Recent developments in denoising medical images using deep learning: An overview of models, techniques, and challenges

Medical imaging plays a critical role in diagnosing and treating various medical conditions. However, interpreting medical images can be challenging even for expert clinicians, as they are often degraded by noise and artifacts that can hinder the accurate identification and analysis of diseases, leading to severe consequences such as patient misdiagnosis or mortality. Various types of noise, including Gaussian, Rician, and Salt-pepper noise, can corrupt the area of interest, limiting the precision and accuracy of algorithms. Denoising algorithms have shown the potential in improving the quality of medical images by removing noise and other artifacts that obscure essential information. Deep learning has emerged as a powerful tool for image analysis and has demonstrated promising results in denoising different medical images such as MRIs, CT scans, PET scans, etc. This review paper provides a comprehensive overview of state-of-the-art deep learning algorithms used for denoising medical images. A total of 120 relevant papers were reviewed, and after screening with specific inclusion and exclusion criteria, 104 papers were selected for analysis. This study aims to provide a thorough understanding for researchers in the field of intelligent denoising by presenting an extensive survey of current techniques and highlighting significant challenges that remain to be addressed. The findings of this review are expected to contribute to the development of intelligent models that enable timely and accurate diagnoses of medical disorders. It was found that 40% of the researchers used models based on Deep convolutional neural networks to denoise the images, followed by encoder-decoder (18%) and other artificial intelligence-based techniques (15%) (Like DIP, etc.). Generative adversarial network was used by 12%, transformer-based approaches (13%) and multilayer perceptron was used by 2% of the researchers. Moreover, Gaussian noise was present in 35% of the images, followed by speckle noise (16%), poisson noise (14%), artifacts (10%), rician noise (7%), Salt-pepper noise (6%), Impulse noise (3%) and other types of noise (9%). While the progress in developing novel models for the denoising of medical images is evident, significant work remains to be done in creating standardized denoising models that perform well across a wide spectrum of medical images. Overall, this review highlights the importance of denoising medical images and provides a comprehensive understanding of the current state-of-the-art deep learning algorithms in this field.

Genotypic Profiling, Functional Analysis, Cholesterol-Lowering Ability, and Angiotensin I-Converting Enzyme (ACE) Inhibitory Activity of Probiotic Lactiplantibacillus plantarum K25 via Different Approaches

Due to its alleged health advantages, several uses in biotechnology and food safety, the well-known probiotic strain Lactiplantibacillus plantarum K25 has drawn interest. This in-depth investigation explores the genetic diversity, makeup, and security characteristics of the microbial genome of L. plantarum K25, providing insightful knowledge about its genotypic profile and functional characteristics. Utilizing cutting-edge bioinformatics techniques like comparative genomics, pan-genomics, and genotypic profiling was carried out to reveal the strain's multidimensional potential in various fields. The results not only add to our understanding of the genetic makeup of L. plantarum K25 but also show off its acceptability in various fields, notably in biotechnology and food safety. The explanation of evolutionary links, which highlights L. plantarum K25's aptitude as a probiotic, is one notable finding from this research. Its safety profile, which is emphasized by the absence of genes linked to antibiotic resistance, is crucial and supports its status as a promising probiotic option.

Whole Genome Analysis of Tibetan Kefir-Derived Lactiplantibacillus Plantarum 12-3 Elucidates Its Genomic Architecture, Antimicrobial and Drug Resistance, Potential Probiotic Functionality and Safety

BACKGROUND

Lactiplantibacillus plantarum 12-3 holds great promise as a probiotic bacterial strain, yet its full potential remains untapped. This study aimed to better understand this potential therapeutic strain by exploring its genomic landscape, genetic diversity, CRISPR-Cas mechanism, genotype, and mechanistic perspectives for probiotic functionality and safety applications.

METHODS

L. plantarum 12-3 was isolated from Tibetan kefir grains and, subsequently, Illumina and Single Molecule Real-Time (SMRT) technologies were used to extract and sequence genomic DNA from this organism. After performing pan-genomic and phylogenetic analysis, Average Nucleotide Identity (ANI) was used to confirm the taxonomic identity of the strain. Antibiotic resistance gene analysis was conducted using the Comprehensive Antibiotic Resistance Database (CARD). Antimicrobial susceptibility testing, and virulence gene identification were also included in our genomic analysis to evaluate food safety. Prophage, genomic islands, insertion sequences, and CRISPR-Cas sequence analyses were also carried out to gain insight into genetic components and defensive mechanisms within the bacterial genome.

RESULTS

The 3.4 Mb genome of L. plantarum 12-3, was assembled with 99.1% completeness and low contamination. A total of 3234 genes with normal length and intergenic spacing were found using gene prediction tools. Pan-genomic studies demonstrated gene diversity and provided functional annotation, whereas phylogenetic analysis verified taxonomic identity. Our food safety study revealed a profile of antibiotic resistance that is favorable for use as a probiotic. Analysis of insertional sequences, genomic islands, and prophage within the genome provided information regarding genetic components and their possible effects on evolution.

CONCLUSIONS

Pivotal genetic elements uncovered in this study play a crucial role in bacterial defense mechanisms and offer intriguing prospects for future genome engineering efforts. Moreover, our findings suggest further in vitro and in vivo studies are warranted to validate the functional attributes and probiotic potential of L. plantarum 12-3. Expanding the scope of the research to encompass a broader range of L. plantarum 12-3 strains and comparative analyses with other probiotic species would enhance our understanding of this organism's genetic diversity and functional properties.

Review of reinforcement learning applications in segmentation, chemotherapy, and radiotherapy of cancer

Owing to early diagnosis and treatment of cancer as a prerequisite in recent times, the role of machine learning has been increased substantially. The mathematically powerful and optimized solutions for the detection and cure of cancer are constantly being explored and novel models based upon standard algorithms are also being developed. Leveraging one such solution is Reinforcement Learning (RL), which is a semi-supervised type of learning. The paper presents a detailed discussion on the various RL techniques, algorithms, and open issues, in addition to the review of literature for diagnosis and treatment of cancer. A smaller number of publications for diagnosis and treatment of cancer have been reported before 2011 but now after the success of Deep Learning (DL) and the advent of Deep Reinforcement Learning (DRL), the publications have grown in number from 2017 onwards. The scope of RL for cancer diagnosis and treatment is also demystified and provides the research community with the insights of how to formulate RL problem as a Cancer diagnostic problem. RL has been found successful for landmark detection in medical images and optimal control of drugs and radiations.

