Fish Fillet Analogue Using Formulation Based on Mushroom (Pleurotus ostreatus) and Enzymatic Treatment: Texture, Sensory, Aromatic Profile and Physicochemical Characterization.

The growing demand for alternative sources of non-animal proteins has stimulated research in this area. Mushrooms show potential in the innovation of plant-based food products. In this study, the aim was to develop prototype fish fillets analogues from Pleurotus ostreatus mushrooms applying enzymatic treatment (ß-glucanase and transglutaminase-TG). A Plackett-Burman 20 experimental design was used to optimize forty variables. Oat flour (OF) exerted a positive effect on the hardness and gumminess texture parameters but a negative effect on cohesiveness and resilience. Soy protein isolate (SPI) exhibited a positive effect on elasticity, gumminess and chewiness, while acacia gum had a negative effect on elasticity, cohesiveness and resilience. After sensory analysis the assay with 1% cassava starch, 5% OF, 5% SPI, 0.1% transglutaminase (240 min/5 °C), 1% coconut oil, 1% soybean oil, 0.2% sodium tripolyphosphate, 0.6% ß-glucanase (80 °C/10 min) and without ß-glucanase inactivation was found to exhibit greater similarity to fish fillet. The classes hydrocarbons, alcohols and aldehydes are the predominant ones in aromatic profile analysis by chromatography and electronic nose. It is concluded that a mushroom-based analogue of fish fillet can be prepared using enzymatic treatment with TG.

Bilirubin Molecular Species Play an Important Role in the Pathophysiology of Acute-on-Chronic Liver Failure.

Bilirubin plays a key role in early diagnosis, prognosis, and prevention of liver diseases. Unconjugated bilirubin (UCB) requires conversion to a water-soluble form through liver glucuronidation, producing monoglucuronide (BMG) or diglucuronide bilirubin (BDG) for bile excretion. This study aimed to assess the roles of bilirubin's molecular species-UCB, BMG, and BDG-in diagnosing and understanding the pathogenesis of liver cirrhosis in patients with acute-on-chronic liver failure (ACLF), compensated liver cirrhosis (LC) patients, and healthy individuals. The study included patients with ACLF and compensated LC of diverse etiologies, along with healthy controls. We collected laboratory and clinical data to determine the severity and assess mortality. We extracted bilirubin from serum samples to measure UCB, BMG, and BDG using liquid chromatography-mass spectrometry (LC-MS). The quantification of bilirubin was performed by monitoring the mass charge (m/z) ratio. Of the 74 patients assessed, 45 had ACLF, 11 had LC, and 18 were healthy individuals. Among ACLF patients, the levels of molecular species of bilirubin were UCB 19.69 µmol/L, BMG 47.71 µmol/L, and BDG 2.120 µmol/L. For compensated cirrhosis patients, the levels were UCB 11.29 µmol/L, BMG 1.49 µmol/L, and BDG 0.055 µmol/L, and in healthy individuals, the levels were UCB 6.42 µmol/L, BMG 0.52 µmol/L, and BDG 0.028 µmol/L. The study revealed marked elevations in the bilirubin species in individuals with ACLF compared to those with compensated cirrhosis and healthy controls, underscoring the progression of liver dysfunction. The correlation of BMG and BDG levels with commonly used inflammatory markers suggests a relationship between bilirubin metabolism and systemic inflammation in ACLF.

Heme metabolism in Strigomonas culicis: Implications of H2O2 resistance induction and symbiont elimination.

