Biology subjects

Joshi, J.

Publications and source records attributed to Joshi, J..

48 records · Page 3Linked to original sources

bioRxiv2021

PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling

Computational methods based on initial screening and prediction of peptides for desired functions have been proven effective alternatives to the lengthy and expensive methods traditionally utilized in peptide research, thus saving time and effort. However, for many researchers, the lack of expertise in utilizing programming libraries and the lack of access to computational resources and flexible pipelines are big hurdles to adopting these advanced methods. To address these barriers, we have implemented the Peptide Design and Analysis Under Galaxy (PDAUG) package, a Galaxy based python powered collection of tools, workflows, and datasets for a rapid in-silico peptide library analysis. PDAUG offers tools for peptide library generation, data visualization, in-built and public database based peptide sequence retrieval, peptide feature calculation, and machine learning modeling. In contrast to the existing methods like standard programming libraries or rigid web-based tools, PDAUG offers a GUI based toolset thus providing flexibility to build and distribute reproducible pipelines and workflows without programming expertise. Additionally, this toolset facilitates researchers to combine PDAUG with hundreds of compatible existing Galaxy tools for limitless analytic strategies. Finally, we demonstrate the usability of PDAUG on predicting anticancer properties of peptides using four different feature sets and assess the suitability of various machine learning algorithms.

bioinformatics↗

bioRxiv2020

Towards a unified theory of plant photosynthesis and hydraulics

The global carbon and water cycles are governed by the coupling of CO2 and water vapour exchanges through the leaves of terrestrial plants, controlled by plant adaptations to balance carbon gains and hydraulic risks. We introduce a trait-based optimality theory that unifies the treatment of stomatal responses and biochemical acclimation of plants to environments changing on multiple timescales. Tested with experimental data from 18 species, our model successfully predicts the simultaneous decline in carbon assimilation rate, stomatal conductance, and photosynthetic capacity during progressive soil drought. It also correctly predicts the dependencies of gas exchange on atmospheric vapour pressure deficit, temperature, and CO2. Model predictions are also consistent with widely observed empirical patterns, such as the distribution of hydraulic strategies. Our unified theory opens new avenues for reliably modelling the interactive effects of drying soil and rising atmospheric CO2 on global photosynthesis and transpiration.

plant biology↗

bioRxiv2020

Spatial patterns of phylogenetic diversity and endemism in the Western Ghats, India: a case study using ancient predatory arthropods

Abstract and keywordsO_ST_ABSAimC_ST_ABSTo study patterns of phylogenetic diversity, endemism and turnover in a community of ancient arthropods across a biodiversity hotspot. Our specific aims were to understand diversity gradients, identify hotspots of endemism and conservation importance, and highlight poorly-studied areas with unique biodiversity. LocationThe Western Ghats (WG), India MethodsWe compiled a location data-set for 19 scolopendrid centipedes species which was used to predict areas of habitat suitability using bioclimatic and geomorphological variables in Maxent. We used predicted distributions and time-calibrated species phylogeny to calculate taxonomic and phylogenetic indices of diversity, endemism and turnover. ResultsWe observed a decreasing gradient in Taxonomic and Phylogenetic Diversity (TD/PD) from the southern to northern WG and high Phylogenetic Endemism (PE) in the southern and northern WG. Southern WG had the highest diversity and was represented by lineages with long branch lengths and short ranges as observed from Relative Phylogenetic Diversity/Endemism (RPD and RPE). Despite having low PD, the northern WG had high values of PE represented by distinct lineages as inferred from RPE. Sites across the Palghat Gap grouped separately in comparisons of species turnover along the WG. Main conclusionsOur findings support expectations from the latitudinal diversity gradient in the WG and the southern WG refuge hypotheses. The high diversity and endemism along with the presence of ancient lineages in the southern WG is consistent with in-situ speciation. Climatic differences or dispersal barriers might have retained this diversity locally. High phylogenetic endemism in lateritic plateaus of the northern WG, albeit with low phylogenetic diversity, indicates the presence of distinct evolutionary lineages that might be adapted to life in these landscapes characterized by poor soil conditions and seasonal ephemeral habitats. Our results from soil arthropods highlight the need to use phylogeny and distribution data while assessing diversity and endemism patterns in the WG.

