Complete mitogenome sequence analysis of an Indian Black Bengal goat, Capra hircus, and its phylogenetic consequences.

Capra hircus (Black Bengal goat) is a prized goat breed reared across the Southeast Asian region. Known for its excellent chevon quality and adaptability to hot and humid climates, it supports the livelihood of millions of farmers. The present study reveals the complete mitogenome of a Black Bengal goat of Indian origin utilizing a next-generation sequencing approach (GenBank acc. no.-MZ073671). This newly assembled whole mitochondrial genome (16,637 bp) is composed of a non-coding control region (D-loop region), two ribosomal RNA (rRNA genes), 13 protein-coding genes, and 22 transfer RNA (tRNA). Overall, the current mitogenome shares 99.77% sequence homology with previously reported mitogenomes of Capra hircus. The phylogenetic analysis inferred that the current mitogenome shares a close relationship with the Teressa goat breed of the Andaman and Nicobar Islands.

Epigenetic disruption of the RARγ complex impairs its function to bookmark AR enhancer interactions required for enzalutamide sensitivity in prostate cancer.

The current study in prostate cancer (PCa) focused on the genomic mechanisms at the cross-roads of pro-differentiation signals and the emergence of lineage plasticity. We explored an understudied cistromic mechanism involving RARγ's ability to govern AR cistrome-transcriptome relationships, including those associated with more aggressive PCa features. The RARγ complex in PCa cell models was enriched for canonical cofactors, as well as proteins involved in RNA processing and bookmarking. Identifying the repertoire of miR-96 bound and regulated gene targets, including those recognition elements marked by m6A, revealed their significant enrichment in the RARγ complex. RARγ significantly enhanced the AR cistrome, particularly in active enhancers and super-enhancers, and overlapped with the binding of bookmarking factors. Furthermore, RARγ expression led to nucleosome-free chromatin enriched with H3K27ac, and significantly enhanced the AR cistrome in G2/M cells. RARγ functions also antagonized the transcriptional actions of the lineage master regulator ONECUT2. Similarly, gene programs regulated by either miR-96 or antagonized by RARγ were enriched in alternative lineages and more aggressive PCa phenotypes. Together these findings reveal an under-investigated role for RARγ, modulated by miR-96, to bookmark enhancer sites during mitosis. These sites are required by the AR to promote transcriptional competence, and emphasize luminal differentiation, while antagonizing ONECUT2.

Polyoxometalate-Guanosine Monophosphate Hydrogels with Haloperoxidase-like Activity for Antibacterial Performance.

Haloperoxidases represent an important class of enzymes that nature adopts as a defense mechanism to combat the colonial buildup of microorganisms on surfaces, commonly known as biofouling. Subsequently, there has been tremendous focus on the development of artificial haloperoxidase mimics that can catalyze the oxidation of X- (halide ion) in the presence of H2O2 to form HOX. The natural intermediate HOX disrupts the bacterial quorum sensing, thus preventing biofilm formation. Herein, we report a simple method for the formation of supramolecular hydrogels through the self-assembly of Keggin-structured polyoxometalates, phosphotungstic acid, and silicotungstic acid with the small biomolecule guanosine monophosphate (GMP) in an aqueous medium. The polyoxometalate-GMP hydrogels that contained highly entangled nanofibers were mechanically robust and showed thixotropic properties. The gelation of the polyoxometalates with GMP not only rendered manifold enhancement in biocompatibility but also the fibril network in the hydrogel provided high water wettability and the polyoxometalates acted as an efficient haloperoxidase mimic to trigger oxidative iodination, as demonstrated by a haloperoxidase assay. The antifouling activity of the phosphotungstic acid-GMP hydrogel was demonstrated against both Gram-positive and Gram-negative bacteria, which showed enhanced antibacterial performance of the hydrogel as compared to the polyoxometalate alone. We envision that the polyoxometalate-GMP hydrogels may facilitate mechanically robust coatings in a simple pathway that can be useful for antifouling applications.

Advancements in Nipah virus treatment: Analysis of current progress in vaccines, antivirals, and therapeutics.

