ATP-cones. The structures reveal considerable flexibility in relative orientation of ATP-cones vs Zn-ribbon domains. The structure of DNA-bound EcoNrdR-ATP-dATP shows that significant conformational rearrangements between ATP-cones and Zn-ribbons accompany DNA binding while the ATP-cones retain the same relative orientation. In contrast, ATP-loaded EcoNrdR filaments show rearrangements of the ATP-cone pairs and sequester the DNA-binding residues of NrdR such that they are unable to bind to DNA. Our results, in combination with a previous structural and biochemical study, point to highly flexible EcoNrdR structures that when loaded with the correct nucleotides adapt to an optimal promoter binding conformation.
The Arabidopsis RS2Z32 and RS2Z33 proteins are dynamic splicing factors whose RNA recognition motif (RRM) domain contributes to protein-protein and protein-RNA interactions
Authors: Fanara Steven , Schloesser Marie , Gérard Méline , De Franco Simona , Vandevenne Marylène , Hanikenne Marc , Motte Patrick
Published: September 2024

The Arabidopsis splicing factors arginine/serine-rich zinc knuckle-containing proteins 32 and 33 (RS2Z32 and RS2Z33) are plant-specific members of the SR family whose molecular functions received little attention. Here, we characterized both RS2Z32 and RS2Z33 by examining their expression profile at different stages of development and their spatial cellular distribution, as well as the contribution of their domains in the establishment of protein-protein interactions and RNA binding specificity. We report that theRS2Z32andRS2Z33promoters are ubiquitously active during vegetative and reproductive growth, and that both RS2Z splicing factors localize in the nucleus (except the nucleolus). We show that the C-terminal arginine/serine-rich (RS) domain, but not the serine/proline-rich (SP) extension, is a determinant of nuclear localization, which likely requires phosphoresidues putatively phosphorylated by kinases of the SRPK family. We demonstrate that their RNA recognition motif (RRM) domain specifically binds pyrimidine-rich RNA motifs via three residues (Y14, Y46, F48), and is also involved in protein-protein interactions with at least three SR proteins, namely SR45, SCL30, and SR34. Finally, we show that mutations in RNA-binding domains (i.e. RRM and zinc knuckles, ZnKs) affect the nucleocytoplasmic dynamics of both RS2Z proteins. Our findings provide molecular evidence for the involvement of plant-specific SR splicing factors into the regulation of the splicing process.

Highlight

Specific domains of theArabidopsisRS2Z splicing factors contribute to their nuclear localization, nucleocytoplasmic dynamics, and ability to contact protein partners and specific pyrimidine-rich RNA motifs.
Calibration of FRET-based biosensors using multiplexed biosensor barcoding
Authors: Wu Jhen-Wei , Yang Jr-Ming , Chen Chao-Cheng , Au Gabriel , Wang Suyang , Chern Gia-Wei , Huang Chuan-Hsiang
Published: September 2024

Förster resonance energy transfer (FRET) between fluorescent proteins (FPs) is widely used in the design of genetically encoded fluorescent biosensors, which are powerful tools for monitoring the dynamics of biochemical activities in live cells. FRET ratio, defined as the ratio between acceptor and donor signals, is often used as a proxy for the actual FRET efficiency, which must be corrected for signal crosstalk using donor-only and acceptor-only samples. However, the FRET ratio is highly sensitive to imaging conditions, making direct comparisons across different experiments and over time challenging. Inspired by a method for multiplexed biosensor imaging using barcoded cells, we reasoned that calibration standards with fixed FRET efficiency can be introduced into a subset of cells for normalization of biosensor signals. Our theoretical analysis indicated that the FRET ratio of high-FRET species relative to non-FRET species slightly decreases at high excitation intensity, suggesting the need for calibration using both high and low FRET standards. To test these predictions, we created FRET donor-acceptor pairs locked in “FRET-ON” and “FRET-OFF” conformations and introduced them into a subset of barcoded cells. Our results confirmed the theoretical predictions and showed that the calibrated FRET ratio is independent of imaging settings. We also provided a strategy for calculating the FRET efficiency. Together, our study presents a simple strategy for calibrated and highly multiplexed imaging of FRET biosensors, facilitating reliable comparisons across experiments and supporting long-term imaging applications.
Going New Places: Successful Adaptation and Genomic Integrity of Grain Amaranth in India
Authors: Singh Akanksha , Stetter Markus G
Published: September 2024