evolutionary biology↗

bioRxiv2020

Expanding the Galaxy's reference data

SummaryProperly and effectively managing reference datasets is an important task for many bioinformatics analyses. Refgenie is a reference asset management system that allows to easily organize, retrieve, and share such datasets. Here, we describe the integration of refgenie into the Galaxy platform. Server administrators are able to configure Galaxy to make use of reference datasets made available on a refgenie instance. Additionally, a Galaxy Data Manager tool has been developed to provide a graphical interface to refgenies remote reference retrieval functionality. A large collection of reference datasets has also been made available using the CVMFS repository from GalaxyProject.org, with mirrors across the United States, Canada, Europe, and Australia, enabling easy use outside of Galaxy. Availability and implementationThe ability of Galaxy to use refgenie assets was added to the core Galaxy framework in version 20.05, which is available from https://github.com/galaxyproject/galaxy under the Academic Free License version 3.0. The refgenie Data Manager tool can be installed via the Galaxy ToolShed, with source code managed at https://github.com/BlankenbergLab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull and released using an MIT license.

bioinformatics↗

bioRxiv2020

Potential For Applying Continuous Directed Evolution To Plant Enzymes

Plant evolution has produced enzymes that may not be optimal for maximizing yield and quality in todays agricultural environments and plant biotechnology applications. By improving enzyme performance, it should be possible to alleviate constraints on yield and quality currently imposed by kinetic properties or enzyme instability. Enzymes can be optimized faster than naturally possible by applying directed evolution, which entails mutating a target gene in vitro and screening or selecting the mutated gene products for the desired characteristics. Continuous directed evolution is a more efficient and scalable version that accomplishes the mutagenesis and selection steps simultaneously in vivo via error-prone replication of the target gene and coupling of the host cells growth rate to the target genes function. However, published continuous systems require custom plasmid assembly, and convenient multipurpose platforms are not available. We discuss two systems suitable for continuous directed evolution of enzymes, OrthoRep in Saccharomyces cerevisiae and EvolvR in Escherichia coli, and our pilot efforts to adapt each system for high-throughput plant enzyme engineering. To test our modified systems, we used the thiamin synthesis enzyme THI4, previously identified as a prime candidate for improvement. Our adapted OrthoRep system shows promise for efficient plant enzyme engineering.

synthetic biology↗

bioRxiv2020

Improving prediction and assessment of global wildfires using neural networks

Fires determine vegetation patterns, impact human societies, and provide complex feedbacks into the global climate system. Empirical and process-based models differ in their scale and mechanistic assumptions, giving divergent predictions of fire drivers and extent. Especially, the role of anthropogenic drivers remains less understood. Taking a data-driven approach, we use an artificial neural network to learn region-specific relationships between fire and its socio-environmental drivers across the globe. As a result, our models achieve higher predictability than previously reported, with global spatial correlation of 0.92, temporal correlation of 0.76, interannual correlation of 0.69, and grid-cell level correlation of 0.6, between predicted and observed burned area. Our analysis reveals universal global patterns in fire-climate interactions, coupled with strong regional differences in fire-human relationships. Given the current socio-anthropogenic conditions, Equatorial Asia, southern Africa, and Australia show a strong sensitivity of fire extent to temperature whereas northern Africa shows a strong negative sensitivity. Overall, forests and shrublands, show a stronger sensitivity of burned area to temperature compared to savannas, potentially weakening their status as carbon sinks under future climate-change scenarios.

ecology↗

bioRxiv2020

The critical ecological role of an endemic, large-bodied frugivore on a small tropical island

Endozoochory, a mutualistic interaction between plants and frugivores, is one of the key processes responsible for maintenance of tropical biodiversity. Islands, which have a smaller subset of plants and frugivores when compared with mainland communities, offer an interesting setting to understand the organization of plant-frugivore communities vis-a-vis the mainland sites. We examined the relative influence of functional traits and phylogenetic relationships on the plant-seed disperser interactions on an island and a mainland site. The island site allowed us to investigate the organization of the plant-seed disperser community in the natural absence of key frugivore groups (bulbuls and barbets) of Asian tropics. The endemic Narcondam Hornbill, was the most abundant frugivore on the island and played a central role in the community. Species strength, a measure of relevance of frugivores for plants, of frugivores was positively associated with their abundance. Among plants, figs had the highest species strength and played a central role in the community. Island-mainland comparison revealed that the island plant-seed disperser community was more asymmetric, connected and nested as compared to the mainland community. Neither phylogenetic relationships or functional traits (after controlling for phylogenetic relationships) were able to explain the patterns of interactions between plants and frugivores on the island or the mainland pointing towards the diffused nature of plant-frugivore interactions. The diffused nature is a likely consequence of plasticity in foraging behavior and trait convergence that contribute to governing the interactions between plants and frugivores.

