bluuebunny/crossref_metadata_2025 huggingface dataset:
ModelSEED v2: High-throughput genome-scale metabolic model reconstruction with enhanced energy biosynthesis pathway prediction
Authors: Faria José P. , Liu Filipe , Edirisinghe Janaka N. , Gupta Nidhi , Seaver Samuel M.D. , Freiburger Andrew P. , Zhang Qizhi , Weisenhorn Pamela , Conrad Neal , Zarecki Raphy , Song Hyun-Seob , DeJongh Matthew , Best Aaron A. , Cottingham Robert W. , Arkin Adam P. , Henry Christopher S.
Published: October 2023

Since the release of ModelSEED in 2010, the systems biology research community has used the ModelSEED genome-scale metabolic model reconstruction pipeline to build over 200,000 draft metabolic reconstructions that support hundreds of publications. Here we describe the first comprehensive update to this reconstruction tool, with new features such as (i) a dramatically improved representation of energy metabolism, which ensures that models produce accurate amounts of ATP per mol of nutrient consumed; (ii) a new template for Archaea model reconstruction; and (iii) a significantly improved curation of all metabolic pathways with mappings to RAST subsystems annotations. We applied the improved pipeline to build and analyze core and genome-scale models for Archaea and Bacteria genomes in KEGG. The new ModelSEED pipeline generates larger models that possess more reactions and genes and require fewer gap-filled reactions. In addition, we see conserved patterns in the ATP biosynthesis mechanism across phylogeny, and identify clades where our understanding of energy biosynthesis is still poor. The ModelSEED v2 pipeline is currently available only as new reconstruction and gap-filling Apps in the KBase platform.
Large-scale discovery of potent, compact and lineage specific enhancers for gene therapy vectors
Authors: Psatha Nikoletta , Sova Pavel , Georgolopoulos Grigorios , Paschoudi Kiriaki , Iwata Mineo , Bloom Jordan , Ulyanova Tatyana , Wang Hao , Kirtsou Alexandra , Vasiloudis Ninos-Ioannis , Wilken Matthew S. , Stamatoyannopoulos John A. , Yannaki Evangelia , Papayanopoulou Thalia , Stamatoyannopoulos George , Vierstra Jeff
Published: October 2023

Regulation of gene expression during cell development and differentiation is chiefly orchestrated by distal noncoding regulatory elements that precisely modulate cell selective gene activity. Gene therapy vectors rely on the cellular and context specificity of regulatory DNA elements to express therapeutic transgenes in the correct location and time. Here, we develop a straight-forward, one-shot approach to screen putative regulatory sequences identified in large-scale epigenomics profiling experiments for precise and programmable control of transgenes encoded within gene therapy viral vectors. We designed a library of 15,000 short sequences (∼200bp) derived from a set of developmentally active DHS elements during humanex vivoerythropoiesis and cloned them into a GFP reporter lentiviral vector. In an erythroid progenitor cell line, these elements display a gradient of transcriptional enhancer activity, with some demonstrating equivalent activity to the canonical β-globin μLCR despite a 9-fold smaller size. We show that these elements are both highly cell type restricted and developmental stage specific bothin vitroandin vivo. Finally, we replace the μLCR element with one of the novel short enhancers in a β-thalassemia lentiviral therapeutic vector and efficiently correct the thalassemic phenotype in patient-derived HSPCs. More broadly, our approach provides further insights into enhancer biology with wider implications into the development of highly cell type specific and efficacious viral vectors for human gene therapy.
Quantitative proteome dynamics across embryogenesis in a model chordate
Authors: Frese Alexander N. , Mariossi Andrea , Levine Michael S. , Wühr Martin
Published: October 2023

The evolution of gene expression programs underlying the development of vertebrates remains poorly characterized. Here, we present a comprehensive proteome atlas of the model chordateCiona, covering eight developmental stages and ∼7,000 translated genes, accompanied by a multi-omics analysis of co-evolution with the vertebrateXenopus. Quantitative proteome comparisons argue against the widely held hourglass model, based solely on transcriptomic profiles, whereby peak conservation is observed during mid-developmental stages. Our analysis reveals maximal divergence at these stages, particularly gastrulation and neurulation. Together, our work provides a valuable resource for evaluating conservation and divergence of multi-omics profiles underlying the diversification of vertebrates.
The socio-spatial ecology of giant anteaters in the Brazilian Cerrado
Authors: Chhen Aimee , Bertassoni Alessandra , Desbiez Arnaud LJ , Noonan Michael J
Published: October 2023

Movement is a key component of an animal’s life history. While there are numerous factors that influence movement, there is an inherent link between a species’ social ecology and its movement ecology. Despite this inherent relationship, the socio-spatial ecology of many species remains unknown, hampering ecological theory and conservation alike. Here, we use fine-scale GPS location data and continuous-time stochastic processes to study the socio-spatial ecology of 23 giant anteaters (Myrmecophaga tridactyla) in the Brazilian Cerrado. We found that individuals occupied stable home ranges with a mean area of 5.45 km2with males having significantly larger home ranges than females. The average amount of home-range overlap was low (0.20, n = 121 dyads), with no evidence that giant anteater home ranges were structured based on territorial, mate guarding, nor other social behaviour. We also identified a total of 2774 encounter events. Interestingly, both female-male and male-male dyads had significantly more encounters than female-female dyads, with two pronounced seasonal peaks in female-male encounters. Though encounters occurred frequently, associations between dyads were generally weak and there was little evidence of any correlated movement (mean amount of total correlation = 0.01). Collectively, these findings suggest giant anteaters are a solitary and largely asocial species that readily share space with conspecifics. Despite their present capacity to share space, the combined pressures of being condensed into smaller areas and decreased food availability due to increased pesticide use may see behavioural changes radiating throughout the population. Our study provides insight into heretofore unknown aspects of the socio-spatial ecology of this iconic, but understudied species, as well as crucial information for proactive area-based management. Ultimately, these findings contribute towards sustainable development while potentially maintaining the ecological integrity of giant anteaters and their habitats.
Capitella teletagets left out: Possible evolutionary shift causes loss of left tissues rather than increased neural tissue from dominant-negative BMPR1
Authors: Webster Nicole B. , Meyer Néva P.
Published: October 2023

