Pub Date : 2024-11-16DOI: 10.1038/s42003-024-07165-7
Demeter Túrós, Jelica Vasiljevic, Kerstin Hahn, Sven Rottenberg, Alberto Valdeolivas
Dissecting tissue compartments in spatial transcriptomics (ST) remains challenging due to limited spatial resolution and dependence on single-cell reference data. We present Chrysalis, a computational method that rapidly uncovers tissue compartments through spatially variable gene (SVG) detection and archetypal analysis without requiring external reference data. Additionally, it offers a unique visualisation approach for swift tissue characterisation and provides access to the underlying gene expression signatures, enabling the identification of spatially and functionally distinct cellular niches. Chrysalis was evaluated through various benchmarks and validated against deconvolution, independently obtained cell type abundance data, and histopathological annotations, demonstrating superior performance compared to other algorithms on both in silico and real-world test examples. Furthermore, we showcased its versatility across different technologies, such as Visium, Visium HD, Slide-seq, and Stereo-seq.
{"title":"Chrysalis: decoding tissue compartments in spatial transcriptomics with archetypal analysis.","authors":"Demeter Túrós, Jelica Vasiljevic, Kerstin Hahn, Sven Rottenberg, Alberto Valdeolivas","doi":"10.1038/s42003-024-07165-7","DOIUrl":"10.1038/s42003-024-07165-7","url":null,"abstract":"<p><p>Dissecting tissue compartments in spatial transcriptomics (ST) remains challenging due to limited spatial resolution and dependence on single-cell reference data. We present Chrysalis, a computational method that rapidly uncovers tissue compartments through spatially variable gene (SVG) detection and archetypal analysis without requiring external reference data. Additionally, it offers a unique visualisation approach for swift tissue characterisation and provides access to the underlying gene expression signatures, enabling the identification of spatially and functionally distinct cellular niches. Chrysalis was evaluated through various benchmarks and validated against deconvolution, independently obtained cell type abundance data, and histopathological annotations, demonstrating superior performance compared to other algorithms on both in silico and real-world test examples. Furthermore, we showcased its versatility across different technologies, such as Visium, Visium HD, Slide-seq, and Stereo-seq.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"7 1","pages":"1520"},"PeriodicalIF":5.2,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11569261/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-16DOI: 10.1038/s42003-024-07248-5
Qing Zhou, Ziyin Li
Faithful chromosome segregation in eukaryotes requires the assembly of a bipolar spindle and the faithful attachment of kinetochores to spindle microtubules, which are regulated by various spindle-associated proteins (SAPs) that play distinct functions in regulating spindle dynamics and microtubule-kinetochore attachment. The protozoan parasite Trypanosoma brucei employs evolutionarily conserved and kinetoplastid-specific proteins, including some kinetoplastid-specific nucleus- and spindle-associated proteins (NuSAPs), to regulate chromosome segregation. Here, we characterized NuSAP4 and its functional interplay with diverse SAPs in promoting chromosome segregation in T. brucei. NuSAP4 associates with the spindle during mitosis and concentrates at spindle poles where it interacts with SPB1 and MAP103. Knockdown of NuSAP4 impairs chromosome segregation by disrupting bipolar spindle assembly and spindle pole protein localization. These results uncover the mechanistic role of NuSAP4 in regulating chromosome segregation by promoting bipolar spindle assembly, and highlight the unusual features of mitotic regulation by spindle-associated proteins in this early divergent microbial eukaryote.
