Aspergillus terreus obtained from mangrove exhibits antagonistic activities against Pythium aphanidermatum-induced damping-off of cucumber
A study was conducted to investigate the potential of Aspergillus terreus obtained from Avicennia marina mangrove roots in inhibiting Pythium aphanidermatum and damping-off disease of cucumber. Aspergillus terreus exhibited in vitro inhibition of Pythium aphanidermatum growth. Electron microscope examination revealed that the antagonistic fungal isolate resulted in shrinking and groves in Pythium hypha. When Aspergillus terreus culture filtrate was added to Pythium aphanidermatum, it resulted in a significant increase (by 73%) in electrolyte leakage from Pythium hypha compared to the control, as well as significant reduction (by 71%) in oospore production. The Aspergillus terreus culture was also found to produce a cellulase enzyme, which is suggested to be involved in the antagonism against Pythium aphanidermatum. Adding Aspergillus terreus to soil infested with Pythium aphanidermatum significantly reduced percent mortality in cucumber seedlings by 70%. Aspergillus terreus, when applied alone on cucumber seedlings, did not show any suppressive effects on cucumber growth (length and fresh and dry weight). This appears to be the first report of isolation from mangrove of Aspergillus terreus with antagonistic activity against Pythium aphanidermatum-induced damping-off of cucumber. The study indicates that fungal isolates obtained from marine environments may serve as potential biocontrol agents against some plant pathogens.
Al-Shibli et al. (2019) Aspergillus terreus obtained from mangrove exhibits antagonistic activities against Pythium aphanidermatum-induced damping-off of cucumber. PeerJ 7:e7884 https://doi.org/10.7717/peerj.7884
Threshold-like associations as a function of disturbance
According to the intelligence-creativity threshold hypothesis, there should be a positive association between intelligence and creative potential up to a certain point, the threshold, after which a further increase in intelligence should have no association with creativity. In the present simulation study, the measured intelligence and creativity of virtual subjects were affected by their true abilities as well as a disturbance factor that varied in magnitude between subjects. The results indicate that the hypothesized threshold-like association could be due to some disturbing factor, for example, low motivation, illness, or linguistic confusion, that varies between individuals and that affects both measured intelligence and measured creativity, especially if the actual association between intelligence and creativity is weak. This, together with previous negative findings, calls the validity of the intelligence-creativity threshold hypothesis into question.
Sorjonen et al. (2019) Threshold-like associations as a function of disturbance. PeerJ 7:e7891 https://doi.org/10.7717/peerj.7891
RNA-seq transcriptome profiling of porcine lung from two pig breeds in response to Mycoplasma hyopneumoniae infection
Background Mycoplasma hyopneumoniae (Mhp) is the main pathogen causing respiratory disease in the swine industry. Mhp infection rates differ across pig breeds, with Chinese native pig breeds that exhibit high fecundity (e.g., Jiangquhai, Meishan, Erhualian) more sensitive than Duroc, Landrace, and other imported pig breeds. However, the genetic basis of the immune response to Mhp infection in different pig breeds is largely unknown. Aims The aims of this study were to determine the relative Mhp susceptibility of the Chinese native Jiangquhai breed compared to the Duroc breed, and identify molecular mechanisms of differentially expressed genes (DEGs) using an RNA-sequencing (RNA-seq) approach. Methods Jiangquhai and Duroc pigs were artificially infected with the same Mhp dose. The entire experiment lasted 28 days. Daily weight gain, Mhp-specific antibody levels, and lung lesion scores were measured to evaluate the Mhp infection susceptibility of different breeds. Experimental pigs were slaughtered on the 28th day. Lung tissues were collected for total RNA extraction. RNA-seq was performed to identify DEGs, which were enriched by gene ontology (GO) and the Kyoto Encyclopedia annotation of Genes and Genomes (KEGG) databases. DEGs were validated with real-time quantitative polymerase chain reaction (RT-qPCR). Results Infection with the same Mhp dose produced a more serious condition in Jiangquhai pigs than in Duroc pigs. Jiangquhai pigs showed poorer growth, higher Mhp antibody levels, and more serious lung lesions compared with Duroc pigs. RNA-seq identified 2,250 and 3,526 DEGs in lung tissue from Jiangquhai and Duroc pigs, respectively. The two breeds shared 1,669 DEGs, which were involved in immune-relevant pathways including cytokine-cytokine receptor interaction, PI3K-Akt signaling pathway, and chemokine signaling pathway. Compared to Jiangquhai pigs, more chemokines, interferon response factors, and interleukins were specifically activated in Duroc pigs; CXCL10, CCL4, IL6 and IFNG genes were significantly up-regulated, which may help Duroc pigs enhance immune response and reduce Mhp susceptibility. Conclusion This study demonstrated differential immune-related DEGs in lung tissue from the two breeds, and revealed an important role of genetics in the immune response to Mhp infection. The biological functions of these important DEGs should be further confirmed and maybe applied as molecular markers that improve pig health.
