bioRxiv Science⌕ Search

Biology subjects

Ram, S.

Publications and source records attributed to Ram, S..

At least 19 recordsLinked to original sources

Individual differences in post-encoding sleep continuity predict context memory accuracy and supporting ERPs in younger and older adults

Post-encoding sleep plays an essential role in episodic memory consolidation. Much of the existing literature on sleep and memory relies on deprivation paradigms or laboratory-controlled sleep. Relatively few studies have examined how naturalistic post-encoding sleep relates to memory retrieval and its supporting neural activity, or whether age-related impairments in this sleep are linked to those in episodic memory. In the present study, we used actigraphy and electroencephalography to examine how post-encoding sleep quality relates to context memory performance and retrieval-related ERPs supporting performance in younger and older adults. Participants encoded object-scene pairs and were tested on matching and mismatching pairs after a 96-hour sleep-filled delay. We found that greater post-encoding sleep continuity predicted better delayed context memory performance for mismatching pairs across age groups. Post-encoding sleep continuity was also associated with larger ERP differences between context hits and misses for context-matching pairs, for ERP effects associated with post-retrieval monitoring operations across age groups. Together, these findings suggest that more continuous, naturalistic post-encoding sleep facilitates episodic memory performance and neural mechanisms supporting episodic memory retrieval across adult age.

neuroscience↗

Structural basis for recognition of a gonococcal lipooligosaccharide epitope by monoclonal antibody 2C7 informs vaccine and immunotherapeutic design

Neisseria gonorrhoeae causes gonorrhea and poses a growing global health threat driven by antimicrobial resistance and the lack of an effective vaccine. The lipooligosaccharide (LOS) epitope recognized by monoclonal antibody (mAb) 2C7 is expressed by most clinical isolates, making it an attractive therapeutic target. To determine the molecular basis for mAb 2C7 recognition, we conducted structural studies of mAb 2C7 in complex with an octasaccharide derived from LOS. NMR epitope mapping demonstrated that mAb 2C7 contacts two of three glycan chains: the {beta}-chain (lactose) and the {gamma}-chain (N-acetylglucosamine). The 1.6-[A] resolution crystal structure of the Fab 2C7-octasaccharide complex revealed that these chains make extensive hydrogen bonds and hydrophobic contacts within a cleft of the Fab. Molecular dynamics (MD) simulations showed that the {beta} and {gamma} chains adopt stable, specific conformations, contrasted with transient interactions of the chain. Informed by these structural data, we synthesized a tetrasaccharide comprising the {beta} and {gamma} chains joined by heptose II. The tetrasaccharide conjugated to a carrier protein bound mAb 2C7 by ELISA and Western blotting. Isothermal titration calorimetry showed that the tetrasaccharide and octasaccharide bound mAb 2C7 with similar affinities, indicating that the smaller oligosaccharide retains the key binding determinants. Binding was enthalpically driven, consistent with the polar interactions observed crystallographically and by MD. NMR experiments with the tetrasaccharide confirmed interactions with all four residues, establishing it as the minimal 2C7 epitope. Together, these studies provide a structural framework for rational design of glycan-based vaccines and antibody therapeutics against antimicrobial-resistant N. gonorrhoeae.

microbiology↗

Pre-clinical efficacy of a C4BP hexameric IgG Fc fusion protein against Neisseria gonorrhoeae

