Biology subjects

Kumar, A.

Publications and source records attributed to Kumar, A..

At least 415 records · Page 23Linked to original sources

bioRxiv2022

Reprogramming Adeno-Associated Virus Tropism Via Displayed Peptides Tiling Receptor-Ligands

Adeno-associated viruses (AAVs) are common gene therapy vectors, however, their effectiveness is hindered by poor target tissue transduction and off-target delivery. Hypothesizing that naturally occurring receptor-ligand interactions could be repurposed to engineer tropism, we fragmented all annotated protein ligands known to bind human receptors into tiling 20-mer peptides and displayed these onto the surface loops of AAV5 and AAV9 capsids at two sites. The resulting four capsid libraries, comprising >1 million AAV variants, were screened across 9 tissues in C57BL/6 mice. Tracking variant abundance, we identified >250,000 variants which packaged into capsids, and >15,000 variants which efficiently transduced at least one mouse organ. We individually validated 21 AAV variants with 74.3% of the organ tropism predictions accurately reproducing, confirming overall screen efficacy. Systematic ligand tiling enabled prediction of putative AAV-receptor interactions, which we successfully validated by targeted genetic perturbations. Comprehensive peptide tiling also enabled examination of homologous peptide activity. Interestingly, we observed functional peptides tended to be derived from specific domains on ligands. Notably, certain peptides also displayed consistent activity across mice strains, capsid insertion contexts, and capsid serotypes, including novel immune orthogonal serotypes. Further analyses of displayed peptides revealed that biophysical attributes were highly predictive of AAV variant packaging, and there was a machine learnable relationship between peptide sequence and tissue tropism. We anticipate this comprehensive ligand peptide tiling and display approach will enable engineering of tropism across diverse viral, viral-like, and non-viral delivery platforms, and shed light into basic receptor-ligand biology.

bioengineering↗

bioRxiv2022

Cd-induced cytosolic proteome changes in the cyanobacterium Anabaena sp. PCC7120 are mediated by LexA as one of the regulatory proteins

LexA, a well-characterized transcriptional repressor of the SOS genes in heterotrophic bacteria, has been shown to regulate diverse genes in cyanobacteria. An earlier study showed that LexA overexpression in a cyanobacterium, Anabaena sp. PCC7120 reduces its tolerance to Cd stress. This was later shown to be due to modulation of photosynthetic redox poising by LexA under Cd stress. However, in light of the global regulatory nature of LexA and the prior prediction of AnLexA-box in a few heavy metal-responsive genes, we speculated that LexA has a broad role in Cd stress tolerance, with regulation over a variety of Cd stress-responsive genes in addition to the regulation on genes related with photosynthetic redox poising. Thus, to further expand the knowledge on the regulatory role of LexA in Cd stress tolerance, a cytosolic proteome profiling of Anabaena constitutively overexpressing LexA upon Cd stress was performed. The proteomic study revealed 25 differentially accumulated proteins (DAPs) in response to the combined effect of LexA overexpression and Cd stress, and the other 11 DAPs exclusively in response to either LexA overexpression or Cd stress. The 36 identified proteins were related with a variety of functions, including photosynthesis, carbon metabolism, antioxidative defence, protein turnover, chaperones, post-transcriptional modifications, and a few unknown and hypothetical proteins. The regulation of LexA on corresponding genes, as well as six previously reported Cd efflux transporters, was further validated by the presence of AnLexA-boxes, transcript, and/or promoter analyses. In a nutshell, this study identifies the regulation of LexA on several genes and proteins of various functional categories in Anabaena that are responsive to Cd stress, hence expanding the regulatory role of LexA under Cd stress. HighlightsO_LILexA overexpression was earlier shown to decrease Cd stress tolerance in Anabaena. C_LIO_LIWe examined the combined effect of LexA overexpression and Cd on Anabaena proteome. C_LIO_LIUpon LexA overexpression or Cd stress or both, 36 differential proteins were found. C_LIO_LIIn silico, transcript and EMSA proved LexA regulation on them and few transporters. C_LIO_LIThe findings of this study extended the regulatory role of LexA in Cd tolerance. C_LI

molecular biology↗

bioRxiv2022

Genome characterization of monkeypox cases detected in India: Identification of three sub clusters among A.2 lineage

