Biology subjects

Altman, J.

Publications and source records attributed to Altman, J..

13 recordsLinked to original sources

bioRxiv2026

Fast and Reliable: Evaluating Smartphone LiDAR App for Stem Diameter Measurement and Tree Mapping

Tree inventories require rapid, accurate measurements of stem diameter at breast height (DBH) and precise tree locations to support monitoring, planning, and informed decision-making. We evaluated a smartphone-based LiDAR app (SBLA), Forest Scanner, against (i) a diameter tape for DBH and (ii) a Vertex ultrasonic device for spatial coordinates. Across DBH of 725 trees, the LiDAR closely matched diameter tape measurements: discrepancies >5 cm occurred in 10.5% and > 10 cm in 3.5% of trees. Errors were concentrated in trees with smaller DBH, where occasional overestimation by SBLA arose from point-cloud misfitting. For medium and large trees, agreement was consistently high. Tree coordinates from SBLA and the ultrasonic device were broadly comparable at fine scales. Field efficiency was substantially improved: a 1,000 m2 plot with 70-80 trees required [~]2 hours using an ultrasonic device and diameter tape versus [~]20 minutes (one person) with SBLA, an [~]85-90% reduction in person-hours. Current limitations of SBLA are primarily software-related (stability, data handling, low-light performance). Overall, SBLA offers an efficient, auditable, and operationally relevant tool for tree inventories, with utility for rapidly updating DBH and spatial data used in management, planning, and asset databases.

ecology↗

bioRxiv2025

Butterfly and moth habitat specialisation changes along an elevational gradient of tropical forests on Mount Cameroon

Niche breadth is a key ecological trait influencing species distribution, persistence, vulnerability to environmental change, and interspecific interactions. While the elevational niche-breadth hypothesis predicts broader ecological niches at higher elevations due to increased environmental stress and heterogeneity, empirical tests have mostly focused on food specialisation, with habitat specialisation remaining largely overlooked. Here, we provide the first direct test of this hypothesis using habitat characteristics, analysing fruit-feeding butterflies and moths along a complete tropical forest gradient on Mount Cameroon. We quantified habitat-related niche breadth using the Outlying Mean Index across 96 forest plots spanning 350-2200 m a.s.l., employing two complementary metrics: absolute niche breadth (ANB) based on the total range of habitat conditions occupied across the gradient, and within-elevation niche breadth (WENB) reflecting the proportion of local habitat heterogeneity utilized at each elevation. Forest structural heterogeneity increased steeply with elevation. In response, butterfly communities showed a substantial upslope broadening of ANB, particularly in Charaxinae and Satyrinae. Moth families exhibited similar but weaker patterns. In contrast, WENB showed no consistent elevational patterns and was more variable among lepidopteran groups. These results support the elevational niche-breadth hypothesis for habitat specialisation in tropical butterflies, likely reflecting increased habitat opportunity space and reduced competition at higher elevations. However, the decoupling of ANB and WENB highlights that broader availability of environmental conditions does not necessarily translate into more generalised local habitat use, suggesting constraints from behavioural preferences, resource distributions, or biotic interactions. By disentangling overall and local habitat niche breadths, our study reveals unrecognised complexity in elevational specialisation patterns and provides new insights into how tropical insect respond to environmental gradients.

ecology↗

bioRxiv2025

From smartphones to satellites: Uniting crowdsourced biodiversity monitoring and Earth observation to fill the gaps in global plant trait mapping

Plant functional traits are fundamental to ecosystem dynamics and Earth system processes, but their global characterization is limited by the availability of field surveys and trait measurements. Recent expansions in biodiversity data aggregation, including large collections of vegetation surveys, citizen science observations, and trait measurements, offer new opportunities to overcome these constraints. Here we demonstrate that combining these diverse data sources with high-resolution Earth observation data enables accurate modeling of key plant traits at up to 1 km resolution. Our approach achieves high predictive power, reaching correlations up to 0.63 (15 of 31 traits exceeding 0.50) and improved spatial transferability, effectively bridging gaps in under-sampled regions. By capturing a broad range of traits with high spatial coverage, these maps can enhance our understanding of plant community properties and ecosystem functioning globally, and can serve as useful tools in modeling global biogeochemical processes and informing worldwide conservation efforts. Ultimately, our framework highlights the power and necessity of crowdsourced biodiversity data in high-resolution plant trait modeling. We anticipate that advancements in biodiversity data collection and remote sensing capabilities will further refine global trait mapping, fostering a dynamic trait-based understanding of the biosphere.