Background

The evolution of centralized nervous systems (CNSs) a fascinating and complex topic; further work is needed to understand the genetic and developmental homology between organisms with a CNS. Research into a limited number of species suggests that CNSs may be homologous across Bilateria. This hypothesis is based in part on similar functions of BMP signaling in establishing fates along the dorsal-ventral (D-V) axis including limiting neural specification to one region of ectoderm. From an evolutionary-developmental perspective, the best way to understand a system is to explore it in a wide range of organisms to create a full picture.

Methods

Here we expand our understanding of BMP signaling in Spiralia, the third major clade of bilaterians, by examining phenotypes after expression of a dominant-negative BMP Receptor 1 and after knock-out of the putative BMP antagonist Chordin-like using CRISPR/Cas9 gene editing in the annelidCapitella teleta(Pleistoannelida).

Results

Ectopic expression of the dominant-negative Cte-BMPR1 did not increase CNS tissue or alter overall D-V axis formation in the trunk. Instead, we observed a unique asymmetric phenotype: a distinct loss of left tissues including the left eye, brain, foregut, and trunk mesoderm. Adding ectopic BMP4 early during cleavage stages reversed the dominant-negative Cte-BMPR1 phenotype, leading to a similar loss or reduction of right tissues instead. Surprisingly, a similar asymmetric loss of left tissues was evident from CRISPR knock-out ofCte-Chordin-likebut concentrated in the trunk rather than the episphere.

Conclusions

We further solidify the hypothesis that the function of BMP signaling during establishment of the D-V axis and CNS is fundamentally different in at least Pleistoannelida, possibly in Spiralia, and is not required for nervous system delimitation in this group. Our results support hypotheses of either multiple evolutionary origins of CNSs across Bilateria or divergence in the molecular mechanisms of CNS specification and D-V axis formation in annelids.
mRNA vaccines encoding membrane-anchored receptor-binding domains of SARS-CoV-2 mutants induce strong humoral responses and can overcome immune imprinting
Authors: Al-Wassiti Hareth A. , Fabb Stewart A. , Grimley Samantha L. , Kochappan Ruby , Ho Joan K. , Wong Chinn Yi , Tan Chee Wah , Payne Thomas J. , Takanashi Asuka , Sicilia Horatio , Teo Serena L.Y. , McAuley Julie , Ellenberg Paula , Cooney James P , Davidson Kathryn C. , Bowen Richard , Pellegrini Marc , Rockman Steven , Godfrey Dale I. , Nolan Terry M. , Wang Lin-fa , Deliyannis Georgia , Purcell Damian F.J. , Pouton Colin W.
Published: October 2023

To address the limitations of whole-spike COVID vaccines, we explored mRNA vaccines encoding membrane-anchored receptor-binding domain (RBD-TMs), each a fusion of a variant RBD, the transmembrane (TM) and cytoplasmic tail (CT) fragments of the SARS-CoV-2 spike protein. In naive mice, RBD-TM mRNA vaccines against ancestral SARS-CoV-2, Beta, Delta, Delta-plus, Kappa, Omicron BA.1 or BA.5, all induced strong humoral responses against the target RBD. Multiplex surrogate viral neutralization (sVNT) assays indicated broad neutralizing activity against a range of variant RBDs. In the setting of a heterologous boost, against the background of exposure to ancestral whole spike vaccines, sVNT studies suggested that RBD-TM vaccines were able to overcome the detrimental effects of immune imprinting. Omicron BA.1 and BA.5 RBD-TM booster vaccines induced serum antibodies with 12 and 22-fold higher neutralizing activity against the target RBD than their equivalent whole spike variants. Boosting with BA.1 or BA.5 RBD-TM provided good protection against more recent variants including XBB and XBB.1.5. Each RBD-TM mRNA is 28% of the length of its whole-spike equivalent. This advantage will enable tetravalent mRNA vaccines to be developed at well-tolerated doses of formulated mRNA.

One Sentence Summary

mRNA vaccines encoding membrane-anchored RBDs of SARS-CoV-2 mutants are effective vaccines that can overcome immune imprinting in mice
Innate immune memory after brain injury drives inflammatory cardiac dysfunction
Authors: Simats A , Zhang S , Messerer D , Cao J , Chong F , Besson-Girard S , Carofiglio O , Filser S , Plesnila N , Braun C , Gökce Ö , Dichgans M , Hatakeyama K , Bonev B , Beltrán E , Schulz C , Liesz A
Published: October 2023

