Effects of rheumatoid arthritis associated transcriptional changes on osteoclast differentiation network in the synovium
Background Osteoclast differentiation in the inflamed synovium of rheumatoid arthritis (RA) affected joints leads to the formation of bone lesions. Reconstruction and analysis of protein interaction networks underlying specific disease phenotypes are essential for designing therapeutic interventions. In this study, we have created a network that captures signal flow leading to osteoclast differentiation. Based on transcriptome analysis, we have indicated the potential mechanisms responsible for the phenotype in the RA affected synovium. Method We collected information on gene expression, pathways and protein interactions related to RA from literature and databases namely Gene Expression Omnibus, Kyoto Encyclopedia of Genes and Genomes pathway and STRING. Based on these information, we created a network for the differentiation of osteoclasts. We identified the differentially regulated network genes and reported the signaling that are responsible for the process in the RA affected synovium. Result Our network reveals the mechanisms underlying the activation of the neutrophil cytosolic factor complex in connection to osteoclastogenesis in RA. Additionally, the study reports the predominance of the canonical pathway of NF-κB activation in the diseased synovium. The network also confirms that the upregulation of T cell receptor signaling and downregulation of transforming growth factor beta signaling pathway favor osteoclastogenesis in RA. To the best of our knowledge, this is the first comprehensive protein–protein interaction network describing RA driven osteoclastogenesis in the synovium. Discussion This study provides information that can be used to build models of the signal flow involved in the process of osteoclast differentiation. The models can further be used to design therapies to ameliorate bone destruction in the RA affected joints.
Harshan et al. (2018) Effects of rheumatoid arthritis associated transcriptional changes on osteoclast differentiation network in the synovium. PeerJ 6:e5743 https://doi.org/10.7717/peerj.5743
Eye movements while judging faces for trustworthiness and dominance
Past studies examining how people judge faces for trustworthiness and dominance have suggested that they use particular facial features (e.g. mouth features for trustworthiness, eyebrow and cheek features for dominance ratings) to complete the task. Here, we examine whether eye movements during the task reflect the importance of these features. We here compared eye movements for trustworthiness and dominance ratings of face images under three stimulus configurations: Small images (mimicking large viewing distances), large images (mimicking face to face viewing), and a moving window condition (removing extrafoveal information). Whereas first area fixated, dwell times, and number of fixations depended on the size of the stimuli and the availability of extrafoveal vision, and varied substantially across participants, no clear task differences were found. These results indicate that gaze patterns for face stimuli are highly individual, do not vary between trustworthiness and dominance ratings, but are influenced by the size of the stimuli and the availability of extrafoveal vision.
Hermens et al. (2018) Eye movements while judging faces for trustworthiness and dominance. PeerJ 6:e5702 https://doi.org/10.7717/peerj.5702
The antioxidant activities, cytotoxic properties, and identification of water-soluble compounds of Ficus deltoidea leaves
Leaves from three varieties of Ficus deltoidea, colloquially termed small- (FDS), medium- (FDM), and big-type leaf (FDB), were subjected to water extraction. The crude extracts were fractionated using water (WF) and ethyl acetate (EAF). The phenolic and flavonoid content, antioxidant activity, and cytotoxicity of the fractions were investigated. The EAF had the highest phenolic and flavonoid content compared to the other FDS fractions. Conversely, the FDM crude extract had the highest phenolic and flavonoid content compared to the other FDM samples. Antioxidant activity was highest in the FDB crude extract. Ultra-high–performance liquid chromatography showed that two compounds, vitexin and coumaric acid, were present in the FDB crude extract. Additionally, the F. deltoidea leaves caused no signs of toxicity in a normal liver cell line. Our findings show that F. deltoidea varieties have excellent antioxidant activity with no cytotoxic effects on normal liver cells.