{"title":"NuSAP4 regulates chromosome segregation in Trypanosoma brucei by promoting bipolar spindle assembly.","authors":"Qing Zhou, Ziyin Li","doi":"10.1038/s42003-024-07248-5","DOIUrl":"10.1038/s42003-024-07248-5","url":null,"abstract":"<p><p>Faithful chromosome segregation in eukaryotes requires the assembly of a bipolar spindle and the faithful attachment of kinetochores to spindle microtubules, which are regulated by various spindle-associated proteins (SAPs) that play distinct functions in regulating spindle dynamics and microtubule-kinetochore attachment. The protozoan parasite Trypanosoma brucei employs evolutionarily conserved and kinetoplastid-specific proteins, including some kinetoplastid-specific nucleus- and spindle-associated proteins (NuSAPs), to regulate chromosome segregation. Here, we characterized NuSAP4 and its functional interplay with diverse SAPs in promoting chromosome segregation in T. brucei. NuSAP4 associates with the spindle during mitosis and concentrates at spindle poles where it interacts with SPB1 and MAP103. Knockdown of NuSAP4 impairs chromosome segregation by disrupting bipolar spindle assembly and spindle pole protein localization. These results uncover the mechanistic role of NuSAP4 in regulating chromosome segregation by promoting bipolar spindle assembly, and highlight the unusual features of mitotic regulation by spindle-associated proteins in this early divergent microbial eukaryote.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"7 1","pages":"1524"},"PeriodicalIF":5.2,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11569230/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pathway analysis is a crucial analytical phase in disease research on single-cell RNA sequencing (scRNA-seq) data, offering biological interpretations based on prior knowledge. However, currently available tools for generating cell-level pathway activity scores (PAS) exhibit computational inefficacy in large-scale scRNA-seq datasets. Additionally, disease-related pathways are often identified through cross-condition comparisons within specific cell types, overlooking potential patterns that involve multiple cell types. Here, we present single-cell pathway activity factor analysis (scPAFA), a Python library designed for large-scale single-cell datasets allowing rapid PAS computation and uncovering biologically interpretable disease-related multicellular pathway modules, which are low-dimensional representations of disease-related PAS alterations in multiple cell types. Application on colorectal cancer (CRC) datasets and large-scale lupus atlas over 1.2 million cells demonstrated that scPAFA can achieve over 40-fold reductions in the runtime of PAS computation and further identified reliable and interpretable multicellular pathway modules that capture the heterogeneity of CRC and transcriptional abnormalities in lupus patients, respectively. Overall, scPAFA presents a valuable addition to existing research tools in disease research, with the potential to reveal complex disease mechanisms and support biomarker discovery at the pathway level.
通路分析是单细胞 RNA 测序(scRNA-seq)数据疾病研究中的一个关键分析阶段,它能根据先前的知识提供生物学解释。然而,目前可用来生成细胞级通路活性评分(PAS)的工具在大规模 scRNA-seq 数据集中表现出计算效率低下的问题。此外,疾病相关通路通常是通过特定细胞类型内的跨条件比较来确定的,忽略了涉及多种细胞类型的潜在模式。在这里,我们介绍了单细胞通路活性因子分析(scPAFA),这是一个专为大规模单细胞数据集设计的 Python 库,可以快速计算 PAS 并发现可从生物学角度解释的疾病相关多细胞通路模块,这些模块是多种细胞类型中疾病相关 PAS 改变的低维表示。在结直肠癌(CRC)数据集和超过120万个细胞的大规模狼疮图谱上的应用表明,scPAFA能将PAS计算的运行时间缩短40倍以上,并进一步确定了可靠且可解释的多细胞通路模块,这些模块分别捕捉了CRC和狼疮患者转录异常的异质性。总之,scPAFA 是对现有疾病研究工具的宝贵补充,有望揭示复杂的疾病机制,支持通路水平的生物标记物发现。
{"title":"Uncovering disease-related multicellular pathway modules on large-scale single-cell transcriptomes with scPAFA.","authors":"Zhuoli Huang, Yuhui Zheng, Weikai Wang, Wenwen Zhou, Yanbo Zhang, Chen Wei, Xiuqing Zhang, Xin Jin, Jianhua Yin","doi":"10.1038/s42003-024-07238-7","DOIUrl":"10.1038/s42003-024-07238-7","url":null,"abstract":"<p><p>Pathway analysis is a crucial analytical phase in disease research on single-cell RNA sequencing (scRNA-seq) data, offering biological interpretations based on prior knowledge. However, currently available tools for generating cell-level pathway activity scores (PAS) exhibit computational inefficacy in large-scale scRNA-seq datasets. Additionally, disease-related pathways are often identified through cross-condition comparisons within specific cell types, overlooking potential patterns that involve multiple cell types. Here, we present single-cell pathway activity factor analysis (scPAFA), a Python library designed for large-scale single-cell datasets