A critical review of machine-learning for "multi-omics" marine metabolite datasets.

During the last decade, genomic, transcriptomic, proteomic, metabolomic, and other omics datasets have been generated for a wide range of marine organisms, and even more are still on the way. Marine organisms possess unique and diverse biosynthetic pathways contributing to the synthesis of novel secondary metabolites with significant bioactivities. As marine organisms have a greater tendency to adapt to stressed environmental conditions, the chance to identify novel bioactive metabolites with potential biotechnological application is very high. This review presents a comprehensive overview of the available "-omics" and "multi-omics" approaches employed for characterizing marine metabolites along with novel data integration tools. The need for the development of machine-learning algorithms for "multi-omics" approaches is briefly discussed. In addition, the challenges involved in the analysis of "multi-omics" data and recommendations for conducting "multi-omics" study were discussed.

Elucidation of the interaction of apocarotenoids with calf thymus DNA by biophysical techniques and in vitro study in MCF-7 cells to explore their potential in cancer therapy.

Objectives: DNA is one of the targets of cancer-therapeutic small molecules. Cisplatin, a DNA intercalator, is one of the first-line drugs in the cancer chemo regimen which comes with health-compromising side effects during chemotherapy. The synergistic effect of natural molecules with cisplatin can help to potentiate its anti-cancer efficacy and decrease its negative effect on health. Here, we report the interaction of cisplatin with calf thymus-DNA (ct-DNA) in combination with natural molecules like apocarotenoids which are reported for their therapeutic properties. Materials and Methods: The combinatorial effect of apocarotenoids on ct-DNA was explored through various biophysical techniques such as UV-Visible spectroscopy, circular dichroism studies, DNA melt curve analysis, viscosity measurements, and an in vitro study in MCF-7 cells by cell cycle analysis. Results: UV-Visible spectroscopy studies suggest apocarotenoids and their combination shows a non-intercalative mode of binding. Circular dichroism analysis showed no major changes in DNA form during the interaction of DNA with apocarotenoids and their respective combinations with cisplatin, which is suggestive of the groove-binding mode of apocarotenoids. DNA melt curve analysis showed a decrease in the intensity of the fluorescence for apocarotenoids with cisplatin which indicates the possibility of DNA interaction through groove binding. Viscosity studies suggested a groove binding mode of interaction of ct-DNA with apocarotenoids and their combination as there was minimal change in the viscosity measurements. The in vitro analysis exhibits that the apocarotenoids and their combination have a considerable effect on DNA synthesis. Conclusion: This study provides a better perspective on the possible mode of interaction between ct-DNA and natural molecules along with cisplatin.

The apocarotenoid production in microbial biofactories: An overview.

Carotenoids are a vast group of natural pigments that come in a variety of colors ranging from red to orange. Apocarotenoids are derived from these carotenoids, which are hormones, pigments, retinoids, and volatiles employed in the textiles, cosmetics, pharmaceutical, and food industries. Due to the high commercial value and poor natural host abundance, they are significantly undersupplied. Microbes like Saccharomyces cerevisiae and Escherichia coli act as heterologous hosts for apocarotenoid production. This article briefly reviews categories of apocarotenoids, their biosynthetic pathway commencing from the MVA and MEP, its significance, the tool enzymes for apocarotenoid biosynthesis like CCDs, their biotechnological production in microbial factories, and future perspectives.

Machine learning in photosynthesis: Prospects on sustainable crop development.

Improving photosynthesis is a promising avenue to increase food security. Studying photosynthetic traits with the aim to improve efficiency has been one of many strategies to increase crop yield but analyzing large data sets presents an ongoing challenge. Machine learning (ML) represents a ubiquitous tool that can provide a more elaborate data analysis. Here we review the application of ML in various domains of photosynthetic research, as well as in photosynthetic pigment studies. We highlight how correlating hyperspectral data with photosynthetic parameters to improve crop yield could be achieved through various ML algorithms. We also propose strategies to employ ML in promoting photosynthetic pigment research for furthering crop yield.

Status of food colorants in India: conflicts and prospects.

