niche modeling

Pseudomonas aeruginosa is a cause of chronic respiratory tract infections in people with cystic fibrosis (CF), non-CF bronchiectasis and chronic obstructive pulmonary disease. Prolonged infection allows accumulation of mutations and horizontal gene transfer, increasing the likelihood of adaptive phenotypic traits. Adaptation is proposed to arise first in bacterial populations colonising upper airway environments. Here, we model this process using an experimental evolution approach. P. aeruginosa PAO1, which is not airway adapted, was serially passaged, separately, in media chemically reflective of upper or lower airway environments...

Phthorimaea operculella is a major potato pest of global importance, early warning and detection of which are of significance. In this study, we analyzed the climate niche conservation of P. operculella during its invasion by comparing the overall climate niche from three dimensions, including the differences between native range (South America) and entire invaded region (excluding South America), the differences bwtween native range (South America) and five invaded continents (North America, Oceania, Asia, Africa, and Europe), as well as the differences between native region (South America) and an invaded region (China)...

Vibrio is a salt-tolerant heterotrophic bacterium that occupies an important ecological niche in marine environments. However, little is known about the contribution of resource diversity to the marine Vibrio diversity and community stability. In this study, we investigated the association among resource diversity, taxonomic diversity, phylogenetic diversity, and community stability of marine Vibrio in the Beibu Gulf. V. campbellii and V. hangzhouensis were the dominant groups in seawater and sediments, respectively, in the Beibu Gulf...

Structurally complex corn bran arabinoxylan (CAX) was used as a model glycan to investigate gut bacteria growth and competition on different AX-based fine structures. Nine hydrolyzate segments of the CAX polymer varying in chemical structure (sugars and linkages), CAX, five less complex non-corn arabinoxylans, and xylose and glucose were ranked from structurally complex to simple. The substrate panel promoted different overall growth and rates of growth of eight Bacteroides xylan-degrading strains. For example, Bacteroides cellulosilyticus DSM 14838 ( Bacteroides cellulosilyticus ) grew well on an array of complex and simple structures, while Bacteroides ovatus 3-1-23 grew well only on the simple structures...

UNLABELLED: Local immune processes within aging tissues are a significant driver of aging associated dysfunction, but tissue-autonomous pathways and cell types that modulate these responses remain poorly characterized. The cytosolic DNA sensing pathway, acting through cyclic GMP-AMP synthase (cGAS) and Stimulator of Interferon Genes (STING), is broadly expressed in tissues, and is poised to regulate local type I interferon (IFN-I)-dependent and independent inflammatory processes within tissues...

UNLABELLED: Multiple myeloma (MM), a cancer of bone marrow plasma cells, is the second-most common hematological malignancy. However, despite immunotherapies like chimeric antigen receptor (CAR)-T cells, relapse is nearly universal. The bone marrow (BM) microenvironment influences how MM cells survive, proliferate, and resist treatment. Yet, it is unclear which BM niches give rise to MM pathophysiology. Here, we present a 3D microvascularized culture system, which models the endosteal and perivascular bone marrow niches, allowing us to study MM-stroma interactions in the BM niche and model responses to therapeutic CAR-T cells...

PREMISE: Functional traits reflect species' responses to environmental variation and the breadth of their ecological niches. Fagus grandifolia and Oreomunnea mexicana have restricted distribution in upper montane cloud forests (1700-2000 m a.s.l.) in Mexico. These species were introduced into plantings at lower elevations (1200-1600 m a.s.l.) that have climates predicted for montane forests in 2050 and 2070. The aim was to relate morphological leaf traits to the ecological niche structure of each species...

Poleward range expansion of marine organisms is commonly attributed to anthropogenic ocean warming. However, the extent to which a single species can migrate poleward remains unclear. In this study, we used molecular data to examine the current distribution of the Pocillopora damicornis species complex in Taiwan waters and applied niche modeling to predict its potential range through the end of the 21st Century. The P. damicornis species complex is widespread across shallow, tropical and subtropical waters of the Indo-Pacific regions...

BACKGROUND: The U.S. antibiotic market failure has threatened future innovation and supply. Understanding when and why clinicians underutilize recently approved gram-negative antibiotics might help prioritize the patient in future antibiotic development and potential market entry rewards. OBJECTIVE: To determine use patterns of recently U.S. Food and Drug Administration (FDA)-approved gram-negative antibiotics (ceftazidime-avibactam, ceftolozane-tazobactam, meropenem-vaborbactam, plazomicin, eravacycline, imipenem-relebactam-cilastatin, and cefiderocol) and identify factors associated with their preferential use (over traditional generic agents) in patients with gram-negative infections due to pathogens displaying difficult-to-treat resistance (DTR; that is, resistance to all first-line antibiotics)...

Here we use population genomic data (ddRAD-Seq) and ecological niche modeling to test biogeographic hypotheses for the divergence of the island-endemic cactus species Cereus insularis Hemsl. (Cereeae; Cactaceae) from its sister species C. fernambucensis Lem. The Cereus insularis grows in the Fernando de Noronha Islands (FNI), a Neotropical archipelago located 350 km off the Brazilian Atlantic Forest (BAF) coast. Phylogeographic reconstructions support a northward expansion by the common ancestor of C...

