Biology subjects

Kaur, P.

Publications and source records attributed to Kaur, P..

52 records · Page 3Linked to original sources

bioRxiv2021

Targeted resurrection of chromosomal arm 1RS in two elite wheat lines with 1BL/1RS translocation for improved end-use quality

1BL/1RS translocation is widely used around the world to enhance wheat yield potential, resistance to various diseases, and adaptation. However, the translocation is combined with inherent quality problems associated with reduced dough strength and dough stickiness due to the presence of Sec-1 on proximal end and absence of GluB3/GliB1 on distal end. Two NILs, one carrying the distal (1RSRW) and the other carrying the proximal (1RSWR) fragment from 1BS, in background of Pavon were used for transferring these two loci in yellow rust resistant version of two elite wheat varieties PBW550+Yr5 and DBW17+Yr5. Foreground and background marker assisted selection was done for the Sec-1- and GluB3+ alongwith Lr26/Yr9/Sr31, Pm8 and 1RS loci in the advancing generation. BC2F5:6 NILs with absence of Secalin and presence of GluB3/GliB1 loci were evaluated for two years in replicated yield trial. A positive correlation of thousand grain weight (TGW), harvest index (HI), and tiller number per meter (TNpM) with yield (YD) with significant GxE effect was observed. Further multivariate analysis of these traits contributed maximum to the effective yield. Thirty promising NILs were identified with Sec-1-/GluB3+ alongwith with high yield contributing parameters.

genetics↗

bioRxiv2021

Targeted drug delivery using Beeswax derived Albendazole-Loaded Solid Lipid Nanoparticles in Haemonchus contortus, an albendazole tolerant nematode.

Targeted delivery has not been achieved for anthelmintic treatment, resulting in the requirement of excess drugs dose leading to side effects and therapeutic resistance. Gastrointestinal helminths ingest lipid droplets from digestive fluid for energy production, development, and defense. Worms habit inspired us to develop biocompatible, oral administrable, bee-wax derived solid lipid nanoparticles (SLN) with excellent drug (albendazole) loading efficiency of 83.3 {+/-} 6.5 mg/g and sustained-release properties (86.4 {+/-} 3.9 % of drug released within 24 h). Rhodamine B-loaded SLN showed time-dependent release and distribution of dye in vivo in Haemonchous contortus. The intestinal sustained-release property was shown by the particles that caused enhancement of albendazole potency for up to 50 folds. Therefore, this formulation has immense potential as an anthelminthic drug delivery vehicle that will not only be able to reduce the dose but will also reduce the drug-induced side effects by enhancing the bioavailability of the drug. HighlightsO_LIAlbendazole-loaded Solid Lipid Nanoparticles (SLN-A) were formulated using Beeswax as stating material showing high drug loading capacity of 83 mg/g with sustained-release properties and 84 {+/-} 3 % of drug release within 24 h. C_LIO_LISLN-A particles showed 50 fold enhancement of Albendazole activity against Haemonchous contortus worm. C_LIO_LIRhodamine B-loaded SLN particles showed the specific uptake and in-vivo sustained release of dye in the worm. C_LI

microbiology↗

bioRxiv2021

Microchromosomes are building blocks of bird, reptile and mammal chromosomes

Microchromosomes, once considered unimportant shreds of the chicken genome, are gene rich elements with a high GC content and few transposable elements. Their origin has been debated for decades. We used cytological and whole genome sequence comparisons, and chromosome conformation capture, to trace their origin and fate in genomes of reptiles, birds and mammals. We find that microchromosomes as well as macrochromosomes are highly conserved across birds, and share synteny with single small chromosomes of the chordate amphioxus, attesting to their origin as elements of an ancient animal genome. Turtles and squamates (snakes and lizards) share different subsets of ancestral microchromosomes, having independently lost microchromosomes by fusion with other microchromosomes or macrochromosomes. Patterns of fusions were quite different in different lineages. Cytological observations show that microchromosomes in all lineages are spatially separated into a central compartment at interphase and during mitosis and meiosis. This reflects higher interaction between microchromosomes than with macrochromosomes, as observed by chromosome conformation capture, and suggests some functional coherence. In highly rearranged genomes fused microchromosomes retain most ancestral characteristics, but these may erode over evolutionary time; surprisingly de novo microchromosomes have rapidly adopted high interaction. Some chromosomes of early branching monotreme mammals align to several bird microchromosomes, suggesting multiple microchromosome fusions in a mammalian ancestor. Subsequently multiple rearrangements fueled the extraordinary karyotypic diversity of therian mammals. Thus microchromosomes, far from being aberrant genetic elements, represent fundamental building blocks of amniote chromosomes, and it is mammals, rather than reptiles, that are atypical. Significance StatementGenomes of birds and reptiles, but not mammals, consist of a few large chromosomes and many tiny microchromosomes. Once considered unimportant shreds of the genome, microchromosomes are gene rich and highly conserved among bird and reptiles, and share homology with one or more of the tiny chromosomes of an invertebrate that diverged from the vertebrate lineage 684 million years ago. Microchromosomes interact strongly and crowd together at the centre of cells, suggesting functional coherence. Many microchromosomes have been lost independently in turtles, snakes and lizards as they have fused with each other, or with larger chromosomes. In mammals they have completely disappeared, yet some chromosomes of the basal platypus line up with several microchromosomes, suggesting that they are the building blocks of the atypically variable chromosomes of mammals.