Global climate change will impact worldwide crop yields, requiring shifts and adaptation of crop varieties. The recent global spread of crops across different continents shows how plants successfully colonized new environments. One such spread is the introduction of the nutritious pseudocereal amaranth to India. Grain amaranth has been domesticated over 6,000 years ago in three different regions of the Americas and was introduced to India approximately 500 years ago. Nowadays numerous local landraces grow throughout the country′s wide climatic conditions. We investigate the introduction of grain amaranth to India to understand the factors allowing successful establishment of crops to novel environments, using whole genome sequencing of almost 200 accessions from India and more than 100 accessions from the crop's native distribution. We find comparable levels of genetic diversity in the Americas and in India, despite the likely population bottleneck during the introduction to India. Surprisingly, the three grain amaranth species that were introduced do not show signs of gene-flow in India, while gene-flow in the Americas was high during the domestication of the crops. Correspondingly, the genetic differentiation between grain species was higher within India than in the native range, indicating a strong isolation between otherwise interbreeding populations. The reconstruction of the population history through demographic modelling of different scenarios suggested rapid expansion in the Indian population but a strong bottleneck in the native population, explaining the comparable diversity and isolation. We identified genomic loci under selection and associated with the climate in India that potentially enabled the adaptation to the new environment. These loci are predicted to provide an advantage under future climate scenarios, even in the native range. Our results suggest that introduced crops can act as reservoirs of genetic diversity, providing additional adaptive potential and resilience to future environmental change.
Neighbor sensing through rhizodeposits in sorghum affects plant physiology and productivity
Authors: Ben-Zeev Shiran , Penn Amanda , Lawrence-Paul Erica H. , Abrams Desa Rae , Ben-Zeev Rotem , Lowry Carolyn , Lasky Jesse R.
Published: September 2024

Plant-plant interactions play a crucial role in shaping the growth environment for crops, impacting their productivity and stress response. The interaction between plants aboveground has been studied and incorporated into breeding programs that select for plants that reduce aboveground competition between plants. However, few studies have focused on belowground interactions, and these looked at combined interactions and root partitioning in the soil. This study focuses on the developmental and physiological responses of sorghum (Sorghum bicolorL.) genotypes to neighboring sorghum plants. In this study, we used two growing methods: i) a focal plant surrounded by neighboring plants in the same pot but without shading, and ii) a focal plant grown either alone or surrounded by neighbors, irrigated with nutrient solution passed through pots (leachates) with or without plants. Our results showed that the presence of neighbors in the same pot led to reduced size-dry weight height, and leaf area of the focal plant. In addition, the presence of neighbors reduced stomatal conductance and PSII quantum yield. While the response direction was similar across tested genotypes, the magnitude varied. The results were repeated when neighboring plants were not grown in the same pot, but the nutrient solution passed through the root system of plants of the neighboring genotype. Furthermore, we saw a reduction in assimilation rate and stomatal conductance when plants were exposed to either the physical presence of neighbors or leachate. We did not find differences in root architecture in either treatment. These results show plants change their growth in response to neighbors and that the signal is carried through the liquid phase of the soil. Our findings provide insights into sorghum plants’ responses to below-ground signaling from neighboring plants and lay the foundation for future studies enabling increased crop performance under high-density planting conditions.
Systemic in utero gene editing as a treatment for cystic fibrosis
Authors: Ricciardi Adele S. , Barone Christina , Putman Rachael , Quijano Elias , Gupta Anisha , Nguyen Richard , Mandl Hanna , Piotrowski-Daspit Alexandra S. , Lopez-Giraldez Francesc , Luks Valerie , Freedman-Weiss Mollie R. , Farrelly James , Ahle Samantha , Glazer Peter M. , Saltzman W. Mark , Stitelman David H. , Egan Marie E.
Published: September 2024