The enormous medical burden of stroke is not only due to the brain injury itself and the acute systemic effects, but is largely determined by chronic comorbidities that develop secondarily after stroke. We hypothesized that the high rate of comorbidity developing after a stroke might have a shared immunological cause, however, the chronic effects of brain injury on systemic immunity have so far been barely investigated. Here, we identified myeloid innate immune memory as a cause of remote organ dysfunction after stroke. Using single-cell sequencing, we identified persistent pro-inflammatory transcriptomic changes in resident monocytes/macrophages in multiple organs one month after experimental ischemic brain injury, which was particularly abundant in the heart and associated with the development of cardiac fibrosis and diastolic dysfunction. A similar phenotype was seen in myocardial autopsy samples from stroke versus control patients. We observed chronic functional changes in myeloid hematopoiesis driven by post-stroke IL-1β-mediated epigenetic changes. These alterations could be transplanted to naïve recipient mice and were sufficient to induce cardiac dysfunction. By effectively blocking the trafficking of pro-inflammatory monocytes from the bone marrow to the heart using a dual CCR2/5 inhibitor, we successfully prevented post-stroke cardiac dysfunction. This approach holds promising potential as a novel immune-targeted secondary prevention therapy. We anticipate that the epigenetic immune reprogramming mechanisms detailed here for the brain-heart axis could be generalized to provide a novel framework for explaining the development of various comorbidities after acute tissue injury in remote organs.
Ultrasound-Induced Reorientation for Multi-Angle Optical Coherence Tomography
Authors: Kvåle Løvmo Mia , Deng Shiyu , Moser Simon , Leitgeb Rainer , Drexler Wolfgang , Ritsch-Marte Monika
Published: October 2023

Organoid and spheroid technology have recently provided great insights into oncology, developmental biology as well as personalized medicine. Among the methods to optically monitor the structural and functional organization of such samples, optical coherence tomography (OCT) has emerged as an excellent, label-free approach. Mature organoids, however, are often too opaque for OCT due to regions of strong attenuation. This leads to severe artifacts and reduced morphological tissue information in the reconstruction, since the far-side of the specimen is not reachable. Access to multi-angle views of OCT is therefore highly desirable. This aligns with another problem affecting certain goals of organoid research: The sample needs to be embedded in a growth scaffold such as Matrigel, whereas freely floating objects would not suffer from confinement and be more easily accessible for mechanical or chemical probing. Here we present ULTrasound-Induced reorientation for Multi-Angle-OCT (ULTIMA-OCT), a solution overcoming these limitations. By inserting a small 3D-printed acoustic trap to a spectral-domain OCT system, acoustic actuation enables contact-free levitation and finely tunable stepwise reorientation of samples such as zebrafish larvae and tumor spheroids, in a controlled and reproducible manner. This enables tomographic reconstruction of (sub-)mm samples with enhanced penetration depth and reduced attenuation artifacts, by means of a model-based algorithm we developed. We show that this approach is able to fuse the diverse multi-angle OCT volumes for a joint recovery of 3D-reconstruction of reflectivity, attenuation, refractive index and position registration for zebrafish larvae. We believe that our approach represents a powerful enabling tool for developmental biology and organoid research.
Juxtacrine DLL4-NOTCH1 signaling between astrocytes drives neuroinflammation via the IL-6-STAT3 axis
Authors: Mora Pierre , Laisné Margaux , Bourguignon Célia , Rouault Paul , Gadeau Alain-Pierre , Renault Marie-Ange , Horng Sam , Couffinhal Thierry , Chapouly Candice
Published: October 2023

Under neuroinflammatory conditions, astrocytes acquire a reactive phenotype that drives acute inflammatory injury as well as chronic neurodegeneration. We hypothesized that astrocytic DLL4 may interact with its receptor NOTCH1 on neighboring astrocytes to regulate astrogliosis via downstream juxtacrine signaling pathways. Here we investigated the role of astrocytic DLL4 on neurovascular unit homeostasis under neuroinflammatory conditions. We probed for downstream effectors of the DLL4-NOTCH1 axis and targeted these for therapy in two models of CNS inflammatory disease. We first demonstrated that astrocytic DLL4 is upregulated during neuroinflammation, both in mice and humans, driving astrogliosis and subsequent blood brain barrier permeability and inflammatory infiltration. We then showed that the DLL4-mediated NOTCH1 signaling in astrocytes directly drives IL-6 levels, induces STAT3 phosphorylation promoting upregulation of astrocyte reactivity markers, pro-permeability factor secretion and consequent blood brain barrier destabilization. Finally we revealed that blocking DLL4 with antibodies improves experimental autoimmune encephalomyelitis symptoms in mice, identifying a potential novel therapeutic strategy for CNS autoimmune demyelinating disease. As a general conclusion, this study demonstrates that DLL4-NOTCH1 signaling is not only a key pathway in vascular development and angiogenesis, but also in the control of astrogliosis during neuroinflammation.
β-catenin inhibition disrupts the homeostasis of osteogenic/adipogenic differentiation leading to the development of glucocorticoid-induced osteonecrosis of femoral head
Authors: Xia Chenjie , Xu Huihui , Fang Liang , Chen Jiali , Yuan Wenhua , Fu Danqing , Wang Xucheng , He Bangjian , Xiao Luwei , Wu Chengliang , Tong Peijian , Chen Di , Wang Pinger , Jin Hongting
Published: October 2023

