The therapeutic applications of antimicrobial peptides (AMPs): a patent review

Antimicrobial peptides (AMPs) are small molecules with a broad spectrum of antibiotic activities against bacteria, yeasts, fungi, and viruses and cytotoxic activity on cancer cells, in addition to anti-inflammatory and immunomodulatory activities. Therefore, AMPs have garnered interest as novel therapeutic agents. Because of the rapid increase in drug-resistant pathogenic microorganisms, AMPs from synthetic and natural sources have been developed using alternative antimicrobial strategies. This article presents a broad analysis of patents referring to the therapeutic applications of AMPs since 2009. The review focuses on the universal trends in the effective design, mechanism, and biological evolution of AMPs.     

Comparative and bioinformatics analyses of pathogenic bacterial secretomes identified by mass spectrometry in <Emphasis Type="Italic">Burkholderia</Emphasis> species

Secreted proteins (secretomes) play crucial roles during bacterial pathogenesis in both plant and human hosts. The identification and characterization of secretomes in the two plant pathogens Burkholderia glumae BGR1 and B. gladioli BSR3, which cause diseases in rice such as seedling blight, panicle blight, and grain rot, are important steps to not only understand the disease-causing mechanisms but also find remedies for the diseases. Here, we identified two datasets of secretomes in B. glumae BGR1 and B. gladioli BSR3, which consist of 118 and 111 proteins, respectively, using mass spectrometry approach and literature curation. Next, we characterized the functional properties, potential secretion pathways and sequence information properties of secretomes of two plant pathogens in a comparative analysis by various computational approaches. The ratio of potential non-classically secreted proteins (NCSPs) to classically secreted proteins (CSPs) in B. glumae BGR1 was greater than that in B. gladioli BSR3. For CSPs, the putative hydrophobic regions (PHRs) which are essential for secretion process of CSPs were screened in detail at their N-terminal sequences using hidden Markov model (HMM)–based method. Total 31 pairs of homologous proteins in two bacterial secretomes were indicated based on the global alignment (identity ≥ 70%). Our results may facilitate the understanding of the species-specific features of secretomes in two plant pathogenic Burkholderia species.     

Effect of the size and shape of silver nanoparticles on bacterial growth and metabolism by monitoring optical density and fluorescence intensity

In this study, we demonstrate the antibacterial activity of silver nanoparticles (AgNPs), depending on their size and shape, on green fluorescent protein (GFP)-expressing E. coli, which provides a facile, rapid, and noninvasive monitoring system. By measuring optical density and fluorescence intensity in the recombinant E. coli, we found that smaller sized plate-shaped AgNPs presented higher antibacterial activity than larger sized, cubic and spherical AgNPs. In the case of 10 nm spherical AgNPs, the optical density was detectable at 15 ng/mL after 12 h incubation, but the fluorescence intensity was not. On the other hand, smaller-sized AgNPs showed higher toxicity than plate-shaped AgNPs based on the measurement of the optical density and fluorescence intensity. The combined analysis of optical density and fluorescence intensity may be helpful for understanding the effect of various materials, including nano- and organic materials, on recombinant bacteria.     

Deoxynivalenol impair skin barrier function through the down regulation of filaggrin and claudin 1/8 in HaCaT keratinocyte

Deoxynivalenol (DON), a typical mycotoxin, is a substance that is biosynthesized mainly by the Fusarium species. It is usually found in wheat and other grains grown in the field. When it enters the human body, it causes severe diarrhea, abdominal pain, vomiting, and even death. In addition, DON is known to induce inflammation of the small and large intestine, and is also associated with the occurrence of cancer. However, until recently, the effects of DON on the human skin were unknown. To investigate how DON affects HaCaT, human immortalized keratinocytes, we used CCK-8 assay and a quantitative real-time RT-PCR method to detect changes in the expression of tight junctions and skin cell regulatory proteins. The CCK-8 assay was performed to determine the growth inhibitory concentration of keratinocytes by DON. DON affected the cell survival rate from 1 μM in a concentration dependent manner, with the minimum set as 1 μM and the maximum as 4 μM for all experiments. DON inhibited the mRNA expression of filaggrin by up to 71% and SERPINA1 up to 75%. The expression of AQP3 was reduced by up to 93% compared to the untreated control group. This may cause problems in the pH control function of the skin and weaken the function of moisturizing. In addition, in the presence of DON, the gene expression of claudin 1 and claudin 8, which are important proteins in the regulation of intercellular skin barrier, decreased by up to 47 and 80%, respectively. Snail/ Slug, suppressors of the claudin gene expression, each increased up to 625 and 974%, respectively. Also, the MMP9 gene increased by up to 515% in a concentrationdependent manner, perhaps causing a weakness of the barrier function of the skin. These results suggest that DON may causing the development of atopic skin by impairing the skin barrier and pH control of skin, as well as intestinal inflammation diseases. Therefore, particular attention should be paid to DON contamination during the development of cosmetic ingredients using grains.     

Enhancement of 2,3-butanediol production from Jerusalem artichoke tuber extract by a recombinant <Emphasis Type="Italic">Bacillus</Emphasis> sp. strain BRC1 with increased inulinase activity

A Bacillus sp. strain named BRC1 is capable of producing 2,3-butanediol (2,3-BD) using hydrolysates of the Jerusalem artichoke tuber (JAT), a rich source of the fructose polymer inulin. To enhance 2,3-BD production, we undertook an extensive analysis of the Bacillus sp. BRC1 genome, identifying a putative gene (sacC) encoding a fructan hydrolysis enzyme and characterizing the activity of the resulting recombinant protein expressed in and purified from Escherichia coli. Introduction of the sacC gene into Bacillus sp. BRC1 using an expression vector increased enzymatic activity more than twofold. Consistent with this increased enzyme expression, 2,3-BD production from JAT was also increased from 3.98 to 8.10 g L^?1. Fed-batch fermentation of the recombinant strain produced a maximal level of 2,3-BD production of 28.6 g L^?1, showing a high theoretical yield of 92.3%.     

