Biology subjects

Unnikrishnan, A.

Publications and source records attributed to Unnikrishnan, A..

At least 19 recordsLinked to original sources

bioRxiv2026

COGNITIVE HETEROGENEITY AND AGING: AN AGE-INDEPENDENT CILIARY GENE PROGRAM TRACKS COGNITIVE RESILIENCE IN MICE

Cognitive decline with age is often viewed as inevitable, yet older animals show striking heterogeneity in functional trajectories, with many preserving cognitive integrity despite physiological decline. The biological basis of this resilience remains poorly understood, partly due to insensitive behavioral testing paradigms. Using an automated home-cage platform and hippocampal RNA sequencing, we integrated behavioral phenotyping with transcriptomic profiling to disentangle molecular programs linked to cognitive performance from chronological age. Behavioral data from 906 C57BL/6 mice across 129 standardized studies, trajectory-based modeling, variance-partitioned correlation, and stability-driven gene prioritization identified a transcriptional signature (271 genes) linked to cognitive state independent of age. Preserved cognition was associated with higher expression of genes governing ciliary structure and motility, neurite organization, and synaptic architecture, while impairment was associated with neuroimmune and metabolic-stress programs. A 38-gene cilia structural module score remained associated with resilience after controlling for age (partial rho = -0.81), with consistent effects across leave-one-out resampling. Because the constituent genes were selected on this same outcome, the module-level magnitude is not an unbiased effect-size estimate; recalibration against a null that reapplies the full selection procedure gave an empirical p of 0.026. This divergence emerged among genetically identical mice, indicating non-genetic, discrete hippocampal molecular signatures underlying individual differences. Cell-type attribution against the Allen Brain Cell Atlas localized the module predominantly to ependymal cells, with 27 of 38 genes ependymal-restricted (median detection 90.2% in ependymal cells versus 1.1% in CA1 glutamatergic neurons) and three genes (Dnah9, Dnai4, Kif9) also detected in CA1. The association was not attributable to ependymal tissue content: the module score was unrelated to Foxj1 expression (rho = -0.016) and the partial correlation was unchanged after adjustment for ependymal and choroid plexus marker panels, indicating that the module reflects how strongly the ciliary program is expressed rather than how many ependymal cells each sample contained. These findings support a conceptual shift: cognitive trajectories appear shaped by intrinsic molecular set points rather than by chronological age, with expression of a motile ciliary program at the cerebrospinal fluid interface, rather than the abundance of the cells carrying it, emerging as a candidate correlate of resilience. This approach offers a generalizable strategy for dissecting functional heterogeneity from aging and identifying pathways for hypothesis-driven tests of resilience across the lifespan.

animal behavior and cognition↗

bioRxiv2026

Enhanced DNA Scanning and Target Specificity via Motif Sequestration

Sequence-specific DNA-binding proteins must efficiently locate their target sequences within large, structurally heterogeneous genomes while avoiding nonproductive off-target interactions. Here, we show that an autoinhibitory conformational state of the site-specific recombinase Cre lowers nonspecific DNA-binding affinity to promote one-dimensional DNA scanning while suppressing off-target assembly of recombinogenic complexes. Recent studies indicate that the C-terminal segment of Cre transiently adopts a sequestered conformation that occludes the catalytic domain's DNA-binding surface. Using NMR spectroscopy, single-molecule fluorescence microscopy, and optical trapping, we investigated how this conformational equilibrium regulates target search. NMR measurements reveal that the sequestered state predominates in the absence of DNA and persists at noncognate sites, whereas binding to cognate loxP sequences relieves autoinhibition. Single-molecule tracking demonstrates that full-length Cre undergoes processive one-dimensional diffusion and transitions to stable binding upon cognate-site recognition, whereas C-terminal truncation impairs scanning efficiency by arresting diffusion. These findings demonstrate how transient motif sequestration coordinates target search with site-specific complex assembly, suggesting a general mechanism by which DNA-modifying enzymes balance search efficiency and target specificity.