Glucocorticoid-induced osteonecrosis of the femoral head (GONFH) is a common refractory joint disease characterized by bone damage and the collapse of femoral head structure. However, the exact pathological mechanisms of GONFH remain unknown. Here, we observed abnormal osteogenesis and adipogenesis associated with decreased β-catenin in the necrotic femoral head of GONFH patients. In vivo and in vitro studies further revealed that glucocorticoid exposure disrupted osteogenic/adipogenic differentiation of bone marrow mesenchymal cells (BMSCs) by inhibiting β-catenin signaling in glucocorticoid-induced GONFH rats. Col2+lineage largely contributes to BMSCs, and was found an osteogenic commitment in the femoral head through 9 months of lineage trace. Specific deletion ofβ-cateninin Col2+cells shifted their commitment from osteoblasts to adipocytes, leading to a full spectrum of disease phenotype of GONFH in adult mice. Overall, we uncover that β-catenin inhibition disrupting the homeostasis of osteogenic/adipogenic differentiation contributes to the development of GONFH, and identify an ideal genetic modified mouse model of GONFH.
Chemokine profiling of melanoma-macrophage crosstalk identifies CCL8 and CCL15 as prognostic factors in cutaneous melanoma
Authors: Barrio-Alonso Celia , Nieto-Valle Alicia , García-Martínez Elena , Gutiérrez-Seijo Alba , Parra-Blanco Verónica , Márquez-Rodas Iván , Avilés-Izquierdo José Antonio , Sánchez-Mateos Paloma , Samaniego Rafael
Published: October 2023

During cancer evolution, tumor cells attract and dynamically interact with monocytes/macrophages. To find biomarkers of disease progression in human melanoma, we used unbiased RNA sequencing and secretome analyses of tumor-macrophage co-cultures. Pathway analysis of genes differentially modulated in human macrophages exposed to melanoma cells revealed a general upregulation of inflammatory hallmark gene sets, particularly chemokines. A selective group of chemokines, including CCL20, CCL15 and CCL8, was actively secreted upon melanoma-macrophage co-culture. Because we previously described the role of CCL20 in melanoma, we focused our study in CCL8 and CCL15, and confirmed that in vitro both chemokines contributed to melanoma survival, proliferation and 3D invasion, through CCR1 signaling. In vivo, both chemokines enhanced primary tumor growth, spontaneous lung metastasis and circulating tumor cell (CTC) survival and lung colonization in mouse xenograft models. Finally, we explored the clinical significance of CCL8 and CCL15 expression in human skin melanoma, screening a collection of 67 primary melanoma samples, by multicolor staining and quantitative image analysis of chemokine-chemokine receptor content at the single cell level. Primary skin melanomas displayed high CCR1 expression, but there was no difference in its level of expression between metastatic and non-metastatic cases. By contrast, the comparative analysis between these two clinically divergent groups showed a highly significant difference in the cancer cell content of CCL8 (P= 0.025) and CCL15 (P< 0.0001). Kaplan–Meier curves showed that high content of CCL8 or CCL15 in cancer cells correlated with shorter disease-free and overall survival (log-rank test, p< 0.001). Our results highlight the role of CCL8 and CCL15, which are highly induced by melanoma-macrophage interactions in biologically aggressive primary melanomas, and could be clinically applicable biomarkers for patient profiling.
Decoding the physics of observed actions in the human brain
Authors: Wurm Moritz F. , Erigüç Doruk Yiğit
Published: October 2023

Recognizing goal-directed actions is a computationally challenging task, requiring not only the visual analysis of body movements, but also analysis of how these movements causally impact, and thereby induce a change in, those objects targeted by an action. We tested the hypothesis that the analysis of body movements and the effects they induce relies on distinct neural representations in superior and anterior inferior parietal lobe (SPL and aIPL). In four fMRI sessions, participants observed videos of actions (e.g. breaking stick, squashing plastic bottle) along with corresponding point-light-display stick figures, pantomimes, and abstract animations of agent-object interactions (e.g. dividing or compressing a circle). Cross-decoding between actions and animations revealed that aIPL encodes abstract representations of action effect structures independent of motion and object identity. By contrast, cross-decoding between actions and point-light-displays revealed that SPL is disproportionally tuned to body movements independent of visible interactions with objects. Lateral occipitotemporal cortex (LOTC) was sensitive to both action effects and body movements. Moreover, cross-decoding between pantomimes and animations suggests that right aIPL and LOTC represent action effects even in response to implied object interactions. These results demonstrate that parietal cortex and LOTC are tuned to physical action features, such as how body parts move in space relative to each other and how body parts interact with objects to induce a change (e.g. in position or shape/configuration). The high level of abstraction revealed by cross-decoding suggests a general neural code supporting mechanical reasoning about how entities interact with, and have effects on, each other.
Multimodal single-cell profiling of T cell specificity and reactivity in lung cancer
Authors: Bieberich Florian , Vazquez-Lombardi Rodrigo , Jin Huixin , Hong Kai-Lin , Herzig Petra , Trefny Marcel , Trüb Marta , Läubli Heinz , Lardinois Didier , Mertz Kirsten , Matter Matthias S. , Zippelius Alfred , Reddy Sai T.
Published: October 2023

Adoptive transfer of autologous tumor-infiltrating lymphocyte T cells (TILs) offers one of the most promising approaches for cancer immunotherapy. However, high variability in patient responses highlight the need for an enhanced understanding of the transcriptional phenotypes of TILs and reactivity of their T cell receptors (TCR). Here, we employ single-cell multiomics approaches and TCR functional screening to investigate TILs from treatment-naive non-small cell lung cancer patients. This comprehensive analysis integrates scRNA-seq, scTCR-seq, and scATAC-seq, enabling a high-resolution examination of TILs within lung cancer tissue, as well as the adjacent non-tumor tissue. We apply a cellular functional screening platform to identify reactive TCRs that represent >1,000 TILs and have specificity towards a multitude of targets, including primary tumor cells, neoantigens, tumor-associated antigens, and viral antigens. Tumor-reactive TILs were primarily associated with dysfunctional phenotypes, whereas viral antigen-reactive TCRs were found in effector phenotype clusters. Key marker genes were identified and used to construct a tumor or viral reactivity score. Comparing clones shared in tumor and non-tumor tissue, a higher fraction of exhausted cells was observed in the tumor tissue, whereas non-tumor adjacent tissue possessed more effector cells, thus providing insight into potential sources for therapeutic T cells. Elucidating the specific T cell populations within TILs and their associated TCRs may support strategies to enhance the efficacy of TIL-based therapies.

