XRN1 deletion induces PKR-dependent cell lethality in interferon-activated cancer cells.

Emerging data suggest that induction of viral mimicry responses through activation of double-stranded RNA (dsRNA) sensors in cancer cells is a promising therapeutic strategy. One approach to induce viral mimicry is to target molecular regulators of dsRNA sensing pathways. Here, we show that the exoribonuclease XRN1 is a negative regulator of the dsRNA sensor protein kinase R (PKR) in cancer cells with high interferon-stimulated gene expression. XRN1 deletion causes PKR pathway activation and consequent cancer cell lethality. Disruption of interferon signaling with the JAK1/2 inhibitor ruxolitinib can decrease cellular PKR levels and rescue sensitivity to XRN1 deletion. Conversely, interferon-ß stimulation can increase PKR levels and induce sensitivity to XRN1 inactivation. Lastly, XRN1 deletion causes accumulation of endogenous complementary sense/anti-sense RNAs, which may represent candidate PKR ligands. Our data demonstrate how XRN1 regulates PKR and how this interaction creates a vulnerability in cancer cells with an activated interferon cell state.

XRN1 deletion induces PKR-dependent cell lethality in interferon-activated cancer cells.

Emerging data suggest that induction of viral mimicry responses through activation of double-stranded RNA (dsRNA) sensors in cancer cells is a promising therapeutic strategy. One approach to induce viral mimicry is to target molecular regulators of dsRNA sensing pathways. Here, we show that the exoribonuclease XRN1 is a negative regulator of the dsRNA sensor protein kinase R (PKR) in cancer cells with high interferon-stimulated gene (ISG) expression. XRN1 deletion causes PKR activation and consequent cancer cell lethality. Disruption of interferon signaling with the JAK1/2 inhibitor ruxolitinib can decrease cellular PKR levels and rescue sensitivity to XRN1 deletion. Conversely, interferon-ß stimulation can increase PKR levels and induce sensitivity to XRN1 inactivation. Lastly, XRN1 deletion causes accumulation of endogenous complementary sense/anti-sense RNAs, which may represent candidate PKR ligands. Our data demonstrate how XRN1 regulates PKR and nominate XRN1 as a potential therapeutic target in cancer cells with an activated interferon cell state.

Non-pathologic components are associated with reduced visual acuity in myopes after spectacle correction.

Purpose: To find the association between reduced best-corrected visual acuity and non-pathologic components after optical correction in individuals with low to high myopia. Methods: Myopic children under 16 years of age were reviewed using electronic medical records and the following data were extracted and recorded: participant's age, gender, uncorrected visual acuity (UCVA), manifest refraction, and best corrected visual acuity (BCVA). Spherical equivalent and cylinder were classified into low, moderate, and high categories based on the magnitude range. Similarly, astigmatism was defined into with-the-rule, against-the-rule, and oblique based on the location of the steepest meridian. Reduced BCVA was defined when the decimal visual acuity was less than 0.66 (equivalent to Snellen's acuity of 6/9 or 20/30). Logistic regression was performed to test the factors associated with reduced visual acuity after optical correction in the absence of myopic pathologic changes. Statistical significance was considered if P < 0.05. Results: Overall 44.9% (N = 242/538) of myopes had reduced best-corrected visual acuity (BCVA) and none of the patients had pathologic myopic lesions. Using logistic regression, we found that high spherical refraction (OR 27.98, 95% CI 14.43-54.25, P < 0.001) and moderate spherical refraction (OR 5.52, 95% CI 2.56-11.91, P < 0.001) were significantly associated with reduced best corrected visual acuity despite any pathological lesions. Additionally, oblique and ATR astigmatism were associated with reduced visual acuity in myopic children with (OR 2.05, 95% CI 0.77-5.42) and (OR 1.59, 95% CI 0.82-3.08). Conclusion: Higher magnitude of refractive error components causes reduced visual acuity in the absence of pathologic changes.

Epsilon poly-lysine in buffalo semen extender: A step towards reducing the development of antibiotic resistance.