In utero gene editing has the potential to modify disease causing genes in multiple developing tissues before birth, possibly allowing for normal organ development, disease improvement, and conceivably, cure. In cystic fibrosis (CF), a disease that arises from mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, there are signs of multiorgan disease affecting the function of the respiratory, gastrointestinal, and reproductive systems already present at birth. Thus, treating CF patients early is crucial for preventing or delaying irreversible organ damage. Here we demonstrate proof-of-concept of multiorgan mutation correction in CF using peptide nucleic acids (PNAs) encapsulated in polymeric nanoparticles and delivered systemically in utero. In utero editing was associated with sustained postnatal CFTR activity, at a level similar to that of wild-type mice, in both respiratory and gastrointestinal tissue, without detection of off-target mutations in partially homologous loci. This work suggests that systemic in utero gene editing represents a viable strategy for treating monogenic diseases before birth that impact multiple tissue types.
Acetylation of lysine 82 initiates TDP-43 nuclear loss of function by disrupting its nuclear import
Authors: Zhang Sitao , Vazquez-Sanchez Sonia , Lu Shan , Baughn Michael W. , Lim Jaisen , Oung Spencer , Gao Lilian , Diedrich Jolene K. , Yates John R , Yu Haiyang , Ravits John , Cleveland Don W.
Published: September 2024

The hallmark of a spectrum of age-dependent neurodegenerative diseases, including Amyotrophic Lateral Sclerosis (ALS), is a TDP-43 proteinopathy that includes nuclear loss of function and cytoplasmic aggregation. Here, reduced proteasome activity, as naturally occurs during aging, is shown to inhibit nuclear import of TDP-43. Quantitative mass spectrometry is used to determine that TDP-43 is the protein whose nuclear localization is most perturbed upon reduction in proteasome activity, culminating in elevated cytoplasmic TDP-43. Interaction of importin-α1 with the bipartiteclassicalnuclear localizationsequence (cNLS) of TDP-43 is shown to be disrupted by partial proteasome inhibition but maintained by replacement with a PY-NLS that is recognized by importin-β2. Mechanistically, this nuclear depletion of TDP-43 is shown to be driven by ubiquitination or acetylation of lysines 79, 82, and 84 within the cNLS when proteasome activity is reduced in human neurons. Specifically, acetylation at lysine 82 is sufficient to abolish TDP-43 binding to importin-α1 and subsequent nuclear import of TDP-43. Moreover, using acetylation-specific TDP-43 antibodies, we detected acetylation of lysine 82 in the motor cortex of sporadic ALS patients but not control subjects. Our findings demonstrate that post-translational acetylation at lysine 82 of TDP-43 drives disruption of its importin-α1-mediated nuclear import and is sufficient to initiate TDP-43 nuclear loss of function and cytoplasmic accumulation, evidence supporting acetylation as a plausible initiator of TDP-43 proteinopathies.
Biologically-Constrained Spiking Neural Network for Neuromodulation in Locomotor Recovery after Spinal Cord Injury
Authors: Chia Raymond , Lin Chin-Teng
Published: September 2024

Presynaptic inhibition after spinal cord injury (SCI) has been hypothesised to disproportionately affect flexion reflex loops in locomotor spinal circuitry. Reducing gamma-aminobutyric acid (GABA) inhibitory activity increases the excitation of flexion circuits, restoring muscle activation, and stepping ability. Conversely, nociceptive sensitisation and muscular spasticity can emerge from insufficient GABAergic inhibition. To investigate the effects of neuromodulation and proprioceptive sensory afferents in the spinal cord, a biologically constrained spiking neural network (SNN) was developed. The network describes the flexor motoneuron (MN) reflex loop with inputs from ipsilateral Ia- and II-fibres and tonically firing interneurons. The model was tuned to a baseline level of locomotive activity before simulating an inhibitory-dominant and body-weight supported (BWS) SCI state. Electrical stimulation (ES) and serotonergic agonists were simulated by the excitation of dorsal fibres and reduced conductance in excitatory neurons. ES was applied across all afferent fibres without phase- or muscle-specific protocols. The present study describes, for the first time, the release of GABAergic inhibition on flexor MNs as a potential mechanism underlying BWS treadmill training. The results demonstrate the synaptic mechanisms by which neuromodulatory therapy tunes the excitation and inhibition of ankle flexor MNs during locomotion for smoother and more coordinated movement.

