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Topic Review
Syndecan-4
Emerging SARS-CoV-2 variants pose threats to vaccination campaigns against COVID-19. Being more transmissible than the original virus, the SARS-CoV-2 B.1.617 lineage, named the Delta variant, swept through the world in 2021. The mutations in the Delta’s spike protein shift the protein towards a net positive electrostatic potential. Compared to the wild-type spike, the Delta one shows a higher affinity towards heparan sulfate proteoglycans than ACE2. Cellular studies showed that syndecan-4, the syndecan isoform abundant in the lung, enhances the transmission of the Delta variant by attaching its mutated spike glycoprotein and facilitating its cellular entry. In addition to the attachment to the polyanionic heparan sulfate chains, the Delta spike’s molecular interactions with syndecan-4 also involve syndecan-4’s cell-binding domain that mediates cell-to-cell adhesion. Exogenously added heparin or syndecan-4 knockdown efficiently blocks the Delta variant’s cellular entry. A profound understanding of syndecan-4-mediated endocytosis enables the development of molecularly targeted yet simple strategies to reduce the Delta variant’s spread.
  • 1.0K
  • 20 Jan 2022
Topic Review
Inhibition of Multidrug Efflux Pumps in Bacterial Pathogens
Of the various bacterial mechanisms for antimicrobial resistance, active efflux is a well-known system that extrudes clinically relevant antimicrobial agents, rendering specific pathogens recalcitrant to the growth-inhibitory effects of multiple drugs. In particular, multidrug efflux pump members of the major facilitator superfamily (MFS) constitute central resistance systems in bacterial pathogens. MFS efflux confer resistance to multiple antimicrobial agents and are thus excellent targets for inhibition. Several efflux pump inhibitors (EPIs) of natural origin have been shown to possess efflux pump inhibition activities and could potentially be used to restore the efficacy of antibacterial drugs. 
  • 1.0K
  • 29 May 2023
Topic Review
Sphinganine-Analog Mycotoxins
Sphinganine-analog mycotoxins (SAMs) including fumonisins and Alternaria alternata f. sp. Lycopersici (AAL) toxins are a group of related mycotoxins produced by plant pathogenic fungi in the Fusarium genus and in A. alternata f. sp. Lycopersici, respectively. SAMs have shown diverse cytotoxicity and phytotoxicity, causing adverse impacts on plants, animals, and humans, and are a destructive force to crop production worldwide.
  • 1.0K
  • 14 Jan 2021
Topic Review
Bacterial Metabolites Correlating with Depression
This comprehensive entry examines the different bacterial metabolites that potentially have implications for mental health issues such as depression.
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  • 06 Jan 2021
Topic Review
Clostridioides Difficile (Bacteria)
Clostridioides difficile (syn. Clostridium difficile), also known as C. difficile, or C. diff (/siː dɪf/), is Gram-positive species of spore-forming bacteria. Clostridioides spp. are anaerobic, motile bacteria, ubiquitous in nature and especially prevalent in soil. Its vegetative cells are rod-shaped, pleomorphic, and occur in pairs or short chains. Under the microscope, they appear as long, irregular (often drumstick- or spindle-shaped) cells with a bulge at their terminal ends (forms subterminal spores). Under Gram staining, C. difficile cells are Gram-positive and show optimum growth on blood agar at human body temperatures in the absence of oxygen. C. difficile is catalase- and superoxide dismutase-negative, and produces up to three types of toxins: enterotoxin A, cytotoxin B and Cytolethal distending toxin. Under stress conditions, the bacteria produce spores that are able to tolerate extreme conditions that the active bacteria cannot tolerate. Clostridioides difficile is an important emerging human pathogen; according to the CDC, in 2017 there were 223,900 cases in hospitalized patients and 12,800 deaths in the United States. Although C. difficile is commonly known as a hospital and antibiotic associated pathogen, at most one third of infections can be traced to transmission from an infected person in hospitals, and only a small number of antibiotics are directly associated with an elevated risk of developing a C. difficile infection (CDI), namely clindamycin, fluoroquinolones and cephalosporins. The majority of infections are acquired outside of hospitals, and most antibiotics have similar elevated risk of infection on par with many non-antibiotic risk factors, such as using stool softeners and receiving an enema. Clostridioides difficile can also become established in the human colon without causing disease. Although early estimates indicated that C. difficile was present in 2–5% of the adult population, more recent research indicates colonization is closely associated with a history of unrelated diarrheal illnesses, such as food poisoning or laxative abuse. Individuals with no history of gastrointestinal disturbances appear unlikely to become asymptomatic carriers. These carriers are thought to be a major reservoir of infection.