ecology↗

bioRxiv2025

RAS pathway activation drives clonal selection and monocytic differentiation in FLT3 and BCL2 inhibitor resistance

Despite efficacy of FLT3 and BCL2 inhibition in acute myeloid leukemia (AML), relapse limits survival. Mutation status and AML monocytic differentiation are implicated in resistance. On-treatment tumor evolution may select for genetically distinct clones or shifts in differentiation not resolvable by bulk sequencing. We performed multiomic single cell (SC) DNA/protein and RNA/protein profiling of patients treated on a clinical trial of the BCL2 inhibitor venetoclax and the FLT3 inhibitor gilteritinib (Ven/Git) to characterize immunophenotypic, transcriptional, and genetic clonal evolution on therapy. We found that while Ven/Gilt effectively eliminated FLT3 mutant clones, it selected for RAS mutations, RAS pathway activation and RAS-associated monocytic differentiation. In an in vitro model of monocytic differentiation associated with heightened RAS pathway activation, we demonstrated that MEK inhibition re-sensitized to Ven/Gilt. These data indicate RAS signaling is central to FLT3 and BCL2 inhibitor resistance, is tightly coupled to monocytic differentiation and can be overcome by RAS pathway inhibition. COIC.C.S. has provided educational talks for Astellas Pharma, served on advisory boards for Genentech/Abbvie and received research funding from Abbvie. B.C., Y.S. and J.H. are employees of Abbvie. M.S. and H.H. are or were previously employees of Genentech. FundingThis work was supported in part by Abbvie. C.C.S. is a Leukemia & Lymphoma Society Scholar in Clinical Research and a Damon Runyon-Richard Lumsden Foundation Clinical Investigator supported (in part) by the Damon Runyon Cancer Research Foundation (CI-99-18). Statement of SignificanceMutational and non-mutational RAS signaling activation drives clonal selection, monocytic differentiation and treatment resistance to FLT3 and BCL2 inhibition in AML. MEK inhibition can resensitize resistant AML cells, suggesting therapeutic potential for combined FLT3, BCL2 and RAS pathway inhibition in AML.

cancer biology↗

bioRxiv2024

deadtrees.earth - An Open-Access and Interactive Database for Centimeter-Scale Aerial Imagery to Uncover Global Tree Mortality Dynamics

Excessive tree mortality is a global concern and remains poorly understood as it is a complex phenomenon. We lack global and temporally continuous coverage on tree mortality data. Ground-based observations on tree mortality, e.g., derived from national inventories, are very sparse, not standardized and not spatially explicit. Earth observation data, combined with supervised machine learning, offer a promising approach to map tree mortality over time. However, global-scale machine learning requires broad training data covering a wide range of environmental settings and forest types. Drones provide a cost-effective source of training data by capturing high-resolution orthophotos of tree mortality events at sub-centimeter resolution. Here, we introduce deadtrees.earth, an open-access platform hosting more than a thousand centimeter-resolution orthophotos, covering already more than 300,000 ha, of which more than 58,000 ha are fully annotated. This community-sourced and rigorously curated dataset shall serve as a foundation for a global initiative to gather comprehensive reference data. In concert with Earth observation data and machine learning it will serve to uncover tree mortality patterns from local to global scales. This will provide the foundation to attribute tree mortality patterns to environmental changes or project tree mortality dynamics to the future. Thus, the open and interactive nature of deadtrees.earth together with the collective effort of the community is meant to continuously increase our capacity to uncover and understand tree mortality patterns.