Author Summary

SCI is a life-altering condition that often leaves young adults paralysed and reliant on others for support. Restoring the ability to walk is a critical goal to help improve independence and quality of life for people living with SCI. Promising new treatments, such as spinal cord stimulation and drug therapies, aim to reawaken the neurons that control walking. However, scientists still do not entirely understand how these treatments work. In this study, we developed a detailed computer model of the neural circuits involved in walking to test how therapies such as serotonin-boosting drugs, ES, and BWS training might help. Our findings suggest that these treatments can work together to reduce excessive inhibition that blocks ankle movement, leading to smoother and more coordinated steps. This research helps uncover how these therapies work and provides insights to develop better rehabilitation strategies for improving walking after SCI.
Gray matter volume increase in the retrosplenial/posterior cingulate cortices of blind soccer players
Authors: Morita Tomoyo , Naito Eiichi
Published: September 2024

Spatial navigation is a crucial brain function that occurs when an individual moves from one location to another. This function normally relies on vision, and the retrosplenial/posterior cingulate cortices (RSC/PCC) and parahippocampal cortex (PHC) play crucial roles. However, an extraordinary adaptation can be observed in blind soccer players, where the human brain can perform spatial navigation without vision. Therefore, this study tested the possible increase in gray matter (GM) volume in the RSC/PCC and PHC in the brains of a world’s top blind soccer player and other blind soccer players. We collected structural magnetic resonance imaging (MRI) scans from six blind soccer players (including the world’s top player) and eight blind non-soccer players. Using voxel-based morphometry (VBM) analysis (single-case VBM approach), we examined GM volume increase in each participant compared to 250 sighted participants (all of whom had never played blind soccer). Compared with the sighted participants, the world’s top blind soccer player had a significant increase in GM volume in the bilateral RSC/PCC. Two of the other five blind soccer players also showed an increase in the left RSC/PCC. However, such an increase in GM volume was not observed in the blind non-soccer players. Eventually, the probability of a significant increase in the RSC/PCC was significantly higher in the blind soccer group than in the blind non-soccer group. In contrast, only one blind soccer player (not the top player) showed a significant increase in the PHC, and no between-group difference was observed in the probability of a significant increase in the PHC. This study, unveiling the characteristics of the brains of the world’s top blind soccer player and of other blind soccer players, for the first time demonstrates that blind soccer training, which requires spatial navigation based on non-visual cues, may enlarge the human RSC/PCC and provide findings that promote understanding the brains of challenged persons playing blind soccer.
Recombination shapes the diversification of thewtfmeiotic drivers
Authors: Wang Yan , Xu Hao , He Qinliu , Wu Zhiwei , Gong Zhen , Han Guan-Zhu
Published: September 2024

Meiotic drivers are selfish genetic elements that distort fair segregation. Thewtfgenes are poison-antidote meiotic drivers that are experiencing rapid diversification in fission yeasts. However, gene duplication alone is insufficient to drive the diversification ofwtfgenes, given the poison encoded by a newly duplicatedwtfgene can be detoxified by the antidote encoded by the originalwtfgene. Here, we analyze the evolution ofwtfgenes across 21 strains ofSchizosaccharomyces pombe. Knocking out each of 25wtfgenes inS. pombestrain 972h- separately does not attenuate the yeast growth, indicating that thewtfgenes might be largely neutral to their carriers in asexual life cycle. Interestingly,wtfgenes underwent recurrent and intricate recombination. As proof-of-principle, we generate a novel meiotic driver through artificial recombination betweenwtfdrivers, and its encoded poison cannot be detoxified by the antidotes encoded by their parentalwtfgenes but can be detoxified by its own antidote. Therefore, we propose that recombination can generate new meiotic drivers and thus shape the diversification of thewtfdrivers.
A novel channel invariant architecture for the segmentation of cells and nuclei in multiplexed images using InstanSeg
Authors: Goldsborough Thibaut , O’Callaghan Alan , Inglis Fiona , Leplat Léo , Filby Andrew , Bilen Hakan , Bankhead Peter
Published: September 2024

The quantitative analysis of bioimaging data increasingly depends on the accurate segmentation of cells and nuclei, a significant challenge for the analysis of high-plex imaging data. Current deep learning-based approaches to segment cells in multiplexed images require reducing the input to a small and fixed number of input channels, discarding imaging information in the process. We present Channel Net, a novel deep learning architecture for generating three-channel representations of multiplexed images irrespective of the number or ordering of imaged biomarkers. When combined with InstanSeg, ChannelNet sets a new benchmark for the segmentation of cells and nuclei on public multiplexed imaging datasets. We provide an open implementation of our method and integrate it in open source software. Our code and models are available onhttps://github.com/instanseg/instanseg.
Discovery of a newPhenuivirusspecies inLachenaliaplants reveals possible co-evolution between 5’ and 3’ RNA sequence motifs
Authors: Dekker Rob J. , de Leeuw Wim C. , van Olst Marina , Ensink Wim A. , van Leeuwen Selina , Breit Timo M. , Jonker Martijs J.
Published: September 2024

