In Silico Functional Annotation of E2102 Hypothetical Protein from Aeromonas veronii

IntroductionSkin and soft tissue infections are common because of exposure to aquatic environment, while severe infections caused by Aeromonas veronii are rare.Case presentationWe report a case of severe skin and soft tissue infection of the left upper limb caused by Aeromonas veronii. A 50-year-old Chinese woman, who had a history of cardiac disease and type 2 diabetes mellitus, accidentally injured her left thumb while cutting a fish. Early antibiotic therapy and surgical debridement was performed before the result of bacterial culture came back. Whole-genome sequencing was further performed to confirm the pathogen and reveal the drug resistance and virulence genes. The wound was gradually repaired after 1 month of treatment, and the left hand recovered well in appearance and function after 3 months of rehabilitation.ConclusionEarly diagnosis, surgical intervention, and administration of appropriate antibiotics are crucial for patients who are suspected of having skin and soft tissue infection, or septicemia caused by Aeromonas veronii.

Bikram DasBackground Aeromonas is a water-dwelling Gram-negative bacillus primarily associated with gastrointestinal tract diseases. Aeromonas sobria causing gastroenteritis has been reported in India. In immunocompromised host, Aeromonas sobria can also present with severe necrotizing skin and soft tissue infection with a high mortality rate. We report a case of Aeromonas sobria sepsis with skin and soft tissue infection in the background of immunosuppression. Case Presentation Fifty-year-old male who underwent an unrelated donor peripheral stem cell transplant for relapsed pre-B acute lymphoblastic leukemia in complete clinical remission on graft versus host disease prophylaxis, post-white blood cell engraftment presented with acute onset lethargy, lower limb pain without fever, or any skin changes initially. He rapidly worsened clinically over few days and developed sepsis, multiorgan dysfunction with the appearance of erythema and blister over the lower limb, and Fournier's gangrene of scrotum. He was found to have Aeromonas sobria bacteremia with isolated resistance to carbapenems while sensitive to all other classes of antibiotics. Despite appropriate antibiotic therapy and supportive measures, he succumbed to death for this invasive bacterial disease. Conclusion Aeromonas should be considered a cause of sepsis in immunosuppressed hosts, especially those with hematological malignancy presenting with necrotizing skin and soft tissue infection. Considering the virulence of this pathogen, despite the very susceptible antibiogram, such patients must be managed aggressively. Early recognition of the disease with a combination of medical and surgical management might help to improve the outcome.

Structural Analysis of the Group II Intron Splicing Factor CRS2 Yields Insights into its Protein and RNA Interaction Surfaces

BackgroundAntibiotic resistance and limited treatment options for severe pathogenic intestinal infections beyond Clostridioides difficile infection (CDI) pose a growing challenge. The purpose of this study is to investigate the potential...

The present study was conducted to examine TAGAP gene of selected mammalian species (Cattle, White tufted ear marmoset, Dog, American Beaver, Beluga whale, Horse, Western European Hedgehog, Western lowland Gorilla, Human, Yangtze River Dolphin, Golden Hamster, Mouse, Yangtze finless porpoise, American Mink, Pacific Walrus, Duckbill platypus, Rat, Bolivian Squirrel Monkey, American black bear, Polar Bear and Western Clawed Frog) by evaluating similarity and identity, evolutionary relationship, physicochemical properties, secondary and tertiary structures, and protein-protein interaction. Amino acid and nucleotide sequences were retrieved using UniProt and NCBI. Using MUSCLE integrated in IVisTMSA the MSA (Multiple Sequence Alignment) was produced, while identity and similarity percentage were determined by E-SICT integrated in IVisTMSA. At the end of the experiment, the results showed that there was lowest similarity and identity percentage (40%) among frog and other selected mammalian species. The evolutionary relationship of human and gorilla, mouse and rat evolves from same cluster while all other mammalian species expands cluster according to their related classes. Physicochemical properties of TAGAP protein revealed that Dog TAGAP protein was the least theoretical pI (5.44) while Duckbill Platypus was the highest (8.46) and protein was found to be not only an intra-cytoplasmic protein but also a soluble protein in all selected mammalian species. The secondary structure included the alpha helix, extended strand, and random coil. It can be concluded that TAGAP gene has identical homologue, functional similarity and highly conserved in all selected mammalian species except Western Clawed Frog. Keywords: TAGAP gene, in-silico analysis, evolution, motifs, STRING, Protein-Protein Interaction (PPI)

