bluuebunny/crossref_metadata_2025 huggingface dataset:
Morphological and molecular effects of short-term water deficiency in barley stamen maturation
Authors: Lange Richard , Zhang Youjun , Fernie Alisdair R. , Acosta Iván F.
Published: November 2024

Water deficiency at the reproductive stage of cereal crops mainly affects the development or function of male organs, which causes strong losses in grain yield. We investigated the effects of short-term drought on the post-meiotic maturation of stamens in barley cultivar Scarlett, where it leads to a stage-dependent decline in fertility. Water deficiency neither affects pollen viability nor the formation of trinuclear pollen. However, it completely blocks pollen starch accumulation. Metabolite profiling suggests that this is due to decreased sugar content at starch-filling stages, probably reflecting impaired carbon supply from photosynthetic tissues to anther sinks. Accordingly, transcriptomic analysis shows that drought reduces the expression of stamen sugar transporters. Moreover, drought causes a strong downregulation of the pollen transcriptional network of auxin signalling and central carbon metabolism genes that controls barley pollen starch production. This wider model of the molecular effects of water deficiency on cereal pollen provides a solid foundation to characterize tolerance mechanisms in potential drought-resistant germplasm.
A single high-zinc activation enhancer can control two genes oriented head-to-head inC. elegans
Authors: Liu Hanwenheng , Earley Brian , Mendoza Adelita , Hunt Patrick , Teng Sean , Schneider Daniel L. , Kornfeld Kerry
Published: November 2024

Enhancers play critical roles in gene expression, but a full understanding of their complex functions has yet to be defined. The cellular response to excess zinc levels inC. elegansrequires the HIZR-1 transcription factor, which binds the high-zinc activation (HZA) enhancer in the promoters of multiple target genes. Cadmium hijacks the excess zinc response by binding and activating HIZR-1. By analyzing the genome-wide transcriptional response to excess zinc and cadmium, we identified two positions in the genome where head-to-head oriented genes are both induced by metals. In both examples, a single predicted HZA enhancer is positioned between the two translational start sites. We hypothesized that a single enhancer can control both head-to- head genes, an arrangement that has not been extensively characterized. To test this hypothesis, we used CRISPR genome editing to precisely delete the HZAmTenhancer positioned betweenmtl-2andT08G5.1, and the HZAcFenhancer positioned betweencdr-1andF35E8.10. In both examples, deleting the enhancer caused both head-to-head genes to lose metal-activated transcription, whereas the induction of more distant genes was not strongly affected. These studies rigorously document that a single HZA enhancer can control two head-to-head genes, advancing our understanding of the diverse functions of enhancers.

Article Summary

Enhancers are critical for gene expression, but a full understanding their functions has yet to be elucidated. We discovered two positions in theC. elegansgenome where a pair of head-to-head oriented genes are both transcriptionally activated by the metals zinc and cadmium; in both cases, one high-zinc activation (HZA) enhancer is positioned between the translation start sites. When these HZA enhancers were deleted by genome engineering, both head-to-head genes lost metal-activated transcription. These results demonstrate that a single HZA enhancer can control two head-to-head genes, advancing the understanding of enhancer function.
Female song elicits increased vocal display effort in both sexes of Alston’s singing mouse
Authors: Tripp Joel A. , Phelps Steven M.
Published: November 2024

Acoustic displays are conspicuous behaviors common across diverse animal taxa. They have long been studied in behavioral ecology, evolutionary biology, and neuroscience. Most of these investigations, however, have focused on male display. For species in which both sexes display, correcting this bias will lead to a fuller understanding of the evolution and function of these behaviors. In this study, we investigated the role of vocal advertisement display in female Alston’s singing mice (Scotinomys teguina). Singing mice are small muroid rodents of the family Cricetidae, native to high altitude cloud forests of Central America. Females and males both produce elaborate advertisement songs used in mate attraction and intra-sexual competition. Prior studies have largely focused on male behavior, though we recently found that both sexes dramatically increase their rate of singing and song duration in response to playback of conspecific male song. Here, we tested how mice of both sexes adjust their song effort in response to female song playback. Our results show that, like male song, female song elicits robust increases in song effort from both female and male mice. This study reveals additional social contexts that promote high song effort in this species, while raising additional questions about the role of song in communication within and between the sexes.
XAI-MRI: An Ensemble Dual-Modality Approach for 3D Brain Tumor Segmentation Using Magnetic Resonance Imaging
Authors: Farhan Ahmeed Suliman , Khalid Muhammad , Manzoor Umar
Published: November 2024

