Peeling off the layers from microbial dark matter (MDM): recent advances, future challenges, and opportunities.

Microbes represent the most common organisms on Earth; however, less than 2% of microbial species in the environment can undergo cultivation for study under laboratory conditions, and the rest of the enigmatic, microbial world remains mysterious, constituting a kind of "microbial dark matter" (MDM). In the last two decades, remarkable progress has been made in culture-dependent and culture-independent techniques. More recently, studies of MDM have relied on culture-independent techniques to recover genetic material through either unicellular genomics or shotgun metagenomics to construct single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs), respectively, which provide information about evolution and metabolism. Despite the remarkable progress made in the past decades, the functional diversity of MDM still remains uncharacterized. This review comprehensively summarizes the recently developed culture-dependent and culture-independent techniques for characterizing MDM, discussing major challenges, opportunities, and potential applications. These activities contribute to expanding our knowledge of the microbial world and have implications for various fields including Biotechnology, Bioprospecting, Functional genomics, Medicine, Evolutionary and Planetary biology. Overall, this review aims to peel off the layers from MDM, shed light on recent advancements, identify future challenges, and illuminate the exciting opportunities that lie ahead in unraveling the secrets of this intriguing microbial realm.

An Integrated Computational Analysis of High-Risk SNPs in Angiopoietin-like Proteins (ANGPTL3 and ANGPTL8) Reveals Perturbed Protein Dynamics Associated with Cancer.

Angiopoietin-like proteins (ANGPTL) constitute a family of eight proteins (1-8) which play a pivotal role in the regulation of various pathophysiological processes. The current study sought to identify high-risk, "non-synonymous, single-nucleotide polymorphisms" (nsSNPs) in both ANGPTL3 and ANGPTL8 to evaluate the role that these nsSNPs play in various types of cancer. We retrieved a total of 301 nsSNPs from various databases; 79 of these candidates constitute high-risk nsSNPs. Moreover, we identified eleven high-risk nsSNPs that cause various types of cancer: seven candidates for ANGPTL3 (L57H, F295L, L309F, K329M, R332L, S348C, and G409R) and four candidates for ANGPTL8 (P23L, R85W, R138S, and E148D). Protein-protein interaction analysis revealed a strong association of ANGPTL proteins with several tumor-suppressor proteins such as ITGB3, ITGAV, and RASSF5. 'Gene-expression profiling interactive analysis' (GEPIA) showed that expression of ANGPTL3 is significantly downregulated in five cancers: sarcoma (SARC); cholangio carcinoma (CHOL); kidney chromophobe carcinoma (KICH); kidney renal clear cell carcinoma (KIRC); and kidney renal papillary cell carcinoma (KIRP). GEPIA also showed that expression of ANGPTL8 remains downregulated in three cancers: CHOL; glioblastoma (GBM); and breast invasive carcinoma (BRCA). Survival rate analysis indicated that both upregulation and downregulation of ANGPTL3 and ANGPTL8 leads to low survival rates in various types of cancer. Overall, the current study revealed that both ANGPTL3 and ANGPTL8 constitute potential prognostic biomarkers for cancer; moreover, nsSNPs in these proteins might lead to the progression of cancer. However, further in vivo investigation will be helpful to validate the role of these proteins in the biology of cancer.

COVID-19: The Ethno-Geographic Perspective of Differential Immunity.

Coronavirus disease 2019 (COVID-19), the agent behind the worst global pandemic of the 21st century (COVID-19), is primarily a respiratory-disease-causing virus called SARS-CoV-2 that is responsible for millions of new cases (incidence) and deaths (mortalities) worldwide. Many factors have played a role in the differential morbidity and mortality experienced by nations and ethnicities against SARS-CoV-2, such as the quality of primary medical health facilities or enabling economies. At the same time, the most important variable, i.e., the subsequent ability of individuals to be immunologically sensitive or resistant to the infection, has not been properly discussed before. Despite having excellent medical facilities, an astounding issue arose when some developed countries experienced higher morbidity and mortality compared with their relatively underdeveloped counterparts. Hence, this investigative review attempts to analyze the issue from an angle of previously undiscussed genetic, epigenetic, and molecular immune resistance mechanisms in correlation with the pathophysiology of SARS-CoV-2 and varied ethnicity-based immunological responses against it. The biological factors discussed here include the overall landscape of human microbiota, endogenous retroviral genes spliced into the human genome, and copy number variation, and how they could modulate the innate and adaptive immune systems that put a certain ethnic genetic architecture at a higher risk of SARS-CoV-2 infection than others. Considering an array of these factors in their entirety may help explain the geographic disparity of disease incidence, severity, and subsequent mortality associated with the disease while at the same time encouraging scientists to design new experimental approaches to investigation.