Image-guided Interstitial Brachytherapy in the Treatment of Primary and Recurrent Vulvovaginal Gynaecological Malignancies

AIMS

To evaluate the use, outcomes and toxicities of high dose rate brachytherapy (HDRB) to the vulvovaginal region in previously irradiated and radiotherapy-naïve patients for primary or recurrent gynaecological malignancies.

MATERIALS AND METHODS

From January 2010 to December 2020, 94 women with a median age of 64 years (range 31-88 years) were treated with interstitial HDRB for vulvovaginal disease. Treatment details, including cumulative radiotherapy doses, were recorded together with reported toxicity, using Common Terminology Criteria for Adverse Events (CTCAE) grading. Dosimetric parameters, including D90, V100 and V150 together with treatment response at 3 months, overall survival, relapse-free survival and long-term toxicity data, were collated from referring centres.

RESULTS

The median follow-up was 78 months (range 2-301). Primary sites of disease included vagina (37), endometrium (29), vulva (16), ovary (7) and cervix (5). Eighty-six (91.5%) patients were treated with curative intent, eight (8.5%) were palliative treatments. Fifty patients received HDRB for recurrent disease, 39 patients for primary disease and five as part of adjuvant treatment. The anatomical site of disease treated with HDRB ranged from vagina (76), vulva (14) and peri-urethral sites (four). The 2- and 5-year local relapse-free survival rates were 76% and 72%, respectively; 15 patients experienced local failure only, whereas six patients had local and nodal/distant failure. The median time to local recurrence was 8 months (range 2-88 months). The 2- and 5-year overall survival rates for all patients were 67% and 47%, respectively; the median overall survival was 59 months. Seventy-nine (84%) patients had a complete response measured with imaging at 3 months. Grade 3 toxicity was reported in 14 patients (14.8%).

CONCLUSION

This retrospective series suggests the use of interstitial brachytherapy for vulvovaginal gynaecological malignancy to be an effective and safe treatment option. Good local control was achieved with a tolerable toxicity profile; it is a valuable treatment modality.

Immobilization of Aspergillus oryzae tyrosine hydroxylase on ZnO nanocrystals for improved stability and catalytic efficiency towards L-dopa production

The current study focuses on the submerged fermentation of tyrosine hydroxylase (TH) from Aspergillus oryzae IIB-9 and its immobilization on zinc oxide nanocrystals (ZnO-NPs) for increased L-dopa production. The volume of Vogel's medium (75 ml), period of incubation (72 h), initial pH (5.5), and size of inoculum (1.5 ml) were optimal for maximum TH activity. The watch glass-dried (WG) and filter paper-dried (FP) ZnO-NPs were prepared and characterized using analytical techniques. The UV-Vis spectra revealed 295 and 285 nm absorption peaks for WG-ZnO-NPs and FP-ZnO-NPs dispersed in isopropanol. X-ray diffraction analysis confirmed the crystalline nature of ZnO-NPs. FTIR spectra band from 740 to 648.1/cm and 735.8/cm to 650.1/cm showed the stretching vibrations of WG-ZnO-NPs and FP-ZnO-NPs, respectively. The particle size of ZnO-NPs observed by scanning electron microscopy (SEM) images was between 130 and 170 nm. Furthermore, the stability of immobilized TH on ZnO-NPs was determined by varying the incubation period (10 min for WG-NPs and 15 min for FP-NPs) and temperature (45 °C and 30 °C for WG and FP-NPs, respectively). Incubating enzymes with various copper, iron, manganese, and zinc salts studied the catalytic efficiency of TH. Immobilization of TH on ZnO-NPs resulted in an 11.05-fold increase in TH activity, thus enhancing stability and catalytic efficiency.

Rainwater harvesting for agriculture development using multi-influence factor and fuzzy overlay techniques

Rainwater harvesting (RWH) is an essential technique for enhancing agricultural development, particularly in regions facing water scarcity or unreliable rainfall patterns. Water shortage, however, is one of the key causes of low crop production especially in mountainous regions like the Khyber Pakhtunkhwa province where most rainwater is lost by runoff. Therefore, rainwater harvesting could be a suitable to make better use of runoff and increase crop production. The study focuses on selecting suitable rainwater harvesting sites in District Karak to enhance agriculture by utilizing multi-influence factor (MIF) and fuzzy overlay techniques. We considered seven factors, i.e., land use land cover (LULC), slope, geology, soil, rainfall, lineament, drainage density, to create a ranking system to understand its application in site selection analysis. The results were combined into one overlay process to produce a rainwater harvesting suitability map. The weighted overlay analysis of the MIF model results reveals that 167.96 km2 area has a very high potential for rainwater harvesting, 874.17 km2 has a high potential, 1182.92 km2 has a moderate and 354.50 km2 has a poor potential for rainwater harvesting. The fuzzy overlay analysis revealed that 257.53 km2 has a very high potential for rainwater harvesting, 896.56 km2 area is classified as high, 1018.30 km2 moderate, and 407.7 km2 has poor potential for rainwater harvesting. The findings of this research work will help the policymakers and decision-makers construct various rainwater harvesting structures in the study area to overcome the water shortage problems.

Influence of quercetin on amiodarone pharmacokinetics and biodistribution in rats

OBJECTIVE

Amiodarone (AMD), a drug of choice to treat cardiac arrhythmias, has a narrow therapeutic index (NTI). It inhibits CYP3A4, CYP2C9, and CYP2D6 enzymes. Quercetin (QUE), a pharmacologically important bioflavonoid in vegetables and fruits, is important in treating cardiovascular comorbidities. QUE alters the bioavailability of drugs used concurrently by dual inhibition of P-glycoproteins (P-gp) and cytochrome (CYP) enzyme systems. The current study aimed to investigate the pre-treatment and co-administration effect of QUE on AMD pharmacokinetics in rats.