Brain tumor segmentation from Magnetic Resonance Images (MRI) presents significant challenges due to the complex nature of brain tumor tissues. This complexity makes distinguishing tumor tissues from healthy tissues difficult, mainly when radiologists perform manual segmentation. Reliable and accurate segmentation is crucial for effective tumor grading and treatment planning. In this paper, we proposed a novel ensemble dual-modality approach for 3D brain tumor segmentation using MRI. Initially, individual U-Net models are trained and evaluated on single MRI modalities (T1, T2, T1ce, and FLAIR) to establish each modality’s performance. Subsequently, we trained U-net models using combinations of the best-performing modalities to exploit the complementary information and improve segmentation accuracy. Finally, we suggested the ensemble dual-modality by combining the best-performing two pre-trained dual-modalities models to enhance segmentation performance. Experimental results show that the proposed model enhanced the segmentation result and achieved a Dice Coefficient of 97.73% and a Mean IoU of 60.08% on the BraTS2020 dataset. The results illustrate that the ensemble dual-modality approach outperforms single-modality and dual-modality models. This study shows that ensemble dual-modality models can help improve the accuracy and dependability of brain tumor segmentation based on MRI. Our code publicly available at:https://github.com/Ahmeed-Suliman-Farhan/Ensemble-Dual-Modality-Approach
Axonal transcriptome reveals upregulation of PLK1 as a protective mechanism in response to increased DNA damage in FUSP525Lspinal motor neurons
Authors: Zimyanin Vitaly , Dash Banaja P. , Großmann Dajana , Simolka Theresa , Glaß Hannes , Verma Riya , Khatri Vivek , Deppmann Christopher , Zunder Eli , Redemann Stefanie , Hermann Andreas
Published: November 2024

Mutations in the geneFUSED IN SARCOMA(FUS) are among the most frequently occurring genetic forms of amyotrophic lateral sclerosis (ALS). Early pathogenesis ofFUS-ALS involves impaired DNA damage response and axonal degeneration. However, it is still poorly understood how these gene mutations lead to selective spinal motor neuron (MN) degeneration and how nuclear and axonal phenotypes are linked. To specifically address this, we applied a compartment specific RNA-sequencing approach using microfluidic chambers to generate axonal as well as somatodendritic compartment-specific profiles from isogenic induced pluripotent stem cells (iPSCs)-derived MNs. We demonstrate high purity of axonal and soma fractions and show that the axonal transcriptome is unique and distinct from that of somas including significantly fewer number of transcripts. Functional enrichment analysis revealed that differentially expressed genes (DEGs) in axons were mainly enriched in key pathways like RNA metabolism and DNA damage, complementing our knowledge of early phenotypes in ALS pathogenesis and known functions of FUS. In addition, we demonstrate a strong enrichment for cell cycle associated genes including significant upregulation of polo-like kinase 1 (PLK1) in FUSP525Lmutant MNs. PLK1 was increased upon DNA damage induction and PLK1 inhibition further increased the number of DNA damage foci in etoposide-treated cells, an effect that was diminished in case ofFUSmutant MNs. In contrast, inhibition of PLK1 increased late apoptotic or necrosis-induced neuronal cell death in mutant neurons. Taken together, our findings provide insights into compartment-specific transcriptomics in humanFUS-ALS MNs and we propose that specific upregulation of PLK1 might represent an early event in the pathogenesis of ALS, possibly modulating DNA damage response and other associated pathways.
NEMF inhibits proliferation and migration of ovarian cancer cells by blocking the PI3K/mTOR pathway
Authors: Wang Qian , Zhu Ying , Zhang Yilin , Chen Chuangzhen , Fan Jing , Yin Aiqi , Guo Suiqun , Liu Yahui
Published: November 2024

Nuclear export mediator factor (NEMF) is considered to be a tumor suppressor in Drosophila. Based on the analysis of data from an online database, NEMF is downregulated in ovarian cancer. However, the mechanism underlying its expression has not been reported thus far.In this study, the immunohistochemistry results showed that the expression of NEMF may be related to patient age and tissue differentiation. In vitro experiments indicated that overexpression of NEMF may inhibit cell proliferation and migration by inhibiting the PI3K/mTOR signaling pathway, thereby blocking cell cycle progression and promoting apoptosis (P < 0.05).Therefore, we speculate that NEMF is a potential tumor suppressor gene. Targeting NEMF may be an innovative therapeutic approach for ovarian cancer.

Summary blurb

NEMF is downregulated in ovarian cancer and the mechanism underlying its expression has not been reported thus far.In vitro experiments indicated that overexpression of NEMF inhibit cell proliferation and migration by inhibiting the PI3K/mTOR signaling pathway,thereby blocking cell cycle progression.
Intrinsic and extrinsic mechanisms alter neural cell fate specification in EPM1 Epilepsy
Authors: Forero Andrea , Pravata Veronica , Pipicelli Fabrizia , Soloperto Alessandro , Di Matteo Francesco , Bekjarova Zagorka , Frenna Elisa , Canafoglia Laura , Ragona Francesca , Maccarrone Giuseppina , Pisfil Mariano Gonzalez , Whal-Schott Christian , Cernilogar Filippo M. , Eder Matthias , Di Giaimo Rossella , Cappello Silvia
Published: November 2024

The extracellular milieu, including extracellular vesicles (EVs), plays a pivotal role in brain development by regulating neural processes such as proliferation, differentiation, and migration. In this study, we sought to elucidate the pathogenesis of progressive myoclonus epilepsy type 1 (EPM1), a disease caused by mutations in theCSTBgene, using cerebral organoids (COs) derived from EPM1 patient cells. The results demonstrate that EPM1 COs display increased electrophysiological activity and a disrupted excitatory/inhibitory balance. Single-cell RNA sequencing (scRNA-seq) analysis of ventral EPM1-Cos revealed an abnormal specification of progenitor fate, with a shift toward dorsal neuron identities at the expense of inhibitory interneurons. In addition, pathological alterations in EV biogenesis and cargo were identified, including aberrant Sonic Hedgehog (SHH) signaling, which may disrupt cortical patterning. These findings suggest that both intrinsic progenitor identity shifts and extrinsic EV-mediated signaling contribute to EPM1 pathology. Our study highlights potential therapeutic strategies mediated by EVs as a novel approach to mitigate disease progression.
Metabolic trade-offs in response to increased acetate metabolism inEscherichia coli
Authors: Pentz Jennifer T. , Koehler Samuel I. , Middlebrook Earl A. , You Mak Kayley T. , Hovde Blake T. , Hanschen Erik R.
Published: November 2024