Nipah virus (NiV) causes severe encephalitis in humans. Three NiV strains NiV-Malaysia (NiVM ), NiV Bangladesh (NiVB ), and NiV India (NiVI reported in 2019) have been circulating in South-Asian nations. Sporadic outbreak observed in South-East Asian countries but human to human transmission raises the concern about its pandemic potential. The presence of the viral genome in reservoir bats has further confirmed that NiV has spread to the African and Australian continents. NiV research activities have gained momentum to achieve specific preparedness goals to meet any future emergency-as a result, several potential vaccine candidates have been developed and tested in a variety of animal models. Some of these candidate vaccines have entered further clinical trials. Research activities related to the discovery of therapeutic monoclonal antibodies (mAbs) have resulted in the identification of a handful of candidates capable of neutralizing the virion. However, progress in discovering potential antiviral drugs has been limited. Thus, considering NiV's pandemic potential, it is crucial to fast-track ongoing projects related to vaccine clinical trials, anti-NiV therapeutics. Here, we discuss the current progress in NiV-vaccine research and therapeutic options, including mAbs and antiviral medications.

The MYC axis in advanced prostate cancer is impacted through concurrent targeting of ERß and AR using a novel ERß-selective ligand alongside Enzalutamide.

We have dissected the role of Estrogen receptor beta (ERß) in prostate cancer (PCa) with a novel ERß ligand, OSU-ERb-12. Drug screens revealed additive interactions between OSU-ERB-12 and either epigenetic inhibitors or the androgen receptor antagonist, Enzalutamide (Enza). Clonogenic and cell biolody studies supported the potent additive effects of OSU-ERB-12 (100nM) and Enza (1µM). The cooperative behavior was in PCa cell lines treated with either OSU-ERB-12 plus Enza or combinations involving 17ß-estradiol (E2). OSU-ERb-12 plus Enza uniquely impacted the transcriptiome, accessible chromatin, and the AR, MYC and H3K27ac cistromes. This included skewed transcriptional responses including suppression of the androgen and MYC transcriptomes, and repressed MYC protein. OSU-ERb-12 plus Enza uniquely impacted chromatin accessibility at approximately 3000 nucleosome-free sites, enriched at enhancers, enriched for basic Helix-Loop-Helix motifs. CUT&RUN experiments revealed combination treatment targeting of MYC, AR, and H3K27ac again shaping enhancer accessibility. Specifically, it repressed MYC interactions at enhancer regions enriched for bHLH motifs, and overlapped with publicly-available bHLH cistromes. Finally, cistrome-transcriptome analyses identified ~200 genes that distinguished advanced PCa tumors in the SU2C cohort with high androgen and low neuroendocrine scores.

Photoacoustic Spectral Response using Ultrasound and Interferometric Sensors: A Correlation Study for a High Bandwidth Real-Time Blood Vasculature Monitoring Application in a Chick-Embryo Chorioallantoic Membrane (CAM) Model.

Photoacoustic (PA) spectral response technique has shown good promise in efficient preclinical tissue diagnosis by depicting mechano-biological properties due to high spatial resolution and penetration depth. The conventional PA-based system is a pump-probe technique that utilizes neodymium-doped yttrium aluminum garnet pulsed laser as a pump and an ultrasound sensor as a probe. For biomedical studies, high-speed PA signals need to be acquired, requiring higher bandwidth ultrasound sensors. While the bandwidth increases, they exhibit a very low signal-to-noise ratio that inhibits acquiring PA signals of biomedical samples. An interferometer-based probe has recently been investigated as a potential ultrasound probe for obtaining PA signals as an alternative. This optical PA detection technique offers high sensitivity by combining low acoustic impedance with high electromechanical coupling. However, there is a lack of exploration of the same for real-time biomedical studies. This work shows the development of a homodyne Mach-Zehnder interferometer-based PA spectral response (PASR) followed by a correlation study between the conventional ultrasound sensor and the interferometer-based sensor. Further, this study demonstrates the capability of continuous monitoring of vascular growth and the effect of an antidrug (Cisplatin) on the vasculature tested on a chick-embryo chorioallantoic membrane model. PASR was able to monitor growth changes within one day, which was not possible with conventional methods. This opens up potential possibilities for using this technique in biomedical applications.

Low Temperature Epitaxial LiMn2O4 Cathodes Enabled by NiCo2O4 Current Collector for High-Performance Microbatteries.

