Unveiling a Shield of Hope: A Novel Multiepitope-Based Immunogen for Cross-Serotype Cellular Defense against Dengue Virus.

Dengue virus (DENV) infection continues to be a public health challenge, lacking a specific cure. Vaccination remains the primary strategy against dengue; however, existing live-attenuated vaccines display variable efficacy across four serotypes, influenced by host serostatus and age, and predominantly inducing humoral responses. To address this limitation, this study investigates a multiepitope-based immunogen designed to induce robust cellular immunity across all DENV serotypes. The chimeric immunogen integrates H-2d specific MHC-I binding T-cell epitopes derived from conserved domains within the DENV envelope protein. Immuno-informatics analyses supported its stability, non-allergenic nature, and strong MHC-I binding affinity as an antigen. To assess the immunogenicity of the multiepitope, it was expressed in murine bone-marrow-derived dendritic cells (BMDCs) that were used to prime mice. In this experimental model, simultaneous exposure to T-cell epitopes from all four DENV serotypes initiated distinct IFNγ-CD8 T-cell responses for different serotypes. These results supported the potential of the multiepitope construct as a vaccine candidate. While the optimization of the immunogen design remains a continuous pursuit, this proof-of-concept study provides a starting point for evaluating its protective efficacy against dengue infection in vivo. Moreover, our results support the development of a multiepitope vaccine that could trigger a pan-serotype anti-dengue CD8 response.

The spatiotemporal pattern of surface ozone and its impact on agricultural productivity in China.

The slowing of agricultural productivity growth globally over the past two decades has brought a new urgency to detect its drivers and potential solutions. We show that air pollution, particularly surface ozone (O3), is strongly associated with declining agricultural total factor productivity (TFP) in China. We employ machine learning algorithms to generate estimates of high-resolution surface O3 concentrations from 2002 to 2019. Results indicate that China's O3 pollution has intensified over this 18-year period. We coupled these O3 estimates with a statistical model to show that rising O3 pollution during nonwinter seasons has reduced agricultural TFP by 18% over the 2002-2015 period. Agricultural TFP is projected to increase by 60% if surface O3 concentrations were reduced to meet the WHO air quality standards. This productivity gain has the potential to counter expected productivity losses from 2°C warming.

Climate vs Energy Security: Quantifying the Trade-offs of BECCS Deployment and Overcoming Opportunity Costs on Set-Aside Land.

Bioenergy with carbon capture and storage (BECCS) sits at the nexus of the climate and energy security. We evaluated trade-offs between scenarios that support climate stabilization (negative emissions and net climate benefit) or energy security (ethanol production). Our spatially explicit model indicates that the foregone climate benefit from abandoned cropland (opportunity cost) increased carbon emissions per unit of energy produced by 14-36%, making geologic carbon capture and storage necessary to achieve negative emissions from any given energy crop. The toll of opportunity costs on the climate benefit of BECCS from set-aside land was offset through the spatial allocation of crops based on their individual biophysical constraints. Dedicated energy crops consistently outperformed mixed grasslands. We estimate that BECCS allocation to land enrolled in the Conservation Reserve Program (CRP) could capture up to 9 Tg C year-1 from the atmosphere, deliver up to 16 Tg CE year-1 in emissions savings, and meet up to 10% of the US energy statutory targets, but contributions varied substantially as the priority shifted from climate stabilization to energy provision. Our results indicate a significant potential to integrate energy security targets into sustainable pathways to climate stabilization but underpin the trade-offs of divergent policy-driven agendas.

Initial COVID-19 Severity and Long-COVID Manifestations: An Observational Analysis.

