Biological Communities Research Articles

Restoring historical grasslands in a desert national park: Resilience or unrecoverable states in an emerging climate?

Ecosystems that supported multiple biological communities during the Holocene and that form alternative stable states pose challenges for identifying appropriate and feasible target communities for ecological restoration and conservation strategies for climate adaptation. In the Chihuahuan Desert, shrubland and perennial grassland alternatively dominated for millennia. However, grassland declined beginning 100–150 years ago during concomitant change in both climate and anthropogenic land use, making it unclear whether restoring grassland is appropriate or feasible in the emerging climate. In Guadalupe Mountains National Park, Texas, USA, we characterized remnant grasslands and performed experiments including outplanting and shrub reduction to assess feasibility and techniques for restoring desert grassland. In remnant patches, grass cover was more temporally variable than shrub cover, as grass cover varied 1.5× between years. Survival of outplanted grasses, either under Larrea tridentata shrubs or in the open with or without woody material encircling outplants for protection, was high (95 %) after seven months but declined to 2 % after 19 months. Response of perennial grass cover was variable after shrub and litter removal on soil surfaces varying in stoniness. Results suggest that 1) restoration can increase native desert grasses but gains may be intermittent; 2) reducing shrubs to facilitate natural expansion of remnant grasses and propagules may be more effective than outplanting grasses; and 3) restoring native grassland by reducing shrubs appears feasible even in dry conditions projected for the emerging climate. Findings that native grasses can increase at least intermittently suggest that practitioners have multiple candidate communities for conservation management and climate change adaptation as grassland, shrubland, and mixed communities each provide unique habitat.

Diatom and macroinvertebrate communities dynamic: A co-occurrence pattern analysis on plastic substrates

Wetlands are habitats that provide numerous ecosystem services, but are often understudied and threatened by anthropogenic pollution, particularly plastic pollution. Macroplastics are a significant component of plastic litter that have high biological impacts but are often understudied. Previous studies have highlighted negative impacts on biota, but there is a lack of information about the communities of micro and macro organisms that settle on macroplastic litter. In this context, we investigated the colonization patterns and community structures of diatoms and macroinvertebrates on virgin substrates composed of two different plastic polymers, polystyrene and polyethylene terephthalate, located at two different depths in a protected wetland in Central Italy over a period of 10 months. The results show that diatom community is not highly structured by competitive forces and aggregation patterns emerges. In contrast, macroinvertebrate community appears to be randomly structured, without the presence of patterns following specific assembly rules. Randomness in macroinvertebrates assemblages could highlight the presence of different niches available for settlement of different taxa. Combined matrix analyses show that diatoms and macroinvertebrates co-occur, and their community assemblages are sometimes structured, while they appeared to be randomly assembled at other times. Whenever non-randomness of diatoms and macroinvertebrates co-occurrences was detected, it suggested aggregation. Moreover, the possible predatory relationship between different macroinvertebrates taxa should be investigated, as it could reveal important scenarios in the establishment of macroinvertebrate structured communities on plastic litter, including taxa that exploit different ecological niches. This could lead to an enrichment of the biological community within areas impacted by plastics.

Structural and functional diversity patterns of macrofaunal communities from a semi-enclosed inlet of Northeast Atlantic: The influence of environmental conditions