ecology↗

bioRxiv2020

Bioinformatic and experimental evidence for suicidal and catalytic plant THI4s

Like fungi and some prokaryotes, plants use a thiazole synthase (THI4) to make the thiazole precursor of thiamin. Fungal THI4s are suicide enzymes that destroy an essential active-site Cys residue to obtain the sulfur atom needed for thiazole formation. In contrast, certain prokaryotic THI4s have no active-site Cys, use sulfide as sulfur donor, and are truly catalytic. The presence of a conserved active-site Cys in plant THI4s and other indirect evidence implies that they are suicidal. To confirm this, we complemented the Arabidopsis tz-1 mutant, which lacks THI4 activity, with a His-tagged Arabidopsis THI4 construct. LC-MS analysis of tryptic peptides of the THI4 extracted from leaves showed that the active-site Cys was predominantly in desulfurated form, consistent with THI4 having a suicide mech-anism in planta. Unexpectedly, transcriptome datamining and deep proteome profiling showed that barley, wheat, and oat have both a widely expressed canonical THI4 with an active-site Cys, and a THI4-like paralog (non-Cys THI4) that has no active-site Cys and is the major type of THI4 in devel-oping grains. Transcriptomic evidence also indicated that barley, wheat, and oat grains synthesize thiamin de novo, implying that their non-Cys THI4s synthesize thiazole. Structure modeling supported this inference, as did demonstration that non-Cys THI4s have significant capacity to complement thia-zole auxotrophy in Escherichia coli. There is thus a prima facie case that non-Cys cereal THI4s, like their prokaryotic counterparts, are catalytic thiazole synthases. Bioenergetic calculations show that, relative to suicide THI4s, such enzymes could save substantial energy during the grain filling period. AbbreviationsDHAla, dehydroalanine; EST, expressed sequence tag; FDR, false discovery rate; IPTG, {beta}-D-1-thiogalactopyranoside

plant biology↗

bioRxiv2019

A multidimensional framework for measuring biotic novelty: How novel is a community?

Anthropogenic changes in climate, land use and disturbance regimes, as well as introductions of non-native species can lead to the transformation of many ecosystems. The resulting novel ecosystems are usually characterized by species assemblages that have not occurred previously in a given area. Quantifying the ecological novelty of communities (i.e. biotic novelty) would enhance the understanding of environmental change. However, quantification remains challenging since current novelty metrics, such as the number and/or proportion of non-native species in a community, fall short of considering both functional and evolutionary aspects of biotic novelty. Here, we propose the Biotic Novelty Index (BNI), an intuitive and flexible multidimensional measure that combines (1) functional differences between native and non-native introduced species with (2) temporal dynamics of species introductions. We show that the BNI is an additive partition of Raos quadratic entropy, capturing the novel interaction component of the communitys functional diversity. Simulations show that the index varies predictably with the relative amount of functional novelty added by recently arrived species, and they illustrate the need to provide an additional standardized version of the index. We present a detailed R-code and two applications of the BNI by (1) measuring changes of biotic novelty of dry grassland plant communities along an urbanization gradient in a metropolitan region and (2) determining the biotic novelty of plant species assemblages at a national scale. Results illustrate the applicability of the index across scales and its flexibility in the use of data of different quality. Both case studies revealed strong connections between biotic novelty and increasing urbanization, a measure of abiotic novelty. We conclude that the BNI framework may help in building a basis for a better understanding of the ecological and evolutionary consequences of global change.

ecology↗

bioRxiv2019

Resilience trinity: safeguarding ecosystem services across three different time horizons and decision contexts

Ensuring ecosystem resilience is an intuitive approach to safeguard future provisioning of ecosystem services (ES). However, resilience is an ambiguous concept and difficult to operationalize. Focusing on resilience mechanisms, such as diversity, network architectures or adaptive capacity, has recently been suggested as means to operationalize resilience. Still, the focus on mechanisms is not specific enough because the usefulness of a mechanism is context-dependent. We suggest a conceptual framework, resilience trinity, to facilitate management of resilience mechanisms in three distinctive decision contexts and time-horizons. i) reactive, when there is an imminent threat to ES resilience and a high pressure to act, ii) adjustive, when the threat is known in general but there is still time to adapt management, and iii) provident when time horizons are very long and the nature of the threats is uncertain, leading to a low willingness to act. This emphasizes that resilience has different interpretations and implications at different time horizons which however need to be reconciled. The inclusion of time into resilience thinking ensures that longer-term management actions are not missed while urgent threats to ES are given priority.

