Browsing by Author "Elmassry, Moamen M. (TTU)"
Now showing 1 - 10 of 10
- Results Per Page
- Sort Options
Item Anti-Pseudomonas aeruginosa Vaccines and Therapies: An Assessment of Clinical Trials(2023) Elmassry, Moamen M. (TTU); Colmer-Hamood, Jane A. (TTUHSC); Kopel, Jonathan (TTUHSC); San Francisco, Michael J. (TTU); Hamood, Abdul N. (TTUHSC)Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that causes high morbidity and mortality in cystic fibrosis (CF) and immunocompromised patients, including patients with ventilator-associated pneumonia (VAP), severely burned patients, and patients with surgical wounds. Due to the intrinsic and extrinsic antibiotic resistance mechanisms, the ability to produce several cell-associated and extracellular virulence factors, and the capacity to adapt to several environmental conditions, eradicating P. aeruginosa within infected patients is difficult. Pseudomonas aeruginosa is one of the six multi-drug-resistant pathogens (ESKAPE) considered by the World Health Organization (WHO) as an entire group for which the development of novel antibiotics is urgently needed. In the United States (US) and within the last several years, P. aeruginosa caused 27% of deaths and approximately USD 767 million annually in health-care costs. Several P. aeruginosa therapies, including new antimicrobial agents, derivatives of existing antibiotics, novel antimicrobial agents such as bacteriophages and their chelators, potential vaccines targeting specific virulence factors, and immunotherapies have been developed. Within the last 2–3 decades, the efficacy of these different treatments was tested in clinical and preclinical trials. Despite these trials, no P. aeruginosa treatment is currently approved or available. In this review, we examined several of these clinicals, specifically those designed to combat P. aeruginosa infections in CF patients, patients with P. aeruginosa VAP, and P. aeruginosa–infected burn patients.Item During bacteremia, Pseudomonas aeruginosa PAO1 adapts by altering the expression of numerous virulence genes including those involved in quorum sensing(2020) Beasley, Kellsie L. (TTUHSC); Cristy, Shane A. (TTU); Elmassry, Moamen M. (TTU); Dzvova, Nyaradzo (TTUHSC); Colmer-Hamood, Jane A. (TTUHSC); Hamood, Abdul N. (TTUHSC)Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that produces numerous virulence factors and causes serious infections in trauma patients and patients with severe burns. We previously showed that the growth of P. aeruginosa in blood from severely burned or trauma patients altered the expression of numerous genes. However, the specific influence of whole blood from healthy volunteers on P. aeruginosa gene expression is not known. Transcriptome analysis of P. aeruginosa grown for 4 h in blood from healthy volunteers compared to that when grown in laboratory medium revealed that the expression of 1085 genes was significantly altered. Quorum sensing (QS), QS-related, and pyochelin synthesis genes were downregulated, while genes of the type III secretion system and those for pyoverdine synthesis were upregulated. The observed effect on the QS and QS-related genes was shown to reside within serum fraction: growth of PAO1 in the presence of 10% human serum from healthy volunteers significantly reduced the expression of QS and QS-regulated genes at 2 and 4 h of growth but significantly enhanced their expression at 8 h. Additionally, the production of QS-regulated virulence factors, including LasA and pyocyanin, was also influenced by the presence of human serum. Serum fractionation experiments revealed that part of the observed effect resides within the serum fraction containing <10-kDa proteins. Growth in serum reduced the production of many PAO1 outer membrane proteins but enhanced the production of others including OprF, a protein previously shown to play a role in the regulation of QS gene expression. These results suggest that factor(s) within human serum: 1) impact P. aeruginosa pathogenesis by influencing the expression of different genes; 2) differentially regulate the expression of QS and QS-related genes in a growth phase- or time-dependent mechanism; and 3) manipulate the production of P. aeruginosa outer membrane proteins.Item GeneHummus: An R package to define gene families and their expression in legumes and beyond(2019) Die, Jose V.; Elmassry, Moamen M. (TTU); LeBlanc, Kimberly H.; Awe, Olaitan I.; Dillman, Allissa; Busby, BenBackground: During the last