Advances in the diagnosis of non-occlusive mesenteric ischemia and challenges in intra-abdominal sepsis patients: a narrative review
Non-occlusive mesenteric ischemia (NOMI) is a type of acute mesenteric ischemia (AMI) with a high mortality rate mainly because of a delayed or misdiagnosis. Intra-abdominal sepsis is one of the risk factors for developing NOMI, and its presence makes early diagnosis much more difficult. An increase in routine abdominal surgeries carries a corresponding risk of abdominal infection, which is a complication that should not be overlooked. It is critical that physicians are aware of the possibility for intestinal necrosis in abdominal sepsis patients due to the poor survival rate of NOMI. This review aims to summarize advances in the diagnosis of NOMI, and focuses on the diagnostic challenges of mesenteric ischemia in patients with intra-abdominal sepsis.
Chen et al. (2023) Advances in the diagnosis of non-occlusive mesenteric ischemia and challenges in intra-abdominal sepsis patients: a narrative review. PeerJ 11:e15307 https://doi.org/10.7717/peerj.15307
Association between Vitamin D receptor (VDR) gene polymorphisms and hypertensive disorders of pregnancy: a systematic review and meta-analysis
Background Hypertensive disorders of pregnancy (HDP) are currently one of the major causes of pregnancy-related maternal and fetal morbidity and mortality worldwide. Recent studies provide evidence that maternal Vitamin D receptor (VDR) gene polymorphisms probably play a key role by affecting the biological function of vitamin D in some adverse pregnancy outcomes, while the relationship between the VDR gene polymorphisms and the risk of HDP remains controversial in current studies. This systematic review and meta-analysis aimed to comprehensively evaluate the association of the VDR gene polymorphisms with HDP susceptibility. Methods This meta-analysis follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement and a protocol has been registered in the PROSPERO (ID: CRD42022344383) before commencing this review. PubMed, Web of Science, Embase, and the Cochrane Library databases were searched until January 21, 2023. Case-control and cohort studies that reported the association of the VDR gene polymorphisms with HDP were included. The quality of the included studies was assessed using the Newcastle-Ottawa Scale (NOS) for non-randomized studies. The odds ratios (ORs) with corresponding 95% confidence intervals (CIs) of the five models (allele model, dominant model, recessive model, homozygous model, heterozygous model) were pooled respectively, and subgroup analysis was performed based on ethnicity. Results A total of ten studies were included. The VDR gene ApaI polymorphism was associated with HDP susceptibility in the dominant model (OR: 1.38; 95% CI [1.07–1.79]; P = 0.014) and the heterozygote model (OR: 1.48; 95% CI [1.12–1.95]; P = 0.006). In subgroup analysis, the heterozygote model (OR: 2.06; 95% CI [1.21–3.52]; P = 0.008) of the ApaI polymorphism was associated with HDP in Asians, but not in Caucasians. Conclusion The VDR gene ApaI polymorphism may be associated with HDP susceptibility. Insufficient evidence to support the existence of ethnic differences in this association.
Guo et al. (2023) Association between Vitamin D receptor (VDR) gene polymorphisms and hypertensive disorders of pregnancy: a systematic review and meta-analysis. PeerJ 11:e15181 https://doi.org/10.7717/peerj.15181
Pyrus calleryana extracts reduce germination of native grassland species, suggesting the potential for allelopathic effects during ecological invasion
Invasive plant species’ success may be a result of allelopathy, or the release of secondary metabolites that are harmful for surrounding plant species. Allelopathy can be mediated through the abiotic environment by chemical sorption or transformation, so the substrate on which interactions occur can lead to differential outcomes in allelopathic potential. One aggressive invader, Pyrus calleryana, has become dominant in many ecosystems throughout Eastern US, and has reduced the abundance of native species where it invades. Thus, our goal was to identify if P. calleryana had allelopathic potential by testing the impact of leaf and flower leachate on gemination of six common grassland species (three grasses and three forbs) in either sterilized sand or field collected soils. Germination of five out of six tested species was reduced by P. calleryana leaf litter, with weaker impacts from flower leachate. This suggests that allelopathy is one mechanism driving the success of P. calleryana and that allelopathic effects may change with plant phenology. For instance, P. calleryana has late leaf senescence in the fall and copious blooming in the spring that may elongate the timeframe that allelopathic inhibition can occur. Further, germination was higher in sand than in soil, suggesting that the context of the abiotic environment can mediate this relationship. In our study, two grass species that could be overabundant in restored grasslands had higher germination rates in soil than sand and one was not altered by P. calleryana suggesting that this relationship could further promote the overabundance of grass species. Taken together, P. calleryana likely inhibits the germination of native species where it invades, but there is context dependency of this relationship with both soil chemistry and seasonality.
