Biology subjects

Singh, G.

Publications and source records attributed to Singh, G..

At least 91 records · Page 5Linked to original sources

bioRxiv2022

A Framework for Designing Efficient Deep Learning-Based Genomic Basecallers

Nanopore sequencing generates noisy electrical signals that need to be converted into a standard string of DNA nucleotide bases using a computational step called basecalling. The performance of basecalling has critical implications for all later steps in genome analysis. Therefore, there is a need to reduce the computation and memory cost of basecalling while maintaining accuracy. We present RUBICON, a framework to develop efficient hardware-optimized basecallers. We demonstrate the effectiveness of RUBICON by developing RUBICALL, the first hardware-optimized mixed-precision basecaller that performs efficient basecalling, outperforming the state-of-the-art basecallers. We believe RUBICON offers a promising path to develop future hardware-optimized basecallers.

genomics↗

bioRxiv2022

Exposure to environmental stress decreases the resistance of river microbial communities towards invasion by antimicrobial resistant bacteria

Environmental microbiomes are constantly exposed to invasion events through foreign, antibiotic resistant bacteria that were enriched in the anthropic sphere. However, the biotic and abiotic factors, as well as the natural barriers that determine the invasion success of these invader bacteria into the environmental microbiomes are poorly understood. A great example of such invasion events are river microbial communities constantly exposed to resistant bacteria originating from wastewater effluents. Here, we aim at gaining comprehensive insights into the key factors that determine their invasion success with a particular focus on the effects of environmental stressors, regularly co-released in wastewater effluents. Understanding invasion dynamics of resistant bacteria is crucial for limiting the environmental spread of antibiotic resistance. To achieve this, we grew natural microbial biofilms on glass slides in rivers for one month. The biofilms were then transferred to laboratory, recirculating flume systems and exposed to a single pulse of a model resistant invader bacterium (E. coli) either in presence or absence of stress induced by Cu2+. The invasion dynamics of E. coli into the biofilms were then monitored for 14 days. Despite an initially successful introduction of E. coli into the biofilms, independent of the imposed stress, over time the invader perished in absence of stress. However, under stress c the invading strain successfully established and proliferated in the biofilms. Noteworthy, the increased establishment success of the invader coincided with a loss in microbial community diversity under stress conditions, likely due to additional niche space becoming available for the invader.

microbiology↗

bioRxiv2022

Consumption of the non-nutritive sweetener stevia for 12 weeks does not alter the composition of the gut microbiota

The use of non-nutritive sweeteners (NNS) as an alternative to caloric sugars has increased in recent years. Stevia is a NNS that has demonstrated beneficial effects on appetite and energy intake. However, the impact on the gut microbiome is not well understood. Therefore, we investigated how regular consumption of stevia, for up to 12 weeks, impacts upon the human gut microbiome. Healthy subjects with a normal body mass index participated in the study; the stevia group (n = 14) were asked to consume five drops of stevia, twice daily, compared against control participants (n = 13). Faecal samples collected before and after treatment were analysed by 16S sequencing. Stevia did not cause significant changes in the beta or alpha diversity when compared to the control groups. When relative abundances of taxa were investigated, no clear differences could be detected. Conversely, random forest analysis could correctly associate the gut microbiome with control and stevia groups with an average of 75% accuracy, suggesting that there are intrinsic patterns that could discriminate between control and stevia use. However, large-scale changes in the gut microbiome were not apparent in this study and therefore, our data suggest that stevia does not significantly impact the gut microbiome.

microbiology↗

bioRxiv2022

Catch bonds in sickle cell disease: shear-enhanced adhesion of red blood cells to laminin