Adaptive laboratory evolution (ALE) is a powerful tool to improve phenotypes in microbial cell factories for biotechnological processes. For example, ALE can be utilized to improve growth on alternative carbon sources such as acetate. Acetate is becoming a promising alternative feedstock to produce a variety of bio-products, but growth on acetate is slow relative to other preferred carbon sources and can be toxic to cells. However, ALE in a homogenous environment can lead to evolutionary trade-offs for growth on other carbon sources, which might be detrimental for feedstocks that contain multiple sugars. Here, we evolvedEscherichia colifor ∼100 generations using continuous culturing in turbidostats in media containing acetate as the sole carbon source to rapidly select for increased growth in acetate. We measured absolute fitness of 119 clones in acetate and glucose separately to characterize trade-offs and found that trade-off patterns were heterogenous amongst measured clones, with 45% of clones showing significantly reduced growth in glucose. Sequencing revealed that the trade-offs were a result of antagonistic pleiotropic effects of early adaptive mutations, but not all high-effect mutations conferred a trade-off, consistent with the model that mutations accumulated in the selected environment can display a range of pleiotropic effects in other environments. Together, these results suggest that ALE in a homogeneous environment needs to be carefully considered for the improvement of metabolic traits in microbial cells as this could limit the use of evolved strains in complex feedstocks that contain multiple sugars.
Enhancing single-cell ATAC sequencing with formaldehyde fixation, cryopreservation, and multiplexing for flexible analysis
Authors: Hohl Tobias , Boenisch Ulrike , Manke Thomas , Arrigoni Laura
Published: November 2024

The assay for transposase-accessible chromatin using sequencing (ATAC-seq) revolutionized the field of epigenetics since its emergence by providing a means to uncover chromatin dynamics and other factors affecting gene expression. The development of single-cell (sc) applications in recent years led to an even deeper understanding of cell type specific gene regulatory mechanisms. One of the major challenges while running ATAC-seq experiments, bulk or sc, is the need for freshly collected cells for successful experiments. While various freezing methods have already been tested and established for bulk and sc ATAC-seq, quality metrics for preserved cells are rather poor or dependent on sampling time when compared to fresh samples. This makes it difficult to conduct all sorts of complex experiments i.e. with multiple conditions, patients, or time course studies. Especially, accounting for batch effects can be difficult if samples need to be processed at different time points of collection. We tackled this issue by adding a fixation step prior to the freezing method. The additional fixation step improved library quality and yield data comparable to fresh samples. The workflow was also tested on multiplexed sc ATAC experiments, set-up for cost-efficient low input sample handling. Sample cross-in, typically encountered in Tn5-based multiplex approaches, were tackled with a computational procedure specifically developed for this approach.
The virulence and motility ofPseudomonas syringaepv.actinidiaemediated by a temperature sensor HktS-HktR
Authors: Xiao Yinan , Liang Yifei , Yang Mingming , Zhou Mingxia , Huang Jing , Wang Nana , Huang Lili
Published: November 2024

Kiwifruit bacterial canker (KBC), caused byPseudomonas syringaepv.actinidiae(Psa) is one of the most devastating diseases of kiwifruit and can damage almost all kiwifruit varieties. The severity of the disease occurrence is closely related to the temperature. Our previous research indicated thatPsashowed stronger pathogenicity and expansion ability at relatively cool temperatures, but howPsasenses environmental temperature and regulates its virulence mechanism remains unclear. In this study, 69 Histidine kinases (HK) inPsawere predicted through bioinformatics analysis, and 9 differentially expressed HK genes were identified at varying temperatures through pathogenicity detection and quantitative reverse transcription PCR (qRT-PCR). Among them, HktS as a temperature signal receiver was identified, and its response regulator (RR) HktR was determined through structure analysis and cotranscription assay. The results showed that HktR can bind to transcription factor RpoD, and RpoD bind tohrpRSpromoter region, thus initiating the expression level of the type III secretion system (T3SS), which plays an important role in the pathogenesis ofPsa. In addition, the motility ofPsawas also regulated by HktS-HktR in a temperature-dependent manner. These findings reveal the molecular mechanism by which HktS-HktR acts as a temperature sensor to regulate bacterial virulence and motility ofPsa, providing a new potential target for KBC control.
Ancestry-specific gene expression in peripheral monocytes mediates risk of neurodegenerative disease
Authors: Wagen Aaron Z , Reynolds Regina H , Nee Foo Jia , Fairbrother-Browne Aine , Gustavsson Emil K , Galgiano-Turin Sarah , Wood Nicholas W , Blauwendraat Cornelis , Gandhi Sonia , Ryten Mina
Published: November 2024