Abrahim et al. (2018) The antioxidant activities, cytotoxic properties, and identification of water-soluble compounds of Ficus deltoidea leaves. PeerJ 6:e5694 https://doi.org/10.7717/peerj.5694
Residue management alters microbial diversity and activity without affecting their community composition in black soil, Northeast China
Residue management is an important agricultural practice for improving soil fertility. To reveal the impact of residue management on soil microbial community, we conducted a field experiment with three treatments: no straw returning (control, CK), straw returning (SR), and straw returning combined with cow manure (SM). Our results indicated that soil organic matter content was significantly higher in SR treatment than CK in both seedling and jointing stages. In seedling stage, the lowest total nitrogen content was observed in CK treatment, and significantly lower than that in SM and SR treatment. Furthermore, soil available phosphorus content was significantly higher in SM and SR treatment than CK in jointing stage. In the seedling stage, the soil microbial average wellcolor development (AWCD) value, microbial McIntosh index, and Shannon index of CK and SM treatments were significantly higher than those in SR treatment. The AWCD value and McIntosh index in the jointing stage showed similar patterns: SM > CK > SR. Permutational multivariate analysis of variance indicated that soil microbial community was significantly affected by growth stage, but unaffected by residue management. The partial Mantel test revealed that the available potassium and the C/N ratio had independent effects on soil microbial community. Overall, our results indicated that straw returning combined with cow manure had a beneficial effect on soil fertility, microbial activity and diversity.
Gu et al. (2018) Residue management alters microbial diversity and activity without affecting their community composition in black soil, Northeast China. PeerJ 6:e5754 https://doi.org/10.7717/peerj.5754
Modulating factors of the abundance and distribution of Achelous spinimanus (Latreille, 1819) (Decapoda, Portunoidea), a fishery resource, in Southeastern Brazil
This is the first study to examine how different environmental factors may influence the distribution of swimming crab Achelous spinimanus across geographically distant and distinct habitats. We analyzed the influence of bottom water temperature and salinity, sediment texture and organic matter content on the spatiotemporal distribution of A. spinimanus. The crabs were collected from January 1998 until December 1999 by trawling with a shrimp fishing boat outfitted with double-rig nets. The sampling took place in Ubatumirim (UBM), Ubatuba (UBA) and Mar Virado (MV) bays, located in the northern coast of São Paulo State (Brazil). These three bays were chosen as they differed in many physiographic features. We captured 1,911 crabs (UBM = 351; UBA = 1,509; MV = 51), and there were significant differences in abundance between bays and between stations. The distribution of A. spinimanus was primarily associated with sediment features: abundance was higher in stations with sandy sediments classified as gravel, very coarse sand, and intermediate sand. Portunoidea usually burrow in the sediment for protection against predators and to facilitate the capture of fast prey. In addition, the station with the highest abundance of A. spinimanus was also naturally protected from fishing activities, and composed of heterogeneous sediment, in terms of grain size. Hence, the combination of a favorable sediment heterogeneity and protection from fishery activities seemed to be effective modulators of the abundance and distribution of A. spinimanus in these bays.
Sousa et al. (2018) Modulating factors of the abundance and distribution of Achelous spinimanus (Latreille, 1819) (Decapoda, Portunoidea), a fishery resource, in Southeastern Brazil. PeerJ 6:e5720 https://doi.org/10.7717/peerj.5720
Could resistance to lactate accumulation contribute to the better swimming performance of Brycon amazonicus when compared to Colossoma macropomum?
Background In the wild, matrinchã (Brycon amazonicus) and tambaqui (Colossoma macropomum) rely strongly on their swimming capacity to perform feeding, migration and reproductive activities. Sustained swimming speed in fishes is performed almost exclusively by aerobic red muscles. The white muscle has high contraction power, but fatigue quickly, being used mainly in sprints and bursts, with a maximum duration of few seconds. The Ucrit test, an incremental velocity procedure, is mainly a measure of the aerobic capacity of a fish, but with a high participation of anaerobic metabolism close to the velocity of fatigue. Our previous study has indicated a high swimming performance of matrinchã (Ucrit) after hypoxia exposure, despite increased levels of lactate in plasma. In contrast, tambaqui with high lactate levels in plasma presented very low swimming performance. Therefore, we aimed to study the resistance of matrinchã and tambaqui to the increased lactate levels in muscle over an incremental velocity test (Ucrit). As a secondary aim, we analyzed the differences in anaerobic metabolism in response to environmental hypoxia, which could also support the better swimming performance of matrinchã, compared to tambaqui. Methods We measured, over incremented velocities in both species, the metabolic rate (the oxygen consumption by the fish; MO2), and the concentrations of lactate and nitrites and nitrates (NOx) in muscles. NOx was measured as an indicator of nitric oxide and its possible role in improving cardiorespiratory capacity in these fishes, which could postpone the use of anaerobic metabolism and lactate production during the swimming test. Also, we submitted fishes until fatigue and hypoxia (0.5 mg L−1) and measured, in addition to the previous parameters, lactate dehydrogenase activity (LDH; the enzyme responsible for lactate production), since that swimming performance could also be explained by the anaerobic capacity of producing ATP. Results Matrinchã exhibited a better swimming performance and higher oxygen consumption rates. Lactate levels were higher in matrinchã only at the moment of fatigue. Under hypoxia, LDH activity increased in the white muscle only in tambaqui, but averages were always higher in matrinchã. Discussion and conclusions The results suggest that matrinchã is more resistant than tambaqui regarding lactate accumulation in muscle at the Ucrit test, but it is not clear how much it contributes to postpone fatigue. The higher metabolic rate possibly allows the accumulated lactate to be used as aerobic fuel by the matrinchã, improving swimming performance. More studies are needed regarding matrinchã’s ability to oxidize lactate, the effects of exercise on muscle acidification, and the hydrodynamics of these species, to clarify why matrinchã is a better swimmer than tambaqui.
