Biology subjects

Krishna, A.

Publications and source records attributed to Krishna, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Reproducible transversal mouse brain sections using low-cost 3D printable resin matrix

Rodent brain matrices that produce coronal or sagittal brain sections for histology confer reproducibility and enable high throughput processing of tissues. However, a stainless steel or acrylic brain matrix that produces tissue sections in a transversal (or horizontal) orientation is currently unavailable as a standard tool. This limits the direct comparison of bilateral brain hemispheres within a single histological section, as freehand trimming to obtain horizontal planes is not easily replicable across samples. To mitigate this challenge, we designed a low-cost (USD 7 per unit), 3D-printed resin-based transverse brain matrix that accommodates mouse brains ranging from 12 to 16 mm in length from the olfactory bulb to the brainstem. Our matrix reproducibly generates horizontal tissue sections with a minimum of 1-mm-thickness without causing visible tissue deformation, which is comparable to the performance of commercial rodent brain matrices. Users may adapt the accompanying CAD code using our video tutorials to customize the transverse brain matrix for their specific needs, including alternative brain size, shape, and tissue thickness.

neuroscience↗

bioRxiv2026

Dissecting human fetal cardiac repair using cardioids

Human cardiac injury responses are governed by dynamic interacting processes that are difficult to resolve. Unlike adults, fetal mammalian hearts regenerate through coordinated remodeling and proliferation supported by a pro-regenerative immune environment, extracellular matrix (ECM), and immature cardiomyocytes, including trabecular subtypes. Here, we establish a modular human cardioid injury platform to dissect these interactions. We show that anti-inflammatory macrophages selectively migrate to the injury, clear debris, and promote ECM remodeling, whereas inflammatory macrophages suppress cardiomyocyte proliferation. Synergistic FGF2-NRG1 signaling induces trabecular identity and morphology in a hyaluronan-dependent manner, conferring enhanced injury repair, characterized by cytoskeletal remodeling and cardiomyocyte proliferation mediated by YAP and WNT signaling. Exogenous YAP, but not WNT, is sufficient to promote repair in non-trabecular cardioids. These findings uncover coordinated immune-ECM-cardiomyocyte interactions governing human fetal regenerative competence and mechanistically resolve remodeling and proliferative components of cardiac repair. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=162 SRC="FIGDIR/small/735236v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@1e647a2org.highwire.dtl.DTLVardef@16911f8org.highwire.dtl.DTLVardef@11ad14eorg.highwire.dtl.DTLVardef@1a35d94_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2025

Shared neural geometries for bilingual semantic representations

The human brain has the remarkable ability to comprehend and express similar concepts in multiple languages. To understand how it does so, we examined responses of hippocampal neurons during passive listening, directed speaking, and spontaneous conversation, in both English and Spanish, in a small group of balanced bilinguals. We find a small number of putative cross-language neurons, whose responses to equivalent words (e.g., "tierra" and "earth") are correlated. However, neurons semantic tunings differed substantially by language, suggesting language-specific neural implementations. Instead, the crucial driver of translation was a preserved geometric organization of neural responses between the two languages, one that did not depend on neuron level functional overlap. Indeed, that geometry was implemented by a common set of neurons along distinct readout axes; this difference in readout may help prevent cross-language interference. Together, these results suggest that hippocampus encodes a language-independent internal model for meaning.

neuroscience↗

bioRxiv2025

Computational biophysical characterization of a superradiant virus-like particle in its ground state

