bluuebunny/crossref_metadata_2025 huggingface dataset:
Unraveling the dynamic transcriptomic changes during the dimorphic transition ofTalaromyces marneffeithrough time-course analysis
Authors: Du Minghao , Tao Changyu , Hu Xueyan , Zhang Yun , Kan Jun , Wang Juan , Yang Ence
Published: June 2023

Systemic dimorphic fungi pose a significant public health challenge, causing over one million new infections annually. The dimorphic transition between saprophytic mycelia and pathogenic yeasts is strongly associated with the pathogenesis of dimorphic fungi. However, despite the dynamic nature of dimorphic transition, the current omics studies focused on dimorphic transition primarily employ static strategies, partly due to the lack of suitable dynamic analytical methods. Here, we firstly conducted time-course transcriptional profiling during the dimorphic transition ofTalaromyces marneffei, a model organism for thermally dimorphic fungi. Then, we identified 5,223 dimorphic transition induced genes (DTIGs) by developing DyGAM-NS (dynamic optimized generalized additive model with natural cubic smoothing), a model that enables the capture of non-uniform and nonlinear transcriptional changes during intricate biological processes. Notably, the DyGAM-NS outperformed other commonly used models, achieving the highest F1-score in DTIGs identification. The cluster analysis of DTIGs suggests differential functional involvement of genes at distinct stages of dimorphic transition. Moreover, we observed divergent gene expression patterns between mycelium-to-yeast and yeast-to-mycelium transitions, indicating the asymmetrical nature of two transition directions. Additionally, leveraging the identified DTIGs, we constructed a regulatory network for the dimorphic transition and identified two zinc finger-containing transcription factors that potentially regulate dimorphic transition inT. marneffei. In summary, our study not only elucidates the dynamic changes in transcriptional profiles during the dimorphic transition ofT. marneffeibut also provides a novel perspective for unraveling the underlying mechanisms of fungal dimorphism.

IMPORTANCE

The dimorphic transition, i.e., morphological switch between saprophytic mycelia and pathogenic yeasts, plays a pivotal role in the pathogenesis of dimorphic fungi. However, the underlying mechanisms of dimorphic transition remain poorly understood, partly due to the lack of dynamic analytical methods suitable for its intricate nature. In the current study, we dissected the dynamic transcriptional profiles of dimorphic transition with a model thermally dimorphic fungus,T. marneffei, by developing a novel analytical method, DyGAM-NS. We proved that DyGAM-NS was more powerful in capturing the non-uniform and nonlinear gene expression variations during the dimorphic transition. With DyGAM-NS, we identified a repertoire of genes associated with dimorphic transition, and comprehensively unraveled distinct functions and expression patterns at different transition stages ofT. marneffei, which offers novel perspectives regarding the mechanistic underpinnings of fungal dimorphism.
Pitch is Not (Always) a Helix: Probing the Structure of Musical Pitch Across Tasks and Experience
Authors: Marjieh Raja , Griffiths Thomas L. , Jacoby Nori
Published: June 2023

Pitch perception is at the core of our experience of both speech and music, and understanding the appropriate representation of musical pitch has intrigued scholars for centuries. The pitch helix, which jointly represents the logarithmic scaling of the periodicity of tones and the heightened similarity between tones separated by an octave, or octave equivalence, is often presented in textbooks as the underlying representation of pitch. However, prior research suggests that the representation of pitch is influenced by task context and musical expertise, although the evidence derives from disparate studies that are small-scale and sometimes contradictory. Here we systematically investigate how the representation of pitch varies across musical expertise levels and task demands. Drawing inspiration from representational similarity analysis in neuroscience, we revisit this problem through a series of nine experiments involving participants with varied levels of musical expertise (N= 592) and paradigms covering both perception and production. We show that, depending on task and musical experience, the best geometrical approximation to the representation of pitch can exhibit an array of structures ranging from linear to double-helical structures, providing strong evidence that a simple helical representation cannot explain the data. Surprisingly, we also found that octave equivalence was strongest in the singing task despite being the most challenging due to production noise. These results suggest a broader, more nuanced understanding of how we perceive pitch.
Rapid measurement and machine learning classification of color vision deficiency
Authors: He Jingyi , Bex Peter J. , Skerswetat Jan
Published: June 2023

Color vision deficiencies (CVDs) indicate potential genetic variations and can be important biomarkers of acquired impairment in many neuro-ophthalmic diseases. However, CVDs are typically measured with insensitive or inefficient tools that are designed to classify dichromacy subtypes rather than track changes in sensitivity. We introduce FInD (Foraging Interactive D-prime), a novel computer-based, generalizable, rapid, self-administered vision assessment tool and applied it to color vision testing. This signal detection theory-based adaptive paradigm computes test stimulus intensity from d-prime analysis. Stimuli were chromatic gaussian blobs in dynamic luminance noise, and participants clicked on cells that contain chromatic blobs (detection) or blob pairs of differing colors (discrimination). Sensitivity and repeatability of FInD Color tasks were compared against HRR, FM100 hue tests in 19 color-normal and 18 color-atypical, age-matched observers. Rayleigh color match was completed as well. Detection and Discrimination thresholds were higher for atypical observers than for typical observers, with selective threshold elevations corresponding to unique CVD types. Classifications of CVD type and severity via unsupervised machine learning confirmed functional subtypes. FInD tasks reliably detect CVD and may serve as valuable tools in basic and clinical color vision science.
Analysis of follow-up data in large biobank cohorts: a review of methodology
Authors: Kolde Anastassia , Koitmäe Merli , Käärik Meelis , Möls Märt , Fischer Krista
Published: June 2023