allowing rapid PAS computation and uncovering biologically interpretable disease-related multicellular pathway modules, which are low-dimensional representations of disease-related PAS alterations in multiple cell types. Application on colorectal cancer (CRC) datasets and large-scale lupus atlas over 1.2 million cells demonstrated that scPAFA can achieve over 40-fold reductions in the runtime of PAS computation and further identified reliable and interpretable multicellular pathway modules that capture the heterogeneity of CRC and transcriptional abnormalities in lupus patients, respectively. Overall, scPAFA presents a valuable addition to existing research tools in disease research, with the potential to reveal complex disease mechanisms and support biomarker discovery at the pathway level.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"7 1","pages":"1523"},"PeriodicalIF":5.2,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11569158/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-16DOI: 10.1038/s42003-024-07139-9
Thanumol Abdul Khader, Waqar Ahmad, Shaima Akhlaq, Neena Gopinathan Panicker, Bushra Gull, Jasmin Baby, Tahir A Rizvi, Farah Mustafa
The mouse mammary tumor virus (MMTV) encodes a 5' element crucial for transcription of its genome along with the Rem/Rem-responsive element (RmRE) responsible for nuclear export of this unspliced RNA. Whether the 5' element is Rem-responsive or has any functional interaction with host/viral factors to facilitate MMTV gene expression was tested in this study. Our results reveal that the 5' element is non-responsive to Rem, but can be transactivated by both HIV Tat and HTLV-1 Tax activators. Reciprocally, MMTV could transactivate not only HIV TAR (similar to HTLV Tax), but also its 5' element. Furthermore, we reveal involvement of pTEFb, a general elongation factor associated with transactivation by Tat/Tax. This makes MMTV the first betaretrovirus to encode both Rem/RRE and Tat/TAR-Tax/TRE-like transcription regulatory systems. This study should enhance not only our understanding of retrovirus replication and virally-induced cancers/immunodeficiency syndromes, but also development of improved retroviral vectors for human gene therapy.
小鼠乳腺肿瘤病毒(MMTV)编码一个对其基因组转录至关重要的 5'元件,以及负责将这种未剪接 RNA 核输出的 Rem/Rem 反应元件(RmRE)。本研究测试了该 5' 元是否具有雷姆响应性,或是否与宿主/病毒因子有任何功能上的相互作用,以促进 MMTV 基因的表达。我们的研究结果表明,5'元件对 Rem 无反应,但可被 HIV Tat 和 HTLV-1 Tax 激活因子转录。反过来,MMTV 不仅能反式激活 HIV TAR(类似于 HTLV Tax),还能反式激活其 5' 元。此外,我们还发现了 pTEFb 的参与,这是一种与 Tat/Tax 的转录活化相关的通用延伸因子。这使 MMTV 成为第一个同时编码 Rem/RRE 和 Tat/TAR-Tax/TRE 类转录调控系统的 betaretrovirus。这项研究不仅加深了我们对逆转录病毒复制和病毒诱导的癌症/免疫缺陷综合征的了解,还有助于开发用于人类基因治疗的改良型逆转录病毒载体。
{"title":"Transactivation of the novel 5' cis-acting element of mouse mammary tumor virus (MMTV) by human retroviral transactivators Tat and Tax.","authors":"Thanumol Abdul Khader, Waqar Ahmad, Shaima Akhlaq, Neena Gopinathan Panicker, Bushra Gull, Jasmin Baby, Tahir A Rizvi, Farah Mustafa","doi":"10.1038/s42003-024-07139-9","DOIUrl":"10.1038/s42003-024-07139-9","url":null,"abstract":"<p><p>The mouse mammary tumor virus (MMTV) encodes a 5' element crucial for transcription of its genome along with the Rem/Rem-responsive element (RmRE) responsible for nuclear export of this unspliced RNA. Whether the 5' element is Rem-responsive or has any functional interaction with host/viral factors to facilitate MMTV gene expression was tested in this study. Our results reveal that the 5' element is non-responsive to Rem, but can be transactivated by both HIV Tat and HTLV-1 Tax activators. Reciprocally, MMTV could transactivate not only HIV TAR (similar to HTLV Tax), but also its 5' element. Furthermore, we reveal involvement of pTEFb, a general elongation factor associated with transactivation by Tat/Tax. This makes MMTV the first betaretrovirus to encode both Rem/RRE and Tat/TAR-Tax/TRE-like transcription regulatory systems. This study should enhance not only our understanding of retrovirus replication and virally-induced cancers/immunodeficiency syndromes, but also development of improved retroviral vectors for human gene therapy.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"7 1","pages":"1521"},"PeriodicalIF":5.2,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11569226/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-15DOI: 10.1038/s42003-024-07182-6
Annika Haessler, Michael Candlish, Jasmin K. Hefendehl, Nathalie Jung, Maike Windbergs