The use of antibiotics in semen extenders can contribute to the development of antibiotic resistance. The objective of the study was to evaluate epsilon-polylysine (Ɛ-PL) as a substitute for antibiotics in the buffalo semen extender. For this, 20 semen ejaculates were collected from four Murrah buffalo bulls. Each ejaculate was divided into three equal aliquots and extended into an egg yolk-based semen extender containing either antibiotics (strepto-penicillin) or different concentrations of Ɛ-PL (0.64 and 1.28 g/L) to make the final concentration 80 million sperm/mL and cryopreserved as per the standard procedure. The antibiogram sensitivity test confirmed that Ɛ-PL is an effective antimicrobial against microbes present in buffalo semen ejaculates. Furthermore, the addition of Ɛ-PL in the semen extender significantly reduces the colony forming unit (CFU)/mL in cryopreserved semen equivalent to strepto-penicillin. The sperm motility and kinematic parameters assessed by a computer-assisted sperm analyser showed that Ɛ-PL did not inhibit either sperm motility not kinematic parameters of cryopreserved sperm. The flow-cytometric evaluation of frozen-thawed sperm revealed interesting results. The extender supplemented with Ɛ-PL protected sperm acrosome and mitochondrial membrane potential greater than the extender supplemented with strepto-penicillin. Further, Ɛ-PL reduced significantly the production of superoxide anions from mitochondria during the cryopreservation process. In this way, Ɛ-PL may be a suitable alternative to antibiotics in semen extenders. In conclusion, Ɛ-PL at a concentration of 0.64 g/L acts as an effective antimicrobial as well as antioxidant in semen extender for cryopreservation of buffalo sperm.

Valorization potential of pine needle waste biomass: recent trends and future perspectives.

Pines play a significant role in forest biodiversity globally and generate huge forest litter. Dry pine needles due to low ignition temperature and high frictional force with the ground catch fire quickly. Annual forest fires in the northern states of India greatly impact the Indian economy besides causing huge loss to biodiversity, livelihood, and environment. Pine needles are also considered unfit for fodder consumption due to presence of tannins. Although the presence of softwood lignin in pine needles makes it difficult to degrade easily, the presence of holocellulose (68.5%) containing 45-51% cellulose makes this biomass a potential substrate to be used in pulp-making industries for low-grade paper sheets. The good fiber length of pine needles (1.3-1.4 mm) with a diameter of 30-32 µm, maybe considered important property for paper making. The use of pine needles in the pharmaceutical and food industries are due to the presence of secondary metabolites (α-pinene, ß-pinene, caryophyllene etc.). The various other potential applications of pine needles are for producing bio-ethanol (yield, 3.98%; purity, 94%), biogas (yield, 23.1 L kg-1), smokeless briquettes (calorific value, 18.77 MJ kg-1), biochar (calorific value, 25.6 MJ kg-1), bio-composites (tensile strength, 21-60 MPa), and bio-pesticides. This paper comprehensively reviews the current applications of pine needles along with its future prospective applications that can have the dual advantage of providing employment opportunities to the people along with environmental protection.

Knowledge, attitude, and practice of childhood myopia among Indian optometrists: A questionnaire-based study.

Purpose: To investigate the knowledge of myopia and its natural history including complications and clinical approaches for management adopted by optometrists across India. Methods: An online survey was distributed to Indian optometrists. A pre-validated questionnaire was adopted from previous literature. Respondents provided information about their demographics (gender, age, practice location, and modality), myopia knowledge, self-reported practice behaviors relating to childhood myopia, the information and evidence base used to guide their practice, and perceived extent of adult caregiver engagement in making management decisions for myopic children. Results: A total of 302 responses were collected from different regions of the country. Most respondents demonstrated knowledge of the association between high myopia and retinal breaks, retinal detachment and primary open-angle glaucoma. Optometrists used a range of techniques to diagnose childhood myopia, with a preference for non-cycloplegic refractive measures. The most common approaches to management were single-vision distance despite most optometrists identifying orthokeratology and low-dose (0.01%) topical atropine as two potentially more effective therapeutic interventions for controlling childhood myopia progression. Almost 90% of respondents considered increasing the time spent outdoors to be beneficial for reducing the rate of myopia progression. The main sources of information used to guide clinical practice were continuing education conferences, seminars, research articles, and workshops. Conclusion: : Indian optometrists appear to be aware of emerging evidence and practices, but are not routinely adopting measures. Clinical guidelines, regulatory approval, and sufficient consultation time may be of value for assisting practitioners in making clinical decisions based on the current available research evidence.