It is hypothesised that peripheral immune states responding to regional environmental triggers contribute to central neurodegeneration. Region-specific genetic selection pressures require this hypothesis to be assessed in an ancestry specific manner. Here we utilise genome-wide association studies and expression quantitative trait loci from African, East Asian and European ancestries to show that genes causing neurodegeneration are preferentially expressed in innate rather than adaptive immune cells, and that expression of these genes mediates the risk of neurodegenerative disease in monocytes in an ancestry-specific manner.
A pair of congenic mice for imaging of transplants by positron emission tomography using anti-transferrin receptor nanobodies
Authors: Balligand Thomas , Carpenet Claire , Olive-Palau Sergi , Jaspers Tom , Suresh Pavana , Liu Xin , Medhi Himadri , Lee Yoon Ho , Rashidian Mohammad , De Strooper Bart , Ploegh Hidde L. , Dewilde Maarten
Published: November 2024

Two anti-transferrin receptor (TfR) nanobodies, VHH123 specific for mouse TfR and VHH188 specific for human TfR (huTfR) were used to track transplants non-invasively by PET/CT in mouse models, without the need for genetic modification of the transferred cells. We provide a comparison of the specificity and kinetics of the PET signals acquired when using nanobodies radiolabeled with89Zr,64Cu and18F. We used a knock-in mouse that expresses a TfR with a human ectodomain (huTfR+/+) as a source of transplants into C57BL/6 recipients and show that VHH188 detects such transplants by PET/CT. Conversely, C57BL/6 transplants into huTfR+/+recipients can be imaged with VHH123. In C57B/6 mice impregnated by huTfR+/+males we saw an intense VHH188 signal in the placenta showing that TfR-specific VHHs accumulate at the placental barrier but do not enter the fetal tissue. The model presented here can be used to track many transplanted cell types by PET/CT, provided cells express TfR, as is typically the case for proliferating cells such as tumor lines.
Predicting inbred parent synchrony at flowering for maize hybrid seed production by integrating crop growth model with whole genome prediction
Authors: Laurent Anabelle , Munaro Eugenia , Zhao Honghua , Technow Frank , Whitted Eric , Clark Randy , Martin Juan Pablo San , Totir Radu
Published: November 2024

One of the challenges of maize hybrid seed production is to ensure synchrony at flowering of the two inbred parents of a hybrid, which depends on the specific parental combination and environmental conditions of the production field. Maize flowering can be simulated using a mechanistic crop growth model that converts thermal time accumulation to leaf numbers based on inbred specific physiological parameter values. Heretofore, these inbred specific physiological parameters need to be measured or assigned based on prior knowledge. Here, we leverage genetic, environmental and management data to predict physiological parameters and simulate flowering phenotypes by using whole genome prediction methodology combined with a crop growth model (CGM-WGP) as part of in-field in-season inbred growth development. We use two estimation sets that differ in terms of management and weather information to test the robustness of our approach. As part of our findings, we demonstrate the importance of defining informative priors to generate biologically meaningful predictions of unobserved physiological parameters. Our CGM-WGP infrastructure is efficient at simulating flowering phenotypes. An important practical application of our method is the ability to recommend differential planting intervals for male and female maize inbreds used in commercial seed production fields to synchronize male and female flowering.

Core ideas

Synchrony at flowering of maize inbred parents is crucial for optimal pollination and consequently seed yield.

Integrating WGP with CGM can accurately predict physiological parameters and simulate maize flowering phenotypes.

CGM-WGP infrastructure can be used to optimize field operations for large scale maize hybrid seed production.
Reciprocal links between methionine metabolism, DNA repair and therapy resistance in glioblastoma
Authors: Korimerla Navyateja , Meghdadi Baharan , Haq Isra , Wilder-Romans Kari , Xu Jie , Becker Nicole , Zhu Ziqing , Kalev Peter , Qi Nathan , Evans Charles , Kachman Maureen , Zhao Zitong , Lin Angelica , Scott Andrew J , O’Brien Alexandra , Kothari Ayesha , Sajjakulnukit Peter , Zhang Li , Palavalasa Sravya , Peterson Erik R , Hyer Marc L , Marjon Katya , Sleger Taryn , Morgan Meredith A , Lyssiotis Costas A , Stone Everett M. , Ferris Sean P. , Lawrence Theodore S , Nagrath Deepak , Zhou Weihua , Wahl Daniel R
Published: November 2024

Glioblastoma (GBM) is uniformly lethal due to profound treatment resistance. Altered cellular metabolism is a key mediator of GBM treatment resistance. Uptake of the essential sulfur-containing amino acid methionine is drastically elevated in GBMs compared to normal cells, however, it is not known how this methionine is utilized or whether it relates to GBM treatment resistance.

Here, we find that radiation acutely increases the levels of methionine-related metabolites in a variety of treatment-resistant GBM models. Stable isotope tracing studies further revealed that radiation acutely activates methionine to S-adenosyl methionine (SAM) conversion through an active signaling event mediated by the kinases of the DNA damage response.In vivotumor SAM synthesis increases after radiation, while normal brain SAM production remains unchanged, indicating a tumor- specific metabolic alteration to radiation. Pharmacological and dietary strategies to block methionine to SAM conversion slowed DNA damage response and increased cell death following radiation in vitro. Mechanistically, these effects are due to depletion of DNA repair proteins and are reversed by SAM supplementation. These effects are selective to GBMs lacking the methionine salvage enzyme methylthioadenosine phosphorylase. Pharmacological inhibition of SAM synthesis hindered tumor growth in flank and orthotopicin vivoGBM models when combined with radiation. By contrast, methionine depletion does not reduce tumor SAM levels and fails to radiosensitize intracranial models, indicating depleting SAM, as opposed to simply lowering methionine, is critical for hindering tumor growth in intracranial models of GBM.