biophysics↗

bioRxiv2026

Maternal Obesity Decreases Offspring Lifespan

Data in mice, nonhuman primates, and in humans demonstrate that exposure to maternal obesity increases the risk of multiple diseases in offspring. However, little is known about the aging effects of maternal obesity on the offspring. This study shows that maternal obesity significantly reduced the lifespan of both male and female mice born to obese dams despite being weaned onto a healthy diet at three weeks of age. This reduction in longevity was linked to an increase in age-related fibrotic pathology across multiple organs, e.g., liver, heart, and kidney. Gompertz analysis of the lifespan data showed that maternal obesity offspring have reduced lifespan due to detrimental changes established early during development rather than factors that modify aging later-in-life. These findings are translationally significant as they demonstrate that the growing prevalence of MO may lead to a decrease in overall lifespan and increase in age-related diseases in the next generation.

physiology↗

bioRxiv2025

NPM1 mislocalization mediated by RNA Pol I inhibition alters chromatin landscape

RNA polymerase I inhibition affects rRNA synthesis from rDNA clusters residing in nucleolar organizer regions (NORs). Here we have demonstrated RNA Pol I inhibition disrupts nucleolar architecture, NPM1 localization, and alters the chromatin landscape using coordinated eraser and writer enzymes. siRNA mediated depletion or dissociation of NPM1 allows HDAC1 loading on the chromatin. HDAC1 mediated deacetylation of H3K9ac creates H3K9 that undegoes SUV39H1-mediated methylation. The stripping of active histone marks leads to enrichment of repressive H3K9me3 in the genome. These altered chromatin landscape corroborates with loss of genome-wide chromatin accessibility and DNA hypermethylation mediated by DNMT1. Chromatin architectural analysis revealed disrupted nucleolar associated domains (NADs) transforming to lamin associated domains (LADs) with specific histone signatures and repressive states. The 3D nuclear architecture was remodeled by A/B compartments reorganization and loss of Hi-C loops at the H3K9ac depleted sites.

molecular biology↗

bioRxiv2025

Structures of Fab-stabilized CHIP reveal a conformational switch important in E3 ligase and chaperone functions

Carboxyl terminus of Hsc70-interacting protein (CHIP/STUB1) is a U-box E3 ligase essential for protein quality control, targeting misfolded or damaged proteins for clearance and conducting chaperone-like functions by suppressing aggregation of proteins, including tau. The previous structure of full-length CHIP identified an asymmetric homodimer in which one U-box is occluded from E2 binding, indicating an unusual half-of-sites activity. However, the flexibility of CHIP has complicated efforts to further characterize its structure and function. Here we leverage two CHIP-targeting fragment antigen-binding (Fab) antibodies to solve structures by cryo-EM. We identify one Fab binds to the CHIP U-box via interactions mimicking E2 contacts and stabilizes three distinct CHIP dimer states, revealing an asymmetric-to-symmetric conformational switch that would enable both U-box domains to be accessible for E2 binding. Conversely, the second Fab targets CHIPs coiled-coil domains, stabilizing the asymmetric dimer with a single accessible U-box. Remarkably, the Fabs exhibit opposing effects on CHIPs inhibition of tau aggregation, wherein binding to coiled-coil domains abolishes inhibition of aggregation, while binding to the U-box greatly potentiates this activity. Together, this work reveals how CHIP conformational states and binding interfaces may regulate ubiquitination cycles and chaperone-like functions.

biochemistry↗

bioRxiv2024

Age, Sex, and mitochondrial-haplotype influence gut microbiome composition and metabolites in a genetically diverse rat model.