Comprehending the mechanisms and circumstances responsible for the dynamics of biological communities is a fundamental step for predicting responses to environmental changes as well as efficient conservation and management efforts. Macrofaunal assemblages support a wide range of ecosystem services, serving as integral components of the biogeochemical cycle. Here, we examine the structure of the subtidal macrofaunal community in a semi-enclosed bay system located in the Northeast Atlantic. Employing a functional approach, our aim is to understand the interplay between water depth, geographical position, colonisation development and the communities. Our findings did not reveal the influence of water depth (range of 4 m–12 m) on the functional structures of the communities. Instead, only significant differences were demonstrated for ‘time of colonisation’ and ‘site’. The community with 1 month of colonisation presented limited functional diversity lacking overall ecological resilience. It was mainly characterised by ‘small-sized’, ‘short-lived’, ‘mobile’, and ‘deposit-feed’ organisms indicating an incipient state of development. Communities Site 2 and Site 3 revealed significant differences in the functional structure of the communities. They exhibited similar levels of functional diversity, yet significant differences emerged in the Biological Trait Analysis. Community Site 2 was characterised by ‘sessile’, ‘long-lived’, ‘large-sized’ ‘suspension feed’ while community Site 3 was characterised by ‘herbivore/grazer’, ‘tubicolous’, and ‘medium-lived’ organisms. Site 2 focuses on the transport of elements from pelagos to the benthos and from benthos to pelagos while Site 3 focus on the transport of elements within the benthos and from benthos to pelagos, and effectively contributes to decomposition and resuspension processes. Moreover, they differ in their sensitivity to disturbance, which suggests that their location in the Ría influences the functional composition of the communities. Understanding these patterns within this environment of significant ecological and economic importance holds profound implications for the effective preservation of ecosystem services.

Spatial and Temporal Characteristics of Winter Diel Vertical Migration of Zooplankton and Nekton in the East China Shelf Seas Based on Multi‐Frequency Echosounder

AbstractThe diel vertical migration (DVM) of plankton and nekton plays an important role in the energy flow and material cycling of marine ecosystems. Especially in shelf seas, seasonal environmental variations may distinguish DVM characteristics in winter mixed water from summer pattern. Therefore, to investigate the patterns and influencing factors of winter DVM in East China Shelf Seas (ECSS), we carried out comprehensive research based on high‐resolution multi‐frequency acoustic data during the winter of 2019/2020. The results showed that: (a) acoustic and zooplankton sampling data can effectively capture the widely existence of winter DVM of different biological community in ECSS and their spatio‐temporal variabilities. (b) In East China Sea, the migration was mainly dominated by the Gas‐bearing class (GB), which had fast migration speed, compared to the Yellow Sea where the migration was dominated by the Fluid‐like class (FL). In addition, GB descends earlier than FL. (c) For large scale factors, during the full moon, the GB will aggregate deeper and the FL shallower, compared to the new moon, and regional temperature is an important factor affecting the distribution of organisms at meridional direction; for small scale processes, cold and warm currents and ocean fronts can also affect migration behavior. In the muddy area with full moon and spring tide, GB and FL show different inconsistent migration compared to normal relatively consistent pattern. These results will help us to better understand the physiological, ecological and environmental elements that control winter DVM, facilitating the management of ecosystem‐based fisheries resources.

A plethora of rodents: Rattlesnake predators generate unanticipated patterns of venom resistance in a grassland ecosystem

Predation has the potential to impart strong selective pressures on organisms within their environments, resulting in adaptive changes in prey that minimize risk of predation. Pressures from venomous snakes present an exceptional challenge to prey, as venom represents a unique chemical arsenal evolutionarily tailored to incapacitate prey. In response, venom resistance has been detected in various snake prey species, and to varying degrees. This study analyzes venom resistance in an eastern Colorado grassland habitat, where the Prairie Rattlesnake (Crotalus viridis) and Desert Massasauga Rattlesnake (Sistrurus tergeminus edwardsii) co-occur with a suite of grassland rodents. We test for venom resistance across rodent and snake pairings using two geographically distant field sites to determine the role of 1) predation pressure and trophic ecology, and 2) sympatric and allopatric patterns of venom resistance. Resistance was measured using serum-based metalloproteinase inhibition assays to determine potential inhibition of proteolytic activity, augmented by median lethal dose (LD50) assays on rodent species to assess toxicity of crude venoms. Resistance is present in several rodent species, with strong resistance present in populations of Eastern Woodrat (Neotoma floridana), Ord's Kangaroo Rat (Dipodomys ordii), and Northern Grasshopper Mouse (Onychomys leucogaster). Resistance is less developed in other species, including the House Mouse (Mus musculus) and Plains Pocket Mouse (Perognathus flavescens). An unexpected differential is present, where Lincoln County Kangaroo Rats are highly resistant to venom of co-occurring Prairie Rattlesnakes yet are sensitive to an allopatric population of Prairie Rattlesnakes in Weld County. Lincoln Co. Northern Grasshopper Mice also demonstrate extremely elevated resistance to Weld Co. Prairie Rattlesnake venoms, and they may possess resistance mechanisms for myotoxin a, an abundant component of Weld Co. C. v viridis venoms. This study illustrates the complexity of venom resistance in biological communities that can exist when incorporating multiple species interactions. Future studies aimed at characterizing resistance mechanisms at the molecular level will provide a more detailed physiological context for understanding mechanisms by which resistance to venoms occurs.