These results highlight a new signaling link between DNA damage and SAM synthesis and define the metabolic fates of methionine in GBMin vivo. Inhibiting radiation-induced SAM synthesis slows DNA repair and augments radiation efficacy in GBM. Using MAT2A inhibitors to deplete SAM may selectively overcome treatment resistance in GBMs with defective methionine salvage while sparing normal brain.
Targeting eIF4G1-dependent translation in melanoma
Authors: Feng Yongmei , Radaeva Mariia , Amiri Mehdi , Deshpande Aniruddha J. , Olson Steven , Jovanovic Predrag , Pass Ian , Deng Qiyun , Lazar Ikrame , Murad Rabi , Molinolo Alfredo , Kim Hyungsoo , Sergienko Eduard , Villaneuva Jessie , Topisirovic Ivan , Jackson Michael , Sonenberg Nahum , Cherkasov Artem , Ronai Ze’ev A.
Published: November 2024

Elevated expression of components of eIF4F translation initiation complex has been documented in cancer, resulting in enhanced translation of mRNAs encoding pro-tumorigenic factors, including oncogenic proteins. We previously identified SBI-756, a small molecule that interferes with the eIF4F assembly and overcomes melanoma resistance to BRAF inhibitors. SBI-756 enhanced anti-tumor immunity in pancreatic cancer and was effective in the treatment of diffuse large B cell lymphoma. Here, we identified the eIF4G1 MA3 (4G1-MA3) domain as the target of SBI-756, attenuating eIF4F complex assembly. Melanoma cells expressing a mutant form of 4G1-MA3 exhibited polysome profiles resembling those of melanoma cells treated with SBI-756. A structure-basedin silicoscreen against the eIF4G1 MA3 domain identified M19, a small molecule inhibitor that exhibited anti-melanoma effects. RNA sequencing (RNA-seq) revealed upregulation of UPR, mTOR, p53, and ROS signaling in M19-treated melanoma cells. Ribosome sequencing identified changes in ribosomal structure and electron transport chain components following M19-6 treatment of melanoma cells. Autophagy and histone deacetylase inhibitors were found to enhance anti-neoplastic activities of M19 or its analog, M19-6. M19-6 conferred a greater effect on melanoma than melanocytes and overcame melanoma resistance to BRAF or MEK inhibitors. Alone, M19-6 reduced melanoma growth and metastasis in a xenograft model. M19-6 offers a new therapeutic modality to overcome resistance and metastasis.
A droplet digital PCR assay for quantification of bacteriophage viral vector titer and purity
Authors: Voorhees Peter J. , Ponek Ronni M. , Liu Jamie D. , Lai Samuel K.
Published: November 2024

Bacteriophage (phage) vectors, bacterial viruses engineered to deliver specific transgenes into target bacteria, offer considerable promise as tools for tuning the microbiome. However, the field currently lacks standardized methods for characterizing phage vectors with the same rigor as those for viral vectors used in human gene therapy. To develop a robust and reproducible viral vector system, it is critical to measure both transduction efficiency and the true dose of vector particles used. Here, we use central composite design to develop a digital droplet PCR (ddPCR) assay for precise quantification of transgene and vector genome-packed phage vector titers following an established production process. This duplex assay uses probes specific to 2 unique DNA barcodes inserted into the vector genome and transgene cassette, enabling precise quantitation of each population with a dynamic range of nearly 3 orders of magnitude. We show biological activity assays can consistently underestimate the number of transgene-packed vectors, potentially greatly overestimating the true transduction efficiency, particularly when contamination by genome-packed vectors is high. This ddPCR approach can be broadly adopted to characterize phage particles for a variety of biomedical applications.
Urban microbial communities shift towards carotenoid-producing species under constant anthropogenic stress
Authors: Sedova V. V. , Demin K. A. , Kulikov M. P. , Prazdnova E.V. , Gorovtsov A.V.
Published: November 2024

During years of investigating soil microbial communities, our research group consistently observed a predominance of carotenoid-producing microbes – characteristically pigmented in hues typical of carotenoids – in urban soil samples, as compared to those from recreational, rural, or non-urban areas. To validate this observation as non-random and to explore the ecological role of carotenoid-producing microorganisms in urban soils, we conducted a series of experiments. Additionally, we extended our study to other components of the urban ecosystem that may harbor and transfer microbial communities, including dust and snow samples. Through ecological monitoring, we assessed the proportion of culturable carotenoid-producing bacteria in those samples. It was found that in urban soils >60% of the isolates are pigmented, and in natural soils only about 30% exhibit carotenoid pigmentation. For snow and dust samples, all sites have shown pigmented bacteria predominance. Further, we analyzed both the physiological traits of individual isolates and the broader characteristics of entire culturomes (comprising all isolates from a single aliquot plated onto Petri dishes). Metagenomic analysis of the culturome washes was also performed to provide deeper insights into the microbial communities present. Metagenome of urban isolates clearly show elevated biodiversity of carotenoid biosynthesis genes and carotenoid-producing taxa, as compared to metagenome of natural habitat. In this study,Flavobacteriumwas identified as the most abundant pigmented genus of urban settings.