Since May 2022, Monkeypox, a zoonotic Orthopox DNA virus was reported in more than 102 countries indicating expansion of its geographic range. We analyzed the complete genomes sequences of Monkeypox cases from Kerala (n=5 travelled from UAE) and Delhi (n=5 no travel history), India confirmed during July to August 2022. All the retrieved MPXV sequences from India covering 90 to 99% genome belong to A.2 lineage of clade IIb. The A.2 MPXV lineage divided in three sub clusters; first cluster Kerala n=5, Delhi n=2 aligned with the USA-2022 ON674051.1; while second of Delhi n=3 aligned with USA-2022 ON675438.1 and third consists of the UK, USA and Thailand. Recent update in MPXV lineage designated all the five sequences from Kerala as A.2.1. In addition to known 16 single nucleotide polymorphisms (SNPs) along with 13 APOBEC3 cytosine deaminase activity determined specific lineage defining mutations in A.2 lineage, 25 additional APOBEC3 mutations were found in 10 reported sequences. The study emphasizes need of enhancing genomic surveillance to understand the mutation and its linkage.

microbiology↗

bioRxiv2022

How short decoding times, stimulus dimensionality and spontaneous activity constrain the shape of tuning curves: A speed-accuracy trade-off

According to the efficient coding hypothesis, sensory neurons are adapted to provide maximal information about the environment given some biophysical constraints. Early sensory neurons modulate their average firing rates in response to some features of the external stimulus, creating tuned responses. In early visual areas, these modulations (or tunings) are predominantly single-peaked. However, periodic tuning, as exhibited by grid cells, has been linked to a significant increase in decoding performance. Does this imply that the tuning curves in early visual areas are sub-optimal? We argue that the time scale at which neurons encode information is imperative to understanding the relative advantages of single-peaked and periodic tuning curves. Because, if decoding ability scales differently with time for the different shapes of tuning curves, the time scale at which the neurons operate becomes critical. Here, we show that the possibility of catastrophic (large) errors due to overlapping neural responses for distinct stimulus conditions creates a trade-off between decoding time and decoding ability. Unfortunately, standard theoretical measures such as Fisher information do not capture these errors. We investigate how (very) short decoding times and stimulus dimensionality affect the optimal shape of tuning curves for stimuli with finite domains. In particular, we focus on the spatial periods of the tuning curves (or the number of "peaks") for a class of circular tuning curves. We show a general trend for minimal decoding time, i.e., the shortest decoding time required to produce a statistically reliable signal, to increase with increasing Fisher information implying a trade-off between accuracy and speed. This trade-off is reinforced whenever the stimulus dimensionality is high or there is ongoing activity. Thus, given constraints on processing speed, we present normative arguments for the existence of single-peaked, rather than a periodic, tuning organization observed in early visual areas.

neuroscience↗

bioRxiv2022

A novel biopolymer for mucosal adjuvant against respiratory pathogens

Mucosal vaccinations for respiratory pathogens provide effective protection as they stimulate localized cellular and humoral immunities at the site of infection. Currently, the major limitation of intranasal vaccination is using effective adjuvants capable of withstanding the harsh environment imposed by the mucosa. Herein, we describe the efficacy of using a novel biopolymer, N-dihydrogalactochitosan (GC), as a nasal mucosal vaccine adjuvant against respiratory infections. Specifically, using COVID as an example, we mixed GC with recombinant SARS-CoV-2 trimeric spike (S) and nucleocapsid (NC) proteins to intranasally vaccinate K18-hACE2 transgenic mice, in comparison with Addavax (AV), an MF-59 equivalent. In contrast to AV, intranasal application of GC induces a robust, systemic antigen-specific antibody response and increases the number of T cells in the cervical lymph nodes. Moreover, GC+S+NC-vaccinated animals were largely resistant to the lethal SARS-CoV-2 challenge and experienced drastically reduced morbidity and mortality, with animal weights and behavior returning to normal 22 days post-infection. In contrast, animals intranasally vaccinated with AV+S+NC experienced severe weight loss, mortality, and respiratory distress, with none surviving beyond 6 days post-infection. Our findings demonstrate that GC can serve as a potent mucosal vaccine adjuvant against SARS-CoV-2 and potentially other respiratory viruses.