Ni et al. (2019) RNA-seq transcriptome profiling of porcine lung from two pig breeds in response to Mycoplasma hyopneumoniae infection. PeerJ 7:e7900 https://doi.org/10.7717/peerj.7900
Classification of RNA backbone conformations into rotamers using 13C′ chemical shifts: exploring how far we can go
The conformational space of the ribose-phosphate backbone is very complex as it is defined in terms of six torsional angles. To help delimit the RNA backbone conformational preferences, 46 rotamers have been defined in terms of these torsional angles. In the present work, we use the ribose experimental and theoretical 13C′ chemical shifts data and machine learning methods to classify RNA backbone conformations into rotamers and families of rotamers. We show to what extent the experimental 13C′ chemical shifts can be used to identify rotamers and discuss some problem with the theoretical computations of 13C′ chemical shifts.
Icazatti et al. (2019) Classification of RNA backbone conformations into rotamers using 13C′ chemical shifts: exploring how far we can go. PeerJ 7:e7904 https://doi.org/10.7717/peerj.7904
A new small device made of glass for separating microplastics from marine and freshwater sediments
Separating microplastics from marine and freshwater sediments is challenging, but necessary to determine their distribution, mass, and ecological impacts in benthic environments. Density separation is commonly used to extract microplastics from sediments by using heavy salt solutions, such as zinc chloride and sodium iodide. However, current devices/apparatus used for density separation, including glass beakers, funnels, upside-down funnel-shaped separators with a shut-off valve, etc., possess various shortcomings in terms of recovery rate, time consumption, and/or usability. In evaluating existing microplastic extraction methods using density separation, we identified the need for a device that allows rapid, simple, and efficient extraction of microplastics from a range of sediment types. We have developed a small glass separator, without a valve, taking a hint from an Utermöhl chamber. This new device is easy to clean and portable, yet enables rapid separation of microplastics from sediments. With this simple device, we recovered 94–98% of <1,000 µm microplastics (polyethylene, polypropylene, polyvinyl chloride, polyethylene terephthalate, and polystyrene). Overall, the device is efficient for various sizes, polymer types, and sediment types. Also, microplastics collected with this glass-made device remain chemically uncontaminated, and can, therefore, be used for further analysis of adsorbing contaminants and additives on/to microplastics.