A simple method for preserving environmental DNA in water samples at ambient temperature by addition of cationic surfactant

Environmental DNA (eDNA) analysis is a powerful tool within ecology for the study of the distribution or abundance of aquatic species, although the simplification of water sampling is required for enabling light and fast field sampling to expand further application of eDNA analysis. Here, certain candidate chemicals belonging to the group of cationic surfactants were examined for their effectiveness as preservatives for eDNA water samples by simply adding the chemicals to water samples to suppress the degradation of eDNA. The quaternary ammonium compound benzalkonium chloride (BAC) at a final concentration of 0.01% was effective to retain 92% of eDNA derived from the bluegill sunfish Lepomis macrochirus in an 8-h incubation test at ambient temperature, which assumed a transportation of water samples in 1-day field sampling during the daytime. Meanwhile, eDNA in water samples without BAC retained only 14% of the initial eDNA. Moreover, an additional long-term incubation test (up to 10 days) revealed BAC-treated samples retained ~70 and 50% of bluegill DNA compared to the initial amount after 1- and 10-day incubation at ambient temperature, respectively. Meanwhile, eDNA in naïve samples reduced to 20% after 1-day incubation and reached undetectable levels after 10 days. Up to now, many eDNA studies have adopted on-site filtration followed by filter fixation, which requires many pieces of equipment. Addition of BAC can protect eDNA in water samples with less effort and equipment resulting in an increase of measurement accuracy of the eDNA quantity and detection probability of rare species by preventing the disappearance of rare sequences in water samples.     

<Emphasis Type="Italic">Legionella</Emphasis> pneumonia due to non-<Emphasis Type="Italic">Legionella pneumophila</Emphasis> serogroup 1: usefulness of the six-point scoring system

Background

Because of a limited number of reports, we aimed to investigate the clinical characteristics of patients with Legionella pneumonia due to non-Legionella pneumophila serogroup 1 and the diagnostic usefulness of the six-point scoring system for such patients compared with patients with pneumonia caused by L. pneumophila serogroup 1.

Methods

We retrospectively analysed patients diagnosed with Legionella pneumonia due to non-L. pneumophila serogroup 1 between March 2001 and June 2016. We examined the clinical characteristics, including symptoms, laboratory findings, radiologic findings, pneumonia severity, initial treatment and prognosis. We also calculated scores using the six-point scoring system in these patients. Furthermore, we compared the clinical characteristics and six-point scores between non-L. pneumophila serogroup 1 patients and L. pneumophila serogroup 1 patients among hospitalized community-acquired pneumonia patients enrolled prospectively between October 2010 and July 2016.

Results

Eleven patients had pneumonia due to non-L. pneumophila serogroup 1; their median age was 66 years and 8 patients (72.7%) were male. The most common pathogen was L. pneumophila serogroup 3 (6/11), followed by L. pneumophila serogroup 9 (3/11), L. pneumophila serogroup 6 (1/11) and L. longbeachae (1/11). Non-specific symptoms, such as fever and cough, were common. Six patients (54.5%) had liver enzyme elevation, but no patient developed hyponatraemia at <130 mEq/L. Nine patients (81.8%) showed lobar pneumonia and 7 patients (63.6%) manifested with consolidation and ground-glass opacity. Patients with mild to moderate severity comprised 10 (90.9%) by CURB-65 and 5 (45.5%) by the Pneumonia Severity Index. Of all patients, 4 were admitted to the intensive care unit and 3 died despite appropriate empiric therapy. The clinical characteristics were not significantly different between non-L. pneumophila serogroup 1 patients and L. pneumophila serogroup 1 patients (n?=?23). At a cut-off value of ≥?2 points, the sensitivity of the six-point scoring system was 54.5% (6/11) for non-L. pneumophila serogroup 1 patients and 95.7% (22/23) for L. pneumophila serogroup 1 patients.

Conclusions

Cases of non-L. pneumophila serogroup 1 pneumonia varied in severity from mild to severe and the clinical characteristics were often non-specific. The six-point scoring system was not useful in predicting such Legionella pneumonia cases.

     

Whole-exome sequencing links a variant in DHDDS to retinitis pigmentosa

Increasingly, mutations in genes causing Mendelian disease will be supported by individual and small families only; however, exome sequencing studies have thus far focused on syndromic phenotypes characterized by low locus heterogeneity. In contrast, retinitis pigmentosa (RP) is caused by >50 known genes, which still explain only half of the clinical cases. In a single, one-generation, nonsyndromic RP family, we have identified a gene, dehydrodolichol diphosphate synthase (DHDDS), demonstrating the power of combining whole-exome sequencing with rapid in vivo studies. DHDDS is a highly conserved essential enzyme for dolichol synthesis, permitting global N-linked glycosylation. Zebrafish studies showed virtually identical photoreceptor defects as observed with N-linked glycosylation-interfering mutations in the light-sensing protein rhodopsin. The identified Lys42Glu variant likely arose from an ancestral founder, because eight of the nine identified alleles in 27,174 control chromosomes were of confirmed Ashkenazi Jewish ethnicity. These findings demonstrate the power of exome sequencing linked to functional studies when faced with challenging study designs and, importantly, link RP to the pathways of N-linked glycosylation, which promise new avenues for therapeutic interventions.