bioengineering↗

bioRxiv2022

Dectin-1 Stimulation Promotes a Distinct Inflammatory Signature in the Setting of HIV-infection and Aging

Dectin-1 is an innate immune receptor that recognizes and binds {beta}-1,3/1,6 glucans on fungi. We evaluated Dectin-1 function in myeloid cells in a cohort of HIV-positive and HIV-negative young and older adults. Stimulation of monocytes with {beta}-D-glucans induced a pro-inflammatory phenotype in monocytes of HIV-infected individuals that was characterized by increased levels of IL-12, TNF-, and IL-6, with some age-associated cytokine increases also noted. Dendritic cells showed a striking HIV-associated increase in IFN- production. These increases in cytokine production paralleled increases in Dectin-1 surface expression in both monocytes and dendritic cells that were noted with both HIV and aging. Differential gene expression analysis showed that HIV-positive older adults had a distinct gene signature compared to other cohorts characterized by a robust TNF- and coagulation response (increased at baseline), a persistent IFN- and IFN-{gamma} response, and an activated dendritic cell signature/M1 macrophage signature upon Dectin-1 stimulation. Dectin-1 stimulation induced a strong upregulation of MTORC1 signaling in all cohorts, although increased in the HIV-Older cohort (stimulation and baseline). Overall, our study demonstrates that the HIV Aging population has a distinct immune signature in response to Dectin-1 stimulation. This signature may contribute to the pro-inflammatory environment that is associated with HIV and Aging.

immunology↗

bioRxiv2022

Asymmetric expression of homoeologous genes in wheat roots modulates the early phase of iron-deficiency signalling

Iron (Fe) limitation leads to dramatic changes in gene expression in plants, to induce iron uptake and mobilization, while at the same time restrict Fe-dependent metabolism and growth. Although transcriptional changes in response to Fe deficiency have recently been charted in wheat, this was performed at a stage when photosynthesis and growth were severely impacted, confounding primary and secondary responses. Here, we specifically uncover the transcriptional landscape of wheat roots during the early stages of the Fe deficiency response (4 and 8 days) and after Fe resupply. Root growth was significantly inhibited at day 4, but chlorosis only became apparent on day 8. The number of differentially expressed genes increased from 1386 on day 4 to 3538 on day 8, with an overlap of 2006 genes. Genes with dynamic changes in expression patterns include membrane transporters and transcription factors shown to be involved in Fe homeostasis in other plant species. Comparative analysis of the Fe deficiency response at 4, 8 and 20 days identified a core set of Fe-regulated genes. Analysis of the expression of homoeologs suggests an increase in induction bias at 8 days compared to 4 days particularly, A genome contributing high at 4 days and the A+D genomes at 8 days. Overall, our work will contribute towards fundamental knowledge of the Fe signalling networks in wheat and point to the interplay of the three sub-genomes in this hexaploid species to fine tune the transcriptional response.

plant biology↗

bioRxiv2022

Genome-Wide Association Study Finds Multiple Loci Associated with Intraocular Pressure in HS Rats