Woods et al. (2023) Pyrus calleryana extracts reduce germination of native grassland species, suggesting the potential for allelopathic effects during ecological invasion. PeerJ 11:e15189 https://doi.org/10.7717/peerj.15189
Annual changes in biomass amount and feeding potential of shrubby rangelands in maquis formation
Background This study evaluated the extent to which the endemic herbaceous and woody species of shrubby rangelands met the roughage needs of grazing animals throughout the year. Methods The biomass, botanical composition, and quality of hay were investigated in the shrubby rangelands in Paşaköy of the Ayvacık districts in Çanakkale over the course of a year. Plant samples were taken from the herbaceous species monthly and from the grazing parts of the shrubs in May and November. Results The total amount of biomass (hay + shrub) in the rangeland was found to be 30.448 kg/ha. Shrubs made up 18.78% of the rangeland, while the annual species comprised 54.96%, and perennial herbs covered 26.26% of the total biomass. Crude protein (CP) ratios of herbaceous species decreased continuously from March (13.58%) to September (6.73%), and then increased. A similar change was also seen in pure ash (PA) ratios. The CP ratios in the shrub species were high in spring and decreased in autumn and there was an irregular variation in PA rates. Oak had the highest PA ratio during the spring, while thuja had the highest ratio in autumn, and Juniperus oxycedrus during the winter months. In herbaceous species, cell wall components (NDF, ADF, and ADL) reached their highest levels in summer and decreased in spring and winter. However, in shrubs, these components varied according to the species and were generally lowest in spring and then increased in autumn and winter. Here, it was determined that year-round grazing is a suitable grazing system in the shrubby rangelands of the Mediterranean zone, and animals are able to find fresh forage in the rangelands due to the presence of shrubs. However, since the contribution of shrubs to the total forage production is low, additional roughage should be provided, except in the spring when the production and quality of hay increase. These practices may contribute to better livestock management.
Alatürk et al. (2023) Annual changes in biomass amount and feeding potential of shrubby rangelands in maquis formation. PeerJ 11:e15204 https://doi.org/10.7717/peerj.15204
CINmetrics: an R package for analyzing copy number aberrations as a measure of chromosomal instability
Genomic instability is an important hallmark of cancer and more recently has been identified in others like neurodegenrative diseases. Chromosomal instability, as a measure of genomic instability, has been used to characterize clinical and biological phenotypes associated with these diseases by measuring structural and numerical chromosomal alterations. There have been multiple chromosomal instability scores developed across many studies in the literature; however, these scores have not been compared because of the lack of a single tool available to calculate and facilitate these various metrics. Here, we provide an R package CINmetrics, that calculates six different chromosomal instability scores and allows direct comparison between them. We also demonstrate how these scores differ by applying CINmetrics to breast cancer data from The Cancer Genome Atlas (TCGA). The package is available on CRAN at https://cran.rproject.org/package=CINmetrics and on GitHub at https://github.com/lasseignelab/CINmetrics.