decade, plant biotechnological laboratories have sparked a monumental revolution with the rapid development of next sequencing technologies at affordable prices. Soon, these sequencing technologies and assembling of whole genomes will extend beyond the plant computational biologists and become commonplace within the plant biology disciplines. The current availability of large-scale genomic resources for non-traditional plant model systems (the so-called 'orphan crops') is enabling the construction of high-density integrated physical and genetic linkage maps with potential applications in plant breeding. The newly available fully sequenced plant genomes represent an incredible opportunity for comparative analyses that may reveal new aspects of genome biology and evolution. The analysis of the expansion and evolution of gene families across species is a common approach to infer biological functions. To date, the extent and role of gene families in plants has only been partially addressed and many gene families remain to be investigated. Manual identification of gene families is highly time-consuming and laborious, requiring an iterative process of manual and computational analysis to identify members of a given family, typically combining numerous BLAST searches and manually cleaning data. Due to the increasing abundance of genome sequences and the agronomical interest in plant gene families, the field needs a clear, automated annotation tool. Results: Here, we present the geneHummus package, an R-based pipeline for the identification and characterization of plant gene families. The impact of this pipeline comes from a reduction in hands-on annotation time combined with high specificity and sensitivity in extracting only proteins from the RefSeq database and providing the conserved domain architectures based on SPARCLE. As a case study we focused on the auxin receptor factors gene (ARF) family in Cicer arietinum (chickpea) and other legumes. Conclusion: We anticipate that our pipeline should be suitable for any taxonomic plant family, and likely other gene families, vastly improving the speed and ease of genomic data processing.Item Geranylgeraniol and Green Tea Polyphenols Mitigate Negative Effects of a High-Fat Diet on Skeletal Muscle and the Gut Microbiome in Male C57BL/6J Mice(2022) Shen, Chwan Li; Elmassry, Moamen M. (TTU); Grue, Katherine (TTU); Joiner, Hayli E. (TTU); Jacobo, A. Unique (TTU); Hamood, Abdul; Chung, EunheeNatural bioactive compounds are proposed as alternatives in mitigating obesity-associated skeletal muscle dysfunction. The objective of this study was to test the hypothesis that the combination of geranylgeraniol (GGOH) and green tea polyphenols (GTPs) can alleviate high-fat-diet (HFD)-induced muscle atrophy and alter gut microbiome composition. Male C57BL/6J mice fed an HFD were assigned to four groups (12 mice each) in a 2 (no GGOH vs. 400 mg GGOH/kg diet) × 2 (no GTPs vs. 0.5% weight/volume GTPs in water) factorial design. After 14 weeks of diet intervention, skeletal muscle and cecal samples were collected and examined. Compared to the control groups, the group that consumed a combination of GGOH and GTPs (GG + GTPs) had significantly decreased body and fat mass but increased skeletal muscle mass normalized by body weight and cross-sectional area. In soleus muscle, the GG + GTP diet increased citrate synthase activity but decreased lipid peroxidation. Gut microbiome beta-diversity analysis revealed a significant difference in the microbiome composition between diet groups. At the species level, the GG + GTP diet decreased the relative abundance of Dorea longicatena, Sporobacter termitidis, and Clostridium methylpentosum, and increased that of Akkermansia muciniphila and Subdoligranulum variabile. These results suggest that the addition of GGOH and GTPs to an HFD alleviates skeletal muscle atrophy, which is associated with changes in the gut microbiome composition.Item Metabolic benefits of annatto-extracted tocotrienol on glucose homeostasis, inflammation, and gut microbiome(2020) Chung, Eunhee; Elmassry, Moamen M. (TTU); Kottapalli, Pratibha; Kottapalli, Kameswara Rao; Kaur, Gurvinder (TTUHSC) (TTU); Dufour, Jannette M. (TTUHSC) (TTU); Wright, Kandis (TTUHSC); Ramalingam, Latha (TTUHSC) (TTU); Moustaid-Moussa, Naima (TTUHSC) (TTU); Wang, Rui (TTUHSC); Hamood, Abdul N. (TTUHSC); Shen, Chwan Li (TTUHSC) (TTU)Emerging evidence suggests that the gut microbiome plays an important role in the pathophysiology