Niche Development Research Articles

Distinct Microbial Communities in the Soils, Waters, and Speleothems of a Hyperalkaline Cave System

AbstractCaves are complex ecosystems with various microbial habitats. Understanding the individual community structures in the key source environments (soils, waters) and those in the sinks (speleothems, cave muds) can help elucidate the extent to which in‐cave communities are a function of their source communities, or if they can successfully adapt and diversify locally. Here, we assess the network of microbial communities existing within a unique British cave system. Poole's Cavern is characterized by alkalinity or even hyperalkalinity (pH > 9) in its drip waters, creating a series of challenging ecological niches for microbes to survive. Samples of soil, drip water, speleothem, and cave sediment were collected for chemical characterization, cell culture assays and DNA sequencing analysis. We show that microbial abundance and diversity were highest in the soils proximal to the cave, and the microbiotas of the hyperalkaline cave chamber were less abundant and less diverse than the cave chamber with lower pH. Proteobacteria and Planctomycetota were the most prevalent bacterial phyla throughout the cave system irrespective of pH, indicating their members are comparatively more metabolically versatile. Predicted essential metabolic pathways were still dominant within all sampling sites, and microorganisms were shown to be capable of utilizing various inorganic or simple organic compounds to survive. Interestingly, co‐occurrence between Poole's samples was limited, never demonstrating more than 50% similarity. This work highlights the diversity of microbial communities within this extreme environment and the development of microbial niches which reflects the adaptation strategy of microorganisms under alkaline‐hyperalkaline conditions.

Mimicry of embryonic circulation enhances the hoxa hemogenic niche and human blood development

Precursors of the adult hematopoietic system arise from the aorta-gonad-mesonephros (AGM) region shortly after the embryonic circulation is established. Here, we develop a microfluidic culture system to mimic the primitive embryonic circulation and address the hypothesis that circulatory flow and shear stress enhance embryonic blood development. Embryonic (HOXA+) hematopoiesis was derived from human pluripotent stem cells and induced from mesoderm by small-molecule manipulation of TGF-β and WNT signaling (SB/CHIR). Microfluidic and orbital culture promoted the formation of proliferative CD34+RUNX1C-GFP+SOX17-mCHERRY+ precursor cells that were released into the artificial circulation from SOX17+ arterial-like structures. Single-cell transcriptomic analysis delineated extra-embryonic (yolk sac) and HOXA+ embryonic blood differentiation pathways. SB/CHIR and circulatory flow enhance hematopoiesis by the formation of proliferative HOXA+RUNX1C+CD34+ precursor cells that differentiate into monocyte/macrophage, granulocyte, erythrocyte, and megakaryocyte progenitors.

Analysis of the barriers to implementing building integrated photovoltaics in Singapore using an interpretive structural modelling approach

Due to global climate change, building-integrated photovoltaics (BIPV) have been recognized as an effective solution to reduce the dependence on fossil fuels and achieve nearly zero-energy buildings. Nevertheless, BIPV implementation remains a niche development. Various studies have discussed the barriers to BIPV implementation. However, very few studies have endeavoured to investigate the complex interrelationships among the barriers to BIPV implementation in Singapore. In this study, the barriers to BIPV implementation in Singapore are first addressed by a literature review and then verified by local academics and industry experts. Additionally, the interpretive structural modelling (ISM) approach is deployed to investigate the contextual interrelationships among the identified barriers. Then, a hierarchical structure of the barriers is developed through the ISM method, and the barriers are categorized by clusters, with cross-impact matrix multiplication applied to the classification technique. In addition to the economic-related issues proposed by previous research, which has concentrated on nonspecific BIPV implementation barriers, the findings show that the lack of professionals and the absence of cost-effective BIPV products and design tools should be given specific attention for BIPV implementation in Singapore. The findings offer valuable information on the overall structure and interrelationships among the barriers to Singapore's BIPV industry, and a three-step plan for unlocking the potential of BIPV implementation is proposed. The findings also have implications for future research and for obtaining effective scientific and administrative solutions to facilitate BIPV deployment in Singapore.