MATERIALS AND METHODS

Two separate animal trials (I and II) were planned to probe the effect of QUE on AMD pharmacokinetics by following previously cited studies. The pre-treatment group received oral doses of QUE for 14 days, and a single dose of AMD on the 15th day. Rats were administered single doses of QUE (20 mg/kg) and AMD (50 mg/kg) concurrently in a carboxymethylcellulose (CMC) in the co-administration study. Blood was collected at pre-determined time points. AMD was quantified by HPLC, and data was analyzed by PK solver software.

RESULTS

In the pre-treated group, peak plasma concentration (Cmax) and area under the curve (AUC0-∞) of AMD were increased by 45.52% and 13.70%, respectively, while time to achieve maximum concentration (tmax), half-life (t1/2) and clearance (CL) were declined by 35.72%, 16.75%, and 11.0% respectively compared to the control. In the co-administered group, compared to controls, Cmax and AUC0-∞ were elevated to 12.90% and 7.80%, respectively, while tmax, t1/2, and CL declined by 16.70%, 2.35%, and 13.40%. Further, AMD was increased in lung tissue of both treated groups, relative to the respective controls.

CONCLUSIONS

A notable pharmacokinetic drug interaction between QUE and AMD was observed in rats and warrants possible drug interaction study in humans, suggesting AMD dose adjustment specifically in patients with arrhythmia having a pre-treatment history and simultaneous administration of QUE-containing products.

Purification of Galacto-oligosaccharide (GOS) by fermentation with Kluyveromyces lactis and Interaction between GOS and casein under simulated acidic fermentation conditions

In the enzymatic synthesis of galacto-oligosaccharide (GOS), the primary by-products include glucose, galactose and unreacted lactose. This This study was aimed to provide a method to to purify GOS by yeat fermentation and explore the interaction between GOS and CAS with a view for expanding the prospects of GOS application in the food industry. The crude GOS(25.70 g/L) was purified in this study using the fermentation method with Kluyveromyces lactis CICC 1773. Optimal conditions for purification with the yeast were 75 g/L of the yeast inoculation rate and 50 g/L of the initial crude GOS concentration for 12 h of incubation. After removing ethanol produced by yeast by low-temperature distillation, GOS content could reach 90.17%. A study of the interaction between GOS and casein (CAS) in a simulated acidic fermentation system by D-(+)-gluconic acid δ-lactone (GDL) showed that the GOS/CAS complexes with higher GOS concentrations, e.g., 4% and 6% (w/v), was more viscoelastic with higher water-holding capacity, but decreased hardness, elasticity, and cohesiveness at 6% (w/v) of GOS. The addition of GOS to CAS suspension significantly caused (p<0.05) decreased particle sizes of the formed GOS/CAS complexes, and the suspension system became more stable. FT-IR spectra confirmed the existence of different forms of molecular interactions between CAS and GOS, e.g., hydrogen bonding and hydrophobic interaction, and the change of secondary structure after CAS binding to GOS.

Recent developments in cervical cancer diagnosis using deep learning on whole slide images: An Overview of models, techniques, challenges and future directions

Integration of whole slide imaging (WSI) and deep learning technology has led to significant improvements in the screening and diagnosis of cervical cancer. WSI enables the examination of all cells on a slide simultaneously and deep learning algorithms can accurately label them as cancerous or non-cancerous. Although many studies have investigated the application of deep learning for diagnosing various diseases, there is a lack of research focusing on the evolution, limitations, and gaps of intelligent algorithms in conjunction with WSI for cervical cancer. This paper provides a comprehensive overview of the state-of-the-art deep learning algorithms used for the timely and precise analysis of cervical WSI images. A total of 115 relevant papers were reviewed, and 37 were selected after screening with specific inclusion and exclusion criteria. Methodological aspects including deep learning techniques, data sources, architectures, and classification techniques employed by the selected studies were analyzed. The review presents the most popular techniques and current trends in deep learning-based cervical classification systems, and categorizes the evolution of the domain based on deep learning techniques, citing an in-depth analysis of various models developed over time. The paper advocates for the implementation of transfer supervised learning when utilizing deep learning models such as ResNet, VGG19, and EfficientNet, and builds a solid foundation for applying relevant techniques in different fields. Although some progress has been made in developing novel models for the diagnosis of cervical cancer, substantial work remains to be done in creating standardized benchmark databases of WSI images for the research community. This paper serves as a comprehensive guide for understanding the fundamental concepts, benefits, and challenges related to various deep learning models on WSI, including their application for cervical system classification. Additionally, it provides valuable insights into future research directions in this area.

Scrutinizing the therapeutic response of Phyllanthus exmblica's different doses to restore the immunomodulation potential in immunosuppressed female albino rats

OBJECTIVE

Immunosuppression and microbial resistance are the major drawbacks in conventional pharmaceutics. The present research work was planned to screen and characterize phytochemical constituents present in Phyllanthus emblica and to explore the immunomodulation potential of P. emblica by evaluating stress markers and different biochemical parameters in animals.

MATERIALS AND METHODS

The phytochemical analysis explored the presence of antioxidant profiles and revealed the radical scavenging activities. In the second phase, an animal trial was performed using female albino rats. Female rats (n=18) were administered three different doses of P. emblica (low dose 100 mg/kg, intermediate 200 mg/kg, and high dose 300 mg/kg) for three weeks. After a significant change (p<0.05) in antioxidant status i.e., TOS and TAS, hematological, biochemical parameters, and immunoregulation i.e., IgM and IgG were elevated. Statistical analysis (ANOVA) illustrates that these selected plants have a great impact on microbial resistance and immunosuppression and have shown highly significant results.

RESULTS

The results of all in vitro and in vivo assays conducted as part of the recent research work offer considerable evidence that the chosen medicinal plant has the ability to induce specific hormone release and boost the immune system.

CONCLUSIONS

Based on our findings, it is proposed that medicinal herbs may be isolated using cutting-edge approaches to tackle the issues of immunosuppression and microbial resistance.