Gonorrhea is the second most common bacterial sexually transmitted infection and affects about 80 million people worldwide annually. The causative agent, Neisseria gonorrhoeae, has become resistant to almost every antibiotic used for its treatment. There is no licensed vaccine against gonorrhea. Therefore, there is an urgent need to develop novel prevention and treatment strategies to curb the spread of gonorrhea. The gonococcus has evolved several mechanisms to evade complement, a key arm of immune defenses against this pathogen, including binding of the human complement inhibitors Factor H (FH) and C4b-binding protein (C4BP). We previously showed that chimeric molecules fusing the gonococcal binding domains of FH and C4BP to IgG Fc and IgM Fc, respectively, mediate complement-dependent killing of gonococci in vitro and attenuate gonococcal colonization of mouse vaginas when administered topically. Here, we fused C4BP domains 1 and 2, which contain the gonococcal binding region, to IgG Fc bearing the IgM tail-piece to facilitate Fc hexamerization. This molecule, called C4BP-Hexa IgG Fc, showed [~]650-fold greater complement-dependent bactericidal activity on a molar basis than monomeric C4BP-IgG1 Fc. C4BP-Hexa IgG Fc enhanced association with and uptake by human neutrophils in a complement-independent manner. Despite off-target complement activation in solution, C4BP-Hexa IgG Fc reduced both the duration and the bacterial burden of gonococcal vaginal colonization in human FH and C4BP transgenic mice when administered intravaginally daily. In conclusion, we show proof-of-concept of the efficacy of a hexameric C4BP IgG Fc fusion molecule against N. gonorrhoeae, which could aid in the fight against this multidrug-resistant pathogen.

immunology↗

C4BP occludes the non-opsonic interaction of Neisseria gonorrhoeae with human neutrophil CEACAMs

Neisseria gonorrhoeae (Gc) causes the sexually transmitted infection gonorrhea, an urgent public health concern. Gc infection elicits a robust neutrophil response and serum leakage, but Gc has developed specialized defenses to evade both complement and neutrophils. We recently reported that the classical complement pathway inhibitor C4b-binding protein (C4BP) binds to Gc and reduces phagocytic killing by neutrophils in a complement-independent manner. Here, we used a Chinese hamster ovary (CHO) expression system and engineered C4BP constructs to define the underlying molecular mechanisms. C4BP inhibited interactions between opacity protein (Opa)-expressing Gc and carcinoembryonic antigen-related cell adhesion molecules (CEACAMs), receptors that drive non-opsonic phagocytosis of Gc by neutrophils. The degree of C4BP-mediated inhibition varied among CEACAMs. By using wild-type and chimeric CEACAMs, we found C4BP was more inhibitory towards the granulocyte-restricted CEACAM3 than the ubiquitously expressed CEACAM1, which we ascribed to CEACAM3s shorter extracellular domain. C4BP also inhibited the association between Opa-expressing Gc and the GPI-anchored CEACAM6. Molecules containing C4BP domains 1 and 2 fused to IgM (C4BP-IgM) or to a hexameric IgG Fc construct (C4BP-Hexa-IgG), proteins similar in diameter and degree of multimerization to native C4BP, inhibited the association of Opa-expressing Gc with CEACAM3-CHO cells to the same degree as C4BP, while C4BP domains 1 and 2 fused to dimeric Fc (C4BP-IgG) did not. C4BP-IgM, but not C4BP-IgG bearing mutations to abrogate Fc gamma receptor interactions, blocked Opa-mediated phagocytosis by primary human neutrophils. These results support a model in which C4BP occludes Opa-CEACAM interactions, which protects Gc from phagocytic killing by neutrophils.

microbiology↗

The sialome of the retina, alteration in age-related macular degeneration (AMD) pathology and potential impacts on Complement Factor H