Environmental Contamination and Remediation
Nakajima et al. (2019) A new small device made of glass for separating microplastics from marine and freshwater sediments. PeerJ 7:e7915 https://doi.org/10.7717/peerj.7915
Mercuric pollution of surface water, superficial sediments, Nile tilapia (Oreochromis nilotica Linnaeus 1758 [Cichlidae]) and yams (Dioscorea alata) in auriferous areas of Namukombe stream, Syanyonja, Busia, Uganda
The mercury content and the contamination characteristics of water, sediments, edible muscles of a non-piscivorous fish (Oreochromis nilotica Linnaeus 1758 [Cichlidae]) and yams (Dioscorea alata) from Namukombe stream in Busia gold district of Uganda were evaluated. Human health risk assessment from consumption of contaminated fish and yams as well as contact with contaminated sediments from the stream were performed. Forty-eight (48) samples of water (n = 12), sediments (n = 12), fish (n = 12) and yams (n = 12) were taken at intervals of 10 m from three gold recovery sites located at up, middle and down sluices of the stream and analyzed for total mercury (THg) using US EPA method 1631. Results (presented as means ± standard deviations) showed that water in the stream is polluted with mercury in the range of < detection limit to 1.21 ± 0.040 mg/L while sediments contain mean THg from < detection limit to 0.14 ± 0.040 ugg−1. Mean THg content of the edible muscles of O. nilotica ranged from < detection limit to 0.11 ± 0.014 ugg−1while D. alata contained from < detection limit to 0.30 ± 0.173 ugg−1mean THg. The estimated daily intake ranged from 0.0049 ugg−1day−1 to 0.0183 ugg−1day−1 and 0.0200 ugg−1day−1 to 0.0730 ugg−1day−1 for fish consumed by adults and children respectively. The corresponding health risk indices ranged from 0.0123 to 0.0458 and 0.0500 to 0.1830. Estimated daily intake was from 0.0042 ugg−1day−1 to 0.1279 ugg−1day−1 and 0.0130 ugg−1day−1 to 0.3940 ugg−1day−1 for D. alata consumed by adults and children respectively. The health risk indices recorded were from 0.011 to 0.320 and 0.033 to 0.985 for adults and children respectively. The mean THg content of the sediments, edible muscles of O. nilotica and D. alata were within acceptable WHO/US EPA limits. About 91.7% of the water samples had mean THg above US EPA maximum permissible limit for mercury in drinking water. Consumption of D. alata grown within 5 m radius up sluice of Namukombe stream may pose deleterious health risks as reflected by the health risk index of 0.985 being very close to one. From the pollution and risk assessments, mercury use should be delimited in Syanyonja artisanal gold mining areas. A solution to abolish mercury-based gold mining in the area needs to be sought as soon as possible to avert the accentuating health, economic and ecological disaster arising from the continuous discharge of mercury into the surrounding areas. Other mercury-free gold recovering methods such as use of borax, sluice boxes and direct panning should be encouraged. Waste management system for contaminated wastewater, used mercury bottles and tailings should be centralized.
Omara et al. (2019) Mercuric pollution of surface water, superficial sediments, Nile tilapia (Oreochromis nilotica Linnaeus 1758 [Cichlidae]) and yams (Dioscorea alata) in auriferous areas of Namukombe stream, Syanyonja, Busia, Uganda. PeerJ 7:e7919 https://doi.org/10.7717/peerj.7919
Effects of the loss of estrogen on the heart’s hypertrophic response to chronic left ventricle volume overload in rats
Aortic valve regurgitation (AR) can result in heart failure from chronic overloading of the left ventricle (LV). Little is known of the role of estrogens in the LV responses to this condition. The aim of the study was to compare LV remodeling in female rats with severe AR in absence of estrogens by ovariectomy (Ovx). In a first study, we investigated over 6 months the development of hypertrophy in four groups of female Wistar rats: AR or sham-operated (sham) and Ovx or not. Ovx reduced normal heart growth. As expected, volume overload (VO) from AR resulted in significant LV dilation (42% and 32% increase LV end-diastolic diameter in intact and Ovx groups vs. their respective sham group; p < 0.0001). LV weight was also significantly and similarly increased in both AR groups (non-Ovx and Ovx). Increase in stroke volume or cardiac output and loss of systolic function were similar between AR intact and AR Ovx groups compared to sham. We then investigated what were the effects of 17beta-estradiol (E2; 0.03 