Enhanced lignin degradation of paddy straw and pine needle biomass by combinatorial approach of chemical treatment and fungal enzymes for pulp making.

Paddy straw (PS) and pine needles (PN) are one of the challenging biomasses in terms of disposal and compost making due to their high silica and tannin contents. Particulate air pollution, loss of biodiversity and respiratory impairments are some of disastrous outcomes caused by burning. However, high percentage of cellulose and hemicellulose makes them potential substrate for paper and pulp industries. The main aim of work was to study and utilize a combinatorial approach of weak chemical treatment and lignin degrading fungal species as agents of effective production of lignin modifying enzymes (LME's) for lignin depolymerisation from the biomasses. Phanerochaete chrysosporium was found to be the best degrader of lignin (47.11 % in PS + PN in 28 days) with maximum LME's production between 10th-17th days. Efficient lignin degradation in the PS and PN biomass will aid further application in pulp production supporting the transition to a circular economy in a greener way.

Aflatoxins in Cereals and Cereal-Based Products: Occurrence, Toxicity, Impact on Human Health, and Their Detoxification and Management Strategies.

Cereals and cereal-based products are primary sources of nutrition across the world. However, contamination of these foods with aflatoxins (AFs), secondary metabolites produced by several fungal species, has raised serious concerns. AF generation in innate substrates is influenced by several parameters, including the substrate type, fungus species, moisture content, minerals, humidity, temperature, and physical injury to the kernels. Consumption of AF-contaminated cereals and cereal-based products can lead to both acute and chronic health issues related to physical and mental maturity, reproduction, and the nervous system. Therefore, the precise detection methods, detoxification, and management strategies of AFs in cereal and cereal-based products are crucial for food safety as well as consumer health. Hence, this review provides a brief overview of the occurrence, chemical characteristics, biosynthetic processes, health hazards, and detection techniques of AFs, along with a focus on detoxification and management strategies that could be implemented for food safety and security.

Nivalenol Mycotoxin Concerns in Foods: An Overview on Occurrence, Impact on Human and Animal Health and Its Detection and Management Strategies.

Mycotoxins are secondary metabolites produced by fungi that infect a wide range of foods worldwide. Nivalenol (NIV), a type B trichothecene produced by numerous Fusarium species, has the ability to infect a variety of foods both in the field and during post-harvest handling and management. NIV is frequently found in cereal and cereal-based goods, and its strong cytotoxicity poses major concerns for both human and animal health. To address these issues, this review briefly overviews the sources, occurrence, chemistry and biosynthesis of NIV. Additionally, a brief overview of several sophisticated detection and management techniques is included, along with the implications of processing and environmental factors on the formation of NIV. This review's main goal is to offer trustworthy and current information on NIV as a mycotoxin concern in foods, with potential mitigation measures to assure food safety and security.

Citrinin Mycotoxin Contamination in Food and Feed: Impact on Agriculture, Human Health, and Detection and Management Strategies.