Ferreira et al. (2018) Could resistance to lactate accumulation contribute to the better swimming performance of Brycon amazonicus when compared to Colossoma macropomum?. PeerJ 6:e5719 https://doi.org/10.7717/peerj.5719
Regional differences in an established population of invasive Indo-Pacific lionfish (Pterois volitans and P. miles) in south Florida
About nine years ago (circa 2009), Indo-Pacific lionfishes (Pterois volitans and P. miles) invaded the south Florida coral reef ecosystem. During the intervening period of time, there has been substantial research on their biology, life history, demography, and habitat preferences; however, little is known concerning their regional population status and trends in the region. Here, we use a large-scale fisheries independent reef fish visual survey to investigate lionfish population status among three south Florida regions: Dry Tortugas, Florida Keys, and southeast Florida. Density estimates (ind ha−1) have been relatively stable since 2012, and are lower than other areas reported in the western Atlantic and Caribbean Sea. Low, stable population densities in south Florida suggest there may be a natural mechanism for lionfish population control. In the Dry Tortugas, lionfish density in 2016 was significantly lower (0.6 ind ha−1 ± 0.15 SE) than the two other south Florida regions. The Dry Tortugas region has the highest percentage of marine protected areas, the lowest level of exploitation, and thus the highest densities of potential lionfish predators and competitors. In the Florida Keys and southeast Florida in 2016, lionfish densities were greater (5.4 ind ha−1 ± 1.0 SE and 9.0 ± 2.7 SE, respectively) than the Dry Tortugas. Fishing pressure on lionfish was higher in these two regions, but densities of several potential predators and competitors were substantially lower. Despite relatively low regional lionfish densities that can be attributed to some combination of fishing mortality and natural biocontrol, lionfish are still well established in the south Florida coral reef ecosystem, warranting continued concern.
Bryan et al. (2018) Regional differences in an established population of invasive Indo-Pacific lionfish (Pterois volitans and P. miles) in south Florida. PeerJ 6:e5700 https://doi.org/10.7717/peerj.5700
Distribution of deep-water corals, sponges, and demersal fisheries landings in Southern California, USA: implications for conservation priorities
Deep-sea corals in Southern California are diverse and abundant but subject to multiple stressors, including bottom-contact fisheries using mobile and fixed gear. There is a need for more information on the distribution of these taxa in relation to the distribution of demersal fishing effort, and the distribution of marine protected areas, in order to improve spatial planning. There are many marine managed areas in Southern California, including essential fish habitat (EFH) areas, conservation areas, and a national marine sanctuary, but specific areas of overlap between bottom fishing and benthic epifauna are poorly known. Groundfish surveys were conducted by the National Marine Fisheries Service using a remotely operated vehicle throughout Southern California between 2003 and 2011 to document abundance and distribution of deep-water rockfish and flatfish to a depth of 500 m. Corals and sponges were also common in these images, providing an opportunity to examine these communities. Analyses of 34,792 still images revealed abundance and diversity of coral and sponge taxa, as well as frequency of fishing debris. The occurrence data were overlaid in a geographic information system with landings data for deep-water (>50 m) demersal fisheries to identify areas of spatial overlap. Corals or sponges were observed in 23% of images. A total of 15 coral genera and six sponge morphotypes were identified. A total of 70 species codes were targeted by deep-water demersal fisheries operating below 50 m for years 2007–2011. A novel priority-setting algorithm was developed to identify areas of high richness, abundance, and fishing intensity (RAFi). Several highly-ranked areas were already protected as EFH (Footprint, Piggy Bank). Other highly-ranked sites (West Catalina Island, San Clemente Island, 9-Mile Bank, Santa Rosa Flats) were encompassed by transient gear restrictions, such as Rockfish conservation areas, but are now recommended for permanent protection by the Pacific Fishery Management Council.
