Biofilm released cells can easily be obtained in a fed-batch system using ica+ but not with ica- isolates
Staphylococcus epidermidis is one of the major opportunistic bacterial pathogens in healthcare facilities, mainly due to its strong ability to form biofilms in the surface of indwelling medical devices. To study biofilms under in vitro conditions, both fed-batch and flow systems are widely used, with the first being the most frequent due to their low cost and ease of use. Aim To assess if a fed-batch system previously developed to obtain biofilm released cells (Brc) from strong biofilm producing S. epidermidis isolates could also be used to obtain and characterize Brc from isolates with lower abilities to form biofilms. Methodology The applicability of a fed-batch system to obtain Brc from biofilms of 3 ica+ and 3 ica− isolates was assessed by quantifying the biofilm and Brc biomass by optical density (OD) and colony-forming units (CFU) measurements. The effect of media replacement procedures of fed-batch systems on the amount of biofilm was determined by quantifying the biofilm and biofilm bulk fluid, by CFU, after consecutive washing steps. Results The fed-batch model was appropriate to obtain Brc from ica+ isolates, that presented a greater ability to form biofilms and release cells. However, the same was not true for ica− isolates, mainly because the washing procedure would physically remove a significant number of cells from the biofilm. Conclusions This study demonstrates that a fed-batch system is only feasible to be used to obtain Brc from S. epidermidis when studying strong and cohesive biofilm-forming isolates.
Gaio et al. (2020) Biofilm released cells can easily be obtained in a fed-batch system using ica+ but not with ica- isolates. PeerJ 8:e9549 https://doi.org/10.7717/peerj.9549
Changes of diazotrophic communities in response to cropping systems in a Mollisol of Northeast China
Nitrogen-fixing microorganisms play important roles in N cycling. However, knowledge related to the changes in the diazotrophic community in response to cropping systems is still rudimentary. In this study, the nifH gene was used to reveal the abundance and community compositions of diazotrophs in the cropping systems of continuous cropping of corn (CC) and soybean (SS) and soybean-corn rotation for growing corn (CSC) and soybean (SCS) in a black soil of Northeast China. The results showed that the abundance of the nifH gene was significantly higher in cropping soybean than in cropping corn under the same cropping system, while remarkably increased in the rotation system under the same crop. The Shannon index in the CC treatment was significantly higher than that in the other treatments, but the OTU number and Chao1 index had no significant change among the four treatments. Bradyrhizobium japonicum was the dominant diazotrophic species, and its relative abundance was at the lowest value in the CC treatment. In contrast, Skermanella sp. had the highest relative abundance in the CC treatment. A PCoA showed that the diazotrophic communities were separated between different cropping systems, and the variation caused by continuous corn cropping was the largest. Among the tested soil properties, the soil available phosphorus was a primary factor in determining diazotrophic community compositions. Overall, the findings of this study highlighted that the diazotrophic communities in black soils are very sensitive to cropping systems.
Zou et al. (2020) Changes of diazotrophic communities in response to cropping systems in a Mollisol of Northeast China. PeerJ 8:e9550 https://doi.org/10.7717/peerj.9550
Beyond loot boxes: a variety of gambling-like practices in video games are linked to both problem gambling and disordered gaming
A variety of practices have recently emerged which relate to both video games and gambling. These range from opening loot boxes, to esports betting, real-money video gaming, token wagering, and social casino spending. It is unknown either how harmful or how widespread many of these activities are. A sample of 1,081 adults from the UK aged 18+ was therefore recruited. This sample was purposively recruited via quota sampling to represent the UK population in terms of sex, age, and ethnicity. Engagement in all forms of gaming-related practices were significantly associated with both problem gambling and disordered gaming. A total of 18.5% of the sample had engaged in these activities at least once in the new year. These results suggest a convergent ecosystem of practices that relate to both video games and gambling. Engagement in each of these activities is linked to problem gambling. However, it remains unclear whether engagement in these activities causes problem gambling.