Elevated intraocular pressure (IOP) is influenced by environmental and genetic factors. Increased IOP is a major risk factor for most types of glaucoma, including primary open angle glaucoma (POAG). Investigating the genetic basis of IOP may lead to a better understanding of the molecular mechanisms of POAG. The goal of this study was to identify genetic loci involved in regulating IOP using outbred heterogeneous stock (HS) rats. HS rats are a multigenerational outbred population derived from eight inbred strains that have been fully sequenced. This population is ideal for genome-wide association studies (GWASs) owing to the accumulated recombinations among well-defined haplotypes, the relatively high allele frequencies, the accessibility to a large collection of tissue samples, and the large allelic effect size compared to human studies. Both male and female HS rats (N=1,812) were used in the study. Genotyping-by-sequencing was used to obtain ~3.5 million single nucleotide polymorphisms (SNP) from each individual. SNP heritability for IOP in HS rats was 0.32, which agrees with other studies. We performed a GWAS for the IOP phenotype using a linear mixed model and used permutation to determine a genome-wide significance threshold. We identified three genome-wide significant loci for IOP on chromosomes 1, 5, and 16. Next, we sequenced the mRNA of 51 whole eye samples to find cis-eQTLs to aid in identification of candidate genes. We report 5 candidate genes within those loci: Tyr, Ctsc, Plekhf2, Ndufaf6 and Angpt2. Tyr, Ndufaf6 and Angpt2 genes have been previously implicated by human GWAS of IOP-related conditions. Ctsc and Plekhf2 genes represent novel findings that may provide new insight into the molecular basis of IOP. This study highlights the efficacy of HS rats for investigating the genetics of elevated IOP and identifying potential candidate genes for future functional testing. Contribution to the field statementGlaucoma is the leading cause of irreversible blindness worldwide. Intraocular pressure (IOP) is the only known modifiable risk factor. This study describes results of the genome-wide association study (GWAS) performed in outbred rats that identifies known and novel genes involved in IOP regulation. To our knowledge, this is the first GWAS performed for IOP in a rat model. Identifying novel candidate genes in the rat model provides insight into the risk factors for glaucoma in humans and potential pharmacological targets for regulating IOP. The rat model is advantageous for studying natural variations in IOP, controlling environmental exposures, and providing easier access to tissue that can be used in phenotyping and gene expression in future studies.

genomics↗

bioRxiv2022

Direct access to millions of mutations by Whole Genome Sequencing of an oilseed rape mutant population

Induced mutations are an essential source of genetic variation in plant breeding. EMS mutagenesis has been frequently applied, and mutants have been detected by phenotypic or genotypic screening of large populations. In this study, a rapeseed M2 population was derived from M1 parent cultivar "Express" treated with EMS. Whole genomes were sequenced from fourfold (4x) pools of 1,988 M2 plants representing 497 M2 families. Detected mutations were not evenly distributed and displayed distinct patterns across the 19 chromosomes with lower mutation rates towards the ends. Mutation frequencies ranged from 32/Mb to 48/Mb. On average, 284,442 single nucleotide polymorphisms per M2 DNA pool were found resulting from EMS mutagenesis. 55% were C[->]T and G[->]A transitions, characteristic for EMS induced ( canonical) mutations, whereas the remaining SNPs were non-canonical transitions (15%) or transversions (30%). Additionally, we detected 88,725 high confidence insertions and deletions (InDels) per pool. On average, each M2 plant carried 39,120 canonical mutations, corresponding to a frequency of one mutation per 23.6 kb. Roughly 82% of such mutations were located either 5 kb upstream or downstream (~56%) of gene coding regions or within intergenic regions (26%). The remaining 18% were located within regions coding for genes. All mutations detected by whole-genome sequencing could be verified by comparison with known mutations. Furthermore, all sequences are accessible via the online tool "EMS Brassica" (http://www.emsbrassica.plantbreeding.uni-kiel.de/), which enables direct identification of mutations in any target sequence. The sequence resource described here will further add value for functional gene studies in rapeseed breeding.

genomics↗

bioRxiv2022

A light sheet fluorescence microscopy protocol for Caenorhabditis elegans larvae and adults

Light sheet fluorescence microscopy (LSFM) has become a method of choice for live imaging because of its fast acquisition and reduced photobleaching and phototoxicity. Despite the strengths and growing availability of LSFM systems, no generalized LSFM mounting protocol has been adapted for live imaging of post-embryonic stages of C. elegans. A major challenge has been to develop methods to limit animal movement using a mounting media that matches the refractive index of the optical system. Here, we describe a simple mounting and immobilization protocol using a refractive-index matched UV-curable hydrogel within fluorinated ethylene propylene (FEP) tubes for efficient and reliable imaging of larval and adult C. elegans stages.

developmental biology↗

bioRxiv2022

UVC-based air disinfection system for rapid inactivation of SARS-CoV-2 present in the air

