Analysis of Transgenic Cotton Plants Containing Universal Stress Protein (GaUSP-1, GaUSP-2) and Zinc Finger Transcriptional Factor (GaZnF) Genes under Drought Stress.

Water is the most limiting factor for plant growth and crop productivity. Drought stress adversely affects crop yield throughout the world. Up to 50% of crop yield in Pakistan is severely affected by the shortage of water. Cotton is an important cash crop for Pakistan known as "white gold." It accounts for 8.2% of the value added in agriculture and about 3.2% of GDP. Besides, being the world's fourth-largest cotton producer, our yield per acre ranks 13th in the world. If we look at the Pakistan scenario, water deficiency is one of the major yield-limiting factors. Limitations related to conventional breeding and the advancements in plant genomics and biotechnology applications have opened new horizons to plant improvements. Therefore, in the current study, we carry out a comparative analysis to evaluate the morphological, physiological biochemical and molecular parameters in transgenic plants containing GaUSP-1, GaUSP-2 and GaZinc Finger genes under different drought stress conditions. Data showed that transgenic plants showed more tolerance as compared to non-transgenic plants. Transgenic and non-transgenic assist us in our better understanding of the drought-responsive mechanism and its effect on different plant growth traits, so, in this way, we would be able to explore drought tolerance mechanism and this will open the doors for the identification of drought-related genes.

Adeno-Associated Virus-Mediated Gene Therapy.

Choice of vector is the most critical step in gene therapy. Adeno-associated viruses (AAV); third generation vectors, are getting much attention of scientists to be used as vehicles due to their non-pathogenicity, excellent safety profile, low immune responses, great efficiency to transduce non-dividing cells, large capacity to transfer genetic material and long-term expression of genetic payload. AAVs have multiple serotypes and each serotype shows tropism for a specific cell. Different serotypes are used to target liver, lungs, muscles, retina, heart, CNS, kidneys, etc. Furthermore, AAV based gene therapies have tremendous marketing applications that can be perfectly incorporated in the anticipated sites of the host target genome resulting in life long expression of transgenes. Some therapeutic products use AAV vectors that are used to treat lipoprotein lipase deficiency (LPLD) and it is injected intramuscularly, to treat mutated retinal pigment epithelium RPE65 (RPE65) that is introduced to subretinal space, an intravenous infusion to treat spinal muscular atrophy and rAAV2-CFTR vector is introduced into nasal epithelial cells to treat cystic fibrosis. AAV therapies and other such interdisciplinary methodologies can create the miracles for the generation of precision gene therapies for the treatment of most serious and sometimes fatal disorders.

Viruses as tools in gene therapy, vaccine development, and cancer treatment.

Using viruses to our advantage has been a huge leap for humanity. Their ability to mediate horizontal gene transfer has made them useful tools for gene therapy, vaccine development, and cancer treatment. Adenoviruses, adeno-associated viruses, retroviruses, lentiviruses, alphaviruses, and herpesviruses are a few of the most common candidates for use as therapeutic agents or efficient gene delivery systems. Efforts are being made to improve and perfect viral-vector-based therapies to overcome potential or reported drawbacks. Some preclinical trials of viral vector vaccines have yielded positive results, indicating their potential as prophylactic or therapeutic vaccine candidates. Utilization of the oncolytic activity of viruses is the future of cancer therapy, as patients will then be free from the harmful effects of chemo- or radiotherapy. This review discusses in vitro and in vivo studies showing the brilliant therapeutic potential of viruses.

An overview of dengue viral infection circulating in Pakistan.