Food colorants are imperative ingredients for attracting consumers and in deciding their preferences. Here we discuss the current status of natural colorants and synthetic food colorants on the Indian market by appraising the growth of the food colorant market both globally and nationally, based on published case studies on synthetic food colorants (SFCs), rules, and regulations implemented by Food Safety and Standards Authority of India on natural food colorants and SFCs. The substantial lacunae in the research on the impacts of SFCs in the Indian population identified through our literature survey signify the scope and need for appraisal of the issues prevailing in the Indian food colorant market as well as the necessity of renewing the food colorant policies. The illegal use of banned food colorants, the adulteration of natural food colorants, mislabelling of SFCs as natural colorants, and the permitted use of internationally banned food colorants, as well as the unawareness among consumers are serious issues recognized. Appropriate labelling to denote natural food colorants' presence, renewed standards of policy to determine the permitted use of food colorants, comprehensive regulations for the production and use of natural food colorants, stringent rules to constrain the production of toxic SFCs are obligatory to breakdown the dilemma on the Indian food market. Most importantly, awareness and responsiveness should be generated among consumers regarding the illegal use and adulteration of colorants and the need to use natural colorants. We also recommend a logo to designate the presence of natural colorants which will aid the consumers to make the right choice.

Carotenoids for lung cancer chemoprevention and chemotherapy: Promises and controversies.

BACKGROUND: Lung cancer is one of the leading causes of malignancy in the world. Several therapeutical and chemopreventive approaches have been practised to mitigate the disease. The use of phytopigments including carotenoids is a well-known approach. However, some of the prominent clinical trials interrogated the efficacy of carotenoids in lung cancer prevention. METHODS: A elaborate literature survey have been performed investigating in vitro, in vivo, and clinical studies reported on the administration of carotenoids for chemoprevention and chemotherapy. RESULTS: Tobacco consumption, genetic factors, dietary patterns, occupational carcinogens, lung diseases, infection, and sex disparities are some of the prominent factors leading to lung cancer. Significant evidence has been found underlining the efficiency of carotenoids in alleviating cancer. In vitro studies have proven that carotenoids act through PI3K/ AKT/mTOR, ERK-MAPK pathways and induce apoptosis through PPAR, IFNs, RAR, which are p53 intermediators in lung cancer signaling. Animal models and cell lines studies showed promising results, while the outcomes of clinical trials are contradictory and require further verification. CONCLUSION: The carotenoids exert chemotherapeutic and chemopreventive effects on lung tumors which has been evidenced in numerous investigations. However, further analyses are necessary to the answer the uncertainties raised by several clinical trials.

Molecular mechanisms of neuroprotective offerings by rosmarinic acid against neurodegenerative and other CNS pathologies.

Rosmarinic acid (RA) is a natural phenolic compound present in culinary herbs of the Boraginaceae, Lamiaceae/Labiatae, and Nepetoideae families. While the medicinal applications of these plants have been known for ages, RA has only been relatively recently established as an effective ameliorative agent against various disorders including cardiac diseases, cancer, and neuropathologies. In particular, several studies have confirmed the neuroprotective potential of RA in multiple cellular and animal models, as well as in clinical studies. The neuroprotective effects mediated by RA stem from its multimodal actions on a plethora of cellular and molecular pathways; including oxidative, bioenergetic, neuroinflammatory, and synaptic signaling. In recent years, RA has garnered tremendous interest as an ideal therapeutic candidate for treating neurodegenerative diseases. This review first briefly discusses the pharmacokinetics of RA and then proceeds to detail the neuroprotective mechanisms of RA at the molecular levels. Finally, the authors focus on the ameliorative potential of RA against several central nervous system (CNS) disorders, ranging from neuropsychological stress and epilepsy to neurodegenerative diseases such as Alzheimer's disease, Huntington's disease, Parkinson's disease, Lewy body dementia, and amyotrophic lateral sclerosis.

An update on CRISPR-Cas12 as a versatile tool in genome editing.

