Biology subjects

Anand, M.

Publications and source records attributed to Anand, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Pilifers provide rapid mechanosensory feedback during floral tracking in hawkmoths

Hawkmoths expertly hover over flowers during feeding, accurately tracking floral movements even as flowers gently sway in the wind. They use visual and mechanosensory feedback to adjust their position, while their long, flexible mouthpart, the proboscis, stays inserted inside the nectar spur. Although much is known about how hawkmoths detect and process visual motion, far less is understood about how hawkmoths detect mechanical motion cues. Pilifers are hair bundles at the proboscis-head joint, well-positioned to provide feedback about floral motion. Here, we tested if pilifers could provide mechanosensory feedback essential for successful floral tracking. We computed bending at the proboscis base during floral tracking in freely flying hawkmoths and found that floral movements induce small yet significantly correlated lateral bending. Recordings from pilifer afferents showed that they respond to lateral motions of amplitudes similar to those seen in natural floral tracking behaviors. They respond to different directions and speeds of proboscis motion with an average latency of 1.9 ms. Neural tracing revealed extensive sensory arborizations in the sub-esophageal ganglion of the brain and ventral nerve cord, indicating a feedback pathway to the neck and flight motor system that enables rapid coordination of appendages and body for successful feeding.

neuroscience↗

bioRxiv2026

The ModelSEED Biochemistry Database, 2026 update: grading multi-source thermodynamics

The ModelSEED Biochemistry Database (https://modelseed.org) supplies foundational mass- and charge-balanced reaction networks for metabolic reconstructions. Here we present an update on the biochemistry where the database has been expanded to [~] 46,000 compounds, and [~] 56,000 reactions, featuring [~] 37,000 metabolic structures. We have expanded our approach for handling thermodynamic data, enabling multiple sources of data to be derived, integrated, and presented to the wider research community. We now publish predictions of pKa, reaction energy (and respective uncertainties), and estimates of reaction direction from multiple independent sources. Each reaction is graded gold, silver or bronze according to the strength of the evidence behind it, so that users can weigh its reliability directly. We also release reaction directions predicted by an ensemble of large language models. This multi-source approach exposes agreements and discrepancies between sources for [~] 33,000 reactions. Finally, to ensure data integrity, a new conflict-resolution pipeline reconciles structures across sources, documenting input from curators. Our work is publicly available at https://github.com/ModelSEED/ModelSEEDDatabase.

biochemistry↗

bioRxiv2026

PARP1 Exhibits an Enzymatically Inactive Chromatin Binding Mode

Poly (ADP-ribose) Polymerase 1 (PARP1) is an abundant nuclear enzyme that dynamically engages chromatin in diverse cellular scenarios. In the context of DNA repair, PARP1 becomes enzymatically activated and subsequently attaches ADP-ribose units onto various proteins, including histones, to signal and coordinate the DNA damage response. In the absence of DNA damage, PARP1 modulates chromatin structure by directly binding to nucleosomes, however, the molecular basis of this interaction is unknown. Here, we define a distinct, enzymatically inactive mode of PARP1 chromatin binding, in which the Zn1, Zn2, Zn3, and BRCT domains cooperatively bind nucleosomal linker DNA and drive compaction of undamaged chromatin. This binding mode does not trigger catalytic activation and therefore is insensitive to PARP inhibitors (PARPi). Together, our results support a model in which PARP1 associates with the genome in an inactive state to compact chromatin and to surveil for DNA lesions. SummaryPARP1 engages undamaged chromatin in a distinct binding mode that results in chromatin compaction but does not lead to enzymatic activation.

biochemistry↗

bioRxiv2024

Trends in Coupled Human-Environment Systems Modelling: A Scoping Review

Classical environmental models assume the influence of humans on environmental systems is constant. However, human and environmental systems respond to one another. As such, coupled human-environment systems (CHES) models have been developed and are becoming more widely studied. In this review, we analyze CHES modelling techniques and study systems over a decade (May 2009-April 2019). We utilized the PRISMA method to filter publications from both Web of Knowledge and PUBMED, yielding 92 relevant papers for our review. Publications more than doubled from the 5-year interval May 2009-December 2013 (28/92) to the 5-year interval January 2014-April 2019 (64/92). CHES models typically used either differential equations (DEs) (44/92) or agent-based models (ABMs) (28/92). We organized the included literature with respect to the technique used to represent human behaviour. We noticed a diversity of approaches in this respect, but primarily optimization techniques (28/92) and game theory (34/92). We noticed a substantial increase in publications using more highly structured models in the second 5-year interval. We attribute this to reduced technological barriers to developing more detailed models, and greater data availability. We discuss the realism of the models and their ability to capture real-world dynamics. Finally, we explore avenues for future research, and discuss unconventional routes such as online communities and artificial intelligence modelling to expand representation of human behaviour in CHES models.

