Published: 27 November 2020
Mehmet Akif Ersoy Üniversitesi Sosyal Bilimler Enstitüsü Dergisi pp 84-99; doi:10.20875/makusobed.780654
Biomolecules, Volume 10; doi:10.3390/biom10121606
The number of researchers using multi-omics is growing. Though still expensive, every year it is cheaper to perform multi-omic studies, often exponentially so. In addition to its increasing accessibility, multi-omics reveals a view of systems biology to an unprecedented depth. Thus, multi-omics can be used to answer a broad range of biological questions in finer resolution than previous methods. We used six omic measurements—four nucleic acid (i.e., genomic, epigenomic, transcriptomics, and metagenomic) and two mass spectrometry (proteomics and metabolomics) based—to highlight an analysis workflow on this type of data, which is often vast. This workflow is not exhaustive of all the omic measurements or analysis methods, but it will provide an experienced or even a novice multi-omic researcher with the tools necessary to analyze their data. This review begins with analyzing a single ome and study design, and then synthesizes best practices in data integration techniques that include machine learning. Furthermore, we delineate methods to validate findings from multi-omic integration. Ultimately, multi-omic integration offers a window into the complexity of molecular interactions and a comprehensive view of systems biology.
Polymers, Volume 12; doi:10.3390/polym12122807
Microfibrillated cellulose films have been gathering considerable attention due to their high mechanical properties and cheap cost. Additionally, it is possible to include compounds within the fibrillated structure in order to confer desirable properties. Ilex paraguariensis A. St.-Hil, yerba mate leaf extract has been reported to possess a high quantity of caffeoylquinic acids that may be beneficial for other applications instead of its conventional use as a hot beverage. Therefore, we investigate the effect of blending yerba mate extract during and after defibrillation of Eucalyptus sp. bleached kraft paper by ultrafine grinding. Blending the extract during defibrillation increased the mechanical and thermal properties, besides being able to use the whole extract. Afterwards, this material was also investigated with high content loadings of starch and glycerine. The results present that yerba mate extract increases film resistance, and the defibrillated cellulose is able to protect the bioactive compounds from the extract. Additionally, the films present antibacterial activity against two known pathogens S. aureus and E. coli, with high antioxidant activity and increased cell proliferation. This was attributed to the bioactive compounds that presented faster in vitro wound healing, suggesting that microfibrillated cellulose (MFC) films containing extract of yerba mate can be a potential alternative as wound healing bandages.
Journal of Marine Science and Engineering, Volume 8; doi:10.3390/jmse8120969
Tidal turbine array optimization is crucial for the further development of the marine sector. It has already been observed that tidal turbines within an array can be heavily affected by excessive aerodynamic interference, thus leading to performance deterioration. Small-scale experimental tests aimed at understanding the physical mechanisms of interaction and identifying optimal distances between machines can be found in the literature. However, often, the relatively narrow channels of laboratories imply high blockage ratios, which could affect the results, making them unreliable if extrapolated to full-scale cases. The main aim of this numerical study was to analyze the effects of the blockage caused by the laboratory channel walls in cases of current and also current surface waves. For this purpose, the performance predictions achieved for two turbines arranged in line for different lateral offsets in case of a typical laboratory scale were compared to the predictions obtained for a full scale, unconfined environment. The methodology consisted in the adoption a hybrid Blade Element Momentum–Computational Fluid Dynamics (BEM-CFD) approach, which was based on the Virtual Blade Model of ANSYS-Fluent. The results indicate that (1) the performance of a downstream turbine can increase up to 5% when this has a lateral separation of 1.5D from an upstream device in a full-scale environment compared to a misleading 15% calculated for the laboratory set-up, and (2) the relative fluctuations of power and thrust generated by waves are not significantly affected by the domain dimensions.
Sci, Volume 2; doi:10.3390/sci2040087
This study assessed farmers’ perception of climate change, and estimated the determinants of, and evaluated the relationship among, adaptation practices using the multivariate probit model. A survey in 300 agricultural households was carried out covering 10 sample districts considering five agro-ecological zones and a vulnerability index. Four adaptation choices (change in planting date, crop variety, crop type and investment in irrigation) were deemed as outcome variables and socioeconomic, demographic, institutional, farm-level and perceptions variables were deployed as explanatory variables. Their marginal effects were determined for three climatic variables—temperature, precipitation and drought. Age, gender and education of head of household, credit access, farm area, rain-fed farming and tenure, were found to be more influential compared to other factors. All four adaptation options were found to be complimentary to each other. Importantly, the intensity of the impact of dependent variables in different models, and for the available adaptation options, were found to be unequal. Therefore, policy options and support facilities should be devised according to climatic variables and adaptation options to achieve superior results.
Nanomaterials, Volume 10; doi:10.3390/nano10122354
Two series of new photocatalysts were synthesized based on modification with Pd of the commercial P25 photocatalyst (EVONIK®). Two techniques were employed to incorporate Pd nanoparticles on the P25 surface: photodeposition (series Pd-P) and impregnation (series Pd-I). Both series were characterized in depth using a variety of instrumental techniques: BET, DRS, XRD, XPS, TEM, FTIR and FESEM. The modified series exhibited a significant change in pore size distribution, but no differences compared to the original P25 with respect to crystalline phase ratio or particle size were observed. The Pd0 oxidation state was predominant in the Pd-P series, while the presence of the Pd2+ oxidation state was additionally observed in the Pd-I series. The photoactivity tests were performed in a continuous photoreactor with the photocatalysts deposited, by dip-coating, on borosilicate glass plates. A total of 500 ppb of NO was used as input flow at a volumetric flow rate of 1.2 L·min−1, and different relative humidities from 0 to 65% were tested. The results obtained show that under UV-vis or Vis radiation, the presence of Pd nanoparticles favors NO removal independently of the Pd incorporation method employed and independently of the tested relative humidity conditions. This improvement seems to be related to the different interaction of the water with the surface of the photocatalysts in the presence or absence of Pd. It was found in the catalyst without Pd that disproportionation of NO2 is favored through its reaction with water, with faster surface saturation. In contrast, in the catalysts with Pd, disproportionation took place through nitro-chelates and adsorbed NO2 formed from the photocatalytic oxidation of the NO. This different mechanism explains the greater efficiency in NOx removal in the catalysts with Pd. Comparing the two series of catalysts with Pd, Pd-P and Pd-I, greater activity of the Pd-P series was observed under both UV-vis and Vis radiation. It was shown that the Pd0 oxidation state is responsible for this greater activity as the Pd-I series improves its activity in successive cycles due to a reduction in Pd2+ species during the photoactivity tests.