This study focuses on key methodological challenges in genome-wide association studies (GWAS) of biobank data with time-to-event outcomes, analyzed using the Cox proportional hazards (CPH) model. We address four primary issues: left-truncation of the data, com-putational inefficiency of standard model-fitting algorithms, related-ness among individuals, and model misspecification. To manage left-truncation, the common practice is to use age as the timescale, with individuals entering the risk set at their age of recruitment. We assess how this choice of timescale influences bias and statistical power, under realistic GWAS conditions of varying effect sizes and censoring rates. In addition, to alleviate the computational burden typical in large-scale data, we propose and evaluate a two-step martingale residual (MR) approach for high-dimensional CPH modeling. Our results show that the timescale choice has minimal effect on accuracy for small hazard ratios, though using birth age as the timescale-ignoring recruitment age-yields the highest power for association detection. We find that relatedness, when ignored, does not substantially bias effect size estimates, while omitting key covariates introduces significant bias. The two-step MR approach proves to be computationally efficient, retaining power for detecting small effect sizes, making it suitable for large-scale association studies. However, when precise effect size estimates are critical, particularly for moderate or larger effect sizes, we recommend recalculating these estimates using the conventional CPH model, with careful attention to left-truncation and relatedness. These conclusions are drawn from simulations and illustrated with data from the Estonian Biobank cohort.
Identification of potential molecular mimicry in pathogen-host interactions
Authors: Rich Kaylee D. , Srivastava Shruti , Muthye Viraj , Wasmuth James D.
Published: June 2023

Pathogens have evolved sophisticated strategies to manipulate host signaling pathways, including the phenomenon of molecular mimicry, where pathogen-derived biomolecules imitate host biomolecules. In this study, we used a sequence-based bioinformatics pipeline to identify potential molecular mimicry candidates between humans and 32 pathogenic species—bacteria, fungi, protozoa, and helminths—of global health importance. We observed considerable variation in the number of mimicry candidates across pathogenic species, with pathogenic bacteria exhibiting fewer candidates compared to fungi and protozoans. Further analysis revealed that the candidate mimicry regions were enriched in solvent-accessible regions, highlighting their potential functional relevance. We identified a total of 1878 mimicked regions in 1439 human proteins, and clustering analysis indicated diverse target proteins across pathogen species. The human proteins containing mimicked regions revealed significant associations between these proteins and various biological processes, with an emphasis on host extracellular matrix organization and cytoskeletal processes. However, immune-related proteins were underrepresented as targets of mimicry. Our findings provide insights into the broad range of host-pathogen interactions mediated by molecular mimicry and highlight potential targets for further investigation. This comprehensive analysis contributes to our understanding of the complex mechanisms employed by pathogens to subvert host defenses and promotes the development of novel therapeutic strategies.
Self-reversal facilitates the resolution of HMCES-DNA protein crosslinks in cells
Authors: Rua-Fernandez Jorge , Lovejoy Courtney A. , Mehta Kavi P.M. , Paulin Katherine A. , Toudji Yasmine T. , Eichman Brandt F. , Cortez David
Published: June 2023

Abasic sites are common DNA lesions that stall polymerases and threaten genome stability. When located in single-stranded DNA (ssDNA), they are shielded from aberrant processing by HMCES via a DNA-protein crosslink (DPC) that prevents double-strand breaks. Nevertheless, the HMCES-DPC must be removed to complete DNA repair. Here, we found that DNA polymerase α inhibition generates ssDNA abasic sites and HMCES-DPCs. These DPCs are resolved with a half-life of approximately 1.5 hours. Resolution does not require the proteasome or SPRTN protease. Instead, HMCES-DPC self-reversal is important for resolution. Biochemically, self-reversal is favored when the ssDNA is converted to duplex DNA. When the self-reversal mechanism is inactivated, HMCES-DPC removal is delayed, cell proliferation is slowed, and cells become hypersensitive to DNA damage agents that increase AP site formation. Thus, HMCES-DPC formation followed by self-reversal is an important mechanism for ssDNA AP site management.
Macromolecular Crowding Tailors the Microtubule Cytoskeleton Through Tubulin Modifications and Microtubule-Associated Proteins
Authors: Shen Yusheng , Ori-McKenney Kassandra M.
Published: June 2023

Cells remodel their cytoskeletal networks to adapt to their environment. Here, we analyze the mechanisms utilized by the cell to tailor its microtubule landscape in response to changes in osmolarity that alter macromolecular crowding. By integrating live cell imaging,ex vivoenzymatic assays, andin vitroreconstitution, we probe the impact of acute perturbations in cytoplasmic density on microtubule-associated proteins (MAPs) and tubulin posttranslational modifications (PTMs), unraveling the molecular underpinnings of cellular adaptation via the microtubule cytoskeleton. We find that cells respond to fluctuations in cytoplasmic density by modulating microtubule acetylation, detyrosination, or MAP7 association, without differentially affecting polyglutamylation, tyrosination, or MAP4 association. These MAP-PTM combinations alter intracellular cargo transport, enabling the cell to respond to osmotic challenges. We further dissect the molecular mechanisms governing tubulin PTM specification, and find that MAP7 promotes acetylation by biasing the conformation of the microtubule lattice, and directly inhibits detyrosination. Acetylation and detyrosination can therefore be decoupled and utilized for distinct cellular purposes. Our data reveal that the MAP code dictates the tubulin code, resulting in remodeling of the microtubule cytoskeleton and alteration of intracellular transport as an integrated mechanism of cellular adaptation.
Mechanically stimulated osteocytes maintain tumor dormancy in bone metastasis of non-small cell lung cancer by releasing small extracellular vesicles
Authors: Xie Jing , Xu Yafei , Liu Xuhua , Long Li , Chen Ji , Huang Chunyan , Shao Yan , Cai Zhiqing , Zhang Zhimin , Zhou Ruixin , Leng Jiarong , Bai Xiaochun , Song Qiancheng
Published: June 2023