We evaluated the impact of sex and mitochondrial-haplotype on the age-related changes in the fecal gut microbiome of the genetically heterogeneous rodent model, the OKC-HETB/W rat. Alpha-diversity, measuring richness and evenness of gut microbiome composition, did not change with age or mitochondrial-haplotype. However, beta-diversity, a measure of microbial differences among samples, was significantly modulated by age in male and female rats in both mitochondrial-haplotypes. The age-related changes in the microbiome differed markedly between male and female rats. Five microbial species changed significantly with age in male rats compared to nine microbial species in female rats. Only three of these microbes changed with age in both male and female rats. The mitochondrial-haplotype of the rats also affected how aging altered the microbiome. Interestingly, most of the microbial species that changed significantly with age were mitochondrial-haplotype and sex specific, i.e., changing in one sex and not the other. We also discovered that sex and mitochondrial-haplotype significantly affected the age-related variations in content of fecal short-chain fatty acids and plasma metabolites that influence or are regulated by the microbiome, e.g., tryptophan derived metabolites and bile acids. This study demonstrates that the hosts sex plays a significant role in how the gut microbiome evolves with age, even within a genetically diverse background. Importantly, this is the first study to show that the mitochondrial-haplotype of a host impacts the age-related changes in the microbiome and supports previous studies suggesting a bidirectional interaction between the gut microbiome and host mitochondria. HighlightsMost age-related changes in microbial species occurred in one sex but not the other Mitochondrial-haplotype altered the microbiome and was generally sex dependent Microbiome associated metabolites differed by age, sex, and mitochondria-haplotype

microbiology↗

bioRxiv2024

Late-life short-term dietary restriction ameliorates intestinal stem cell function and impacts intestinal stem cell DNA methylation

Aging reduces the function of intestinal stem cells (ISCs) and dietary restriction (DR) has been shown to improve ISC function in young mice. However, there are no studies to-date that has evaluated the effect of short-term DR (stDR) implemented late-in-life on ISC function. Data from our laboratory shows for the first time that stDR can ameliorate the age-related decline in ISC function by in-vitro enteroid forming assay. Transcriptomic analysis of the Lgr5+ ISCs identified genes not commonly known for ISC function but showed a robust change with age which were reversed by stDR. Evaluation of the methylation status of selected genes (Slc28a3, Ly9, Cd2, Platr4) showed association between changes in 5mCG levels in the cis-acting regions of the genes and their expression. Our data suggest a potential role for DNA methylation in stDRs effect on ISC function.

molecular biology↗

bioRxiv2023

Environmental Factors Associated with Incidence and Distribution of V. parahaemolyticus and V. vulnificus in Chesapeake Bay, Maryland, USA: A three-year case study

Members of the genus Vibrio are ecologically significant bacteria native to aquatic ecosystems globally, and a few can cause diseases in humans. Vibrio-related illnesses have increased in recent years, primarily attributed to changing environmental conditions. Therefore, understanding the role of environmental factors in the occurrence and growth of pathogenic strains is crucial for public health. Water, oyster, and sediment samples were collected between 2009 and 2012 from Chester River and Tangier Sound sites in Chesapeake Bay, Maryland, USA, to investigate the relationship between water temperature, salinity, and chlorophyll with the incidence and distribution of Vibrio parahaemolyticus (VP) and Vibrio vulnificus (VV). Odds ratio analysis was used to determine association between the likelihood of VP and VV presence and these environmental variables. Results suggested that water temperature threshold of 20{degrees}C or higher was associated with an increased risk, favoring the incidence of Vibrio spp. A significant difference in salinity was observed between the two sampling sites, with distinct ranges showing high odds ratio for Vibrio incidence, especially in water and sediment, emphasizing the impact of salinity on VP and VV incidence and distribution. Notably, salinity between 9-20 PPT consistently favored the Vibrio incidence across all samples. Relationship between chlorophyll concentrations and VP and VV incidence varied depending on sample type. However, chlorophyll range of 0-10 {micro}g/L was identified as critical in oyster samples for both vibrios. Analysis of odds ratios for water samples demonstrated consistent outcomes across all environmental parameters, indicating water samples offer a more reliable indicator of Vibrio spp. incidence. ImportanceUnderstanding the role of environmental parameters in the occurrence of Vibrio species posing significant public health risks and economic burdens such as Vibrio parahaemolyticus and Vibrio vulnificus are of paramount importance. These aquatic bacteria are responsible for various human diseases, including gastroenteritis and wound infections, which can be severe and sometimes fatal. Recent observations suggest that certain environmental conditions may favor the growth of Vibrio, leading to more severe disease outcomes. By investigating the environmental factors that influence the occurrence of Vibrio parahaemolyticus and Vibrio vulnificus, the need to gain insights into the favorable ranges of environmental variables is apparent. The significance of this research is in identifying the favorable ranges of environmental and ecological factors, which holds the potential to provide an aid in the intervention and mitigation strategies through the development of predictive models, ultimately enhancing our ability to manage and control diseases caused by these pathogens.

ecology↗

bioRxiv2023

Dysregulated expression of Hoxa1 isoforms in hematopoietic stem and progenitor cells causes myelodysplastic syndromes.