Could the phenomenon of catch bonding--force-strengthened cellular adhesion--play a role in sickle cell disease, where abnormal red blood cell (RBC) adhesion obstructs blood flow? Here we investigate the dynamics of sickle RBCs adhering to a surface functionalized with the protein laminin (a component of the extracellular matrix around blood vessels) under physiologically relevant micro-scale flow. First, using total internal reflectance microscopy we characterize the spatial fluctuations of the RBC membrane above the laminin surface before detachment. The complex dynamics we observe suggest the possibility of catch bonding, where the mean detachment time of the cell from the surface initially increases to a maximum and then decreases as a function of shear force. We next conduct a series of shear-induced detachment experiments on blood samples from 25 sickle cell disease patients, quantifying the number and duration of adhered cells under both sudden force jumps and linear force ramps. The experiments reveal that a subset of patients does indeed exhibit catch bonding. By fitting the data to a theoretical model of the bond dynamics, we can extract the mean bond lifetime versus force for each patient. The results show a striking heterogeneity among patients, both in terms of the qualitative behavior (whether or not there is catch bonding) and in the magnitudes of the lifetimes. Patients with large bond lifetimes at physiological forces are more likely to have certain adverse clinical features, like a diagnosis of pulmonary arterial hypertension and intracardiac shunts. By introducing an in vitro platform for fully characterizing RBC-laminin adhesion dynamics, our approach could contribute to the development of patient-specific anti-adhesive therapies for sickle cell disease. The experimental setup is also easily generalizable to studying adhesion dynamics in other cell types, for example leukocytes or cancer cells, and can incorporate disease-relevant environmental conditions like oxygen deprivation. SIGNIFICANCEAbnormal red blood cell adhesion to the walls of blood vessels is a central feature of sickle cell disease. We study this adhesion by experimentally measuring how long on average red blood cells adhere to a protein-covered surface, and how the strength of the cell-protein bond depends on the force resulting from the surrounding fluid flow. The results vary widely from patient to patient, with some cases showing an unusual regime where the mean bond strength increases with force. We connect these measurements to clinical aspects of the disease, which may aid in the design of individualized therapies in the future.

biophysics↗

bioRxiv2022

Protein kinase gene declines linearly with elevation: a shared genomic feature across species and continents in lichenized fungi suggests role in climate adaptation

Intraspecific genomic variability affects a species adaptive potential towards climatic conditions. Variation in gene content across populations and environments may point at genomic adaptations to specific environments. The lichen symbiosis, a stable association of fungal and photobiont partners, offers an excellent system to study environmentally driven gene content variation. Many species have remarkable environmental tolerances, and often form populations in different climate zones. Here we combine comparative and population genomics to assess the presence and absence of genes in high elevation and low elevation genomes of two lichenized fungi of the genus Umbilicaria. The two species have non-overlapping ranges, but occupy similar climatic niches in North America (U. phaea) and Europe (U. pustulata): high elevation populations are located in the cold temperate zone and low elevation populations in the Mediterranean zone. We assessed gene content variation along replicated elevation gradients in each of the two species, based on a total of 2050 individuals across 26 populations. Specifically, we assessed shared orthologs across species within the same climate zone, and tracked which genes increase or decrease in abundance within populations along elevation. In total, we found 16 orthogroups with shared orthologous genes in genomes at low elevation and 13 at high elevation. Coverage analysis revealed one ortholog that is exclusive to genomes at low elevation. Conserved domain search revealed domains common to the protein kinases (PKs) superfamily. We traced the discovered ortholog in populations along five replicated elevation gradients on both continents. The protein kinase gene linearly declined in abundance with increasing elevation, and was absent in the highest populations. We consider the parallel loss of an ortholog in two species and in two geographic settings a rare find, and a step forward in understanding the genomic underpinnings of climatic tolerances in lichenized fungi. In addition, the tracking of gene content variation provides a widely applicable framework for retrieving biogeographical determinants of gene presence/absence patterns. Our work provides insights into gene content variation of lichenized fungi in relation to climatic gradients, suggesting a new research direction with implications for understanding evolutionary trajectories of complex symbioses in relation to climatic change.

genomics↗

bioRxiv2022

Site of vulnerability on SARS-CoV-2 spike induces broadly protective antibody to antigenically distinct omicron SARS-CoV-2 subvariants

The rapid evolution of SARS-CoV-2 Omicron variants has emphasized the need to identify antibodies with broad neutralizing capabilities to inform future monoclonal therapies and vaccination strategies. Herein, we identify S728-1157, a broadly neutralizing antibody (bnAb) targeting the receptor-binding site (RBS) and derived from an individual previously infected with SARS-CoV-2 prior to the spread of variants of concern (VOCs). S728-1157 demonstrates broad cross-neutralization of all dominant variants including D614G, Beta, Delta, Kappa, Mu, and Omicron (BA.1/BA.2/BA.2.75/BA.4/BA.5/BL.1). Furthermore, it protected hamsters against in vivo challenges with wildtype, Delta, and BA.1 viruses. Structural analysis reveals that this antibody targets a class 1 epitope via multiple hydrophobic and polar interactions with its CDR-H3, in addition to common class 1 motifs in CDR-H1/CDR-H2. Importantly, this epitope is more readily accessible in the open and prefusion state, or in the hexaproline (6P)-stabilized spike constructs, as compared to diproline (2P) constructs. Overall, S728-1157 demonstrates broad therapeutic potential, and may inform target-driven vaccine design against future SARS-CoV-2 variants.