Gene editing techniques, which help in modification of any DNA sequence at ease, have revolutionized the world of Genetic engineering. Although there are other gene-editing techniques, CRISPR has emerged as the chief and most preferred tool due to its simplicity and capacity to execute effective gene editing in a wide range of organisms. Although Cas9 has widely been employed for genetic modification over the years, Cas12 systems have lately emerged as a viable option. This review primarily focuses on assessing Cas12-mediated mutagenesis and elucidating the editing efficacy of both Cpf1 (Cas12a) and C2c1 (Cas12b) systems in microbes, plants, and other species. Also, we reviewed several genetic alterations that have been performed with these Cas12 systems to improve editing efficiency. Furthermore, the experimental benefits and applications of Cas12 systems are highlighted in this study.

Multispectroscopic, virtual and in vivo insights into the photoaging defense mediated by the natural food colorant bixin.

An upsurge in early onset of photoaging due to repeated skin exposure to environmental stressors such as UV radiation is a challenge for pharmaceutical and cosmeceutical divisions. Current reports indicate severe side effects because of chemical or synthetic inhibitors of matrix metalloproteases (MMPs) in anti-skin aging cosmeceuticals. We evaluated the adequacy of bixin, a well-known FDA certified food additive, as a scavenger of free radicals and its inhibitory mechanism of action on MMP1, collagenase, elastase, and hyaluronidase. The anti-skin aging potential of bixin was evaluated by several biotechnological tools in silico, in vitro and in vivo. Molecular docking and simulation dynamics studies gave a virtual insight into the robust binding interaction between bixin and skin aging-related enzymes. Absorbance and fluorescence studies, enzyme inhibition assays, enzyme kinetics and in vitro bioassays of human dermal fibroblast (HDF) cells highlighted bixin's role as a potent antioxidant and inhibitor of skin aging-related enzymes. Furthermore, in vivo protocols were carried out to study the impact of bixin administration on UVA induced photoaging in C57BL/6 mice skin. Here, we uncover the UVA shielding effect of bixin and its efficacy as a novel anti-photoaging agent. Furthermore, the findings of this study provide a strong foundation to explore the pharmaceutical applications of bixin in several other biochemical pathways linked to MMP1, collagenase, elastase, and hyaluronidase.

Smart Nanoformulations for Brain Cancer Theranostics: Challenges and Promises.

Despite their low prevalence, brain tumors are among the most lethal cancers. They are extremely difficult to diagnose, monitor and treat. Conventional anti-cancer strategies such as radio- and chemotherapy have largely failed, and to date, the development of even a single effective therapeutic strategy against central nervous system (CNS) tumors has remained elusive. There are several factors responsible for this. Brain cancers are a heterogeneous group of diseases with variable origins, biochemical properties and degrees of invasiveness. High-grade gliomas are amongst the most metastatic and invasive cancers, which is another reason for therapeutic failure in their case. Moreover, crossing the blood brain and the blood brain tumor barriers has been a significant hindrance in the development of efficient CNS therapeutics. Cancer nanomedicine, which encompasses the application of nanotechnology for diagnosis, monitoring and therapy of cancers, is a rapidly evolving field of translational medicine. Nanoformulations, because of their extreme versatility and manipulative potential, are emerging candidates for tumor targeting, penetration and treatment in the brain. Moreover, suitable nanocarriers can be commissioned for theranostics, a combinatorial personalized approach for simultaneous imaging and therapy. This review first details the recent advances in novel bioengineering techniques that provide promising avenues for circumventing the hurdles of delivering the diagnostic/therapeutic agent to the CNS. The authors then describe in detail the tremendous potential of utilizing nanotechnology, particularly nano-theranostics for brain cancer imaging and therapy, and outline the different categories of recently developed next-generation smart nanoformulations that have exceptional potential for making a breakthrough in clinical neuro-oncology therapeutics.

Untapping the protective role of carotenoids against respiratory diseases.