OBJECTIVE: New-onset or persistent symptoms beyond after 4 weeks from COVID-19 are termed "long-COVID." Whether the initial severity of COVID-19 has a bearing on the clinicoradiological manifestations of long COVID is an area of interest. MATERIAL AND METHODS: We did an observational analysis of the long-COVID patients after categorizing them based on their course of COVID-19 illness into mild, moderate, and severe groups. The clinical and radiological profile was compared across these groups. RESULTS: Out of 150 long-COVID patients recruited in the study, about 79% (118), 14% (22), and 7% (10) had a history of mild, moderate, and severe COVID-19, respectively. Fatigue (P = .001), breathlessness (P = .001), tachycardia (P = .002), tachypnea (P < .001), raised blood pressure (P < .001), crepitations (P = .04), hypoxia at rest (P < .001), significant desaturation in 6-minute walk test (P = .27), type 1 respiratory failure (P = .001), and type 2 respiratory failure (P = .001) were found to be significantly higher in the long-COVID patients with a history of severe COVID-19. These patients also had the highest prevalence of abnormal chest X-ray (60%) and honeycombing in computed tomography scan thorax (25%, P = .027). CONCLUSION: The course of long COVID bears a relationship with initial COVID-19 severity. Patients with severe COVID-19 are prone to develop more serious long-COVID manifestations.

Identification of suitable house-keeping genes during chikungunya virus infection.

PURPOSE: Quantitative PCR (qPCR) is a reliable and robust technique for gene expression analysis, but its efficacy is dependent on the normalization of qPCR data with the stably expressed reference gene. Selection of a suitable reference gene is mandatory for accurate gene expression analysis, till data the most appropriate reference gene during chikungunya virus infection has not been elucidated. METHOD: In this study the expression of reference genes(GAPDH, GUSB, HPRT, Beta-actin, 18S rRNA) was analysed during chikungunya virus infection by quantitative PCR. The stability of the house-keeping genes was evaluated with three bioinformatics softwares: BestKeeper, NormFinder and GeNorm. RESULT: The significant variation in the expression of house-keeping genes (GusB, Beta-actin, HPRT) was observed during chikungunya virus infection; whereas GAPDH and 18S rRNA was most stable. The stability of reference genes analysed by the bioinformatics software further corroborate the results of qPCR. CONCLUSION: This is first study that identifies and validates the most suitable reference gene for normalization of qPCR data during chikungunya based gene expression analysis. This could serve as a reference study for the researchers working on different aspects of chikungunya virus infections.

Implications of Biorefinery Policy Incentives and Location-Specific Economic Parameters for the Financial Viability of Biofuels.

Cellulosic biofuels are part of a portfolio of solutions to address climate change; however, their production remains expensive and federal policy interventions (e.g., Renewable Fuel Standard) have not spurred broad construction of cellulosic biorefineries. A range of state-level interventions have also been enacted, but their implications for the financial viability of biorefineries are not well understood. To address this gap, this study evaluated the efficacy of 20 state-level tax incentives from 14 states and their interactions with other location-specific economic parameters (e.g., state income tax rates, electricity prices). To characterize implications of location-specific policies and parameters on biorefinery cash flows, we developed a new BioSTEAM Location-Specific Evaluation (BLocS) module for the open-source software BioSTEAM. Leveraging BLocS and BioSTEAM, we characterized the minimum ethanol selling price (MESP) for a cellulosic biorefinery (using corn stover as feedstock) and two conventional biorefineries (using corn or sugarcane as feedstock) for comparison. Among state-specific scenarios, nonincentivized MESPs for the corn stover biorefinery ranged from 0.74 $·L-1 (4.20 $·gallon gasoline equivalent [gge]-1) [0.69-0.79 $·L-1; 3.91-4.48 $·gge-1; Oklahoma] to 1.02 $·L-1 (5.78 $·gge-1) [0.95-1.09 $·L-1; 5.39-6.18 $·gge-1; New York], while the tax incentive-induced MESP reduction ranged from negligible (Virginia) to 5.78% [5.43-6.20%; Iowa]. Ultimately, this work can inform the design of policy incentives for biorefineries under specific deployment contexts.

Pharmacological Manipulation of UPR: Potential Antiviral Strategy Against Chikungunya Virus.