Zendle (2020) Beyond loot boxes: a variety of gambling-like practices in video games are linked to both problem gambling and disordered gaming. PeerJ 8:e9466 https://doi.org/10.7717/peerj.9466
Identification of potential biomarkers and their clinical significance in gastric cancer using bioinformatics analysis methods
Background Alternative splicing (AS) is an important mechanism for regulating gene expression and proteome diversity. Tumor-alternative splicing can reveal a large class of new splicing-associated potential new antigens that may affect the immune response and can be used for immunotherapy. Methods The RNA-seq transcriptome data and clinical information of stomach adenocarcinoma (STAD) cohort were downloaded from The Cancer Genome Atlas (TCGA) database data portal, and data of splicing events were obtained from the SpliceSeq database. Predicting genes were validated by Asian cancer research group (ACRG) cohort and Oncomine database. RT-qPCR was used to analysis the expression of ECT2 in STAD. Results A total of 32,166 AS events were identified, among which 2,042 AS events were significantly associated with patients survival. Biological pathway analysis indicated that these genes play an important role in regulating gastric cancer-related processes such as GTPase activity and PI3K-Akt signaling pathway. Next, we derived a risk signature, using alternate acceptor, that is an independent prognostic marker. Moreover, high ECT2 expression was associated with poorer prognosis in STAD. Multivariate survival analysis demonstrated that high ECT2 expression was an independent risk factor for overall survival. Gene set enrichment analysis revealed that high ECT2 expression was enriched for hallmarks of malignant tumors. The ACRG cohort and Oncomine also showed that high ECT2 expression was associated with poorer prognosis in gastric cancer patients. Finally, RT-qPCR showed ECT2 expression was higher in STAD compared to the normal tissues. Conclusion This study excavated the alternative splicing events in gastric cancer, and found ECT2 might be a biomarkers for diagnosis and prognosis.
Liu et al. (2020) Identification of potential biomarkers and their clinical significance in gastric cancer using bioinformatics analysis methods. PeerJ 8:e9174 https://doi.org/10.7717/peerj.9174
Establishment and characterization of fantail goldfish fin (FtGF) cell line from goldfish, Carassius auratus for in vitro propagation of Cyprinid herpes virus-2 (CyHV-2)
Background Herpesviral hematopoietic necrosis disease, caused by cyprinid herpesvirus-2 (CyHV-2), is responsible for massive mortalities in the aquaculture of goldfish, Carassius auratus. Permissive cell lines for the isolation and propagation of CyHV-2 have been established from various goldfish tissues by sacrificing the fish. Here, we report the development of a cell line, FtGF (Fantail Goldfish Fin), from caudal fin of goldfish using non-lethal sampling. We also describe a simple protocol for successful establishment and characterization of a permissive cell line through explant method and continuous propagation of CyHV-2 with high viral titer using this cell line. Methods Caudal fin tissue samples were collected from goldfish without killing the fish. Cell culture of goldfish caudal fin cells was carried out using Leibovitz’s L-15 (L-15) medium containing 20% FBS and 1X concentration of antibiotic antimycotic solution, incubated at 28 °C. Cells were characterized and origin of the cells was confirmed by sequencing fragments of the 16S rRNA and COI genes. CyHV-2 was grown in the FtGF cells and passaged continuously 20 times. The infectivity of the CyHV-2 isolated using FtGF cells was confirmed by experimental infection of naïve goldfish. Results The cell line has been passaged up to 56 times in L-15 with 10% FBS. Karyotyping of FtGF cells at 30th, 40th and 56th passage indicated that modal chromosome number was 2n = 104. Species authentication of FtGF was performed by sequencing of the 16S rRNA and COI genes. The cell line was used for continuous propagation of CyHV-2 over 20 passages with high viral titer of 107.8±0.26 TCID50/mL. Following inoculation of CyHV-2 positive tissue homogenate, FtGF cells showed cytopathic effect by 2nd day post-inoculation (dpi) and complete destruction of cells was observed by the 10th dpi. An experimental infection of naïve goldfish using supernatant from infected FtGF cells caused 100% mortality and CyHV-2 infection in the challenged fish was confirmed by the amplification of DNA polymerase gene, histopathology and transmission electron microscopy. These findings provide confirmation that the FtGF cell line is highly permissive to the propagation of CyHV-2.