of both obesity and type 2 diabetes mellitus. We previously reported that dietary annatto-extracted tocotrienol exerts beneficial effects by modulating inflammatory responses in mice fed a high-fat diet (HFD). The purpose of this study was to test the hypothesis that tocotrienol supplementation when combined with an HFD would result in an altered gut microbiota composition. For 14 weeks, forty-eight male C57BL/6J mice were assigned to 4 groups—low-fat diet, HFD, HFD supplemented with annatto-extracted tocotrienol at 800 mg/kg diet (AT), and HFD supplemented with metformin at 200 mg/kg diet. Glucose homeostasis was assessed by glucose and insulin tolerance tests, serum and pancreas insulin levels, and histological assessments of insulin and glucagon in pancreatic tissue. The concentrations of adipokines were measured in white adipose tissues. For the gut microbiome analysis, cecal content was collected, DNA was extracted, and 16S rRNA gene sequencing was performed. AT supplementation improved glucose homeostasis and lowered resistin, leptin, and interleukin-6 levels in white adipose tissue. Relative to the HFD group, AT-supplemented mice showed a decrease in the Firmicutes to Bacteroidetes ratio and had a lower abundance of Ruminococcus lactaris, Dorea longicatena, and Lachnospiraceae family. The relative abundance of Akkermansia muciniphila was increased in the AT group compared to the low-fat diet group. The association between the metabolic improvements and the identified bacterial taxa suggests a potential metabolic modulation caused by AT supplementation through the gut microbiota composition in mice fed an HFD.Item Pseudomonas aeruginosa Alters Its Transcriptome Related to Carbon Metabolism and Virulence as a Possible Survival Strategy in Blood from Trauma Patients(2019) Elmassry, Moamen M. (TTU); Mudaliar, Nithya S. (TTUHSC); Kottapalli, Kameswara Rao (TTU); Dissanaike, Sharmila (TTUHSC); Griswold, John A. (TTUHSC); San Francisco, Michael J. (TTU); Colmer-Hamood, Jane A. (TTUHSC); Hamood, Abdul N. (TTUHSC)Trauma patients (TPs) are highly susceptible to infections, which often lead to sepsis. Among the numerous causative agents, Pseudomonas aeruginosa is especially important, as P. aeruginosa sepsis is often fatal. Understanding the mechanism of its pathogenesis in bloodstream infections is imperative; however, this mechanism has not been previously described. To examine the effect of trauma-induced changes in blood on the expression of P. aeruginosa genes, we grew strain UCBPP-PA14 (PA14) in blood samples from eight TPs and seven healthy volunteers (HVs). Compared with its growth in blood from HVs, the growth of PA14 in blood from TPs significantly altered the expression of 285 genes. Genes whose expression was significantly increased were related to carbon metabolism, especially malonate utilization and mannitol uptake, and efflux of heavy metals. Genes whose expression was significantly reduced included genes of the type VI secretion system, genes related to uptake and metabolism of amino acids, and genes related to biosynthesis and transport of the siderophores pyoverdine and pyochelin. These results suggest that during systemic infection in trauma patients, and to adapt to the trauma-induced changes in blood, P. aeruginosa adjusts positively and negatively the expression of numerous genes related to carbon metabolism and virulence, respectively. IMPORTANCE While a considerable body of knowledge regarding sepsis in trauma patients is available, the potential influence of trauma-induced changes in the blood of these patients on the pathogenesis of Pseudomonas aeruginosa is basically an unexplored area. Rather than using standard laboratory media, we grew P. aeruginosa in whole blood from either healthy volunteers or trauma patients. The specific changes in the P. aeruginosa transcriptome in response to growth in blood from trauma patients reflect the adaptation of this organism to the bloodstream environment. This knowledge is vital for understanding the strategies this pathogen uses to adapt and survive within the host during systemic infection. Such information will help researchers and clinicians to develop new approaches for treatment of sepsis caused by P. aeruginosa in trauma patients, especially in terms of recognizing the effects of specific therapies (e.g., iron, zinc, or mannitol) on the organism. Further, this information can most likely be extrapolated to all patients with P. aeruginosa septicemia.Item