mg/kg/day) treatment on the parameters studied in Ovx rats. Ovx reduced uterus weight by 85% and E2 treatment restored up to 65% of the normal weight. E2 also helped normalize heart size to normal values. On the other hand, it did not influence the extent of the hypertrophic response to AR. In fact, E2 treatment further reduced LV hypertrophy in AR Ovx rats (41% over Sham Ovx + E2). Systolic and diastolic functions parameters in AR Ovx + E2 were similar to intact AR animals. Ovx in sham rats had a significant effect on the LV gene expression of several hypertrophy markers. Atrial natriuretic peptide (Nppa) gene expression was reduced by Ovx in sham-operated females whereas brain natriuretic peptide (Nppb) expression was increased. Alpha (Myh6) and beta (Myh7) myosin heavy chain genes were also significantly modulated by Ovx in sham females. In AR rats, LV expression of both Nppa and Nppb genes were increased as expected. Ovx further increased it of AR rats for Nppa and did the opposite for Nppb. Interestingly, AR in Ovx rats had only minimal effects on Myh6 and Myh7 genes whereas they were modulated as expected for intact AR animals. In summary, loss of estrogens by Ovx in AR rats was not accompanied by a worsening of hypertrophy or cardiac function. Normal cardiac growth was reduced by Ovx in sham females but not the hypertrophic response to AR. On the other hand, Ovx had important effects on LV gene expression both in sham and AR female rats.
Walsh-Wilkinson et al. (2019) Effects of the loss of estrogen on the heart’s hypertrophic response to chronic left ventricle volume overload in rats. PeerJ 7:e7924 https://doi.org/10.7717/peerj.7924
Spatio-temporal patterns of the oceanic conditions and nearshore marine community in the Mid-Atlantic Bight (New Jersey, USA)
Oceanic environmental conditions influence, shape, and control the geographical range, spatial distribution, abundance, and size composition of marine fauna. Water temperature, salinity, dissolved oxygen, depth, and sediment type influence select fish life-history characteristics and community structure. Marine communities are vulnerable to major changes in environmental conditions, but the response and severity depends on various biological or ecological factors, such as resilience to stress or adaptation. Researchers around the world have predicted and documented numerous alterations in fish communities caused by ongoing significant physicochemical shifts associated with natural and potentially unnatural sources, but published studies describing the historical conditions are lacking for most regions around the world, including the coastal waters off New Jersey. Given the need to understand these processes, a multifaceted investigation was undertaken to describe, evaluate, and compare the oceanic conditions and nearshore marine fauna community off New Jersey during 1988 through 2015. Findings showed the oceanic conditions varied over time and space. Mean surface water temperature increased significantly about 0.6 °C per decade, mean salinity decreased about 1.3 psu per decade, and dissolved oxygen increased 0.09 mg/l per decade. Over 20.4 million fish and invertebrates (1,338.3 mt) representing 214 (water temperature preference classified) species (not including unidentified species) were collected within 15 strata (areas: 12−26) off the coast of New Jersey from 1988 to 2015. Three marine fauna water temperature preference groups (coldwater-adapted, warmwater-adapted, and subtropic-adapted) were identified in the study area. The main coldwater-adapted species collected were longfin squid (Loligo pealei) (n = 2, 225, 975), Atlantic herring (Clupea harengus) (n = 544, 032), and little skate (Leucoraja erinacea) (n = 316, 356), while Atlantic butterfish (Peprilus triacanthus) (n = 2, 873, 138), scup (Stenotomus chrysops) (n = 1, 318, 569), and northern searobin (Prionotus carolinus) (n = 503, 230) represented the warmwater-adapted group. Bay anchovy (Anchoa mitchilli) (n = 9, 227, 960), striped anchovy (Anchoa hepsetus) (n = 245, 214), and Atlantic moonfish (Vomer setapinnis) (n = 38, 691) denoted the subtropic-adapted group. Subtropic-adapted species were the most abundant and coldwater-adapted were the least abundant water temperature preference group. The estimated abundance of coldwater-adapted species declined, warmwater-adapted species slightly increased, and subtropic-adapted species decreased with time, which suggest the environmental conditions are influencing and thereby shifting the marine community.