Herpesviral capsids are assembled in the host cell nucleus and are subsequently translocated to the cytoplasm. During this process it has been demonstrated that the human cytomegalovirus proteins pUL50 and pUL53 interact and form, together with other viral and cellular proteins, the nuclear egress complex at the nuclear envelope. In this study we provide evidence that specific residues of a conserved N-terminal region of pUL50 determine its intranuclear interaction with pUL53. In silico evaluation and biophysical analyses suggested that the conserved region forms a regular secondary structure adopting a globular fold. Importantly, site-directed replacement of individual amino acids by alanine indicated a strong functional influence of specific residues inside this globular domain. In particular, mutation of the widely conserved residues Glu-56 or Tyr-57 led to a loss of interaction with pUL53. Consistent with the loss of binding properties, mutants E56A and Y57A showed a defective function in the recruitment of pUL53 to the nuclear envelope in expression plasmid-transfected and human cytomegalovirus-infected cells. In addition, in silico analysis suggested that residues 3-20 form an amphipathic α-helix that appears to be conserved among Herpesviridae. Point mutants revealed a structural role of this N-terminal α-helix for pUL50 stability rather than a direct role in the binding of pUL53. In contrast, the central part of the globular domain including Glu-56 and Tyr-57 is directly responsible for the functional interaction with pUL53 and thus determines formation of the basic nuclear egress complex.

Objective Leptin is an important protein hormone produced by white adipose tissue, which participates in the regulation of energy metabolism. Its research on improving metabolic mechanism after bariatric surgery is attracting more and more attention. The purpose of this study is to analyze Leptin’s structure and predict its function by bioinformatics, in order to further explore the role of leptin in the treatment of obesity by bariatric surgery. Methods Tools of ExPASy Server were employed to analyze the physicochemical properties of Leptin protein. The secondary structure was predicted by Jpred 4 and its three-level structure by Swiss-Mode. STRINGS database is used to predict interactions between Leptin and other proteins. Results The Leptin protein consisted of 167 amino acids with an isoelectric point of 5.88, an instability index of 47.52, and a fat coefficient of 110.84. There were 5 α-helicesand 1 β-sheet in the secondary structure prediction. The number of amino acids constituting alpha helix accounted for 50.9% of the total protein. Three possible tertiary structure models were simulated. From the prediction model, the protein was mainly alpha-helix, which was consistent with the prediction results of secondary structure. According to the trend of similar waveform, prediction model A is the most stable. The protein interaction network found that the protein families interacting with Leptin include Leptin receptor (LEPR), Signal transducer and activator of transcription 3 (STAT3), Peroxisome proliferator-activated receptor gamma (PPARG), Suppressor of cytokine signaling 3 (SOCS3), Glucagon (GCG), Tyrosine-protein kinase JAK2, Insulin receptor substrate 1 (IRS1), C-reactive protein (CRP), Tyrosine-protein phosphatase non-receptor type 1 (PTPN1) and Insulin (INS). Conclusion Leptin protein is an unstable lipophilic protein mainly composed of alpha-helix. It is secreted by white adipose tissue and mainly acts on the outside of cells. It inhibits the synthesis of adipocytes by participating in the regulation of sugar, fat and energy metabolism, thus reducing body weight. Key words: Leptin; Bariatric Surgery; Bioinformatics

Aeromonas species are opportunistic bacteria causing a vast spectrum of human diseases, including skin and soft tissue infections, meningitis, endocarditis, peritonitis, gastroenteritis, and finally hemorrhagic septicemia. The aim of our research was to indicate the molecular alterations in proteins and lipids profiles resulting from Aeromonas sobria and A. salmonicida subsp. salmonicida infection in trout kidney tissue samples. We successfully applied FT-IR (Fourier transform infrared) spectroscopy and MALDI-MSI (matrix-assisted laser desorption/ionization mass spectrometry imaging) to monitor changes in the structure and compositions of lipids, secondary conformation of proteins, and provide useful information concerning disease progression. Our findings indicate that the following spectral bands’ absorbance ratios (spectral biomarkers) can be used to discriminate healthy tissue from pathologically altered tissue, for example, lipids (CH2/CH3), amide I/amide II, amide I/CH2 and amide I/CH3. Spectral data obtained from 10 single measurements of each specimen indicate numerous abnormalities concerning proteins, lipids, and phospholipids induced by Aeromonas infection, suggesting significant disruption of the cell membranes. Moreover, the increase in the content of lysolipids such as lysophosphosphatidylcholine was observed. The results of this study suggest the application of both methods MALDI-MSI and FT-IR as accurate methods for profiling biomolecules and identifying biochemical changes in kidney tissue during the progression of Aeromonas infection.

