Mass Spectrometry Applications to Study Human Microbiome

Microbiotas are an adaptable component of ecosystems, including human ecology. Microorganisms influence the chemistry of their specialized niche, such as the human gut, as well as the chemistry of distant surroundings, such as other areas of the body. Metabolomics based on mass spectrometry (MS) is one of the primary methods for detecting and identifying small compounds generated by the human microbiota, as well as understanding the functional significance of these microbial metabolites. This book chapter gives basic knowledge on the kinds of untargeted mass spectrometry as well as the data types that may be generated in the context of microbiome study. While data analysis remains a barrier, the emphasis is on data analysis methodologies and integrative analysis, particularly the integration of microbiome sequencing data. Mass spectrometry (MS)-based techniques have resurrected culture methods for studying the human gut microbiota, filling in the gaps left by high-throughput sequencing methods in terms of culturing minor populations.

Applications of Proteomics in Probiotics Having Anticancer and Chemopreventive Properties

Proteomics has grown in importance in molecular sciences because it gives vital information on protein identification, expression levels, and alteration. Cancer is one of the world's major causes of death and is the major focus of much research. Cancer risk is determined by hereditary variables as well as the body's immunological condition. Probiotics have increasing medical importance due to their therapeutic influence on the human body in the prevention and treatment of numerous chronic illnesses, including cancer, with no adverse effects. Several anticancer, anti-inflammatory, and chemopreventive probiotics are studied using different proteomic approaches like two-dimensional gel electrophoresis, liquid chromatography-mass spectrometry, and matrix-assisted laser desorption/ionization mass spectrometry. To gain relevant information about probiotic characteristics, data from the proteomic analysis are evaluated and processed using bioinformatics pipelines. Proteomic studies showed the significance of different proteomic approaches in characterization, comparing strains, and determination of oxidative stress of different probiotics. Moreover, proteomic approaches identified different proteins that are involved in glucose metabolism and the formation of cell walls or cell membranes, and the differences in the expression of critical enzymes in the HIF-1 signaling pathway, starch, and sucrose metabolism, and other critical metabolic pathways.

Associations between Nutrigenomic Effects and Incidences of Microbial Resistance against Novel Antibiotics

Nutrigenomics is the study of the impact of diets or nutrients on gene expression and phenotypes using high-throughput technologies such as transcriptomics, proteomics, metabolomics, etc. The bioactive components of diets and nutrients, as an environmental factor, transmit information through altered gene expression and hence the overall function and traits of the organism. Dietary components and nutrients not only serve as a source of energy but also, through their interactions with genes, regulate gut microbiome composition, the production of metabolites, various biological processes, and finally, health and disease. Antimicrobial resistance in pathogenic and probiotic microorganisms has emerged as a major public health concern due to the presence of antimicrobial resistance genes in various food products. Recent evidence suggests a correlation between the regulation of genes and two-component and other signaling systems that drive antibiotic resistance in response to diets and nutrients. Therefore, diets and nutrients may be alternatively used to overcome antibiotic resistance against novel antibiotics. However, little progress has been made in this direction. In this review, we discuss the possible implementations of nutrigenomics in antibiotic resistance against novel antibiotics.

Advances in the Applications of Bioinformatics and Chemoinformatics

Chemoinformatics involves integrating the principles of physical chemistry with computer-based and information science methodologies, commonly referred to as "in silico techniques", in order to address a wide range of descriptive and prescriptive chemistry issues, including applications to biology, drug discovery, and related molecular areas. On the other hand, the incorporation of machine learning has been considered of high importance in the field of drug design, enabling the extraction of chemical data from enormous compound databases to develop drugs endowed with significant biological features. The present review discusses the field of cheminformatics and proposes the use of virtual chemical libraries in virtual screening methods to increase the probability of discovering novel hit chemicals. The virtual libraries address the need to increase the quality of the compounds as well as discover promising ones. On the other hand, various applications of bioinformatics in disease classification, diagnosis, and identification of multidrug-resistant organisms were discussed. The use of ensemble models and brute-force feature selection methodology has resulted in high accuracy rates for heart disease and COVID-19 diagnosis, along with the role of special formulations for targeting meningitis and Alzheimer's disease. Additionally, the correlation between genomic variations and disease states such as obesity and chronic progressive external ophthalmoplegia, the investigation of the antibacterial activity of pyrazole and benzimidazole-based compounds against resistant microorganisms, and its applications in chemoinformatics for the prediction of drug properties and toxicity-all the previously mentioned-were presented in the current review.