Assessing the probiotic potential, antioxidant, and antibacterial activities of oat and soy milk fermented with Lactiplantibacillus plantarum strains isolated from Tibetan Kefir

Sufficient intake of probiotics has been shown to help in the digestion, protect the body against pathogenic microorganisms and boost the immune system. Recently, due to high prevalence of milk allergies and lactose intolerance in population, the non-dairy based probiotic alternative are becoming increasing popular. In this context, the oat milk and soya milk-based fermented products can be an ideal alternative for the development of Lactic acid bacteria bacteria based probiotics. These bacteria can not only improve the product's flavor and bioavailability but also increases its antibacterial and antioxidant capabilities due to fermentation process. The purpose of the resent work was to assess the antioxidant and probiotic properties of oat and soy milk that had been fermented with three different strains of Lactiplantibacillus plantarum (L. plantarum) including L. plantarum 12-3, L. plantarum K25, and L. plantarum YW11 isolated from Tibetan Kefir. Different validated assays were used to evaluate the probiotic properties, adhesion and survival in the digestive system (stomach, acid and bile salts resistance), antioxidant and antimicrobial activities and safety (ABTS and DPPH scavenging assays) of these strains. Results of the study showed that soya milk and oat milk fermented with L. plantarum strains possess promising probiotic, antibacterial and antioxidant properties. These results can be helpful to produce dairy-free probiotic replacements, which are beneficial for those who are unable to consume dairy products due to dietary or allergic restrictions.

Investigation of VEGF (rs 699947) polymorphism in the progression of Rheumatoid Arthritis (RA) and in-silico nanoparticle drug delivery of potential phytochemicals to cure RA

Mutation in the VEGF gene disturbs the production of chondrocytes and angiogenesis which are essential for cartilage health. Cytokines and chemokines produced by auto-activation of B-cells degrade cartilage. Bruton's Tyrosine Kinase (BTK) plays a crucial role in the activation of these B-cells. VEGF has a central part in angiogenesis, in the recruitment of endothelial cells, and is involved in mechanisms that result in tumour formation. The objective of this research is to investigate the potential role of VEGF polymorphism in the development of Rheumatoid Arthritis (RA) and the screening of potential natural, synthetic BTK inhibitor compounds as possible in-silico chemotherapeutic agents to control auto-activation of B-cells and cartilage degrading cytokines. In this study, it had been shown that allele A frequency was significantly higher than that of allele C in RA-positive patients as compared to controls. Hence it depicts that allele A of VEGF (rs699947) can increase the risk of RA while allele C has a protective role. The phytochemicals which showed maximum binding affinity at the inhibitory site of BTK include beta boswellic acid, tanshinone, and baicalin. These phytochemicals as BTK inhibitor give insights to use them as anti-arthritic compounds by nanoparticle drug delivery mechanism.

Enhancement of shelf-life of food items via immobilized enzyme nanoparticles on varied supports. A sustainable approach towards food safety and sustainability

This study was designed to extend the shelf life of fruits and vegetables through a novel technique based on utilization of microbially driven enzyme glucose oxidase and casting a fine layer of hydrogen peroxide on the food item that protected the fruit from decay. The produced nanoparticles (ZnO, Ag) were ligated with Glucose Oxidize (GOx) purified from Aspergillus niger. Post ligation studies revealed that ligated enzymes display relatively enhanced activity. Four types of sprays were prepared in order to compare their effectiveness. Glucose oxidase/silver nanoparticles (GOx/AgNPs), glucose oxidase/zinc oxide nanoparticles (GOx/ZnONPs), AgNPs and ZnONPs sprays were applied to guava fruit samples as post-harvest therapeutic agents for a period of 15 days. Fruit quality parameters such as total suspended solids (TSS), pH, weight loss, DPPH free radical capturing performance and firmness confirms that usage of the bioconjugates especially that of GOx/ZnONP was curiously active to maintain the physical appearance of fruit well along with no such deterioration in chemical composition of fruit. Consequently, enzymes ligated on the surface of nanoparticles (ZnONP) are exceptional for extension of post-harvest shelf life of fruits such as guava.

Evaluating the influence of Aloe barbadensis extracts on edema induced changes in C-reactive protein and interleukin-6 in albino rats through in vivo and in silico approaches

The current study investigated the in-vivo and in-silico anti-inflammatory effect of Aloe barbadensis in edema induced rat and its blood biomarkers. 60 albino rats (160-200 g) were divided into 4 groups. The 1st group (control) comprised of 6 rats that were treated with saline. The 2nd group (standard) comprised of 6 rats that were treated with diclofenac. The 3rd and 4th experimental groups consisted of 48 rats, treated with A. barbadensis gel ethanolic and aqueous extracts respectively at doses of 50, 100, 200 and 400 mg/kg. According to paw sizes, groups III and IV showed 51% and 46% inhibition respectively at the 5th hour, as compared to group II with 61% inhibition. Correlation was negative between biomarkers in group III, while, positive in group IV. Blood samples were collected; C-reactive protein and interleukin-6 were measured using commercially available ELISA kits. Similarly, biomarkers showed significant effect in dose-dependent manner. In molecular docking, for CRP both ligands aloe emodin and emodin showed -7.5 kcal/mol binding energy as compared to diclofenac with -7.0 kcal/mol. For IL-1beta, both ligands showed -4.7 kcal/mol binding energy as compared to diclofenac -4.4 kcal/mol. Hence, we concluded that A. barbadensis extracts can be used as an effective drug for managing inflammation.

Comparative genomics of food-derived probiotic Lactiplantibacillus plantarum K25 reveals its hidden potential, compactness, and efficiency

This study aimed to investigate the intricate genetic makeup of the Lactiplantibacillus plantarum K25 strain by conducting a comprehensive analysis of comparative genomics. The results of our study demonstrate that the genome exhibits a high-level efficiency and compactness, comprising a total of 3,199 genes that encode proteins and a GC content of 43.38%. The present study elucidates the evolutionary lineage of Lactiplantibacillus plantarum strains through an analysis of the degree of gene order conservation and synteny across a range of strains, thereby underscoring their closely interrelated evolutionary trajectories. The identification of various genetic components in the K25 strain, such as bacteriocin gene clusters and prophage regions, highlights its potential utility in diverse domains, such as biotechnology and medicine. The distinctive genetic elements possess the potential to unveil innovative therapeutic and biotechnological remedies in future. This study provides a comprehensive analysis of the L. plantarum K25 strain, revealing its remarkable genomic potential and presenting novel prospects for utilizing its unique genetic features in diverse scientific fields. The present study contributes to the existing literature on Lactiplantibacillus plantarum and sets the stage for prospective investigations and practical implementations that leverage the exceptional genetic characteristics of this adap organism.