genomics↗

bioRxiv2020

TIN2 facilitates TRF1-mediated trans- and cis-interactions on physiologically relevant long telomeric DNA

The shelterin complex consisting of TRF1, TRF2, RAP1, TIN2, TPP1, and POT1, functions to prevent false recognition of telomeres as double-strand DNA breaks, and to regulate telomerase and DNA repair protein access. TIN2 is a core component linking double-stranded telomeric DNA binding proteins (TRF1 and TRF2) and proteins at the 3 overhang (TPP1-POT1). Since knockdown of TIN2 also removes TRF1 and TRF2 from telomeres, determining TIN2s unique mechanistic function has been elusive. Here, we investigated DNA molecular structures promoted by TRF1-TIN2 using complementary single-molecule imaging platforms, including atomic force microscopy (AFM), total internal reflection fluorescence microscopy (TIRFM), and the DNA tightrope assay. We demonstrate that TIN2S and TIN2L isoforms facilitate TRF1-mediated DNA compaction (cis-interactions) and DNA-DNA bridging (trans-interactions) in a telomeric sequence- and length-dependent manner. On the short telomeric DNA substrate (6 TTAGGG repeats), the majority of TRF1 mediated telomeric DNA-DNA bridging events are transient with a lifetime of ~1.95 s. On longer DNA substrates (270 TTAGGG), TIN2 forms multi-protein complexes with TRF1 and stabilizes TRF1-mediated DNA-DNA bridging events that last for at least minutes. Preincubation of TRF1 with its regulator protein Tankyrase 1 significantly reduces TRF1-TIN2 mediated DNA-DNA bridging, whereas TIN2 protects the disassembly of TRF1-TIN2 mediated DNA-DNA bridging upon Tankyrase 1 addition. Our study provides evidence that TIN2 functions to promote TRF1 mediated trans-interactions of telomeric DNA, leading to new mechanistic insight into sister telomere cohesion.

biophysics↗

bioRxiv2020

Mapping the landscape of chromatin dynamics during naïve CD4+ T-cell activation.

T-cell activation induces context-specific gene expression programs that promote energy generation and biosynthesis, progression through the cell cycle and ultimately cell differentiation. The aim of this study was to apply the omni ATAC-seq method to characterize the landscape of chromatin changes induced by T-cell activation in mature naive CD4+ T-cells. Using a well-established ex vivo protocol of canonical T-cell receptor signaling, we generated genome-wide chromatin maps of naive T-cells from pediatric donors in quiescent or recently activated states. We identified thousands of individual chromatin accessibility peaks that are associated with T-cell activation. The majority of these were localized to intronic and intergenic enhancer regions, marked by active histone modifications whilst quiescence was maintained by repressive histone marks. Regions of activation-associated gains in chromatin accessibility were enriched for well-known pioneer transcription factor motifs, and super-enhancer regions associated with distinct gene regulatory networks. These cis-regulatory elements together brought about distinct transcriptional signatures in activated cells including TNFa-NFkB signaling, hormone-responsive genes, inflammatory response genes and IL2-STAT5 signaling. Our data provides novel insights into the chromatin dynamics and motif usage of T-cell receptor signaling events in early life. The characterized pathways demonstrate the utility of chromatin profiling techniques applied to bio-banked samples for characterizing gene regulatory elements.

immunology↗

bioRxiv2020

Composite modeling of leaf shape across shoots discriminates Vitis species better than individual leaves