Maximizing Societal Benefit Across Multiple Hyperspectral Earth Observation Missions: A User Needs Approach

AbstractImaging spectroscopy is a powerful tool used to support diverse Earth science and applications objectives, ranging from understanding and mitigating widespread impacts of climate change to management of water at farm‐scale. Community studies, such as those deployed by NASA's Surface Biology and Geology and ESA's Copernicus Hyperspectral Imaging Mission for the Environment, have offered new and tangible insights into user needs that are then incorporated into overall mission planning and design. These technologies and tools will be key to develop and consolidate downstream services for users and resource management, given the current pressures on the environment posed by climate change and population growth. This process has highlighted the degree to which planned mission capabilities are responsive to community needs. In this study, we analyze user requirements belonging to the Italian Copernicus User Forum and to the user pool of NASA's Surface Biology and Geology community for the synergic use of hyperspectral imaging technology, providing a reference for the development of earth observation services and the consolidation of existing ones. In addition, potential cross‐mission coordination is analyzed to highlight key benefits—(a) addressing shared community needs around products requiring more frequent temporal revisit and (b) shared resources and community expertise around algorithm development. This paper discusses the critical role of early engagement with users to establish a community of practice ready to work with high spatial resolution imaging spectroscopy data sets. The main outcome is a guide for the synergetic use of hyperspectral mission and data together with the identification of the main gaps between user needs and satellite capabilities influencing the development of key national and trans‐national downstream services.

On the De Novo Emergence of Ecological Interactions during Evolutionary Diversification: A Conceptual Framework and Experimental Test.

AbstractEcological interactions are crucial to the structure and function of biological communities, but we lack a causal understanding of the forces shaping their emergence during evolutionary diversification. Here we provide a conceptual framework linking different modes of diversification (e.g., ecological diversification), which depend on environmental characteristics, to the evolution of different forms of ecological interactions (e.g., resource partitioning) in asexual lineages. We tested the framework by examining the net interactions in communities of Pseudomonas aeruginosa produced via experimental evolution in nutritionally simple (SIM) or complex (COM) environments by contrasting the productivity and competitive fitness of whole evolved communities relative to their component isolates. As expected, we found that nutritional complexity drove the evolution of communities with net positive interactions whereas SIM communities had similar performance as their component isolates. A follow-up experiment revealed that high fitness in two COM communities was driven by rare variants (frequency <0.1%) that antagonized PA14, the ancestral strain and common competitor used in fitness assays. Our study suggests that the evolution of de novo ecological interactions in asexual lineages is predictable at a broad scale from environmental conditions. Further, our work demonstrates that rare variants can disproportionately impact the function of relatively simple microbial communities.

Analysis of population size of Pterygoplichthys multiradiatus and its intake of microplastics in streams with different land uses

Most freshwater habitats have been substantially affected by anthropogenic factors such as fish introductions, plastic pollution, and river regulation. Urban rivers are highly vulnerable to impacts associated with land use changes resulting from increasing urbanization, including altering habitat and establishing aquatic biological communities in these areas. In turn, the introduction of exotic species into sensitive and threatened ecosystems such as tropical urban streams and their rapid establishment, such as Pterygoplichthys multiradiatus, was used as an ecological model to determine the relative population size of the species. Also, the species was used to evaluate the presence of microplastics (MPs) in the gastrointestinal tract (GIT) of fish in rivers with different land use history. Our results showed significant differences in pleco abundance between areas with high and low urban (LU) development in the watersheds. The study demonstrated that abiotic environmental factors directly influence the relative abundance of plecos at the range and watershed scales. In a total of 42 fish examined, only 85.7% showed MPs retained in the GIT, with fibers and fragments being the most common. A total of 22 pieces of microplastic were identified with Nile Red staining by slide analysis. A significant difference was found between the abundance of microplastic ingested per total fish length between streams with high and LU development reaches. Therefore, in relatively small amounts, microplastic ingestion appears to be common in P. multiradiatus species, regardless of the habitat in which they are found and the diet present.