Oza et al. (2023) CINmetrics: an R package for analyzing copy number aberrations as a measure of chromosomal instability. PeerJ 11:e15244 https://doi.org/10.7717/peerj.15244
Characterization of the populations of upside-down jellyfish in Jardines de la Reina National Park, Cuba
Upside-down jellyfish are a group of benthic scyphozoans belonging to the genus Cassiopea, whose members are in symbiosis with dinoflagellates and inhabit tropical and subtropical waters. Although there are some studies of the genus in the Caribbean, these are limited. In Cuba, the group’s studies are restricted to reports on taxonomic lists and, as far as we know, no one has performed any analyzes of the densities of these jellyfish in seagrass or mangrove ecosystems in Cuba. In this work, the populations of Cassiopea spp. in Jardines de la Reina National Park (JRNP) were characterized, for the first time for this Marine Protected Area and Cuba. One hundred 1m2 square frames were placed at 14 JRNP sites. For each site, the species, density, size of the individuals and abiotic factors were determined. Density and diameter comparisons were made between sites, zones and regions within the JRNP. The percentage of the benthic cover was determined and a correlation was made between density and diameter. A total of 10,803 individuals were recorded, of which 7,618 belong to Cassiopea xamachana and 3,185 belong to Cassiopea frondosa. Both species share a niche and no evident segregation was detected according to abiotic variables. Significant differences were detected in comparisons of density and size across sites and zones. Density and size in the JRNP were negatively correlated, and higher aggregations of the species were observed at lower sizes. Density mean values ranged from 2.18 to 14.52 ind. /m2 with maximum values of 79 ind. /m2. Cayo Alcatraz was the site found to have the highest density while Cachiboca was the site with the lowest density. The average bell diameter size of the individuals ranged from 9.34 to 15.31 cm for the sampled sites, with minimum and maximum values of 2.5 cm and 32.6 cm. The smallest size was recorded at Cayo Alcatraz while the largest size was reported for Boca de las Anclitas. The environmental factors evaluated showed no significant relationship with the density or diameter of Cassiopea, while the Thalassia testudinum cover was negatively correlated with Cassiopea density at all fourteen sites in the JRNP. The percentage of Cassiopea coverage was higher than those reported in the literature, with four sites exceeding 20% coverage. In general, the populations of Cassiopea spp. in the JRNP did not differ greatly, although a higher density was observed towards the eastern region of the park. It was shown for the first time for the species that density and size have a negative correlation. Future studies are required to quantify the impact of Cassiopea on coastal marine ecosystem processes, and to further determine how anthropogenic changes may be altering the function of these tropical ecosystems.
Morejón-Arrojo et al. (2023) Characterization of the populations of upside-down jellyfish in Jardines de la Reina National Park, Cuba. PeerJ 11:e15254 https://doi.org/10.7717/peerj.15254
Macroevolutionary patterns in intragenomic rDNA variability among planktonic foraminifera
Ribosomal intragenomic variability in prokaryotes and eukaryotes is a genomic feature commonly studied for its inflationary impact on molecular diversity assessments. However, the evolutionary mechanisms and distribution of this phenomenon within a microbial group are rarely explored. Here, we investigate the intragenomic variability in 33 species of planktonic foraminifera, calcifying marine protists, by inspecting 2,403 partial SSU sequences obtained from single-cell clone libraries. Our analyses show that polymorphisms are common among planktonic foraminifera species, but the number of polymorphic sites significantly differs among clades. With our molecular simulations, we could assess that most of these mutations are located in paired regions that do not affect the secondary structure of the SSU fragment. Finally, by mapping the number of polymorphic sites on the phylogeny of the clades, we were able to discuss the evolution and potential sources of intragenomic variability in planktonic foraminifera, linking this trait to the distinctive nuclear and genomic dynamics of this microbial group.