The homeobox gene, Hoxa1, has two different isoforms generated by alternative splicing: a full-length homeodomain-containing Hoxa1 (Hoxa1-FL), and a truncated Hoxa1 (Hoxa1-T), that lacks the homeodomain. The effects of the distinct Hoxa1 isoforms in hematopoiesis have not been investigated. Oncoretroviral studies revealed that Hoxa1-T acts in a dominant negative manner, regulating transcriptionally active Hoxa1. Oncoretroviral overexpression of wildtype Hoxa1 (WT-Hoxa1), which generates both Hoxa1 isoforms, in murine hematopoietic stem and progenitor cells (HSPCs) perturbed hematopoiesis, resulting in transplantable myelodysplastic syndromes (MDS) in mice. Overexpression of a mutated Hoxa1 cDNA (MUT-Hoxa1) that generates Hoxa1-FL, but not Hoxa1-T, led to a more severe MDS that transformed to secondary acute myeloid leukemia (sAML). DNA damage repair pathways were downregulated in Hoxa1-overexpressing hematopoietic progenitor cells, accompanied by increased {gamma}H2AX foci. In silico analyses revealed that CD34+ cells from approximately 50% of patients with MDS had elevated HOXA1-FL expression. Conditional knock-in WT-Hoxa1 and MUT-Hoxa1 mice were generated and had features of pre-MDS, developing altered hematopoiesis within 4 months of Hoxa1 isoform overexpression in HSPCs. HSPCs were significantly reduced in all knock-in mice, accompanied by significantly increased apoptosis in WT-Hoxa1 HSPCs. Healthy wildtype recipients transplanted with bone marrow cells from Hoxa1 knock-in mice developed trilineage MDS, with Hoxa1 isoform and gene dosage dependent phenotypes. Collectively our data identify a role for HOXA1 in the pathogenesis of MDS. Our Hoxa1 mouse models capture different stages of progression of disease from pre-MDS to MDS to sAML and provide novel, clinically relevant tools to study MDS. Key pointsHOXA1 is upregulated in approximately 50% of MDS patient CD34+ BM cells, highlighting a potential role for HOXA1 in the pathogenesis of MDS. Dysregulated expression of Hoxa1 isoforms in murine hematopoietic stem and progenitor cells predisposes mice to pre-MDS and MDS.

cancer biology↗

bioRxiv2022

Single cell genotyping of matched bone marrow and peripheral blood cells in treatment naive and AZA-treated MDS and CMML

Progressively acquired somatic mutations in hematopoietic stem cells are central to pathogenesis in myelodysplastic syndromes (MDS) and chronic myelomonocytic leukemia (CMML). They can lead to proliferative advantages, impaired differentiation and progressive cytopenias. MDS or CMML patients with high-risk disease are treated with hypomethylating agents including 5-azacytidine (AZA). Clinical improvement does not require eradication of mutated cells and may be related to improved differentiation capacity of mutated hematopoietic stem and progenitor cells (HSPCs). However, the contribution of mutated HSPCs to steadystate hematopoiesis in MDS and CMML is unclear. To address this, we characterised the somatic mutations of individual stem, progenitor (common myeloid progenitor, granulocyte monocyte progenitor, megakaryocyte erythroid progenitor), and matched circulating (monocyte, neutrophil, naive B cell) haematopoietic cells in treatment naive and AZA-treated MDS and CMML via high-throughput single cell genotyping. The mutational burden was similar across multiple hematopoietic cell types, and even the most mutated stem and progenitor clones maintained their capacity to differentiate to mature myeloid and, in some cases, lymphoid cell types in vivo. Our data show that even highly mutated HSPCs contribute significantly to circulating blood cells in MDS and CMML, prior to and following AZA treatment. Key points* Highly mutated HSPCs contribute significantly to circulating blood cells in MDS and CMML, prior to and following AZA treatment. * The mutational burden in matched bone marrow and peripheral blood cells in MDS and CMML was similar throughout myelopoiesis.