ecology↗

bioRxiv2024

novoStoic2.0: An integrated framework for pathway synthesis, thermodynamic evaluation, and enzyme selection

Computational pathway design and retro-biosynthetic approaches can facilitate the development of innovative biochemical production routes, biodegradation strategies, and the funneling of multiple precursors into a single bioproduct. However, effective pathway design necessitates a comprehensive understanding of biochemistries, enzyme activities, and thermodynamic feasibility. Herein, we introduce novoStoic2.0, an integrated platform that combines tools for estimating overall stoichiometry, designing de novo synthesis pathways, assessing thermodynamic feasibility, and selecting enzymes. novoStoic2.0 offers a unified web-based interface as a part of the AlphaSynthesis platform (http://novostoic.platform.moleculemaker.org/) tailored for the synthesis of thermodynamically viable pathways as well as the selection of enzymes for re-engineering required for novel reaction steps. We exemplify the utility of the platform to identify novel pathways for hydroxytyrosol synthesis, which are shorter than the known pathways and require reduced cofactor usage. In summary, novoStoic2.0 aims to streamline the process of pathway design contributing to the development of sustainable biotechnological solutions.

synthetic biology↗

bioRxiv2023

SARS-CoV-2 Nsp13 is a viral RHIM protein promoting cell death linked to Z-RNA sensing and ZBP1-RIPK3 signaling

RHIM is a protein motif in cell death proteins that assembles higher-order signaling complexes and triggers regulated cell death, which in itself limits virus spread and additionally triggers inflammation for mounting immune responses. A few DNA viruses employ viral RHIMs mimicking host RHIMs. However, these viral RHIMs counteract host cell death by interacting with host RHIM proteins and blocking complex formation to alleviate antiviral defenses. Whether RNA viruses operate such viral RHIMs remains unknown. RHIM-protein signaling promotes lung damage and cytokine storm in respiratory RNA virus infections, arguing the presence of viral RHIMs. Here, we report the novel viral RHIMs in Nsp13 and Nsp14 of SARS-CoV-2 and other bat RNA viruses, providing the basis for bats as the hosts for their evolution. Nsp13 promoted cell death in bat and human cells, however, viral RHIM of Nsp13 is more critical for human cell death than bat cells, suggesting species-specific regulation. The conformation of RNA-binding channel in Nsp13 is critical for cell death in bat and human cells. Nsp13 showed RHIM-dependent interactions with ZBP1 and RIPK3 and promoted the formation of large insoluble complexes of ZBP1 and RIPK3. Also, Nsp13 promoted ZBP1-RIPK3 signaling-mediated cell death dependent on intracellular RNA ligands. Intriguingly, the SARS-CoV-2 genome consists of bona fide Z-RNA-forming segments. These SARS-CoV-2 Z-RNA segments promoted Nsp13-dependent cell death, further revealing Nsp13s association with Z-RNA sensing and ZBP1-RIPK3 signaling. Our findings reveal the functional viral RHIMs of bat-originated RNA viruses regulating host cell death associated with Z-RNA sensing and ZBP1-RIPK3 signaling activation. These observations allow the understanding of mechanisms of cellular damage and cytokine storm in SARS-CoV-2 and other bat-originated RNA virus infections. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=144 SRC="FIGDIR/small/554434v2_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@f71c5aorg.highwire.dtl.DTLVardef@1666aa5org.highwire.dtl.DTLVardef@e37d82org.highwire.dtl.DTLVardef@145020f_HPS_FORMAT_FIGEXP M_FIG C_FIG One-sentence summaryBat-associated RNA viruses employ viral RHIMs and regulate host cell death.

immunology↗

bioRxiv2022

TCID50 Measurements of anti-viral efficacy on metal printed masks and plastic surfaces