Abstract: Viruses invade the host cells and maneuver the cellular translation machinery to translate the viral proteins in substantial amounts, which may disturb Endoplasmic Reticulum homeostasis leading to induction of Unfolded Protein Response (UPR), a host response pathway involved in viral pathogenesis. Here, we investigated the effect of UPR pathways on the pathogenesis of chikungunya virus infection. We observed that chikungunya virus mediated the modulation of UPR. A positive modulation was observed in the activation of IRE1 and ATF6 branch while the PERK branch of UPR observed suppressed upon virus infection. We further investigated the effect of the inhibition of UPR pathways on chikungunya virus replication using inhibitors for each branch. Cells treated with 3-ethoxy-5,6-dibromosalicylaldehyde (IRE1 inhibitor) and AEBSF (ATF6 inhibitor) significantly inhibits the viral replication process. This study has provided a novel perspective in designing antivirals against chikungunya virus. Supplementary Information: The online version contains supplementary material available at 10.1007/s12088-022-01046-5.

Current Insights into the Host Immune Response to Respiratory Viral Infections.

Respiratory viral infections often lead to severe illnesses varying from mild or asymptomatic upper respiratory tract infections to severe bronchiolitis and pneumonia or/and chronic obstructive pulmonary disease. Common viral infections, including but not limited to influenza virus, respiratory syncytial virus, rhinovirus and coronavirus, are often the leading cause of morbidity and mortality. Since the lungs are continuously exposed to foreign particles, including respiratory pathogens, it is also well equipped for recognition and antiviral defense utilizing the complex network of innate and adaptive immune cells. Immediately upon infection, a range of proinflammatory cytokines, chemokines and an interferon response is generated, thereby making the immune response a two edged sword, on one hand it is required to eliminate viral pathogens while on other hand it's prolonged response can lead to chronic infection and significant pulmonary damage. Since vaccines to all respiratory viruses are not available, a better understanding of the virus-host interactions, leading to the development of immune response, is critically needed to design effective therapies to limit the severity of inflammatory damage, enhance viral clearance and to compliment the current strategies targeting the virus. In this chapter, we discuss the host responses to common respiratory viral infections, the key players of adaptive and innate immunity and the fine balance that exists between the viral clearance and immune-mediated damage.

Assessing Marginal Land Availability Based on Land Use Change Information in the Contiguous United States.

Utilization of marginal land for growing dedicated bioenergy crops for second-generation biofuels is appealing to avoid conflicts with food production. This study develops a novel framework to quantify marginal land for the Contiguous United States (CONUS) based on a history of satellite-observed land use change (LUC) over the 2008-2015 period. Frequent LUC between crop and noncrop is assumed to be an indicator of economically marginal land; this land is also likely to have a lower opportunity cost of conversion from food crop to bioenergy crop production. We first present an approach to identify cropland in transition using the time series of Cropland Data Layer (CDL) land cover product and determine the amount of land that can be considered marginal with a high degree of confidence vs with uncertainty across the CONUS. We find that the biophysical characteristics of this land and its productivity and environmental vulnerability vary across the land and lie in between that of permanent cropland and permanent natural vegetation/bare areas; this land also has relatively low intrinsic value and agricultural profit but a high financial burden and economic risk. We find that the total area of marginal land with confidence vs with uncertainty is 10.2 and 58.4 million hectares, respectively, and mainly located along the 100th meridian. Only a portion of this marginal land (1.4-2.2 million hectares with confidence and 14.8-19.4 million hectares with uncertainty) is in the rainfed region and not in crop production and, thus, suitable for producing energy crops without diverting land from food crops in 2016. These estimates are much smaller than the estimates obtained by previous studies, which consider all biophysically low-quality land to be marginal without considering economical marginality. The estimate of marginal land for bioenergy crops obtained in this study is an indicator of the availability of economically marginal land that is suitable for bioenergy crop production; whether this land is actually converted to bioenergy crops will depend on the market conditions. We note the inability to conduct field-level validation of cropland in transition and leave it to future advances in technology to ground-truth land use change and its relationship to economically marginal land.

Maladaptation of U.S. corn and soybeans to a changing climate.