Toxicological Responses of α-Pinene-Derived Secondary Organic Aerosol and Its Molecular Tracers in Human Lung Cell Lines.

Secondary organic aerosol (SOA) is a major component of airborne fine particulate matter (PM2.5) that contributes to adverse human health effects upon inhalation. Atmospheric ozonolysis of α-pinene, an abundantly emitted monoterpene from terrestrial vegetation, leads to significant global SOA formation; however, its impact on pulmonary pathophysiology remains uncertain. In this study, we quantified an increasing concentration response of three well-established α-pinene SOA tracers (pinic, pinonic, and 3-methyl-1,2,3-butanetricarboxylic acids) and a full mixture of α-pinene SOA in A549 (alveolar epithelial carcinoma) and BEAS-2B (bronchial epithelial normal) lung cell lines. The three aforementioned tracers contributed ∼57% of the α-pinene SOA mass under our experimental conditions. Cellular proliferation, cell viability, and oxidative stress were assessed as toxicological end points. The three α-pinene SOA molecular tracers had insignificant responses in both cell types when compared with the α-pinene SOA (up to 200 µg mL-1). BEAS-2B cells exposed to 200 µg mL-1 of α-pinene SOA decreased cellular proliferation to ∼70% and 44% at 24- and 48-h post exposure, respectively; no changes in A549 cells were observed. The inhibitory concentration-50 (IC50) in BEAS-2B cells was found to be 912 and 230 µg mL-1 at 24 and 48 h, respectively. An approximate 4-fold increase in cellular oxidative stress was observed in BEAS-2B cells when compared with untreated cells, suggesting that reactive oxygen species (ROS) buildup resulted in the downstream cytotoxicity following 24 h of exposure to α-pinene SOA. Organic hydroperoxides that were identified in the α-pinene SOA samples likely contributed to the ROS and cytotoxicity. This study identifies the potential components of α-pinene SOA that likely modulate the oxidative stress response within lung cells and highlights the need to carry out chronic exposure studies on α-pinene SOA to elucidate its long-term inhalation exposure effects.

Spiking dependence of SARS-CoV-2 pathogenicity on TMPRSS2.

Epidemiological data shows a discrepancy in COVID-19 susceptibility and outcomes with some regions being more heavily affected than others. However, the factors that determine host susceptibility and pathogenicity remain elusive. An increasing number of publications highlight the role of Transmembrane Serine Protease 2 (TMPRSS2) in the susceptibility of the host cell to SARS-CoV-2. Cleavage of viral spike protein via the host cell's TMPRSS2 enzyme activity mediates viral entry into the host cell. The enzyme synthesis is regulated by the TMPRSS2 gene, which has also been implicated in the entry mechanisms of previously reported Coronavirus infections. In this review, we have investigated the pathogenicity of SARS-CoV-2 and disease susceptibility dependence on the TMPRSS2 gene as expressed in various population groups. We further discuss how the differential expression of this gene in various ethnic groups can affect the SARS-CoV-2 infection and Coronavirus disease (COVID)-19 outcomes. Moreover, promising new TMPRSS2 protease blockers and inhibitors are discussed for COVID-19 treatment.

Carbon-dot wrapped ZnO nanoparticle-based photoelectrochemical sensor for selective monitoring of H2O2 released from cancer cells.

