Biogeography of the Southern Ocean: environmental factors driving mesoplankton distribution South of Africa
Spatial distribution of zooplankton communities depends on numerous factors, especially temperature and salinity conditions (hydrological factor), sampled depth, chlorophyll concentration, and diel cycle. We analyzed and compared the impact of these factors on mesoplankton abundance, biodiversity, quantitative structure based on proportion of taxa and qualitative structure based on presence/absence of taxa in the Southern Ocean. Samples (43 stations, three vertical strata sampled at each station, 163 taxa identified) were collected with a Juday net along the SR02 transect in December 2009. Mesoplankton abundance in discrete vertical layers ranged from 0.2 to 13,743.6 ind. m−3, i.e., five orders of magnitude, maximal and minimal values were recorded in the upper mixed and in the deepest layer, respectively. Within the combined 300-m layer, abundances ranged from 16.0 to 1,455.0 ind. m−3, i.e., two orders of magnitude suggesting that integral samples provide little information about actual variations of mesoplankton abundances. A set of analyses showed that depth was the major driver of mesoplankton distribution (abundance, biodiversity, quantitative structure), hydrological factors influenced two of them (quantitative and qualitative structure), chlorophyll concentration strongly affected only quantitative structure, and diel cycle had an insignificant effect on mesoplankton distribution. Using our current knowledge of the fine structure of the Antarctic Circumpolar Current, we compared effects of four hydrological fronts, i.e., boundaries between different water-masses with distinct environmental characteristics, and eight dynamic jets (narrow yet very intense currents) on mesoplankton distribution. Subtropical, Polar, and Subantarctic Fronts drove quantitative and qualitative structure of mesoplankton assemblages (decreasing in order of influence), while the Southern Boundary affected only qualitative structure. Effects of dynamic jets were insignificant. We suggest that mesoplankton composition is driven by hydrological parameters and further maintained through compartmentalization by fronts. Impact of local eddies and meanders on biodiversity, abundance, qualitative and quantitative structure of mesoplankton is comparable to that of hydrological fronts. Qualitative structure of mesoplankton assemblages mirrors hydrological structure of the Southern Ocean better than quantitative structure and may be recommended for biogeographic analyses of the Southern Ocean. Comparisons with previous reports from the same area retrieved no significant changes in mesoplankton distribution during the period 1992–2009.
Vereshchaka et al. (2021) Biogeography of the Southern Ocean: environmental factors driving mesoplankton distribution South of Africa. PeerJ 9:e11411 https://doi.org/10.7717/peerj.11411
Nostolepis scale remains (stem Chondrichthyes) from the Lower Devonian of Qujing, Yunnan, China
Based initially on microfossils, Nostolepis is one of the first known ‘acanthodians’, which constitute a paraphyletic assemblage of plesiomorphic members of the total group Chondrichthyes. Its wide distribution has potential implications for stratigraphic comparisons worldwide. Six species of Nostolepis have been reported in China, including one species from the Xitun Formation (Lochkovian, Lower Devonian) of Qujing, eastern Yunnan. Acid preparation of rock samples from the Xitun Formation has yielded abundant acanthodian remains. Based on both morphological and histological examinations, here we identify five species of Nostolepis, including two new species. N. qujingensis sp. nov. is characterized by thin scales devoid of the neck anteriorly and the dentine tubules rarely present in the anterior part of the crown. N. digitus sp. nov. is characterized by parallel ridges on anterior and lateral margins of the crown, and the neck constricted and ornamented with pore openings. We extend the duration of N. striata in China from the Pridoli of Silurian (Yulungssu Formation) to the Lower Devonian in Qujing and report the first occurrences of N. amplifica and N. consueta in this region. This study increases the diversity of the Lower Devonian Xitun Fauna and provides a better understanding of the paleogeographic distribution of Nostolepis.