We quantify long-run adaptation of U.S. corn and soybean yields to changes in temperature and precipitation over 1951-2017. Results show that although the two crops became more heat- and drought-tolerant, their productivity under normal temperature and precipitation conditions decreased. Over 1951-2017, heat- and drought-tolerance increased corn and soybean yields by 33% and 20%, whereas maladaptation to normal conditions reduced yields by 41% and 87%, respectively, with large spatial variations in effects. Changes in climate are projected to reduce average corn and soybean yields by 39-68% and 86-92%, respectively, by 2050 relative to 2013-2017 depending on the warming scenario. After incorporating estimated effects of climate-neutral technological advances, the net change in yield ranges from (-)13 to 62% for corn and (-)57 to (-)26% for soybeans in 2050 relative to 2013-2017. Our analysis uncovers the inherent trade-offs and limitations of existing approaches to crop adaptation.

Targeting unfolded protein response: a new horizon for disease control.

Unfolded protein response (UPR) is an evolutionarily conserved pathway triggered during perturbation of endoplasmic reticulum (ER) homeostasis in response to the accumulation of unfolded/misfolded proteins under various stress conditions like viral infection, diseased states etc. It is an adaptive signalling cascade with the main purpose of relieving the stress from the ER, which may otherwise lead to the initiation of cell death via apoptosis. ER stress if prolonged, contribute to the aetiology of various diseases like cancer, type II diabetes, neurodegenerative diseases, viral infections etc. Understanding the role of UPR in disease progression will help design pharmacological drugs targeting the sensors of signalling cascade acting as potential therapeutic agents against various diseases. The current review aims at highlighting the relevance of different pathways of UPR in disease progression and control, including the available pharmaceutical interventions responsible for ameliorating diseased state via modulating UPR pathways.

Water Quality Effects of Economically Viable Land Use Change in the Mississippi River Basin under the Renewable Fuel Standard.

Demand for biofuel production driven by the Renewable Fuel Standard (RFS2) has coincided with increased land in corn production and increasing nitrogen (N) loss to the Gulf of Mexico. Diversifying cropland with perennial energy crops (miscanthus and switchgrass) may reduce N loss and improve water quality. However, the extent of these benefits depends on the mix of biomass feedstocks (corn stover, perennials) incentivized by the RFS2 and the extent to which energy crops displace N-intensive row crops. We developed an integrated economic-biophysical model to quantify the water quality impacts of three potential policy scenarios that provided corn ethanol at levels before the RFS2 (RFS1 baseline); 15 billion gallons of corn ethanol (corn ethanol only); or 16 billion gallons of cellulosic ethanol in addition to corn ethanol (corn + cellulosic ethanol). Our results showed that economically optimal locations for perennial energy crop production were distributed across idle cropland with lower intrinsic N loss than active cropland. We found stover removal incentivized by the RFS2 offset N loss benefits of perennial energy crops. This finding suggests that targeted incentives for N loss reduction are needed to supplement the RFS2 to induce displacement of N-intensive row crops with energy crops to reduce N losses.

Assessing the Returns to Land and Greenhouse Gas Savings from Producing Energy Crops on Conservation Reserve Program Land.

Using land already enrolled in the Conservation Reserve Program (CRP) in the eastern region of the U.S. for producing energy crops for bioenergy while reducing land rental payments offers the potential for lowering the program costs, increasing returns to CRP landowners, and displacing greenhouse gas (GHG) emissions from fossil fuels. We develop an integrated modeling approach to analyze the combination of biomass prices and CRP land rental payment reductions that can incentivize energy crop production on CRP land and its potential to increase soil carbon stocks and displace fossil fuel emissions. We find that conversion of 3.4 million ha in the CRP can be economically viable at a minimum biomass price of $75 Mg-1 with full CRP land rental payment or at $100 Mg-1 with 75% of this land rental payment; this conversion can result in savings of 0.52 and 1.25 billion Mg CO2-eq in life-cycle emissions through the displacement of energy-equivalent fossil fuels and coal-based electricity, respectively, and an additional 0.11 billion Mg CO2-eq soil carbon sequestration relative to the status quo, with CRP left unharvested over the 2016-2030 period. The soil carbon debt due to the transition from unharvested CRP land to energy crops is short-lived and more than offset by the reduction in fossil fuel emissions. The net discounted benefits from producing energy crops on CRP land through a reduced need for government payments to maintain existing enrollment, higher returns to CRP landowners, and the value of the reduction in GHG emissions could be as high as $16-$30 billion by using them for cellulosic biofuels to displace gasoline and $35-$68 billion by displacing coal-based electricity over the 2016-2030 period if biomass prices are $75-$125 Mg-1 and land rental payments are reduced by 25%.