ecology↗

bioRxiv2024

Broad-spectrum RNA antiviral inspired by ISG15-/- deficiency

Type I interferons (IFN-I) are cytokines with potent antiviral and inflammatory capacities. IFN-I signaling drives the expression of hundreds of IFN-I stimulated genes (ISGs), whose aggregate function results in the control of viral infection. A few of these ISGs are tasked with negatively regulating the IFN-I response to prevent overt inflammation. ISG15 is a negative regulator whose absence leads to persistent, low-grade elevation of ISG expression and concurrent, self-resolving mild autoinflammation. The limited breadth and low-grade persistence of ISGs expressed in ISG15 deficiency are sufficient to confer broad-spectrum antiviral resistance. Inspired by ISG15 deficiency, we have identified a nominal collection of 10 ISGs that recapitulate the broad antiviral potential of the IFN-I system. The expression of the 10 ISG collection in an IFN-I non-responsive cell line increased cellular resistance to Zika, Vesicular Stomatitis, Influenza A (IAV), and SARS-CoV-2 viruses. A deliverable prophylactic formulation of this syndicate of 10 ISGs significantly inhibited IAV PR8 replication in vivo in mice and protected hamsters against a lethal SARS-CoV-2 challenge, suggesting its potential as a broad-spectrum antiviral against many current and future emerging viral pathogens. One-Sentence SummaryHuman inborn error of immunity-guided discovery and development of a broad-spectrum RNA antiviral therapy

immunology↗

bioRxiv2021

Sticking around: plant persistence strategies on edaphic islands

O_LISpecies extinction risk at local scales can be partially offset by strategies promoting in-situ persistence. We explored how persistence-related traits of clonal and non-clonal plants in temperate dry grasslands respond intra- and interspecifically to variation in environmental conditions (soil, climate) and insularity. C_LIO_LIWe focused on edaphic island specialist species, hypothesizing that plants experiencing harsh soil environments and strong insularity are distinguished by traits supporting enhanced persistence, such as small stature, long lifespan and resource-conservative strategies. We used linear mixed-effect models and bivariate ordinary least squares linear models to explore the response of species triats to environmental and biogeographic predictors. C_LIO_LIWe found general support for this hypothesis. Soil properties and insularity emerged as the most important drivers of trait patterns. However, clonal species showed more consistent responses to variation in environmental conditions and insularity than non-clonal plants, which were characterized by distinct species-specific responses. C_LIO_LISoil properties and insularity confirmed their major role in shaping the persistence strategies of edaphic island plant species. These drivers may exert their effect on specific functions (e.g. belowground resource conservation captured by BDMC). Additionally, we unambiguously identified that clonal species had different persistence strategies than non-clonal ones. C_LI

ecology↗

bioRxiv2021

Comparative anatomy of leaf petioles in temperate trees and shrubs

Petioles are important plant organs connecting stems with leaf blades and affecting light-harvesting leaf ability as well as transport of water, nutrient and biochemical signals. Despite petioles high diversity in size, shape and anatomical settings, little information is available about their structural adaptations across evolutionary lineages and environmental conditions. To fill our knowledge gap, we investigated the variation of petiole morphology and anatomy in 95 European woody plant species using phylogenetic comparative models. Two major axes of variation were related to leaf area (from large and soft to small and tough leaves), and plant size (from cold-adapted shrubs to warm-adapted tall trees). Larger and softer leaves are found in taller trees of more productive habitats. Their petioles are longer, with a circular outline, thin cuticles without trichomes, and are anatomically characterised by the predominance of sclerenchyma, larger vessels, interfascicular areas with fibers, indistinct phloem rays, and the occurrence of prismatic crystals and druses. In contrast, smaller and tougher leaves are found in shorter trees and shrubs of colder or drier habitats. Their petioles are characterized by teret outline, thick cuticle, simple and non-glandular trichomes, epidermal cells smaller than cortex cells, phloem composed of small cells and radially arranged vessels, fiberless xylem, lamellar collenchyma, acicular crystals and secretory elements. Individual anatomical traits were linked to different internal and external drivers. The petiole length and vessel conduit size increase, while cuticle thickness decreases, with increasing leaf blade area. Epidermis cell walls are thicker in leaves with higher specific leaf area. Collenchyma becomes absent with increasing temperature, epidermis cell size increases with plant height and temperature, and petiole outline becomes polygonal with increasing precipitation. We conclude that species temperature and precipitation optima, plant height, leaf area and thickness exerted a significant control on petiole anatomical and morphological structures not confounded by phylogenetic inertia. Unrelated species with different evolutionary histories but similar thermal and hydrological requirements have converged to similar petiole anatomical structures. Our findings contribute to improving current knowledge about the functional morphoanatomy of the petiole as the key organ that plays a crucial role in the hydraulic pathways in plants.