Aβ plaques are a main feature of Alzheimer’s disease, and pathological alterations especially in their microenvironment have recently come into focus. However, a holistic imaging approach unveiling these changes and their biochemical nature is still lacking. In this context, we leverage confocal Raman microscopy as unbiased tool for non-destructive, label-free differentiation of progressive biomolecular changes in the Aβ plaque microenvironment in brain tissue of a murine model of cerebral amyloidosis. By developing a detailed approach, overcoming many challenges of chemical imaging, we identify spatially-resolved molecular signatures of disease-associated structures. Specifically, our study reveals nuclear condensation, indicating cellular degeneration, and increased levels of cytochrome c, showing mitochondrial dysfunction, in the vicinity of Aβ plaques. Further, we observe severe accumulation of especially unsaturated lipids. Thus, our study contributes to a comprehensive understanding of disease progression in the Aβ plaque microenvironment, underscoring the prospective of Raman imaging in neurodegenerative disorder research. Multivariate analysis of hyperspectral Raman imaging data unveils severe cellular toxicity and lipid dysregulation in the chemically complex Aβ plaque microenvironment.
{"title":"Mapping cellular stress and lipid dysregulation in Alzheimer-related progressive neurodegeneration using label-free Raman microscopy","authors":"Annika Haessler, Michael Candlish, Jasmin K. Hefendehl, Nathalie Jung, Maike Windbergs","doi":"10.1038/s42003-024-07182-6","DOIUrl":"10.1038/s42003-024-07182-6","url":null,"abstract":"Aβ plaques are a main feature of Alzheimer’s disease, and pathological alterations especially in their microenvironment have recently come into focus. However, a holistic imaging approach unveiling these changes and their biochemical nature is still lacking. In this context, we leverage confocal Raman microscopy as unbiased tool for non-destructive, label-free differentiation of progressive biomolecular changes in the Aβ plaque microenvironment in brain tissue of a murine model of cerebral amyloidosis. By developing a detailed approach, overcoming many challenges of chemical imaging, we identify spatially-resolved molecular signatures of disease-associated structures. Specifically, our study reveals nuclear condensation, indicating cellular degeneration, and increased levels of cytochrome c, showing mitochondrial dysfunction, in the vicinity of Aβ plaques. Further, we observe severe accumulation of especially unsaturated lipids. Thus, our study contributes to a comprehensive understanding of disease progression in the Aβ plaque microenvironment, underscoring the prospective of Raman imaging in neurodegenerative disorder research. Multivariate analysis of hyperspectral Raman imaging data unveils severe cellular toxicity and lipid dysregulation in the chemically complex Aβ plaque microenvironment.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":" ","pages":"1-11"},"PeriodicalIF":5.2,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42003-024-07182-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142636960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-15DOI: 10.1038/s42003-024-07200-7
Hang Zhou, Viola Neudecker, Jose F. Perez-Zoghbi, Ansgar M. Brambrink, Guang Yang
Anesthesia can influence cerebral blood flow by altering vessel diameter. Using in vivo two-photon imaging, we examined the effects of volatile anesthetics, sevoflurane and isoflurane, on vessel diameter in young and adult mice. Our results show that these anesthetics induce robust dilation of cortical arterioles and arteriole-proximate capillaries in adult mice, with milder effects in juveniles and no dilation in infants. This anesthesia-induced vasodilation correlates with decreased cytosolic Ca2+ levels in NG2+ vascular mural cells. Optogenetic manipulation of these cells bidirectionally regulates vessel diameter, and their ablation abolishes the vasodilatory response to anesthetics. In immature brains, NG2+ mural cells are fewer in number and express lower levels of Kir6.1, a subunit of ATP-sensitive potassium channels. This likely contributes to the age-dependent differences in vasodilation, as Kir6.1 activation promotes, while its inhibition reduces, anesthesia-induced vasodilation. These findings highlight the essential role of NG2+ mural cells in mediating anesthesia-induced cerebral vasodilation. Live animal imaging reveals age-dependent cerebral vasodilatory responses to volatile anesthetics, pronounced in adult mice and diminished or absent in developing brains. These effects are mediated by NG2+ mural cells and Kir6.1 signaling.