Graphical Abstract

Multimodal single cell profiling and reactivity testing of TILs

(A) CD8+T cells of treatment naive non-small cell lung cancer patients and adjacent lung tissue were isolated by fluorescence-activated cell sorting (FACS) and were then subjected to scRNA-seq + scTCR-seq or scATAC-seq. (B) TCRs were functionally screened using a cellular platform (TnT cells) and target cells (tumor cells, antigen-pulsed antigen-presenting cells, PBMCs) by flow cytometry and deep sequencing. (C) scRNA-seq + scATAC-seq allowed trajectory inference of transcription factors and genes along pseudotime. (D) Gene scores for tumor- and virus-reactivity were developed by combining functional reactivity and transcriptomic profiling for each CD8+T cell. (E) TIL scRNA-seq pre and post IL-2 treatment in tumor suspension displayed as alluvial plot shows change of clonal cell state composition.
JAK/STAT mediated insulin resistance in muscles is essential for effective immune response
Authors: McMullen Ellen , Strych Lukas , Chodáková Lenka , Krebs Amber , Dolezal Tomas
Published: October 2023

The metabolically demanding nature of immune response requires nutrients to be preferentially directed towards the immune system at the expense of peripheral tissues. We study the mechanisms by which this metabolic reprograming occurs using the parasitoid infection ofDrosophilalarvae. To overcome such an immune challenge hemocytes differentiate into lamellocytes, which encapsulate and melanize the parasitoid egg. Hemocytes acquire the energy for this process by expressing JAK/STAT ligands upd2 and upd3, which activates JAK/STAT signaling in muscles and redirects carbohydrates away from muscles in favor of immune cells. Absence of upd/JAK/STAT signaling leads to an impaired immune response and increased mortality. We demonstrate how JAK/STAT signaling in muscles leads to suppression of insulin signaling through activation of ImpL2, the inhibitor of Drosophila insulin like peptides. We reveal the crucial function of muscles during immune response and show the benefits of insulin resistance as an adaptive mechanism that is necessary for survival.
Employing a honeybee olfactory neural circuit as a novel gas sensor for the detection of human lung cancer biomarkers
Authors: Parnas Michael , Cox Elyssa , Sanchez Simon , Farnum Alexander , Lefevre Noël , Miller Sydney , Saha Debajit
Published: October 2023

Human breath contains biomarkers (odorants) that can be targeted for early disease detection. It is well known that honeybees have a keen sense of smell and can detect a wide variety of odors at low concentrations. Here, for the first time, we employ honeybee olfactory neuronal circuitry to classify human lung cancer volatile biomarkers and their mixtures at concentration ranges relevant to human breath, parts-per-billion to parts-per-trillion. Different lung cancer biomarkers evoked distinct spiking response dynamics in the honeybee antennal lobe neurons indicating that those neurons encoded biomarker-specific information. By investigating lung cancer biomarker-evoked population neuronal responses from the honeybee antennal lobe, we could classify individual human lung cancer biomarkers successfully (88% success rate). When we mixed six lung cancer biomarkers at different concentrations to create ‘synthetic lung cancer’ vs. ‘synthetic healthy breath’, honeybee population neuronal responses were also able to classify those complex breath mixtures successfully (100% success rate with a leave-one-trial-out method). Finally, we used separate training and testing datasets containing responses to the synthetic lung cancer and healthy breath mixtures. We identified a simple metric, the peak response of the neuronal ensemble, with the ability to distinguish synthetic lung cancer breath from the healthy breath with 86.7% success rate. This study provides proof-of-concept results that a powerful biological gas sensor, the honeybee olfactory system, can be used to detect human lung cancer biomarkers and their complex mixtures at biological concentrations.
Harnessing Landrace Diversity Empowers Wheat Breeding for Climate Resilience
Authors: Cheng Shifeng , Feng Cong , Wingen Luzie U. , Cheng Hong , Riche Andrew B. , Jiang Mei , Leverington-Waite Michelle , Huang Zejian , Collier Sarah , Orford Simon , Wang Xiaoming , Awal Rajani , Barker Gary , O’Hara Tom , Lister Clare , Siluveru Ajay , Quiroz-Chávez Jesús , Ramírez-González Ricardo H. , Bryant Ruth , Berry Simon , Bansal Urmil , Bariana Harbans S. , Bennett Malcolm J. , Bicego Breno , Bilham Lorelei , Brown James K.M. , Burridge Amanda , Burt Chris , Buurman Milika , Castle March , Chartrain Laetitia , Chen Baizhi , Denbel Worku , Elkot Ahmed F. , Fenwick Paul , Feuerhelm David , Foulkes John , Gaju Oorbessy , Gauley Adam , Gaurav Kumar , Hafeez Amber N. , Han Ruirui , Horler Richard , Hou Junliang , Iqbal Muhammad S. , Kerton Matthew , Kondic-Spica Ankica , Kowalski Ania , Lage Jacob , Li Xiaolong , Liu Hongbing , Liu Shiyan , Lovegrove Alison , Ma Lingling , Mumford Cathy , Parmar Saroj , Philp Charlie , Playford Darryl , Przewieslik-Allen Alexandra M. , Sarfraz Zareen , Schafer David , Shewry Peter R. , Shi Yan , Slafer Gustavo , Song Baoxing , Song Bo , Steele David , Steuernagel Burkhard , Tailby Phillip , Tyrrell Simon , Waheed Abdul , Wamalwa Mercy N. , Wang Xingwei , Wei Yanping , Winfield Mark , Wu Shishi , Wu Yubing , Wulff Brande B.H. , Xian Wenfei , Xu Yawen , Xu Yunfeng , Yuan Quan , Zhang Xin , Edwards Keith J. , Dixon Laura , Nicholson Paul , Chayut Noam , Hawkesford Malcolm J. , Uauy Cristobal , Sanders Dale , Huang Sanwen , Griffiths Simon
Published: October 2023