ecology↗

bioRxiv2021

Insight into Canary Island pine physiology provided by stable isotope patterns of water and plant tissues along an altitudinal gradient

The Canary Islands, an archipelago east of Moroccos Atlantic coast, present steep altitudinal gradients covering various climatic zones from hot deserts to subalpine Mediterranean, passing through fog-influenced cloud forests. Unlike the majority of the Canarian flora, Pinus canariensis grow along most of these gradients, allowing the study of plant functioning in contrasting ecosystems. Here we assess the water sources (precipitation, fog) of P. canariensis and its physiological behavior in its different natural environments. We analyzed carbon and oxygen isotope ratios of water and organics from atmosphere, soil and different plant organs and tissues (including 10-year annual time series of tree-ring cellulose) of six sites from 480 to 1990 m asl on the Canary island La Palma. We found a decreasing {delta}18O trend in source water that was overridden by an increasing {delta}18O trend in needle water, leaf assimilates and tree-ring cellulose with increasing altitude, suggesting site-specific tree physiological responses to relative humidity. Fog-influenced and fog-free sites showed similar {delta}13C values, suggesting photosynthetic activity to be limited by stomatal closure and irradiance at certain periods. Besides, we observed an 18O-depletion (fog-free and timberline sites) and 13C-depletion (fog-influenced and fog-free sites) in latewood compared to earlywood caused by seasonal differences in: (i) water uptake (i.e. deeper ground water during summer drought, fog water frequency and interception) and (ii) meteorological conditions (stem radial growth and latewood {delta}18O correlated with winter precipitation). In addition, we found evidence for foliar water uptake and strong isotopic gradients along the pine needle axis in water and assimilates. These gradients are likely the reason for an unexpected underestimation of pine needle water {delta}18O when applying standard leaf water {delta}18O models. Our results indicate that soil water availability and air humidity conditions are the main drivers of the physiological behavior of pine along the Canary Islands altitudinal gradients.

ecology↗

bioRxiv2021

Distance decay 2.0 - a global synthesis of taxonomic and functional turnover in ecological communities.

Understanding the variation in community composition and species abundances, i.e., {beta}-diversity, is at the heart of community ecology. A common approach to examine {beta}-diversity is to evaluate directional turnover in community composition by measuring the decay in the similarity among pairs of communities along spatial or environmental distances. We provide the first global synthesis of taxonomic and functional distance decay along spatial and environmental distance by analysing 149 datasets comprising different types of organisms and environments. We modelled an exponential distance decay for each dataset using generalized linear models and extracted r2 and slope to analyse the strength and the rate of the decay. We studied whether taxonomic or functional similarity has stronger decay across the spatial and environmental distances. We also unveiled the factors driving the rate of decay across the datasets, including latitude, spatial extent, realm, and organismal features. Taxonomic distance decay was stronger along spatial and environmental distances compared with functional distance decay. The rate of taxonomic spatial distance decay was the fastest in the datasets from mid-latitudes while the rate of functional decay increased with latitude. Overall, datasets covering larger spatial extents showed a lower rate of decay along spatial distances but a higher rate of decay along environmental distances. Marine ecosystems had the slowest rate of decay. This synthesis is an important step towards a more holistic understanding of patterns and drivers of taxonomic and functional {beta}-diversity.

ecology↗

bioRxiv2021

Climate fluctuations drive the recruitment and growth of temperate grassland plants