cancer biology↗

bioRxiv2021

Mesoderm-Derived PDGFRA+ Cells Regulate the Emergence of Hematopoietic Stem Cells in the Dorsal Aorta

Mouse hematopoietic stem cells (HSCs) first emerge at embryonic day 10.5 (E10.5) on the ventral surface of the dorsal aorta, by endothelial-to-hematopoietic transition (EHT). We investigated whether cells with mesenchymal stem cell-like activity, which provide an essential niche for long-term HSCs (LT-HSCs) in the bone marrow, reside in the aorta- gonad-mesonephros (AGM) and contribute to the structural development of the dorsal aorta and EHT. Using transgenic mice, we demonstrate a lineage hierarchy for AGM stromal cells and traced the E10.5/E11.5 aortic endothelium and HSCs to mesoderm derived (Mesp1) PDGFRA+ stromal cells (Mesp1der PSCs). Mesp1der PSCs dominate the sub-endothelial and ventral stroma in the E10.5-E11.5 AGM but by E13.5 were replaced by neural crest (Wnt1) derived PDGFRA+ stromal cells (Wnt1der PSCs). Co-aggregating non-hemogenic embryonic and adult endothelial cells with Mesp1der PSCs but not with Wnt1der PSCs resulted in activation of a hematopoietic transcriptional program in endothelial cells accompanied by EHT and generation of LT-HSCs. Dose-dependent inhibition of PDGFRA signalling or BMP, WNT, NOTCH signalling interrupted this reprogramming event. This partnership between endothelial cells and AGM Mesp1der PSCs could potentially be harnessed to manufacture LT-HSCs from endothelium.

developmental biology↗

bioRxiv2021

A Reevaluation of the Effect of Dietary Restriction on Different Recombinant Inbred (RI) Lines of Male and Female Mice

Dietary restriction (DR) was reported to either have no effect or reduced the lifespan of the majority of the 41-recombinant inbred (RI)-lines studied (Liao et al., 2010). In an appropriately power longevity study (n > 30 mice/group), we measured the lifespan of the four RI-lines (115-RI, 97-RI, 98-RI, and 107-RI) that were reported to have the greatest decrease in lifespan when fed 40% DR. DR increased the median lifespan of female and male 115-RI mice and female 97-RI and 107-RI mice. DR had little effect (less than 4%) on the median lifespan of female and male 98-RI mice and male 97-RI mice and reduced the lifespan of male 107-RI mice over 20%. While our study was unable to replicate the effect of DR on the lifespan of the RI-mice (except male 107-RI mice) reported by Liao et al. (2010), we found that the genotype of a mouse had a major impact on the effect of DR on lifespan, with the effect of DR ranging from a 50% increase to a 22% decrease. No correlation was observed between the changes in either body composition or glucose tolerance induced by DR and the changes observed in lifespan of the four RI-lines of male and female mice. These four RI-lines of mice give the research community a unique resource where investigators for the first time can study the anti-aging mechanism of DR by comparing mice in which DR increases lifespan to mice where DR has either no effect or reduces lifespan. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/449984v1_ufig1.gif" ALT="Figure 1"> View larger version (11K): org.highwire.dtl.DTLVardef@1a11d22org.highwire.dtl.DTLVardef@7fd855org.highwire.dtl.DTLVardef@153b5bborg.highwire.dtl.DTLVardef@c013f3_HPS_FORMAT_FIGEXP M_FIG C_FIG Brief AbstractIn this study we reevaluate the effect of the genotype and sex of the recombinant inbred strains of mice on their response to dietary restriction. Out of the eight lines studied, half of the groups showed an increase in lifespan when the diet was restricted by 40% and the other half either did not respond or showed a decrease in lifespan. The recombinant inbred lines used in this study are potentially important resource for aging research to identify pathways and understand the mechanism involved in the anti-aging action of DR.