BACKGROUND: Recent studies revealed a substantial role of carotenoids to treat respiratory diseases. This review aimed to give an updated overview of the investigational evidence on the preventive properties of carotenoids against respiratory diseases both in vitro and in vivo along with their pathophysiology and mechanisms of action. HYPOTHESIS: Carotenoids as a potential therapeutic class of bioactive compounds to treat respiratory diseases. RESULTS: Carotenoids such as ß-carotene, lycopene, crocin, bixin, lutein, and astaxanthin show beneficial effects against chronic lung diseases (e.g., asthma, emphysema, fibrosis, COPD, acute lung injury, and lung cancer). Moreover, in vitro and in vivo studies also supported the preventive role of carotenoids. These carotenoids showed a beneficial role by activation of the NRF2/HO-1 pathway and inhibition of the NF-кB, MAPK, JAK/STAT-3, and PI3K/AKT pathways. Additionally, epidemiological studies also showed that dietary intake of carotenoids lowers the risk of lung diseases. CONCLUSION: Carotenoids may be used as drugs or can be given in combination with other drugs to prevent and treat respiratory diseases. Although in vitro and in vivo results are encouraging, further well-conducted randomized clinical trials are required to approve carotenoids as drug candidates.

The role of photosynthesis related pigments in light harvesting, photoprotection and enhancement of photosynthetic yield in planta.

Photosynthetic pigments are an integral and vital part of all photosynthetic machinery and are present in different types and abundances throughout the photosynthetic apparatus. Chlorophyll, carotenoids and phycobilins are the prime photosynthetic pigments which facilitate efficient light absorption in plants, algae, and cyanobacteria. The chlorophyll family plays a vital role in light harvesting by absorbing light at different wavelengths and allowing photosynthetic organisms to adapt to different environments, either in the long-term or during transient changes in light. Carotenoids play diverse roles in photosynthesis, including light capture and as crucial antioxidants to reduce photodamage and photoinhibition. In the marine habitat, phycobilins capture a wide spectrum of light and have allowed cyanobacteria and red algae to colonise deep waters where other frequencies of light are attenuated by the water column. In this review, we discuss the potential strategies that photosynthetic pigments provide, coupled with development of molecular biological techniques, to improve crop yields through enhanced light harvesting, increased photoprotection and improved photosynthetic efficiency.

Endophytism of Fusarium Solani in Meristems of Delonix Regia (Bojer ex Hook.) Raf.

A bright yellow pigment-producing endophytic fungus strain GMRS1 was isolated from the meristems of Delonix regia (Bojer ex Hook.) Raf. The fungus was identified as Fusarium solani on grounds of morphological and molecular analysis. The chemical composition of the crude pigments was partially analyzed by Quadrupole Time-of-flight Liquid chromatography/Mass spectrometry/Mass spectrometry and the major compounds were reported. The crude pigments were proved toxic and unsafe by acute oral toxicity study on Wistar rats. The total cholesterol and glucose levels of the rats ingested with crude pigments were significantly elevated than the control rats. The treatment rats were further observed with damaged liver and kidney tissues. The LD50 value of the crude pigments was higher than 1000 mg/kg of body weight. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-021-00968-w.

Cardioprotective effects of phytopigments via multiple signaling pathways.

BACKGROUND: Cardiovascular diseases (CVDs) are among the deadliest non-communicable diseases, and millions of dollars are spent every year to combat CVDs. Unfortunately, the multifactorial etiology of CVDs complicates the development of efficient therapeutics. Interestingly, phytopigments show significant pleiotropic cardioprotective effects both in vitro and in vivo. PURPOSE: This review gives an overview of the cardioprotective effects of phytopigments based on in vitro and in vivo studies as well as clinical trials. METHODS: A literature-based survey was performed to collect the available data on cardioprotective activities of phytopigments via electronic search engines such as PubMed, Google Scholar, and Scopus. RESULTS: Different classes of phytopigments such as carotenoids, xanthophylls, flavonoids, anthocyanins, anthraquinones alleviate major CVDs (e.g., cardiac hypertrophy, atherosclerosis, hypertension, cardiotoxicities) via acting on signaling pathways related to AMPK, NF-κB, NRF2, PPARs, AKT, TLRs, MAPK, JAK/STAT, NLRP3, TNF-α, and RA. CONCLUSION: Phytopigments represent promising candidates to develop novel and effective CVD therapeutics. More randomized, placebo-controlled clinical studies are recommended to establish the clinical efficacy of phytopigments.