Exploring the origin of the cancer stem cell niche and its role in anti-angiogenic treatment for glioblastoma

Cancer stem cells are thought to be the main drivers of tumorigenesis for malignancies such as glioblastoma (GBM). They are maintained through a close relationship with the tumor vasculature. Previous literature has well-characterized the components and signaling pathways for maintenance of this stem cell niche, but details on how the niche initially forms are limited. This review discusses development of the nonmalignant neural and hematopoietic stem cell niches in order to draw important parallels to the malignant environment. We then discuss what is known about the cancer stem cell niche, its relationship with angiogenesis, and provide a hypothesis for its development in GBM. A better understanding of the mechanisms of development of the tumor stem cell niche may provide new insights to potentially therapeutically exploit.

An interplay between cellular growth and atypical fusion defines morphogenesis of a modular glial niche in Drosophila

Neural stem cells (NSCs) live in an intricate cellular microenvironment supporting their activity, the niche. Whilst shape and function are inseparable, the morphogenetic aspects of niche development are poorly understood. Here, we use the formation of a glial niche to investigate acquisition of architectural complexity. Cortex glia (CG) in Drosophila regulate neurogenesis and build a reticular structure around NSCs. We first show that individual CG cells grow tremendously to ensheath several NSC lineages, employing elaborate proliferative mechanisms which convert these cells into syncytia rich in cytoplasmic bridges. CG syncytia further undergo homotypic cell–cell fusion, using defined cell surface receptors and actin regulators. Cellular exchange is however dynamic in space and time. This atypical cell fusion remodels cellular borders, restructuring the CG syncytia. Ultimately, combined growth and fusion builds the multi-level architecture of the niche, and creates a modular, spatial partition of the NSC population. Our findings provide insights into how a niche forms and organises while developing intimate contacts with a stem cell population.

РОССИЯ НА ЕВРОПЕЙСКОМ НЕФТЯНОМ РЫНКЕ: ВЫБОР ВЕКТОРА ГЕОПОЛИТИЧЕСКОГО РАЗВИТИЯ

It is expected that the fulfillment of obligations under the Paris Climate Agreement (2015) by 2035 will lead to a sharp drop in global oil demand. However, today, for the countries of the European Union (EU), the shortage of energy carriers and the high dependence in their supply from external sources, especially from Russia, continues to be a serious problem. The purpose of the study is to consider changes in demand for Russian crude oil from the countries of the European Union (EU) and other European countries in the first half of 2022. The main factors determining the dynamics of the world oil market in recent decades are analyzed. The contribution of crude oil imports from Russia to the EU countries to meet their needs for fossil fuel sources, as well as to form the revenue side of the Russian budget in 2019-2021 has been determined. The regions of European countries with an increased demand for petroleum products have been identified. The level of dependence of different countries within the EU on the import of Russian oil is considered. The role of tanker and pipeline transport in the supply of Russian crude oil to the countries of Western Europe is revealed. For Russia, the export of fuel and energy resources is a geopolitical factor of power in the international system. Therefore, the narrowing of its positions in the traditional European energy markets with the introduction by the EU and UK authorities of an embargo on Russian oil prices necessitates both changes in the existing oil transportation strategies to European consumers and the active development of new niches in other external energy markets.

Islands as Playing and Breeding Grounds for Incumbents, Entrepreneurial Technologists, Policymakers, and Engaged Citizens: The Case of Energy Transition on Ameland

Increasingly, discussions on sustainability, in particular in relation to energy transition, are finding their way to the regional and local political arena. Although for analysing transition pathways on these sub-national scales, conceptual frameworks such as the multi-level perspective may be helpful, some issues remain relatively unaddressed: the relevance of citizens and their social networks and the precise interactions between place, the local context, and external conditions. This paper aims to better understand energy transition processes on the local and regional scale by analysing the case of the Dutch island of Ameland. Since 2006, Ameland has been on a sustainability pathway towards self-sufficiency, in particular in terms of reducing CO2 emissions. In this case study, we conducted in-depth empirical analysis, using a mixed-methods approach, including document analysis and ethnographic techniques. In a five-stage development process, a combination of place-related niche development, regime developments, and the involvement of citizens have created a protective space for several socio-technological innovations to emerge. The unique combination of specific local conditions, in particular political and cultural, and external influences, national policy, and ‘enlightened’ companies have shaped ideal conditions for Ameland to become an inspiring example of innovation in regional transition processes.