Monoxenous trypanosomatid Strigomonas culicis harbors an endosymbiotic bacterium, which enables the protozoa to survive without heme supplementation. The impact of H2O2 resistance and symbiont elimination on intracellular heme and Fe2+ availability was analyzed through a comparison of WT strain with both WT H2O2-resistant (WTR) and aposymbiotic (Apo) protozoa. The relative quantification of the heme biosynthetic pathway through label-free parallel reaction monitoring targeted mass spectrometry revealed that H2O2 resistance does not influence the abundance of tryptic peptides. However, the Apo strain showed increased coproporphyrinogen III oxidase and ferrochelatase levels. A putative ferrous iron transporter, homologous to LIT1 and TcIT from Leishmania major and Trypanosoma cruzi, was identified for the first time. Label-free parallel reaction monitoring targeted mass spectrometry also showed that S. culicis Iron Transporter (ScIT) increased 1.6- and 16.4-fold in WTR and Apo strains compared to WT. Accordingly, antibody-mediated blockage of ScIT decreased by 28.0% and 40.0% intracellular Fe2+concentration in both WTR and Apo strains, whereas no effect was detected in WT. In a heme-depleted medium, adding 10 µM hemin decreased ScIT transcript levels in Apo, whereas 10 µM PPIX, the substrate of ferrochelatase, increased intracellular Fe2+ concentration and ferric iron reduction. Overall, the data suggest mechanisms dependent on de novo heme synthesis (and its substrates) in the Apo strain to overcome reduced heme availability. Given the importance of heme and Fe2+ as cofactors in metabolic pathways, including oxidative phosphorylation and antioxidant systems, this study provides novel mechanistic insights associated with H2O2 resistance in S. culicis.

Proteomic changes of the bovine blood plasma in response to heat stress in a tropically adapted cattle breed.

Background: Identifying molecular mechanisms responsible for the response to heat stress is essential to increase production, reproduction, health, and welfare. This study aimed to identify early biological responses and potential biomarkers involved in the response to heat stress and animal's recovery in tropically adapted beef cattle through proteomic analysis of blood plasma. Methods: Blood samples were collected from 14 Caracu males during the heat stress peak (HSP) and 16 h after it (heat stress recovery-HSR) assessed based on wet bulb globe temperature index and rectal temperature. Proteome was investigated by liquid chromatography-tandem mass spectrometry from plasma samples, and the differentially regulated proteins were evaluated by functional enrichment analysis using DAVID tool. The protein-protein interaction network was evaluated by STRING tool. Results: A total of 1,550 proteins were detected in both time points, of which 84 and 65 were downregulated and upregulated during HSR, respectively. Among the differentially regulated proteins with the highest absolute log-fold change values, those encoded by the GABBR1, EPHA2, DUSP5, MUC2, DGCR8, MAP2K7, ADRA1A, CXADR, TOPBP1, and NEB genes were highlighted as potential biomarkers because of their roles in response to heat stress. The functional enrichment analysis revealed that 65 Gene Ontology terms and 34 pathways were significant (P < 0.05). We highlighted those that could be associated with the response to heat stress, such as those related to the immune system, complement system, hemostasis, calcium, ECM-receptor interaction, and PI3K-Akt and MAPK signaling pathways. In addition, the protein-protein interaction network analysis revealed several complement and coagulation proteins and acute-phase proteins as important nodes based on their centrality and edges. Conclusion: Identifying differentially regulated proteins and their relationship, as well as their roles in key pathways contribute to improve the knowledge of the mechanisms behind the response to heat stress in naturally adapted cattle breeds. In addition, proteins highlighted herein are potential biomarkers involved in the early response and recovery from heat stress in tropically adapted beef cattle.

Recent advances in the chromatographic analysis of endocannabinoids and phytocannabinoids in biological samples.

Endocannabinoid system, including endocannabinoid neurotransmitters (eCBs), has gained much attention over the last years due to its involvement with the pathophysiology of diseases and the potential use of Cannabis sativa (marijuana). The identification of eCBs and phytocannabinoids in biological samples for forensic, clinical, or therapeutic drug monitoring purposes constitutes a still significant challenge. In this scoping review, the recent advantages, and limitations of the eCBs and phytocannabinoids quantification in biological samples are described. Published studies from 2018-2023 were searched in 8 databases, and after screening and exclusions, the selected 38 articles had their data tabulated, summarized, and analyzed. The main characteristics of the eCBs and phytocannabinoids analyzed and the potential use of each biological sample were described, indicating gaps in the literature that still need to be explored. Well-established and innovative sample preparation protocols, and chromatographic separations, such as GC, HPLC, and UHPLC, are reviewed highlighting their respective advantages, drawbacks, and challenges. Lastly, future approaches, challenges, and tendencies in the quantification analysis of cannabinoids are discussed.