Li et al. (2021) Nostolepis scale remains (stem Chondrichthyes) from the Lower Devonian of Qujing, Yunnan, China. PeerJ 9:e11093 https://doi.org/10.7717/peerj.11093
Type of organic fertilizer rather than organic amendment per se increases abundance of soil biota
Addition of organic amendments is a commonly used practice to offset potential loss of soil organic matter from agricultural soils. The aim of the present study was to examine how long-term addition of organic matter affects the abundance of different soil biota across trophic levels and the role that the quality of the organic amendments plays. Here we used a 17-year-old fertilization experiment to investigate soil biota responses to four different organic fertilizers, compared with two mineral nitrogen fertilizers and no fertilization, where the organic fertilizers had similar carbon content but varied in their carbon to nitrogen ratios. We collected soil samples and measured a wide range of organisms belonging to different functional groups and trophic levels of the soil food web. Long-term addition of organic and mineral fertilizers had beneficial effects on the abundances of most soil organisms compared with unfertilized soil, but the responses differed between soil biota. The organic fertilizers generally enhanced bacteria and earthworms. Fungi and nematodes responded positively to certain mineral and organic fertilizers, indicating that multiple factors influenced by the fertilization may affect these heterogeneous groups. Springtails and mites were less affected by fertilization than the other groups, as they were present at relatively high abundances even in the unfertilized treatment. However, soil pH had a great influence on springtail abundance. In summary, the specific fertilizer was more important in determining the numerical and compositional responses of soil biota than whether it was mineral or organic. Overall, biennial organic amendments emerge as insufficient, by themselves, to promote soil organisms in the long run, and would need to be added annually or combined with other practices affecting soil quality, such as no or reduced tillage and other crop rotations, to have a beneficial effect.
Viketoft et al. (2021) Type of organic fertilizer rather than organic amendment per se increases abundance of soil biota. PeerJ 9:e11204 https://doi.org/10.7717/peerj.11204
The regulation of immune checkpoints by the hypoxic tumor microenvironment
The tumor microenvironment (TME) influences the occurrence and progression of tumors, and hypoxia is an important characteristic of the TME. The expression of programmed death 1 (PD1)/programmed death-ligand 1 (PDL1), cytotoxic T-lymphocyte-associated antigen 4 (CTLA4), and other immune checkpoints in hypoxic malignant tumors is often significantly increased, and is associated with poor prognosis. The application of immune checkpoint inhibitors (ICIs) for treating lung cancer, urothelial carcinoma, and gynecological tumors has achieved encouraging efficacy; however, the rate of efficacy of ICI single-drug treatment is only about 20%. In the present review, we discuss the possible mechanisms by which the hypoxic TME regulates immune checkpoints. By activating hypoxia-inducible factor-1α (HIF-1α), regulating the adenosine (Ado)-A2aR pathway, regulating the glycolytic pathway, and driving epithelial-mesenchymal transition (EMT) and other biological pathways, hypoxia regulates the expression levels of CTLA4, PD1, PDL1, CD47, lymphocyte activation gene 3 (LAG3), T-cell immunoglobulin and mucin domain 3 (TIM3), and other immune checkpoints, which interfere with the immune effector cell anti-tumor response and provide convenient conditions for tumors to escape immune surveillance. The combination of HIF-1α inhibitors, Ado-inhibiting tumor immune microenvironment regulatory drugs, and other drugs with ICIs has good efficacy in both preclinical studies and phase I-II clinical studies. Exploring the effects of TME hypoxia on the expression of immune checkpoints and the function of infiltrating immune cells has greatly clarified the relationship between the hypoxic TME and immune escape, which is of great significance for the development of new drugs and the search for predictive markers of the efficacy of immunotherapy for treating malignant tumors. In the future, combination therapy with hypoxia pathway inhibitors and ICIs may be an effective anti-tumor treatment strategy.