  • 1.0K
  • 24 Oct 2022
Topic Review
Control of Clubroot Disease Caused by Plasmodiophora brassicae
Clubroot caused by the soil-living, obligate biotrophic protist Plasmodiophora brassicae Woronin belongs to the most devastating diseases of cruciferous crops worldwide. As with many plant pathogens, the spread is closely related to the cultivation of suitable host plants. In addition, temperature and water availability are crucial determinants for the occurrence and reproduction of clubroot disease. Current global changes are contributing to the widespread incidence of clubroot disease. On the one hand, global trade and high prices are leading to an increase in the cultivation of the host plant rapeseed worldwide. On the other hand, climate change is improving the living conditions of the pathogen P. brassicae in temperate climates and leading to its increased occurrence. Since chemical control of the clubroot disease is not possible or not ecologically compatible, more and more alternative control options are being investigated.
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  • 25 Mar 2022
Topic Review
Medicinal Plants against Candida spp.
The use of natural products to promote health is as old as human civilization. In recent years, the perception of natural products derived from plants as abundant sources of biologically active compounds has driven their exploitation towards the search for new chemical products that can lead to further pharmaceutical formulations. Candida fungi, being opportunistic pathogens, increase their virulence by acquiring resistance to conventional antimicrobials, triggering diseases, especially in immunosuppressed hosts. They are also pointed to as the main pathogens responsible for most fungal infections of the oral cavity. This increased resistance to conventional synthetic antimicrobials has driven the search for new molecules present in plant extracts, which have been widely explored as alternative agents in the prevention and treatment of infections.
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  • 24 Nov 2021
Topic Review
Bacterial Adaptation to Nano-Titania
Microbes could have prolonged exposure to nanomaterials because of their deposition in the natural environment and wide use in several fields. This could be responsible for the emergence, prevalence, and spread of microbial adaption/resistance to nanoparticles. The emergence of resistance is due to the selective pressure exerted by nanomaterials together with the peculiar flexibility of the microbial genome. This is particularly relevant for nano-titania (TiO2 nanoparticles (NPs)) because of its wide use and release into the environment. TiO2 NPs have been also investigated for their antibacterial activity showing a good performance against bacteria, alone or in combination with antibiotics. However, bacteria are able to invoke multiple response mechanisms in an attempt to adapt to TiO2 NPs. Mechanisms of nanoparticle resistance are different from those of antibiotic resistance because of the peculiar features of nanomaterials. As the antimicrobial activity of nanoparticles depends on their size, shape, and surface properties, the modification of these features by interaction with environmental components influences antibacterial properties, and thereafter the possible development of resistance. Bacterial adaption arises from global changes in metabolic pathways via the modulation of regulatory networks and can be related to single-cell or multicellular communities. The impact of TiO2 NPs on bacteria leads to several changes in microorganisms, mainly during long-term exposure, that can evolve towards adaptation and/or increased virulence.
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  • 08 Nov 2022
Topic Review
Ascomycota genomics, phylogenomics and proteomics
Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments.
  • 1.0K
  • 29 Dec 2020
Topic Review
Microbial Communities of Peat in the Aapa-Type Mire
Large areas in the northern hemisphere are covered by extensive wetlands, which represent a complex mosaic of raised bogs, eutrophic fens, and aapa mires all in proximity to each other. Aapa mires differ from other types of wetlands by their concave surface, heavily watered by the central part, as well as by the presence of large-patterned string-flark complexes. The microbial communities in raised strings were clearly distinct from those in submerged flarks. Strings were dominated by the Alpha- and Gammaproteobacteria. Other abundant groups were the Acidobacteriota, Bacteroidota, Verrucomicrobiota, Actinobacteriota, and Planctomycetota. Archaea accounted for only 0.4% of 16S rRNA gene sequences retrieved from strings. By contrast, they comprised about 22% of all sequences in submerged flarks and mostly belonged to methanogenic lineages. Methanotrophs were nearly absent. Other flark-specific microorganisms included the phyla Chloroflexi, Spirochaetota, Desulfobacterota, Beijerinckiaceae- and Rhodomicrobiaceae-affiliated Alphaproteobacteria, and uncultivated groups env.OPS_17 and vadinHA17 of the Bacteroidota. Such pattern probably reflects local anaerobic conditions in the submerged peat layers in flarks. 
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  • 06 Feb 2022
Topic Review
Binding of Various Aminopolycarboxylates
Synthetic aminopolycarboxylates like ethylenediaminetetraacetate (EDTA) are common chelating agents. EDTA-degrading bacterium Chelativorans sp. BNC1 uses an ABC-type transporter for the uptake of free EDTA into its cells for biodegradation. The key component of the transporter is a periplasmic EDTA-binding protein, EppA, and the structural and functional analyses indicate that EppA is a general binding protein for the uptake of free aminopolycarboxylates, suggesting that stable metal-chelate complexes are not transported into the cells for biodegradation and explaining the persistence of stable metal-EDTA complexes in the environment.