Phenotypic plasticity can be adaptive in fluctuating environments by providing rapid environment-phenotype matching and this applies particularly in seasonal environments. African Bicyclus butterflies have repeatedly colonized seasonal savannahs from ancestral forests around the Late Miocene and many species now exhibit seasonal polyphenism. On a macroevolutionary scale, it can be expected that savannah species will exhibit higher plasticity due to them experiencing stronger environmental seasonality than forest species...

AbstractThe nonrandom association between landscape characteristics and the dominant life history strategies observed in species pools is a typical pattern in nature. Here, we argue that these associations determine predictable changes in the relative importance of assembly mechanisms along broadscale geographic gradients (i.e., the geographic context of metacommunity dynamics). To demonstrate that, we employed simulation models in which groups of species with the same initial distribution of niche breadths and dispersal abilities interacted across a wide range of landscapes with contrasting characteristics...

Species-to-species and species-to-environment interactions are key drivers of community dynamics. Disentangling these drivers in species-rich assemblages is challenging due to the high number of potentially interacting species (the 'curse of dimensionality'). We develop a process-based model that quantifies how intraspecific and interspecific interactions, and species' covarying responses to environmental fluctuations, jointly drive community dynamics. We fit the model to reef fish abundance time series from 41 reefs of Australia's Great Barrier Reef...

Animal and human dirofilariosis is a vector-borne zoonotic disease, being one of the most important diseases in Europe. In Serbia, there are extensive studies reporting the presence of Dirofilaria immitis and D. repens , mainly in the north of the country, where the human population is concentrated and where there is a presence of culicid mosquitoes that transmit the disease. Ecological niche modeling (ENM) has proven to be a very good tool to predict the appearance of parasitosis in very diverse areas, with distant orography and climatologies at a local, continental, and global level...

Rock hind (Epinephelus adscensionis) and spotted moray (Gymnothorax moringa) are ubiquitous mesopredators that co-occur in the nearshore waters of Ascension Island in the South Atlantic Ocean, where they have significant cultural and subsistence value, but management of their non-commercial take is limited. This isolated volcanic system is home to high biomass and low species diversity, which poses two key questions: How can two mesopredators that perform similar ecological roles coexist? And if these two species are so ecologically similar, can they be managed using the same approach? Here, we combined acoustic telemetry, stomach content analysis, and stable isotope analysis to (i) explore space use and diet choices within and between these two species and (ii) to assess appropriate species-specific management options...

Bursaphelenchus xylophilus (Steiner&Buhrer) Nickle is a global quarantine pest that causes devastating mortality in pine species. The rapid and uncontrollable parasitic spread of this organism results in substantial economic losses to pine forests annually. In this study, we used the MaxEnt model and GIS software ArcGIS10.8 to predict the distribution of B. xylophilus based on collected distribution points and 19 environmental variables (with a correlation coefficient of|R| > 0.8) for the contemporary period (1970-2000), 2041-2060 (2050s), 2061-2080 (2070s), and 2081-2100 (2090s) under four shared socioeconomic pathways (SSPs)...

Although several phylogeographic studies of Asian snakes have been conducted, most have focused on pitvipers, with non-venomous snakes, such as colubrids or natricids, remaining poorly studied. The Chinese keelback water snake ( Trimerodytes percarinatus Boulenger) is a widespread, semiaquatic, non-venomous species occurring in China and southeastern Asia. Based on mitochondrial DNA (mtDNA) and single nucleotide polymorphism (SNP) data, we explored the population genetic structure, genetic diversity, and evolutionary history of this species...

Species distribution and resource utilization are a fundamental aspect of ecology. By analyzing the tree space usage by birds and determining the species composition of birds across different parts of trees, our study could shed light on the mechanisms shaping co-occurrence patterns in bird communities. Therefore, our study aimed to determine the species composition of birds across different parts of trees. We investigated whether species richness differs between positions on a tree and how these positions influence the probability of occurrence of the 10 most frequently observed bird species...

Cancer stem cells (CSCs), which are critical targets for cancer therapy as they are involved in drug resistance to anticancer drugs, and metastasis, are maintained by angiocrine factors produced by particular niches that form within tumor tissue. Secreted frizzled-related protein 1 (Sfrp1) is an extracellular protein that modulates Wnt signaling. However, the cells that produce Sfrp1 in the tumor environment and its function remain unclear. We aimed to elucidate angiocrine factors related to CSC maintenance, focusing on Sfrp1...

High-elevation arid regions harbor microbial communities reliant on metabolic niches and flexibility to survive under biologically stressful conditions, including nutrient limitation that necessitates the utilization of atmospheric trace gases as electron donors. Geothermal springs present "oases" of microbial activity, diversity, and abundance by delivering water and substrates, including reduced gases. However, it is unknown whether these springs exhibit a gradient of effects, increasing the spatial reach of their impact on trace gas-oxidizing microbes in the surrounding soils...