This study reports the discovery of a new Phenuivirus species, named Lachenalia Phenuivirus-1 (LacPhV-1), from Lachenalia plants in an urban botanic garden in Amsterdam. Using a combination of smallRNA-seq, RNA-seq, and advanced bioinformatics, we identified a segmented negative-strand RNA virus in the Phenuiviridae family. Our findings show significant divergence between this new virus and known Phenuiviruses, such as Tulip Streak Virus (TuSV) and Lactuca Big Vein associated Phlebovirus (LBVaPV), supporting its classification as a distinct species. Notably, the sequence differences found in the conserved 5’ and 3’ ends of these segments suggest potential co-evolution. Despite the observed genomic distances, there is significant conservation in the RdRp subdomain, underscoring evolutionary relationships among LacPhV-1, TuSV, and LBVaPV. Our findings expand the known global virome and highlight the importance of exploring plant viromes in diverse ecological settings to better understand virus evolution and diversity.
Pupil self-regulation modulates markers of cortical excitability and cortical arousal
Authors: Weijs Marieke Lieve , Missura Silvia , Potok-Szybińska Weronika , Bächinger Marc , Badii Bianca , Dominguez Manuel Carro , Wenderoth Nicole , Meissner Sarah Nadine
Published: September 2024

The brain’s arousal state (i.e., central arousal) is regulated by multiple neuromodulatory nuclei in the brainstem and significantly influences high-level cognitive processes. By exploiting the mechanistic connection between the locus coeruleus (LC), a key regulator of central arousal, and pupil dynamics, we recently demonstrated that participants can gain volitional control over arousal-regulating centers including the LC using a pupil-based biofeedback approach. Here, we test whether pupil-based biofeedback modulates electrophysiological markers of cortical excitability, cortical arousal, and phasic LC activity. Combining pupil-based biofeedback with single-pulse TMS, EEG recordings, and an auditory oddball task revealed three main results: pupil self-regulation significantly modulates (i) cortical excitability, (ii) the EEG spectral slope, a marker of cortical arousal, and (iii) the P300 response to target tones, an event-related potential suggested to be tightly linked to phasic LC activity. Interestingly, pupil self-regulation strength was linearly linked to the modulation of the spectral slope, suggesting a common physiological mechanism. Here, we have shown that pupil-based biofeedback modulates fundamental aspects of brain function. Whether this method could further be used to modulate these aspects in case of disturbances associated with neurological and psychiatric disorders needs to be investigated in future studies.
Impact of Acetate and Optimized Nitrate Levels on Mixotrophic Growth and Protein Dynamics inChlorella Sorokiniana
Authors: Chen Sunni , Wang Ruiqi , Kim Youn Joong , Radican Emily , Lei Yu , Cho Yongku , Xiao Zhenlei , Qiao Mingyu , Luo Yangchao
Published: September 2024

Microalgae are well-known for their role as sustainable bio-factories, offering a promising solution to the global food and nutrition crisis. To clarify the potential ofChlorella sorokinianaUTEX 1230 for food applications, particularly as an alternative protein source, the study employed a mixotrophic cultivation mode with sodium acetate (NaAc) as a cost-effective organic carbon (NaAc-C) source. Varying levels of NaAc-C and nitrate-sourced nitrogen were investigated, optimizing the effect of metabolic characteristics of the microalgal growth. The designed heterotrophic cultivation confirmed the ability ofC. sorokinianaUTEX 1230 to grow on NaAc-C, and then the mixotrophic cultures, when supported by both NaAc-C and CO2, exhibited superior growth performance, achieving double the biomass concentration compared to the autotrophic control. The addition of nitrogen (750 mg/L NaNO₃) facilitated the thorough metabolism of NaAc-C and enhanced photosynthetic activity indicated by a 196% increase in pigment levels, which resulted in a maximum biomass concentration of 2.82 g/L in the 150 mM NaAc-C group. A detailed analysis of nitrogen and protein concentrations over time revealed that higher nitrogen availability led to greater protein accumulation which was then degraded to support essential life activities under nitrogen starvation. Therefore, it is suggested that supplementing nitrate on the 3rdday and harvesting on the 4thday could be strategically implemented to increase protein yield from 0.17 g/L/d to 0.34 g/L/d. These findings offer theoretical guidance for further refining this microalgal strain for use as an alternative protein.