Impact of the near-physiological temperature on the in vitro maturation of bovine oocytes: A comparative proteomic approach.

In vivo, the temperature inside preovulatory follicles of cows is approximately 1 °C lower than rectal temperature. However, standard bovine oocyte in vitro maturation (IVM) protocols use 38.5 °C based on rectal temperature. This study evaluated the effect of reducing IVM temperature to 37.5 °C on the proteomic profile of oocytes compared to the routine 38.5 °C. Nuclear maturation rate and cumulus cell (CC) expansion (30 COCs per group, 21 replicates) were assessed by observing the first polar body and using a subjective scoring method (0-4). Total nitrite concentrations in the culture medium were measured using the Griess method. Differential proteomics was performed using LC-MS/MS on pooled oocyte samples (500 matured oocytes per group, three replicates), followed by gene ontology enrichment, protein-protein interaction, and putative miRNA target analyses. No significant differences were observed between the groups in nuclear maturation, CC expansion, or nitrite concentration (P > 0.05). A total of 806 proteins were identified, with 7 up-regulated and 12 down-regulated in the treatment group compared to the control. Additionally, 12 proteins were unique to the control group, and 8 were unique to the treatment group. IVM at 37.5 °C resulted in the upregulation of proteins involved in protein folding and GTP binding, and the downregulation of enzymes with oxidoreductase activity and proteins involved in cytoskeletal fiber formation. Furthermore, 43 bovine miRNAs potentially regulating these genes (DES, HMOX2, KRT75, FARSA, IDH2, CARHSP1) were identified. We conclude that IVM of bovine oocytes at 37.5 °C induces significant proteomic changes without impacting nuclear maturation, cumulus cell expansion, or nitrite concentration in the IVM medium.

Porphyrin Production by Corynebacterium diphtheriae Strains from Clinical Isolates.

Porphyrins are intermediate metabolites in the biosynthesis of vital molecules, including heme, cobalamin, and chlorophyll. Bacterial porphyrins are known to be proinflammatory and have been associated with biofilm production. This study investigated porphyrin production by strains of Corynebacterium diphtheriae using emission spectroscopy, high-performance liquid chromatography with fluorescence detection, a diode array detector, and mass spectrometry. Emission spectroscopy revealed characteristic porphyrin emission spectra in all strains, with coproporphyrin III predominating. Qualitative analysis via different chromatography methods revealed identified coproporphyrin III, uroporphyrin I, and protoporphyrin IX in all the strains. Quantitative analysis revealed strain-dependent coproporphyrin III production. More studies are needed to investigate the relationship between porphyrin production and the virulence potential of Corynebacterium diphtheriae.

On the PhyloQuant protein expression profiles approach to the taxonomic problem.

Inferring evolutionary relationships among organisms has been a fundamental problem in evolutionary biology. The current phylogenetic molecular methods serve as the baseline model to test new evolutionary hypotheses with taxonomic purposes. Leishmaniinae trypanosomatids subfamily includes protozoan parasites of clinical importance to humans. They have an intricate taxonomic history defined by morphological elements, host range, and molecular phylogenies. Unraveling the increasing diversity of this group has shown limitations in reconstructing the true evolutionary relationships among Trypanosomatidae species. Toward the goal of inferring evolutionary relationships that help to resolve phylogenetic and taxonomic controversies among parasites of the subfamily Leishmaniinae, Mule et al. propose the method PhyloQuant as a valuable approach, based on differential protein expression obtained from high throughput mass spectrometry data. Employing a pioneering methodological approach, Mule et al. assess the taxonomic problem for species hypothesis within Leishmaniinae, from quantitative phenetic protein expression profiles, in contrast to the standard multilocus phylogenetic approaches.