The neuroprotective potential of carotenoids in vitro and in vivo.

BACKGROUND: Despite advances in research on neurodegenerative diseases, the pathogenesis and treatment response of neurodegenerative diseases remain unclear. Recent studies revealed a significant role of carotenoids to treat neurodegenerative diseases. The aim of this study was to systematically review the neuroprotective potential of carotenoids in vivo and in vitro and the molecular mechanisms and pathological factors contributing to major neurodegenerative diseases (Alzheimer's disease, Huntington's disease, Parkinson's disease, amyotrophic lateral sclerosis, and stroke). HYPOTHESIS: Carotenoids as therapeutic molecules to target neurodegenerative diseases. RESULTS: Aggregation of toxic proteins, mitochondrial dysfunction, oxidative stress, the excitotoxic pathway, and neuroinflammation were the major pathological factors contributing to the progression of neurodegenerative diseases. Furthermore, in vitro and in vivo studies supported the beneficiary role of carotenoids, namely lycopene, ß-carotene, crocin, crocetin, lutein, fucoxanthin and astaxanthin in alleviating disease progression. These carotenoids provide neuroprotection by inhibition of neuro-inflammation, microglial activation, excitotoxic pathway, modulation of autophagy, attenuation of oxidative damage and activation of defensive antioxidant enzymes. Additionally, studies conducted on humans also demonstrated that dietary intake of carotenoids lowers the risk of neurodegenerative diseases. CONCLUSION: Carotenoids may be used as drugs to prevent and treat neurodegenerative diseases. Although, the in vitro and in vivo results are encouraging, further well conducted clinical studies on humans are required to conclude about the full potential of neurodegenerative diseases.

Unraveling the versatility of CCD4: Metabolic engineering, transcriptomic and computational approaches.

Carotenoids are economically valuable isoprenoids synthesized by plants and microorganisms, which play a paramount role in their overall growth and development. Carotenoid cleavage dioxygenases are a vast group of enzymes that specifically cleave thecarotenoids to produce apocarotenoids. Recently, CCDs are a subject of talk because of their contributions to different aspects of plant growth and due to their significance in the production of economically valuable apocarotenoids. Among them, CCD4 stands unique because of its versatility in performing metabolic roles. This review focuses on the multiple functionalities of CCD4 like pigmentation, volatile apocarotenoid production, stress responses, etc. Interestingly, through our literature survey we arrived at a conclusion that CCD4 could perform functions of other carotenoid cleaving enzymes.The metabolic engineering, transcriptomic, and computational approaches adopted to reveal the contributions of CCD4 were also considered here for the study.Phylogenetic analysis was performed to delve into the evolutionary relationships of CCD4 in different plant groups. A tree of 81CCD genes from 64 plant species was constructed, signifying the presence of well-conserved families. Gene structures were illustrated and the difference in the number and position of exons could be considered as a factor behind functional versatility and substrate tolerance of CCD4 in different plants.

Strategies to meet the global demand for natural food colorant bixin: A multidisciplinary approach.

Bixin is an apocarotenoid derived from Bixa orellana L. well known as a food colorant along with its numerous industrial and therapeutic applications. With the current surge in usage of natural products, bixin has contributed immensely to the world carotenoid market and showcases a spike in its requirement globally. To bridge the gap between bixin availability and utility, owed to its bioactivity and demand as a colouring agent in industries the sustainable production of bixin is critical. Therefore, to meet up this challenge effective use of multidisciplinary strategies is a promising choice to enhance bixin quantity and quality. Here we report, an optimal blend of approaches directed towards manipulation of bixin biosynthesis pathway with an insight into the impact of regulatory mechanisms and environmental dynamics, engineering carotenoid degradation in plants other than annatto, usage of tissue culture techniques supported with diverse elicitations, molecular breeding, application of in silico predictive tools, screening of microbial bio-factories as alternatives, preservation of bixin bioavailability, and promotion of eco-friendly extraction techniques to play a collaborative role in promoting sustainable bixin production.