BACKGROUND & OBJECTIVES: Dengue virus (DENV) is an RNA virus that infects approximately 2.5 billion people around the world. The incidence of dengue fever has rapidly increased at an alarming rate in the last few years and has affected thousands of people in Pakistan. This review explores the prevalence, serotypes and pathogenesis of dengue virus circulating in Pakistan. METHODS: A systematic review of observational studies published between 1994 and December 2019 was performed. All records of the confirmed outbreak of dengue fever in Pakistan were reviewed and articles containing no primary data were excluded. RESULTS: Four identified serotypes of dengue virus (DENV 1-4) circulate in different regions of the world causing epidemics. The most prevalent serotype, which is still epidemic and dominant in Pakistan, is DENV-2. Many factors like over-population, rapid urbanization, travelling, lack of vector control in dengue endemic areas and inadequate health-care are responsible of dynamic and huge raise of dengue in Pakistan. INTERPRETATION & CONCLUSION: Currently there is no specific treatment for prevention of dengue virus. Recently some antiviral compounds were being tested to eradicate this disease. There is a need to develop an efficient and safe vaccine for all four serotypes to combat dengue viral infection globally and particularly in Pakistan.

Dengue Vaccines: Ongoing Challenges and Current Status in the Advancement of Different Candidates.

Dengue is a vector-borne highly systemic infectious disease of the tropical and subtropical countries and is devastating millions of lives worldwide. It may be self-eliminated like a mild fever or may cause life-threatening fatal complications as dengue hemorrhagic fever and dengue shock syndrome. The lack of specific and effective antiviral drugs and vaccines amplify its transmission rate across the world. The development of the dengue vaccine has been an ambitious task due to the presence of four different dengue serotypes capable of carrying antibody enhancement complex mechanisms. In this review, we have summarized the ongoing challenges in the construction of a dengue vaccine and the current status of the vaccine development. Limited knowledge of immune responses against dengue infection, lack of human or animal model of disease, and suboptimal assay strategies to detect immune responses after infection or vaccination, are some barriers to vaccine and drug development. A tetravalent vaccine with low cost, high efficiency, and capable of eliciting immune responses against all four serotypes is needed to minimize the epidemics. Currently, only one live attenuated chimeric dengue vaccine, the CYD Dengue Vaccine, has completed its third phase and has been licensed. DENVax and TetraVax-DV-TV003 (TV003) are in the third phase while others are still in the first trial phase.

Novel Coronavirus: A Review from Origin to Current Status of Therapeutic Strategies.

Coronaviruses (CoVs) are continuously emerging, highly transmissible, and pathogenic agents that primarily target the human respiratory system. Previous outbreaks of severe acute respiratory syndrome-CoV and Middle East respiratory syndrome-CoV remain life-threatening and global public health concerns. A novel CoV outbreak that occurred in December 2019 in Wuhan, China was declared a pandemic outbreak that has since killed millions of individuals worldwide. Rapid transmission, genetic variations, and unavailability of specific therapeutic drugs are major factors that led to this alarming and deadly situation. Currently, > 200 clinical vaccine trials are underway to combat infection. This review summarizes reports related to CoV origin, genetic variations, drug options, status of nine vaccines that were in phase III trials, and novel therapies including convalescent plasma and stem cell treatment.

Association of Interleukin 28B Polymorphism with Clearance of Hepatitis C Virus: A Mini Review.

The highly infectious hepatitis C virus (HCV) is the major cause of chronic hepatitis around the globe. Approximately 3% of the world's population has been affected by both chronic and acute HCV. In this study, we highlight the relationship between single-nucleotide proteins (SNPs) and interleukin (IL) IL28B on chromosome 19 with the treatment response of chronic HCV infection along with its sustained virologic response (SVR). Four SNPs are strongly linked with HCV self-clearance: rs8099917 TT, rs12980275 AA, rs8105790 TT, and rs10853728 CC. Most SNPs, including rs12979860, are located upstream of the IL28B gene fragment, encoding interferon (IFN)-λ3. We find that IL28B variants rs8099917 and rs12979860 strongly influence results of combined pegylated (PEG)-IFN/ribavirin (RBV) therapy. In the case of SNP rs12979860, the CC genotype is linked with greater than a twofold higher SVR than that with TT or CT genotypes. These SNPs are associated with expression of intrahepatic IFN-stimulated genes in liver. Past research shows that females are more efficient in resolving HCV infection, regardless of IL28B genotype. Similar results of IL28B polymorphisms associated with spontaneous HCV clearance were also obtained in Chinese and Taiwanese HCV patients. Another report of RBV and PEG-IFN-treated patients revealed that age, viral load, rs8099917 genotype, and fibrosis were major predictors of antiviral therapeutic response. To select favorable antiviral regimes for treatment using IFN, a combination of host genetic data and viral genotyping may be useful in treating chronic HCV. We propose that these predictive factors must be considered before commencing treatment in HCV patients.