Lipidomic Analysis Reveals Branched-Chain and Cyclic Fatty Acids from Angomonas deanei Grown under Different Nutritional and Physiological Conditions.

Angomonas deanei belongs to Trypanosomatidae family, a family of parasites that only infect insects. It hosts a bacterial endosymbiont in a mutualistic relationship, constituting an excellent model for studying organelle origin and cellular evolution. A lipidomic approach, which allows for a comprehensive analysis of all lipids in a biological system (lipidome), is a useful tool for identifying and measuring different expression patterns of lipid classes. The present study applied GC-MS and NMR techniques, coupled with principal component analysis (PCA), in order to perform a comparative lipidomic study of wild and aposymbiotic A. deanei grown in the presence or absence of FBS. Unusual contents of branched-chain iso C17:0 and C19:0-cis-9,10 and-11,12 fatty acids were identified in A. deanei cultures, and it was interesting to note that their content slightly decreased at the log phase culture, indicating that in the latter growth stages the cell must promote the remodeling of lipid synthesis in order to maintain the fluidity of the membrane. The combination of analytical techniques used in this work allowed for the detection and characterization of lipids and relevant contributors in a variety of A. deanei growth conditions.

An intense 60-day weight-loss course leads to an 18 kg body weight reduction and metabolic reprogramming of soldiers with obesity.

Soldiers of the Mexican Army with obesity were subjected to an intense 60-day weight-loss course consisting of a controlled diet, daily physical training, and psychological sessions. The nutritional treatment followed the European Society of Cardiology (ESC) recommendations, incorporating elements of the traditional milpa diet in the nutritional intervention. The total energy intake was reduced by 200 kcal every 20 days, starting with 1,800 kcal and ending with 1,400 kcal daily. On average, the participants reduced their body weight by 18 kg. We employed an innovative approach to monitor the progress of the twelve soldiers who completed the entire program. We compared the untargeted metabolomics profiles of their urine samples, taken before and after the course. The data obtained through liquid chromatography and high-resolution mass spectrometry (LC-MS) provided insightful results. Classification models perfectly separated the profiles pre and post-course, indicating a significant reprogramming of the participants' metabolism. The changes were observed in the C1-, vitamin, amino acid, and energy metabolism pathways, primarily affecting the liver, biliary system, and mitochondria. This study not only demonstrates the potential of rapid weight loss and metabolic pathway modification but also introduces a non-invasive method for monitoring the metabolic state of individuals through urine mass spectrometry data.

Characterizing lipid constituents of B. moojeni snake venom: a comparative approach for chemical and biological investigations.

Snake venoms are complex mixtures majorly composed of proteins with well-studied biological effects. However, the exploration of non-protein components, especially lipids, remains limited despite their potential for discovering bioactive molecules. This study compares three liquid-liquid lipid extraction methods for both chemical and biological analyses of Bothrops moojeni snake venom. The methods evaluated include the Bligh and Dyer method (methanol, chloroform, water), considered standard; the Acunha method, a modification of the Bligh and Dyer protocol; and the Matyash method (MTBE/methanol/water), featuring an organic phase less dense than the aqueous phase. Lipidomic analysis using liquid chromatography with high-resolution mass spectrometry (LC-HRMS) system revealed comparable values of lipid constituents' peak intensity across different extraction methods. Our results show that all methods effectively extracted a similar quantity of lipid species, yielding approximately 17-18 subclasses per method. However, the Matyash and Acunha methods exhibited notably higher proportions of biologically active lipids compared to the Bligh and Dyer method, particularly in extracting lipid species crucial for cellular structure and function, such as sphingomyelins and phosphatidylinositol-phosphate. In conclusion, when selecting a lipid extraction method, it is essential to consider the study's objectives. For a biological approach, it is crucial to evaluate not only the total quantity of extracted lipids but also their quality and biological activity. The Matyash and Acunha methods show promise in this regard, potentially offering a superior option for extracting biologically active lipids compared to the Bligh and Dyer method.

