AbstractFungi are an understudied, biotechnologically valuable group of organisms. Due to the immense range of habitats that fungi inhabit, and the consequent need to compete against a diverse array of other fungi, bacteria, and animals, fungi have developed numerous survival mechanisms. The unique attributes of fungi thus herald great promise for their application in biotechnology and industry. Moreover, fungi can be grown with relative ease, making production at scale viable. The search for fungal biodiversity, and the construction of a living fungi collection, both have incredible economic potential in locating organisms with novel industrial uses that will lead to novel products. This manuscript reviews fifty ways in which fungi can potentially be utilized as biotechnology. We provide notes and examples for each potential exploitation and give examples from our own work and the work of other notable researchers. We also provide a flow chart that can be used to convince funding bodies of the importance of fungi for biotechnological research and as potential products. Fungi have provided the world with penicillin, lovastatin, and other globally significant medicines, and they remain an untapped resource with enormous industrial potential.
Enrico Gugliandolo, Bilal Mghili, Francesca Fabrizi
et al.
This study examines the occurrence of bacteria resistant to antibiotics and heavy metals in Terra Nova Bay, a coastal area of the Ross Sea in Antarctica that is increasingly recognised as vulnerable to human influence. During the 37th Italian Antarctic Expedition (2021–2022), researchers collected seawater, sediment, and fish samples from the notothenioid species <i>Trematomus bernacchii</i> to evaluate microbial resistance in an environment once considered largely pristine. Fifty heterotrophic bacterial isolates were obtained and tested against twenty-eight antibiotics, revealing a notable presence of multidrug resistance. These multidrug-resistant isolates were then assessed for their tolerance to eight heavy metal salts to understand whether resistance traits extended beyond antimicrobials. Twelve isolates showing resistance to both antibiotics and metals were selected for further genetic screening, targeting key resistance genes linked to tetracycline, vancomycin, sulphonamides, and other antimicrobial classes. The detection of multiple resistance genes in genera such as <i>Pseudomonas</i>, <i>Pseudoalteromonas</i>, and <i>Psychrobacter</i> indicates that both natural selective pressures and local, human-related contamination may be shaping resistance patterns in this region. Overall, the study demonstrates that even remote Antarctic marine ecosystems can host bacteria with complex resistance profiles. While these ecosystems are largely isolated, human activities such as scientific research, tourism, and the introduction of pollutants may contribute to the dissemination of antibiotic resistance genes, raising important ecological and potential public health considerations regarding the spread of resistance in polar environments.
Antonio Musolino, Marco Roversi, Mariateresa Romaniello
et al.
Introduction: Pneumococcal vaccination has significantly decreased the burden of invasive pneumococcal disease in the general population, however studies on effectiveness in Down syndrome (DS) are heterogeneous. In this cross-sectional study we evaluated the prevalence of adequate immune response in children with DS after pneumococcal vaccination and we searched for possible clinical predictors associated with it, in order to provide data to optimize vaccination strategies in this high-risk group. Methods: Data of children with DS referred to the DS outpatient Clinic of Bambino Gesù Children's Hospital, Rome, Italy, between September 2021 and March 2022 were reviewed. Clinical and laboratory predictors of immunological response to PCV vaccine, defined as an anti-pneumococcal IgG titer threshold above 0.35 μg/mL were compared and evaluated with bivariate analyses and logistic regression. Results: In this cohort of 406 patients the mean age was 8.4 years and 56.2 % of individuals were male. Most of them had congenital cardiopathy (57.8 %) and recurrent respiratory infections (57.4 %). An anti-pneumococcal Ig titer ≥0.35 μg/mL was found in 50.5 % of patients. Those with Ig < 0.35 μg/mL were significantly younger (p < 0.001) and less likely to have autoimmune disorders or hypothyroidism. Logistic regression showed that a positive history of previous surgery increased the likelihood of Ig ≥ 0.35 μg/mL (OR 2.25, p = 0.001), as well as hypothyroidism (OR 3.14, p = 0.016) and celiac disease (OR 3.70, p = 0.030). Additionally, older age at last PCV13 dose positively correlated with higher Ig levels (p = 0.018). Conclusion: Our findings confirm a lower prevalence of adequate immune response after anti-pneumococcal vaccination in individuals with DS. Older age at last PCV13 dose was found to be correlated to higher specific IgG titers; we suggest a tailored vaccination schedule or a booster dose in individuals with DS that could improve their immune protection.