immunology↗

bioRxiv2022

Astrocytic Sleep Homeostasis Model

Sleep awake cycle is critical for cognitive and functional abilities. Conventional sleep homeostasis mechanisms are neuronal in nature and recent views indicate glial regulation of the sleep-wake process. Mechanisms of homeostatic regulation of sleep remain to be understood. A simplified astrocytic sleep-awake homeostasis mathematical model with sleep pressure and synaptic strength dynamics is proposed using feedback control loops. The model provides insights into the emergence of two discrete states through sleep and awake promoting neuronal populations giving rise to a homeostatic process S and oscillatory process C is regulated by astrocytic sleep pressure. It also explains the variations seen in synaptic strength dynamics during sleep and awake states.

neuroscience↗

bioRxiv2022

Therapy Induced Tumor Senescence Model

Senescent cell accumulation and defective clearance of the senescent cells by the immune system occur with aging and increase the prevalence of diseases like cancer. Anti-tumor therapies can induce senescence in the tumor cells. Senescence Associated Secretory Phenotypes (SASP) secretion by these senescent tumor cells activates the innate NK cells which can detect and eliminate them. Mechanisms are unclear about how does it occur? A combination of immunotherapy and senotherapy has shown the possibility to reduce the tumor burden and increase the health span. The temporal and intensity dynamics of the therapeutic dose regimen remains to be studied. Therefore, a simplified therapy-induced senescence (TIS) phenomenological model is proposed to explain the mechanism of senescent tumor cell clearance by the NK immune cells and understand the possibility of a two-punch therapy technique in regulating tumors. Interaction strength changes for the cellular population within a healthy and an aged tumor microenvironment. The simulation result shows an oscillatory behavior existing between the tumor and immune cells. Tumor heterogeneity acts as inherent noise in sustaining the tumor for relapse emergence despite therapeutic clearance. The model indicates the formation of a robust oscillatory loop between the tumor, immune, and senescence cells which they can tune by modifying the phenotypic fitness landscape through secreted factors making them resistant despite selective removal of the sensitive populations by various therapies. The model highlights the importance of modified and aged tumor microenvironment by senescence tumor cells in obstructing clearance of both senescence and tumor cells by the innate immune system. Cancer therapies along with senolytics may have a robust and effective regulatory potential over tumor and senescence cells. The model also provides a preliminary analysis of the therapy temporal and intensity dosage regimen causing a therapeutic shift in tumors.

systems biology↗

bioRxiv2022

Biophysical Characterization of an Essential Mammalian Protein; Transcription Termination Factor I (TTF1)

Mammalian Transcription Terminator Factor 1 (TTF1) is an essential protein which plays diverse cellular physiological functions like transcription regulation (both initiation and termination), replication fork blockage, chromatin remodelling, DNA damage repair etc. Hence, understanding the structure and mechanism conferred by its variable confirmations becomes significantly important. But so far, almost nothing is known about the structure of either the full-length protein or any of its domain in isolation. Moving towards achieving the above goals, our lab has codon optimised, expressed and purified N-terminal 190 amino acid deleted TTF1 ({Delta}N190TTF1) protein, since full length protein even after multiple trials could not be purified in soluble form. In this article, we have characterized this essential protein by studying its homogeneity, molecular size and secondary structure using tools like dynamic light scattering (DLS), circular dichroism (CD) spectroscopy, Raman spectroscopy and atomic force microscopy (AFM). By CD and DLS we have shown that the purified protein is homogenous and soluble. CD spectroscopy also revealed that {Delta}N190TTF1 is a helical protein which was further confirmed by analysis of Raman spectra and Amide I region deconvolution studies. AFM imaging data discovered the size of single protein molecule to be 94 nm which is in agreement with the size determined by the DLS study as well. Our structural and biophysical characterization of this essential protein will open avenues towards solving the structure to atomic resolution and also will encourage the research to investigate the mechanism behind its diverse functions attributed to its various domains.