Premise of studyLeaf morphology is dynamic, continuously deforming during leaf expansion and among leaves within a shoot. We measured leaf morphology from over 200 vines over four years, and modeled changes in leaf shape along the shoot to determine if a composite "shape of shapes" can better capture variation and predict species identity compared to individual leaves. MethodsUsing homologous universal landmarks found in grapevine leaves, we modeled various morphological features as a polynomial function of leaf node. The resulting functions are used to reconstruct modeled leaf shapes across shoots, generating composite leaves that comprehensively capture the spectrum of possible leaf morphologies. ResultsWe found that composite leaves are better predictors of species identity than individual leaves from the same plant. We were able to use composite leaves to predict species identity of previously unassigned vines, which were verified with genotyping. DiscussionObservations of individual leaf shape fail to capture the true diversity between species. Composite leaf shape--an assemblage of modeled leaf snapshots across the shoot--is a better representation of the dynamic and essential shapes of leaves, as well as serving as a better predictor of species identity than individual leaves.

plant biology↗

bioRxiv2020

Calcitriol, the active form of vitamin D, is a promising candidate for COVID-19 prophylaxis

COVID-19, the disease caused by SARS-CoV-2 (1), was declared a pandemic by the World Health Organization (WHO) in March 2020 (2). While awaiting a vaccine, several antivirals are being used to manage the disease with limited success (3, 4). To expand this arsenal, we screened 4 compound libraries: a United States Food and Drug Administration (FDA) approved drug library, an angiotensin converting enzyme-2 (ACE2) targeted compound library, a flavonoid compound library as well as a natural product library. Of the 121 compounds identified with activity against SARS-CoV-2, 7 were shortlisted for validation. We show for the first time that the active form of Vitamin D, calcitriol, exhibits significant potent activity against SARS-CoV-2. This finding paves the way for consideration of host-directed therapies for ring prophylaxis of contacts of SARS-CoV-2 patients.

microbiology↗

bioRxiv2020

A rapid, low cost, and highly sensitive SARS-CoV-2 diagnostic based on whole genome sequencing

Early detection of infection with SARS-CoV-2 is key to managing the current global pandemic, as evidence shows the virus is most contagious on or before symptom onset. Here, we introduce a low-cost, high-throughput method for diagnosing and studying SARS-CoV-2 infection. Dubbed Pathogen-Oriented Low-Cost Assembly & Re-Sequencing (POLAR), this method amplifies the entirety of the SARS-CoV-2 genome. This contrasts with typical RT-PCR-based diagnostic tests, which amplify only a few loci. To achieve this goal, we combine a SARS-CoV-2 enrichment method developed by the ARTIC Network (https://artic.network/) with short-read DNA sequencing and de novo genome assembly. Using this method, we can reliably (>95% accuracy) detect SARS-CoV-2 at a concentration of 84 genome equivalents per milliliter (GE/mL). Almost all diagnostic methods currently authorized for use by the United States Food and Drug Administration with the Coronavirus Disease 2019 (COVID-19) Emergency Use Authorization require larger concentrations of the virus to achieve this degree of accuracy. In addition, we can reliably assemble the SARS-CoV-2 genome in the sample, often with no gaps and perfect accuracy. The genotypic data contained in these genome assemblies enable the more effective analysis of disease spread than is possible with an ordinary binary diagnostic. These data can also help identify vaccine and drug targets. Finally, we show that the diagnoses obtained using POLAR of both positive and negative clinical nasopharyngeal swab samples 100% match the diagnoses obtained in a clinical diagnostic lab using the Center for Disease Controls 2019-Novel Coronavirus test. Using POLAR, a single person can manually process 192 samples over an 8- hour experiment at the cost of [~]$36 per patient (as of December 7th, 2022), enabling a 24-hour turnaround with sequencing and data analysis time. We anticipate that further testing and refinement will allow greater sensitivity in this approach.

genomics↗

bioRxiv2019

Application of Optogenetic Amyloid-β Distinguishes Between Metabolic and Physical Damage in Neurodegeneration

The brains of Alzheimers Disease patients show a decrease in brain mass and a preponderance of extracellular Amyloid-{beta} plaques. These plaques are formed by aggregation of polypeptides that are derived from Amyloid Precursor Protein (APP). Amyloid-{beta} plaques are thought to play either a direct or an indirect role in disease progression, however the exact role of aggregation and plaque formation in the ethology of Alzheimers Disease is subject to debate, not least because the biological effects of soluble and aggregated Amyloid-{beta} peptides are difficult to separate in vivo. To investigate the consequences of formation of Amyloid-{beta} oligomers in living tissues, we developed a fluorescently tagged, optogenetic Amyloid-{beta} peptide that oligomerizes rapidly in the presence of blue light. We applied this system to the crucial question of how intracellular Amyloid-{beta} oligomers underlie the pathologies of Alzheimers Disease. We show that, although both expression and induced oligomerization of Amyloid-{beta} were detrimental to lifespan and healthspan, we were able to separate the metabolic and physical damage caused by light-induced Amyloid-{beta} oligomerization from Amyloid-{beta} expression alone. The physical damage caused by Amyloid-{beta} oligomers also recapitulated the catastrophic tissue loss that is a hallmark of late AD. We show that the lifespan deficit induced by Amyloid-{beta} oligomers was reduced with Li+ treatment. Our results present the first model to separate different aspects of disease progression.