Cadmium (Cd) contamination in soil poses a threat to crop production and food safety. Rhizosphere microorganisms are crucial for crop growth and production. However, sufficient evidence regarding Cd-responsive bacteria and fungi within crop rhizosphere remains largely unknown. Here, we investigated the impacts of Cd on soil microbial communities in wheat rhizosphere by performing 16S and ITS sequencing under normal (CK) and Cd (10 μM) conditions. We found that the lower concentration of Cd significantly increased Cd concentration in wheat grains (nearly 0.2 mg kg−1), but it had no obvious growth inhibition. Interestingly, bacterial abundance and diversity were significantly decreased in soil rhizosphere when exposed to Cd, whereas little changes were observed in fungi. A total of 259 CK-specific and 45 Cd-specific operational taxonomic units (OTUs) in bacteria, as well as 3 CK-specific and 2 Cd-specific OTUs in fungi were identified. The function of identified bacteria were enriched in human diseases, organismal systems, metabolism, genetic information processing and environmental information processing. We also revealed a complicated bacterial co-occurrence network responding to Cd, including the core bacteria of Acidobacteria, Nitrospirae and Chloroflexi phylums. This study revealed Cd-responding bacteria and fungi communities in wheat rhizosphere, which may provide new insights into beneficial microorganisms for food safety.
Rawan Amr Elmasri, Alaa A. Rashwan, Sarah Hany Gaber
et al.
A non-negligible part of our DNA has been proven to be transcribed into non-protein coding RNA and its intricate involvement in several physiological processes has been highly evidenced. The significant biological role of non-coding RNAs (ncRNAs), including long non-coding RNAs (lncRNAs) has been variously reported. In the current review, the authors highlight the multifaceted role of myocardial infarction-associated transcript (MIAT), a well-known lncRNA, in hepatocellular carcinoma (HCC). Since its discovery, MIAT has been described as a regulator of carcinogenesis in several malignant tumors and its overexpression predicts poor prognosis in most of them. At the molecular level, MIAT is closely linked to the initiation of metastasis, invasion, cellular migration, and proliferation, as evidenced by several in-vitro and in-vivo models. Thus, MIAT is considered a possible theranostic agent and therapeutic target in several malignancies. In this review, the authors provide a comprehensive overview of the underlying molecular mechanisms of MIAT in terms of its downstream target genes, interaction with other classes of ncRNAs, and potential clinical implications as a diagnostic and/or prognostic biomarker in HCC.
The various strains of influenza virus cause respiratory symptoms in humans every year and annual vaccinations are recommended. Due to its RNA-type genes and segmented state, it belongs to a virus that mutates frequently with antigenic drift and shift, giving rise to various strains. Each year, the World Health Organization identifies the epidemic strains and operates a global surveillance system to suggest the viral composition for the influenza vaccine. Influenza viruses, which have multiple viral strains, are produced in the format of multivalent vaccine. However, the multivalent vaccine has a possibility of causing immune interference by introducing multiple strain-specific antigens in a single injection. Therefore, evaluating immune interference phenomena is essential when assessing multivalent vaccines. In this study, the protective ability and immunogenicity of multivalent and monovalent vaccines were evaluated in mice to assess immune interference in the multivalent vaccine. Monovalent and multivalent vaccines were manufactured using the latest strain of the 2022–2023 seasonal influenza virus selected by the World Health Organization. The protective abilities of both types of vaccines were tested through hemagglutination inhibition test. The immunogenicity of multivalent and monovalent vaccines were tested through enzyme-linked immunosorbent assay to measure the cellular and humoral immunity expression rates. As a result of the protective ability and immunogenicity test, higher level of virus neutralizing ability and greater amount of antibodies in both IgG1 and IgG2 were confirmed in the multivalent vaccine. No immune interference was found to affect the protective capacity and immune responses of the multivalent vaccines.