biochemistry↗

bioRxiv2022

Attenuated Dengue Virus PV001-DV Induces Oncolytic Cell Death and Potent Anti-Tumor Immunity

Viral therapies developed for cancer treatment have classically prioritized direct oncolytic effects over their immune activating properties. However, recent clinical insights have challenged this longstanding prioritization and have shifted the focus to more immune-based mechanisms. Through the potential utilization of novel, inherently immune-stimulating, oncotropic viruses there is a therapeutic opportunity to improve anti-tumor outcomes through virus-mediated immune activation. PV001-DV, is an attenuated strain of Dengue virus (DEN-1 #45AZ5) with a favorable clinical safety profile that also maintains the potent immune stimulatory properties known of Dengue virus. In this study, we examined the anti-tumor effects of PV001-DV as a potential novel cancer immunotherapy. In vitro assays demonstrated that PV001-DV possesses the ability to directly kill human melanoma cells lines as well as patient melanoma tissue ex vivo. Importantly, further in vitro work demonstrated that, when patient peripheral blood mononuclear cells (PBMCs) were exposed to PV001-DV, a substantial induction in production of apoptotic factors and immunostimulatory cytokines was detected. When tumor cells were cultured with the resulting soluble mediators from these PBMCs, rapid cell death of melanoma and breast cancer cell lines was observed. The direct tumor-killing and immune-mediated tumor cytotoxicity facilitated by PV001-DV contributes support of its upcoming clinical evaluation in patients with advanced melanoma who have failed prior therapy (NCT03989895).

cancer biology↗

bioRxiv2022

Systematic Design of Pulse Dosing to Eradicate Persister Bacteria

A small fraction of infectious bacteria use persistence as a strategy to survive exposure to antibiotics. Periodic pulse dosing of antibiotics has long been considered a potentially effective strategy towards eradication of persisters. Recent studies have demonstrated through in vitro experiments that it is indeed feasible to achieve such effectiveness. However, systematic design of periodic pulse dosing regimens to treat persisters is currently lacking. Here we rigorously develop a methodology for the systematic design of optimal periodic pulse dosing strategies for rapid eradication of persisters. A key outcome of the theoretical analysis, on which the proposed methodology is based, is that bactericidal effectiveness of periodic pulse dosing depends mainly on the ratio of durations of the corresponding on and off parts of the pulse. Simple formulas for critical and optimal values of this ratio are derived. The proposed methodology is supported by computer simulations and in vitro experiments. Author SummaryAdministering antibiotics in periodic pulses that alternate between high and low concentration has long been known as a possible dosing strategy to treat stubborn infections caused by bacteria known as persisters. Such bacteria use clever mechanisms to survive otherwise lethal temporary exposure to antibiotics and to resume normal activity upon antibiotic removal. Persisters pose a serious health problem. Recent studies have elucidated mechanisms of persistence and have confirmed that pulse dosing, if designed appropriately, can indeed be effective. However, effective pulse dosing design has been mainly handled by trial and error, requiring relatively extensive experimentation. Here we develop a method for rapid systematic design of effective pulse dosing. The method relies on a simple mathematical model and a minimal amount of standard experimental data. We derive corresponding design formulas that explicitly characterize the shape of generally effective or optimal periodic pulses. We tested our method through computer simulations and in vitro experiments, as well as on prior literature data. In all cases, the outcomes on persister bacteria eradication predicted by our method were confirmed. These results pave the way for ultimately developing effective pulse dosing regimens in realistic situations in vivo.

systems biology↗

bioRxiv2022

Genome mining as a biotechnological tool for the discovery of novel biosynthetic genes in lichens

The ever-increasing demand for novel drugs highlights the need for bioprospecting unexplored taxa for their biosynthetic potential. Lichen-forming fungi (LFF) are a rich source of natural products but their implementation in pharmaceutical industry is limited, mostly because the genes corresponding to a majority of their natural products is unknown. Furthermore, it is not known to what extent these genes encode structurally novel molecules. Advance in next-generation sequencing technologies has expanded the range of organisms that could be exploited for their biosynthetic potential. In this study, we mine the genomes of nine lichen-forming fungal species of the genus Umbilicaria for biosynthetic genes, and categorize the BGCs as "associated product structurally known", and "associated product putatively novel". We found that about 25-30% of the biosynthetic genes are divergent when compared to the global database of BGCs comprising of 1,200,000 characterized biosynthetic genes from planta, bacteria and fungi. Out of 217 total BGCs, 43 were only distantly related to known BGCs, suggesting they encode structurally and functionally unknown natural products. Clusters encoding the putatively novel metabolic diversity comprise PKSs (30), NRPSs (12) and terpenes (1). Our study emphasizes the utility of genomic data in bioprospecting microorganisms for their biosynthetic potential and in advancing the industrial application of unexplored taxa. We highlight the untapped structural metabolic diversity encoded in the lichenized fungal genomes. To the best of our knowledge, this is the first investigation identifying genes coding for NPs with potentially novel therapeutic properties in LFF.