Dharmaratnam et al. (2020) Establishment and characterization of fantail goldfish fin (FtGF) cell line from goldfish, Carassius auratus for in vitro propagation of Cyprinid herpes virus-2 (CyHV-2). PeerJ 8:e9373 https://doi.org/10.7717/peerj.9373
The validity of activity trackers is affected by walking speed: the criterion validity of Garmin Vivosmart® HR and StepWatch™ 3 for measuring steps at various walking speeds under controlled conditions
Introduction The use of activity trackers has increased both among private consumers and in healthcare. It is therefore relevant to consider whether a consumer-graded activity tracker is comparable to or may substitute a research-graded activity tracker, which could further increase the use of activity trackers in healthcare and rehabilitation. Such use will require knowledge of their accuracy as the clinical implications may be significant. Studies have indicated that activity trackers are not sufficiently accurate, especially at lower walking speeds. The present study seeks to inform decision makers and healthcare personnel considering implementing physical activity trackers in clinical practice. This study investigates the criterion validity of the consumer-graded Garmin Vivosmart® HR and the research-graded StepWatch™ 3 compared with manual step count (gold standard) at different walking speeds under controlled conditions. Methods Thirty participants, wearing Garmin Vivosmart® HR at the wrist and StepWatch™ 3 at the ankle, completed six trials on a treadmill at different walking speeds: 1.6 km/h, 2.4 km/h, 3.2 km/h, 4.0 km/h, 4.8 km/h, and 5.6 km/h. The participants were video recorded, and steps were registered by manual step count. Medians and inter-quartile ranges (IQR) were calculated for steps and differences in steps between manually counted steps and the two devices. In order to assess the clinical relevance of the tested devices, the mean absolute percentage error (MAPE) was determined at each speed. A MAPE ≤3% was considered to be clinically irrelevant. Furthermore, differences between manually counted steps and steps recorded by the two devices were presented in Bland–Altman style plots. Results The median of differences in steps between Garmin Vivosmart® HR and manual step count ranged from −49.5 (IQR = 101) at 1.6 km/h to −1 (IQR = 4) at 4.0 km/h. The median of differences in steps between StepWatch™ 3 and manual step count were 4 (IQR = 14) at 1.6 km/h and 0 (IQR = 1) at all other walking speeds. The results of the MAPE showed that differences in steps counted by Garmin Vivosmart® HR were clinically irrelevant at walking speeds 3.2–4.8 km/h (MAPE: 0.61–1.27%) as the values were below 3%. Differences in steps counted by StepWatch™ 3 were clinically irrelevant at walking speeds 2.4–5.6 km/h (MAPE: 0.08–0.35%). Conclusion Garmin Vivosmart® HR tended to undercount steps compared with the manual step count, and StepWatch™ 3 slightly overcounted steps compared with the manual step count. Both the consumer-graded activity tracker (Garmin Vivosmart® HR) and the research-graded (StepWatch™ 3) are valid in detecting steps at selected walking speeds in healthy adults under controlled conditions. However, both activity trackers miscount steps at slow walking speeds, and the consumer graded activity tracker also miscounts steps at fast walking speeds.
Svarre et al. (2020) The validity of activity trackers is affected by walking speed: the criterion validity of Garmin Vivosmart® HR and StepWatch™ 3 for measuring steps at various walking speeds under controlled conditions. PeerJ 8:e9381 https://doi.org/10.7717/peerj.9381
Targeting secretory leukocyte protease inhibitor (SLPI) inhibits colorectal cancer cell growth, migration and invasion via downregulation of AKT
The secretory leukocyte protease inhibitor (SLPI) is a serine protease inhibitor which plays important role in bacterial infection, inflammation, wound healing and epithelial proliferation. Dysregulation of SLPI has been reported in a variety of human cancers including glioblastoma, lung, breast, ovarian and colorectal carcinomas and is associated with tumor aggressiveness and metastatic potential. However, the pathogenic role of SLPI in colorectal cancer is still unclear. Here we showed that SLPI mRNA level was significantly upregulated in colorectal cancer tissues compared to adjacent normal controls. Targeting SLPI by siRNA inhibited proliferation, migration and invasion of colorectal cancer cells lines HT29 and HT116 in vitro. Mechanistically, blockage of cancer cell growth and metastasis after SLPI knockdown was associated with down-regulation of AKT signaling. In conclusion, SLPI regulated colorectal cell growth and metastasis via AKT signaling. SLPI may be a novel biomarker and therapeutic target for colorectal cancer. Targeting AKT signaling may be effective for colorectal cancer treatment.
Wei et al. (2020) Targeting secretory leukocyte protease inhibitor (SLPI) inhibits colorectal cancer cell growth, migration and invasion via downregulation of AKT. PeerJ 8:e9400 https://doi.org/10.7717/peerj.9400
Siderophore and indolic acid production by Paenibacillus triticisoli BJ-18 and their plant growth-promoting and antimicrobe abilities
Paenibacillus triticisoli BJ-18, a N2-fixing bacterium, is able to promote plant growth, but the secondary metabolites that may play a role in promoting plant growth have never been characterized. In this study, untargeted metabolomics profiling of P. triticisoli BJ-18 indicated the existence of 101 known compounds, including N2-acetyl ornithine, which is the precursor of siderophores, plant growth regulators such as trehalose 6-phosphate, betaine and trigonelline, and other bioactive molecules such as oxymatrine, diosmetin, luotonin A, (-)-caryophyllene oxide and tetrahydrocurcumin. In addition, six compounds were also isolated from P. triticisoli BJ-18 using a combination of silica gel chromatography, sephadex LH-20, octadecyl silane (ODS), and high-performance liquid chromatography (HPLC). The compound structures were further analyzed by Nuclear Magnetic Resonance (NMR), Mass Spectrometry (MS), and Electronic Circular Dichroism (ECD). The six compounds included three classical siderophore fusarinines identified as deshydroxylferritriacetylfusigen, desferritriacetylfusigen, and triacetylfusigen, and three indolic acids identified as paenibacillic acid A, 3-indoleacetic acid (IAA), and 3-indolepropionic acid (IPA). Both deshydroxylferritriacetylfusigen and paenibacillic acid A have new structures. Fusarinines, which normally occur in fungi, were isolated from bacterium for the first time in this study. Both siderophores (compounds 1 and 2) showed antimicrobial activity against Escherichia coli, Staphylococcus aureus and Bacillus subtilis, but did not show obvious inhibitory activity against yeast Candida albicans, whereas triacetylfusigen (compound 3) showed no antibiosis activity against these test microorganisms. Paenibacillic acid A, IAA, and IPA were shown to promote the growth of plant shoots and roots, and paenibacillic acid A also showed antimicrobial activity against S. aureus. Our study demonstrates that siderophores and indolic acids may play an important role in plant growth promotion by P. triticisoli BJ-18.