developmental biology↗

bioRxiv2018

Selectivity among anti-σ factors by Mycobacterium tuberculosis ClpX influences intracellular levels of Extracytoplasmic Function σ factors

Extracytoplasmic Function {sigma} factors that are stress inducible are often sequestered in an inactive complex with a membrane-associated anti-{sigma} factor. M. tuberculosis membrane-associated anti-{sigma} factors have a small stable RNA gene A-like degron for targeted proteolysis. Interaction between the unfoldase, ClpX, and the substrate with an accessible degron initiates energy-dependent proteolysis. Four anti-{sigma} factors with a mutation in the degron provided a set of natural substrates to evaluate the influence of the degron on degradation strength in ClpX-substrate processivity. We note that a point mutation in the degron (XXX-Ala-Ala) leads to an order of magnitude difference in the dwell time of the substrate on ClpX. Differences in ClpX/anti-{sigma} interactions were correlated with change in unfoldase activity. GFP chimeras or polypeptides of identical length with the anti-{sigma} degron also demonstrate degron-dependent variation in ClpX activity. We show that degron-dependent ClpX activity leads to differences in anti-{sigma} factor degradation thereby regulating the release of free {sigma} from the {sigma}/anti-{sigma} complex. M. tuberculosis ClpX activity thus influences changes in gene expression by modulating the cellular abundance of ECF {sigma} factors.\n\nImportanceThe ability of Mycobacterium tuberculosis to quickly adapt to the changing environmental stimuli occurs by maintaining protein homeostasis. Extra-cytoplasmic function (ECF) {sigma} factors play a significant role in coordinating the transcription profile to changes in environmental conditions. Release of the {sigma} factor from the anti-{sigma} is governed by the ClpXP2P1 assembly. M. tuberculosis ECF anti-{sigma} factors have a ssrA-like degron for targeted degradation. A point mutation in the degron leads to differences in ClpX mediated proteolysis and affects the cellular abundance of ECF {sigma}-factors. ClpX activity thus synchronizes changes in gene expression with environmental stimuli affecting M. tuberculosis physiology.

biochemistry↗

bioRxiv2018

Hi-C yields chromosome-length scaffolds for a legume genome, Trifolium subterraneum

We present a chromosome-length assembly of the genome of subterranean clover, Trifolium subterraneum, a key Australian pasture legume. Specifically, in situ Hi-C data (48X) was used to correct misjoins and anchor, order, and orient scaffolds in a previously published genome assembly (TSUd_r1.1; scaffold N50: 287kb). This resulted in an improved genome assembly (TrSub3; scaffold N50: 56Mb) containing eight chromosome-length scaffolds that span 95% of the sequenced bases in the input assembly.

genomics↗

bioRxiv2018

Recapitulation of human germline coding variation in an ultra-mutated infant leukemia

BackgroundMixed lineage leukemia/Histone-lysine N-methyltransferase 2A gene rearrangements occur in 80% of infant acute lymphoblastic leukemia, but the role of cooperating events is unknown. While infant leukemias typically carry few somatic lesions, we identified a case with over 100 somatic point mutations per megabase and here report unique genomic-features of this case.\n\nResultsThe patient presented at 82 days of age, one of the earliest manifestations of cancer hypermutation recorded. The transcriptional profile showed global similarities to canonical cases. Coding lesions were predominantly clonal and almost entirely targeting alleles reported in human genetic variation databases with a notable exception in the mismatch repair gene, MSH2. There were no rare germline alleles or somatic mutations affecting proof-reading polymerase genes POLE or POLD1, however there was a predicted damaging mutation in the error prone replicative polymerase, POLK. The patients diagnostic leukemia transcriptome was depleted of rare and low-frequency germline alleles due to loss-of-heterozygosity, while somatic point mutations targeted low-frequency and common human alleles in proportions that offset this discrepancy. Somatic signatures of ultra-mutations were highly correlated with germline single nucleotide polymorphic sites indicating a common role for 5-methylcytosine deamination, DNA mismatch repair and DNA adducts.\n\nConclusionsThese data suggest similar molecular processes shaping population-scale human genome variation also underlies the rapid evolution of an infant ultra-mutated leukemia.