Breeding crops resilient to climate change is urgently needed to help ensure food security. A key challenge is to harness genetic diversity to optimise adaptation, yield, stress resilience and nutrition. We examined the genetic and phenotypic diversity of the A.E. Watkins landrace collection of bread wheat (Triticum aestivum), a major global cereal, through whole-genome re-sequencing (827 Watkins landraces and 208 modern cultivars) and in-depth field evaluation spanning a decade. We discovered that modern cultivars are derived from just two of the seven ancestral groups of wheat, leaving five groups as previously untapped sources for breeding. This provides access to landrace-specific functional variations using structured germplasm, genotyping and informatics resources. Employing complementary genetic populations and approaches, we identified thousands of high-resolution quantitative trait loci (QTL) and significant marker–trait associations for major traits, revealing many Watkins-unique loci that can confer superior traits in modern wheat. Furthermore, we identified and functionally verified causative genes for climate-change adaptation, nutritional enhancement and resistance to wheat blast. Finally, we assessed the phenotypic effects of 44,338 Watkins-unique haplotypes, introgressed from 143 prioritised QTL in the context of modern cultivars, bridging the gap between landrace diversity and current breeding. This study establishes a framework for systematically utilising genetic diversity in crop improvement to achieve sustainable food security.
A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics
Authors: Eisenhofer Raphael , Nesme Joseph , Santos-Bay Luisa , Koziol Adam , Sørensen Søren Johannes , Alberdi Antton , Aizpurua Ostaizka
Published: October 2023

Shotgun metagenomics enables the reconstruction of complex microbial communities at a high level of detail. Such an approach can be conducted using both short-read and long-read sequencing data, as well as a combination of both. To assess the pros and cons of these different approaches, we used 22 faecal DNA extracts collected weekly for 11 weeks from two respective lab mice to study seven performance metrics over four combinations of sequencing depth and technology: i) 20 Gbp of Illumina short-read data, ii) 40 Gbp of short-read data, iii) 20 Gbp of PacBio HiFi long-read data, and iv) 40 Gbp of hybrid (20 Gbp of short-read + 20 Gbp of long-read) data. No strategy was best for all metrics, but instead, each one excelled across different metrics. The long-read approach yielded the best assembly statistics, with the highest N50 and lowest number of contigs. The 40 Gbp short-read approach yielded the highest number of refined bins. Finally, the hybrid approach yielded the longest assemblies, and the highest mapping rate to the bacterial genomes. Our results suggest that while long-read sequencing significantly improves the quality of reconstructed bacterial genomes, it is more expensive and requires deeper sequencing than short-read approaches to recover a comparable amount of reconstructed genomes. The most optimal strategy is study-specific, and depends on how researchers assess the tradeoff between the quantity and quality of recovered genomes.

Importance

Our understanding of microbial communities is limited by the technologies we employ. Here, we test several different DNA sequencing techniques to better understand the pros and cons of each. Long read DNA sequencing allowed for the reconstruction of higher quality and even complete microbial genomes, however, the cost was greater than commonly used short-read DNA sequencing. We suggest researchers consider the trade-offs between each method and decide based on the goals of their research question/s.
Pumping the brakes: rostromedial tegmental inhibition of compulsive cocaine seeking
Authors: Vento Peter J. , Watson Jacob R. , Pullmann Dominika , Black Samantha L. , Tomberlin Jensen S. , Jhou Thomas C.
Published: October 2023

Addiction is marked by aberrant decision-making and an inability to suppress inappropriate and often dangerous behaviors. We previously demonstrated that inactivation of the rostromedial tegmental nucleus (RMTg) in rats causes persistent food seeking despite impending aversive footshock, an effect strikingly similar to the punishment resistance observed in people with a history of protracted drug use [1]. Here, we extend these studies to demonstrate chemogenetic silencing of RMTg axonal projections to the ventral tegmental area (VTA) (RMTg◊VTA pathway) causes rats to endure significantly more footshock to receive cocaine infusions. To further test whether activation of this circuit is sufficient to suppress reward seeking in the absence of an overtly aversive stimulus, we used temporally specific optogenetic stimulation of the RMTg◊VTA pathway as a “punisher” in place of footshock following lever pressing for either food or cocaine reward. While optical stimulation of the RMTg◊VTA pathway robustly suppressed lever pressing for food, we found that stimulation of this circuit had only modest effects on suppressing responding for cocaine infusions. Even though optical RMTg◊VTA stimulation was not particularly effective at reducingongoingcocaine use, this experience nevertheless had long-lasting consequences, as reinstatement of drug seeking in response to cocaine-associated cues was profoundly suppressed when tested nearly two weeks later. These results suggest the RMTg may serve as a useful target for producing enduring reductions in drug craving, particularly during periods of abstinence from drug use.
Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry
Authors: Bhat-Nakshatri Poornima , Gao Hongyu , Khatpe Aditi S. , McGuire Patrick C. , Erdogan Cihat , Chen Duojiao , Jiang Guanglong , New Felicia , German Rana , Storniolo Anna Maria , Liu Yunlong , Nakshatri Harikrishna
Published: October 2023