Role of MicroRNAs in Establishing Latency of Human Immunodeficiency Virus.

Acquired immunodeficiency syndrome (AIDS) emerged as an epidemic in Africa in 1981, and now it has become a most destructive global pandemic. Human immunodeficiency virus (HIV) is responsible for the pathogenesis of AIDS, and it is usually transmitted through unsafe sexual activities. HIV is a lentivirus that can remain latent in the host cells for a long period, and it has various mechanisms to establish latency. The HIV genome encodes several microRNAs (miRNA-TAR, miRNA-H1, miRNA-H3, and miRNA-Nef-367) that act as posttranscriptional control by targeting mRNA sequences. The miRNA-TAR, miRNA-Nef-367, and miRNA-H1 have established roles in HIV latency, whereas miRNA-H3 can activate the latent reservoirs of HIV. The human genome also encodes several miRNAs that have defensive roles against infections. Cellular miRNAs (miRNA-29a, miRNA-146a, miRNA-34c-5'p, miRNA-186, miRNA-210 and miRNA-222) also contribute to viral latency. The most challenging hurdle in the development of effective HIV therapeutics is viral latency. A complete understanding of latency will enable us to develop efficient therapeutics and to eradicate HIV from the globe.

Paradoxical Role of Dengue Virus Envelope Protein Domain III Antibodies in Dengue Virus Infection.

Every year, approximately 100 million individuals are infected with dengue viral infections. Severe dengue infection, characterized as dengue hemorrhagic fever, leads to loss of intravascular fluids and severe bleeding. During dengue virus (DENV) secondary infection, the body produces neutralizing antibodies that cause a strong immune response, resulting in severe hemolysis and plasma leakage. DENV infections in humans stimulate production of virus serotype-specific and cross-reactive antibodies. The envelope (E) protein of DENV contains potent antigenic sites, with one known as E protein domain III (EDIII). Studies of DENV EDIII in mouse models have shown that strongly neutralizing mouse monoclonal antibodies (mAbs) are DENV-serotype specific and bind to an epitope on EDIII that is unique to each serotype. Unlike DENV-serotype-specific mouse mAbs, cross-reactive mAbs that bind to EDIII have moderate-to-weak neutralizing activity. Studies with mouse mAbs resulted in identification and mapping of different epitopes on the lateral ridge of DENV EDIII.

Drug Resistance in Hepatitis C Virus: Future Prospects and Strategies to Combat It.

Induction of highly pathogenic hepatitis C virus (HCV) causes chronic hepatitis round the world. This virus is easily prone to developing resistance against antiviral drugs because of two viral polymerases that do not possess the proofreading and overlapping reading frame abilities. There is more than one explanation for how this virus builds up resistance against antiviral drug treatments. Assays are now available to detect HCV-resistant variants, based on phenotypic and genotypic assays, and next generation sequencing. But these assays are of a little value at baseline, because they are not influential enough for making therapeutic decisions in HCV patients. Moreover, HCV monitoring is now an essential part of clinical practice. Special patients, such as those with thalassemia, renal transplant due to renal failure, and the patients undergoing hemodialysis, are at higher risk for acquiring this infection. Management of HCV infection in these patient groups is complicated by multiple side effects, including flu-like symptoms, neutropenia, fever, and neuropsychiatric disorders, thus limiting the use of ribavirin and coexisting iron overload. In HCV patients suffering from depression, the treatment may be discontinued because of some defects in neurochemical pathways caused by interferon, which can enhance the level of depression in these patients. In addition, obesity has been found to be a marker of failure of HCV treatment. There will be many resistance tolerant HCV treatment options available in the near future.