Superradiance (SR) arises when fluorophores radiate collectively rather than independently, producing ultrabright emission bursts. Recent experiments show that dye-labeled virus-like particles (VLPs) can exhibit SR at room temperature, where the VLP scaffold organizes dyes into a macrodipole of coherent emitters under pulsed excitation. To elucidate the biophysical basis of this phenomenon, microsecond-scale all-atom molecular dynamics (MD) simulations were performed on intact Brome mosaic virus (BMV) VLPs, comparing the native scaffold to a capsid decorated with Oregon Green 488 (OG). Results show that OG conjugation at K105 induces only subtle structural changes: a slight expansion of VLP volume and marginally higher inter-subunit flexibility, while overall shell morphology and pore architecture remain intact. However, dianionic OG alters VLP electrostatics, increasing water exchange across the shell and reducing chloride permeability. Dyes bound in pentamers are more closely packed and conformationally restricted than those in hexamers, and their transition dipoles more frequently adopt parallel orientations predicted to favor excitonic coupling and cooperative emission. By examining the role of scaffold architecture in dye interactions and dynamics, this work offers a mechanistic framework and design principles for engineering SR-VLPs as next-generation fluorescent probes and photonic materials.

biophysics↗

bioRxiv2025

Influence of duty-cycle recording on measuring bat activity in passive acoustic monitoring

Echolocating bats provide vital ecosystem services and can be monitored effectively using passive acoustic monitoring (PAM) techniques. Duty-cycle subsampling is widely used to collect PAM data at regular ON/OFF cycles to circumvent battery and storage capacity constraints for long-term monitoring. However, the impact of duty-cycle subsampling and potential detector errors on estimating bat activity has not been systematically investigated for bats. Here, we simulate the influence of duty-cycle subsampling in measuring bat activity via three metrics-Call Rate (CR), Activity Index (AI), and Bout-Time Percentage (BTP)-using three months of continuous recordings spanning summer to fall in a temperate urban natural area. Our simulations show that subsampled bat activity estimates more accurately track true values when the listening ratio is high and the cycle length is low, when the true call activity is high, or when recorded calls have lower frequency content. Generally, among the three metrics, AI provides the best subsampling estimates and is robust against false negatives but sensitive to false positives, whereas BTP provides better temporal resolution compared to AI and is robust against both false positives and false negatives. Our results offer important insights into selecting sampling parameters and measurement metrics for long-term bat PAM.

ecology↗

bioRxiv2025

Quantifying the effects of antibiotic resistance and within-host competition on strain fitness in Streptococcus pneumoniae

Competition plays a key role in shaping the structure and diversity of bacterial populations. In many clinically important bacterial species, strains compete at multiple scales: at the between-host scale for new hosts to colonise, and at the within-host scale during co-colonisation. Characterising these multiple facets of competition plays an important role in understanding bacterial ecology. This is particularly relevant for antibiotic resistance, where competition between antibiotic-susceptible and resistant strains determines resistance dynamics. In this work, we perform survival analyses on a large longitudinal dataset of Streptococcus pneumoniae carriage to quantify how within-host competition affects the rates of clearance and establishment of pneumococcal strains. We find that the presence of a within-host competitor is associated with a 33% increase in clearance and a 54% reduction in establishment. Priority effects and serotype differences partially predict the outcomes of this within-host competition. Further, we quantify the effects of antibiotic resistance on betweenand within-host components of fitness. Antibiotic consumption is associated with increased clearance rate for both susceptible and resistant strains, albeit to a higher extent in susceptible strains. In the absence of antibiotics, we find some evidence that resistance is associated with increased susceptibility to within-host competition, suggesting a fitness cost of resistance. Overall, our work provides quantitative insights into pneumococcal competition across scales and the role of this competition in shaping pneumococcal epidemiology.

ecology↗

bioRxiv2024

Competition strategies driving resource partitioning in chitin degrading communities

Resource competition strongly shapes microbial community dynamics and function. In polysaccharide-degrading communities, primary degraders secrete monomer-releasing enzymes and exploiters consume released products without investing in enzymes. By investigating competitive strategies between chitin degraders and N-acetylglucosamine (GlcNAc) exploiters, we uncover several interacting factors, including GlcNAc liberation rates, diffusive loss, and resource partitioning between competitors, which determine community viability and growth dynamics at early stages of degradation. Aside from cases involving antibiotic secretion or aggregation on particles to privatize degrading enzymes, exploiters also inhibit degraders by siphoning away limiting GlcNAc flux during early stages of particle degradation, when degraders must overcome diffusive GlcNAc loss to sustain chitinase production. Analogous to the Allee effect in population biology, these effects lead to sensitive dependences on initial species densities for a community to thrive. This study elucidates how metabolic competition at early stages of particle degradation shapes species interactions, resource partitioning, and ultimately community viability.