The novel coronavirus disease 2019 (COVID-19) infections have rapidly spread throughout the world, and the virus has acquired an ability to spread via aerosols even at long distances. Hand washing, face-masking, and social distancing are the primary preventive measures against infections. With mounting scientific evidence, World Health Organisation (WHO) declared COVID-19 an air-borne disease. This ensued the need to disinfect air to reduce the transmission. Ultraviolet C (UVC) comprising the light radiation of 200-280 nm range is a commonly used method for inactivation of pathogens. The heating, ventilation, and air conditioning (HVAC) systems are not beneficial in closed spaces due to poor or no ability to damage circulating viruses. Therefore, standard infection-prevention practices coupled with a strategy to reduce infectious viral load in air substantially might be helpful in reducing virus transmissibility. In this study, we implemented UV light-based strategies to combat COVID-19 and future pandemics. We tested various disinfection protocols by using UVC-based air purification systems and currently installed such a system in workspaces, rushed out places, hospitals and healthcare facilities for surface, air, and water disinfection. In this study, we designed a prototype device to test the dose of UVC required to inactivate SARS-CoV-2 in aerosols and demonstrate that the radiation rapidly destroys the virus in aerosols. The UVC treatment renders the virus non-infectious due to chemical modification of nucleic acid. We also demonstrate that UVC treatment alters the Spike protein conformation that may further affect the infectivity of the virus. We show by using a mathematical model based on the experimental data that UVC-based air disinfection strategy can substantially reduce the risk of virus transmission. The systematic treatment by UVC of air in the closed spaces via ventilation systems could be helpful in reducing the active viral load in the air.

microbiology↗

bioRxiv2022

The PREGCARE study: Personalized recurrence risk assessment following the birth of a child with a pathogenic de novo mutation

Next-generation sequencing has led to a dramatic improvement in molecular diagnoses of serious pediatric disorders caused by apparently de novo mutations (DNMs); by contrast, clinicians ability to counsel the parents about the risk of recurrence in a future child has lagged behind. Owing to the possibility that one of the parents could be mosaic in their germline, a recurrence risk of 1-2% is frequently quoted, but for any specific couple, this figure is usually incorrect. We present a systematic approach to providing individualized recurrence risk stratification, by combining deep-sequencing of multiple tissues in the mother-father-child trio with haplotyping to determine the parental origin of the DNM. In the first 58 couples analysed (total of 59 DNMs in 49 different genes), the risk for 35 (59%) DNMs was decreased below 0.1% but for 6 (10%) couples it was increased owing to parental mosaicism - that could be quantified in semen (recurrence risks of 5.6-12.1%) for the paternal cases. Deep-sequencing of the DNM efficiently identifies couples at greatest risk for recurrence and may qualify them for additional reproductive technologies. Haplotyping can further reassure many other couples that their recurrence risk is very low, but its implementation is more technically challenging and will require better understanding of how couples respond to information that reduces their risks.

genetics↗

bioRxiv2022

Temporal regulation of TAK1 to counteract muscular dystrophy

Muscular dystrophy is a group of genetic neuromuscular disorders that involves severe muscle wasting. Transforming growth factor {beta}-activated kinase 1 (TAK1) is an important signaling protein that regulates cell survival, growth, and inflammation. TAK1 has been recently found to promote myofiber growth in skeletal muscle of adult mice. However, the role of TAK1 in muscle disorders remains poorly understood. In the present study, we have investigated how TAK1 affects progression of dystrophic phenotype in the mdx mouse model of Duchnne muscular dystrophy (DMD). TAK1 is highly activated during peak necrotic phase in mdx mice. Targeted inducible inactivation of TAK1 inhibits muscle injury, necroptosis, and accumulation of macrophages in dystrophic muscle of mdx mice. Additionally, targeted inactivation of TAK1 leads to the activation of autophagy and Notch and Wnt signaling in the dystrophic muscle. However, inactivation of TAK1 significantly reduces myofiber size and muscle contractile function in both young and adult mdx mice. Forced activation of TAK1 in skeletal muscle after peak necrotic phase induces myofiber growth and improves muscle histopathology in mdx mice. Our results suggest that targeted activation of TAK1 can ameliorate disease progression and improve muscle growth in DMD. One Sentence SummaryOur results demonstrate that duly regulation of TAK1 activity ameliorates dystrophic phenotype in a mouse model of Duchnne Muscular Dystrophy.