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  • 02 Nov 2020
Topic Review
Biogenesis of Outer Membrane Vesicles
Outer membrane vesicles (OMVs) are spheroidal proteoliposomes ranging from ~20 to 200 nm in diameter that originate from the outer membrane of Gram-negative bacteria. The biogenesis of OMVs has been a topic of intense research due to the diverse roles that OMVs play in bacterial pathogenesis, immune modulation, and potential therapeutic applications. 
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  • 04 Sep 2023
Topic Review
Characteristics of Ascochyta Blight in Chickpea
Chickpea (Cicer arietinum L.), one of the most cultivated legumes worldwide, is crucial for the economy of several countries and a valuable source of nutrients. Yields may be severely affected by Ascochyta blight, a disease caused by the fungus Ascochyta rabiei. 
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  • 27 Apr 2023
Topic Review
Alt a 1 Protein Family in Phylogenetic-Related Alternaria
Alternaria is a genus of worldwide fungi found in different habitats such as soil, the atmosphere, plants or indoor environments. Alternaria species are saprobic—largely involved in the decomposition of organic material—but they can also act as animal pathogens, causing disease in humans and animals, developing infections, toxicosis and allergic diseases. A. alternata is considered one of the most important sources of fungal allergens worldwide and it is associated with severe asthma and respiratory status. In fact,  Alt a 1, the main allergen of A. alternata, is an important marker for assessing the risk factor and severity of allergic respiratory disease. Another role of Alt a 1, from a evolutionary point of view, would be to define a family of proteins that would allow establishing taxonomic relationships between different fungal divisions. Finally, Alt a 1 has been shown to be a very useful marker for the identification of pathogenic molds contaminating plants and fruits.
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  • 28 Apr 2022
Topic Review
Role of GI Microbiota in Spiny Lobsters
Indigenous intestinal microbiota influences the physiological function of the host GI tract. These influences are evident in scientific articles reporting intestinal microflora abnormalities in a variety of organisms, including germ-free animals, animals, and humans. As observed in higher organisms, humans, terrestrial animals, or aquatic animals, the presence of GI microbiota in spiny lobsters influences the host and brings various benefits to its host. The symbiosis between the GI microbiota and the host is important to ensure the nutrition and health of the host. The human GI tract comprises 1000 culturable microflora species, where 92 species are from eukarya, 8 from archaea, and 957 from bacteria. The complex and diverse microflora community in the GI tract of humans co-exists and contributes to the prevention of metabolic diseases. The GI microbiota in the human body possesses both beneficial and harmful traits. It has been proven that GI microbes are associated with obesity, inflammatory bowel disease, cancers, diabetes, autism, and asthma. The role of fish GI microbiota is based on the host’s dietary needs. Herbivorous fishes, such as grass carp, are associated with cellulolytic bacteria, which help in plant fibre intake. Meanwhile, nitrogen-fixing bacteria are the dominant species in the GI tract of wood-eating fish. The GI bacteria of carnivorous fish species consist of mostly lipase- and protease-synthesising bacteria. In aquatic invertebrates, an earlier experiment by Harris proved that the presence of GI bacteria has specific roles and functions.
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  • 27 May 2022
Topic Review
Phytochemicals as Antimicrobials
Among all available antimicrobials, antibiotics hold a prime position in the treatment of infectious diseases. However, the emergence of antimicrobial resistance (AMR) has posed a serious threat to the effectiveness of antibiotics, resulting in increased morbidity, mortality, and escalation in healthcare costs causing a global health crisis. The overuse and misuse of antibiotics in global healthcare setups have accelerated the development and spread of AMR, leading to the emergence of multidrug-resistant (MDR) pathogens, which further limits treatment options. This creates a critical need to explore alternative approaches to combat bacterial infections. Phytochemicals have gained attention as a potential source of alternative medicine to address the challenge of AMR. Phytochemicals are structurally and functionally diverse and have multitarget antimicrobial effects, disrupting essential cellular activities.
  • 1.0K
  • 28 Jun 2023
Topic Review
Control of Greenhouse Gas Fluxes
Covering up to 25% of the land surface and acting as a rapid CH4 sink and alternately as a CO2 source or sink, karstic subterranean ecosystems play a decisive role in the carbon cycle in terms of their contribution to the global balance of greenhouse gases. Recent data indicate that microbiota must play a significant ecological role in the biogeochemical processes that control the composition of the subterranean atmosphere, as well as in the availability of nutrients for the ecosystem. Nevertheless, there are still essential gaps in our knowledge concerning the budgets of greenhouse gases at the ecosystem scale and the possible feedback mechanisms between environmental-microclimatic conditions and the rates and type of activity of microbial communities in subterranean ecosystems.