The SARS-CoV-2 pandemic has created a need for effective personal protective equipment (PPE) to prevent viral spread. PPE like face masks contain the spread of virus-filled droplets and thus reduce infection rates, has been a critical tool in stopping the spread of SARS-CoV-2. PET plastic barriers have also been used in public settings to reduce face to face viral transmission. However, in some cases, they have provided additional contact with the virus due to contamination. In order study, we evaluated the effectiveness of face masks and PET plastics coated in different metals in reducing viral load. We compared PPE printed with silver, copper, or zinc for their ability to inactivate live human coronavirus HCoV 229E. Our results show that silver and copper have significant anti-viral efficacy when printed on nonwoven fabric compared to the controls. The metal-printed PET showed around 70% anti-viral efficacy with any formulations, with copper performing the best. This work builds more data to support the development of metal printed materials for enhanced protection against coronaviruses.

bioengineering↗

bioRxiv2022

Acclimating to degraded environments: The social rationale for swift action on restoration

As environmental degradation progresses, economies and societies adapt to the loss of ecosystem services and public attention to degradation subsides. In systems experiencing such societal acclimation to degradation, net incentives for stakeholder mitigation peak during early degradation phases and subside over time. Using harmful algae blooms in western Lake Erie as a case study, we illustrate how declines in public attention and societal reliance on lake recreation (i.e., finding recreation alternatives) reduce the incentives for stakeholders to reduce pollution runoff (i.e., mitigation efforts throughout the watershed). We then analyze how acclimation can affect a broad array of conservation challenges by developing a general socio-ecological model of societal response to degradation. We find that delays in initiating stakeholder-driven mitigation efforts can exponentially prolong restoration projects. Furthermore, when alleviating intense degradation relies upon voluntary commitments by many individuals, windows of opportunity for mitigation can be very limited because feedback loops of societal adaptation doom late restoration efforts to failure and lock human-environment systems into degraded states. These windows of opportunity can be particularly narrow when a) stakeholder mitigation requires supportive public opinion or b) even modestly valuable alternative services are available in degraded ecosystems. In such cases, maintaining undegraded human-environment regimes may hinge on quickly initiating stakeholder mitigation movements and allocating limited government conservation funds soon after degradation begins instead of spreading mitigation efforts out over decades. Such initiatives, regardless of whether acclimation is slow or rapid in a given system, also greatly accelerate the pace of environmental restoration. Significance StatementAs societies acclimate to degraded environments, mitigation efforts that hinge on action by many stakeholders can erode. Developing a socio-ecological model of acclimation, we reveal how social and environmental processes intertwine to create alternative stable socio-ecological regimes, with either: 1) undegraded ecosystem states sustained by widespread mitigation adoption, or 2) degraded states where societies neither maintain nor continue relying on traditional, local ecosystem services. This dynamic places a premium on prompt mitigation efforts, which may face narrow opportunity windows to get started and avert degraded regimes in systems that rely on stakeholder-driven mitigation. Moreover, in any system requiring stakeholder action, societal acclimation will increase the importance of early action because decaying mitigation incentives exponentially lengthen restoration efforts.

ecology↗

bioRxiv2022

Single-Molecule Analysis of DNA Base-Stacking Energetics Using Patterned DNA Nanostructures

DNA double helix structure is stabilized by the base-pairing and the base-stacking interactions. Base-stacking interactions originating from hydrophobic interactions between the nucleobases predominantly contribute to the duplex stability. A comprehensive understanding of dinucleotide base-stacking interactions is lacking owing to the unavailability of sensitive techniques that can measure these weak interactions. Earlier studies attempting to address this question only managed to estimate the base-pair stacking interactions, however, disentangling individual base-stacking interactions was enigmatic. By combining multiplexed DNA-PAINT imaging with designer DNA nanostructures, we experimentally measure the free energy of dinucleotide base-stacking at the single-molecule level. Multiplexed imaging enabled us to extract binding kinetics of an imager strand with and without additional dinucleotide stacking interactions in a single imaging experiment, abolishing any effects of experimental variations. The DNA-PAINT data showed that a single additional dinucleotide base-stacking results in as much as 250-fold stabilization of the imager strand binding. We found that the dinucleotide base-stacking energies vary from -1.18 {+/-} 0.17 kcal/mol to -3.57 {+/-} 0.08 kcal/mol for C|T and A|C base-stackings, respectively. We demonstrate the application of base-stacking energetics in designing DNA-PAINT probes for multiplexed super-resolution imaging. Our results will aid in designing functional DNA nanostructures, DNA and RNA aptamers, and facilitate better predictions of the local DNA structure.

biophysics↗

bioRxiv2021

Local overfishing patterns have regional effects on health of coral, and economic transitions can promote its recovery