Zhang et al. (2020) Siderophore and indolic acid production by Paenibacillus triticisoli BJ-18 and their plant growth-promoting and antimicrobe abilities. PeerJ 8:e9403 https://doi.org/10.7717/peerj.9403
Utilization of brewery wastes in food industry
Beer is the most popular low-alcohol beverage consumed in large amounts in many countries each year. The brewing industry is an important global business with huge annual revenues. It is profitable and important for the economies of many countries around the world. The brewing process involves several steps, which lead to fermentation of sugars contained in malt and conversion thereof into alcohol and carbon dioxide by yeasts. Beer brewing generates substantial amounts of by-products. The three main brewing industry wastes include brewer’s spent grain, hot trub, and residual brewer’s yeast. Proper management of these wastes may bring economical benefits and help to protect the environment from pollution caused by their excessive accumulation. The disposal of these wastes is cumbersome for the producers, however they are suitable for reuse in the food industry. Given their composition, they can serve as a low-cost and highly nutritional source of feed and food additives. They also have a potential to be a cheap material for extraction of compounds valuable for the food industry and a component of media used in biotechnological processes aimed at production of compounds and enzymes relevant for the food industry.
Rachwał et al. (2020) Utilization of brewery wastes in food industry. PeerJ 8:e9427 https://doi.org/10.7717/peerj.9427
Correlation between emotional regulation and peripheral lymphocyte counts in colorectal cancer patients
Background Colorectal cancer is one of the most common cancers worldwide. Psychological morbidity has an important impact on quality of life and major clinical outcomes. Several data have shown that the immune system may be a key player on the relation between psychological features and cancer outcomes. Natural Killer (NK) cells have been shown to be influenced by psychological factors. The aim of this investigation was to assess the impact of anxiety, depression, and anger state, trait, and expression on the immune response, particularly, their effect on NK cells and CD8+ T cells in surgical colorectal cancer patients. Methods We studied 54 surgical colorectal cancer patients and assessed patients pre-surgically, post-surgically, and 12 months after surgery (follow-up). We applied the Hospital Anxiety and Depression Scale and the State-Trait Anger Expression Inventory and measured peripheral T cells, CD8+ T cells, and NK cells. We did a cross-sectional analysis as well as a longitudinal assessment of the variables during the follow-up period. Results Pre-surgical assessment: Trait anger, angry reaction, and anger-out had a significant negative correlation with NK cells. The lymphocytes values were unaffected by the presence of clinical anxiety or depression. Post-surgical assessment: Patients without clinical anxiety had higher levels of T cells. Angry reaction was negatively correlated with NK cells. Lymphocytes values were unaffected by the presence of clinical depression. Follow-up assessment: Patients without clinical depression had higher T cell counts. Trait anger and angry reaction were negatively correlated with the levels of NK cells. The lymphocytes values were unaffected by the presence of clinical anxiety. Longitudinal assessment: Angry-temperament, anger expression, and anger-in reduced significantly from the first to the second assessment. Anxiety, state anger, and trait anger significantly diminished from the pre-surgical to the follow-up assessment. Depression levels did not alter during the follow-up period. The lymphocyte count, and particularly T cells and CD8+ T cells, was significantly higher in the follow-up when compared with the pre-surgical assessment. Conclusion Our study suggests the existence of a relation between psychological response and immune response in colorectal cancer patients. We identified the importance of emotional regulation as a potential modulator for NK cell counts. Higher values of propensity to experience anger states and express them outwards seem to be associated with lower NK cell counts.
Kakoo Brioso et al. (2020) Correlation between emotional regulation and peripheral lymphocyte counts in colorectal cancer patients. PeerJ 8:e9475 https://doi.org/10.7717/peerj.9475