TubULAR: tracking in toto deformations of dynamic tissues via constrained maps.

A common motif in biology is the arrangement of cells into tubes, which further transform into complex shapes. Traditionally, analysis of dynamic tissues has relied on inspecting static snapshots, live imaging of cross-sections or tracking isolated cells in three dimensions. However, capturing the interplay between in-plane and out-of-plane behaviors requires following the full surface as it deforms and integrating cell-scale motions into collective, tissue-scale deformations. Here, we present an analysis framework that builds in toto maps of tissue deformations by following tissue parcels in a static material frame of reference. Our approach then relates in-plane and out-of-plane behaviors and decomposes complex deformation maps into elementary contributions. The tube-like surface Lagrangian analysis resource (TubULAR) provides an open-source implementation accessible either as a standalone toolkit or as an extension of the ImSAnE package used in the developmental biology community. We demonstrate our approach by analyzing shape change in the embryonic Drosophila midgut and beating zebrafish heart. The method naturally generalizes to in vitro and synthetic systems and provides ready access to the mechanical mechanisms relating genetic patterning to organ shape change.

Envisaging a global infrastructure to exploit the potential of digitised collections

Tens of millions of images from biological collections have become available online over the last two decades. In parallel, there has been a dramatic increase in the capabilities of image analysis technologies, especially those involving machine learning and computer vision. While image analysis has become mainstream in consumer applications, it is still used only on an artisanal basis in the biological collections community, largely because the image corpora are dispersed. Yet, there is massive untapped potential for novel applications and research if images of collection objects could be made accessible in a single corpus. In this paper, we make the case for infrastructure that could support image analysis of collection objects. We show that such infrastructure is entirely feasible and well worth investing in.

Workshop on 3D mapping of habitats and biological communities with underwater photogrammetry

For the past decades, photogrammetry has been increasingly used for monitoring spatial arrangement or temporal dynamics of submerged man-made structures and natural systems. As photogrammetry remains a nascent technique for data collection in the underwater environment, acquisition workflows have evolved constrained by specific methodological practicalities (e.g. euphotic environments vs. deep-sea waters). The annual GeoHab conference gathers a world-wide range of scientists interested in mapping and is, therefore, an adequate event to set up a state-of-the-art workshop on (underwater) photogrammetry. More specifically, a preliminary survey identified the overall lack of photogrammetry knowledge from the audience. A programme was conceptualised to explore within a day theoretical concepts, sampling design and practicalities and a wide range of case studies in various underwater environments. Furthermore, we provided manual training on data acquisition and processing. In overall, a post-survey demonstrated the audience’s satisfaction despite a remaining lack of confidence for implementing their own photogrammetry studies. As this workshop gathers a diversity of materials and a training relevant for a scientific audience, it sets the stage for a reproducible event and leaves room for future improvements. Finally, it provided relevant materials and discussions that enabled us to identify the aspects limiting photogrammetry methodology across scientific applications and institutes, in order to work towards standardisation.

Ephedra shrubs facilitate local arthropod communities in the Andean Puna: Implications for conservation and habitat restoration

In high-altitude deserts, the vegetation is spatially structured as a mosaic of patches with vegetation and interpatches of bare soil. Shrub patches create microhabitats that facilitate the persistence of other organisms by ameliorating climate extremes and increasing soil nutrients and moisture. Although this facilitative effect has been studied mainly on shrub understorey plants, the positive influence of desert shrubs may extend to the local arthropod community. In this study, we examined the hypothesis that plant facilitation by the desert shrub species Ephedra multiflora and E. breana positively influences the epigeal arthropod communities of the Andean Puna. We found that arthropod abundance, richness and diversity were all higher on Ephedra shrub microsites relative to paired open microsites. The harsh environmental conditions prevailing in the Puna ecosystems and the protection and resources provided by plants could jointly explain the positive influence of Ephedra shrubs over the arthropod community. The growth of tourism and the boom for lithium, as well as the increasing drought expected for the region under climate change scenarios, strengthens the importance of conserving shrub cover in these ecosystems to sustain biodiversity and ecosystem functioning. Our results are also relevant for restoration projects that consider the whole biological community, where using Ephedra as foundation shrubs to support desert endemics could be a strategy for land restoration.