molecular biology↗

bioRxiv2020

Calorie Restriction Prevents Age-Related Changes in the Intestinal Microbiota

The effect of calorie restriction (CR) on the microbiome, fecal metabolome, and colon transcriptome of adult and old male mice was compared. Life-long CR increased microbial diversity and the Bacteriodetes/Fermicutes ratio and prevented the age-related changes in the microbiota, shifting it to a younger microbial and fecal metabolite profile in both C57BL/6JN and B6D2F1 mice. Old mice fed CR were enriched in the Rikenellaceae, S24-7 and Bacteroides families. The changes in the microbiome that occur with age and CR were initiated in the cecum and further modified in the colon. Short-term CR in adult mice had a minor effect on the microbiome but a major effect on the transcriptome of the colon mucosa. These data suggest that the primary impact of CR is on the physiological status of the gastrointestinal system, maintaining it in a more youthful state, which in turn results in a more diverse and youthful microbiome.

molecular biology↗

bioRxiv2020

Litter expansion alters metabolic homeostasis in a sexually divergent manner

Nutritional manipulations early in life have been shown to influence growth rate and elicit long lasting effects which in turn has been found to impact lifespan. Therefore, we studied the long-term effects of pre-weaning dietary restriction implemented by litter expansion (4, 6, 8, 10, and 12 pups per dam: LS4, LS6, LS8, LS10, LS12) on male and female C57BL/6 mice. After weaning, these mice were fed ad libitum a commercial lab chow for the 15-month duration of the study. The mice from large litter sizes (LS12) were significantly leaner and had reduced total fat mass compared to the normal size litters (LS 6) starting from weaning through to 15 months of age. Male LS10 & 12 mice showed significant reduction in their fat depot masses at 15 months of age: gonadal, subcutaneous, and brown fat whereas the females did not mimic these findings. At 9 months of age, both male and female LS10 and 12 mice showed improved glucose tolerance; however, only male LS10 and LS12 mice showed improved insulin tolerance starting at 5 months of age. In addition, we found that the male LS8, 10 & 12 mice at 15 months of age showed significantly reduced IGF-1 levels in the serum and various other organs (liver, gastrocnemius and brain cortex). Interestingly, the female LS8, 10, 12 mice showed a different pattern with reduced IGF-1 levels in serum, liver and gastrocnemius but not in the brain cortex. Similarly, the litter expanded mice showed sexual divergence in levels of FGF21 and adiponectin with only the male mice showing increased FGF21 and adiponectin levels at 15 months of age. In summary, our data show that, litter expansion results in long-lasting metabolic changes that are age and sex dependent with the male mice showing an early and robust response compared to female mice.

molecular biology↗

bioRxiv2020

Health benefits attributed to 17α-estradiol, a lifespan-extending compound, are mediated through estrogen receptor α

Metabolic dysfunction underlies several chronic diseases, many of which are exacerbated by obesity. Dietary interventions can reverse metabolic declines and slow aging, although compliance issues remain paramount. 17-estradiol treatment improves metabolic parameters and slows aging in male mice. The mechanisms by which 17-estradiol elicits these benefits remain unresolved. Herein, we show that 17-estradiol elicits similar genomic binding and transcriptional activation through estrogen receptor (ER) to that of 17{beta}-estradiol. In addition, we show that the ablation of ER completely attenuates the beneficial metabolic effects of 17-E2 in male mice. Our findings suggest that 17-E2 acts primarily through the liver and hypothalamus to improve metabolic parameters in male mice. Lastly, we also determined that 17-E2 improves metabolic parameters in male rats, thereby proving that the beneficial effects of 17-E2 are not limited to mice. Collectively, these studies suggest ER may be a drug target for mitigating chronic diseases in male mammals.

physiology↗

bioRxiv2020

DNA Binding Induces a cis to trans Switch in Cre Recombinase to Enable Intasome Assembly