Although preclinical and clinical studies have shown that exercise can inhibit bone metastasis progression, the mechanism remains poorly understood. Here, we found that non-small cell lung cancer (NSCLC) cells adjacent to bone tissue had a much lower proliferative capacity than the surrounding tumor cells. Subsequently, it was demonstrated that osteocytes, sensing mechanical stimulation generated by exercise, inhibit NSCLC cell proliferation and sustain the dormancy thereof by releasing small extracellular vesicles with tumor suppressor microRNAs, such as miR-99b-3p. Furthermore, mechanical loading of the tibia inhibited the bone metastasis progression of NSCLC. Notably, bone metastasis progression of NSCLC was inhibited by moderate exercise, and combinations with zoledronic acid had additive effects. Moreover, exercise preconditioning effectively suppressed bone metastasis progression. This study significantly advances the understanding of the mechanism underlying exercise-afforded protection against bone metastasis progression.
The LINC complex ensures accurate centrosome positioning during prophase
Authors: Lima Joana T. , Pereira António J. , Ferreira Jorge G.
Published: June 2023

Accurate centrosome separation and positioning during early mitosis relies on force- generating mechanisms regulated by a combination of extracellular, cytoplasmic, and nuclear cues. The identity of the nuclear cues involved in this process remains largely unknown. Here, we investigate how the prophase nucleus contributes to centrosome positioning during the initial stages of mitosis, by using a combination of cell micropatterning, high-resolution live-cell imaging and quantitative 3D cellular reconstruction. We show that in untransformed RPE-1 cells, centrosome positioning is regulated by a nuclear signal, independently of external cues. This nuclear mechanism relies on the linker of nucleoskeleton and cytoskeleton (LINC) complex that controls the timely loading of dynein on the nuclear envelope (NE), providing spatial cues for robust centrosome positioning on the shortest nuclear axis, prior to nuclear envelope permeabilization (NEP). Our results demonstrate how nuclear-cytoskeletal coupling maintains a robust centrosome positioning mechanism to ensure efficient mitotic spindle assembly.

Summary blurb

Centrosome positioning in prophase is essential for efficient spindle assembly. Here, we show that centrosome positioning requires LINC complex-mediated loading of dynein on the nuclear envelope.
Symbiotic nutrient exchange enhances the long-term survival of cassiosomes, the autonomous stinging-cell structures ofCassiopea
Authors: Toullec Gaëlle , Lyndby Niclas Heidelberg , Banc-Prandi Guilhem , Pogoreutz Claudia , Olmos Cristina Martin , Meibom Anders , Rädecker Nils
Published: June 2023

Medusae of the widely distributed and locally invasive upside-down jellyfishCassiopearelease autonomous, mobile stinging structures. These so-called cassiosomes are a major contributor to ‘contactless’ stinging incidents in (sub-)tropical shallow waters. While the presence of endosymbiotic dinoflagellates in cassiosomes has previously been observed, their potential contribution to the metabolism and long-term survival of cassiosomes is unknown. Combining stable isotope labeling and correlative SEM and NanoSIMS imaging with a long-termin vitroexperiment, this study reveals a mutualistic symbiosis based on nutritional exchanges in dinoflagellate-bearing cassiosomes. We were able to show that organic carbon input from the dinoflagellates fuels the metabolism of the host tissue and enables anabolic nitrogen assimilation. Thanks to this symbiotic nutrient exchange, cassiosomes showed enhanced survival in the light compared to dark conditions for at least one monthin vitro. Overall, this study demonstrates that cassiosomes, in analogy withCassiopeamedusae, are photosymbiotic holobionts. Cassiosomes thus promise to be a powerful new miniaturized model system for in-depth ultrastructural and molecular investigation of cnidarian photosymbioses.
Quantifying innervation facilitated by deep learning in wound healing
Authors: Mehta Abijeet Singh , Teymoori Sam , Recendez Cynthia , Fregoso Daniel , Gallegos Anthony , Yang Hsin-Ya , Isseroff Roslyn Rivkah , Zhao Min , Gomez Marcella
Published: June 2023