Based on data obtained in this work, and similar literature data on urban microbial communities, we propose that the unique combination of environmental factors in urban settings fosters the selective enrichment of carotenoid-producing microorganisms. Finally, we offer a model to explain this selective process.
Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish
Authors: Huang Delai , Kapadia Emaan , Liang Yipeng , Shriver Leah P. , Dai Shengkun , Patti Gary J. , Humbel Bruno M. , Laudet Vincent , Parichy David M.
Published: November 2024

The often-prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes, and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish, a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells, “melanoleucophores.” To identify mechanisms underlying this conversion we used ultrastructural, transcriptomic, mutational and other approaches. We show that melanophore– melanoleucophore transition depends on regional BMP signals transduced through non-canonical receptors (Rgmb-Neo1a-Lrig2) as well as BMP-dependent signaling by Agouti genes,asip1andasip2b. These signals lead to expression of transcription factor genes includingfoxd3andrunx3that are necessary to induce loss of melanin by an autophagy-like process, curtail new melanin production, and deploy a pathway for accumulating guanine crystals that, together, confer a white phenotype. These analyses uncover an important role for positional information in specifying ornamentation in zebrafish and show how tissue environmental cues and a novel gene regulatory program have allowed terminal addition of a distinct phenotype to a pre-existing cell type.

Significance

Fish often have striking color patterns with important functions in behavior. In zebrafish, the familiar striped pattern forms through self-organizing interactions between pigment cells, yet the white highlights on their fins arise differently—through the transformation of black pigment cells into white ones. This study reveals how this dramatic cell transformation happens: signals from the surrounding tissue, specifically BMP and Agouti proteins, instruct black cells to change their fate. These signals trigger expression of specific genes that cause the cells to break down their black pigment while acquiring white, crystal-like structures. This work shows how local signals in tissues can drive the development of ornamental features and provides insights into how new cell types evolve.
A systematic assessment of phylogenomic approaches for microbial species tree reconstruction
Authors: Weiner Samson , Feng Yutian , Gogarten J. Peter , Bansal Mukul S.
Published: November 2024

A key challenge in microbial phylogenomics is that microbial gene families are often affected by extensive horizontal gene transfer (HGT). As a result, most existing methods for microbial phylogenomics can only make use of a small subset of the gene families present in the microbial genomes under consideration, potentially biasing their results and affecting their accuracy. To address this challenge, several methods have recently been developed for inferring microbial species trees from genome-scale datasets of gene families affected by evolutionary events such as HGT, gene duplication, and gene loss.

In this work, we use extensive simulated and real biological datasets to systematically assess the accuracies of four recently developed methods for microbial phylogenomics, SpeciesRax, ASTRAL-Pro 2, PhyloGTP, and AleRax, under a range of different conditions. Our analysis reveals important insights into the relative performance of these methods on datasets with different characteristics, identifies shared weaknesses when analyzing complex biological datasets, and demonstrates the importance of accounting for gene tree inference error/uncertainty for improved species tree reconstruction. Among other results, we find that (i) AleRax, the only method that explicitly accounts for gene tree inference error/uncertainty, shows the best species tree reconstruction accuracy among all tested methods, (ii) PhyloGTP shows the best overall accuracy among methods that do not account for gene tree error and uncertainty, (iii) ASTRAL-Pro 2 is less accurate than the other methods across nearly all tested conditions, and (iv) explicitly accounting for gene tree inference error/uncertainty can lead to substantial improvements in species tree reconstruction accuracy. Importantly, we also find that all methods, including AleRax and PhyloGTP, are susceptible to biases present in complex real biological datasets and can sometimes yield misleading phylogenies.
Vaccination with a Replication-Dead Murine Gammaherpesvirus Lacking Viral Pathogenesis Genes Inhibits WT Virus Infection
Authors: Mitra Dipanwita , Oldenburg Darby , Forrest J. Craig , Krug Laurie T.
Published: November 2024

Gammaherpesviruses are oncogenic pathogens that establish lifelong infections. There are no FDA-approved vaccines against Epstein-Barr virus or Kaposi sarcoma herpesvirus. Murine gammaherpesvirus-68 (MHV68) infection of mice provides a system for investigating of gammaherpesvirus pathogenesis and testing vaccine strategies. Prime-boost vaccination with a replication-dead virus (RDV) that does not express the essential replication and transactivator protein (RTA) encoded byORF50 (RDV-50.stop) protected against WT virus replication and reduce latency in C57BL/6 mice and prevented lethal disease inIfnar1-/-mice. To further improve the RDV vaccine and more closely model KSHV vaccine design, we generated an RDV lacking the unique M1-M4 genes and the non-coding tRNA-miRNA-encoded RNAs (TMERs) 6, 7, and 8 that collectively promote latency of MHV68in vivo. Prime-boost vaccination of mice with RDV-50.stopΔM1-M4 elicited neutralizing antibodies and virus-specific CD8 T-cell responses in lungs and spleens, the respective sites of acute replication and latency, that were comparable to RDV-50.stop vaccination. When challenged with WT MHV68, vaccinated mice exhibited a near-complete block of lytic replication and a reduction in latency and reactivation. We conclude that major determinants of MHV68 pathogenesis are not required components for eliciting a protective immune response.
Mechanisms of growth-dependent regulation of the Gin4 kinase
Authors: Diaz Francisco Mendez , Godinez David Sanchez , Solano Francisco , Jasani Akshi , Alcaide Maria , Kellogg Douglas R.
Published: November 2024