Mechanistic understanding of DNA recombination in the Cre-loxP system has largely been guided by crystallographic structures of tetrameric synaptic complexes. Those studies have suggested a role for protein conformational dynamics that has not been well characterized at the atomic level. We used solution NMR to discover the link between intrinsic flexibility and function in Cre recombinase. TROSY-NMR spectra show the N-terminal and C-terminal catalytic domains (CreNTD, CreCat) to be structurally independent. Amide 15N relaxation measurements of the CreCat domain reveal fast time scale dynamics in most regions that exhibit conformational differences in active and inactive Cre protomers in crystallographic tetramers. However, the C-terminal helix N, implicated in assembly of synaptic complexes and regulation of DNA cleavage activity via trans protein-protein interactions, is unexpectedly rigid in free Cre. Chemical shift perturbations and intra- and inter-molecular paramagnetic relaxation enhancement (PRE) NMR data reveal an alternative auto-inhibitory conformation for the N region of free Cre, wherein it packs in cis over the protein DNA binding surface and active site. Moreover, binding to loxP DNA induces a conformational change that dislodge the C-terminus, resulting in a cis to trans switch that is likely to enable protein-protein interactions required for assembly of recombinogenic Cre intasomes. These findings necessitate a re-examination of the mechanisms by which this widely-utilized gene editing tool selects target sites, avoids spurious DNA cleavage activity, and controls DNA recombination efficiency. SIGNIFICANCE STATEMENTThe Cre-loxP system is a widely used gene editing tool that has enabled transformative advances in immunology, neuroscience and cardiovascular research. Still, off-target activities confound research results and present obstacles to biomedical applications. Overcoming those limitations requires understanding the steps leading to assembly of recombination complexes, intasomes. We measured the magnetic properties of nitrogen nuclei in the backbone of the enzyme to correlate its intrinsic dynamics with its function in DNA recognition and cleavage. Remarkably, we found that in the absence of DNA the C-terminus of Cre appears to block the DNA binding surface and active site of the enzyme. Binding to loxP DNA induces a conformational switch that would enable the intermolecular protein-protein interactions required for assembly of recombinogenic Cre intasomes.

biophysics↗

bioRxiv2020

RNA splicing alterations induce a cellular stress response associated with poor prognosis in AML

RNA splicing is a fundamental biological process that generates protein diversity from a finite set of genes. Recurrent somatic mutations of splicing factor genes are relatively uncommon in Acute Myeloid Leukemia (AML, < 20%). We examined whether RNA splicing differences exist in AML even in the absence of splicing factor mutations. Analyzing RNA-seq data from two independent cohorts of AML patients, we identified recurrent differential alternative splicing between patients with poor and good prognosis. These alternative splicing events occurred even in patients without any discernible splicing factor mutations. The alternative splicing events recurrently occurred in genes involved in specific molecular functions, primarily related to protein translation. Developing informatics tools to predict the functional impact of alternative splicing on the translated protein, we discovered that ~45% of the splicing events directly affected highly conserved protein domains. Several splicing factors were themselves misspliced in patients, and the splicing of their target transcripts were also altered. By studying differential gene expression in the same patients, we identified that alternative splicing of protein translation genes in ELNAdv patients resulted in the induction of an integrated stress response and up- regulation of inflammation-related genes. Lastly, using machine learning techniques, we identified a set of four genes whose alternative splicing can refine the accuracy of existing risk prognosis schemes and validated it in a completely independent cohort. Our discoveries therefore identify aberrant alternative splicing as a molecular feature of adverse AML with clinical relevance.

cancer biology↗

bioRxiv2019

Biodiversity clock and conservation triangle: Integrative platform for biodiversity monitoring, evaluation, and preemptive conservation intervention

Business-as-usual is no more an option on the table for biodiversity conservation. Disruptive transformation at both policy and polity levels are pressing needs. The possibilities presented by the current wave of information and communication technology can act as travelators to meet the conservation targets. Here, we introduce twin concepts of biodiversity clock and conservation triangle that posit as convergence plane to seamlessly consolidate ongoing discrete efforts and convey real-time biodiversity information in a lucid schematic form. In its present form, the biodiversity clock depicts 12 ecological and 6 biophysical components. The universal consistency in clock-reading facilitates the biodiversity clock to be read and interpreted identically across the world. A ternary plot of the International Union of Conservation of Nature (IUCN) species conservation status is presented as the conservation triangle. Together, the biodiversity clock and the conservation triangle are invaluable in strategizing biodiversity conservation, post-2020. Leveraged smartly, they make possible pre-emptive intervention for biodiversity conservation.

ecology↗