Spatial and Geographic Information Science
Salgado et al. (2018) Distribution of deep-water corals, sponges, and demersal fisheries landings in Southern California, USA: implications for conservation priorities. PeerJ 6:e5697 https://doi.org/10.7717/peerj.5697
Production of exopolysaccharide by strains of Lactobacillus plantarum YO175 and OF101 isolated from traditional fermented cereal beverage
Lactobacillus plantarum YO175 and OF101 isolates from Nigerian traditional fermented cereal gruel ‘ogi’, were investigated on the basis of their capability to produce exopolysaccharide (EPS) on sucrose modified deMan Rogosa Sharpe medium (mMRS). Functional groups analysis of the EPSs produced (EPS-YO175 and EPS-OF101) by Fourier-transform infrared (FT-IR) spectroscopy revealed the presence of –OH, C=O and C–H groups. The chemical composition of EPS-YO175 and EPS-OF101 showed the presence of 87.1% and 80.62% carbohydrates and 1.21% and 1.47% protein. For maximum EPS yield, three significant factors were optimized using central composite design and response surface methodology, the predicted maximum EPS produced was 1.38 g/L and 2.19 g/L, while the experimental values were 1.36 g/L and 2.18 g/L for EPS-YO175 and EPS-OF101. The EPS samples showed strong antioxidant activities in-vitro. The scale-up of the production process of the EPS will find its potential application in food industries.
Adesulu-Dahunsi et al. (2018) Production of exopolysaccharide by strains of Lactobacillus plantarum YO175 and OF101 isolated from traditional fermented cereal beverage. PeerJ 6:e5326 https://doi.org/10.7717/peerj.5326
Population structure in the Andaman keelback, Xenochrophis tytleri: geographical distance and oceanic barriers to dispersal influence genetic divergence on the Andaman archipelago
Limited gene flow between populations due to geographic distance, presence of barriers or inherent low dispersal ability leads to the formation of genetically structured populations. Strong population structure indicates lowered levels or absence of gene flow which might lead to inbreeding and loss of genetic capacity to recuperate from anthropogenic stress and natural calamities. Terrestrial reptiles are generally known to have low dispersal abilities and few studies have explored drivers of their population structure on continental islands, where both anthropogenic stress and natural calamities are relatively common. We investigated the population structure and drivers of diversification of the Andaman keelback (Xenochrophis tytleri), an endemic, terrestrial and freshwater snake species in the Andaman archipelago, a continental group of islands in the Bay of Bengal. Data was collected from 86 individuals from seven islands and 78 individuals were sequenced for the gene Nuclear Dehydrogenase subunit 4 to identify the number of populations and distribution of genetic diversity across populations. We found 11 haplotypes on seven islands and observed high genetic differentiation between seven populations defined island-wise (FST = 0.82). We further tested the number of populations by incorporating spatial data into Bayesian Clustering Analysis (GENELAND) and identified six populations of the Andaman keelback. We tested for the influence of Isolation-by-distance on these populations. While the overall trend showed a positive correlation between geographic and genetic distance, a correlogram revealed that the positive correlation disappears beyond ∼20–40 km. We also tested for the presence of geographical barriers to gene flow using Monmonier’s algorithm (SPADS), which identified five barriers to dispersal confirming that there are oceanic barriers to dispersal for some island populations of the Andaman keelback. As the Andaman Islands are arranged almost in a straight line from North to South, our data are insufficient to tease apart the roles of geographical distance and barriers to gene flow. We conclude that salt waters between near islands are weak barriers and as the geographical distance between islands increases, so does the strength of the barrier.
Mohan et al. (2018) Population structure in the Andaman keelback, Xenochrophis tytleri: geographical distance and oceanic barriers to dispersal influence genetic divergence on the Andaman archipelago. PeerJ 6:e5752 https://doi.org/10.7717/peerj.5752