Blood-based gene expression profile of oxidative stress and antioxidant genes for identifying surrogate markers of liver tissue injury in chronic hepatitis C patients.

Oxidative stress is the process by which reactive molecules and free radicals are formed in cells. In this study, we report the blood-based gene expression profile of oxidative stress and antioxidant genes for identifying surrogate markers of liver tissue in chronic hepatitis C (CHC) patients by using real-time PCR. A total of 144 untreated patients diagnosed with CHC having genotype 3a and 20 healthy controls were selected for the present study. Liver biopsy staging and grading of CHC patients were performed using the METAVIR score. Total RNA was extracted from liver tissue and blood samples, followed by cDNA synthesis and real-time PCR. The relative expression of genes was calculated using the ΔΔCt method. The expression profile of 84 genes associated with oxidative stress and antioxidants was determined in liver tissue and blood samples. In liver tissue, 46 differentially expressed genes (upregulated, 27; downregulated, 19) were identified in CHC patients compared to normal samples. In blood, 61 genes (upregulated, 51; downregulated; 10) were significantly expressed in CHC patients. A comparison of gene expression in liver and whole blood showed that 20 genes were expressed in a similar manner in the liver and blood. The expression levels of commonly expressed liver and blood-based genes were also correlated with clinical factors in CHC patients. A receiver operating curve (ROC) analysis of oxidative stress genes (ALB, CAT, DHCR24, GPX7, PRDX5, and MBL2) showed that infections in patients with CHC can be distinguished from healthy controls. In conclusion, blood-based gene expression can reflect the behavior of oxidative stress genes in liver tissue, and this blood-based gene expression study in CHC patients explores new blood-based non-invasive biomarkers that represent liver damage.

Evolution of efficacious pangenotypic hepatitis C virus therapies.

Hepatitis C compromises the quality of life of more than 350 million individuals worldwide. Over the last decade, therapeutic regimens for treating hepatitis C virus (HCV) infections have undergone rapid advancements. Initially, structure-based drug design was used to develop molecules that inhibit viral enzymes. Subsequently, establishment of cell-based replicon systems enabled investigations into various stages of HCV life cycle including its entry, replication, translation, and assembly, as well as role of host proteins. Collectively, these approaches have facilitated identification of important molecules that are deemed essential for HCV life cycle. The expanded set of putative virus and host-encoded targets has brought us one step closer to developing robust strategies for efficacious, pangenotypic, and well-tolerated medicines against HCV. Herein, we provide an overview of the development of various classes of virus and host-directed therapies that are currently in use along with others that are undergoing clinical evaluation.

HSV-1 Infection: Role of Viral Proteins and Cellular Receptors.

The interaction between herpes simplex virus type 1 (HSV-1) and its host starts with the attachment of the virus for entry and spreading into host cells involving viral glycoproteins and host receptors. Once entered, it remains persistent as a latent infection throughout the host's life as it cannot be cleared completely by the immune system. Viral regulatory proteins and host factors determine whether the virus will enter into the acute or latent mode of infection. Acute viral infection is usually asymptomatic and self-limiting whereas latent infection may remain in the trigeminal ganglion of oropharyngeal mucosa, where it can be activated at any time depending upon the stimulus. Host innate and adaptive immune elements play important roles in limiting HSV-1 infection by interfering with viral replication but are unable to remove the virus completely. In this review, we update how the major proteins involved in entry and pathogenesis of viruses and immune responses against infection.

Deadly outbreak of chickenpox at district Faisalabad, Pakistan: possible causes, and preventive way forward.

This article details our recommendations for the deadly outbreak of chickenpox to consider the additional referral of the absence of a monitoring system of prevention and control along with poor vaccination system for children in low-resource settings. The recent spread of chickenpox outbreak in Pakistan has claimed dozens of lives. The deaths in this current outbreak in quick successions are beyond understanding. Re-emergence of chickenpox in the area has raised many questions. Keeping in view the spread of chickenpox mainly in Faisalabad and its international reputation in trading, chickenpox breakout needs international attention to control its spread. It should be taken as an eye opener for the Government of Pakistan and government should develop and implement Centralized Infectious Disease Reporting Information Management System that will help to narrow down the pathogens as far as the epidemics are concerned and also for early preventive and countermeasure response.