COVID-19: A Cloud with a Silver Lining for Renewable Energy?

COVID-19 has led to an unprecedented reduction in demand for energy for transportation and electricity, a crash in prices and employment in the fossil fuel industries and record-breaking reductions in global carbon emissions. This paper discusses whether this "demand destruction" could spell the beginning of the end for fossil fuels or a temporary recession and the imperative to recover from the current crisis by "building back better" and not the same as before. There are encouraging signs for the renewable energy industry that could make COVID-19 a cloud with a silver lining; whether this is the case will depend not only on the technological realities and social response to the crisis but also on political will and foresight.

Regulation of Host Innate Immunity by Non-Coding RNAs During Dengue Virus Infection.

An estimated 3.9 billion individuals in 128 nations (about 40% of global population) are at risk of acquiring dengue virus infection. About 390 million cases of dengue are reported each year with higher prevalence in the developing world. A recent modeling-based report suggested that half of the population across the globe is at risk of dengue virus infection. In any given dengue outbreak, a percentage of infected population develops severe clinical manifestations, and this remains one of the "unsolved conundrums in dengue pathogenesis". Although, host immunity and virus serotypes are known to modulate the infection, there are still certain underlying factors that play important roles in modulating dengue pathogenesis. Advanced genomics-based technologies have led to identification of regulatory roles of non-coding RNAs. Accumulating evidence strongly suggests that viruses and their hosts employ non-coding RNAs to modulate the outcome of infection in their own favor. The foremost ones seem to be the cellular microRNAs (miRNAs). Being the post-transcriptional regulators, miRNAs can be regarded as direct switches capable of turning "on" or "off" the viral replication process. Recently, role of long non-coding RNAs (lncRNAs) in modulating viral infections via interferon dependent or independent signaling has been recognized. Hence, we attempt to identify the "under-dog", the non-coding RNA regulators of dengue virus infection. Such essential knowledge will enhance the understanding of dengue virus infection in holistic manner, by exposing the specific molecular targets for development of novel prophylactic, therapeutic or diagnostic strategies.

Characteristics of COVID-19 at a non-COVID tertiary pulmonary care centre in Delhi, India.

The pandemic of COVID-19 has emerged as a serious health crisis globally and India too has been extensively affected with 604,641 active cases reported, till date. The present study focuses on the demographic, clinical and laboratory profile of such patients from a tertiary level non-COVID respiratory care hospital. This is a retrospective observational study. Seventy-seven sick patients fulfilling COVID suspect criteria were admitted to the isolation area. Their RT-PCR test was done from the designated laboratory and 35 of them  were confirmed to be COVID-19 patients. The detailed demographic, clinical and laboratory profile of these COVID-19 patients was studied. The mean age was 46±17 years with male predominance (57%). Majority  of the cases (83%) were symptomatic. The most common symptom was cough (66%) followed by breathlessness and fever. Nineteen (54.3%) patients had one or the other co-morbidity and 16 (45.7%) had chronic lung diseases as one of the comorbidities. Nearly half of the patients (51%) required supplementary oxygen on presentation. Two patients were put on invasive mechanical ventilation while 4 patients required non-invasive ventilation before being shifted to the COVID hospital. Hence, it can be concluded that COVID-19 in patients of chronic respiratory diseases  manifests with higher prevalence of symptoms and also higher severity of disease. Further, the  symptomatology of COVID-19 closely mimics the acute exacerbation of chronic lung diseases, so cautious screening and testing should be done, especially at the pulmonary department.

Potential for large-scale CO2 removal via enhanced rock weathering with croplands.