microbiology↗

bioRxiv2024

Novel spirocyclic dimer, SpiD3, targets chronic lymphocytic leukemia survival pathways with potent preclinical effects

Chronic lymphocytic leukemia (CLL) cell survival and growth is fueled by the induction of B-cell receptor (BCR) signaling within the tumor microenvironment (TME) driving activation of NF- {kappa}B signaling and the unfolded protein response (UPR). Malignant cells have higher basal levels of UPR posing a unique therapeutic window to combat CLL cell growth using pharmacological agents that induce accumulation of misfolded proteins. Frontline CLL therapeutics that directly target BCR signaling such as Bruton-tyrosine kinase (BTK) inhibitors (e.g., ibrutinib) have enhanced patient survival. However, resistance mechanisms wherein tumor cells bypass BTK inhibition through acquired BTK mutations, and/or activation of alternative survival mechanisms have rendered ibrutinib ineffective, imposing the need for novel therapeutics. We evaluated SpiD3, a novel spirocyclic dimer, in CLL cell lines, patient-derived CLL samples, ibrutinib-resistant CLL cells, and in the E{micro}-TCL1 mouse model. Our integrated multi-omics and functional analyses revealed BCR signaling, NF-{kappa}B signaling, and endoplasmic reticulum stress among the top pathways modulated by SpiD3. This was accompanied by marked upregulation of the UPR and inhibition of global protein synthesis in CLL cell lines and patient-derived CLL cells. In ibrutinib-resistant CLL cells, SpiD3 retained its anti-leukemic effects, mirrored in reduced activation of key proliferative pathways (e.g., PRAS, ERK, MYC). Translationally, we observed reduced tumor burden in SpiD3-treated E{micro}-TCL1 mice. Our findings reveal that SpiD3 exploits critical vulnerabilities in CLL cells including NF-{kappa}B signaling and the UPR, culminating in profound anti-tumor properties independent of TME stimuli. STATEMENT OF SIGNIFICANCESpiD3 demonstrates cytotoxicity in CLL partially through inhibition of NF-{kappa}B signaling independent of tumor-supportive stimuli. By inducing the accumulation of unfolded proteins, SpiD3 activates the UPR and hinders protein synthesis in CLL cells. Overall, SpiD3 exploits critical CLL vulnerabilities (i.e., the NF-{kappa}B pathway and UPR) highlighting its use in drug-resistant CLL. VISUAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=137 HEIGHT=200 SRC="FIGDIR/small/578283v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1dd7a38org.highwire.dtl.DTLVardef@1831c85org.highwire.dtl.DTLVardef@c571f9org.highwire.dtl.DTLVardef@bdce53_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Investigating Sensitivity, Specificity and Accuracy of Variant Calling Pipelines for Analyzing SARS-CoV-2 Data

The rapidly increasing popularity of Next Generation Sequencing and analysis methods in clinical and research settings necessitates an understanding of ideal combinations in identifying genomic variants. Especially with the importance of detecting accurate variants for the development of targeted SARS-CoV-2 vaccines. This research compares the results of two Mapping Algorithms , BWA-MEM and Bowtie2, and two Variant Calling Algorithms , LoFreq and FreeBayes, and their combinatory Variant Calling Pipelines on the analyses of Next Generation Sequencing (NGS) data of five SARS-CoV-2 samples collected from patients in the USA, India, Italy, and Malawi and sourced for this research from the publicly available NCBI SRA database. Our analysis of mapping algorithms found that BWA-MEM likely has higher sensitivity and specificity than Bowtie2 for mapping reads, and their specificity and sensitivity vary with read length. Furthermore, the accuracy of variant calling algorithms increases with the number of reads, while higher read length possibly leads to divergence in accuracy and sensitivity. Overall, FreeBayes was found to likely be more sensitive to detecting variants when used with Bowtie2 rather than BWA-MEM for analyzing SARS-CoV-2 data.