Assessing the niche development of carbon capture and storage through strategic niche management approach: The case of China

Carbon capture and storage (CCS) is an important strategic technology choice for the future reduction of greenhouse gas emissions, which plays a crucial role as part of an economically sustainable route. Although some studies have discussed CCS demonstration projects and early developments, CCS has not been investigated as an innovative niche for sustainable transition. In an attempt to fill this gap, this study studies CCS as an innovative niche and assess the niche development of CCS in China by using a strategic niche management (SNM) framework. The evolution of three interlinked niche processes (expectations, social networks and learning process) is analysed with a comprehensive analytical approach that includes policy, social network and bibliometric analysis. Results show that a CCS niche has formed in China, but it is at a relatively low level of niche development in terms of the three internal processes. The expectations for CCS evolved linearly and are constantly being reinforced. The actor network supporting CCS niche development is sparse, and network cohesion is gradually decreasing. CCS learning continues to deepen but remains insufficient; it focuses on technical aspects and provides little attention to policy and social issues. The results indicate that expectations have been well-established at various levels in China, but the network and the learning process still need to be improved. Our findings help to identify problems in the development of technology and provide useful references for technology planning and the further development of CCS.

Tumor cell-conditioned media drives collagen remodeling via fibroblast and pericyte activation in an in vitro premetastatic niche model

SummaryPrimary tumors secrete large quantities of cytokines and exosomes into the bloodstream, which are uptaken at downstream sites and induce a pro-fibrotic, pro-inflammatory premetastatic niche. Niche development is associated with later increased metastatic burden, but the cellular and matrix changes in the niche that facilitate metastasis are yet unknown. Furthermore, there is no current standard model to study this phenomenon. Here, biofabricated collagen and hyaluronic acid hydrogel models were employed to identify matrix changes elicited by pericytes and fibroblasts after exposure to colorectal cancer-secreted factors. Focusing on myofibroblast activation and collagen remodeling, we report fibroblast activation and pericyte stunting in response to tumor signaling. In addition, we characterize contributions of both cell types to matrix dysregulation via collagen degradation, deposition, and architectural remodeling. With these findings, we discuss potential impacts on tissue stiffening and vascular leakiness and suggest pathways of interest for future mechanistic studies of metastatic cell-premetastatic niche interactions.

Myeloid Derived Suppressor Cells Migrate in Response to Flow and Lymphatic Endothelial Cell Interaction in the Breast Tumor Microenvironment.

Simple SummaryMyeloid-derived suppressor cells (MDSCs) are a subset of immune cells that contribute to a pro-tumorigenic microenvironment, promoting immunosuppression in multiple tumors. In breast cancer, they have been mostly studied in pre-clinical mouse models. These models allow for examination of the development of pre-metastatic niches and immune infiltration at the primary tumor site, but are difficult to use to extricate complex intercellular signaling events and MDSC migration. Here, we describe the development of a breast tumor microenvironment model that includes primary-derived mouse MDSCs. We use this model to identify interactions that drive MDSC migration through both biophysical and cellular signaling events within the tumor microenvironment.At the site of the tumor, myeloid derived suppressor cells (MDSCs) infiltrate and interact with elements of the tumor microenvironment in complex ways. Within the invading tumor, MDSCs are exposed to interstitial fluid flow (IFF) that exists within the chronic inflammatory tumor microenvironment at the tumor–lymphatic interface. As drivers of cell migration and invasion, the link between interstitial fluid flow, lymphatics, and MDSCs have not been clearly established. Here, we hypothesized that interstitial fluid flow and cells within the breast tumor microenvironment modulate migration of MDSCs. We developed a novel 3D model to mimic the breast tumor microenvironment and incorporated MDSCs harvested from 4T1-tumor bearing mice. Using live imaging, we found that sorted GR1+ splenocytes had reduced chemotactic index compared to the unsorted population, but their speed and displacement were similar. Using our adapted tissue culture insert assay, we show that interstitial fluid flow promotes MDSC invasion, regardless of absence or presence of tumor cells. Coordinating with lymphatic endothelial cells, interstitial fluid flow further enhanced invasion of MDSCs in the presence of 4T1 cells. We also show that VEGFR3 inhibition reduced both MDSC and 4T1 flow response. Together, these findings indicate a key role of interstitial fluid flow in MDSC migration as well as describe a tool to explore the immune microenvironment in breast cancer.