The peripheral nerves (PNs) innervate the dermis and epidermis, which have been suggested to play an important role in wound healing. Several methods to quantify skin innervation during wound healing have been reported. Those usually require multiple observers, are complex and labor-intensive, and noise/background associated with the Immunohistochemistry (IHC) images could cause quantification errors/user bias. In this study, we employed the state-of-the-art deep neural network, DnCNN, to perform pre-processing and effectively reduce the noise in the IHC images. Additionally, we utilized an automated image analysis tool, assisted by Matlab, to accurately determine the extent of skin innervation during various stages of wound healing. The 8mm wound is generated using a circular biopsy punch in the wild-type mouse. Skin samples were collected on days 3,7,10 and 15, and sections from paraffin-embedded tissues were stained against pan-neuronal marker- protein-gene-product 9.5 (PGP 9.5) antibody. On day 3 and day 7, negligible nerve fibers were present throughout the wound with few only on the lateral boundaries of the wound. On day 10, a slight increase in nerve fiber density appeared, which significantly increased on day 15. Importantly we found a positive correlation (R-2= 0.933) between nerve fiber density and re-epithelization, suggesting an association between re-innervation and re-epithelization. These results established a quantitative time course of re-innervation in wound healing, and the automated image analysis method offers a novel and useful tool to facilitate the quantification of innervation in the skin and other tissues.
Positive association between alleles at selectively neutral loci
Authors: Potapova Nadezhda A. , Kondrashov Alexey S.
Published: June 2023

Linkage disequilibrium (LD) is a non-independent distribution of alleles at different loci and might be defined using directional and directionless approaches. While analytical theory is available for directionless LD, analytical theory for directional LD is less developed. In this study we investigated directional LD generated by random drift between two selectively neutral loci. When the sign of LD is determined by the ancestral-derived status of these alleles, its expected value is zero. In contrast, computer simulations show that random drift leads to a tendency of rare, as well as of common, alleles to occur together. This observation is supported by a straightforward analytical argument. If only those generations where both loci are polymorphic are taken into account, the magnitude of the resulting directional LD depends only on Ne. These observations might give an opportunity to directly estimate Nefrom the data on genetic variation within a single generation.
RAVER1 interconnects lethal EMT and miR/RISC activity by the control of alternative splicing
Authors: Wedler Alice , Bley Nadine , Glaß Markus , Müller Simon , Schian Laura , Obika Kingsley-Benjamin , Lederer Marcell , Misiak Claudia , Fuchs Tommy , Köhn Marcel , Jacob Roland , Gutschner Tony , Ihling Christian , Sinz Andrea , Hüttelmaier Stefan
Published: June 2023

The RAVER1 protein was proposed to serve as a co-factor in guiding the PTBP-dependent control of alternative splicing (AS). Whether RAVER1 solely acts in concert with PTBPs and how it affects cancer cell fate remained elusive. Here we provide the first comprehensive investigation of RAVER1-controlled AS in cancer cell models and reveal a pro-oncogenic role of RAVER1 in tumor growth. This unravels that RAVER1 guides AS in synergy with PTBPs but more prominently serves PTBP1-independent roles in splicing. In cancer cells, one major function of RAVER1 is the control of proliferation and apoptosis, which involves the modulation of AS events within the miR/RISC pathway. Associated with this regulatory role, RAVER1 antagonizes lethal, TGFB-driven epithelial-mesenchymal-transition (EMT) by limiting TGFB signaling. RAVER1-modulated splicing events affect the insertion of protein interaction modules in factors guiding miR/RISC-dependent gene silencing. Most prominently, in all three human TNRC6 proteins, RAVER1 controls AS of GW-enriched motifs, which are essential for AGO2-binding. Disturbance of RAVER1-guided AS events in TNRC6 proteins and other facilitators of miR/RISC activity compromise miR/RISC activity which is essential to restrict TGFB signaling and lethal EMT.
Sexual antagonism evolves when autosomes influence offspring sex ratio
Authors: Sloat Solomon , Rockman Matthew
Published: June 2023

Sex allocation theory generally assumes maternal control of offspring sex and makes few predictions for populations evolving under paternal control. Using population genetic simulations, we show that maternal and paternal control of the sex ratio lead to different equilibrium sex ratios in structured populations. Sex ratios evolved under paternal control are more female biased. This effect is dependent on the population subdivision; fewer founding individuals leads to both more biased sex ratios and a greater difference between the paternal and maternal equilibria. In addition, sexual antagonism evolves in simulations with both maternally- and paternally-acting loci. Maternally-acting loci continuously accumulate ever more female-biasing effects as male-biasing effects accumulate at paternally-acting loci. The difference in evolved sex-ratio equilibria and the evolution of sexual antagonism can be largely explained by differences in the between-group variance of maternal and paternal effects in the founding generation. These theoretical results apply to any system with biparental autosomal influence over offspring sex, opening up an exciting new line of questioning.
Alterations in the Mammary Gland and Tumor Microenvironment of Formerly Obese Mice
Authors: Kuziel Genevra , Moore Brittney N. , Haugstad Grace P. , Xiong Yue , Williams Abbey E. , Arendt Lisa M.
Published: June 2023

Obesity is a risk factor for breast cancer, and women with obesity that develop breast cancer have a worsened prognosis. Within the mammary gland, obesity causes chronic, macrophage-driven inflammation and adipose tissue fibrosis. To examine the impact of weight loss on the mammary microenvironment, mice were fed high-fat diet to induce obesity, then switched to a low-fat diet. In formerly obese mice, we observed reduced numbers of crown-like structures and fibrocytes in mammary glands, while collagen deposition was not resolved with weight loss. Following transplant of TC2 tumor cells into the mammary glands of lean, obese, and formerly obese mice, diminished collagen deposition and cancer-associated fibroblasts were observed in tumors from formerly obese mice compared to obese mice. When TC2 tumor cells were mixed with CD11b+CD34+myeloid progenitor cells, collagen deposition within the tumors was significantly greater compared to when tumor cells were mixed with CD11b+CD34-monocytes, suggesting that fibrocytes contribute to early collagen deposition in mammary tumors of obese mice. Overall, these studies show that weight loss resolved some of the microenvironmental conditions within the mammary gland that may contribute to tumor progression.
Krause corpuscles of the genitalia are vibrotactile sensors required for normal sexual behavior
Authors: Qi Lijun , Iskols Michael , Handler Annie , Ginty David D.
Published: June 2023