Abstract

Cell cycle progression is dependent upon cell growth. Cells must therefore translate growth into a proportional signal that can be used to determine when there has been sufficient growth for cell cycle progression. In budding yeast, the protein kinase Gin4 is required for normal control of cell growth and undergoes gradual hyperphosphorylation and activation that are dependent upon growth and proportional to the extent of growth, which suggests that Gin4 could function in mechanisms that measure cell growth. However, the molecular mechanisms that drive hyperphosphorylation of Gin4 are poorly understood. Here, we used biochemical reconstitution and genetic analysis to test hypotheses for the mechanisms that drive phosphorylation of Gin4. We ruled out a previous model in which phosphatidylserine delivered to sites of plasma membrane growth binds Gin4 to initiate autophosphorylation. Instead, we show that Elm1, a homolog of the mammalian Lkb1 tumor suppressor kinase, is sufficient to promote hyperphosphorylation of Gin4 in vitro, likely via initiation of Gin4 autophosphorylation. Furthermore, we show that casein kinase I is required for growth-dependent hyperphosphorylation of Gin4 and also for normal regulation of Elm1. Together, these discoveries lead to new insight into mechanisms that link cell cycle progression to cell growth.
The human claustrum activates across multiple cognitive tasks
Authors: Huang Celine H.L. , Stewart Brent W. , Liu Chun Yin , Phylactou Phivos , Mathur Brian N. , Seminowicz David A.
Published: November 2024

Cognitive control, the ability to manage information during purposeful actions, is crucial for everyday functioning and can become impaired in a variety of neuropsychiatric disorders. The claustrum, a subcortical brain structure, has recently been implicated in functional mechanisms underlying cognitive control. A current theory on the claustrum’s function, the Network Instantiation in Cognitive Control (NICC) model, proposes that the claustrum acts as a cortical network hub synchronizing distant parts of the brain to optimize task performance across cognitive domains. Testing this in this study, we examined the claustrum signal within a dataset (n = 55) that includes functional MRI (fMRI) of healthy participants engaged in four well-established cognitive tasks: the Stroop task, AX-continuous performance task (AX-CPT), cued task-switching, and Sternberg working memory task. Bilateral claustrum activation was observed during certain conditions and trial phases of all four tasks, particularly during active use of cognitive control, and coinciding with task-positive cortical network activations. These findings provide further support for the NICC model of claustrum function, demonstrating claustrum activation across multiple cognitive tasks, and potentially paving the way for new insights into how cognitive processes can become compromised in neuropsychiatric disorders.
Ezh2 Delays Activation of Differentiation Genes During Normal Cerebellar Granule Neuron Development and in Medulloblastoma
Authors: Purzner James , Brown Alexander S. , Purzner Teresa , Ellis Lauren , Broski Sara , Litzenburger Ulrike , Andrews Kaytlin , Sharma Aryaman , Wang Xin , Taylor Michael D. , Cho Yoon-Jae , Fuller Margaret T. , Scott Matthew P.
Published: November 2024

Medulloblastoma (MB) is the most common malignant brain tumour in children. The Sonic Hedgehog (SHH)-medulloblastoma subtype arises from the cerebellar granule neuron lineage. Terminally differentiated neurons are incapable of undergoing further cell division, so an effective treatment for this tumour could be to force neuronal differentiation. Differentiation therapy provides a potential alternative for patients with medulloblastoma who harbor mutations that impair cell death pathways (TP53), which is associated a with high mortality. To this end, our goal was to explore epigenetic regulation of cerebellar granule neuron differentiation in medulloblastoma cells. Key regulators were discovered using chromatin immunoprecipitation with high-throughput sequencing. DNA-bound protein and chromatin protein modifications were investigated across all genes. We discovered that Ezh2-mediated tri-methylation of the H3 histone (H3K27me3), occurred on more than half of the 787 genes whose transcription normally increases as granule neurons terminally differentiate. Conditional knockout ofEzh2led to early initiation of differentiation in granule neuron precursors (GNPs), but only after cell cycle exit had occurred. Similarly, in MB cells, neuronal differentiation could be induced by preventing H3K27me3 modifications using an Ezh2 inhibitor (UNC1999), but only when UNC1999 was combined with forced cell cycle exit driven by a CDK4/6 inhibitor (Palbociclib). Ezh2 emerges as a powerful restraint upon post-mitotic differentiation during normal GNP development and combination of Ezh2 inhibition with cell cycle exit leads to MB cell differentiation.
Anthropogenic noise can decrease tomato reproductive success by hindering bumblebee-mediated pollination
Authors: Varga-Szilay Zsófia , Szövényi Gergely , Pozsgai Gábor
Published: November 2024