physiology↗

bioRxiv2022

Antibiotic induced biofilm formations in Pseudomonas aeruginosa strains KPW.1-S1 and HRW.1-S3 are associated with increased production of eDNA and exoproteins, increased ROS generation, and increased cell surface hydrophobicity

Pseudomonas aeruginosa is a medically important bacteria due to its ability to form biofilm and is also an opportunistic pathogen. Pseudomonas aeruginosa has the intrinsic ability to form biofilm as one of the defense mechanisms for their survival. The fact that it can form biofilms on various medical implants makes it more harmful clinically. Although various antibiotics are used to treat Pseudomonas aeruginosa infections, previous studies have shown that sub-MIC levels of antibiotics cause biofilm formation in this type of bacteria. The present study thus deals with the effect of the aminoglycoside antibiotic gentamicin on the biofilm dynamics of two Pseudomonas aeruginosa strains KPW.1-S1 and HRW.1-S3. Biofilm formation was seen to be increasing with increased gentamicin concentrations in growth media. Confocal laser scanning microscopy and scanning electron microscopy accompanied with other biochemical tests deduced that biofilm-forming components like exoproteins, eDNA, and exolipids as exopolymeric substances in Pseudomonas aeruginosa biofilms were increased in the presence of gentamicin. An increase in reactive oxygen species generation along with increased cell surface hydrophobicity was also seen in both strains when treated with gentamicin. The observed increase in the adherence of the cells accompanied by an increase in exopolymeric substances, eDNA, and exolipids may have largely contributed to the increased biofilm production by the Pseudomonas aeruginosa strains KPW.1-S1 and HRW.1-S3 under the stress of the antibiotic treatment.

microbiology↗

bioRxiv2022

An accessible infrastructure for artificial intelligence using a docker-based Jupyterlab in Galaxy

Artificial intelligence (AI) programs that train on a large amount of data require powerful compute infrastructure. Jupyterlab notebook provides an excellent framework for developing AI programs but it needs to be hosted on a powerful infrastructure to enable AI programs to train on large data. An open-source, docker-based, and GPU-enabled jupyterlab notebook infrastructure has been developed that runs on the public compute infrastructure of Galaxy Europe for rapid prototyping and developing end-to-end AI projects. Using such a notebook, long-running AI model training programs can be executed remotely. Trained models, represented in a standard open neural network exchange (ONNX) format, and other resulting datasets are created in Galaxy. Other features include GPU support for faster training, git integration for version control, the option of creating and executing pipelines of notebooks, and the availability of multiple dashboards for monitoring compute resources. These features make the jupyterlab notebook highly suitable for creating and managing AI projects. A recent scientific publication that predicts infected regions of COVID-19 CT scan images is reproduced using multiple features of this notebook. In addition, colabfold, a faster implementation of alphafold2, can also be accessed in this notebook to predict the 3D structure of protein sequences. Jupyterlab notebook is accessible in two ways - first as an interactive Galaxy tool and second by running the underlying docker container. In both ways, long-running training can be executed on Galaxys compute infrastructure. The scripts to create the docker container are available under MIT license at https://github.com/anuprulez/ml-jupyter-notebook. Contactkumara@informatik.uni-freiburg.de anup.rulez@gmail.com

bioinformatics↗

bioRxiv2022

Gamma (γ)-radiation stress response of the cyanobacterium Anabaena sp. PCC7120: Regulatory role of LexA and photophysiological changes

High radioresistance of the cyanobacterium, Anabaena sp. PCC7120 has been attributed to efficient DNA repair, protein recycling, and oxidative stress management. However, the regulatory network involved in these batteries of responses remains unexplored. In the present study, the role of a global regulator, LexA in modulating gamma ({gamma})-radiation stress response of Anabaena was investigated. Comparison of the cytosolic proteome profiles upon {gamma}-radiation in recombinant Anabaena strains, AnpAM (vector-control) and AnlexA+ (LexA-overexpressing), revealed 41 differentially accumulated proteins, corresponding to 29 distinct proteins. LexA was found to be involved in the regulation of 27 of the corresponding genes based on the presence of AnLexA-Box, EMSA, and/or qRT-PCR studies. The majority of the regulated genes were found to be involved in C-assimilation either through photosynthesis or C-catabolism and oxidative stress alleviation. Photosynthesis, measured in terms of PSII photophysiological parameters and thylakoid membrane proteome was found to be affected by {gamma}-radiation in both AnpAM and AnlexA+ cells, with LexA affecting them even under control growth conditions. Thus, LexA functioned as one of the transcriptional regulators involved in modulating {gamma}-radiation stress response in Anabaena. This study could pave the way for a deeper understanding of the regulation of {gamma}-radiation-responsive genes in cyanobacteria at large. HighlightsO_LI{gamma}-radiation alters PSII photophysiology and thylakoid proteome profile in Anabaena. C_LIO_LILexA modulates the cytosolic and thylakoid proteome of Anabaena under {gamma}-radiation. C_LIO_LILexA functions as one of the regulators of radiation-responsive genes in Anabaena. C_LI