bioinformatics↗

bioRxiv2023

The everting Drosophila wing disc is a shape-programmed material

How complex 3D tissue shape emerges during animal development remains an important open question in biology and biophysics. In this work, we study eversion of the Drosophila wing disc pouch, a 3D morphogenesis step when the epithelium transforms from a radially symmetric dome into a curved fold shape via an unknown mechanism. To explain this morphogenesis, we take inspiration from inanimate "shape-programmable" materials, which are capable of undergoing blueprinted 3D shape transformations arising from in-plane gradients of spontaneous strains. Here, we show that active, in-plane cellular behaviors can similarly create spontaneous strains that drive 3D tissue shape change and that the wing disc pouch is shaped in this way. We map cellular behaviors in the wing disc pouch by developing a method for quantifying spatial patterns of cell behaviors on arbitrary 3D tissue surfaces using cellular topology. We use a physical shape-programmability model to show that spontaneous strains arising from measured active cell behaviors create the tissue shape changes observed during eversion. We validate our findings using a knockdown of the mechanosensitive molecular motor MyoVI, which we find to reduce active cell rearrangements and disrupt wing pouch eversion. This work shows that shape programming is a mechanism for animal tissue morphogenesis and suggests that there exist intricate patterns in nature that could present novel designs for shape-programmable materials.

biophysics↗

bioRxiv2023

Mutational scanning reveals oncogenic CTNNB1 mutations have diverse effects on signalling and clinical traits

CTNNB1, the gene encoding {beta}-catenin, is a frequent target for oncogenic mutations activating the canonical Wnt signalling pathway, typically via missense mutations within a degron hotspot motif in exon 3. Here, we combine saturation genome editing with a fluorescent reporter assay to quantify signalling phenotypes for all 342 missense mutations in the mutation hotspot, including 74 recurrent mutations reported in over 6000 tumours. Our data define the genetic requirements for {beta}-catenin degron function and reveal diverse levels of signal activation among known driver mutations. Tumorigenesis in different human tissues involves selection for CTNNB1 mutations spanning distinct ranges of effect size. In hepatocellular carcinoma, mutations that activate {beta}-catenin relatively weakly are associated with worse prognosis compared to stronger activating mutations, despite greater immune cell infiltration in the tumour microenvironment. Our work therefore provides a resource to understand mutational diversity within a pan-cancer mutation hotspot, with potential implications for targeted therapy.

cancer biology↗

bioRxiv2023

Quantifying nutrient colimitation of microbial growth

Resource availability dictates how fast and how much microbial populations grow. Quantifying the relationship between microbial growth and resource concentrations makes it possible to promote, inhibit, and predict microbial activity. Microbes require many resources, including macronutrients (e.g., carbon and nitrogen), micronutrients (e.g., metals), and complex nutrients like vitamins and amino acids. When multiple resources are scarce, as occurs in nature, microbes may experience resource colimitation in which more than one resource limits growth simultaneously. Despite growing evidence for colimitation, the data is difficult to interpret and compare due to a lack of quantitative measures of colimitation and systematic tests of resource conditions. We hypothesize that microbes experience a continuum of nutrient limitation states and that nutrient colimitation is common in the laboratory and in nature. To address this, we develop a quantitative theory of resource colimitation that captures the range of possible limitation states and describes how they can change dynamically with resource conditions. We apply this approach to clonal populations of Escherichia coli to show that colimitation occurs in common laboratory conditions. We also show that growth rate and growth yield are colimited differently, reflecting their different underlying biology. Finally, we analyze environmental data to provide intuition for the continuum of limitation and colimitation conditions in nature. Altogether our results provide a quantitative framework for understanding and quantifying colimitation of microbes in biogeochemical, biotechnology, and human health contexts.