This study reports on a simple approach for the fabrication of an electrode modified with biocompatible C-dot wrapped ZnO nanoparticles for selective photoelectrochemical monitoring of H2O2 released from living cells. The biocompatibility of the ZnO nanoparticles was confirmed through in-vitro cellular testing using the MTT assay on Huh7 cell lines. The ZnO nanoparticles wrapped with dopamine-derived C-dots possess numerous catalytically active sites, excessive surface defects, good electrical conductivity, and efficient separation ability of photo-induced electrons and holes. These properties offer highly sensitive and selective non-enzymatic photo-electrochemical monitoring of H2O2 released from HeLa cells after stimulation with N-formylmethionyl-leucyl-phenylalanine. The sensor has a wide linear range (20-800 nM), low detection limit (2.4 nM), and reliable reproducibility, this implying its suitability for biological and biomedical applications. Graphical abstract Schematic of the fabrication of ZnO nanoparticles by using a plant extract as a reducing agent. Wrapping of ZnO with C-dots enhances the photoelectrocatalytic efficacy. Sensitive and selective photoelectrochemical monitoring of H2O2 released from cancer cells is demonstrated.

Structure-based pharmacophore models to probe anticancer activity of inhibitors of protein kinase B-beta (PKB ß).

Protein kinase B-beta (PKBß/Akt2) is a non-receptor kinase that has attracted a great deal of attention as a promising cancer therapy drug target. In mammalian cells, hyperactivation of Akt2 exclusively facilitates the survival of solid tumors by interfering with cell cycle progression. This definite function of Akt2 in tumor survival/maintenance provides the basis for the development of its antagonists with the aim of desensitizing cell proliferation. In order to find novel and potent Akt2 inhibitors, structure-based pharmacophore models have been developed and validated by the test set prediction. The final pharmacophore model was used for hits identification using public chemical databases. The hits were further prioritized using drug-like filters which revealed 14 potential hit compounds having novel chemical scaffolds. Our results elucidate the importance of three hydrogen bond acceptors (A), one hydrogen bond donor (D), one hydrophobic group (H), and one positive ionic charge (P) toward inhibition of the Ak2. One of our selected hits showed 68% cell apoptosis at 8 µg/ml concentration. We proposed various chemical scaffolds including benzamide, carboxamide, and methyl benzimidazole targeting Akt2 and thus may act as potential leads for the further development of new anticancer agents.

Bisphenol A (BPA) the mighty and the mutagenic.

Bisphenol A (BPA) is one of the most widely used synthetic compounds on the planet. Upon entering the diet, its highest concentration (1-104 ng/g of tissue) has been recorded in the placenta and fetus. This accumulation of BPA can have many health hazards ranging from the easy to repair single strand DNA breaks (SSBs) to error prone double strand DNA breaks (DSBs). Although the Human liver can efficiently metabolize BPA via glucuronidation and sulfation pathways, however the by-product Bisphenol-o-quinone has been shown to act as a DNA adduct. Low doses of BPA have also been shown to interact with various signaling pathways to disrupt normal downstream signaling. Analysis has been made on how BPA could interact with several signaling pathways such as NFκB, JNK, MAPK, ER and AR that eventually lead to disease morphology and even tumorigenesis. The role of low dose BPA is also discussed in dysregulating Ca2+ homeostasis of the cell by inhibiting calcium channels such as SPCA1/2 to suggest a new direction for future research in the realms of BPA induced disease morphology and mutagenicity.

Bystander signaling via oxidative metabolism.

The radiation-induced bystander effect (RIBE) is the initiation of biological end points in cells (bystander cells) that are not directly traversed by an incident-radiation track, but are in close proximity to cells that are receiving the radiation. RIBE has been indicted of causing DNA damage via oxidative stress, besides causing direct damage, inducing tumorigenesis, producing micronuclei, and causing apoptosis. RIBE is regulated by signaling proteins that are either endogenous or secreted by cells as a means of communication between cells, and can activate intracellular or intercellular oxidative metabolism that can further trigger signaling pathways of inflammation. Bystander signals can pass through gap junctions in attached cell lines, while the suspended cell lines transmit these signals via hormones and soluble proteins. This review provides the background information on how reactive oxygen species (ROS) act as bystander signals. Although ROS have a very short half-life and have a nanometer-scale sphere of influence, the wide variety of ROS produced via various sources can exert a cumulative effect, not only in forming DNA adducts but also setting up signaling pathways of inflammation, apoptosis, cell-cycle arrest, aging, and even tumorigenesis. This review outlines the sources of the bystander effect linked to ROS in a cell, and provides methods of investigation for researchers who would like to pursue this field of science.

Nanomedicine and cancer immunotherapy: focus on indoleamine 2,3-dioxygenase inhibitors.