Levesque (2019) Spatio-temporal patterns of the oceanic conditions and nearshore marine community in the Mid-Atlantic Bight (New Jersey, USA). PeerJ 7:e7927 https://doi.org/10.7717/peerj.7927
The distribution and mitochondrial genotype of the hydroid Aglaophenia latecarinata is correlated with its pelagic Sargassum substrate type in the tropical and subtropical western Atlantic Ocean
The pelagic brown macroalga Sargassum supports rich biological communities in the tropical and subtropical Atlantic region, including a variety of epiphytic invertebrates that grow on the Sargassum itself. The thecate hydroid Aglaophenia latecarinata is commonly found growing on some, but not all, Sargassum forms. In this study, we examined the relationship between A. latecarinata and its pelagic Sargassum substrate across a broad geographic area over the course of 4 years (2015–2018). The distribution of the most common Sargassum forms that we observed (Sargassum fluitans III and S. natans VIII) was consistent with the existence of distinct source regions for each. We found that A. latecarinata hydroids were abundant on both S. natans VIII and S. fluitans III, and also noted a rare observation of A. latecarinata on S. natans I. For the hydroids on S. natans VIII and S. fluitans III, hydroid mitochondrial genotype was strongly correlated with the Sargassum substrate form. We found significant population genetic structure in the hydroids, which was also consistent with the distributional patterns of the Sargassum forms. These results suggest that hydroid settlement on the Sargassum occurs in type-specific Sargassum source regions. Hydroid species identification is challenging and cryptic speciation is common in the Aglaopheniidae. Therefore, to confirm our identification of A. latecarinata, we conducted a phylogenetic analysis that showed that while the genus Aglaophenia was not monophyletic, all A. latecarinata haplotypes associated with pelagic Sargassum belonged to the same clade and were likely the same species as previously published sequences from Florida, Central America, and one location in Brazil (São Sebastião). A nominal A. latecarinata sequence from a second Brazilian location (Alagoas) likely belongs to a different species.
Govindarajan et al. (2019) The distribution and mitochondrial genotype of the hydroid Aglaophenia latecarinata is correlated with its pelagic Sargassum substrate type in the tropical and subtropical western Atlantic Ocean. PeerJ 7:e7814 https://doi.org/10.7717/peerj.7814
Determining the optimal maximal and submaximal voluntary contraction tests for normalizing the erector spinae muscles
Background This study aimed to identify which maximum voluntary isometric contraction (MVIC) and sub-MVIC tests produce the highest activation of the erector spinae muscles and the greatest reduction in inter-individual variability, to put them forward as reference normalization maneuvers for future studies. Methods Erector spinae EMG activity was recorded in 38 healthy women during five submaximal and three maximal exercises. Results None of the three MVIC tests generated the maximal activation level in all the participants. The maximal activation level was achieved in 68.4% of cases with the test performed on the roman chair in the horizontal position (96.3 ± 7.3; p < 0.01). Of the five submaximal maneuvers, the one in the horizontal position on the roman chair produced the highest percentage of activation (61.1 ± 16.7; p < 0.01), and one of the lowest inter-individual variability values in the normalized signal of a trunk flexion-extension task. Conclusions A modified Sorensen MVIC test in a horizontal position on a roman chair and against resistance produced the highest erector spinae activation, but not in 100% of participants, so the execution of several normalization maneuvers with the trunk at different inclinations should be considered to normalize the erector spinae EMG signal. A modified Sorensen test in a horizontal position without resistance is the submaximal maneuver that produces the highest muscle activation and the greatest reduction in inter-individual variability, and could be considered a good reference test for normalization.
Biviá-Roig et al. (2019) Determining the optimal maximal and submaximal voluntary contraction tests for normalizing the erector spinae muscles. PeerJ 7:e7824 https://doi.org/10.7717/peerj.7824