  • 1.0K
  • 07 Jan 2021
Topic Review
Enteropathy-associated T-cell Lymphoma
Enteropathy-associated T-cell lymphoma (EATL), previously termed enteropathy-associated T-cell lymphoma, type I and at one time termed enteropathy-type T-cell lymphoma (ETTL), is a complication of coeliac disease in which a malignant T-cell lymphoma develops in areas of the small intestine affected by the disease's intense inflammation. While a relatively rare disease, it is the most common type of primary gastrointestinal T-cell lymphoma. EATL had been defined as a single type of small intestine lymphoma, but in 2008, the World Health Organization (WHO) divided the disease into two subtypes: 1) EATL type I, which occurs in individuals with coeliac disease, a chronic immune disorder causing inflammatory responses to dietary gluten primarily in the upper reaches (i.e. jejunum and duodenum) of the small intestine; and 2) EATL type II, a disorder similar to EATL type I that occurs without coeliac disease. While type I and II EATL share many similar features, post-2008 studies found some significant differences between the two types. In 2016, the WHO redefined the two diseases as separate entities, keeping the term enteropathy-associated T-cell lymphoma for the coeliac disease-associated lymphoma and terming type 2 disease as monomorphic epitheliotropic intestinal T cell lymphoma (MEITL). EATL is five to ten times more common than is MEITL. The WHO also defined a third type of intestinal T-cell lymphoma that cannot not be classified as EATL or MEITL as peripheral T-cell lymphoma not otherwise specified (ITCL-NOS). EATL arises from the malignant transformation of small-intestinal intraepithelial lymphocytes (IEL). IEL are a heterogeneous group of principally T-cell lymphocytes residing in epithelial tissues that interface the environment, such as the mucosa of the bronchi, reproductive tract and gastrointestinal tract. At these sites, IEL are exposed and regulate immune responses to non-dietary and dietary antigens, pathogenic and non-pathogenic organisms and injured self tissues. Gastrointestinal tract IEL appear in the epithelium of the small intestine, colon, stomach and esophagus, residing between the epithelial cells that line these organs' lumens. These IEL often exhibit natural killer and cytotoxic T-cell cell activation markers, contain various toxic agents (e.g. perforin, granzyme) and therefore are capable, if activated, of causing severe tissue injuries. With coeliac disease, the IEL react to the glutelins in dietary gluten by increasing their numbers, becoming pathologically active, producing chronic inflammation that injures intestinal cells, interfering with nutrient absorption and creating an environment conducive to their malignant transformation into EATL. Optimal treatment of EATL has used regimens consisting of intensive chemotherapy, hematopoietic stem cell transplantation and, in cases with bulky, obstructive and/or perforated bowel disease, surgical intervention. The disease has a five-year overall survival rate of only ~20%. However, recent studies focusing on the malignant IEL in EATL have increased understanding of the disease and suggested newer chemotherapy-based strategies and novel molecular targets that might be attacked therapeutically to improve the disease's prognosis.
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  • 17 Nov 2022
Topic Review
Antimicrobial Peptides-Silver Nanoparticles for Methicillin-Resistance Staphylococcus aureus
Antibiotics are regarded as a miracle in the medical field as it prevents disease caused by pathogenic bacteria. Since the discovery of penicillin, antibiotics have become the foundation for modern medical discoveries. However, bacteria soon became resistant to antibiotics, which puts a burden on the healthcare system. Methicillin-resistant Staphylococcus aureus (MRSA) has become one of the most prominent antibiotic-resistant bacteria in the world since 1961. MRSA primarily developed resistance to beta-lactamases antibiotics and can be easily spread in the healthcare system. Thus, alternatives to combat MRSA are urgently required. Antimicrobial peptides (AMPs), an innate host immune agent and silver nanoparticles (AgNPs), are gaining interest as alternative treatments against MRSA. Both agents have broad-spectrum properties which are suitable candidates for controlling MRSA. Although both agents can exhibit antimicrobial effects independently, the combination of both can be synergistic and complementary to each other to exhibit stronger antimicrobial activity. The combination of AMPs and AgNPs also reduces their own weaknesses as their own, which can be developed as a potential agent to combat antibiotic resistance especially towards MRSA. 
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  • 25 Jul 2022
Topic Review
Secondary Metabolites of Aspergillus sydowii
Marine-derived fungi are renowned as a source of astonishingly significant and synthetically appealing metabolites that are proven as new lead chemicals for chemical, pharmaceutical, and agricultural fields. Aspergillus sydowii is a saprotrophic, ubiquitous, and halophilic fungus that is commonly found in different marine ecosystems. This fungus can cause aspergillosis in sea fan corals leading to sea fan mortality with subsequent changes in coral community structure.
  • 1.0K
  • 11 Aug 2023
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