genomics↗

bioRxiv2022

miR-34a negatively regulates cell cycle factor Cdt2/DTL in HPV infected Cervical Cancer Cells

MicroRNAs have emerged as an important factor in regulating cell cycle and various other cellular processes. Aberration in microRNAs has been linked with development of several cancers and other diseases but still very little is known about the mechanism behind their function in regulating cellular processes. 99% of cervical cancer is caused by the infection of high-risk HPVs (HR HPVs) which suppresses multiple tumor suppressors and checkpoint factors of the host cell. It also stabilizes oncogenic proteins, one of them is Cdt2/DTL which promotes cell transformation and proliferation. In this study, we have reported that in cervical cancer cell lines miR-34a by targeting HPV E6 protein, regulates Cdt2/DTL protein level and leads to its destabilization. Destabilization of Cdt2 stabilizes onco-suppressor proteins like p21 and Set8 in these cell lines. We have also shown that the overexpression of miR-34a suppresses cell proliferation, invasion and migration capabilities of HPV positive cervical cancer cells which was reverted by overexpression of either HPV E6 or Cdt2 genes. This is the first-ever report to show that miR-34a regulates cell cycle factor Cdt2 by suppressing viral E6 protein level, which opens up the scope of exploring miR-34a as a specific therapy for cervical cancer treatment. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/486030v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@723381org.highwire.dtl.DTLVardef@1937614org.highwire.dtl.DTLVardef@2d1ce1org.highwire.dtl.DTLVardef@1c31bc5_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2022

Trivalent NDV-HXP-S vaccine protects against phylogenetically distant SARS-CoV-2 variants of concern in mice

Equitable access to vaccines is necessary to limit the global impact of the coronavirus disease 2019 (COVID-19) pandemic and the emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. In previous studies, we described the development of a low-cost vaccine based on a Newcastle Disease virus (NDV) expressing the prefusion stabilized spike protein from SARS-CoV-2, named NDV-HXP-S. Here, we present the development of next-generation NDV-HXP-S variant vaccines, which express the stabilized spike protein of the Beta, Gamma and Delta variants of concerns (VOC). Combinations of variant vaccines in bivalent, trivalent and tetravalent formulations were tested for immunogenicity and protection in mice. We show that the trivalent preparation, composed of the ancestral Wuhan, Beta and Delta vaccines, substantially increases the levels of protection and of cross-neutralizing antibodies against mismatched, phylogenetically distant variants, including the currently circulating Omicron variant.

immunology↗

bioRxiv2022

A mRNA vaccine encoding for a RBD 60-mer nanoparticle elicits neutralizing antibodies and protective immunity against the SARS-CoV-2 delta variant in transgenic K18-hACE2 mice

Two years into the COVID-19 pandemic there is still a need for vaccines to effectively control the spread of novel SARS-CoV-2 variants and associated cases of severe disease. Here we report a messenger RNA vaccine directly encoding for a nanoparticle displaying 60 receptor binding domains (RBDs) of SARS-CoV-2 that acts as a highly effective antigen. A construct encoding the RBD of the delta variant elicits robust neutralizing antibody response with neutralizing titers an order of magnitude above currently approved mRNA vaccines. The construct also provides protective immunity against the delta variant in a widely used transgenic mouse model. We ultimately find that the proposed mRNA RBD nanoparticle-based vaccine provides a flexible platform for rapid development and will likely be of great value in combatting current and future SARS-CoV-2 variants of concern.

immunology↗

bioRxiv2022

Symbolic quantitative cognition in wild zebrafish (Danio rerio)