Autophagy-independent functions of UVRAG are essential for peripheral naive T-cell homeostasis.

UV radiation resistance-associated gene (UVRAG) encodes a tumor suppressor with putative roles in autophagy, endocytic trafficking, and DNA damage repair but its in vivo role in T cells is unknown. Because conditional homozygous deletion of Uvrag in mice results in early embryonic lethality, we generated T-cell-specific UVRAG-deficient mice that lacked UVRAG expression specifically in T cells. This loss of UVRAG led to defects in peripheral homeostasis that could not be explained by the increased sensitivity to cell death and impaired proliferation observed for other autophagy-related gene knockout mice. Instead, UVRAG-deficient T-cells exhibited normal mitochondrial clearance and activation-induced autophagy, suggesting that UVRAG has an autophagy-independent role that is critical for peripheral naive T-cell homeostatic proliferation. In vivo, T-cell-specific loss of UVRAG dampened CD8(+) T-cell responses to LCMV infection in mice, delayed viral clearance, and impaired memory T-cell generation. Our data provide novel insights into the control of autophagy in T cells and identify UVRAG as a new regulator of naïve peripheral T-cell homeostasis.

HCV-induced regulatory alterations of IL-1ß, IL-6, TNF-α, and IFN-ϒ operative, leading liver en-route to non-alcoholic steatohepatitis.

Over the course of time, Hepatitis C has become a universal health menace. Its deleterious effects on human liver encompass a lot of physiological, genetic as well as epigenetic alterations. Fatty liver (Hepatic steatosis) is an inflammation having multifactorial ancestries; one of them is HCV (steatohepatitis). HCV boosts several cellular pathways involving up-regulation of a number of cytokines. Current study reviews the regulation of some selective key cytokines during HCV infection, to help generate an improved understanding of their role. These cytokines, IL-1ß, IL-6, TNF-α, and IFN-ϒ, are inflammatory markers of the body. These particular markers along with others help hepatocytes against viral infestation. However, recently, their association has been found in degradation of liver on the trail heading to non-alcoholic steatohepatitis (NASH). Consequently, the disturbance in their equilibrium has been repeatedly reported during HCV infection. Quite a number of findings are affirming their up-regulation. Although these cell markers are stimulated by hepatocytes as their standard protection mechanism, but modern studies have testified the paradoxical nature of this defense line. Nevertheless, direct molecular or epigenetic research is needed to question the actual molecular progressions and directions commanding liver to steatosis, cirrhosis, or eventually HCC (Hepatocellular Carcinoma).

Progression of fibrosis in patients with chronic viral hepatitis is associated with IL-17(+) neutrophils.

BACKGROUND & AIMS: The pro-inflammatory cytokine IL-17 plays a crucial role in liver diseases associated with hepatic fibrosis and increased risk of cancer development. Nevertheless, the cellular source of this cytokine has never been characterized in patients with liver fibrosis. METHODS: In this study, we investigated liver biopsies from 49 patients with chronic viral hepatitis at different stages of liver fibrosis. We monitored IL-17 production by intracellular flow cytometry, immunofluorescence and immunohistochemical in situ stainings, allowing a precise quantification, characterization and localization of IL-17(+) cells. RESULTS: Density of IL-17(+) cells increased with the stage of liver fibrosis specifically in fibrotic septa and portal areas (correlation coefficient r = 0.7373; P < 0.0001). Data clearly show that the frequency of intrahepatic IL-17(+) lymphocytes (including T, NKT and NK cells) was independent on stage of liver fibrosis, and we observed no statistical differences in number of IL-17(+) macrophages during progression of fibrosis. On the other hand, the number of IL-17(+) neutrophils in fibrotic septa and portal areas strongly correlated with the stages of fibrosis (correlation coefficient r = 0.6986; P < 0.0001), contributing significantly to total IL-17 production in liver tissue. CONCLUSIONS: Our data indicate that neutrophils represent an important source of IL-17 in the human liver, especially in late fibrosis stages. Inhibition of this specific harmful subset of neutrophils may offer therapeutic opportunities in fibrotic liver.