PurposeLittle is known about sialic acids of the human retina, despite their integral role in self/non-self-discrimination by complement factor H (CFH), the alternative complement pathway inhibitor. MethodsA custom sialoglycan microarray was used to characterize the sialic acid-binding specificity of native CFH or recombinant molecules where IgG Fc was fused to CFH domains 16-20 (contains a sialic acid-binding site), domains 6-7 (contains a glycosaminoglycan-binding site) or the CFH-related proteins (CFHRs) 1 and 3. We analyzed macular and peripheral retinal tissue from post-mortem ocular globes for amount, type, and presentation (glycosidic linkage type) of sialic acid in individuals with age-related macular degeneration (AMD) and age-matched controls using fluorescent lectins and antibodies to detect sialic acid and endogenous CFH. Released sialic acids from neural retina, retinal pigmented epithelium (RPE) cells and the Bruchs membrane (BrM) were labelled with 1,2-diamino-4,5-methylenedioxybenzene-2HCl (DMB), separated and quantified by high-performance liquid chromatography (DMB-HPLC). ResultsBoth native CFH and the recombinant CFH domains 16-20 recognized Neu5Ac and Neu5Gc that is 2-3-linked to the underlying galactose. 4-O-Actylation of sialic acid and sulfation of GlcNAc did not inhibit binding. Different linkage types of sialic acid were localized at different layers of the retina. The greatest density of 2-3-sialic acid, which is the preferred ligand of CFH, did not colocalize with endogenous CFH. The level of sialic acids at the BrM/choroid interface of macula and peripheral retina of individuals with AMD were significantly reduced. ConclusionsThe sialome of the human retina is altered in AMD. This can affect CFH binding and consequently, alternative complement pathway regulation.

biochemistry↗

Global survey of secondary metabolism in Aspergillus niger via activation of specific transcription factors

Genomics analysis confirmed the status of the filamentous fungi as a rich source of novel secondary metabolites; however, the discovery of these compounds is hampered by the cryptic nature of their biosynthetic pathways under laboratory conditions. Consequently, despite substantial research effort over the past decades, much of the secondary metabolome remains uncharacterized in fungal organisms. Our manual curation of biosynthetic gene clusters (BGCs) in the Aspergillus niger NRRL3 genome revealed that only 13 of 86 BGCs have had their cognate secondary metabolite products confirmed or reliably inferred. We also identified 60 transcription factors associated with cryptic BGCs. To further characterize A. niger secondary metabolism, we created a collection of strains each overexpressing a single BGC-associated transcription factor. We analyzed the strain collection using a standardized pipeline where we monitored phenotypic changes and compound production using mass spectrometry. Strains showing evidence of secondary metabolism activation were selected for gene expression analysis. Our approach resulted in the production of multiple potentially novel secondary metabolites and linked a specific BGC to tensidol production in A. niger. More broadly, this study found evidence counter to the existing paradigm of BGC expression controlled by co-localized transcription factors, lending credence to the emerging picture of a complex regulatory network governing fungal secondary metabolism. Significance StatementFungi produce an array of chemically diverse compounds that are routinely found to harbour valuable bioactivity. The products of secondary metabolism, these compounds have been a source of antimicrobials, anti-cancer agents, and other biopharmaceutical compounds termed natural products. Despite their demonstrated economic value, much is still unknown about the biosynthesis, regulation, and identities of these compounds. This study adopted a genome-wide approach to improve our understanding of the regulatory mechanisms that control fungal secondary metabolism, improving our ability to investigate the pathways responsible for natural product production.

microbiology↗

The long non-coding RNA NEAT1 regulates the transcriptional landscape of cardiomyocytes

Long non-coding RNAs (lncRNAs) play a crucial role in fine-tuning the gene expression. In the present study, we identified that the lncRNA NEAT1 is upregulated in failing murine hearts and in human hypertrophic cardiomyopathies. Further investigations demonstrated that NEAT1 expression is regulated by calcium dependent NFAT (nuclear factor of activated T cells). Overexpression of NEAT1 led to increased cardiomyocyte size and elevated expression of cardiac stress markers while its depletion had the opposite effect. Through transcriptomic analysis in NEAT1-KO cells, we demonstrated the cis-regulatory role of NEAT1, wherein it maintains the transcription of neighboring genes by interacting with the coactivator p300. Additionally, NEAT1 depletion resulted in decreased expression of GRK2 (G protein-coupled receptor kinase 2), a key player in the development of cardiac hypertrophy, suggesting that NEAT1 contributes to the development of cardiac hypertrophy by regulating GRK2 expression. Consistent with this, Neat1-/- mice are resistant to {beta}-adrenergic stimulation. Overall, our study provides enough evidence that NEAT1 is a calcium-regulated, pro-hypertrophic lncRNA that exerts significant control over the transcriptional landscape of cardiomyocytes during heart failure.