molecular biology↗

bioRxiv2022

Novel class of yellow emitting carbon dots stimulate collective cell migration and 3D uptake in vivo

We present a new class of nitrogen-doped yellow fluorescent carbon dots, synthesized using a one-step hydrothermal method. These bright fluorescent nanoparticles have excitation and emission spectra near the red region of the visible light spectrum that are quite useful for bioimaging applications. Using organic molecules like ortho- phenylenediamine (OPDA), L-ascorbic acid and urea, yellow fluorescent carbon dots (CDs) were synthesized. We obtained a scalable number of CDs having an average size of 3 nm. The CDs show significant emission spectra in the yellow fluorescence region ({lambda}em= 557 nm). The CDs show remarkable stability in their fluorescence in different pH conditions, ionic stability, photostability as well as thermal stability. These CDs are efficiently uptaken by mammalian cells through clathrin-mediated pathway. Apart from in vitro studies we have also used zebrafish larvae as a 3D in vivo model, and showed that CDs were uptaken efficiently by larvae showing maximum accumulation and fluorescence in the yolk sac region and the notochord region. The CDs also offer enhancement in cell proliferation, hence showing the application in wound healing. The fluorescence of CDs is quite robust and is not affected by most external stimuli, hence can be explored as a promising bioimaging tool for targeted bioimaging and biomedical applications.

bioengineering↗

bioRxiv2022

Preclinical efficacy of bacosides-lauric acid nano-herbal formulation incomparison to rivastigmine for treatment of Alzheimer's disease

Despite decades of rigorous scientific endeavors for Alzheimers disease (AD) drug development, massive failures in clinical trials is continuously posing healthcare and societal burden. Currently recommended single targeted drugs including rivastigmine with limited bioavailability can alleviate AD symptoms only for a limited period of time but unable to reverse the disease progression. Recent evidences consider poly-pharmacological and multi-targeted agents aiming at amyloid and tau burden, neuroinflammation, neuroprotection and cognitive enhancement as potential treatment options. In this regard, bioactive herbal compounds with holistic action and minimal adversities have gained prominence, though lacunae in their scientific validation and limited bio-permeability to cross BBB represent major hurdles. Previously, we showed that lactoferrin conjugated PEG-S-S-PLA-PCL-OH efficaciously delivered herbal compounds to brain and such nano-herbal formulation of bacosides-lauric acid (BAN-LAN) attenuated neuronal damages induced by scopolamine in vitro. Here, we tested the preclinical potential of BAN-LAN in reversal of AD pathologies in 5XFAD transgenic mice. Our nano-herbal formulation substantially reduced amyloid burden by clearing A{beta} plaques in the hippocampus of 5XFAD mice and also attenuated a{beta}42 induced alterations in AD associated gene expression in hippocampal neurons in vitro. It showed neuroprotection by rescuing neuronal damage and promoting neurogenesis in the hippocampus of AD transgenic mice. Anti-neuroinflammatory properties were also exhibited by the formulation as evident from inhibition of hippocampal astrocytic and microglial activation in 5XFAD mice. BAN-LAN showed cognitive efficacy by restoring memory impairment in AD transgenic mice and effects were more pronounced than unconjugated natural form and rivastigmine. These findings suggest that BAN-LAN may serve as a promising therapeutic agent for AD with better brain penetration and targeting multiple AD pathways.

pharmacology and toxicology↗