Isolation and characterization of indigenous bacterial assemblage for biodegradation of persistent herbicides in the soil

Extensive pesticides (herbicides) use is negatively disturbing the environment and humans. Pesticide bioremediation with eco-friendly techniques bears prime importance. This study aimed to isolate and characterize three different herbicides (metribuzin, clodinafop- propargyl, MCPA (2-methyl, 4 chlorophenoxyacetic acids) and Bromoxynil) degrading bacterial strains from agricultural fields of Punjab University, Pakistan. Among the 12 bacterial isolates, 5 were metribuzin degrading, 3 were clodinafop propargyl degrading and, 4 were MCPA and Bromoxynil degrading bacteria. Morphological, microscopic, and molecular characterization revealed that the majority of these bacterial strains were gram-negative and belonged to Bacillus and Pseudomonas genera. The isolates A6, B3, and C1 were subjected to respective herbicide degradation and the data was confirmed through GC-MS analysis. The effect of herbicide concentrations, pH, and temperature on bacterial growth was determined at OD600. The strain A6 degraded 14.8% metribuzin out of the provided concentration of 50 ppm by following the deamination pathway. While the isolates B3 and C1 degraded 23.2% and 33.9% clodinafop, MCPA and bromo-xynil, respectively, at a spiking concentration of 50ppm. The clodinafop, MCPA and Bromoxynil were metabolized into less toxic products i.e., dicarboxylic acids and 2-methyl phenol respectively, and metabolized via decarboxylation and dehalogenation mechanism. The present study evaluates the herbicides degrading bacterial strains that could potentially be used for bioremediation of agricultural contaminated sites.

Particle Nanoarchitectonics for Nanomedicine and Nanotherapeutic Drugs with Special Emphasis on Nasal Drugs and Aging

Aging is a multifunctional physiological manifestation. The nasal cavity is considered a major site for easy and cost-effective drug and vaccine administration, due to high permeability, low enzymatic activity, and the presence of a high number of immunocompetent cells. This review article primarily focuses on aging genetics, physical parameters, and the use of nanoparticles as delivery systems of drugs and vaccines via the nasal cavity. Studies have identified various genes involved in centenarian and average-aged people. VEGF is a key mediator involved in angiogenesis. Different therapeutic approaches induce vascular function and angiogenesis. FOLR1 gene codes for folate receptor alpha protein that helps in regulating the transport of vitamin B folate, 5-methyltetrahydrofolate and folate analogs inside the cell. This gene also aids in slowing the aging process down by cellular regeneration and promotes healthy aging by reducing aging symptoms. It has been found through the literature that GATA 6, Yamanaka factors, and FOLR1 work in synchronization to induce healthy and delayed aging. The role and applications of genes including CBS, CISD, SIRT 1, and SIRT 6 play a significant role in aging.

Myogenesis and Analysis of Antimicrobial Potential of Silver Nanoparticles (AgNPs) against Pathogenic Bacteria

The widespread and indiscriminate use of broad-spectrum antibiotics leads to microbial resistance, which causes major problems in the treatment of infectious diseases. However, advances in nanotechnology have opened up new domains for the synthesis and use of nanoparticles against multidrug-resistant pathogens. The traditional approaches for nanoparticle synthesis are not only expensive, laborious, and hazardous but also have various limitations. Therefore, new biological approaches are being designed to synthesize economical and environmentally friendly nanoparticles with enhanced antimicrobial activity. The current study focuses on the isolation, identification, and screening of metallotolerant fungal strains for the production of silver nanoparticles, using antimicrobial activity analysis and the characterization of biologically synthesized silver nanoparticles by X-ray diffraction (XRD) spectroscopy, energy-dispersive X-ray spectroscopy (EDX), and scanning electron microscopy (SEM). In total, 11 fungal isolates were isolated and screened for the synthesis of AgNPs, while the Penicillium notatum (K1) strain was found to be the most potent, demonstrating biosynthetic ability. The biologically synthesized silver nanoparticles showed excellent antibacterial activity against the bacteria Escherichia coli (ATCC10536), Bacillus subtilis, Staphylococcus aureus (ATCC9144), Pseudomonas aeruginosa (ATCC10145), Enterococcus faecalis, and Listeria innocua (ATCC13932). Furthermore, three major diffraction peaks in the XRD characterization, located at the 2θ values of 28.4, 34.8, 38.2, 44, 64, and 77°, confirmed the presence of AgNPs, while elemental composition analysis via EDX and spherical surface topology with a scanning electron microscope indicated that its pure crystalline nature was entirely composed of silver. Thus, the current study indicates the enhanced antibacterial capability of mycologically synthesized AgNPs, which could be used to counter multidrug-resistant pathogens.

Genome Investigation and Functional Annotation of Lactiplantibacillus plantarum YW11 Revealing Streptin and Ruminococcin-A as Potent Nutritive Bacteriocins against Gut Symbiotic Pathogens

All nutrient-rich feed and food environments, as well as animal and human mucosae, include lactic acid bacteria known as Lactobacillus plantarum. This study reveals an advanced analysis to study the interaction of probiotics with the gastrointestinal environment, irritable bowel disease, and immune responses along with the analysis of the secondary metabolites’ characteristics of Lp YW11. Whole genome sequencing of Lp YW11 revealed 2297 genes and 1078 functional categories of which 223 relate to carbohydrate metabolism, 21 against stress response, and the remaining 834 are involved in different cellular and metabolic pathways. Moreover, it was found that Lp YW11 consists of carbohydrate-active enzymes, which mainly contribute to 37 glycoside hydrolase and 28 glycosyltransferase enzyme coding genes. The probiotics obtained from the BACTIBASE database (streptin and Ruminococcin-A bacteriocins) were docked with virulent proteins (cdt, spvB, stxB, and ymt) of Salmonella, Shigella, Campylobacter, and Yersinia, respectively. These bacteria are the main pathogenic gut microbes that play a key role in causing various gastrointestinal diseases. The molecular docking, dynamics, and immune simulation analysis in this study predicted streptin and Ruminococcin-A as potent nutritive bacteriocins against gut symbiotic pathogens.