cell biology↗

Gardnerella vaginolysin potentiates glycan molecular mimicry by Neisseria gonorrhoeae

Bacterial vaginosis (BV) is a condition of the vaginal microbiome in which there are lower levels of "healthy" Lactobacillus species and an outgrowth of diverse anaerobic bacteria. BV is associated with increased risk of infection by the bacterium Neisseria gonorrhoeae - the causative agent of gonorrhea. Here we test if one known facet of BV - the presence of bacterial cytolysins - leads to the mobilization of specific intracellular contents that aid in gonococcal virulence. We cloned and expressed recombinant vaginolysin (VLY), a cytolysin produced by the BV-associated bacterium Gardnerella, verifying that it liberates the contents of red blood cells and cervical epithelial (HeLa) cells while vector control preparations made in parallel did not. We tested if VLY mediates a well-known virulence mechanism of gonococcus - the molecular mimicry of host glycans. To evade host immunity, N. gonorrhoeae caps its surface lipooligosaccharide (LOS) with 2-3-linked sialic acid. To do this, gonococci must scavenge an intermediate metabolite made and used inside host cells. Flow-cytometry based lectin-binding assays showed that, compared to controls, gonococci exposed to vaginolysin-liberated contents of HeLa cells displayed greater sialic acid capping of their LOS. This higher level of bacterial sialylation was accompanied by increased binding of the complement regulatory protein Factor H, and greater resistance to complement attack. Together these results suggest that cytolytic activities present during BV may enhance the ability of N. gonorrhoeae to capture intracellular metabolites and evade host immunity via glycan molecular mimicry.

microbiology↗

Bacterial cell widening alters periplasmic size and activates envelope stress responses

The Rcs signal transduction system is a phosphorelay responsible for sensing a wide variety of enterobacterial cell envelope stresses. In Escherichia coli, the Rcs system is required to survive A22 and mecillinam treatment, two drugs that perturb cell size. To test whether cell size changes might be correlated with envelope damage and thereby sensed by the Rcs system, we tuned E. coli cell size via drug inhibition with A22, point mutations to the cell-shape determinant MreB, and mechanically confined growth. In all conditions, cell width was strongly correlated with Rcs activation, with wider cells exhibiting more activation than wild-type. In all conditions, RcsF, the outer membrane-localized upstream component of the Rcs system, was essential for responding to cell width changes. Consistently, several envelope gene deletions known to induce the Rcs system via RcsF resulted in cells that were wider than wild-type. Cryo- electron microscopy revealed that the periplasm of a wide MreB mutant was on average [~]3 nm thinner than wild-type, thereby bringing RcsF closer to the downstream components of the signaling cascade in the inner membrane. Conversely, extending the flexible linker region of RcsF by [~]3 nm increased Rcs activity in wild-type cells. In summary, we propose that the Rcs system responds to changes in cell width because of altered periplasmic thickness.

microbiology↗

Gramicidin S and Melittin - Potential anti-viral therapeutic peptides to treat SARS-CoV-2 infection

The COVID19 pandemic has resulted in multipronged approaches for treatment of the disease. Since de novo discovery of drugs is time consuming, repurposing of molecules is now considered as one of the alternative strategies to treat COVID19. Antibacterial peptides are being recognized as attractive candidates for repurposing to treat viral infections. In this study, we describe the anti-SARS-CoV-2 activity of gramicidin S and melittin peptides obtained from Bacillus brevis and bee venom respectively. Our in vitro antiviral assay results showed significant decrease in the viral load compared to the untreated group with no/very less cytotoxicity. The EC50 values for gramicidin S and melittin are calculated as 1.571g and 0.656g respectively. Both the peptides treated to the SARS-CoV-2 infected Vero cells showed viral clearance from 12 hours onwards with a maximal clearance after 24 hours post infection. Based on proteome analysis it was found that more than 250 proteins were found to be differentially regulated in the gramicidin S and melittin treated SARS-CoV-2 infected Vero cells against control SARS-CoV-2 infected Vero cells after 24 and 48 hours post infection. The identified proteins were found to be associated in the metabolic and mRNA processing of the Vero cells post-treatment and infection. Both these peptides could be attractive candidates for repurposing to treat SARS-CoV-2 infection.