ecology↗

bioRxiv2018

Emergence of social inequality in a spatial-ecological public goods game

Spatial ecological public goods, such as forests, grasslands, and fish stocks risk being overexploited by selfish consumers, a phenomenon called \"the tragedy of commons\". The spatial and ecological dimensions introduce new features absent in non spatio-ecological contexts, such as consumer mobility, incomplete information availability, and rapid evolution by social learning. It is unclear how these different processes interact to influence the harvesting and dispersal strategies of consumers. To answer these questions, we develop and analyze an individual-based, spatially-structured evolutionary model with explicit resource dynamics. We find that, 1) When harvesting efficiency is low, consumers evolve a sedentary harvesting strategy, with which resources are harvested sustainably, but harvesting rates remain far below their maximum sustainable value. 2) As harvesting efficiency increases, consumers adopt a mobile consume-and-disperse strategy, which is sustainable, equitable, and allows for maximum sustainable yield. 3) Further increase in harvesting efficiency leads to large-scale overexploitation. 4) If costs of dispersal are significant, increased harvesting efficiency also leads to social inequality between frugal sedentary consumers and overexploitative mobile consumers. Whereas overexploitation can occur without social inequality, social inequality always leads to overexploitation. Thus, we identify four conditions, which are characteristic (and as such positive) features of modern societies resulting from technological progress, but also risk promoting social inequality and unsustainable resource use: high harvesting efficiency, moderately low costs of dispersal, high consumer density, and consumers tendency to rapidly adopt new strategies. We also show that access to global information, which is also a feature of modern societies, may help mitigate these risks.

evolutionary biology↗

bioRxiv2017

Mobility can promote the evolution of cooperation via emergent self-assortment dynamics

The evolution of costly cooperation, where cooperators pay a personal cost to benefit others, requires that cooperators interact more frequently with other cooperators. This condition, called positive assortment, is known to occur in spatially-structured viscous populations, where individuals typically have low mobility and limited dispersal. However many social organisms across taxa, from cells and bacteria, to birds, fish and ungulates, are mobile, and live in populations with considerable inter-group mixing. In the absence of information regarding others traits or conditional strategies, such mixing may inhibit assortment and limit the potential for cooperation to evolve. Here we employ spatially-explicit individual-based evolutionary simulations to incorporate costs and benefits of two coevolving costly traits: cooperative and local cohesive tendencies. We demonstrate that, despite possessing no information about others traits or payoffs, mobility (via self-propulsion or environmental forcing) facilitates assortment of cooperators via a dynamically evolving difference in the cohesive tendencies of cooperators and defectors. We show analytically that this assortment can also be viewed in a multilevel selection framework, where selection for cooperation among emergent groups can overcome selection against cooperators within the groups. As a result of these dynamics, we find an oscillatory pattern of cooperation and defection that maintains cooperation even in the absence of well known mechanisms such as kin interactions, reciprocity, local dispersal or conditional strategies that require information on others strategies or payoffs. Our results offer insights into differential adhesion based mechanisms for positive assortment and reveal the possibility of cooperative aggregations in dynamic fission-fusion populations.\n\nAuthor SummaryCooperation among animals is ubiquitous. In a cooperative interaction, the cooperator confers a benefit to its partner at a personal cost. How does natural selection favour such a costly behaviour? Classical theories argue that cooperative interactions among genetic relatives, reciprocal cooperators, or among individuals within groups in viscous population structures are necessary to maintain cooperation. However, many organisms are mobile, and live in dynamic (fission-fusion) groups that constantly merge and split. In such populations, the above mechanisms may be inadequate to explain cooperation. Here, we develop a minimal model that explicitly accounts for mobility and cohesion among organisms. We find that mobility can support cooperation via emergent dynamic groups, even in the absence of previously known mechanisms. Our results may offer insights into the evolution of cooperation in animals that live in fission fusion groups, such as birds, fish or mammals, or microbes living in turbulent media, such as in oceans or in the bloodstreams of animal hosts.

evolutionary biology↗