The percutaneous cecostomy tube in the management of fecal incontinence in children.

PURPOSE: To retrospectively evaluate experience with percutaneous cecostomies and their long-term outcomes. MATERIALS AND METHODS: Between June 1994 and March 2009, 290 patients (mean age, 10.1 y) with fecal incontinence underwent percutaneous cecostomy tube placement and subsequent tube management. Technical success, procedural complications, and long-term follow-up until March 2012 were evaluated. RESULTS: A cecostomy was successfully placed in 284 patients (98%), and 257 of 280 patients (92%) underwent a successful exchange to a low-profile tube. A total of 1,431 routine exchanges to low-profile tubes were reviewed in 258 patients (mean, 1.6 ± 1.3 routine tube changes per 1,000 days). Eighty-five patients (29%) experienced one or more early problems after cecostomy, and 10 (3%) had major complications. In the total 463,507 tube-days, 938 late problems were noted: 917 (98%) minor and 22 (2%) major. Forty patients had the cecostomy catheter removed and 141 "graduated" to an adult health care facility. CONCLUSIONS: The percutaneous cecostomy procedure provides a safe management option for fecal incontinence in the pediatric population.

De Novo modeling of Envelope 2 protein of HCV isolated from Pakistani patient and epitopes prediction for vaccine development.

Hepatitis C virus (HCV) is a universal health issue and a significant risk factor leading to hepatocellular carcinoma. HCV has infected approximately 170 million individuals worldwide. It is a member of Flaviviridae with positive sense RNA genome. In the absence of any effective vaccine against HCV, pegylated interferon with ribavirin is the standard of treatment against HCV infection. In this study, sequence and structural analysis of envelope 2 (E2) protein was performed which was isolated from patients of HCV genotype 3a in Pakistan. Then, epitopes were predicted which were specific for both B-cells and T-cells. Later, conservancy of epitopes was checked with the HCV 3a and 1a sequences from different countries. A total of 6 conserved epitopes were found from extra-membranous regions of E2 protein. Presence of conserved epitopes in E2 protein generates the possibility that these epitopes can be used to elicit the immune response against HCV.

Acidic nuclear phosphoprotein 32kDa (ANP32)B-deficient mouse reveals a hierarchy of ANP32 importance in mammalian development.

The highly conserved ANP32 proteins are proposed to function in a broad array of physiological activities through molecular mechanisms as diverse as phosphatase inhibition, chromatin regulation, caspase activation, and intracellular transport. On the basis of previous analyses of mice bearing targeted mutations of Anp32a or Anp32e, there has been speculation that all ANP32 proteins play redundant roles and are dispensable for normal development. However, more recent work has suggested that ANP32B may in fact have functions that are not shared by other ANP32 family members. Here we report that ANP32B expression is associated with a poor prognosis in human breast cancer, consistent with the increased levels of Anp32b mRNA present in proliferating wild-type (WT) murine embryonic fibroblasts and stimulated WT B and T lymphocytes. Moreover, we show that, contrary to previous assumptions, Anp32b is very important for murine embryogenesis. In a mixed genetic background, ANP32B-deficient mice displayed a partially penetrant perinatal lethality that became fully penetrant in a pure C57BL/6 background. Surviving ANP32B-deficient mice showed reduced viability due to variable defects in various organ systems. Study of compound mutants lacking ANP32A, ANP32B, and/or ANP32E revealed previously hidden roles for ANP32A in mouse development that became apparent only in the complete absence of ANP32B. Our data demonstrate a hierarchy of importance for the mammalian Anp32 genes, with Anp32b being the most critical for normal development.