Variation of food web structure in macrobenthic communities in low diversity system as determined by stable isotope-based community-wide metrics

Recognition of spatial and temporal variations of food webs is of fundamental importance for understanding ecological processes and biodiversity management. Changes in trophic organization alter routing patterns and dynamics of energy fluxes among ecosystem compartments and ultimately affect the ecosystem functioning. In this study, stable isotopes of carbon and nitrogen (δ13C and δ15N) were employed to define trophic niche and diversity as well as redundancy of four macrofaunal benthic communities in a low diversity, brackish system of the Puck Lagoon (southern Baltic Sea). The Bayesian mixing models were used to delineate community-wide metrics at different trophic levels. Benthic macrovegetation appeared to facilitate directly and indirectly development of different trophic niches for consumers by diversification of basic carbon resources and providing habitat structure. In habitat with dense vegetation, diverse food sources supported benthic fauna of different feeding modes. Communities from sandy bottom with low biomass of macrophytes showed compact food webs of lower trophic diversity. Reliance on one dominant resource (suspended particulate organic matter-SPOM, and phytoplankton) resulted here in simplification of food web structure with a large proportion of species with one feeding mode (suspension feeders). Widening of δ13C range (CR) and δ15N range (NR) in the cold season was related to the extended carbon isotope ratios of organic matter sources and the presence of omnivorous and carnivorous fish that migrated towards the shoreline. A decreased trophic diversity during a vegetative season (spring-summer) was attributed to a narrowed isotopic range of primary producers that incorporated isotopically similar biogenic substances. Geographical and seasonal differences of trophic structure highlighted important natural variation of benthic communities which can benefit ecological restoration programmes and biodiversity management of coastal and marine areas.

Integrating spatial transcriptomics with single-cell transcriptomics reveals a spatiotemporal gene landscape of the human developing kidney

BackgroundResearch on spatiotemporal gene landscape can provide insights into the spatial characteristics of human kidney development and facilitate kidney organoid cultivation. Here, we profiled the spatiotemporal gene programs of the human embryonic kidneys at 9 and 18 post-conception weeks (PCW) by integrating the application of microarray-based spatial transcriptomics and single-cell transcriptomics.ResultsWe mapped transcriptomic signatures of scRNA-seq cell types upon the 9 and 18 PCW kidney sections based on cell-type deconvolution and multimodal intersection analyses, depicting a spatial landscape of developing cell subpopulations. We established the gene characteristics in the medullary regions and revealed a strong mitochondrial oxidative phosphorylation and glycolysis activity in the deeper medullary region. We also built a regulatory network centered on GDNF-ETV4 for nephrogenic niche development based on the weighted gene co-expression network analysis and highlighted the key roles of Wnt, FGF, and JAG1-Notch2 signaling in maintaining renal branching morphogenesis.ConclusionsOur findings obtained by this spatiotemporal gene program are expected to improve the current understanding of kidney development.

The application of blockchain technology in smart sustainable energy business model

Blockchain technology is considered to be a disruptive technology that has real potential for change after steam engines, electricity, and the Internet. However, in terms of power generation, the current level of hydropower development in my country is only 39%. Compared with developed countries, there is still a big gap and a high development space. This article proposes a research on the application of blockchain technology in smart sustainable energy business models, studies the conversion path of sustainable energy systems, introduces integrated energy service blockchain technology, and builds a sustainable energy transition model. The selection of practical dimensions requires both Quantitative indicators also require cultural and behavioral qualitative indicators; finally, through the analysis of social development trends and government policies, the external variable landscape signals are parameterized. Sustainable energy rather than fossil energy is the energy of the future. Weak landscape signals have significantly weakened the development of the sustainable energy niche: the proportion of coal consumption has declined slowly. Although it has transformed from a system to a niche, it has always been higher than that of other energy types. Only with long-term landscape pressure, positive changes to sustainable energy technologies and infrastructure, and continuous changes in consumer preferences, can sustainable energy ultimately dominate.