Community assembly of the human piercing microbiome.

Predicting how biological communities respond to disturbance requires understanding the forces that govern their assembly. We propose using human skin piercings as a model system for studying community assembly after rapid environmental change. Local skin sterilization provides a 'clean slate' within the novel ecological niche created by the piercing. Stochastic assembly processes can dominate skin microbiomes due to the influence of environmental exposure on local dispersal, but deterministic processes might play a greater role within occluded skin piercings if piercing habitats impose strong selection pressures on colonizing species. Here we explore the human ear-piercing microbiome and demonstrate that community assembly is predominantly stochastic but becomes significantly more deterministic with time, producing increasingly diverse and ecologically complex communities. We also observed changes in two dominant and medically relevant antagonists (Cutibacterium acnes and Staphylococcus epidermidis), consistent with competitive exclusion induced by a transition from sebaceous to moist environments. By exploiting this common yet uniquely human practice, we show that skin piercings are not just culturally significant but also represent ecosystem engineering on the human body. The novel habitats and communities that skin piercings produce may provide general insights into biological responses to environmental disturbances with implications for both ecosystem and human health.

Protecting our streams by defining measurable targets for riparian management in a forestry context

Abstract Generally, governments and industry have implemented some degree of protection to reduce the impacts of forestry on aquatic ecosystems. Here, we consider the widespread application of streamside management in terms of riparian buffer retention to protect freshwaters from forestry practices across three jurisdictions with large and intensive forestry sectors (British Columbia, Finland and Sweden). This perspective was developed by working with researchers, practitioners and policymakers on mitigation measures to decrease the impacts of forestry on streams. We demonstrate that it is exceedingly rare for policies and guidelines to specify concrete objectives and measurable targets that can be assessed against riparian buffer management outcomes. Most often, policy objectives for riparian management prescribe ‘to prevent or mitigate impacts’, and this vagueness is insufficient to protect our waters. We argue that we should be clearer about the targets (outcomes) for riparian management and go beyond the simple idea that buffer presence, without further specification of its conditions, is always a successful protection strategy. One cannot measure the effectiveness of rules and guidelines without quantitative targets. Policy implications: In this paper, we suggest that locally developed and adjusted targets for riparian buffers must include quantifiable, measurable goals that specify what is supposed to be achieved and protected with respect to ecological functions, biological communities or other values. It should be relatively simple to move from current vague objectives such as ‘protect and prevent’ to a defined range of values for ecological parameters that buffers are supposed to provide. For example, these can include region‐specific shading levels and microclimate targets, large wood volumes, or riparian forest species composition. We stress that these targets must be developed through an open dialogue between agencies, practitioners, land owners and scientists. We acknowledge that there are trade‐offs between being too prescriptive and too vague. However, when excessively broad goals are the norm, we lose the capacity to effectively implement, monitor or evaluate the outcomes of protection measures.

On the spatiotemporal structures of ratio-dependent prey–predator model of ecological system

Ecological system is the interaction of biological community with other organisms and their physical environments. One of the important models is spatiotemporal prey–predator model of Michaelis–Menten-type functional response and reaction diffusion with constant harvest rate. This paper investigates the spatiotemporal structures of ratio-dependent prey and predator densities under different constraint conditions and suitable parameters. The [Formula: see text] model expansion technique is followed to extract these densities. The prey and predator densities behave differently depending on the diffusion coefficients and other parametric ratios. The 3D and 2D behavior of these densities are also plotted and observed. These results may help for better understanding to study the biological community in a real marine environment or ecological system.