Revealing the constituents of Egypt’s oldest beer using infrared and mass spectrometry(2019) Farag, Mohamed A.; Elmassry, Moamen M. (TTU); Baba, Masahiro; Friedman, RenéePrevious studies have shown that the Ancient Egyptians used malted wheat and barley as the main ingredients in beer brewing, but the chemical determination of the exact recipe is still lacking. To investigate the constituents of ancient beer, we conducted a detailed IR and GC-MS based metabolite analyses targeting volatile and non-volatile metabolites on the residues recovered from the interior of vats in what is currently the world’s oldest (c. 3600 BCE) installation for large-scale beer production located at the major pre-pharaonic political center at Hierakonpolis, Egypt. In addition to distinguishing the chemical signatures of various flavoring agents, such as dates, a significant result of our analysis is the finding, for the first time, of phosphoric acid in high level probably used as a preservative much like in modern beverages. This suggests that the early brewers had acquired the knowledge needed to efficiently produce and preserve large quantities of beer. This study provides the most detailed chemical profile of an ancient beer using modern spectrometric techniques and providing evidence for the likely starting materials used in beer brewing.Item Sixty-One Volatiles Have Phylogenetic Signals Across Bacterial Domain and Fungal Kingdom(2020) Elmassry, Moamen M. (TTU); Farag, Mohamed A.; Preissner, Robert; Gohlke, Björn Oliver; Piechulla, Birgit; Lemfack, Marie C.Microorganisms are diverse in their genome sequences and subsequently in their encoded metabolic pathways, which enabled them to adapt to numerous environmental conditions. They produce thousands of small molecules, many of which are volatiles in nature and play important roles in signaling in intra- and inter-species to kingdom and domain interactions, survival, or virulence. Many of these compounds have been studied, characterized, and organized in the mVOC 2.0 database. However, such dataset has not been investigated comprehensively in terms of its phylogeny to determine key volatile markers for certain taxa. It was hypothesized that some of the volatiles described in the mVOC 2.0 database could function as a phylogenetic signal since their production is conserved among certain taxa within the microbial evolutionary tree. Our meta-analysis revealed that some volatiles were produced by a large number of bacteria but not in fungal genera such as dimethyl disulfide, acetic acid, 2-nonanone, dimethyl trisulfide, 2-undecanone, isovaleric acid, 2-tridecanone, propanoic acid, and indole (common bacterial compounds). In contrast, 1-octen-3-ol, 3-octanone, and 2-pentylfuran (common fungal compounds) were produced primarily by fungal genera. Such chemical information was further confirmed by investigating genomic data of publicly available databases revealing that bacteria or fungi harbor gene families involved in these volatiles’ biosynthesis. Our phylogenetic signal testing identified 61 volatiles with a significant phylogenetic signal as demonstrated by phylogenetic D statistic P-value < 0.05. Thirty-three volatiles were phylogenetically conserved in the bacterial domain (e.g., cyclocitral) compared to 17 volatiles phylogenetically conserved in the fungal kingdom (e.g., aristolochene), whereas 11 volatiles were phylogenetically conserved in genera from both bacteria and fungi (e.g., geosmin). These volatiles belong to different chemical classes such as heterocyclic compounds, long-chain fatty acids, sesquiterpenoids, and aromatics. The performed approaches serve as a starting point to investigate less explored volatiles with potential roles in signaling, antimicrobial therapy, or diagnostics.Item Tai Chi Improves Brain Functional Connectivity and Plasma Lysophosphatidylcholines in Postmenopausal Women With Knee Osteoarthritis: An Exploratory Pilot Study(2022) Shen, Chwan Li (TTUHSC); Watkins, Bruce A.; Kahathuduwa, Chanaka (TTUHSC); Chyu, Ming Chien (TTUHSC); Zabet-Moghaddam, Masoud (TTU); Elmassry, Moamen M. (TTU); Luk, Hui Ying (TTUHSC); Brismée, Jean Michel (TTUHSC); Knox, Ami (TTUHSC); Lee, Jaehoon (TTUHSC); Zumwalt, Mimi (TTUHSC); Wang, Rui (TTUHSC); Wager, Tor D.; Neugebauer, Volker (TTUHSC)Objective: A pre/post pilot study was designed to investigate neurobiological mechanisms and plasma metabolites in an 8-week Tai-Chi (TC) group intervention in subjects with knee osteoarthritis. Methods: Twelve postmenopausal women underwent Tai-Chi group exercise for 8 weeks (60 min/session, three times/week). Outcomes were measured before and after Tai Chi intervention including pain intensity (VAS), Brief Pain Inventory (BPI), Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), plasma metabolites (amino acids and lipids), as well as resting-state functional magnetic resonance imaging (rs-fMRI, 10 min, eyes open), diffusion tensor imaging (DTI, 12 min), and structural MRI (4.5 min) in a subgroup. Clinical data was analyzed using paired t-tests; plasma metabolites were analyzed using Wilcoxon signed-rank tests; and rs-fMRI data were analyzed using seed-based correlations of the left and right amygdala in a two-level mixed-effects model (FSL software). Correlations between amygdala-medial prefrontal cortex (mPFC) connectivity and corresponding changes in clinical outcomes were examined. DTI connectivity of each amygdala was modeled using a Bayesian approach and probabilistic tractography. The associations between neurobiological effects and pain/physical function were examined. Results: Significant pre/post changes were observed with reduced knee pain (VAS with most pain: p = 0.018; WOMAC-pain: p = 0.021; BPI with worst level: p = 0.018) and stiffness (WOMAC-stiffness, p = 0.020), that likely contributed to improved physical function (WOMAC-physical function: p = 0.018) with TC. Moderate to large effect sizes pre/post increase in rs-fMRI connectivity were observed between bilateral mPFC and the amygdala seed regions (i.e., left: d = 0.988, p = 0.355; right: d = 0.600, p = 0.282). Increased DTI connectivity was observed between bilateral mPFC and left amygdala (d = 0.720, p = 0.156). There were moderate-high correlations (r = 0.28–0.60) between TC-associated pre-post changes in amygdala-mPFC functional connectivity and pain/physical function improvement. Significantly higher levels of lysophosphatidylcholines were observed after TC but lower levels of some essential amino acids. Amino acid levels (alanine, lysine, and methionine) were lower after 8 weeks of TC and many of the lipid metabolites were higher after TC. Further, plasma non-HDL cholesterol levels were lower after TC. Conclusion: This pilot study showed moderate to large effect sizes, suggesting an important role that cortico-amygdala interactions related to TC have on pain and physical function in subjects with knee osteoarthritis pain. Metabolite analyses revealed a metabolic shift of higher lyso-lipids and lower amino acids that might suggest greater fatty acid catabolism, protein turnover and changes in lipid redistribution in response to TC exercise. The results also support therapeutic strategies aimed at strengthening functional and structural connectivity between the mPFC and the amygdala. Controlled clinical trials are warranted to confirm these observed preliminary effects.Item The characterization of flavored hookahs aroma profile and in response to heating as analyzed via headspace solid-phase microextraction (SPME) and chemometrics(2018) Farag, Mohamed A.; Elmassry, Moamen M. (TTU); El-Ahmady, Sherweit H.Flavors profiling in flavored hookah tobacco is an issue of increasing scrutiny for the health sector owing to its adverse effects on humans, especially being heated to produce smoke. This study aims at tackling the components involved in the flavored hookah tobacco from a chemical and biological point of view. Detecting individual flavor compounds, within a complex hookah tobacco matrix was accomplished using headspace solid phase microextraction (SPME). A total of 114 volatiles were identified in 13 flavored hookah tobacco products, with esters amounting for the major component up to 40%. Whereas oxygenated monoterpenes presented another major volatile class, contributing up to 23%, including (E)-anethole. Superheating flavored hookah tobacco at 190 °C resulted in the release of a mixture of phenol derivatives and polycyclic aromatic compounds that are indicative of coal tar, a major component produced during hookah tobacco usage with potential health hazards. This study provides the first comprehensive volatile profile of hookah tobacco products from different origins identifying chemical components involved in flavors. It is expected to serve as informative grounds for the better understanding of hookah tobacco production and usage. The information presented is also expected to raise awareness on the health risks of hookah tobacco smoking.