Microorganisms, Volume 8; doi:10.3390/microorganisms8121877
Cattle are an established reservoir of the foodborne bacterial pathogen Campylobacter jejuni. Our six-month study aimed to evaluate sources and pathways governing long-term presence of C. jejuni in a pasture-based dairy herd. C. jejuni was detected in all sample types (soil, pasture, stock drinking water, bird, rodents and cow faeces). It was persistently detected from cow (54%; 49/90 samples) and bird (36%; 77/211) faeces. Genetic comparison of 252 C. jejuni isolates identified 30 Multi-Locus Sequence Types (ST). ST-61 and ST-42 were persistent in the herd and accounted for 43% of the cow isolates. They were also detected on pasture collected from fields both recently and not recently grazed, indicating that grazed pasture is an important pathway and reservoir for horizontal transmission among cows. ST-61 accounted for 9% of the bird isolates and was detected at four of the six sampling events, suggesting that bird populations might contribute to the cycling of ruminant-adapted genotypes on-farm. Overall, the results indicated that management of grazed pasture and supplementary feed contaminated by bird droppings could be targeted to effectively reduce transmission of C. jejuni to dairy herds, the farm environment and ultimately to humans.
Applied Sciences, Volume 10; doi:10.3390/app10238463
Cyclodextrin-based nanosponges (CD-NS) are a novel class of polymers cross-linked with a three-dimensional network and can be obtained from cyclodextrins (CD) and pyromellitic dianhydride. Their properties, such as their ability to form an inclusion complex with drugs, can be used in biomedical science, as nanosponges influence stability, toxicity, selectivity, and controlled release. Most pharmaceutical research use CD-NS for the delivery of drugs in cancer treatment. Application of molecular targeting techniques result in increased selectivity of CD-NS; for example, the addition of disulfide bridges to the polymer structure makes the nanosponge sensitive to the presence of glutathione, as it can reduce such disulfide bonds to thiol moieties. Other delivery applications include dermal transport of pain killers or photosensitizers and delivery of oxygen to heart cells. This gives rise to the opportunity to transition to medical scaffolds, but more, in modern times, to create an ultrasensitive biosensor, which employs the techniques of surface-modified nanoparticles and molecularly imprinted polymers (MIP). The following review focuses on the biomedical research of cyclodextrin polymers cross-linked via dianhydrides of carboxylic acids.
Applied Sciences, Volume 10; doi:10.3390/app10238459
Quality parameters are always of major importance in fruit sensory perception and they are influenced by the agriculture and environmental strategies of water-use efficiency that in the last few years are being developed due to water scarcity. Blueberry fruit quality depends on several factors, such as variety, water availability or cultivation system. The purpose of this work was to determine the effect of deficit irrigation and cultivation systems on the quality of three blueberry cultivars along two consecutive seasons. Three blueberry varieties (‘Rocio’, V2 and V3) were subjected to two irrigation regimes (100% and 80% crop evapotranspiration) and grown under two cultivation systems (open field and plastic tunnels). Their quality attributes (color, sugars, acidity, firmness, size and weight) were evaluated over two consecutive seasons (2011–2012). The application of deficit irrigation did not significantly affect the quality parameters, except for an increase in firmness. The cultivation system used influenced the quality attributes of blueberries cultivated under plastic tunnels in both seasons, increasing the soluble solids content and decreasing the titratable acidity. All the studied quality parameters were significantly affected by genetic factors. The V2 cultivar was the most influenced by the cultivation system. In conclusion, the use of deficit irrigation and plastic tunnels in blueberry cultivation is a good alternative to obtain fruits with enhanced quality features.
Sustainability, Volume 12; doi:10.3390/su12239917
Plant growth-promoting bacteria (PGPB) afford plants several advantages (i.e., improvement of nutrient acquisition, growth, and development; induction of abiotic and biotic stress tolerance). Numerous PGPB strains have been isolated and studied over the years. However, only a few of them are available on the market, mainly due to the failed bacterial survival within the formulations and after application inside agroecosystems. PGPB strains with these challenging limitations can be used for the formulation of cell-free supernatants (CFSs), broth cultures processed through several mechanical and physical processes for cell removal. In the scientific literature there are diverse reviews and updates on PGPB in agriculture. However, no review deals with CFSs and the CFS metabolites obtainable by PGPB. The main objective of this review is to provide useful information for future research on CFSs as biostimulant and biocontrol agents in sustainable agriculture. Studies on CFS agricultural applications, both for biostimulant and biocontrol applications, have been reviewed, presenting limitations and advantages. Among the 109 articles selected and examined, the Bacillus genus seems to be the most promising due to the numerous articles that support its biostimulant and biocontrol potentialities. The present review underlines that research about this topic needs to be encouraged; evidence so far obtained has demonstrated that PGPB could be a valid source of secondary metabolites useful in sustainable agriculture.