Vid Mlakar, Laurence Lesne, Stefania Vossio
et al.
Abstract Cloning is a key molecular biology procedure for obtaining a genetically homogenous population of organisms or cell lines. It requires the expansion of new cell populations starting from single genetically modified cells. Despite the technical progress, cloning of many cell lines remains difficult. Cloning often fails either due to the strenuous conditions associated with manipulating cells or because many cells don’t tolerate a single-cell state. Here we describe a new cloning method utilizing low adhesion microcavity plates. This new technique, named microcavity-assisted cloning (MAC) was developed to clone difficult-to-clone HepG2 cells. The clones were produced following CRISPR/Cas9 knockout of the GSTA1 gene by a random distribution of 200, 400, and 800 cells into 550 microcavities of a 24-well low adhesion plate originally designed for the culture of spheroids. The knockout of GSTA1 was verified at the protein level using Western blotting. The advantages of the MAC method are its low cost, ease of the procedure, and the possibility of scaling up the throughput and automatization.
Chih-Hsiang Yu, Ya-Hsuan Chang, Der-Shiun Wang
et al.
Abstract Mercaptopurine intolerance is an adverse effect of mercaptopurine administration in pediatric patients with acute lymphoblastic leukemia (ALL). NUDT15 variants have emerged as major determinants of mercaptopurine intolerance, especially in the Asian population. Two variants, c.55_56insGAGTCG in exon 1 and c.415C > T in exon 3, were commonly detected in the same allele, named NUDT15*1/*2. Although rare, compound heterozygous mutations also occur, with the two variants on different alleles (NUDT15*3/*6), which may confer tolerance to considerably lesser mercaptopurine dosage. Sanger sequencing or pyrosequencing can determine the NUDT15 variants but not the phase. Here, we designed an allele-specific PCR (AS-PCR) with locked nucleic acid-modified primers. A cohort of 63 patients harboring heterozygous c.55_56insGAGTCG and c.415C > T NUDT15 variations was selected for haplotyping using AS-PCR. Of the 63 patients, 60 harbored the NUDT15*1/*2 variant and three harbored compound heterozygous mutations, including two NUDT15*3/*6 and one NUDT15*2/*7 variants. These findings suggest that AS-PCR can determine NUDT15 diplotype and identify patients with compound heterozygous NUDT15 variants, which may enable precise genetic diagnosis of NUDT15. Nevertheless, a larger clinical trial is required to understand the clinical significance of NUDT15*3/*6 in pediatric patients with ALL because of its low incidence rate and challenges in detecting this variant.
Uzair Muhammad Khan, Iqrar Ahmad Rana, Nabeel Shaheen
et al.
Abstract Very long-chain fatty acids (VLCFAs) possess more than twenty carbon atoms and are the major components of seed storage oil, wax, and lipids. FAE (Fatty Acid Elongation) like genes take part in the biosynthesis of VLCFAs, growth regulation, and stress responses, and are further comprised of KCS (Ketoacyl-CoA synthase) and ELO (Elongation Defective Elongase) sub-gene families. The comparative genome-wide analysis and mode of evolution of KCS and ELO gene families have not been investigated in tetraploid Brassica carinata and its diploid progenitors. In this study, 53 KCS genes were identified in B. carinata compared to 32 and 33 KCS genes in B. nigra and B. oleracea respectively, which suggests that polyploidization might has impacted the fatty acid elongation process during Brassica evolution. Polyploidization has also increased the number of ELO genes in B. carinata (17) over its progenitors B. nigra (7) and B. oleracea (6). Based on comparative phylogenetics, KCS, and ELO proteins can be classified into eight and four major groups, respectively. The approximate date of divergence for duplicated KCS and ELO genes varied from 0.03 to 3.20 million years ago (MYA). Gene structure analysis indicated that the maximum number of genes were intron-less and remained conserved during evolution. The neutral type of selection seemed to be predominant in both KCS and ELO genes evolution. String-based protein-protein interaction analysis suggested that bZIP53, a transcription factor might be involved in the activation of transcription of ELO/KCS genes. The presence of biotic and abiotic stress-related cis-regulatory elements in the promoter region suggests that both KCS and ELO genes might also play their role in stress tolerance. The expression analysis of both gene family members reflect their preferential seed-specific expression, especially during the mature embryo development stage. Furthermore, some KCS and ELO genes were found to be specifically expressed under heat stress, phosphorus starvation, and Xanthomonas campestris infection. The current study provides a basis to understand the evolution of both KCS and ELO genes in fatty acid elongation and their role in stress tolerance.