Epitaxial cathodes in lithium-ion microbatteries are ideal model systems to understand mass and charge transfer across interfaces, plus interphase degradation processes during cycling. Importantly, if grown at <450 °C, they also offer potential for complementary metal-oxide-semiconductor (CMOS) compatible microbatteries for the Internet of Things, flexible electronics, and MedTech devices. Currently, prominent epitaxial cathodes are grown at high temperatures (>600 °C), which imposes both manufacturing and scale-up challenges. Herein, we report structural and electrochemical studies of epitaxial LiMn2O4 (LMO) thin films grown on a new current collector material, NiCo2O4 (NCO). We achieve this at the low temperature of 360 °C, ∼200 °C lower than existing current collectors SrRuO3 and LaNiO3. Our films achieve a discharge capacity of >100 mAh g-1 for ∼6000 cycles with distinct LMO redox signatures, demonstrating long-term electrochemical stability of our NCO current collector. Hence, we show a route toward high-performance microbatteries for a range of miniaturized electronic devices.

Increased renal elimination of endogenous and synthetic pyrimidine nucleosides in concentrative nucleoside transporter 1 deficient mice.

Concentrative nucleoside transporters (CNTs) are active nucleoside influx systems, but their in vivo roles are poorly defined. By generating CNT1 knockout (KO) mice, here we identify a role of CNT1 in the renal reabsorption of nucleosides. Deletion of CNT1 in mice increases the urinary excretion of endogenous pyrimidine nucleosides with compensatory alterations in purine nucleoside metabolism. In addition, CNT1 KO mice exhibits high urinary excretion of the nucleoside analog gemcitabine (dFdC), which results in poor tumor growth control in CNT1 KO mice harboring syngeneic pancreatic tumors. Interestingly, increasing the dFdC dose to attain an area under the concentration-time curve level equivalent to that achieved by wild-type (WT) mice rescues antitumor efficacy. The findings provide new insights into how CNT1 regulates reabsorption of endogenous and synthetic nucleosides in murine kidneys and suggest that the functional status of CNTs may account for the optimal action of pyrimidine nucleoside analog therapeutics in humans.

A comprehensive diffusion-induced stress coupled multiscale modeling and analysis in hard-carbon electrodes of Li-ion batteries.

Particle fracture due to diffusion-induced stress (DIS) in electrodes is a key factor for lithium-ion battery (LIB) failure. Among many ways to minimize DIS, optimization of particle size and C-rates using state of charge (SOC) dependent varying properties can be a noble approach. Herein, a comprehensive multiscale modeling approach has been proposed to optimize the particle size by studying the DIS in hard carbon (HC) particles as the potential anode materials for high-energy LIBs. To accomplish this, density functional theory (DFT) was used to calculate the SOC dependent coefficient of volume expansion (CVE). Similarly, SOC dependent diffusivity and elastic modulus are calculated via molecular dynamics (MD) simulations. These results are transferred to a continuum model to examine the evolution of concentrations and DISs in hard carbon particles of radius 100-1000 nm lithiated at various C-rates (1C, 2C, 5C, and 10C). Our model successfully incorporates the variation of Li+ diffusivity and elastic modulus with SOC and tracks stress relaxation and volume expansion in the particles during lithiation. An optimized particle size has been recommended for hard carbon, considering both stresses for different C-rates. Our study provides a more realistic multiscale modeling framework for optimizing the DIS and can act as a guiding method towards achieving an optimum particle size so that capacity fading due to cracking can be avoided.

Combination of Tissue Microarray Profiling and Multiplexed IHC Approaches to Investigate Transport Mechanism of Nucleoside Analog Drug Resistance.

Nucleoside analogs (NAs) are an established class of anticancer agents being used clinically for the treatment of diverse cancers, either as monotherapy or in combination with other established anticancer or pharmacological agents. To date, nearly a dozen anticancer NAs are approved by the FDA, and several novel NAs are being tested in preclinical and clinical trials for future applications. However, improper delivery of NAs into tumor cells because of alterations in expression of one or more drug carrier proteins (e.g., solute carrier (SLC) transporters) within tumor cells or cells surrounding the tumor microenvironment stands as one of the primary reasons for therapeutic drug resistance. The combination of tissue microarray (TMA) and multiplexed immunohistochemistry (IHC) is an advanced, high-throughput approach over conventional IHC that enables researchers to effectively investigate alterations to numerous such chemosensitivity determinants simultaneously in hundreds of tumor tissues derived from patients. In this chapter, taking an example of a TMA from pancreatic cancer patients treated with gemcitabine (a NA chemotherapeutic agent), we describe the step-by-step procedure of performing multiplexed IHC, imaging of TMA slides, and quantification of expression of some relevant markers in these tissue sections as optimized in our laboratory and discuss considerations while designing and carrying out this experiment.