{"title":"Age-dependent cerebral vasodilation induced by volatile anesthetics is mediated by NG2+ vascular mural cells","authors":"Hang Zhou, Viola Neudecker, Jose F. Perez-Zoghbi, Ansgar M. Brambrink, Guang Yang","doi":"10.1038/s42003-024-07200-7","DOIUrl":"10.1038/s42003-024-07200-7","url":null,"abstract":"Anesthesia can influence cerebral blood flow by altering vessel diameter. Using in vivo two-photon imaging, we examined the effects of volatile anesthetics, sevoflurane and isoflurane, on vessel diameter in young and adult mice. Our results show that these anesthetics induce robust dilation of cortical arterioles and arteriole-proximate capillaries in adult mice, with milder effects in juveniles and no dilation in infants. This anesthesia-induced vasodilation correlates with decreased cytosolic Ca2+ levels in NG2+ vascular mural cells. Optogenetic manipulation of these cells bidirectionally regulates vessel diameter, and their ablation abolishes the vasodilatory response to anesthetics. In immature brains, NG2+ mural cells are fewer in number and express lower levels of Kir6.1, a subunit of ATP-sensitive potassium channels. This likely contributes to the age-dependent differences in vasodilation, as Kir6.1 activation promotes, while its inhibition reduces, anesthesia-induced vasodilation. These findings highlight the essential role of NG2+ mural cells in mediating anesthesia-induced cerebral vasodilation. Live animal imaging reveals age-dependent cerebral vasodilatory responses to volatile anesthetics, pronounced in adult mice and diminished or absent in developing brains. These effects are mediated by NG2+ mural cells and Kir6.1 signaling.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":" ","pages":"1-16"},"PeriodicalIF":5.2,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11568297/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142638654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-15DOI: 10.1038/s42003-024-07239-6
Tobias Richter, Lisa Geres, Sebastian König, Kristin H Braziunas, Cornelius Senf, Dominik Thom, Claus Bässler, Jörg Müller, Rupert Seidl, Sebastian Seibold
Mountain forests are biodiversity hotspots with competing hypotheses proposed to explain elevational trends in habitat specialization and species richness. The altitudinal-niche-breadth hypothesis suggests decreasing specialization with elevation, which could lead to decreasing species richness and weaker differences in species richness and beta diversity among habitat types with increasing elevation. Testing these predictions for bacteria, fungi, plants, arthropods, and vertebrates, we found decreasing habitat specialization (represented by forest developmental stages) with elevation in mountain forests of the Northern Alps - supporting the altitudinal-niche-breadth hypothesis. Species richness decreased with elevation only for arthropods, whereas changes in beta diversity varied among taxa. Along the forest developmental gradient, species richness mainly followed a U-shaped pattern which remained stable along elevation. This highlights the importance of early and late developmental stages for biodiversity and indicates that climate change may alter community composition not only through distributional shifts along elevation but also across forest developmental stages.