microbiology↗

bioRxiv2023

Pre-patterned epithelial invagination prevents mechanical instability during fly gastrulation

Mechanical forces are crucial for driving and shaping tissue morphogenesis during embryonic development, but their relevance for the evolution of development remains poorly understood. Here, we show that a morphogenetic innovation present in fly embryos--a deep epithelial fold known as the cephalic furrow--plays a mechanical role during Drosophila gastrulation. By integrating in vivo experiments and in silico simulations, we find that the formation of the cephalic furrow prevents mechanical instabilities at the head-trunk epithelium by absorbing the compressive stresses generated by concurrent morphogenetic movements of gastrulation, the expansion of mitotic domains and the germ band extension. Furthermore, by comparing the expression of known and novel genes involved in cephalic furrow formation between fly species, we find that the presence of the cephalic furrow is linked to changes in the expression of buttonhead transcription factor at the head-trunk boundary. These data suggest that the genetic control of cephalic furrow formation was established through the integration of a new player into the ancestral head-trunk patterning system, and that mechanical instability may have been the selective pressure associated with the evolution of the cephalic furrow. Our findings uncover empirical evidence for how mechanical forces can influence the evolution of morphogenetic innovations in early development.

developmental biology↗

bioRxiv2022

Core PCP mutations affect short time mechanical properties but not tissue morphogenesis in the Drosophila pupal wing

How morphogenetic movements are robustly coordinated in space and time is a fundamental open question in biology. We study this question using the wing of Drosophila melanogaster, an epithelial tissue that undergoes large-scale tissue flows during pupal stages. We showed previously (Etournay et al., 2015) that pupal wing morphogenesis involves both cellular behaviors that allow relaxation of mechanical tissue stress, as well as cellular behaviors that appear to be actively patterned. The core planar cell polarity (PCP) pathway influences morphogenetic cell movements in many other contexts, which suggests that it could globally pattern active cellular behaviors during pupal wing morphogenesis. We show here, however, that this is not the case: there is no significant phenotype on the cellular dynamics underlying pupal morphogenesis in mutants of core PCP. Furthermore, using laser ablation experiments, coupled with a rheological model to describe the dynamics of the response to laser ablation, we conclude that while core PCP mutations affect the fast timescale response to laser ablation, they do not affect overall tissue mechanics. In conclusion, our work shows that cellular dynamics and tissue shape changes during Drosophila pupal wing morphogenesis are independent of one potential chemical guiding cue, core PCP.

developmental biology↗

bioRxiv2022

Size-dependent transition from steady contraction to waves in actomyosin networks with turnover

Actomyosin networks play essential roles in many cellular processes including intracellular transport, cell division, and cell motility, exhibiting a myriad of spatiotemporal patterns. Despite extensive research, how the interplay between network mechanics, turnover and geometry leads to these different patterns is not well understood. We focus on the size-dependent behavior of contracting actomyosin networks in the presence of turnover, using a reconstituted system based on cell extracts encapsulated in water-in-oil droplets. We find that the system can self-organize into different global contraction patterns, exhibiting persistent contractile flows in smaller droplets and periodic contractions in the form of waves or spirals in larger droplets. The transition between continuous and periodic contraction occurs at a characteristic length scale that is inversely dependent on the network contraction rate. These dynamics are recapitulated by a theoretical model, which considers the coexistence of different local density-dependent mechanical states with distinct rheological properties. The model shows how large-scale contractile behaviors emerge from the interplay between network percolation essential for long-range force transmission and rearrangements due to advection and turnover. Our findings thus demonstrate how varied contraction patterns can arise from the same microscopic constituents, without invoking specific biochemical regulation, merely by changing the systems geometry.