1. Kohashi T, Sakai H, Marumo F, Sato C: Aeromonas sobria infection with severe muscle degeneration in a patient with alcoholic liver cirrhosis. American Journal of Gastroenterology (1995) 90 :2234–2235 2. Daily OP, Joseph SW, Coolbaugh JC, Walker RI, Merrell BR, Rollins DM, Seidler RJ, Colwell RR, Lissner CR: Association of Aeromonas sobria with human infection. Journal of Clinical Microbiology (1981) 13 :769–777 3. Gold WL, Salit IE: Aeromonas hydrophila infections of skin and soft tissue: report of 11 cases and review. Clinical Infectious Diseases (1993) 16 :69–74 4. King GE, Werner SB, Kizer KW: Epidemiology of Aeromonas infections in California. Clinical Infectious Diseases (1992) 15 :449–452 5. Snower DP, Ruef C, Kuritza AP, Edberg SC: Aeromonas hydrophila infection associated with the use of medicinal leeches. Journal of Clinical Microbiology (1989) 27 :1421–1422 6. Lineaweaver WC, Hill MK, Buncke GM, Follansbee S, Buncke HJ, Wong RKM, Manders EK, Grotting JC, Anthony J, Mathes SJ: Aeromonas hydrophila infections following use of medicinal leeches in replantation and flap surgery. Annals of Plastic Surgery (1992) 29 :238–244 7. Adams SL: The medicinal leech. Annals of Internal Medicine (1988) 109 :399–405 8. Kelly KA, Koelher JM, Ashdown LR: Spectrum of extraintestinal disease due to Aeromonas species in tropical Queensland, Australia. Clinical Infectious Diseases (1993) 16 :574–579 9. Janda JM, Brenden R: Importance of Aeromonas sobria in Aeromonas bacteremia. Journal of Infectious Diseases (1987) 155 :589–591 10. Koelher JM, Ashdown LR: In vitro susceptibilities of tropical strains of Aeromonas species in tropical Queensland, Australia, to 22 antimicrobial agents. Antimicrobial Agents and Chemotherapy (1993) 37 :905–907 11. Jones BL, Wilcox MH: Aeromonas infections and their treatment. Journal of Antimicrobial Chemotherapy (1995) 35 :453–461

Clinical significance and distribution of putative virulence markers of 116 consecutive clinical Aeromonas isolates in southern Taiwan

Aeromonas veronii is an important zoonotic and aquatic pathogen that causes a number of illnesses in both humans and animals. It is related to gastroenteritis, skin and soft tissue infections and bacteremia in humans, as well as causing significant economic losses in aquaculture owing to fish sepsis. Here, we constructed the flagellar cap gene (fliD) mutant strain of A. veronii by suicide plasmid-mediated homologous recombination system and analysed its characteristics. It was found that the deletion of fliD had no effect on growth and biochemical properties and could be inherited stably. However, the motility of A. veronii ΔfliD was significantly reduced, the flagellum was defective and the biofilm formation was attenuated compared with that of A. veronii wild-type strain. In vivo experiments revealed that the colonization capacity of ΔfliD was significantly lower than that of the wild-type strain in the period of first 24 h, and the median lethal dose (LD50 ) was 56 times higher than that of the wild-type strain. The Cyprinus carpio infected with the wild-type strain indicated faster death speed and more severe clinical signs compared to ΔfliD strain. These results suggest that fliD is closely related to the virulence of A. veronii and plays an important role in pathogenicity, providing the foundation for pathogenic mechanism studies of A. veronii.

Aeromonas sobria causes a rare Gram-negative bacterial water-borne infection. It has been found in waters of North Queensland and South-east Asia. Of all Aeromonas species, A. sobria is the most virulent and invasive and has been reported to cause soft tissue infection and corneal ulcer. A 14-year-old Caucasian male from North Queensland presented following a penetrating eye injury in which a water bird (cormorant species) had pecked his eye while he was fishing. A fulminant endophthalmitis developed despite treatment with intravenous, intravitreal and topical antibiotics and initial wound repair. Enucleation was performed. Aeromonas sobria was isolated from the vitreous aspirate. Aeromonas sobria infection should be suspected in water-contaminated penetrating eye injuries. The prognosis in this case was poor.