Krause corpuscles, first discovered in the 1850s, are enigmatic sensory structures with unknown physiological properties and functions found within the genitalia and other mucocutaneous tissues. Here, we identified two distinct somatosensory neuron subtypes that innervate Krause corpuscles of the mouse penis and clitoris and project to a unique sensory terminal region of the spinal cord. Usingin vivoelectrophysiology and calcium imaging, we found that both Krause corpuscle afferent types are A-fiber rapid-adapting low-threshold mechanoreceptors, optimally tuned to dynamic, light touch and mechanical vibrations (40-80 Hz) applied to the clitoris or penis. Optogenetic activation of male Krause corpuscle afferent terminals evoked penile erection, while genetic ablation of Krause corpuscles impaired intromission and ejaculation of males as well as reduced sexual receptivity of females. Thus, Krause corpuscles, which are particularly dense in the clitoris, are vibrotactile sensors crucial for normal sexual behavior.
Single-cell transcriptomic analysis of pea shoot development and cell-type-specific responses to boron deficiency
Authors: Chen Xi , Ru Yanqi , Takahashi Hirokazu , Nakazono Mikio , Shabala Sergey , Smith Steven M. , Yu Min
Published: June 2023

Understanding how nutrient stress impacts plant growth is fundamentally important to the development of approaches to improve crop production under nutrient limitation. Here we applied single-cell RNA sequencing to shoot apices ofPisum sativumgrown under boron (B) deficiency. We identified up to fifteen cell clusters based on the clustering of gene expression profiles and verified cell identity with cell-type-specific marker gene expression. Different cell types responded differently to B deficiency. Specifically, the expression of photosynthetic genes in mesophyll cells (MCs) was down-regulated by B deficiency, consistent with impaired photosynthetic rate. Furthermore, the down-regulation of stomatal development genes in guard cells (GCs), including homologs ofMUTEandTOO MANY MOUTHS, correlated with a decrease in stomatal density under B deficiency. We also constructed the developmental trajectory of the shoot apical meristem (SAM) cells and a transcription factor (TF) interaction network. The developmental progression of SAM to MC was characterized by up-regulation of genes encoding histones and chromatin assembly and remodeling proteins including homologs of FASCIATA1 (FAS1) and SWITCH DEFECTIVE/SUCROSE NON-FERMENTABLE (SWI/SNF) complex. However, B deficiency suppressed their expression, which helps to explain impaired SAM development under B deficiency. These results represent a major advance over bulk-tissue RNA-seq analysis in which cell-type-specific responses are lost and hence important physiological responses to B deficiency are missed. The reported approach and resources have potential applications well beyondP. sativumspecies and could be applied to various legumes to improve their adaptability to multiple nutrient or abiotic stresses.
VIGA: an one-stop tool for eukaryotic Virus Identification and Genome Assembly from next-generation-sequencing data
Authors: Fu Ping , Wu Yifan , Zhang Zhiyuan , Qiu Ye , Wang Yirong , Peng Yousong
Published: June 2023

Identification of viruses and further assembly of viral genomes from the next-generation-sequencing (NGS) data are essential steps in virome studies. This study presented an one-stop tool named VIGA (available athttps://github.com/viralInformatics/VIGA) for eukaryotic virus identification and genome assembly from NGS data. It was composed of four modules including identification, taxonomic annotation, assembly and novel virus discovery which integrated the homology-based method for virus identification and both the reference-based andde novoassemblers for accurate and effective assembly of virus genomes. Evaluation on multiple simulated and real virome datasets showed that VIGA assembled more complete virus genomes than its competitors on both the metatranscriptomic and metagenomic data, and also performed well in assembling virus genomes at the strain level. Finally, VIGA was used to investigate the virome in metatranscriptomic data from the Human Microbiome Project and revealed different composition and positive rate of viromes in diseases of Prediabetes, Crohn’s disease and Ulcerative colitis. Overall, VIGA would help much in identification and characterization of viromes in future studies.
Hybrid Modeling of Engineered Biological Systems through Coupling Data-Driven Calibration of Kinetic Parameters with Mechanistic Prediction of System Performance
Authors: Cheng Zhang , Ronen Avner , Yuan Heyang
Published: June 2023

Mechanistic models can provide predictive insight into the design and optimization of engineered biological systems, but the kinetic parameters in the models need to be frequently calibrated and uniquely identified. This limitation can be addressed by integrating mechanistic models with data-driven approaches, a strategy known as hybrid modeling. Herein, we developed a hybrid modeling strategy using bioelectrochemical systems as a platform system. The data-driven component of the model consisted of artificial neural networks (ANNs) that were trained by using mechanistically derived parameter values (e.g., the maximum specific growth rate µmaxand the maximum substrate utilization rate kmaxfor the fermentative, electroactive, and methanogenic populations, and the mediator yield for electroactive microbes YM) as outputs to compute error signals. The hybrid model was built using 148 samples collected from 25 publications. After ten-fold cross-validation, the model was tested with another 28 samples. Internal resistance was accurately predicted with a relative root-mean-square error (RMSE) of 3.9%. Microbial kinetic parameters were also calibrated using the data-driven component. They were fed into the mechanistic component to predict system performance. The R2between the predicted and observed organic removal and current production for systems fed with a simple substrate were 0.90 and 0.94, respectively, significantly higher than those obtained with a standalone data-driven model (0.51 and 0) and a standalone mechanistic model (0.07 and 0.15). The hybrid modeling strategy can potentially be applied to a variety of engineered biological systems forin silicosystem design and optimization.