cell biology↗

Anti-SARS-CoV-2 potential of Cissampelos pareira L. identified by Connectivity map-based analysis and in vitro studies

BackgroundViral infections have a history of abrupt and severe eruptions through the years in the form of pandemics. And yet, definitive therapies or preventive measures are not present. PurposeHerbal medicines have been a source of various antiviral compounds. An accelerated repurposing potential of antiviral herbs can provide usable drugs and identify druggable targets. In this study, we dissect the anti-coronavirus activity of Cissampelos pareira L (Cipa). using an integrative approach. MethodsWe analysed the signature similarities between predicted antiviral agents and Cipa using the connectivity map (https://clue.io/). Next, we tested the anti-SARS-COV-2 activity of Cipa in vitro. A three-way comparative analysis of Cipa transcriptome, COVID-19 BALF transcriptome and CMAP signatures of small compounds was also performed. ResultsSeveral predicted antivirals showed a high positive connectivity score with Cipa such as apcidin, emetine, homoharringtonine etc. We also observed 98% inhibition of SARS-COV-2 replication in infected Vero cell cultures with the whole extract. Some of its prominent pure constituents e.g pareirarine, cissamine, magnoflorine exhibited 40-80% inhibition. Comparison of genes between BALF and Cipa showed an enrichment of biological processes like transcription regulation and response to lipids, to be downregulated in Cipa while being upregulated in COVID-19. CMAP also showed that Triciribine, torin-1 and VU-0365114-2 had positive connectivity with BALF 1 and 2, and negative connectivity with Cipa.

systems biology↗

Integrative physiological, biochemical and transcriptomic analysis of hexaploid wheat roots and shoots provides new insights into the molecular regulatory network during Fe & Zn starvation

In plants, iron (Fe) & zinc (Zn) uptake and transportation from the rhizosphere to the grain is a critical process regulated by complex transcriptional regulatory networks. However, understanding the combined effect of Fe & Zn starvation on their uptake and transportation and the molecular regulatory networks that control them lack in wheat. Here, we performed a comprehensive physiological, biochemical and transcriptome analysis in two bread wheat genotypes, i.e. Narmada 195 and PBW 502, differing in inherent Fe & Zn content to understand the mechanism of Fe & Zn homeostasis. Compared to PBW 502, Narmada 195 exhibited increased tolerance to Fe & Zn withdrawal by an increased level of antioxidant enzymes and DPPH radical scavenging activity along with less malondialdehyde (MDA), H2O2 level, increased PS accumulation and lower reduction of root and shoot Fe & Zn content and length, leaf chlorosis, and leaf area. By integrating physiological and biochemical data along with co-expression & functional genome annotation and gene expression analysis, we identified 25 core genes associated with four key pathways, i.e. Met cycle (10), PS biosynthesis (4), antioxidant (3) and transport system (8) that were significantly modulated by Fe & Zn withdrawal in both the genotypes. Genes of these four pathways were more considerably up-regulated in Narmada 195, allowing better tolerance to Fe & Zn withdrawal and efficient uptake and transportation of Fe & Zn. Chromosomal distribution and sub-genome wise mapping of these genes showed a contribution from all the chromosomes except group 5 chromosomes with the highest number of genes mapped to chromosome 4 (24%) and sub-genome D (40%). Besides, we also identified 26 miRNAs targeting 14 core genes across the four pathways. Together, our work provides a crucial angle for an in-depth understanding of regulatory cross-talk among physiological, biochemical and transcriptional reprogramming underlying Fe & Zn withdrawal in wheat. Core genes identified can serve as valuable resources for further functional research for genetic improvement of Fe & Zn content in wheat grain. HighlightOur work provides a crucial angle for a comprehensive understanding of the regulatory mechanism underlying Fe & Zn withdrawal associated with physiological, biochemical and transcriptional reprogramming in wheat.