biophysics↗

bioRxiv2022

Matrix topology guides collective cell migration in vivo

Diverse modes of cell migration shape organisms in health and disease and much research has focused on the role of intracellular and extracellular components in different cell migration phenomena. What is less explored, however, is how the arrangement of the underlying extracellular matrix that many cells move upon in vivo influences migration. Combining novel transgenic lines and image analysis pipelines, reveals that during zebrafish optic cup formation cells use cryptopodia-like protrusions to migrate collectively and actively over a topologically changing matrix. These changing topologies correspond to different cell-matrix interactions. Interference with matrix topology results in loss of cryptopodia and inefficient migration. Thus, matrix topology influences the efficiency of directed collective cell migration during eye morphogenesis, a concept likely conserved in other developmental and disease contexts. One-Sentence SummaryDynamic cell-matrix interactions, crucial for successful collective rim cell migration, rely on extracellular matrix topologies during optic cup development in vivo.

developmental biology↗

bioRxiv2021

Fine-mapping of nuclear compartments using ultra-deep Hi-C shows that active promoter and enhancer elements localize in the active A compartment even when adjacent sequences do not

Megabase-scale intervals of active, gene-rich and inactive, gene-poor chromatin are known to segregate, forming the A and B compartments. Fine mapping of the contents of these A and B compartments has been hitherto impossible, owing to the extraordinary sequencing depths required to distinguish between the long-range contact patterns of individual loci, and to the computational complexity of the associated calculations. Here, we generate the largest published in situ Hi-C map to date, spanning 33 billion contacts. We also develop a computational method, dubbed PCA of Sparse, SUper Massive Matrices (POSSUMM), that is capable of efficiently calculating eigenvectors for sparse matrices with millions of rows and columns. Applying POSSUMM to our Hi-C dataset makes it possible to assign loci to the A and B compartment at 500 bp resolution. We find that loci frequently alternate between compartments as one moves along the contour of the genome, such that the median compartment interval is only 12.5 kb long. Contrary to the findings in coarse-resolution compartment profiles, we find that individual genes are not uniformly positioned in either the A compartment or the B compartment. Instead, essentially all (95%) active gene promoters localize in the A compartment, but the likelihood of localizing in the A compartment declines along the body of active genes, such that the transcriptional termini of long genes (>60 kb) tend to localize in the B compartment. Similarly, nearly all active enhancers elements (95%) localize in the A compartment, even when the flanking sequences are comprised entirely of inactive chromatin and localize in the B compartment. These results are consistent with a model in which DNA-bound regulatory complexes give rise to phase separation at the scale of individual DNA elements.

genomics↗

bioRxiv2020

Control of Vein-Forming, Striped Gene-Expression by Auxin Signaling

Activation of gene expression in striped domains is a key building block of biological patterning, from the recursive formation of veins in plant leaves to that of ribs and vertebrae in our bodies. In animals, gene expression is activated in striped domains by the differential affinity of broadly expressed transcription factors for their target genes and the combinatorial interaction between such target genes. In plants, how gene expression is activated in striped domains is instead unknown. We address this question for the broadly expressed MONOPTEROS (MP) transcription factor and its target gene ARABIDOPSIS THALIANA HOMEOBOX FACTOR8 (ATHB8). We find that ATHB8 promotes vein formation and that such vein-forming function depends on both levels of ATHB8 expression and width of ATHB8 expression domains. We further find that ATHB8 expression is activated in striped domains by a combination of (1) activation of ATHB8 expression through binding of peak levels of MP to a low-affinity MP-binding site in the ATHB8 promoter and (2) repression of ATHB8 expression by MP target genes of the INDOLE-3-ACETIC-ACID-INDUCIBLE family such as BODENLOS. Our findings suggest that a common regulatory logic controls activation of gene expression in striped domains in both plants and animals despite the independent evolution of their multicellularity.

plant biology↗