The power of computational proteomics platforms to decipher protein-protein interactions.

Adopting computational tools for analyzing extensive biological datasets has profoundly transformed our understanding and interpretation of biological phenomena. Innovative platforms have emerged, providing automated analysis to unravel essential insights about proteins and the complexities of their interactions. These computational advancements align with traditional studies, which employ experimental techniques to discern and quantify physical and functional protein-protein interactions (PPIs). Among these techniques, tandem mass spectrometry is notably recognized for its precision and sensitivity in identifying PPIs. These approaches might serve as important information enabling the identification of PPIs with potential pharmacological significance. This review aims to convey our experience using computational tools for detecting PPI networks and offer an analysis of platforms that facilitate predictions derived from experimental data.

Exploring Maillard reaction markers and melanoidins to investigate toxicological and antioxidant profiles of optimized expanded snacks from corn/common bean mixtures.

BACKGROUND: Extrusion cooking of cereal-legume flour mixture is an innovative strategy to introduce nutrient-enriched ready-to-eat snacks to the market. However, this thermal process triggers the formation of compounds that could impact safety aspects of these products. Maillard reaction markers and the end products known as melanoidins were evaluated to assess the toxicological and bioactive profiles of extruded snacks from corn-plus-common-bean-flour combinations. Different molecular weight fractions were isolated and purified to analyze their antioxidant activity and to investigate the role of melanoidins. RESULTS: The snack formulated with an 84:16 ratio of corn:common bean flours exhibited an enhanced toxicological profile. It displayed the lowest levels of acrylamide and furanic compounds, along with reduced blockage of lysine residues in the protein. Extrusion increased the antioxidant activity of uncooked flours (30 to 64%) and total phenolic compounds (26 to 50%), and decreased the available lysine (-72.7 to -79.5%). During the fractionation process, it was established that compounds within the range of 3-10 kDa made the greatest contribution to antioxidant activity. The fraction greater than 10 kDa, which included melanoidins, displayed 7 to 33% lower antioxidant activity. The purification of the fraction greater than 10 kDa revealed that pure melanoidins represented approximately one-third of the antioxidant activity in that fraction. Non-covalent adducts linked to the melanoidin core therefore had a relevant role in the antioxidant action of formulated snacks. CONCLUSION: This investigation illustrates the importance of considering both potential risks and associated benefits of compounds formed during the Maillard reaction while developing new extruded snacks. © 2024 The Author(s). Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Anthocyanin Profiles in the Tropical Fruits Eugenia jambolana and Inga edulis: A Comparative Study Using Paper Spray Ionization (PSI-MS), Tissue Spray Ionization (TSI-MS), and Direct Infusion (DI-MS).

Paper spray ionization (PSI-MS) and tissue spray ionization (TSI-MS) mass spectrometry are simple and rapid ambient ionization mass spectrometry techniques that offer numerous advantages over conventional analysis methods. This study aims to analyze the efficiency of detecting anthocyanins from Eugenia jambolana fruit peel and Inga edulis seeds using PSI-MS, TSI-MS, and DI-MS (direct infusion). DI-MS exhibited high efficiency, detecting all compounds in abundance, with anthocyanins malvidin 3,5-O-diglucoside (1) and petunidin 3,5-O-diglucoside (2) being the most prevalent. PSI-MS, however, struggled to detect delphinidin 3-O-glucoside and showed lower abundances for compounds 1, 2, 3 (delphinidin 3,5-O-diglucoside), and 4 (petunidin 3-O-glucoside) compared to DI-MS, attributed to the technique's challenges with molecular weight and polarity. TSI-MS was least effective, detecting only compounds 1, 2, and 3 at low intensities. The overall unique compounds identified across techniques were 134, emphasizing the importance of comprehensively employing multiple methods to analyze anthocyanins in these edible plants.

Basal release of 6-cyanodopamine from rat isolated vas deferens and its role on the tissue contractility.