Characterization of an Aedes ADP-Ribosylation Protein Domain and Role of Post-Translational Modification during Chikungunya Virus Infection.

Poly ADP-ribose polymerases (PARPs) catalyze ADP-ribosylation, a subclass of post-translational modification (PTM). Mono-ADP-ribose (MAR) moieties bind to target molecules such as proteins and nucleic acids, and are added as part of the process which also leads to formation of polymer chains of ADP-ribose. ADP-ribosylation is reversible; its removal is carried out by ribosyl hydrolases such as PARG (poly ADP-ribose glycohydrolase), TARG (terminal ADP-ribose protein glycohydrolase), macrodomain, etc. In this study, the catalytic domain of Aedes aegypti tankyrase was expressed in bacteria and purified. The tankyrase PARP catalytic domain was found to be enzymatically active, as demonstrated by an in vitro poly ADP-ribosylation (PARylation) experiment. Using in vitro ADP-ribosylation assay, we further demonstrate that the chikungunya virus (CHIKV) nsp3 (non-structural protein 3) macrodomain inhibits ADP-ribosylation in a time-dependent way. We have also demonstrated that transfection of the CHIKV nsP3 macrodomain increases the CHIKV viral titer in mosquito cells, suggesting that ADP-ribosylation may play a significant role in viral replication.

Impact of CHIKV Replication on the Global Proteome of Aedes albopictus Cells.

Arboviruses are some of the important causative agents of mosquito-mediated viral diseases. These viruses are transmitted between vector and host during the blood meal. Upon viral entry, host replication machinery is hijacked, supporting new virus particle production and thereby allowing viral survival in the host. In this process, host proteins interact with viral proteins to either facilitate viral replication, or they may provide antiviral defense mechanisms. In this study, we analyzed the impact of chikungunya virus (CHIKV) infection on the global proteome of Dicer active Aedes albopictus cells during the early and late time points of infection. We utilized a bottom-up approach of global proteomics analysis, and we used label-free quantitative mass spectrometry to identify the global protein signatures of Ae. albopictus at two different time points upon CHIKV infection. The mass spectrometry data analysis of the early time point revealed that proteins belonging to pathways such as translation, RNA processing, and cellular metabolic processes were less in abundance, whereas those belonging to pathways such as cellular catabolic process and organic substance transport were significantly abundant. At later time points, proteins belonging to pathways such as cellular metabolic processes, primary metabolic process, organonitrogen compound metabolic process, and organic substance metabolic process were found to be decreased in their presence, whereas those belonging to pathways such as RNA processing, gene expression, macromolecule metabolic processing, and nitrogen compound metabolic processing were found to be abundant during CHIKV infection, indicating that modulation in gene expression favoring cell survival occurs at a later time point, suggesting a survival strategy of Aedes cells to counter prolonged CHIKV infection.

Green Synthesis of Endolichenic Fungi Functionalized Silver Nanoparticles: The Role in Antimicrobial, Anti-Cancer, and Mosquitocidal Activities.