Md. Rakhibul Hasan, Surid Mohammad Chowdhury, Md. Abdul Aziz
et al.
In this in silico study, thirty-five ciprofloxacin analogs were docked to the active site of DNA gyrase, the prime target of ciprofloxacin type antibiotics. Prior to docking all the structures were optimized using MM2 force field parameters. The study revealed that five candidates, namely 6MePQ_3, 6MePQ_11, A6MePQ_3, HPQ_11, and PQ_7, exhibited promising binding to DNA gyrase. Upon analysis of the ligand-receptor complex, it is also divulged that this binding has been stabilized by the interaction between different neutral, nonpolar, aromatic amino-acid residues of DNA gyrase and the ciprofloxacin analogs. Moreover, the interaction between ciprofloxacin analogs and DNA gyrase was mainly governed by hydrophobic interactions and, to a lesser extent, hydrogen bonds. Halogen bonds, electrostatic interactions, and other types of interactions were almost absent in all cases. Molecular dynamic simulation was performed to recognize the structural variations and the complexes' stability of suggested ligands. This study indicates that 6MePQ_3 forms a stable drug-protein complex. On the other site, Pharmacokinetic filtering done using SwissADME server, reveals that 6MePQ_3 is well absorbed from the GI tract, does not cross BBB and is not a P-gp substrate. But it is possible to check and confirm its all “in silico” pharmacodynamics and pharmacokinetics characteristics in real life by synthesis and subsequent analysis of this ligand.
Computer applications to medicine. Medical informatics
Intracellular protein trafficking processes consisting of three intracellular states are described by three differential equations. To solve the equations, a quadratic equation is required, and its roots are generally real or complex. The purpose of the present study is to clarify the meanings of roots of real and complex numbers. To clarify the point, we define that: 1) ‘kI’ is the insertion rate from an insertion state trafficking to the plasma membrane state; 2) ‘kE’, the endocytotic rate from the plasma membrane state trafficking to a recycling state; 3) ‘kR’, the recycling rate from the recycling state trafficking to the insertion state. Amounts of proteins in three states are expressed as αelt+βemt+γ with α,β,γ = constant and l and m are roots of a quadratic equation, r2+kI+kE+kRr+kIkE+kIkR+kEkR=0. When l and m are real kI2+kE2+kR2>2kIkE+kEkR+kRkI, amounts of proteins in three states shows no oscillatory change but a monotonic change after a transient increase (or decrease); when l and m are complex kI2+kE2+kR2<2kIkE+kEkR+kRkI, amounts of proteins in three states are expressed as αelt+βemt+γ=2g2+h2sinbt+σeat+γ (α, β, l, m = complex and γ, a,b,g,h,σ = real: α,β = conjugate each other; l,m = conjugate each other), showing an oscillatory change with time. The frequency of oscillatory change appearance is evaluated to be 60% at random combinations of three trafficking rates, kI, kE and kR. The present study indicates that complex numbers have an essentially important meaning in appearance of oscillatory phenomena in bodily and cellular function.