SYNOPSIS

A hybrid modeling strategy was developed to predict the performance of engineered biological systems without the need for laborious experiment-based parameter calibration.
EphB3 receptor negatively regulates osteogenesis in mice
Authors: Rodríguez-Sosa Mariano R. , Alfaro David , Castillo Luis M. del , Belarra Adrián , Zapata Agustín G.
Published: June 2023

Bone homeostasis is a complex process in which some Eph kinase receptors and their Ephrin ligands appear to be involved. In the present study, we address this issue by examining the capacity of adipose tissue-derived mesenchymal stromal cells (Ad-MSC) derived from either WT,EphB2-andEphB3-KO mice to differentiate into bone tissue. Differentiation capacities were evaluated in cultured MSC by RT-qPCR and histological staining, revealing that whereasEphB2-/-MSC cultured in a specific medium expressed mainly pro-adipogenic transcription factors,EphB3-/-MSC showed abundant osteogenic transcripts, such asRunx2,Msx2andOsterix.In addition, the lack of EphB3 signaling alters the genetic profile of differentiating Ad-MSC, reducing the expression of many inhibitory molecules and antagonists of the BMP signaling pathway, and increasingBmp7expression, a robust bone inductor. Then, to confirm the osteogenic role of EphB3in vivo, we studied the condition of two animal models of induced osteoporosis (ovariectomy or long-term glucocorticoid treatment). Interestingly, in both models, both WT andEphB2-/-mice equally developed the disease butEphB3-/-mice did not exhibit the typical bone loss, nor did they show increased urine Ca2+or blood serum CTX-1. The proportions of osteoprogenitor cells and pre-osteoblasts were also found to be significantly higher inEphB3-KO mice, and the osteoclasts significantly reduced, as compared to WT andEphB2-KO mice. We conclude that EphB3 acts as a negative regulator of the osteogenic differentiation, and its absence prevents the development of experimentally-induced osteoporosis.
Untargeted metabolomics reveals PTI-associated metabolites in tomato
Authors: Muñoz Hoyos Lina , Wan Petra Anisha , Meng Chen , Kleigrewe Karin , Dawid Corinna , Hückelhoven Ralph , Stam Remco
Published: June 2023

Plants employ a multi-layered innate immune system to detect and fend off invading fungal pathogens. In one such layer, recognition of Pathogen- or Microbe-Associated Molecular Patterns or elicitors, triggers a signaling cascade that leads to defence against the pathogen and ultimately Pattern-Triggered Immunity (PTI). Secondary Metabolites (SMs) are expected to play an important role in this kind of resistance, because they are potentially mycotoxic compounds. Tomato plants inoculated withAlternaria solanishow clear symptoms of infection 5 days after inoculation. Whereas plants inoculated withAlternaria alternataremain symptomless. We hypothesized that pattern-triggered induction of resistance-related metabolites inSolanum lycopersicumcontribute to the resistance againstA. alternata, yet such SMs are suppressed in a compatible interaction. We compared the metabolomic profile (metabolome) ofS. lycopersicumat two time points (3 and 24 hours) after treatments withA. alternata, A. solaniand the fungal elicitor chitin and identified SMs that are involved in the early defence response of tomato plants. Our study revealed differential metabolome fingerprints and shows that the molecular composition ofA. alternataand chitin-induced indeed show larger overlap with each other than with theA. solani-induced metabolome. We identify 65 candidate metabolites possibly associated with pattern-triggered resistance in tomato plants, including the alkaloid, trigonelline, for which we can confirm that it inhibits fungal growthin vitrowhen supplied at physiological concentrations. Our findings show that a true, pattern-triggered, chemical defence is mounted againstA. alternataand that it contains mycotoxin compounds previously unidentified in tomato, that could be interesting for future crop protection strategies.
Anti-CD117 CAR T cells incorporating a safety switch eradicate human acute myeloid leukemia and hematopoietic stem cells
Authors: Magnani Chiara F. , Myburgh Renier , Brunn Silvan , Chambovey Morgane , Ponzo Marianna , Volta Laura , Pellegrino Christian , Pascolo Steve , Miskey Csaba , Ivics Zoltán , Shizuru Judith A. , Neri Dario , Manz Markus G.
Published: June 2023