COVID-19 signalome: Pathways for SARS-CoV-2 infection and impact on COVID-19 associated comorbidity

The COVID-19 pandemic has been the focus of research the past two years. The major breakthrough was made by discovering pathways related to SARS-CoV-2 infection through cellular interaction by angiotensin-converting enzyme (ACE2) and cytokine storm. The presence of ACE2 in lungs, intestines, cardiovascular tissues, brain, kidneys, liver, and eyes shows that SARS-CoV-2 may have targeted these organs to further activate intracellular signalling pathways that lead to cytokine release syndrome. It has also been reported that SARS-CoV-2 can hijack coatomer protein-I (COPI) for S protein retrograde trafficking to the endoplasmic reticulum-Golgi intermediate compartment (ERGIC), which, in turn, acts as the assembly site for viral progeny. In infected cells, the newly synthesized S protein in endoplasmic reticulum (ER) is transported first to the Golgi body, and then from the Golgi body to the ERGIC compartment resulting in the formation of specific a motif at the C-terminal end. This review summarizes major events of SARS-CoV-2 infection route, immune response following host-cell infection as an important factor for disease outcome, as well as comorbidity issues of various tissues and organs arising due to COVID-19. Investigations on alterations of host-cell machinery and viral interactions with multiple intracellular signaling pathways could represent a major factor in more effective disease management.

Effectiveness of chondrofascial 'cigar' graft in contouring the nasal dorsum

Irregularities of the nasal dorsum after rhinoplasty are frustrating for the patient and the surgeon. Different grafts and implants have been adopted to camouflage this nasal imperfection. This study was performed to assess the outcome of a composite chondrofascial 'cigar' graft for contouring an irregular nasal dorsum. Thirty-six patients who underwent rhinoplasty between May 2014 and October 2016 were studied prospectively. The cartilaginous core of the graft was obtained from the septal or conchal cartilage, while the graft outer sleeve was harvested from the right lateral thigh fascia lata. The graft was secured over the nasal dorsum through an external rhinoplasty approach. The patients were followed up for at least 18 months postoperative. All participants were evaluated objectively by two independent rhinoplasty surgeons and subjectively by Rhinoplasty Outcome Evaluation (ROE) score. Donor site morbidity was also assessed. All patients had satisfactory aesthetic results with no apparent irregularities detected over the nasal dorsum. The ROE score improved, from a mean of 20.94±8.67 (range 8-58) preoperatively to a mean of 79.56±10.65 (range 50-96) postoperatively. Insignificant donor site morbidity was encountered, with inconsequential effects. The chondrofascial cigar graft is a reliable method for contouring dorsal irregularities, particularly in patients with thin nasal skin.

Olfactory bulb neuroplasticity: A prospective cohort study in patients with chronic rhinosinusitis with nasal polyps

OBJECTIVES

To compare the olfactory bulb volumes (OBVs) in patients with chronic rhinosinusitis with nasal polyps (CRSwNP) to healthy individuals, and to assess the changes of the OBVs in patients with CRSwNP before and after the endoscopic sinus surgery (ESS) utilising magnetic resonance imaging (MRI) with specialised software.

DESIGN

This is a prospective cohort study.

SETTING

Tanta University hospital (tertiary referral hospital), Egypt.

PARTICIPANTS

Thirty patients with CRSwNP (Group A) were compared with thirty healthy individuals (Group B) as regards the OBVs. Patients with CRSwNP underwent ESS where the Smell Identification Test-40 (SIT-40) and the OBVs were assessed pre-operatively and at least 6 months postoperatively. Assessment of the OBVs was carried out using MRI with specialised software.

MAIN OUTCOME MEASURES

Assessment of the volumetric changes of the olfactory bulbs in patients with CRSwNP before and after endoscopic sinus surgery utilise magnetic resonance imaging.

RESULTS

The OBVs were significantly smaller in Group A (58.94 ± 7.96 mm³ and 60.79 ± 8.14 mm³ on the right and left sides, respectively) as compared with the Group B (73.46 ± 8.54 mm³ and 72.96 ± 9.74 mm³ on the right and left sides, respectively). There was also a significant increase in the olfactory bulb volumes as well as improvement of the SIT-40 6 months postoperatively in the Group A.

CONCLUSIONS

The olfactory bulb is characterised by neural plasticity, and its volume may be affected by the peripheral olfactory function.