Integrated genome based evaluation of safety and probiotic characteristics of Lactiplantibacillus plantarum YW11 isolated from Tibetan kefir

The comparative genomic analysis of Lactiplantibacillus plantarum YW11 (L. plantarum YW11) isolated from Tibetan kefir involves comparison of the complete genome sequences of the isolated strain with other closely related L. plantarum strains. This type of analysis can be used to identify the genetic diversity among strains and to explore the genetic characteristics of the YW11 strain. The genome of L. plantarum YW11 was found to be composed of a circular single chromosome of 4,597,470 bp with a G + C content of 43.2%. A total of 4,278 open reading frames (ORFs) were identified in the genome and the coding density was found to be 87.8%. A comparative genomic analysis was conducted using two other L. plantarum strains, L. plantarum C11 and L. plantarum LMG21703. Genomic comparison revealed that L. plantarum YW11 shared 72.7 and 75.2% of gene content with L. plantarum C11 and L. plantarum LMG21703, respectively. Most of the genes shared between the three L. plantarum strains were involved in carbohydrate metabolism, energy production and conversion, amino acid metabolism, and transcription. In this analysis, 10 previously sequenced entire genomes of the species were compared using an in-silico technique to discover genomic divergence in genes linked with carbohydrate intake and their potential adaptations to distinct human intestinal environments. The subspecies pan-genome was open, which correlated with its extraordinary capacity to colonize several environments. Phylogenetic analysis revealed that the novel genomes were homogenously grouped among subspecies of l Lactiplantibacillus. L. plantarum was resistant to cefoxitin, erythromycin, and metronidazole, inhibited pathogens including Listeria monocytogenes, Clostridium difficile, Vibrio cholera, and others, and had excellent aerotolerance, which is useful for industrial operations. The comparative genomic analysis of L. plantarum YW11 isolated from Tibetan kefir can provide insights into the genetic characteristics of the strain, which can be used to further understand its role in the production of kefir.

On-Site Application of Solar-Activated Membrane (Cr-Mn-Doped TiO2@Graphene Oxide) for the Rapid Degradation of Toxic Textile Effluents

Solar-activated water treatment has become an emerging research field due to its eco-friendly nature and the economic feasibility of green photocatalysis. Herein, we synthesized promising, cost-effective, and ultralong-semiconductor TiO₂ nanowires (NW), with the aim to degrade toxic azo dyes. The band gap of TiO₂ NW was tuned through transition metals, i.e., chromium (Cr) and manganese (Mn), and narrowed by conjugation with high surface area graphene oxide (GO) sheets. Cr-Mn-doped TiO₂ NWs were chemically grafted onto GO nanosheets and polymerized with sodium alginate to form a mesh network with an excellent band gap (2.6 eV), making it most suitable to act as a solar photocatalytic membrane. Cr-Mn-doped TiO₂ NW @GO aerogels possess high purity and crystallinity confirmed by Energy Dispersive X-ray spectroscopy and X-ray diffraction pattern. A Cr-Mn-doped TiO₂ NW @GO aerogels membrane was tested for the photodegradation of Acid Black 1 (AB 1) dye. The synthesized photocatalytic membrane in the solar photocatalytic reactor at conditions optimized by response surface methodology (statistical model) and upon exposure to solar radiation (within 180 min) degraded 100% (1.44 kg/m³/day) AB 1dye into simpler hydrocarbons, confirmed by the disappearance of dye color and Fourier transform infrared spectroscopy. An 80% reduction in water quality parameters defines Cr-Mn-doped TiO₂ NW @GO aerogels as a potential photocatalytic membrane to degrade highly toxic pollutants.

Functional Annotation of Lactiplantibacillus plantarum 13-3 as a Potential Starter Probiotic Involved in the Food Safety of Fermented Products

The important role of Lactiplantibacillus plantarum strains in improving the human mucosal and systemic immunity, preventing non-steroidal anti-provocative drug-induced reduction in T-regulatory cells, and as probiotic starter cultures in food processing has motivated in-depth molecular and genomic research of these strains. The current study, building on this research concept, reveals the importance of Lactiplantibacillus plantarum 13-3 as a potential probiotic and bacteriocin-producing strain that helps in improving the condition of the human digestive system and thus enhances the immunity of the living beings via various extracellular proteins and exopolysaccharides. We have assessed the stability and quality of the L. plantarum 13-3 genome through de novo assembly and annotation through FAST-QC and RAST, respectively. The probiotic-producing components, secondary metabolites, phage prediction sites, pathogenicity and carbohydrate-producing enzymes in the genome of L. plantarum 13-3 have also been analyzed computationally. This study reveals that L. plantarum 13-3 is nonpathogenic with 218 subsystems and 32,918 qualities and five classes of sugars with several important functions. Two phage hit sites have been identified in the strain. Cyclic lactone autoinducer, terpenes, T3PKS, and RiPP-like gene clusters have also been identified in the strain evidencing its role in food processing. Combined, the non-pathogenicity and the food-processing ability of this strain have rendered this strain industrially important. The subsystem and qualities characterization provides a starting point to investigate the strain’s healthcare-related applications as well.

Effect of Chilled Storage on Antioxidant Capacities and Volatile Flavors of Synbiotic Yogurt Made with Probiotic Yeast Saccharomyces boulardii CNCM I-745 in Combination with Inulin

Fermentation of available sugars in milk by yogurt starter culture initially and later by Saccharomyces boulardii (Probiotic yeast) improves the bioavailability of nutrients and produces bioactive substances and volatile compounds that enhance consumer acceptability. The combination of S. boulardii, a unique species of probiotic yeast, and inulin, an exopolysaccharide used as a prebiotic, showed remarkable probiotic and hydrocolloid properties in dairy products. The present study was designed to study the effect of fermentation and storage on antioxidant and volatile capacities of probiotic and synbiotic yogurt by incorporation of S. boulardii and inulin at 1%, 1.5%, and 2% (w/v), compared with the probiotic and control plain yogurt. All samples were stored at 4 °C, and during these four weeks, they were analyzed in terms of their antioxidant and volatile compounds. The synbiotic yogurt samples having inulin and S. boulardii displayed significantly higher DPPH (2,2-diphenyl-1-picrylhydrazyl) free radical activity values and more values of TPC (total phenol contents) than control plain yogurt. A total of 16 volatile compounds were identified in S5-syn2 and S4-syn1.5, while S3-syn1 and S2-P had 14, compared with the control S1-C plain yogurt samples, which had only 6. The number of volatile compounds increased with the increasing concentration of inulin throughout the storage period. Therefore, this novel synbiotic yogurt with higher antioxidant and volatile compounds, even with chilling storage conditions, will be a good choice for consumer acceptability.