Single nuclei analysis is allowing robust classification of cell types in an organ that helps to establish relationships between cell-type specific gene expression and chromatin accessibility status of gene regulatory regions. Using breast tissues of 92 healthy donors of various genetic ancestry, we have developed a comprehensive chromatin accessibility and gene expression atlas of human breast tissues. Integrated analysis revealed 10 distinct cell types in the healthy breast, which included three major epithelial cell subtypes (luminal hormone sensing, luminal adaptive secretory precursor, and basal-myoepithelial cells), two endothelial subtypes, two adipocyte subtypes, fibroblasts, T-cells, and macrophages. By integrating gene expression signatures derived from epithelial cell subtypes with spatial transcriptomics, we identify specific gene expression differences between lobular and ductal epithelial cells and age-associated changes in epithelial cell gene expression patterns and signaling networks. Among various cell types, luminal adaptive secretory cells and fibroblasts showed genetic ancestry dependent variability. A subpopulation of luminal adaptive secretory cells with alveolar progenitor (AP) cell state were enriched in Indigenous American (IA) ancestry and fibroblast populations were distinct in African ancestry. ESR1 expression pattern was distinctly different in cells from IA compared to the rest, with a high level of ESR1 expression extending to AP cells and crosstalk between growth factors and Estrogen Receptor signaling being evident in these AP cells. In general, cell subtype-specific gene expression did not uniformly correlate with cell-specific chromatin accessibility, suggesting that transcriptional regulation independent of chromatin accessibility governs cell type-specific gene expression in the breast.
Automated Surface-Based Segmentation of Deep Gray Matter Regions Based on Diffusion Tensor Images Reveals Unique Age Trajectories Over the Healthy Lifespan
Authors: Little Graham , Acosta-Franco J. Alejandro , Beaulieu Christian
Published: October 2023

Many studies have demonstrated unique trajectories of deep gray matter (GM) volumes over development and aging, suggesting but not measuring microstructural alterations over the lifespan. Only a few studies have measured diffusion tensor imaging (DTI) parameters in deep GM or reported these values across a wide age range in a large cohort. To enable efficient DTI studies of deep GM in large cohorts without the need of T1-weighted images, an automated segmentation technique is proposed here that works solely on parametric maps calculated from DTI. The algorithm segments the globus pallidus, striatum, thalamus, hippocampus and amygdala per hemisphere by deforming 3D models of these structures to their boundaries visible on the contrast provided by diffusion tensor maps and images alone. This new DTI-only method is compared against standard T1-weighted image segmentation for (i) 1.25 mm isotropic diffusion data from the Human Connectome Project (HCP) test-retest cohort (n=44) and (ii) 1.5 mm isotropic test-retest diffusion data from a local normative study (n=24). Dice coefficients of voxel overlap between methods in the HCP test-retest cohort were high (>0.7) for 7 of 10 structures, but were low for the left globus pallidus (0.54) and left/right amygdala (0.67, 0.69). The proposed DTI-only segmentation qualitatively appeared more accurate and yielded smaller volumes than T1w for 8/10 structures in both cohorts, with the exception of the globus pallidus which showed larger volumes in the HCP test-retest data but lower volumes in the local normative study data. The DTI-only segmentation method was then applied to two local single site development/aging ‘lifespan’ cohorts (cohort 1: n=365 5-90 years, cohort 2: n= 164 5-74 years) to assess age changes in volume, fractional anisotropy (FA) and mean diffusivity (MD). In both cohorts, MD trajectories were quadratic for all five structures, decreasing slightly and then increasing after ∼30-35 years. In cohort #1, FA trajectories remained flat from 5 to ∼25 years and then started to decrease for the globus pallidus and hippocampus and over 5 to 90 years, FA decreased linearly for amygdala, increased linearly for striatum, and remained constant for the thalamus. In the second cohort, using an alternate acquisition protocol, the FA trajectories of all 5 structures across all ages were similar, except for the globus pallidus and thalamus which both increased in value from 5 ∼ 20 years and likely reflect differences in acquisition details. Notably, the development and aging trajectories for DTI were distinct from those of the deep GM volumes. The proposed automated deep GM segmentation method on DTI-only will facilitate the analysis of deep GM DTI (currently ignored in nearly all studies despite the data there within the field-of-view) and will be advantageous particularly for studies that do not have a T1-weighted scan, as in many clinical populations.
A portable, easy-to-use paper-based biosensor for rapid in-field detection of fecal contamination on fresh produce farms
Authors: Wang Jiangshan , Kaur Simerdeep , Kayabasi Ashley , Ranjbaran Mohsen , Rath Ishaan , Benschikovski Ilan , Raut Bibek , Ra Kyungyeon , Rafiq Nafisa , Verma Mohit S.
Published: October 2023