{"title":"Effects of climate and forest development on habitat specialization and biodiversity in Central European mountain forests.","authors":"Tobias Richter, Lisa Geres, Sebastian König, Kristin H Braziunas, Cornelius Senf, Dominik Thom, Claus Bässler, Jörg Müller, Rupert Seidl, Sebastian Seibold","doi":"10.1038/s42003-024-07239-6","DOIUrl":"10.1038/s42003-024-07239-6","url":null,"abstract":"<p><p>Mountain forests are biodiversity hotspots with competing hypotheses proposed to explain elevational trends in habitat specialization and species richness. The altitudinal-niche-breadth hypothesis suggests decreasing specialization with elevation, which could lead to decreasing species richness and weaker differences in species richness and beta diversity among habitat types with increasing elevation. Testing these predictions for bacteria, fungi, plants, arthropods, and vertebrates, we found decreasing habitat specialization (represented by forest developmental stages) with elevation in mountain forests of the Northern Alps - supporting the altitudinal-niche-breadth hypothesis. Species richness decreased with elevation only for arthropods, whereas changes in beta diversity varied among taxa. Along the forest developmental gradient, species richness mainly followed a U-shaped pattern which remained stable along elevation. This highlights the importance of early and late developmental stages for biodiversity and indicates that climate change may alter community composition not only through distributional shifts along elevation but also across forest developmental stages.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"7 1","pages":"1518"},"PeriodicalIF":5.2,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11568152/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142638655","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-15DOI: 10.1038/s42003-024-07232-z
Johnny A Waters, Jan Bohatý, D Bradford Macurda
Echinoderms are a diverse phylum with a rich fossil record. The five extant classes of echinoderms are characterised by a pentameral (or pseudo-pentameral) symmetry, a water vascular system, a mesodermal skeleton of calcite stereom, and Mutable Collagenous Tissue (MCT), a unique type of connective tissue. Difficulties in tracing the geologic history of these traits complicates phylogenetic analyses of echinoderms. We present evidence herein of MCT in an extinct class of echinoderms, the Blastoidea. Blastoids have composite hair-like structures, brachioles, which formed a feeding filtration fan. Rare specimens from the Devonian of Germany demonstrate the presence of MCT by preserving brachioles as long rigid structures making a feeding fan with MCT in a rigid state. Specimens show brachioles in different configurations in the same specimen, which may indicate nervous control of MCT in individual brachioles. Other specimens appear to indicate the transition of MCT from a rigid to a compliant state as rigid brachioles begin to curve. Still other specimens show a majority of brachioles as limp hair-like structures swept by currents while a minority of brachioles remain rigid. These remarkable specimens could capture MCT transitioning from its rigid to compliant states in individual specimens indicating rapid burial and preservation.
{"title":"Feeding postures as indicators of mutable collagenous tissue in extinct echinoderms.","authors":"Johnny A Waters, Jan Bohatý, D Bradford Macurda","doi":"10.1038/s42003-024-07232-z","DOIUrl":"10.1038/s42003-024-07232-z","url":null,"abstract":"<p><p>Echinoderms are a diverse phylum with a rich fossil record. The five extant classes of echinoderms are characterised by a pentameral (or pseudo-pentameral) symmetry, a water vascular system, a mesodermal skeleton of calcite stereom, and Mutable Collagenous Tissue (MCT), a unique type of connective tissue. Difficulties in tracing the geologic history of these traits complicates phylogenetic analyses of echinoderms. We present evidence herein of MCT in an extinct class of echinoderms, the Blastoidea. Blastoids have composite hair-like structures, brachioles, which formed a feeding filtration fan. Rare specimens from the Devonian of Germany demonstrate the presence of MCT by preserving brachioles as long rigid structures making a feeding fan with MCT in a rigid state. Specimens show brachioles in different configurations in the same specimen, which may indicate nervous control of MCT in individual brachioles. Other specimens appear to indicate the transition of MCT from a rigid to a compliant state as rigid brachioles begin to curve. Still other specimens show a majority of brachioles as limp hair-like structures swept by currents while a minority of brachioles remain rigid. These remarkable specimens could capture MCT transitioning from its rigid to compliant states in individual specimens indicating rapid burial and preservation.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"7 1","pages":"1516"},"PeriodicalIF":5.2,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11568118/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142638656","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-15DOI: 10.1038/s42003-024-07187-1