Acute Myeloid Leukemia originates from the accumulation of mutations in hematopoietic stem and progenitor cells, leading to the emergence of leukemia-initiating cells, which sustain blast formation. CAR T cells specific for the CD117 antigen can deplete malignant and healthy hematopoietic stem cells. Here we exploit non-viral technology to achieve early termination of CAR T cell activity to prevent incoming graft rejection. Transient expression of an anti-CD117 CAR by mRNA conferred T cells the ability to eliminate CD117+ targets in vitro and in vivo. As an alternative approach, we used a Sleeping Beauty transposon vector for the generation of CAR T cells incorporating an inducible Caspase 9 safety switch. Stable CAR expression was associated with high proportion of T memory stem cells, low levels of exhaustion markers, and potent cellular cytotoxicity. Anti-CD117 CAR T cells mediated depletion of leukemic cells and healthy hematopoietic stem cells in NSG mice reconstituted with human leukemia or CD34+ cord blood cells, respectively, and could be chemically terminated in vivo. The use of a non-viral technology to control CAR T cell pharmacokinetic properties is attractive for a first-in-human study in patients with acute myeloid leukemia prior to hematopoietic stem cell transplantation.
Vitamin B12 status and folic acid supplementation influence mitochondrial heteroplasmy levels in mice as they age
Authors: Walsh Darren J , Bernard David J , Fiddler Joanna L , Pangilinan Faith , Esposito Madison , Harold Denise , Field Martha S , Parle-McDermott Anne , Brody Lawrence C
Published: June 2023

One-carbon metabolism is a complex network of metabolic reactions that are essential for cellular function including DNA synthesis. Vitamin B12 and folate are micronutrients that are utilized in this pathway and their deficiency can result in the perturbation of one-carbon metabolism and subsequent perturbations in DNA replication and repair. This effect has been well characterized in nuclear DNA but to date, mitochondrial DNA (mtDNA) has not been investigated extensively. Mitochondrial variants have been associated with several inherited and age-related disease states; therefore, the study of factors that impact heteroplasmy are important for advancing our understanding of the mitochondrial genome’s impact on human health.

Heteroplasmy studies require robust and efficient mitochondrial DNA enrichment to carry out in-depth mtDNA sequencing. Many of the current methods for mtDNA enrichment can introduce biases and false positive results. Here we use a method that overcomes these limitations and have applied it to assess mitochondrial heteroplasmy in mouse models of altered one-carbon metabolism. Vitamin B12 deficiency was found to cause increased levels of mitochondrial DNA heteroplasmy across all tissues that were investigated. Folic acid supplementation also contributed to elevated mitochondrial DNA heteroplasmy across all mouse tissues investigated. Heteroplasmy analysis of human data from the Framingham Heart Study suggested a potential sex-specific effect of folate and vitamin B12 status on mitochondrial heteroplasmy. This is a novel relationship that may have broader consequences for our understanding of one-carbon metabolism, mitochondrial related disease and the influence of nutrients on DNA mutation rates.

Significance Statement

Using a sensitive method for mitochondrial heteroplasmy analysis, we show that both vitamin B12 and folic acid can impact mitochondrial DNA mutation. This effect requires further investigation of the potential impact on humans.
Notes on the diet composition of Anoles lizards,Anolis(Dactyloidae), in the Yasuni National Park (Ecuador)
Authors: Pinto Javier
Published: June 2023

In this study, we observed and briefly described the diet of six species of lizards of the genus Anolis in the Yasuni National Park, located in the western part of the Amazon Rainforest. A total of 241 items found in the stomachs of the lizards were classified. We noted that Aranea and Hymenoptera were the most frequent diet categories used by the lizard community. In terms of volume, Hemiptera and insect larvae were the most representative prey. We aim that the description of the diet ofAnolisprovided by this study can be further combined with information pertaining to their natural history, thus shedding light on ecological mechanisms that influence adaptation.
Improved RNA stability estimation through Bayesian modeling reveals mostSalmonellatranscripts have sub-minute half-lives
Authors: Jenniches Laura , Michaux Charlotte , Popella Linda , Reichardt Sarah , Vogel Jörg , Westermann Alexander J. , Barquist Lars
Published: June 2023

RNA decay is a crucial mechanism for regulating gene expression in response to environmental stresses. In bacteria, RNA-binding proteins (RBPs) are known to be involved in post-transcriptional regulation, but their global impact on RNA half-lives has not been extensively studied. To shed light on the role of the major RBPs ProQ and CspC/E in maintaining RNA stability, we performed RNA sequencing ofSalmonella entericaover a time course following treatment with the transcription initiation inhibitor rifampicin (RIF-seq) in the presence and absence of these RBPs. We developed a hierarchical Bayesian model that corrects for confounding factors in rifampicin RNA stability assays and enables us to identify differentially decaying transcripts transcriptome-wide. Our analysis revealed that the median RNA half-life inSalmonellain early stationary phase is less than 1 minute, a third of previous estimates. We found that over half of the 500 most long-lived transcripts are bound by at least one major RBP, suggesting a general role for RBPs in shaping the transcriptome. Integrating differential stability estimates with CLIP-seq revealed that approximately 30% of transcripts with ProQ binding sites and more than 40% with CspC/E binding sites in coding or 3’ untranslated regions decay differentially in the absence of the respective RBP. Analysis of differentially destabilized transcripts identified a role for ProQ in the oxidative stress response. Our findings provide new insights into post-transcriptional regulation by ProQ and CspC/E, and the importance of RBPs in regulating gene expression.