6-Cyanodopamine is a novel catecholamine released from rabbit isolated heart. However, it is not known whether this catecholamine presents any biological activity. Here, it was evaluated whether 6-cyanodopamine (6-CYD) is released from rat vas deferens and its effect on this tissue contractility. Basal release of 6-CYD, 6-nitrodopamine (6-ND), 6-bromodopamine, 6-nitrodopa, and 6-nitroadrenaline from vas deferens were quantified by LC-MS/MS. Electric-field stimulation (EFS) and concentration-response curves to noradrenaline, adrenaline, and dopamine of the rat isolated epididymal vas deferens (RIEVD) were performed in the absence and presence of 6-CYD and /or 6-ND. Expression of tyrosine hydroxylase was assessed by immunohistochemistry. The rat isolated vas deferens released significant amounts of both 6-CYD and 6-ND. The voltage-gated sodium channel blocker tetrodotoxin had no effect on the release of 6-CYD, but it virtually abolished 6-ND release. 6-CYD alone exhibited a negligible RIEVD contractile activity; however, at 10 nM, 6-CYD significantly potentiated the noradrenaline- and EFS-induced RIEVD contractions, whereas at 10 and 100 nM, it also significantly potentiated the adrenaline- and dopamine-induced contractions. The potentiation of noradrenaline- and adrenaline-induced contractions by 6-CYD was unaffected by tetrodotoxin. Co-incubation of 6-CYD (100 pM) with 6-ND (10 pM) caused a significant leftward shift and increased the maximal contractile responses to noradrenaline, even in the presence of tetrodotoxin. Immunohistochemistry revealed the presence of tyrosine hydroxylase in both epithelial cell cytoplasm of the mucosae and nerve fibers of RIEVD. The identification of epithelium-derived 6-CYD and its remarkable synergism with catecholamines indicate that epithelial cells may regulate vas deferens smooth muscle contractility.

Analysis of chlordecone and its transformation products in environmental waters by a new SPME-GC-MS method and comparison with LLE-GC-MS/MS and LLE-LC-MS/MS: A case study in the French West Indies.

Among the numerous organochlorines (OCs) applied in the French West Indies (FWI), chlordecone (hydrated form C10Cl10O2H2; CLD) still causes major environmental pollution nowadays. A recent report revealed the unexpected presence in FWI environment of transformation products (TPs) of CLD not routinely monitored due to a lack of commercial standards. Here, we present a method for surface waters and groundwaters to analyze CLD, its main TPs (hydroCLDs, chlordecol (CLDOH), 10-monohydroCLDOH and polychloroindenes) and other OCs. We developed an SPME-GC-SIM/MS method with a PDMS-DVB fiber. Since CLDOH-d commonly used as internal standard (IS) proved unsuitable, we synthesized several IS candidates, and finally identified 10-monohydro-5-methyl-chlordecol as a satisfactory IS for CLDOH and 10-monohydroCLDOH avoiding the use of 13C-labelled analogue. LODs for CLD and its TPs varied from 0.3 to 10 ng/L, equal to or below LODs of the two laboratories, BRGM (the French geological survey) and LDA26 (one of the French Departmental Analytical Laboratories), requested in FWI pollution monitoring that used liquid-liquid extractions and advanced facilities (LLE-GC-MS/MS and LLE-LC-MS/MS methods, respectively). Then, we extended the multi-residue method to 30 OCs (CLD and its TPs, mirex, ß-HCH, lindane, dieldrin, aldrin, HCB, hexachlorobutadiene, TCE, PCE) and applied it to 30 surface and ground waters from FWI. While CLD, 8- and 10-monohydroCLD, CLDOH, 10-monohydroCLDOH, dieldrin, and ß-HCH were detected and quantified, pentachloroindene, another CLD TP, was sporadically found in trace levels. A comparison with BRGM and LDA26 confirmed the interest of the SPME method. Results suggested an underestimation of CLDOH and an overestimation of high CLD concentrations with one of the currently used routine protocol. In light of these findings, previous temporal monitoring of environmental waters in FWI were re-examined and revealed some atypical values, which may indeed be due to analytical bias. These discrepancies call for intensified efforts to reliably quantify CLD and its TPs.