Nanomedicine application in cancer immunotherapy is currently one of the most challenging areas in cancer therapeutic intervention. Innovative solutions have been provided by nanotechnology to deliver cytotoxic agents to the cancer cells partially affecting the healthy cells of the body during the process. Nanoparticle-based drug delivery is an emerging approach to stimulate the immune responses against cancer. The inhibition of indoleamine 2,3-dioxygenase (IDO) is a pivotal area of research in cancer immunotherapy. IDO is a heme-containing immunosuppressive enzyme, which is responsible for the degradation of tryptophan while increasing the concentration of kynurenine metabolites. Various preclinical studies showed that IDO inhibition in certain diseases may result in significant therapeutic effects. Here, we provide a review of the natural and synthetic inhibitors of IDO. These inhibitors are classified according to their source, inhibitory concentrations, the chemical structure, and the mechanism of action. Tumor-targeted chemotherapy is an advanced technique and has more advantages as compared to the conventional chemotherapy. Search for more efficient and less toxic nanoparticles in conjunction with compounds to inhibit IDO is still an area of interest for several research groups worldwide, especially revealing to be an extensive and a promising area in cancer therapeutic innovations.

Contemplating the Importance of Toll-like Receptors I and II Regarding Human Viral Pathogenesis.

BACKGROUND: Toll-like receptors (TLRs) play a major role in innate immunity, since they detect conserved pathogen-associated molecular patterns (PAMPs) on a range of microbes, including viruses, leading to innate immune activation and orchestration of the adaptive immune response. OBJECTIVES: The current study aimed to discuss earlier evidence implicating TLRs I and II in the innate immune response to viruses, in the light of more recent clinical data demonstrating that TLRs are important for anti-viral immunity in humans. MATERIALS AND METHODS: A literature search was performed via accessing research articles from PakMediNet, Pubmed and Google Scholar with key words of Toll-like receptors I and II Regarding human viral pathogenesis. The valued information on the recent scientific horizons was subjected to critical analysis. RESULTS: Comprehensive literature review illustrates important signaling pathways involved in TLR1/TLR2 mediated regulation of viral pathogenesis. TLRs mediated activation of apoptosis tends to contribute towards defense strategies utilized by innate immune response. Activation of antiviral TLR1-dependent signaling cascade would ultimately lead to activation of NF-kappa B which promotes antiviral responses via induction of specific genes. TLR1/TLR2 dimer generates intracellular signaling via IRAK4 mediated activation of IRAK1/2 which results in activation of NF-kappa B, p38 and JNK proteins in cytoplasm. NF- kappa B, p38 and JNK enter the nucleus thereby causing activation of various pro-inflammatory cytokines such as IL-1 beta, TNF-alpha, IL-6, IL-8 and IL-18. Among the chronic HCV infection, the HCV core protein induces TNF-α and IL-10 from the macrophages thereby causing reduction in release of interferon alpha. Abnormal TLR1/TLR2 signaling may contribute to the enhancement of infection-related morbidity and mortality. CONCLUSIONS: To date, a large number of viruses are proved to trigger innate immunity via TLRs, suggesting that these receptors are likely to be important in the outcome of viral infection. This suggestion is supported by the observation that many viruses have evolved mechanisms not only to evade the innate immune system, but also to subvert it for the benefit of the virus.

Radiation induced bystander effect and DNA damage.

Bystander effects (BSEs) have been investigated for a long time but without much deliberation as to the cause in targeted cells and the subsequent effect in naïve cells. BSEs have traditionally been associated with radiation. Currently, this phenomenon is at a juncture where nuclear DNA damage is being debated as either essential or nonessential. If DNA damage is essential for the bystander signal (BSS) production then, this raises a number of questions about, radiotherapy and chemotherapy of cancer patients. This review presents a detailed analysis of the work done to investigate nuclear DNA damage versus exclusively cytoplasmic targeting with ionizing radiations and measurement of bystander end-points in naïve cells. The review also analyzes some of the research work done to investigate cell models that were developed specifically to study and track radiation-induced DNA damage to construct mutation spectra. Production of reactive oxygen species and reactive nitrogen species as possible candidates of the elusive BSS are also discussed besides the signal transduction pathways implicated in reception of a BSS by the naïve cell.