Greco et al. (2023) Macroevolutionary patterns in intragenomic rDNA variability among planktonic foraminifera. PeerJ 11:e15255 https://doi.org/10.7717/peerj.15255
East Timor as an important source of cashew (Anacardium occidentale L.) genetic diversity
Background Cashew (Anacardium occidentale L.) is a crop currently grown in several tropical countries because of the economic importance of cashew nuts. Despite its enormous economic worth, limited research has been conducted on the molecular diversity of cashew genetic resources. In this study, a wide comprehensive assessment of the genetic diversity of cashew trees in East Timor was performed using microsatellites (SSRs) to evaluate intraspecific diversity and population structuring. Methods A total of 207 individual cashew trees, including trees from East Timor (11), and outgroup populations from Indonesia (one) and Mozambique (two), were analyzed with 16 cashew-specific SSRs. A comprehensive sampling of cashew trees within East Timor was performed, covering the distribution of cashew orchards in the country. Genetic diversity indices were calculated, and population structuring was determined using three different approaches: genetic distances (UPGMA and NJ), AMOVA, and individual-based clustering methods through Bayesian (STRUCTURE) and multivariate (DAPC) analyses. Results The population structuring analysis revealed that the genetic diversity of cashew populations in East Timor was higher in this study than previously reported for cashew trees. A higher allelic richness was found within cashew populations in East Timor compared with the outgroup populations (Mozambique and Indonesia), reinforced by the presence of private alleles. Moreover, our study showed that cashew populations in East Timor are grouped into two dissimilar genetic groups, which may suggest multiple cashew introductions over time. These new cashew genetic resources could be explored for future crop improvement. Conclusions Crop diversity underpins the productivity, resilience, and adaptive capacity of agriculture. Therefore, this study provides useful information regarding genetic diversity and population structure that can be harnessed to improve cashew production in East Timor. This data is also important to creating a country-specific genetic cashew signature to increase cashew market value.
Guterres et al. (2023) East Timor as an important source of cashew (Anacardium occidentale L.) genetic diversity. PeerJ 11:e14894 https://doi.org/10.7717/peerj.14894
Personality traits, rank attainment, and siring success throughout the lives of male chimpanzees of Gombe National Park
Personality traits in many taxa correlate with fitness. Several models have been developed to try to explain how variation in these traits is maintained. One model proposes that variation persists because it is linked to trade-offs between current and future adaptive benefits. Tests of this model’s predictions, however, are scant in long-lived species. To test this model, we studied male chimpanzees living in Gombe National Park, Tanzania. We operationalized six personality traits using ratings on 19 items. We used 37 years of behavioral and genetic data to assemble (1) daily rank scores generated from submissive vocalizations and (2) records of male siring success. We tested whether the association between two personality traits, Dominance and Conscientiousness, and either rank or reproductive success, varied over the life course. Higher Dominance and lower Conscientiousness were associated with higher rank, but the size and direction of these relationships did not vary over the life course. In addition, independent of rank at the time of siring, higher Dominance and lower Conscientiousness were related to higher siring success. Again, the size and direction of these relationships did not vary over the life course. The trade-off model, therefore, may not hold in long-lived and/or slowly reproducing species. These findings also demonstrate that ratings are a valid way to measure animal personality; they are related to rank and reproductive success. These traits could therefore be used to test alternative models, including one that posits that personality variation is maintained by environmental heterogeneity, in studies of multiple chimpanzee communities.
Weiss et al. (2023) Personality traits, rank attainment, and siring success throughout the lives of male chimpanzees of Gombe National Park. PeerJ 11:e15083 https://doi.org/10.7717/peerj.15083
In silico screening of chalcones and flavonoids as potential inhibitors against yellow head virus 3C-like protease
Yellow head virus (YHV) is one of the most important pathogens in prawn cultivation. The outbreak of YHV could potentially result in collapses in aquaculture industries. Although a flurry of development has been made in searching for preventive and therapeutic approaches against YHV, there is still no effective therapy available in the market. Previously, computational screening has suggested a few cancer drugs to be used as YHV protease (3CLpro) inhibitors. However, their toxic nature is still of concern. Here, we exploited various computational approaches, such as deep learning-based structural modeling, molecular docking, pharmacological prediction, and molecular dynamics simulation, to search for potential YHV 3CLpro inhibitors. A total of 272 chalcones and flavonoids were in silico screened using molecular docking. The bioavailability, toxicity, and specifically drug-likeness of hits were predicted. Among the hits, molecular dynamics simulation and trajectory analysis were performed to scrutinize the compounds with high binding affinity. Herein, the four selected compounds including chalcones cpd26, cpd31 and cpd50, and a flavonoid DN071_f could be novel potent compounds to prevent YHV and GAV propagation in shrimp. The molecular mechanism at the atomistic level is also enclosed that can be used to further antiviral development.
Boonthaworn et al. (2023) In silico screening of chalcones and flavonoids as potential inhibitors against yellow head virus 3C-like protease. PeerJ 11:e15086 https://doi.org/10.7717/peerj.15086