Post Natal Microbial and Metabolite Transmission: The Path from Mother to Infant.

The entero-mammary pathway is a specialized route that selectively translocates bacteria to the newborn's gut, playing a crucial role in neonatal development. Previous studies report shared bacterial and archaeal taxa between human milk and neonatal intestine. However, the functional implications for neonatal development are not fully understood due to limited evidence. This study aimed to identify and characterize the microbiota and metabolome of human milk, mother, and infant stool samples using high-throughput DNA sequencing and FT-ICR MS methodology at delivery and 4 months post-partum. Twenty-one mothers and twenty-five infants were included in this study. Our results on bacterial composition suggest vertical transmission of bacteria through breastfeeding, with major changes occurring during the first 4 months of life. Metabolite chemical characterization sheds light on the growing complexity of the metabolites. Further data integration and network analysis disclosed the interactions between different bacteria and metabolites in the biological system as well as possible unknown pathways. Our findings suggest a shared bacteriome in breastfed mother-neonate pairs, influenced by maternal lifestyle and delivery conditions, serving as probiotic agents in infants for their healthy development. Also, the presence of food biomarkers in infants suggests their origin from breast milk, implying selective vertical transmission of these features.

Cultivation of Chlorella vulgaris in wastewater: biodiesel potential and wastewater remediation.

The present investigation has evaluated the use of effluents from a secondary municipal wastewater treatment plant for biomass production and potential of the biomass for biodiesel production. Cultivations of Chlorella vulgaris using wastewater, wastewater with supplementation, and WC medium were carried out. Effect of wastewater collected in different months on biomass productivity (BP) and lipid composition was studied. Methods based on NMR and GC-MS techniques were applied for determining the composition of the lipids and their fatty acid profile including poly unsaturated fatty acids (PUFAs). Lipids extracted are comprised of both neutral (tri acyl glycerides, TAG; free fatty acids, FFA) and polar (glyco glycero/phospho) lipids. The TAG content of the extracted lipids was determined in the range of 22.5-41.3% w/w. The NMR and GC-MS compositional results of microalgal lipids of biomasses cultivated in wastewater without nutrient supplementation, collected in different months, showed potential for biodiesel production. The fatty acid profiles of neutral and polar lipids, which are mainly comprised of saturated and unsaturated long alkyl chain (C16-C22) fatty acids, are potential sources for the biodiesel and food industry. The concentration of nitrates (45-78 mg L-1) in wastewater without supplementation, collected in different months, was found to be optimum to enable cultivation of biomasses with reasonably good BP of 21.5-28.1 mg L-1 day-1. Similar results have been obtained in the present work as well as reported in the literature in the case of WC medium (nitrate, 69 mg L-1) with BP of 25.5-28.2 mg L-1 day-1, thus highlighted the significance of the presented work.

Identification of Novel Bacterial Microproteins Encoded by Small Open Reading Frames Using a Computational Proteogenomics Workflow.

Genome annotation has historically ignored small open reading frames (smORFs), which encode a class of proteins shorter than 100 amino acids, collectively referred to as microproteins. This cutoff was established to avoid thousands of false positives due to limitations of pure genomics pipelines. Proteogenomics, a computational approach that combines genomics, transcriptomics, and proteomics, makes it possible to accurately identify these short sequences by overlaying different levels of omics evidence. In this chapter, we showcase the use of µProteInS, a bioinformatics pipeline developed for the identification of unannotated microproteins encoded by smORFs in bacteria. The workflow covers all the steps from quality control and transcriptome assembly to the scoring and post-processing of mass spectrometry data. Additionally, we provide an example on how to apply the pipeline's machine learning method to identify high-confidence spectra and pinpoint the most reliable identifications from large datasets.