Overfishing has the potential to severely disrupt coral reef ecosystems worldwide, while harvesting at more sustainable levels instead can boost fish yield without damaging reefs. The dispersal abilities of reef species mean that coral reefs form highly connected environments, and the viability of reef fish populations depends on spatially explicit processes such as the spillover effect and unauthorized harvesting inside marine protected areas. However, much of the literature on coral conservation and management has only examined overfishing on a local scale, without considering how different spatial patterns of fishing levels can affect reef health both locally and regionally. Here, we simulate a coupled human-environment model to determine how coral and herbivorous reef fish respond to overfishing across multiple spatial scales. We find that coral and reef fish react in opposite ways to habitat fragmentation driven by overfishing, and that a potential spillover effect from marine protected areas into overfished patches helps coral populations far less than it does reef fish. We also show that ongoing economic transitions from fishing to tourism have the potential to revive fish and coral populations over a relatively short timescale, and that large-scale reef recovery is possible even if these transitions only occur locally. Our results show the importance of considering spatial dynamics in marine conservation efforts, and demonstrate the ability of economic factors to cause regime shifts in human-environment systems.

ecology↗

bioRxiv2021

Implications of trade network structure and population dynamics for food security and equality

Given trades importance to maintaining food security, it is crucial to understand the relationship between human population growth, land use, food supply, and trade. We develop a metapopulation model coupling human population dynamics to agricultural land use and food production in "patches" (regions and countries) connected via trade networks. Patches that import sparingly or fail to adjust their demand sharply in response to changes in food per capita experience food insecurity. They fall into a feedback loop between increasing population growth and decreasing food per capita, particularly if they are peripheral to the network. A displacement effect is also evident; patches that are more central and/or import more heavily preserve their natural land states. Their reliance on imports means other patches must expand their agricultural land. These results emphasize that strategies for improving food security and equality must account for the combined effects of network topology and patch-level characteristics.

ecology↗

bioRxiv2021

Deep learning for early warning signals of regime shifts

Many natural systems exhibit regime shifts where slowly changing environmental conditions suddenly shift the system to a new and sometimes very different state. As the tipping point is approached, the dynamics of complex and varied systems all simplify down to a small number of possible normal forms that determine how the new regime will look. Indicators such as increasing lag-1 autocorrelation and variance provide generic early warning signals (EWS) by detecting how dynamics slow down near the tipping point. But they do not indicate what type of new regime will emerge. Here we develop a deep learning algorithm that can detect EWS in systems it was not explicitly trained on, by exploiting information about normal forms and scaling behaviour of dynamics near tipping points that are common to many dynamical systems. The algorithm detects EWS in 268 empirical and model time series from ecology, thermoacoustics, climatology, and epidemiology with much greater sensitivity and specificity than generic EWS. It can also predict the normal form that will characterize the oncoming regime shift. Such approaches can help humans better manage regime shifts. The algorithm also illustrates how a universe of possible models can be mined to recognize naturally-occurring tipping points.

ecology↗

bioRxiv2020

Debates about vaccines and climate change on social media networks: a study in contrasts

Vaccines and climate change have much in common. In both cases, a scientific consensus contrasts with a divided public opinion. They also exemplify coupled human-environment systems involving common pool resources. Here we used machine learning algorithms to analyze the sentiment of 87 million tweets on climate change and vaccines in order to characterize Twitter user sentiment and the structure of user and community networks. We found that the vaccine conversation was characterized by much less interaction between individuals with differing sentiment toward vaccines. Community-level interactions followed this pattern, showing less interaction between communities of opposite sentiment toward vaccines. Additionally, vaccine community networks were more fragmented and exhibited numerous isolated communities of neutral sentiment. Finally, pro-vaccine individuals overwhelmingly believed in anthropogenic climate change, but the converse was not true. We propose mechanisms that might explain these results, pertaining to how the spatial scale of an environment system can structure human populations.