Green nanotechnology is currently a very crucial and indispensable technology for handling diverse problems regarding the living planet. The concoction of reactive oxygen species (ROS) and biologically synthesized silver nanoparticles (AgNPs) has opened new insights in cancer therapy. The current investigation caters to the concept of the involvement of a novel eco-friendly avenue to produce AgNPs employing the wild endolichenic fungus Talaromyces funiculosus. The synthesized Talaromyces funiculosus-AgNPs were evaluated with the aid of UV visible spectroscopy, dynamic light scattering (DLS), Fourier infrared spectroscopy (ATR-FTIR), X-ray diffraction (XRD), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). The synthesized Talaromyces funiculosus-AgNPs (TF-AgNPs) exhibited hemo-compatibility as evidenced by a hemolytic assay. Further, they were evaluated for their efficacy against foodborne pathogens Staphylococcus aureus, Streptococcus faecalis, Listeria innocua, and Micrococcus luteus and nosocomial Pseudomonas aeruginosa, Escherichia coli, Vibrio cholerae, and Bacillus subtilis bacterial strains. The synthesized TF-AgNPs displayed cytotoxicity in a dose-dependent manner against MDA-MB-231 breast carcinoma cells and eventually condensed the chromatin material observed through the Hoechst 33342 stain. Subsequent analysis using flow cytometry and fluorescence microscopy provided the inference of a possible role of intracellular ROS (OH-, O-, H2O2, and O2-) radicals in the destruction of mitochondria, DNA machinery, the nucleus, and overall damage of the cellular machinery of breast cancerous cells. The combined effect of predation by the cyclopoid copepod Mesocyclops aspericornis and TF-AgNPS for the larval management of dengue vectors were provided. A promising larval control was evident after the conjunction of both predatory organisms and bio-fabricated nanoparticles. Thus, this study provides a novel, cost-effective, extracellular approach of TF-AgNPs production with hemo-compatible, antioxidant, and antimicrobial efficacy against both human and foodborne pathogens with cytotoxicity (dose dependent) towards MDA-MB-231 breast carcinoma.

Emerging Biomedical Applications of the Vesicular Stomatitis Virus Glycoprotein.

Nanoparticles (NPs) made of metals, polymers, micelles, and liposomes are increasingly being used in various biomedical applications. However, most of these NPs are hazardous for long- and short-term use and hence have restricted biomedical applications. Therefore, naturally derived, biocompatible, and biodegradable nanoconstructs are being explored for such applications. Inspired by the biology of viruses, researchers are exploring the viral proteins that hold considerable promise in biomedical applications. The viral proteins are highly stable and further amenable to suit specific biological applications. Among various viral proteins, vesicular stomatitis virus glycoprotein (VSV-G) has emerged as one of the most versatile platforms for biomedical applications. Starting with their first major use in lentivirus/retrovirus packaging systems, the VSV-G-based reagents have been tested for diverse biomedical use, many of which are at various stages of clinical trials. This manuscript discusses the recent advancements in the use of the VSV-G-based reagents in medical, biological research, and clinical applications particularly highlighting emerging applications in biomedical imaging.

Solute Carrier Nucleoside Transporters in Hematopoiesis and Hematological Drug Toxicities: A Perspective.

Anticancer nucleoside analogs produce adverse, and at times, dose-limiting hematological toxicities that can compromise treatment efficacy, yet the mechanisms of such toxicities are poorly understood. Recently, cellular nucleoside transport has been implicated in normal blood cell formation with studies from nucleoside transporter-deficient mice providing additional insights into the regulation of mammalian hematopoiesis. Furthermore, several idiopathic human genetic disorders have revealed nucleoside transport as an important component of mammalian hematopoiesis because mutations in individual nucleoside transporter genes are linked to various hematological abnormalities, including anemia. Here, we review recent developments in nucleoside transporters, including their transport characteristics, their role in the regulation of hematopoiesis, and their potential involvement in the occurrence of adverse hematological side effects due to nucleoside drug treatment. Furthermore, we discuss the putative mechanisms by which aberrant nucleoside transport may contribute to hematological abnormalities and identify the knowledge gaps where future research may positively impact treatment outcomes for patients undergoing various nucleoside analog therapies.

Role of Doxorubicin on the Loading Efficiency of ICG within Silk Fibroin Nanoparticles.

The effective loading or encapsulation of multimodal theranostic agents within a nanocarrier system plays an important role in the clinical development of cancer therapy. In recent years, the silk fibroin protein-based delivery system has been drawing significant attention to be used in nanomedicines due to its biocompatible and biodegradable nature. In this study, silk fibroin nanoparticles (SNPs) have been synthesized by a novel and cost-effective ultrasonic atomizer-based technique for the first time. The fabricated SNPs were coencapsulated by the FDA-approved indocyanine green (ICG) dye and the chemotherapeutic drug doxorubicin (DOX). The synthesized SNPs are spherical, with an average diameter of ∼37 ± 4 nm, and the ICG-DOX-coencapsulated SNPs (ID-SNPs) have a diameter size of ∼47 ± 6 nm. For the first time, here we demonstrate that DOX helps in the higher loading of ICG within the ID-SNPs, which enhances the encapsulation efficiency of ICG by ∼99%. This could be attributed to the interaction of ICG and DOX molecules with the silk fibroin protein, which helps ICG to get loaded more efficiently within these nanoparticles. The overall finding of this study suggests that the ID-SNPs could be utilized for enhanced ICG-complemented multimodal deep-tissue bioimaging and synergistic chemo-photothermal therapy.