Anthropogenic noise is a little-studied type of pollution that negatively affects the physiology, nervous function and development of insects, thereby it has the potential to disrupt even key ecological services such as pollination. Here, we investigate the effects of anthropogenic noise on the pollination success of theBombus terrestrison tomatoes in controlled conditions. We expect that bumblebees avoid flowers exposed to noise more than flowers in non-noisy environments, leading to less efficient pollination and lower fruit quality. The experiment was conducted in Hungary, in 2023. Three treatments were applied to randomly chosen flowers: noisy (with played traffic noise); and two non-noisy, one allowing bumblebees and one excluding them. The flowers were enclosed with nets before maturity to avoid pollination, opened exclusively during treatment, and re-enclosed for three more days post-treatment. We recorded the marketing value of the fruits and the number of seeds they produced. We found no significant differences in the marketing value of fruits among treatments, but the number of seeds differed significantly suggesting that anthropogenic noise has a substantial effects on bumblebee-mediated pollination. Although these effects may be mitigated by habituation, loud external noise of various machines (e.g. irrigation systems) within polytunnels is still likely to contribute to the everyday noise exposure of bumblebees and could thus potentially lead to hidden economic losses in production. Therefore, further research is needed to understand the behavioural effects of both direct and indirect noise pollution on bumblebees.
Modeling Mountain Pine Beetle Abundance in Novel Hosts
Authors: Xie Xiaoqi , Brush Micah , Johnson Evan , Cullingham Catherine , Duffy Jessica , Lewis Mark A.
Published: November 2024

The mountain pine beetle has recently expanded its range into northern and central Alberta, posing an immediate threat to the novel host, jack pine. To date, some experiments suggest that jack pine has limited defensive capabilities despite of the restrictions from the physical environment. In this work, we explore the susceptibility of jack pine compared to the primary host, lodgepole pine, evaluating the risk of potential range expansion into Canada’s boreal forest. We employ a hierarchical model, incorporating environmental and ecological covariates, to examine mountain pine beetle dynamics in a pine forest with lodgepole, hybrid and jack pines. Our results show that pine species significantly influence the probability of being killed, with jack pine being less likely to be infested than lodgepole pine, all else being equal. The hierarchical model demonstrates that beetles perform poorer in jack pine, characterized by a reproduction rate 0.16 times that of non-jack pine. Although jack pine is a suitable host, our results indicate that the number of infestations in jack pine could be lower than in lodgepole pine, with a reduced probability of emerging beetles.
Switchable client specificity in a dual functional chaperone coordinates light harvesting complex biogenesis
Authors: Siegel Alex R. , Kroon Gerard , Wright Peter E. , Shan Shu-ou
Published: November 2024

The proper assembly of light harvesting complexes (LHCs) is critical for photosynthesis and requires the biogenesis of light-harvesting chlorophyll a,b-binding proteins (LHCPs) to be coordinated with the biosynthesis of chlorophylls (Chl). The mechanism underlying this coordination is not well understood. Here we show that a conserved molecular chaperone in chloroplasts, cpSRP43, provides a molecular thermostat that helps maintain this coordination. cpSRP43 undergoes a conformational rearrangement between a well-foldedclosedstate and a partially disorderedopenstate.ClosedcpSRP43 is dedicated to thede novobiogenesis of LHCPs, whereasopencpSRP43 protects multiple Chl biosynthesis enzymes from heat-induced destabilization. Rising temperature shifts cpSRP43 to theopenstate and thus enables it to protect Chl biosynthesis enzymes that are heat-destabilized. Our results reveal the molecular basis of a post-translational mechanism for the thermo-adaptation of LHC biogenesis. They also demonstrate how an ATP-independent chaperone uses conformational dynamics to switch its activity and client selectivity, thereby adapting to different proteostatic demands under shifting environmental conditions.

Teaser

A thermo-switchable molecular chaperone helps coordinate light harvesting complex assembly during photosynthesis.
Exploring the Neural Basis and Validity of Ordinal Emotion Representation through EEG
Authors: Chen Xuyang , Xu Xin , Zhang Dan , Liu Quanying , Shen Xinke
Published: November 2024

Accurately measuring emotion is a major challenge in advancing the understanding of human emotion and developing emotional artificial intelligence. In many existing studies, participants’ emotional ratings in interval scales are considered the true reflection of their emotional experiences. However, recent research suggests that ordinal annotations of emotions can more accurately capture the emotional expression process, providing a potential method for more precise emotion measurement. However, our understanding of the characteristics and validity of this new form of emotion representation is still relatively lacking. In particular, there is a lack of research using neural signals to explore the validity and neural basis of ordinal emotion representation. In this study, we used a video-elicited EEG dataset (n = 123) to identify the neural basis of ordinal emotion representation and demonstrate its validity from a neural perspective. Furthermore, we explored various characteristics of ordinal emotion representation, showing how it is superior to the interval form. First, we conducted inter-situation representational similarity analysis (RSA) and inter-subject RSA to test the degree to which ordinal representation captures both group commonalities and individual differences of emotion. Next, we investigated the characteristics of ordinal representation under different combinations of emotion items, including uni-variate and multivariate emotions, positive and negative emotions. Our results show that both group commonalities and inter-subject variations in EEG features are better explained by ordinal emotion representations than by interval ones. Multivariate ordinal representations showed better inter-subject reliability and higher representational similarity with EEG features compared to univariate counterparts, highlighting the co-occurrence nature of human emotions. Compared to negative emotions, ordinal representation showed greater improvements for positive emotions, suggesting that the complexity of positive emotions is well captured by ordinal representations. Taken together, these findings demonstrate that multivariate ordinal emotion ratings provide a more accurate measure of real emotional experience, which is crucial for enabling machines to precisely understand and express human emotions.