ecology↗

bioRxiv2020

Quaternary climate change explains global patterns of tree beta-diversity

Both historical and contemporary environmental conditions determine present biodiversity patterns, but their relative importance is not well understood. One way to disentangle their relative effects is to assess how different dimensions of beta-diversity relate to past climatic changes, i.e., taxonomic, phylogenetic and functional compositional dissimilarity, and their components generated by replacement of species, lineages and traits (turnover) and richness changes (nestedness). Here, we quantify global patterns of each of these aspects of beta-diversity among neighboring sites for angiosperm trees using the most extensive global database of tree species-distributions (43,635 species). We found that temperature change since the Last Glacial Maximum (LGM) was the major influence on both turnover and nestedness components of beta-diversity, with a negative correlation to turnover and a positive correlation to nestedness. Moreover, phylogenetic and functional nestedness was higher than expected from taxonomic beta-diversity in regions that experienced large temperature changes since the LGM. This pattern reflects relatively greater losses of phylogenetic and functional diversity in species-poor assemblages, possibly caused by phylogenetically and functionally selective species extinction and recolonization during glacial-interglacial oscillations. Our results send a strong warning that rapid anthropogenic climate change is likely to result in a long-lasting phylogenetic and functional compositional simplification, potentially impairing forest ecosystem functioning.

ecology↗

bioRxiv2020

Coupled social-land dynamics and the future of sustainable consumption

Dietary patterns have long been a driver of global land use. Increasingly, they also respond to it, in part because of social forces that support adoption of sustainable diets. Here we develop a coupled social-land use dynamics model parameterised for 164 countries. We project global land use under 20 scenarios for future population, income, and agricultural yield. When future yields are low and/or population size is high, coupled social-land feedbacks can reduce the peak global land use by up to 2 billion hectares, if socio-economic barriers to adopting a sustainable diet are sufficiently low. In contrast, when population growth is low or yield is high, reductions in income elasticity can increase peak land use by 100 million hectares. The model also exhibits a regime of synergistic effects whereby simultaneous changes to multiple social and economic parameters are required to change land use projections. This research demonstrates the value of including coupled social-land feedbacks in land use projections.

evolutionary biology↗

bioRxiv2020

When conflicts get heated, so does the planet: social-climate dynamics under inequality

Climate dynamics are inextricably linked to processes in social systems that are highly unequal. This suggests a need for coupled social-climate models that capture pervasive real-world asymmetries in the population distribution of the consequences of anthropogenic climate change and climate (in)action. Here we develop a simple social-climate model with group structure to investigate how anthropogenic climate change and population heterogeneity co-evolve. We find that greater homophily and resource inequality cause an increase in the global peak temperature anomaly by as much as 0.7{degrees}C. Also, climate change can structure human populations by driving opinion polarization. Finally, climate mitigation achieved by reducing the cost of mitigation measures paid by individuals tends to be contingent upon socio-economic conditions, whereas policies that achieve communication between different strata of society show climate mitigation benefits across a broad socio-economic regime. We conclude that advancing climate change mitigation efforts can benefit from a social-climate systems perspective.

ecology↗

bioRxiv2020

Paleoclimate and current climate collectively shape the phylogenetic and functional diversity of trees worldwide

Trees are of vital importance for ecosystem functioning and services at local to global scales, yet we still lack a detailed overview of the global patterns of tree diversity and the underlying drivers, particularly the imprint of paleoclimate. Here, we present the high-resolution (110 km) worldwide mapping of tree species richness, functional and phylogenetic diversities based on [~]7 million quality-assessed occurrences for 46,752 tree species (80.5% of the estimated total number of tree species), and subsequent assessments of the influence of paleo-climate legacies on these patterns. All three tree diversity dimensions exhibited the expected latitudinal decline. Contemporary climate emerged as the strongest driver of all diversity patterns, with Pleistocene and deeper-time (>107 years) paleoclimate as important co-determinants, and, notably, with past cold and drought stress being linked to reduced current diversity. These findings demonstrate that tree diversity is affected by paleoclimate millions of years back in time and highlight the potential for tree diversity losses from future climate change.

ecology↗

bioRxiv2020

Half of the world's tree biodiversity is unprotected and is increasingly threatened by human activities

Although trees are key to ecosystem functioning, many forests and tree species across the globe face strong threats. Preserving areas of high biodiversity is a core priority for conservation; however, different dimensions of biodiversity and varied conservation targets make it difficult to respond effectively to this challenge. Here, we (i) identify priority areas for global tree conservation using comprehensive coverage of tree diversity based on taxonomy, phylogeny, and functional traits; and (ii) compare these findings to existing protected areas and global biodiversity conservation frameworks. We find that ca. 51% of the top-priority areas for tree biodiversity are located in current protected areas. The remaining half top-priority areas are subject to moderate to high human pressures, indicating conservation actions are needed to mitigate these human impacts. Our findings emphasize the effectiveness of using tree conservation priority areas for future global conservation planning.

ecology↗