Recent climate warming is associated with the increasing magnitude and frequency of extreme events, including heatwaves and drought periods worldwide. Such events can have major effects on the species composition of plant communities, hence on biodiversity and ecosystem functioning. Here we studied responses of Central European dry grassland plants to fluctuating temperature and precipitation over the last thirty years with monthly temporal resolution. We assessed the seasonal and annual dynamics of plant recruitment and growth based on the analysis of annual growth rings from the root collar. Although most studies so far applied such methods to trees and shrubs, we focused on typical grassland plants, two forbs and two chamaephytes. We related the recruitment and annual growth to monthly and annual precipitation, temperature and aridity between 1991 and 2019. We revealed species-specific responses, namely the (i) recruitment of deep-rooted, heavy-seeded species was positively affected by precipitation in both late winter-early spring and summer, whereas recruitment of shallow-rooted, light-seeded species was weakly influenced by climate fluctuations; (ii) growth of shallow-rooted species was more adversely affected by high summer temperature and drought than the growth of deep-rooted species. The population age structure of all the studied species was affected by the climate of the past decades. Most individuals established in the wet period of the 2000s, fewer in the precipitation-poorer 1990s, and the establishment was considerably reduced in the dry and warm period of the 2010s. Our findings indicate that the change towards warmer and drier climate has a profound effect even on drought-adapted ecosystems such as temperate dry grasslands. However, plant responses to various climatic extremes are species-specific, depending on their characteristics, such as life form or rooting depth. Consequently, the ongoing and anticipated climate warming will likely result in complex changes in species composition and other ecosystem properties of temperate grasslands

ecology↗

bioRxiv2020

Does rainforest biodiversity stand on the shoulders of giants? Effect of disturbances by forest elephants on trees and insects on Mount Cameroon

Natural disturbances are essential for dynamics of tropical rainforests, contributing to their tremendous biodiversity. In the Afrotropical rainforests, megaherbivores have played a key role before their recent decline. Although the influence of savanna elephants on ecosystems has been documented, their close relatives, forest elephants, remain poorly studied. Few decades ago, in the unique natural enclosure experiment on Mount Cameroon, West/Central Africa, the rainforests were divided by lava flows which are not crossed by the local population of forest elephants. We assessed communities of trees, butterflies and two ecological guilds of moths in disturbed and undisturbed forests split by the longest lava flow at upland and montane elevations. Altogether, we surveyed 32 forest plots resulting in records of 2,025 trees of 97 species, and 7,853 butterflies and moths of 437 species. The disturbed forests differed in reduced tree density, height, and high canopy cover, and in increased DBH. Forest elephants also decreased tree species richness and altered their composition, probably by selective browsing and foraging. The elephant disturbance also increased species richness of butterflies and had various effects on species richness and composition of all studied insect groups. These changes were most probably caused by disturbance-driven alterations of (micro)habitats and species composition of trees. Moreover, the abandonment of forests by elephants led to local declines of range-restricted butterflies. Therefore, the current appalling decline of forest elephant populations across the Afrotropics most probably causes important changes in rainforest biodiversity and should be reflected by regional conservation authorities.

ecology↗

bioRxiv2019

Homozygous STAT2 gain-of-function mutation by loss of USP18 activity in a patient with type I interferonopathy

Type I interferonopathies are monogenic disorders characterized by enhanced Type I interferon (IFN-I) activity. Inherited ISG15 and USP18 deficiencies underlie type I interferonopathies by preventing the regulation of late responses to IFN-I. Specifically, ISG15/USP18 are induced by IFN-I and sterically hinder JAK1 from binding to the IFNAR2 subunit of IFN-I receptor. We report an infant who died of autoinflammation due to a homozygous missense mutation (R148Q) in STAT2. The variant is gain-of-function (GOF) for ISGF3-dependent induction of late but not early response to IFN-I. Surprisingly, the mutation does not enhance the intrinsic transcriptional activity of ISGF3. Rather, the STAT2 R148Q variant is GOF because it fails to appropriately interact with and traffic USP18 to IFNAR2, preventing USP18 from negatively regulating responses to IFN-I. Overall, a STAT2 missense mutation that fails to facilitate USP18-mediated signal termination in the homozygous state underlies a novel genetic etiology of type I interferonopathy.

immunology↗