Increasing risk of radiation exposure can be due to various reasons such as terrorist attacks, detonation of nuclear reactors, nuclear weapons, as well as acute radiation exposure on large scale poses high risk to humankind. Therefore, there is a critical need of identification and authentication of fast and early-response radiation induced harm biomarkers to distinguish between exposed and non-exposed individuals on a large-scale basis. This study deals with structural characterization of radiation induced proteins that are probable biomarkers such as Flt3L using database tools such as prot-param for physio-chemical properties, GOR IV to predict the secondary structure, swiss modelling for 3D model of protein, stitch and string analysis for protein-chemical interaction and protein-protein interaction respectively. In-silico analysis showcasing, protein Flt3L physical parameters such as theoretical PI 8.72, hydrophobicity 0.100, aliphatic index 111.81. Secondary structure, alpha helix 41.38%, extended strand 11.64%. Homology modelling showing sequence identity 74.26%, coverage 0.50 and range 1-101. In stich, Flt3 activating KITLG and showing binding affinity to Zn molecule. Identification of protein-protein interacting functional partner of Flt3L using string shows interactions with polyubiquitin-C (UBC), KITLG, Nras proto onco genes, etc, it showed experimental evidence of Flt3L and KITLG protein. Hence, by using in-silico analysis we can perform a preliminary study to predict the structures and chemical interaction of potential radiation induced probable biomarkers that can be utilized for rapid detection of radiation exposure and drugdiscovery.

There has been a multiple evidence of enteroviral infection reported in human which cause various diseases. The work is based on in-silico analysis of coksackie virus induced Insulin Dependent Diabetes Mellitus(IDDM) and the possible interactions between host and viral proteins.The infection of this coxsackie virus strain has been reported to cause IDDM. The exact pathway of the viral-host protein interactions are still unknown. We used IntAct database and found that the viral VP4 protein interacts with the DAF proteins of Human beta cells. The DAF protein is responsible for prevention of compliment attacks in the host cell.The microarray data and the viral-host gene interaction pathways are used to understand the infection progression pathway. Protein-protein docking was used to obtain the locus for the viral protein(VP4) and host protein(DAF) interaction (Etotal value -444.41 EShape value -444.41). The data obtained from protein-protein docking became the basis of this research. The amino acid involved in VP4-DAF interaction was found by analyzing the docked complex, using ArgusLab.The VP4 proteindrug complex failed to bind the beta cell DAF receptor. By using linkage maps we found the evolutionary linkage of coksackie virus B4 strain. This helped in gathering information about possible mutations in viral genome which was useful in designing the drug using Desloratadine and Cannabidiol as a template which could bind to conserved domain of VP4 protein near DAF binding site to prevent VP4-DAF interaction. The drug molecule was converted into pdb format and docked. We selected drug configuration showing best drug-protein complex E value after docking.

This prospective study aimed to investigate the clinical and microbiological characteristics of different Aeromonas species. Clinical isolates of Aeromonas species between 2016 to 2018 were collected in a university hospital in southern Taiwan. The species was determined by rpoD or gyrB sequencing. A total of 222 Aeromonas isolates from 160 patients in 164 episodes were identified. The crude in-hospital mortality was 17.2%. The most frequently isolated species was Aeromonas veronii (30.6%), followed by A. caviae (24.8%), A. hydrophila (23%), and A. dhakensis (16.7%). The major clinical manifestations were primary bacteremia (31.1%), skin and soft tissue infection (22.6%), and biliary tract infection (18.3%). The most common underlying diseases were malignancy (45.1%), diabetes mellitus (27.4%), and liver cirrhosis or chronic hepatitis (26.2%). A. hydrophila and A. dhakensis predominated in the skin and soft tissue infection (p<0.0001), whereas A. vernoii and A. caviae prevailed in primary bacteremia and biliary tract infections (p=0.012). Pneumonia, malignancy, and ascF-ascG genotype were independent factors associated with mortality. Ertapenem susceptibility was decreased in A. sobria (42.9%), A. veronii (66.7%), A. dhakensis (73%), and A. hydrophila (84.3%). Cefotaxime resistance was found in 30.9% of A. caviae and 18.9% of A. dhakensis isolates, much more prevalent than the other species. The metallo-β-lactamase blaCphA was almost invariably present in A. dhakensis, A. hydrophila, and A. veronii (100%, 100% and 89.9%, respectively). Amp-C β-lactamases such as blaMOX and blaAQU-1 were identified in all A. caviae and 91.9% of A. dhakensis isolates. Cefepime, fluoroquinolones and tigecycline showed good in vitro activity against aeromonads.