Cytogenetic abnormalities in patients with hematological malignancies in Lahore city, Pakistan

Hematological and hematopoietic cells malignancies of the genes and hematopoietic cells are associated with the genetic mutation, often at the chromosomal level. The standard cytogenetic study is widely accepted as one of the main diagnostics and prognostic determinants in patients. Therefore, the current descriptive and cross-sectional study sought to determine the cytogenetic analysis of frequent hematological malignancies in Pakistan. A total of 202 peripheral bone marrow or blood samples from patients with benign and malignant hematological malignancy were taken using a conventional G-banding technique. Among enrolled patients, the mean age was 21.5 years ± 23.4, and gender-wise distribution showed a marked predominance of the male 147 (73%) population compared to the female 55 (27%). Patients in the age group (2-10 years) had the highest frequency, 48 (24%), of hematological neoplasms, followed by age (11-20 years) with 40 (20%). Normal karyotypes (46, XX/46, XY) was found in 51% (n=103) patients. Furthermore, the frequency of complex karyotype was 30 (15%), while normal was seen in 171 (85%) patients. Pre-B Acute Lymphoblastic Leukemia (Pre-B ALL) was the most prevalent malignancy of 66 (33%), followed by Chronic Myelogenous Leukemia (CML) of 41 (20%) and Acute Lymphocytic Leukemia of 29 (14%). Translocation was the most prevalent 50 (25%), followed by hypotriploidy 14 (7%) and monosomy 8 (4%) on chromosome aberration analysis. In addition, t(9:22) translocation was found to be 20 (10%) in CML, with the majority in the age group (31-40 years). This study recommends that karyotyping should be tested frequently in hematological conditions because it may provide insight into the relative chromosomal changes associated with particular malignancies.

Antioxidant Activity of Novel Casein-Derived Peptides with Microbial Proteases as Characterized via Keap1-Nrf2 Pathway in HepG2 Cells

Casein-derived antioxidant peptides by using microbial proteases have gained increasing attention. Combination of two microbial proteases, Protin SD-NY10 and Protease A "Amano" 2SD, was employed to hydrolyze casein to obtain potential antioxidant peptides that were identified by LCMS/ MS, chemically synthesized and characterized in a oxidatively damaged HepG2 cell model. Four peptides, YQLD, FSDIPNPIGSEN, FSDIPNPIGSE, YFYP were found to possess high 1,1-diphenyl-2-picrylhydrazyl (DPPH) scavenging ability. Evaluation with HepG2 cells showed that the 4 peptides at low concentrations (< 1.0 mg/ml) protected the cells against oxidative damage. The 4 peptides exhibited different levels of antioxidant activity by stimulating mRNA and protein expression of the antioxidant enzymes such as superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GSH-Px), as well as nuclear factor erythroid-2-related factor 2 (Nrf2), but decreasing the mRNA expression of Kelch-like ECH-associated protein 1 (Keap1). Furthermore, these peptides decreased production of reactive oxygen species (ROS) and malondialdehyde (MDA), but increased glutathione (GSH) production in HepG2 cells. Therefore, the 4 casein-derived peptides obtained by using microbial proteases exhibited different antioxidant activity by activating the Keap1-Nrf2 signaling pathway, and they could serve as potential antioxidant agents in functional foods or pharmaceutic preparation.

Biotransformation of linoleic acid into different metabolites by food derived Lactobacillus plantarum 12-3 and in silico characterization of relevant reactions

Lactic acid bacteria have been reported to be capable of converting polyunsaturated fatty acids, e.g. linoleic acid (LA) into bioactive and other fatty acid metabolites that are not toxic to the bacteria themselves, but the mechanism of this conversion is not clear. Here we reported for the first time that probiotic L. plantarum 12-3 derived from Tibet kefir when supplemented with LA from 1% to 10% in the MRS medium transformed LA to various fatty acid derivatives. These derivatives formed in the medium were identified with gas chromatography and mass spectrometry. In silico studies were done to confirm the enzymatic reactions responsible for this conversion. We found that L. plantarum 12-3 could convert LA at different concentrations to 8 different fatty acid derivatives. Putative candidate enzymes involved in biotransformation of LA into fatty acid derivatives were identified via whole genome of L. plantarum 12-3, including linoleate isomerase, acetoacetate decarboxylase and dehydrogenase. Therefore, the present study provides further understanding of the mechanism of conversion of LA to health-beneficial fatty acid metabolites in probiotic L. plantarum, which can be explored for potential application in functional foods.

Antiadhesion and antibiofilm potential of Fagonia indica from Cholistan desert against clinical multidrug resistant bacteria

High resistance to antimicrobials is associated with biofilm formation responsible for infectious microbes to withstand severe conditions. Therefore, new alternatives are necessary as biofilm inhibitors to control infections. In this study, the antimicrobial and antibiofilm activities of Fagonia indica extracts were evaluated against MDR clinical isolates. The extract exhibited its antibiofilm effect by altering adherence and disintegration of bacterial cell wall. Fagonia indica has antibacterial effect as minimum inhibitory concentration (MIC) values ranging from 125 to 500 µg mL-1 and minimum bactericidal concentration (MBC) value was 500-3000 µg mL-1 against multidrug resistant (MDR) clinical isolates. The extract exhibited its antibiofilm effect by altering adherence and disintegration of bacterial cell wall. Fagonia indica had antibacterial effect as minimum inhibitory concentration (MIC) values ranging from 125 to 500 µg mL-1 and minimum bactericidal concentration (MBC) value was 500-3000 µg mL-1 against MDR isolates. The maximum inhibitory effects of Fagonia indica chloroform extract on biofilm formation was observed on Staphylococcus aureus (71.84%) followed by Klebsiella pneumoniae (70.83%) after 48 hrs showing that inhibition is also time dependent. Our results about bacterial cell protein leakage indicated that MDR isolates treated with chloroform extract of Fagonia indica showed maximum protein leakage of K. pneumoniae (59.14 µg mL-1) followed by S. aureus (56.7 µg mL-1). Cell attachment assays indicated that chloroform extract resulted in a 43.5-53.5% inhibition of cell adherence to a polystyrene surface. Our results revealed that extracts of Fagonia indica significantly inhibited biofilm formation among MDR clinical isolates, therefore, could be applied as antimicrobial agents and cost effective biofilm inhibitor against these MDR isolates.