From backyard to backcountry: changes in mammal communities across an urbanization gradient

Abstract Urbanization often results in biodiversity loss and homogenization, but this result is not universal and there is substantial variability in the spatiotemporal effects of urbanization on wildlife across cities and taxa. Areas with lower population and housing density are some of the fastest-growing regions in the western United States; thus, more research in these areas could offer additional insight into the effects of urbanization on wildlife and the potential importance of wild spaces in maintaining a diverse biotic community surrounding developed areas. To address this need, we conducted a study to identify the effects of urbanization (i.e. housing density) on mammals along a housing density gradient from wilderness to suburbia in Missoula, Montana. We deployed 178 motion-activated trail cameras at random sites within urban/suburban, exurban, rural, and wild regions from May to October 2019 to 2020. We identified all mammals &amp;gt;150 g, then evaluated how housing density influenced: (i) occupancy and (ii) species richness using multispecies occupancy models; (iii) relative abundance using Poisson models; and (iv) diel activity patterns using kernel density estimation and logistic regression. Urbanization was the strongest driver of mammal distribution, with a linear decline in mammal species richness as housing density increased. Urbanization also had strong effects on occupancy and detection rates, with larger-bodied mammals generally having stronger negative associations. Overall, mammal relative abundance was highest in suburban regions; however, this effect was largely driven by White-tailed Deer. Natural environmental factors explained most changes in mammal nocturnal activity; however, urbanization strongly affected nocturnality in some species, with Black Bear and White-tailed Deer becoming more nocturnal and Red Fox and Northern Raccoon becoming less nocturnal as housing density increased. While our study confirms that some mammals can live and thrive in developed areas, it emphasizes the importance of maintaining wild areas for those species that cannot.

Asynchronous multitrophic level regime shifts show resilience to lake browning

Lake browning is widespread due to increased supply of dissolved organic carbon under climate warming and nitrogen deposition. However, multitrophic level responses to lake browning are poorly understood. Our study aims to explore such responses across multitrophic levels based on sedimentary records of diatoms, chrysophyte stomatocysts and chironomids in a remote headwater lake in the Three Gorges Reservoir region, central China. Although all biotic proxies were analysed in the same core, the timing of shifts in chironomids (1886 ± 18 CE) preceded that in chrysophyte stomatocysts (∼1914 ± 10 CE) and diatoms (∼1941 ± 6 CE). Shifts in biotic communities were closely linked to rising temperature, δ15N depletion (a proxy for nitrogen deposition), δ13C enrichment (a proxy for littoral moss expansion), as well as biotic interactions, whereas the relative importance of the driving forces varied among the three biotic groups. Our results suggest that the zoobenthos grazing effect might be more important than bottom-up pathways in humic environments. Additionally, the coexistence of benthic, littoral and pelagic algae after the 1950s suggested that mixotrophic chrysophytes could reduce lake browning through heterotrophic processes and sustain the ecological equilibrium between littoral, pelagic and benthic productivity. Therefore, lake browning ecosystem regime shifts require analyses of multiple trophic levels. Our results suggest that heterotrophy may become more important in lake ecosystem carbon cycling with water brownification in Mulong Lake, as well as similar montane lakes.

An Ecoregional Conservation Assessment for Forests and Woodlands of the Mogollon Highlands Ecoregion, Northcentral Arizona and Southwestern New Mexico, USA