Neisseria genes required for persistence identified via in vivo screening of a transposon mutant library.

The mechanisms used by human adapted commensal Neisseria to shape and maintain a niche in their host are poorly defined. These organisms are common members of the mucosal microbiota and share many putative host interaction factors with Neisseria meningitidis and Neisseria gonorrhoeae. Evaluating the role of these shared factors during host carriage may provide insight into bacterial mechanisms driving both commensalism and asymptomatic infection across the genus. We identified host interaction factors required for niche development and maintenance through in vivo screening of a transposon mutant library of Neisseria musculi, a commensal of wild-caught mice which persistently and asymptomatically colonizes the oral cavity and gut of CAST/EiJ and A/J mice. Approximately 500 candidate genes involved in long-term host interaction were identified. These included homologs of putative N. meningitidis and N. gonorrhoeae virulence factors which have been shown to modulate host interactions in vitro. Importantly, many candidate genes have no assigned function, illustrating how much remains to be learned about Neisseria persistence. Many genes of unknown function are conserved in human adapted Neisseria species; they are likely to provide a gateway for understanding the mechanisms allowing pathogenic and commensal Neisseria to establish and maintain a niche in their natural hosts. Validation of a subset of candidate genes confirmed a role for a polysaccharide capsule in N. musculi persistence but not colonization. Our findings highlight the potential utility of the Neisseria musculi-mouse model as a tool for studying the pathogenic Neisseria; our work represents a first step towards the identification of novel host interaction factors conserved across the genus.

Bringing a governance perspective to plastic litter: A structural analysis of the German PET industry

The challenge for a circular plastics economy transition is to focus policies on key leverage points that initiate actual system transitions. This requires a systemic perspective on the plastics industries. This study takes such a systemic perspective by employing a network approach to examine the often-underestimated complexity of interrelating markets in a circular plastics economy, and their structural sensitivity to governance interventions. Based on the case of polyethylene terephthalate (PET) markets in Germany, we investigate the structures and underlying dynamics of increasing circularity in the PET industry. Concerns about plastic litter accumulating in the natural environment have facilitated the development of niche markets for the recycling of plastic litter recovered from the environment. We systematically reveal that recycling markets connecting diverse waste sources with a broad range of new applications are key areas of intervention in the structural transitions towards circular industries. By connecting otherwise disconnected parts of the system, the recycling of recovered plastic litter is a key leverage point for the circular economy transition. We recommend to focus governance efforts on such key leverage markets as powerful venues to initiate systemic change.

The Regulation of Lymph Node Pre-Metastatic Niche Formation in Head and Neck Squamous Cell Carcinoma.

In many distinct forms of malignancies, there is a close relationship between lymph node (LN) metastases and further dissemination to distant organs, and this is a critical prognostic factor. At the beginning of the process, the original tumor secretes soluble substances or releases extracellular vesicles (EVs) that are carried through lymphatic channels to draining (sentinel) LN. The tumor-derived factors then drive LN remodeling. These significant alterations occur prior to the emergence of the first metastatic cell, bringing about the development of a pre-metastatic niche that allows metastatic cells to survive and thrive. In this review, we discuss current information available about the regulation of lymph node pre-metastatic niche in head and neck squamous cell carcinoma (HNSCC), and the role of EVs in forming the pre-metastatic niche.