Enhanced silicate rock weathering (ERW), deployable with croplands, has potential use for atmospheric carbon dioxide (CO2) removal (CDR), which is now necessary to mitigate anthropogenic climate change1. ERW also has possible co-benefits for improved food and soil security, and reduced ocean acidification2-4. Here we use an integrated performance modelling approach to make an initial techno-economic assessment for 2050, quantifying how CDR potential and costs vary among nations in relation to business-as-usual energy policies and policies consistent with limiting future warming to 2 degrees Celsius5. China, India, the USA and Brazil have great potential to help achieve average global CDR goals of 0.5 to 2 gigatonnes of carbon dioxide (CO2) per year with extraction costs of approximately US$80-180 per tonne of CO2. These goals and costs are robust, regardless of future energy policies. Deployment within existing croplands offers opportunities to align agriculture and climate policy. However, success will depend upon overcoming political and social inertia to develop regulatory and incentive frameworks. We discuss the challenges and opportunities of ERW deployment, including the potential for excess industrial silicate materials (basalt mine overburden, concrete, and iron and steel slag) to obviate the need for new mining, as well as uncertainties in soil weathering rates and land-ocean transfer of weathered products.

Development of BacMam Induced Hepatitis E Virus Replication Model in Hepatoma Cells to Study the Polyprotein Processing.

The processing of polyprotein(s) to form structural and non-structural components remains an enigma due to the non-existence of an efficient and robust Hepatitis E Virus (HEV) culture system. We used the BacMam approach to construct an HEV replication model in which the HEV genome was cloned in the BacMam vector under the CMV promoter. The recombinant BacMam was used to infect Huh7 cells to transfer the HEV genome. HEV replication was authenticated by the presence of RNAs of both the polarity (+) and (-) and formation of hybrid RNA, a replication intermediate. The presence of genes for Papain-like Cysteine Protease (PCP), methyltransferase (MeT), RNA dependent RNA polymerase (RdRp), and ORF2 was confirmed by PCR amplification. Further, the infectious nature of the culture system was established as evidenced by the cross-infection of uninfected cells using the cell lysate from the infected cells. The HEV replication model was validated by detection of the ORF1 (Open Reading Frame1) encoded proteins, identified by Western blotting and Immunofluorescence by using epitope-specific antibodies against each protein. Consequently, discrete bands of 18, 35, 37, and 56 kDa corresponding to PCP, MeT, RdRp, and ORF2, respectively, were seen. Besides demonstrating the presence of non-structural enzymes of HEV along with ORF2, activity of a key enzyme, HEV-methyltransferase has also been observed. A 20% decrease in the replicative forms of RNA could be seen in presence of 100 µM Ribavirin after 48 h of treatment. The inhibition gradually increased from 0 to 24 to 48 h post-treatment. Summarily, infectious HEV culture system has been established, which could demonstrate the presence of HEV replicative RNA forms, the structural and non-structural proteins and the methyltransferase in its active form. The system may also be used to study the mechanism of action of Ribavirin in inhibiting HEV replication and develop a therapy.

Natural Products as a Paradigm for the Treatment of Coxsackievirus - induced Myocarditis.

Coxsackievirus B3 (CVB3), a member of the Picornaviridae family, is considered to be one of the most important infectious agents to cause virus-induced myocarditis. Despite improvements in studying viral pathology, structure and molecular biology, as well as diagnosis of this disease, there is still no virus-specific drug in clinical use. Structural and nonstructural proteins produced during the coxsackievirus life cycle have been identified as potential targets for blocking viral replication at the step of attachment, entry, uncoating, RNA and protein synthesis by synthetic or natural compounds. Moreover, WIN (for Winthrop) compounds and application of nucleic-acid based strategies were shown to target viral capsid, entry and viral proteases, but have not reached to the clinical trials as a successful antiviral agent. There is an urgent need for diverse molecular libraries for phenotype-selective and high-throughput screening.

Data highlighting miR-155 and GAPDH correlation.

This data represents the effect of miR-155 on the expression of commonly used housekeeping genes, GAPDH, Beta Actin, RPL13A, and U6. The human miR-155 and control RNA were transfected to A549 cells by electroporation. Expression of these genes was compared in both groups by real-time PCR. The significant up-regulation in the expression of GAPDH was observed in the miR-155 transfected samples as compared to control while no major change was observed in the expression of the other three genes.