The Mogollon Highlands, Arizona/New Mexico, USA, spans a large biogeographical region of 11 biotic communities, 63 land cover types, and 7 ecoregions. This 11.3 M ha region has high levels of beta diversity across topo-edaphic gradients that span deserts to mountain tops. The main stressors affecting the region’s forests and woodlands include climate change, livestock grazing, and frequent mechanical removals of large amounts of forest biomass for fire concerns. We present an ecoregion conservation assessment for robust conservation area design that factors in appropriate wildfire response to protect communities from increasing threats of climate-induced wildfires spreading into urban areas. We focused mainly on maintaining connectivity for endangered focal species (grizzly bear (Ursus arctos horribilis) and Mexican wolf (Canis lupus baileyi)) along with protecting mature and old-growth (MOG) forests, Piñon (Pinus spp.)–Juniper (Juniperus spp.) Woodlands, and riparian areas. Over half the region is managed by federal agencies where new protected areas can be integrated with tribal co-management and prescribed burning, defensible space, and home hardening to protect communities from the growing threat of climate-induced wildfires. However, just 9% of the study area is currently protected, and even with the inclusion of proposed protected areas, only 24% would be protected, which is below 30 × 30 targets. The potential grizzly bear habitat, wolf habitat connectivity, and MOG forests (1.6 M ha (14.2%) of the study area; 18% protected) are concentrated mainly in the central and eastern portions of the MHE. There were 824 fires (2 to 228,065 ha) from 1984–2021, with 24% overlapping the wildland–urban interface. Regional temperatures have increased by 1.5 °C, with a 16% reduction in precipitation and stream flow since 1970 that under worst-case emission scenarios may increase temperatures another 3 to 8 °C by the century’s end. The unique biodiversity of the MHE can be better maintained in a rapidly changing climate via at least a three-fold increase in protected areas, co-management of focal species with tribes, and strategic use of fuel treatments nearest communities.

A simeprevir-inducible molecular switch for the control of cell and gene therapies

Chemical inducer of dimerization (CID) modules can be used effectively as molecular switches to control biological processes, and thus there is significant interest within the synthetic biology community in identifying novel CID systems. To date, CID modules have been used primarily in engineering cells for in vitro applications. To broaden their utility to the clinical setting, including the potential to control cell and gene therapies, the identification of novel CID modules should consider factors such as the safety and pharmacokinetic profile of the small molecule inducer, and the orthogonality and immunogenicity of the protein components. Here we describe a CID module based on the orally available, approved, small molecule simeprevir and its target, the NS3/4A protease from hepatitis C virus. We demonstrate the utility of this CID module as a molecular switch to control biological processes such as gene expression and apoptosis in vitro, and show that the CID system can be used to rapidly induce apoptosis in tumor cells in a xenograft mouse model, leading to complete tumor regression.

What happens when salinization meets eutrophication? A test using stream microcosms

Nutrient and salt pollution often co-occur in rivers and streams due to human activities (e.g., agriculture, urbanization). Thus, understanding the interactive effects of nutrients and salinity on freshwater ecosystems is critical for environmental management. We experimentally assessed the interactive effects of nutrient and salt pollution on stream microcosms using biofilm and macroinvertebrates as model systems. Six treatments were performed in triplicate: control (C: N-NH4+ = 0.05; P- PO43− = 0.037; Cl- = 33.5 mg L−1), intermediate nutrient (IN: N-NH4+ = 0.4; P- PO43− = 0.271; Cl- = 33. 5 mg L−1), high nutrient (HN: N-NH4+ = 0.84; P- PO43− = 0.80; Cl- = 33.5 mg L−1), salt (S: N-NH4+ = 0.05; P- PO43− = 0.037; Cl- = 3000 mg L−1), salt with intermediate nutrient (SIN: N-NH4+ = 0.4; P- PO43− = 0.27; Cl- = 3000 mg L−1) and salt with high nutrient (SHN: N-NH4+ = 0.84; P- PO43− = 0.80; Cl- = 3000 mg L−1). After 14 days of exposure, biofilm chlorophyll-a increased across all treatments, with cyanobacteria replacing diatoms and green algae. Treatments with no added nutrients (C and S) had more P uptake capacity than the rest. The indicator species analysis showed 8 significant taxa, with Orthocladius (Orthocladius) gr. Wetterensis and Virganytarsus significantly associated with the salinity treatment. Overall, salt pollution led to a very strong decline in macroinvertebrate richness and diversity. However, salt toxicity seemed to be ameliorated by nutrient addition. Finally, both structural equation models and biotic-abiotic interaction networks showed that complex biological interactions could be modulating the response of the biological communities to our treatments. Thus, our study calls for species-level assessments of salt and nutrient effects on river ecosystems and advocates for better management of co-occurring pollutants.