Citrinin (CIT) is a mycotoxin produced by different species of Aspergillus, Penicillium, and Monascus. CIT can contaminate a wide range of foods and feeds at any time during the pre-harvest, harvest, and post-harvest stages. CIT can be usually found in beans, fruits, fruit and vegetable juices, herbs and spices, and dairy products, as well as red mold rice. CIT exerts nephrotoxic and genotoxic effects in both humans and animals, thereby raising concerns regarding the consumption of CIT-contaminated food and feed. Hence, to minimize the risk of CIT contamination in food and feed, understanding the incidence of CIT occurrence, its sources, and biosynthetic pathways could assist in the effective implementation of detection and mitigation measures. Therefore, this review aims to shed light on sources of CIT, its prevalence in food and feed, biosynthetic pathways, and genes involved, with a major focus on detection and management strategies to ensure the safety and security of food and feed.

Trichothecenes in food and feed: Occurrence, impact on human health and their detection and management strategies.

Trichothecenes (TCNs) are the mycotoxins produced by many fungal species such as Fusarium, Myrothecium, and Stachybotrys and pose a considerable health risk. Based on their characteristic functional moieties, they are divided into four categories: Type A (T-2, HT-2, diacetoxyscirpenol (DAS), harzianum A, neosolaniol (NEO) and trichodermin), Type B (deoxynivalenol (DON), nivalenol (NIV), trichothecin and fusarenon X), Type C (crotocin) and Type D (satratoxin G & H, roridin A and verrucarin A) with types A and B being the most substantial. TCNs cause growth retardation in eukaryotes, suppress seedling growth or regeneration in plants and could be a reason for animal reproductive failure. Due to the increased frequency of occurrence and widespread distribution of TCNs in food and feed, knowledge of their sources of occurrence is essential to strategise their control and management. Hence, this review provides an overview of various types and sources of TCNs, the associated biosynthetic pathways and genes responsible for production in food and feed. Further, various processing and environmental effects on TCNs production, detection techniques and management strategies are also briefly outlined.

Accurate Quantification of Overlapping Herpesvirus Transcripts from RNA Sequencing Data.

Herpesviruses employ extensive bidirectional transcription of overlapping genes to overcome length constraints on their gene product repertoire. As a consequence, many lytic transcripts cannot be measured individually by reverse transcription-quantitative PCR (RT-qPCR) or conventional RNA sequencing (RNA-seq) analysis. A. G. Bruce, S. Barcy, T. DiMaio, E. Gan, et al. (Pathogens 6:11, 2017, https://doi.org/10.3390/pathogens6010011) have proposed an approximation method using unique coding sequences (UCDS) to estimate lytic gene abundance from Kaposi's sarcoma-associated herpesvirus (KSHV) RNA-seq data. Although UCDS has been widely employed, its accuracy, to our knowledge, has never been rigorously validated for any herpesvirus. In this study, we use cap analysis of gene expression sequencing (CAGE-seq) as a gold-standard to determine the accuracy of UCDS for estimating Epstein-Barr virus (EBV) lytic gene expression levels from RNA-seq data. We also introduce the Unique TranScript (UTS) method, which, like UCDS, estimates transcript abundance from changes in mean RNA-seq read depth. UTS is distinguished by its use of empirically determined 5' and 3' transcript ends rather than coding sequence annotations. Compared to conventional read assignment, both UCDS and UTS improved the accuracy of quantitation of overlapping genes, with UTS giving the most-accurate results. The UTS method discards fewer reads and may be advantageous for experiments with less sequencing depth. UTS is compatible with any aligner and, unlike isoform-aware alignment methods, can be implemented on a laptop computer. Our findings demonstrate that the accuracy achieved by complex and expensive techniques such as CAGE-seq can be approximated using conventional short-read RNA-seq data when read assignment methods address transcript overlap. Although our study focuses on EBV transcription, the UTS method should be applicable across all herpesviruses as well as to other genomes with extensively overlapping transcriptomes. IMPORTANCE Many viruses employ extensively overlapping transcript structures. This complexity makes it difficult to quantify gene expression by using conventional methods, including RNA-seq. Although high-throughput techniques that overcome these limitations exist, they are complex, expensive, and scarce in the herpesvirus literature relative to short-read RNA-seq. Here, using Epstein-Barr virus (EBV) as a model, we demonstrate that conventional RNA-seq analysis methods fail to accurately quantify the abundances of many overlapping transcripts. We further show that the previously described Unique CoDing Sequence (UCDS) method and our Unique TranScript (UTS) method greatly improve the accuracy of EBV lytic gene measurements obtained from RNA-seq data. The UTS method has the advantages of discarding fewer reads and being implementable on a laptop computer. Although this study focuses on EBV, the UCDS and UTS methods should be applicable across herpesviruses and for other viruses that make extensive use of overlapping transcription.