Separation of Storage Proteins (7S and 11S) from Soybean Seed, Meals and Protein Isolate Using an Optimized Method Via Comparison of Yield and Purity

The primary purpose of this study was to extract β-conglycinin (7S) and glycinin (11S) from soybean seed, soybean meals and soybean protein isolate and compare their yield and purity. The previous methods were modified for the extraction and isolation of 7S and 11S globulins. The adjustment mainly included sample to solution ratio of 1:10 (previously 1:15). Comparing the yield of 11S fraction in Tris-HCl and water as extractable solutions, it was almost doubled in soybean seed (16.97% to 32.41%) with purity from 96 to 98% respectively. In case of soybean meal, samples yield increased from 45.46 to 61.86% with purity from 94 to 98%. On contrary, 7S yield was significantly improved in soybean protein isolate sample from 30.33 to 53.81% along with no contamination in its purity while soybean seed and soybean meal samples had less increase in both yield and purity in Tris-HCl and water as extractable solutions. Results of this study will bring new insights into soybean 7S and 11S separation and purification techniques as well as pave the way for their application in food industry.

Screening of folate-producing lactic acid bacteria and modulatory effects of folate-biofortified yogurt on gut dysbacteriosis of folate-deficient rats

Folate deficiency is accompanied by gut dysbacteriosis. To understand dietary intervention in folate deficiency, a folate-deficient rat model was used to evaluate the modulatory effects of folate-producing lactic acid bacteria (LAB) and biofortified yogurt on gut dysbacteriosis. The high folate-producing strain was screened from 12 LABs, and its variant, namely Lactobacillus plantarum GSLP-7 V, with folate productivity in yogurt at 3.72 μg mL-1, was obtained by stressing with 5.0 mg L-1 methotrexate and 100.00 mg L-1 Ca2+. To our knowledge, this is the highest folate productivity in yogurt by LAB strains ever reported. To further examine the folate supplement effect in vivo, a folate-deficient rat model was established and fed a folate-free diet for 8 weeks. Also, the effects of L. plantrum GSLP-7 V, yogurt fermented with L. plantrum GSLP-7 V, plain yogurt, and chemical folic acid on folate deficiency and gut dysbacteriosis were examined. Analysis of the change in gut microbiota showed that the gut dysbacteriosis was significantly correlated with folate deficiency. Administration of L. plantrum GSLP-7 V and its fermented yogurt for 10 days restored the disrupted gut microbiota and recovered the serum folate and homocysteine to normal levels, while chemical folic acid worsened the gut dysbacteriosis. Chemical folic acid only enriched Akkermansia, while L. plantrum GSLP-7 V and its fermented yogurt modulated the gut microbiota comprehensively through 7 and 10 key genera, respectively. This study confirmed the effectiveness of dietary intervention with folate-biofortified yogurt through modulating gut microbiota, suggesting the potential of the folate-producing LAB as an agent for the treatment of folate-deficiency related diseases.

Paper currency harbours antibiotic-resistant coliform bacteria and integron integrase

AIMS

This study was designed to analyse the prevalence of class 1 and class 2 integron integrase genes among antibiotic-resistant coliform bacteria isolated from paper currency circulating in Pakistan.

METHODS AND RESULTS

A total of 500 individual currency notes were collected from different food vending sites at Lahore, Pakistan. Bacterial population were identified by biochemical and PCR techniques. Antimicrobial susceptibility testing was performed by disc diffusion assay. The highest bacterial population on currency was found from street vendors and butcher shops. Escherichia coli was found to be the most prevalent coliform bacteria followed by Klebsiella sp. and Enterobacter sp. PCR amplification of antimicrobial resistance gene showed the presence of ampC, bla_TEM , bla_NDM-1 , qnrA, tet(A) and tet(B) genes among coliform isolates. A total of 47 integron integrase bearing strains of coliform bacteria were analysed. Sequence analysis showed the presence of dfrA1-aadA1, dfrA1, dfrA5, dfrA7, aadA1, aadA4 cassette arrays in class 1 integron and dfrA1-sat2-aadA1 in class 2 integrase genes.

CONCLUSION

Circulating currency was heavily contaminated with antimicrobial-resistant coliform bacteria bearing class 1 and class 2 integron integrase genes.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study describes a potential threat of severe bacterial infections due to improper hand hygiene and community sanitation when dealing with the currency notes.

Dose-dependent production of linoleic acid analogues in food derived Lactobacillus plantarum K25 and in silico characterization of relevant reactions

The objective of this study was to assess and scrutinize the competency of probiotic L. plantarum K25 to produce linoleic acid analogues in the medium supplemented with different concentrations of linoleic acid, ranging from 1% to 10%, in a dose dependent manner. The analogues produced were identified and quantitated by GC-MS and in silico studies were done to confirm enzymatic reactions involved in its conversion. The results showed that L. plantarum K25 could convert linoleic acid at different concentrations to 9 different fatty acid analogues at concentrations ranging from 0.01 to 17.24 mg/L. Among these metabolites, formation of an essential fatty acid, the linolenic acid, in media supplemented with 9% linoleic acid, is being reported for the first time. Putative candidate enzymes involved in biotransformation of linoleic acid into linoleic acid analogues were identified in the whole genome of L. plantarum K25, which was sequenced previously. In silico studies confirmed that many enzymes, including linoleate isomerase and dehydrogenase, may be involved in biotransformation of linoleic acid into linoleic acid analogues. Both enzymes could effectively bind the linoleic acid molecule, mainly by forming hydrogen bonding between the acidic groups of linoleic acid and the proline residues at the active sites of the enzymes, validating putative reaction partners.