Laboratory-based nucleic acid amplification tests (NAATs) are highly sensitive and specific, but they require the transportation of samples to centralized testing facilities and have long turnaround times. During the Coronavirus Disease 2019 (COVID-19) pandemic, substantial advancement has been achieved with the development of paper-based point-of-care (POC) NAATs, offering features such as low cost, being easy to use, and providing rapid sample-to-answer times. Although most of the POC NAATs innovations target clinical settings, we have developed a portable, paper-based loop-mediated isothermal amplification (LAMP) testing platform for on-farm applications, capable of detectingBacteroidalesas a fecal contamination biomarker. Our integrated platform includes a drop generator, a heating and imaging unit, and paper-based biosensors, providing sensitive results (limit of detection 3 copies ofBacteroidalesper cm2) within an hour of sample collection. We evaluated this integrated platform on a commercial lettuce farm with a concordance of 100% when compared to lab-based tests. Our integrated paper-based LAMP testing platform holds great promise as a reliable and convenient tool for on-site NAATs. We expect that this innovation will encourage the fresh produce industry to adopt NAATs as a complementary tool for decision-making in growing and harvesting. We also hope that our work can stimulate further research in the development of on-farm diagnostic tools for other agricultural applications, leading to improved food safety and technology innovation.
Grove-level analysis of titer and prevalence of “CandidatusLiberibacter asiaticus” andWolbachiainDiaphorina citri,vector of citrus Huanglongbing
Authors: Mann Marina , Thompson Luke , Johnson Lynn , Heck Michelle
Published: October 2023

Huanglongbing (HLB, or citrus greening disease) affects all citrus varieties world-wide. In the USA, Asia, and South America the causal agent is “CandidatusLiberibacter asiaticus” (CLas), a phloem-limited, uncultured, alphaproteobacterium. The hemipteran insect vector,Diaphorina citri(Asian citrus psyllid) acquires and transmitsCLas in a circulative, propagative manner. In addition toCLas,D. citrihosts multiple symbiotic bacterial species includingWolbachia(wDi). InD. citri, wDi has been sequenced and studied but specific roles inD. citribiology are unknown. Using well established quantitative PCR methods we measuredCLas titer inD. citricollected from four groves in central Florida with distinct HLB management strategies and tested whetherCLas and wDi titer were correlated in a sub-set of these insects. Grove site had the largest effect onCLas titer. Sex had no effect onCLas titer, while higher wDi titer was correlated with non-infected insects. Our results suggest that more directed follow-up research is necessary and important to clarify whether field management tactics influenceCLas titer inD. citriand to better understand gene-by-environment interactions amongD. citri, wDi andCLas. Now that millions of trees in Florida have been treated with injectable formulations of oxytetracycline, which is likely to decrease bacterial populations inD. citri, this study may represent the last biologically meaningful snapshot of grove-level vector-pathogen ecology in the state during the HLB epidemic.
Dedifferentiated early postnatal lung myofibroblasts redifferentiate in adult disease
Authors: Chandran Rachana R. , Adams Taylor , Kabir Inamul , Gallardo Eunate , Kaminski Naftali , Gomperts Brigitte , Greif Daniel M.
Published: October 2023

Alveolarization ensures sufficient lung surface area for gas exchange, and during bulk alveolarization in mice (postnatal day [P] 4.5-14.5), alpha-smooth muscle actin (SMA)+myofibroblasts accumulate, secrete elastin, and lay down alveolar septae. Herein, we delineate the dynamics of the lineage of early postnatal SMA+myofibroblasts during and after bulk alveolarization and in response to lung injury. SMA+lung myofibroblasts first appear at ∼P2.5 and proliferate robustly. Lineage tracing shows that, at P14.5 and over the next few days, the vast majority of SMA+myofibroblasts downregulate smooth muscle cell markers and undergo apoptosis. Of note, ∼8% of these dedifferentiated cells and another ∼1% of SMA+myofibroblasts persist to adulthood. Single cell RNA sequencing analysis of the persistent SMA-cells and SMA+myofibroblasts in the adult lung reveals distinct gene expression profiles. For instance, dedifferentiated SMA-cells exhibit higher levels of tissue remodeling genes. Most interestingly, these dedifferentiated early postnatal myofibroblasts re-express SMA upon exposure of the adult lung to hypoxia or the pro-fibrotic drug bleomycin. However, unlike during alveolarization, these cells that re-express SMA do not proliferate with hypoxia. In sum, dedifferentiated early postnatal myofibroblasts are a previously undescribed cell type in the adult lung and redifferentiate in response to injury.
A phylogenetic method linking nucleotide substitution rates to rates of continuous trait evolution
Authors: Gemmell Patrick , Sackton Timothy B. , Edwards Scott V. , Liu Jun S.
Published: October 2023

Genomes contain conserved non-coding sequences that perform important biological functions, such as gene regulation. We present a phylogenetic method, PhyloAcc-C, that associates nucleotide substitution rates with changes in a continuous trait of interest. The method takes as input a multiple sequence alignment of conserved elements, continuous trait data observed in extant species, and a background phylogeny and substitution process. Gibbs sampling is used to assign rate categories (background, conserved, accelerated) to lineages and explore whether the assigned rate categories are associated with increases or decreases in the rate of trait evolution. We test our method using simulations and then illustrate its application using mammalian body size and lifespan data previously analyzed with respect to protein coding genes. Like other studies, we find processes such as tumor suppression, telomere maintenance, and p53 regulation to be related to changes in longevity and body size. In addition, we also find that skeletal genes, and developmental processes, such as sprouting angiogenesis, are relevant. The R/C++ software package implementing our method is available under an open source license fromhttps://github.com/phyloacc/PhyloAcc-C.