Zebrafish (Danio rerio) constitute an excellent model system to investigate the neural and genetic basis of quantitative cognition We tested the ability of reward quantity discrimination of wild-type zebrafish in an associative learning task. We used an operant conditioning paradigm in which the number of horizontal lines zebrafish approached in a 2-alternative forced choice task predicted the number of food reward pellets they would receive. Zebrafish did not learn a preference for the 2-line stimulus predictive of receiving 2 food pellets. However, a subset of the fish performed significantly above chance in a discrimination task with the same apparatus, in which the 2-line stimulus was associated with the same reward but the choice of the 1-line stimulus was not rewarded. Zebrafish also showed a population level learning in a simpler spatial association task with the same apparatus. We also explored the explanatory value of alternative spatial learning hypotheses such as a Win-Stay, Lose-Shift (WSLS) strategy at the individual level for fish in navigating these spatially randomised tasks.

animal behavior and cognition↗

bioRxiv2022

Discovery of a SARS-CoV-2 Broadly-Acting Neutralizing Antibody with Activity against Omicron and Omicron + R346K Variants

The continual emergence of SARS-CoV-2 variants of concern, in particular the newly emerged Omicron (B.1.1.529) variant, has rendered ineffective a number of previously EUA approved SARS-CoV-2 neutralizing antibody therapies. Furthermore, even those approved antibodies with neutralizing activity against Omicron are reportedly ineffective against the subset of Omicron variants that contain a R346K substitution, demonstrating the continued need for discovery and characterization of candidate therapeutic antibodies with the breadth and potency of neutralizing activity required to treat newly diagnosed COVID-19 linked to recently emerged variants of concern. Following a campaign of antibody discovery based on the vaccination of Harbour H2L2 mice with defined SARS-CoV-2 spike domains, we have characterized the activity of a large collection of Spike-binding antibodies and identified a lead neutralizing human IgG1 LALA antibody, STI-9167. STI-9167 has potent, broad-spectrum neutralizing activity against the current SARS-COV-2 variants of concern and retained activity against the Omicron and Omicron + R346K variants in both pseudotype and live virus neutralization assays. Furthermore, STI-9167 nAb administered intranasally or intravenously provided protection against weight loss and reduced virus lung titers to levels below the limit of quantitation in Omicron-infected K18-hACE2 transgenic mice. With this established activity profile, a cGMP cell line has been developed and used to produce cGMP drug product intended for use in human clinical trials.

microbiology↗

bioRxiv2022

A candidate gene cluster for the bioactive natural product gyrophoric acid in lichen-forming fungi

Natural products of lichen-forming fungi are structurally diverse and have a variety of medicinal properties. Despite this, they a have limited implementation in industry, because the corresponding genes remain unknown for most of the natural products. Here we implement a long-read sequencing and bioinformatic approach to identify the biosynthetic gene cluster of the bioactive natural product gyrophoric acid (GA). Using 15 high-quality genomes representing nine GA-producing species of the lichen-forming fungal genus Umbilicaria, we identify the most likely GA cluster and investigate cluster gene organization and composition across the nine species. Our results show that GA clusters are promiscuous within Umbilicaria, with only three genes that are conserved across species, including the PKS gene. In addition, our results suggest that the same cluster codes for different but structurally similar NPs, i.e., GA, umbilicaric acid and hiascic acid, bringing new evidence that lichen metabolite diversity is also generated through regulatory mechanisms at the molecular level. Ours is the first study to identify the most likely GA cluster, and thus provides essential information to open new avenues for biotechnological approaches to producing and modifying GA and similar lichen-derived compounds. We show that bioinformatics approaches are useful in linking genes and potentially associated natural products. Genome analyses help unlocking the pharmaceutical potential of organisms such as lichens, which are biosynthetically diverse but slow growing, and difficult to cultivate due to their symbiotic nature. ImportanceThe implementation of natural products in the pharmaceutical industry relies on the possibility of modifying the natural product (NP) pathway to optimize yields and pharmacological effects. Characterization of genes and pathways underlying natural product biosynthesis is a major bottleneck for the use of natural products in the pharmaceutical industry. Genome mining is a promising and relatively cost- and time-effective approach to exploit unexplored NP resources for drug discovery. In this study, we identify the most likely gene cluster for the lichen-forming fungal depside gyrophoric acid in nine Umbilicaria species. This compound shows cytotoxic and antiproliferative properties against several cancer cell lines, and is also a broad-spectrum antimicrobial agent. We identify the putative GA cluster from nine Umbilicaria species. This information paves the way for generating GA analogs with modified properties by selective activation/deactivation of genes.

genomics↗