A generalist–specialist trade-off between switchgrass cytotypes impacts climate adaptation and geographic range

Polyploidy results from whole-genome duplication and is a unique form of heritable variation with pronounced evolutionary implications. Different ploidy levels, or cytotypes, can exist within a single species, and such systems provide an opportunity to assess how ploidy variation alters phenotypic novelty, adaptability, and fitness, which can, in turn, drive the development of unique ecological niches that promote the coexistence of multiple cytotypes. Switchgrass, Panicum virgatum, is a widespread, perennial C4 grass in North America with multiple naturally occurring cytotypes, primarily tetraploids (4×) and octoploids (8×). Using a combination of genomic, quantitative genetic, landscape, and niche modeling approaches, we detect divergent levels of genetic admixture, evidence of niche differentiation, and differential environmental sensitivity between switchgrass cytotypes. Taken together, these findings support a generalist (8×)–specialist (4×) trade-off. Our results indicate that the 8× represent a unique combination of genetic variation that has allowed the expansion of switchgrass’ ecological niche and thus putatively represents a valuable breeding resource.

Exploring the role of extracellular vesicles and their protein cargo in lung cancer metastasis: A review.

Extracellular vesicles (EV) are membrane-enclosed structures of varying size released from all cells and contain a variety of cargo including proteins, lipids, and nucleic acids. They are postulated to play a pivotal role in cancer metastasis through delivery of oncogenic material to neighbouring and distant cells to promote development of a metastatic niche and tumour seeding. Here we reviewed protein data in relevant literature to determine whether specific proteins known to be involved in metastasis can be reliably identified in lung cancer EV, whether these proteins are important in all or specific lung cancers, and whether results from in-vitro cell studies are supported by research examining EV in human biofluids. Our analysis suggests that specific proteins may be more important for individual lung cancers, but interpretation of the literature is currently limited by a relative lack of research investigating EV proteins in some cancers and in clinical studies using biofluids.

Abnormal Development of Neural Stem Cell Niche in the Dentate Gyrus of Menkes Disease.

Background and ObjectivesMenkes disease (MNK) is a rare X-linked recessive disease, caused by mutations in the copper transporting ATP7A gene that is required for copper homeostasis. MNK patients experience various clinical symptoms including neurological defects that are closely related to the prognosis of MNK patients. Neural stem cells (NSCs) in the hippocampal dentate gyrus (DG) produce new neurons throughout life, and defects in DG neurogenesis are often correlated with cognitive and behavioral problems. However, neurodevelopmental defects in the DG during postnatal period in MNK have not been understood yet.Methods and ResultsMottled-brindled (MoBr/y) mice (MNK mice) and littermate controls were used in this study. In vivo microCT imaging and immunohistochemistry results demonstrate that blood vasculatures in hippocampus are abnormally decreased in MNK mice. Furthermore, postnatal establishment of NSC population and their neurogenesis are severely compromised in the DG of MNK mice. In addition, in vitro analyses using hippocampal neurosphere culture followed by immunocytochemistry and immunoblotting suggest that neurogenesis from MNK NSCs is also significantly compromised, corresponding to defective neurogenic gene expression in MNK derived neurons.ConclusionsOur study is the first reports demonstrating that improper expansion of the postnatal NSC population followed by significant reduction of neurogenesis may contribute to neurodevelopmental symptoms in MNK. In conclusion, our results provide new insight into early neurodevelopmental defects in MNK and emphasize the needs for early diagnosis and new therapeutic strategies in the postnatal central nerve system damage of MNK patients.

Examining the vehicle-to-grid niche in Australia through the lens of a trial project

Vehicle-to-grid is a promising source of the shallow storage needed for Australia’s energy transition. However, it is a niche innovation dependent on other new technologies. The paper describes the Australian vehicle-to-grid niche via examination of a trial and sets an agenda for niche development. The multi-level perspective provides understanding of the processes of socio-technical transitions and strategic niche management provides a tool for facilitating development and linking with policy. The study found that the Australian vehicle-to-grid niche is at an embryonic stage and is yet to stabilise into a dominant form. Variety and non-technical learning are lacking and expectations underestimate the significance of existing infrastructures and user factors as well as the scope of complementary technologies. Greater experimentation with users and installation premises are recommended, plus engaging more actors and intermediaries. The study concludes with directions for further research in multi-system interactions and transitions in importer countries like Australia.