Mycosynthesis of novel lactone in foliar endophytic fungus isolated from Bixa orellana L.

There is a colossal demand for natural pigments and its applications in recent times. In the study, a novel lactone pigment was isolated from a predominant endophytic fungus residing in Bixa orellana L. (Bixaceae) leaves. The endophyte was identified as Fusarium verticillioides through morphological and molecular investigations. The optimum growth parameters of the endophyte for pigment production were at 33 ºC with pH 6.5 in dark. Through comprehensive spectroscopic studies, the structure of the isolated lactone was resolved and identified as (E)-3, 3-dimethyl-4-(pent-1-en-1-yl)-4-propyldihydrofuran-2(3H)-one. The acute oral toxicity study of the pigment investigated upon female Wistar rats indicated the median lethal dose (LD50) value above 1000 mg/kg body weight affirming safety. Thus, the red pigment from the isolated endophyte may be employed as a sustainable source for natural colorant in industries owing to its non-toxicity. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-020-02566-x.

Molecular dynamics simulations to decipher the structural and functional consequences of pathogenic missense mutations in the galactosylceramidase (GALC) protein causing Krabbe's disease.

Krabbe disease (KD), also known as globoid cell leukodystrophy disease, is an autosomal recessive lysosomal storage genetic disorder, which is caused by the deficiency of galactocerebrosidase (GALC) coding gene (GALC). This study aimed to use extensive computational pipelines in understanding the missense mutations in GALC. We retrieved 176 mutations from the public databases and subjected them to pathogenicity, stability, and conservation analyses. The PredictSNP, iStable, and ConSurf prediction tools predicted 45, 95, and 47 mutations to be deleterious, destabilizing, and highly conserved, respectively. The R396L and R396W were the most deleterious and destabilizing to GALC, and were therefore prioritized for further analysis. Systematic validation on the impact of the R396L and R396W mutations to the chaperone alpha lobeline was performed using the molecular docking approach. The docking analysis revealed that the mutant R396W interacted with minimal binding affinity compared with both the R396L mutant and native GALC. Furthermore, the repetitive molecular dynamics simulation analysis showed that the mutant R396W demonstrated less compactness and reduced number of intramolecular hydrogen bonds compared with the mutant R396L and the native GALC. Overall, we observed higher structural and functional modifications in R396W positioned in the substrate-binding site. This was highly supported by the MMPBSA and DSSP analysis of the GROMACS. DSSP showed the transformation of turns to bends, indicating a loss of stability due to the R396W mutation. This study is expected to serve as a platform for prioritizing mutant proteins that could be a platform for both drug and target therapeuticsCommunicated by Ramaswamy H. Sarma.

Photosynthesis in non-foliar tissues: implications for yield.

Photosynthesis is currently a focus for crop improvement. The majority of this work has taken place and been assessed in leaves, and limited consideration has been given to the contribution that other green tissues make to whole-plant carbon assimilation. The major focus of this review is to evaluate the impact of non-foliar photosynthesis on carbon-use efficiency and total assimilation. Here we appraise and summarize past and current literature on the substantial contribution of different photosynthetically active organs and tissues to productivity in a variety of different plant types, with an emphasis on fruit and cereal crops. Previous studies provide evidence that non-leaf photosynthesis could be an unexploited potential target for crop improvement. We also briefly examine the role of stomata in non-foliar tissues, gas exchange, maintenance of optimal temperatures and thus photosynthesis. In the final section, we discuss possible opportunities to manipulate these processes and provide evidence that Triticum aestivum (wheat) plants genetically manipulated to increase leaf photosynthesis also displayed higher rates of ear assimilation, which translated to increased grain yield. By understanding these processes, we can start to provide insights into manipulating non-foliar photosynthesis and stomatal behaviour to identify novel targets for exploitation in continuing breeding programmes.