Satyabrata Parida, Kimberly Yurasits, Victoria E Cancel, Maggie E Zink, Claire Mitchell, Meredith C Ziliak, Audrey V Harrison, Edward L Bartlett, Aravindakshan Parthasarathy
Current tests of hearing fail to diagnose pathologies in ~10% of patients seeking help for hearing difficulties. Neural ensemble responses to perceptually relevant cues in the amplitude envelope, termed envelope following responses (EFR), hold promise as an objective diagnostic tool to probe these 'hidden' hearing difficulties. But clinical translation is impeded by current measurement approaches involving static amplitude modulated (AM) tones, which are time-consuming and lack optimal spectrotemporal resolution. Here we develop a framework to rapidly measure EFRs using dynamically varying AMs combined with spectrally specific analyses. These analyses offer 5x improvement in time and 30x improvement in spectrotemporal resolution, and more generally, are optimal for analyzing time-varying signals with known spectral trajectories of interest. We validate this approach across several mammalian species, including humans, and demonstrate robust responses that are highly correlated with traditional static EFRs. Our analytic technique facilitates rapid and objective neural assessment of temporal processing throughout the brain that can be applied to track auditory neurodegeneration using EFRs, as well as tracking recovery after therapeutic interventions.
{"title":"Rapid and objective assessment of auditory temporal processing using dynamic amplitude-modulated stimuli.","authors":"Satyabrata Parida, Kimberly Yurasits, Victoria E Cancel, Maggie E Zink, Claire Mitchell, Meredith C Ziliak, Audrey V Harrison, Edward L Bartlett, Aravindakshan Parthasarathy","doi":"10.1038/s42003-024-07187-1","DOIUrl":"10.1038/s42003-024-07187-1","url":null,"abstract":"<p><p>Current tests of hearing fail to diagnose pathologies in ~10% of patients seeking help for hearing difficulties. Neural ensemble responses to perceptually relevant cues in the amplitude envelope, termed envelope following responses (EFR), hold promise as an objective diagnostic tool to probe these 'hidden' hearing difficulties. But clinical translation is impeded by current measurement approaches involving static amplitude modulated (AM) tones, which are time-consuming and lack optimal spectrotemporal resolution. Here we develop a framework to rapidly measure EFRs using dynamically varying AMs combined with spectrally specific analyses. These analyses offer 5x improvement in time and 30x improvement in spectrotemporal resolution, and more generally, are optimal for analyzing time-varying signals with known spectral trajectories of interest. We validate this approach across several mammalian species, including humans, and demonstrate robust responses that are highly correlated with traditional static EFRs. Our analytic technique facilitates rapid and objective neural assessment of temporal processing throughout the brain that can be applied to track auditory neurodegeneration using EFRs, as well as tracking recovery after therapeutic interventions.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"7 1","pages":"1517"},"PeriodicalIF":5.2,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11568220/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142638657","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The Pacific saury (Cololabis saira) is a pelagic fish commonly found in the North Pacific Ocean. Its population diversity and migratory lifestyle have long captured global attention. Despite the inherent complexity of the C. saira genome, characterized by extremely high heterozygosity, we successfully assembled a phased chromosome-level genome. The genome analysis revealed the expansion and natural selection of numerous functional genes, likely contributing to its enduring and extensive migratory lifestyle. Notably, gpr35 and igh genes showed significant expansion in the C. saira genome, potentially associated with regulating the immune response against environmental parasites and pathogens. Moreover, genes involved in DNA repair/replication and peroxisome function, including atm, ercc6, pex14, and pex16, displayed evidence of positive selection. Based on genome-sequencing of 80 individuals from eight sampling sites, we demonstrated that the genomic divergence among C. saira populations is relatively low. However, the sampling sites could be grouped into two distinct clusters, roughly corresponding to the migratory route of C. saira. This suggests a possible genome-wide divergence for C. saira within the open ocean region. Furthermore, the trmu gene, responsible for controlling otolith development and sharpness, exhibited differentiation between the two groups, consistent with previously reported differences in otolith morphology. This study has provided a reference genome and insights into the evolution, ecology, and conservation of Pacific saury and closely-related species. Phased chromosome-level genome provides insights into the molecular adaptation for enduring and extensive migratory lifestyle and population diversity for Pacific saury.