molecular biology↗

Dry Swab Method of sample collection for SARS-CoV2 testing can be used for culturing virus

Back groundEarlier studies suggested the use of dry swab method for SARS-CoV-2 detection as it does not need VTM and subsequent RNA extraction step making the process cheaper, safer and faster. In this study we explore whether the virus in the dry swab is viable and can be cultured and propagated. MethodSwabs were spiked with SARS-CoV-2 and stored in three different conditions: a) as dry swab (SD, eluted in 1 mL DMEM), b) in 1 mL of Viral Transport Medium (SVTM), and c) in 1 mL of Tris-EDTA buffer (STE). The sample groups were stored either at room temperature (RT, 25{degrees}C{+/-}1{degrees}C) or at 4{degrees}C for 1, 4, 8, 12, 24, 48 and 72 hours before being used as viral inoculums for the propagation studies in Vero cells. ResultsThe RT-qPCR data suggests that SD incubated both at RT and 4{degrees}C harbors viral particles that are viable and culturable at par with SVTM and STE. ConclusionThe dry swab method, in addition to its advantages in detection of the virus, also renders viable viral particles that can be cultured and propagated.

microbiology↗

Traditional use of Cissampelos pareira L. for hormone disorder and fever provides molecular links of ESR1 modulation to viral inhibition

Bioactive fractions or compounds obtained from medicinal plants have been used for the treatment of multiple diseases. This effect could be due to common pathways underlying these conditions that are targeted by such medicines. In this study, we explored the molecular basis of action of one such herbal formulation Cissampelos pareira, used for the treatment of female hormone disorders and fever. Genome-wide expression studies on MCF7 cell lines treated with Cipa extract were carried out using Affymetrix arrays. Transcriptome analysis revealed a downregulation of signatures of estrogen response governed by estrogen receptor (ER). Molecular docking analysis identified 38 constituent molecules in Cipa that potentially bind ({Delta}G< -7.5) with ER at the same site as estrogen. Cipa transcriptome signatures show high positive connectivity (https://clue.io/) scores with protein translation inhibitors such as emetine (score: 99.61) and knockdown signatures of genes linked to the antiviral response such as ribosomal protein RPL7 (score: 99.92), which is also an ER coactivator. Cipa exhibits antiviral activity in dengue infected MCF7 cells that is decreased upon ESR1 (estrogen receptor 1) gene knockdown. This approach reveals a novel pathway involving ESR1-RPL7 axis that could be a potential target in dengue viral infection.

genomics↗

Host tropism determination by convergent evolution of immunological evasion in the Lyme disease system

Microparasites selectively adapt in some hosts, known as host tropism. Transmitted through ticks and carried mainly by mammals and birds, the Lyme disease (LD) bacterium is a well-suited model to study such tropism. LD bacteria species vary in host ranges through mechanisms eluding characterization. By feeding ticks infected with different LD bacteria species, utilizing feeding chambers and live mice and quail, we found species-level differences of bacterial transmission. These differences localize on the tick blood meal, and complement, a defense in vertebrate blood, and a bacterial polymorphic protein, CspA, which inactivates complement by binding to a host complement inhibitor, FH. CspA selectively confers bacterial transmission to vertebrates that produce FH capable of allele-specific recognition. Phylogenetic analyses revealed convergent evolution as the driver of such findings, which likely emerged during the last glacial maximum. Our results identify LD bacterial determinants of host tropism, defining an evolutionary mechanism that shapes host-microparasite associations.