Significance Statement

Together with transcription and translation, RNA decay is one of the major processes governing protein production. Here, we have developed a new statistical approach that corrects for confounding effects when estimating RNA decay rates from RNA-seq in bacteria. Our more accurate decay rate estimates indicate thatSalmonellatranscripts have half-lives about three times shorter than previously thought. This approach allowed us to measure the effects of RNA-binding proteins (RBPs) on decay rates, identifying large cohorts of transcripts with changes in stability following RBP deletion and conditions where post-transcriptional regulation affects survival. Our method should lead to a reevaluation of RNA stability estimates across diverse bacteria and new insights into the role of RBPs in shaping the transcriptome.
DidMoldehaweraflowers evolve through mimicry with oil-producing Malpighiaceae?
Authors: de Queiroz Luciano Paganucci , Costa Jorge Antonio Silva , Costa Cristiana Barros Nascimento
Published: June 2023

Floral mimicry is a captivating phenomenon wherein flowers imitate traits of other species to attract specific pollinators. The Caesalpinioideae legumes in general have relatively unspecialized flowers, which has allowed the development of disparate morphologies associated with adaptation to different types of pollinators. This study describes the pollination ofMoldenhawera nutansand explores its potential floral mimicry towards Malpighiaceae flowers. Our investigation revealed thatM. nutansis pollinated by species ofCentrisFabricius, 1804 andXylocopaLatreille, 1802. It also presents compelling evidence supporting the hypothesis of floral mimicry, including striking similarities in floral display, shared oil-collecting pollinators, oil collection behavior inM. nutansdespite the absence of oil production, and the reliance on exogenous pollen for reproduction. These findings suggest that species ofCentrisbees visitM. nutansflowers under the mistaken impression of oil availability, subsequently transitioning to pollen collection. We explored other potential cases of floral mimicry with Malpighiaceae in the Caesalpinioideae legumes by optimizing the Malpighiaceae-like floral display on a dated phylogeny of this subfamily. However, current information does not allow us to determine whether the similarities in floral morphology represent cases of floral mimicry, phylogenetic inertia, or simple convergence. Several hypothesis tests are suggested that can guide the study of these fascinating evolutionary processes in the group.
Evolution ofShewanella oneidensisMR-1 in competition withCitrobacter freundii
Authors: Zhao Biyi , Chen Geng , Chen Wei , Xiao Yong
Published: June 2023

Interspecific competition is one of the most important metabolic interactions within microbial communities, and exoelectrogenic bacteria that can conduct extracellular electron transfer act essential roles in nature and engineering systems for pollutants removal. In the present study we investigated the long-term impact of substrate competition from non-exoelectrogenicCitrobacter freundiiAn1 on exoelectrogenicShewanella oneidensisMR-1. Without additional electron acceptor or with electron acceptor of oxygen,C. freundiiAn1 typically suppressed the growth ofS. oneidensisMR-1. In contrast,S. oneidensisMR-1 grown better with electron acceptor of ferrihydrite by taking advantage of extracellular electron transfer. However, the presence of ferrihydrite did not enhance the ferrihydrite reduction ofS. oneidensisMR-1 after the 160 d-acclimation. The whole genome resequencing showed a complex evolution ofS. oneidensisMR-1 when the strain faced the competition fromC. freundiiAn1 for substrate.
MeasuringC. elegansAgeing Through Non-Invasive Monitoring of Movement across Large Populations
Authors: Zavagno Giulia , Raimundo Adelaide , Kirby Andy , Saunter Christopher , Weinkove David
Published: June 2023

Finding new interventions that slow ageing and maintain human health is a huge challenge of our time. The nematodeCaenorhabditis elegans, offers a rapidin vivomethod to determine whether a compound extends its 2-3 week lifespan. However, the standardC. eleganslifespan assay is hard to scale for large screens. Lifespan analysis produces only one data point per animal with no information about health. Here we describe automated monitoring of movement from early to mid-adulthood as a healthspan-based alternative to measure ageing. Using our WormGazer™ technology, over 100 petri dishes containingC. elegansworms are imaged simultaneously and non-invasively by an array of cameras. This approach demonstrates that most functional decline inC. elegansoccurs during the first week of adulthood. We find 7 days of imaging is sufficient to measure the dose-dependent efficacy of sulfamethoxazole to slow ageing, compared to 40 days required for a parallel lifespan experiment. Understanding any negative consequences of interventions that slow ageing is important. We show that the long-lived mutantage-1(hx546)stays active for longer than the wild type but it moves slower in early adulthood. Thus, continuous analysis of movement can rapidly identify interventions that slow ageing while simultaneously revealing any negative effects on health.
Conformation-based refinement of 18-mer DNA structures
Authors: Svoboda Jakub , Berdár Daniel , Kolenko Petr , Černý Jiří , Nováková Zora , Pavlíček Jiří , Schneider Bohdan
Published: June 2023

Nine new crystal structures of CG-rich DNA 18-mers with the sequence 5′-GGTGGGGGC-XZ-GCCCCACC-3′, which are related to the bacterial repetitive extragenic palindromes, are reported. 18-mer oligonucleotides with the central XZ dinucleotide systematically mutated to all 16 sequences show complex behavior in solution, but all ten so far successfully crystallized 18-mers crystallized as A-form duplexes. The refinement protocol benefited from the recurrent use of geometries of the dinucleotide conformer (NtC) classes as refinement restraints in regions of poor electron density. The restraints are automatically generated at the dnatco.datmos.org web service and are available for download. This NtC-driven protocol significantly helped to stabilize the structure refinement. The NtC-driven refinement protocol can be adapted to other low-resolution data such as cryo-EM maps. To test the quality of the final structural models, a novel validation method based on comparison of the electron density and conformational similarity to the NtC classes was employed.