Recombination drives the emergence of orf virus diversity: evidence from the first complete genome sequence of an Indian orf virus isolate and comparative genomic analysis.

Contagious pustular dermatitis is a disease that primarily infects small ruminants and possesses zoonotic potential. It is caused by orf virus (ORFV), a member of the genus Parapoxvirus. In this study, we evaluated an ORFV outbreak in goats in Madhya Pradesh, a state in central India, during 2017. The transboundary potential of this virus was evaluated by constructing phylogenetic trees. The complete genome sequence of an ORFV isolate named Ind/MP/17 was found to be 139,807 bp in length with 63.7% GC content and 132 open reading frames (ORFs) flanked by 3,910-bp inverted terminal repeats (ITRs). An investigation into evolutionary parameters such as selection pressure (θ = dN/dS) and nucleotide diversity (π) demonstrated that ORFV has undergone purifying selection. A total of 40 recombination events were identified, 21 of which were evident in the Ind/MP/17 genome, indicating its ability to generate new variants.

Genome-wide identification and characterization of microsatellite markers within the Avipoxviruses.

Microsatellite markers or Simple Sequence Repeats (SSRs) are gaining importance for molecular characterization of the virus as well as estimation of evolution patterns due to its high-polymorphic nature. The Avipoxvirus is the causative agent of pox-like lesions in more than 300 birds and one of the major diseases for the extinction of endangered avian species. Therefore, we conducted a genome-wide analysis to decipher the type, distribution pattern of 14 complete genomes derived from the Avipoxvirus genus. The in-silico screening deciphered the existence of 917-2632 SSRs per strain. In the case of compound SSRs (cSSRs), the value was obtained 44-255 per genome. Our analysis indicates that the di-nucleotide repeats (52.74%) are the most abundant, followed by the mononucleotides (34.79), trinucleotides (11.57%), tetranucleotides (0.64%), pentanucleotides (0.12%) and hexanucleotides (0.15%) repeats. The specific parameters like Relative Abundance (RA) and Relative Density (RD) of microsatellites ranged within 5.5-8.12 and 33.08-53.58 bp/kb. The analysis of RA and RD value of compound microsatellites resulted between 0.25-0.82 and 4.64-15.12 bp/kb. The analysis of motif composition of cSSR revealed that most of the compound microsatellites were made up of two microsatellites, with some unique duplicated pattern of the motif like, (TA)-x-(TA), (TCA)-x-(TCA), etc. and self-complementary motifs, such as (TA)-x-(AT). Finally, we validated forty sets of compound microsatellite markers through an in-vitro approach utilizing clinical specimens and mapping the sequencing products with the database through comparative genomics approaches. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03169-4.

EMT alterations in the solute carrier landscape uncover SLC22A10/A15 imposed vulnerabilities in pancreatic cancer.

The involvement of membrane-bound solute carriers (SLCs) in neoplastic transdifferentiation processes is poorly defined. Here, we examined changes in the SLC landscape during epithelial-mesenchymal transition (EMT) of pancreatic cancer cells. We show that two SLCs from the organic anion/cation transporter family, SLC22A10 and SLC22A15, favor EMT via interferon (IFN) α and γ signaling activation of receptor tyrosine kinase-like orphan receptor 1 (ROR1) expression. In addition, SLC22A10 and SLC22A15 allow tumor cell accumulation of glutathione to support EMT via the IFNα/γ-ROR1 axis. Moreover, a pan-SLC22A inhibitor lesinurad reduces EMT-induced metastasis and gemcitabine chemoresistance to prolong survival in mouse models of pancreatic cancer, thus identifying new vulnerabilities for human PDAC.