microbiology↗

Pixelwise H-score: a novel digital image analysis based-metric to quantify membrane biomarker expression from immunohistochemistry images

Immunohistochemistry (IHC) assays play a central role in evaluating biomarker expression in tissue sections for diagnostic and research applications. Manual scoring of IHC images, which is the current standard of practice, is known to have several shortcomings in terms of reproducibility and scalability to large scale studies. Here, by using a digital image analysis-based approach, we introduce a new metric called the pixelwise H-score (pix H-score) that quantifies biomarker expression from whole-slide scanned IHC images. The pix H-score is an unsupervised algorithm that only requires the specification of intensity thresholds for the biomarker and the nuclear-counterstain channels. We present the detailed implementation of the pix H-score in two different whole-slide image analysis software packages Visiopharm and HALO. We consider three biomarkers P-cadherin, PD-L1, and 5T4, and show how the pix H-score exhibits tight concordance to multiple orthogonal measurements of biomarker abundance such as the biomarker mRNA transcript and the pathologist H-score. We also compare the pix H-score to existing automated image analysis algorithms and demonstrate that the pix H-score provides either comparable or significantly better performance over these methodologies. We also present results of an empirical resampling approach to assess the performance of the pix H-score in estimating biomarker abundance from select regions within the tumor tissue relative to the whole tumor resection. We anticipate that the new metric will be broadly applicable to quantify biomarker expression from a wide variety of IHC images. Moreover, these results underscore the benefit of digital image analysis-based approaches which offer an objective, reproducible, and highly scalable strategy to quantitatively analyze IHC images.

pathology↗

Characterizing intra-tumor and inter-tumor variability of immune cell infiltrates in murine syngeneic tumors

By using serial-sectioning methodology combined with immunohistochemistry (IHC) and whole-slide digital image analysis (DIA), we present a systematic analysis of intra-tumor and inter-tumor variability in the abundance of nine immune cell biomarkers in multiple murine tumor models. Our analysis shows that inter-tumor variability is typically the dominant source of variation in measurements of immune cell densities. Statistical power analysis reveals how group size and variance in immune cell density estimates affect the predictive power for detecting a statistically meaningful fold-change in immune cell density. Inter-tumor variability in the ratio of immune cell densities show distinct patterns in select tumor models and reveal the existence of strong correlations between select biomarker pairs. Further, we show that the relative proportion of immune cells at different depths across tumor samples is preserved in some but not all tumor models thereby revealing the existence of compositional heterogeneity. The results and analyses presented here reveal the complex nature of immunologic heterogeneity that exists in murine tumor models and provide guidelines for designing preclinical studies for immuno-oncology research and drug development.

cancer biology↗

Information theoretic analysis of hyperspectralimaging systems with applications to fluorescencemicroscopy

We present a general stochastic model for hyperspectral imaging data and derive analytical expressions for the Fisher information matrix for the underlying spectral unmixing problem. We investigate the linear mixing model as a special case and define a linear unmixing performance bound by using the Cramer-Rao inequality. As an application, we consider fluorescence imaging and show how the performance bound provides a spectral resolution limit that predicts how accurately a pair of spectrally similar fluorescent labels can be spectrally unmixed. We also report a novel result that shows how the spectral resolution limit can be overcome by exploiting the phenomenon of anti-Stokes shift fluorescence. In addition, we investigate how photon statistics, channel addition and channel splitting affect the performance bound. Finally by using the performance bound as a benchmark, we compare the performance of the least squares and the maximum likelihood estimators for spectral unmixing. For the imaging conditions tested here, our analysis shows that both estimators are unbiased and that the standard deviation of the maximum likelihood estimator is consistently closer to the performance bound than that of the least squares estimator. The results presented here are based on broad assumptions regarding the underlying data model and are applicable to hyperspectral data acquired with point detectors, sCMOS, CCD and EMCCD imaging detectors.\n\nEDICS: ELI-COL, COI-MCI.

bioengineering↗