太平洋秋刀鱼(Cololabis saira)是一种常见于北太平洋的中上层鱼类。长期以来,它的种群多样性和洄游生活方式一直吸引着全球的目光。尽管太平洋秋刀鱼基因组本身非常复杂,杂合度极高,但我们还是成功地组装了一个分阶段的染色体级基因组。基因组分析揭示了大量功能基因的扩增和自然选择,这可能是其持久而广泛的迁徙生活方式的原因。值得注意的是,gpr35 和 igh 基因在 C. saira 基因组中有显著扩增,可能与调节对环境寄生虫和病原体的免疫反应有关。此外,参与 DNA 修复/复制和过氧物酶体功能的基因,包括 atm、ercc6、pex14 和 pex16,也显示出正选择的证据。通过对来自八个采样点的 80 个个体进行基因组测序,我们发现赛拉蛙种群间的基因组差异相对较小。然而,采样点可分为两个不同的群组,大致与 C. saira 的迁徙路线相对应。这表明在公海区域内,西拉鱼可能存在全基因组的分化。此外,负责控制耳石发育和尖锐度的 trmu 基因在两组之间表现出分化,这与之前报道的耳石形态差异一致。这项研究为太平洋秋刀鱼及其近缘物种的进化、生态学和保护提供了参考基因组和见解。
{"title":"Phased chromosome-level genome provides insights into the molecular adaptation for migratory lifestyle and population diversity for Pacific saury, Cololabis saira","authors":"Yang Liu, Yanping Luo, Penghao Wang, Wenjia Li, Hao Tian, Chang Cao, Zhiqiang Ye, Hongan Long, Tongtong Lin, Shengjun Wang, Xiaohui Yuan, Shijun Xiao, Yoshiro Watanabe, Yongjun Tian","doi":"10.1038/s42003-024-07126-0","DOIUrl":"10.1038/s42003-024-07126-0","url":null,"abstract":"The Pacific saury (Cololabis saira) is a pelagic fish commonly found in the North Pacific Ocean. Its population diversity and migratory lifestyle have long captured global attention. Despite the inherent complexity of the C. saira genome, characterized by extremely high heterozygosity, we successfully assembled a phased chromosome-level genome. The genome analysis revealed the expansion and natural selection of numerous functional genes, likely contributing to its enduring and extensive migratory lifestyle. Notably, gpr35 and igh genes showed significant expansion in the C. saira genome, potentially associated with regulating the immune response against environmental parasites and pathogens. Moreover, genes involved in DNA repair/replication and peroxisome function, including atm, ercc6, pex14, and pex16, displayed evidence of positive selection. Based on genome-sequencing of 80 individuals from eight sampling sites, we demonstrated that the genomic divergence among C. saira populations is relatively low. However, the sampling sites could be grouped into two distinct clusters, roughly corresponding to the migratory route of C. saira. This suggests a possible genome-wide divergence for C. saira within the open ocean region. Furthermore, the trmu gene, responsible for controlling otolith development and sharpness, exhibited differentiation between the two groups, consistent with previously reported differences in otolith morphology. This study has provided a reference genome and insights into the evolution, ecology, and conservation of Pacific saury and closely-related species. Phased chromosome-level genome provides insights into the molecular adaptation for enduring and extensive migratory lifestyle and population diversity for Pacific saury.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":" ","pages":"1-13"},"PeriodicalIF":5.2,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42003-024-07126-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142616280","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}