Bioformulation development via valorizing silica-rich spent mushroom substrate with Trichoderma asperellum for plant nutrient and disease management.

The present investigation was performed to valorize paddy straw (PS) based silica (Si) rich Spent Mushroom Substrate (SMS) of Pleurotus ostreatus for Plant Nutrient and Disease Management in wilt (caused by F. oxysporum f. sp. lycopersici) susceptible tomato plant F1 Hybrid King 180. Raw PS and SMS generated by P. ostreatus cultivated on PS only, and PS amended with 5% soybean cake (SC) were bio-fortified with Trichoderma asperellum (TA). SMS (PS+ 5% SC) was found supporting the growth of T. asperellum to an extent of 12.37 × 1013 conidia/g substrate. GC-MS analysis of SMS detected several bioactive metabolites like Palmitic acid, Oleic acid, Methyl linoleate, Stigmasterol, etc., known for plant health management. Bioformulations were developed employing Press Mud (PM) and Talcum Powder (TP) as carrier materials. Among the different bioformulations tested in pots study; SMS (PS+ 5% SC) SiTAPM, collectively named as TF-I, provided improved levels of morpho-biochemical and nutritional parameters, i.e., Plant Biomass (2.27 folds), Root Volume (1.75 folds), Chlorophyll (2.66 folds), Carotenoids (2.42 folds), Number of Fruits (1.76 folds), Fruit Biomass (2.02 folds), Total Soluble Sugars (2.32 folds), Total Soluble Proteins (1.70 folds), and nutraceutical parameters as Lycopene (1.42 folds), ß-carotene (2.65 folds) and Ascorbic Acid (1.54 folds), along with significant (p < 0.05) reduction in the Disease Severity Index (84.34%-21.23%), over the pathogen affected plant taken as control. The fruits and leaves garnered under TF-I displayed Total Polyphenol Content (TPC) of 74.5 and 126.9 mg g-1 gallic acid, respectively, with 83.73% DPPH and 72.25% FRAP activity, indicating the elicitation of antioxidant properties in tomato fruits. EDS analyses showed 21.53% Si in SMS, and plant mapping investigation indicated a substantial accumulation of Si, which is well conceded to promote growth, disease resistance, and antioxidant parameters. The study also endorsed the use of PM over TP, as TF-I recorded an acceptable conidial count (2.22 × 108 cfu/g) towards the end of six months storage period over other bioformulations. Overall, the study envisages the development and application of innovative methodology (TF-I), offering an eco-friendly alternative for producing quality crops and a sustainable solution to waste management, thus delivering a holistic contribution towards the circular economy.

Post-traumatic bilateral vesicocutaneous fistula of thighs treated with buccal mucosa graft urethroplasty and cyanoacrylate glue instillation: a novel treatment for management of a complicated fistula.

Post-traumatic vesicocutaneous fistula (VCF) is a rare variant of urinary fistulas. These fistulas may externally communicate to abdomen, perineum, buttocks, scrotum or very rarely thigh. These fistulas usually develop at a variable time duration after trauma and are usually preceded with thigh swelling or abscess formation followed by spontaneous rupture. We, hereby, report a case of VCF of bilateral thighs with associated penobulbar urethral stricture after road traffic accident which was managed with dual modality of buccal mucosa graft urethroplasty surgery and cyanoacrylate glue injection in the fistulous tracts. To the best of our knowledge, this is first report of bilateral VCFs communicating externally to thighs. In literature, very few cases of VCFs of thigh are reported and are rarely managed with adhesive glue application.