cancer biology↗

bioRxiv2017

Gene networks underlying faster flowering induction in response to far-red light

Light is one of the main signals that regulates flowering. Low red to far-red ratios accelerate flowering in a wide range of species. The central gene pathways controlling flowering time in Arabidopsis, appear to be largely conserved in legumes. However, numerous examples exist of gene duplication and loss. The role of CONSTANS-LIKE genes as integrators of the photoperiod response has been questioned in several dicot species, including legumes. In this study on subterranean clover, using RNA-seq and controlled light spectra, we identified 13 differentially expressed genes related to light signalling, meristem identity and flowering promotion. Of these, we pinpointed genes which seem to link photoperiod and far-red light signalling coding for a With no lysine kinase, a CCT motif related to CONSTANS, a FLOWERING LOCUS T b2 like protein, and their active downstream cascade. The earlier down-regulation of these genes under blue compared to far-red-enriched light may explain their role in floral induction. A second independent approach (qPCR analysis) confirmed our findings. Contrasting responses to light quality related to reproduction and defence mechanisms were also found. These results will contribute to a better understanding of the molecular basis of flowering in response to light quality in long-day plants.

genetics↗

bioRxiv2017

Large-scale structural variation detection in subterranean clover subtypes using optical mapping validated at nucleotide level

Whole genome sequencing has been widely used to detect structural variations (SVs). However, the limited single molecule size makes it difficult to characterize large-scale SVs in a genome because they cannot fully cover such vast and complex regions. Recently, optical mapping in nanochannels has provided novel resolution to detect large-scale SVs by comparing the physical location of the nickase recognition sequence in genomes. Other than in humans, SVs discovered in plants by optical mapping have not been validated. To assess the accuracy of SV calling in plants by optical mapping, we selected two genetically diverse subspecies of the Trifolium model species, subterranean clover cvs. Daliak and Yarloop. The SVs discovered by BioNano optical mapping (BOM) were validated using Illumina short reads. In the analysis, BOM identified 12 large-scale regions containing deletions and 19 containing insertions in Yarloop. The 12 large-scale regions contained 71 small deletions when validated by Illumina short reads. The results suggest that BOM could detect the total size of deletions and insertions, but it could not precisely report the location and actual quantity of SVs in the genome. Nucleotide-level validation is crucial to confirm and characterize SVs reported by optical mapping. The accuracy of SV detection by BOM is highly dependent on the quality of reference genomes and the density of selected nickases.

bioinformatics↗

bioRxiv2017

An Embryonic System To Assess Wnt Transcriptional Targets

During animal development, complex signals determine and organize a vast number of tissues using a very small number of signal transduction pathways. These developmental signaling pathways determine cell fates through a coordinated transcriptional response that remains poorly understood. The Wnt pathway is involved in a variety of these cellular functions, and its signals are transmitted in part through a {beta}-catenin/TCF transcriptional complex. Here we report an in vivo Drosophila assay that can be used to distinguish between activation, de-repression and repression of transcriptional responses, separating upstream and downstream pathway activation and canonical/non-canonical Wnt signals in embryos. We find specific sets of genes downstream of both {beta}-catenin and TCF with an additional group of genes regulated by Wnt, while the non-canonical Wnt4 regulates a separate cohort of genes. We correlate transcriptional changes with phenotypic outcomes of cell differentiation and embryo size, showing our model can be used to characterize developmental signaling compartmentalization in vivo.

developmental biology↗

bioRxiv2017

Coupling optogenetics and light-sheet microscopy to study signal transduction in vivo

Optogenetics allows precise, fast and reversible intervention in biological processes. Light-sheet microscopy allows observation of the full course of embryonic development from egg to larva. Bringing the two approaches together allows unparalleled precision into the temporal regulation of signaling pathways and cellular processes in vivo. To develop this method, we investigated the regulation of canonical Wnt signaling during anterior-posterior patterning of the Drosophila embryonic epidermis. Cryptochrome 2 (CRY2) from Arabidopsis Thaliana was fused to mCherry fluorescent protein and Drosophila {beta}-catenin to form an easy to visualize optogenetic switch. Blue light illumination caused oligomerization of the fusion protein and inhibited downstream Wnt signaling in vitro and in vivo. Temporal inactivation of {beta}-catenin confirmed that Wnt signaling is required not only for Drosophila pattern formation, but also for maintenance later in development. We anticipate that this method will be easily extendable to other developmental signaling pathways and many other experimental systems.

developmental biology↗