Hu et al. (2021) The regulation of immune checkpoints by the hypoxic tumor microenvironment. PeerJ 9:e11306 https://doi.org/10.7717/peerj.11306
DNA methylome and transcriptome analysis established a model of four differentially methylated positions (DMPs) as a diagnostic marker in esophageal adenocarcinoma early detection
Background Esophageal carcinogenesis involves in alterations of DNA methylation and gene transcription. This study profiled genomic DNA methylome vs. gene expression using transcriptome data on esophageal adenocarcinoma (EAC) tissues from the online databases in order to identify methylation biomarkers in EAC early diagnosis. Materials and Methods The DNA methylome and transcriptome data were downloaded from the UCSC Xena, Gene Expression Omnibus (GEO), and The Cancer Genome Atlas (TCGA) databases and then bioinformatically analyzed for the differentially methylated positions (DMPs) vs. gene expression between EAC and normal tissues. The highly methylated DMPs vs. reduced gene expression in EAC were selected and then stratified with those of the corresponding normal blood samples and other common human cancers to construct an EAC-specific diagnostic model. The usefulness of this model was further verified in other three GEO datasets of EAC tissues. Result A total of 841 DMPs were associated with expression of 320 genes, some of which were aberrantly methylated in EAC tissues. Further analysis showed that four (cg07589773, cg10474350, cg13011388 and cg15208375 mapped to gene IKZF1, HOXA7, EFS and TSHZ3, respectively) of these 841 DMPs could form and establish a diagnostic model after stratified them with the corresponding normal blood samples and other common human cancers. The data were further validated in other three GEO datasets on EAC tissues in early EAC diagnosis. Conclusion This study revealed a diagnostic model of four genes methylation to diagnose EAC early. Further study will confirm the usefulness of this model in a prospective EAC cases.
Peng et al. (2021) DNA methylome and transcriptome analysis established a model of four differentially methylated positions (DMPs) as a diagnostic marker in esophageal adenocarcinoma early detection. PeerJ 9:e11355 https://doi.org/10.7717/peerj.11355
Transgenerational effects on development following microplastic exposure in Drosophila melanogaster
Background Plastic pollution affects all ecosystems, and detrimental effects to animals have been reported in a growing number of studies. However, there is a paucity of evidence for effects on terrestrial animals in comparison to those in the marine realm. Methods We used the fly Drosophila melanogaster to study the effects that exposure to plastics may have on life history traits and immune response. We reared flies in four conditions: In media containing 1% virgin polyethylene, with no chemical additives; in media supplemented with 1% or 4% polyvinyl chloride, known to have a high content of added chemicals; and control flies in non-supplemented media. Plastic particle size ranged from 23–500 µm. We studied fly survival to viral infection, the length of the larval and pupal stage, sex ratios, fertility and the size of the resultant adult flies. We then performed crossings of F1 flies in non-supplemented media and looked at the life history traits of the F2. Results Flies treated with plastics in the food media showed changes in fertility and sex ratio, but showed no differences in developmental times, adult size or the capacity to fight infections in comparison with controls. However, the offspring of treated flies reared in non-supplemented food had shorter life cycles, and those coming from both polyvinyl chloride treatments were smaller than those offspring of controls.
Jimenez-Guri et al. (2021) Transgenerational effects on development following microplastic exposure in Drosophila melanogaster. PeerJ 9:e11369 https://doi.org/10.7717/peerj.11369
The impact of COVID-19 pandemic on nitrogen dioxide levels in Nigeria
The Coronavirus disease (COVID-19) has been transmitted worldwide over a very short time after it originated in China in December 2019. In an attempt to control its spread and reduce its health impacts, several countries including those in the African continent imposed restrictive measures that was termed “lockdown”. The outcomes of this lockdown have been reported to be beneficial to air quality worldwide. The main objective of this study is to assess the impact of lockdown due to COVID-19 on nitrogen dioxide (NO2) levels over six major cities in Nigeria. Maps extracted from satellite (Sentinel-5P) were used to indicate the significant reduction in the level of NO2 in the selected cities in Nigeria during two time-intervals, pre-lockdown (December, 2019) and during lockdown (April, 2020). The results show a significant reduction in NO2 levels during the lockdown period compared with its levels during the pre-lockdown period in 2019. The reduction in NO2 concentration levels during lockdown is likely due to less traffic, social distancing and restrictions on business and human activities. There could be an element of uncertainty in the results due to seasonality, as the comparison is done with a different season. However, the magnitude of change due to lockdown is probably much higher than the seasonal variability. Although COVID-19 has negatively impacted the health and economic status of all regions worldwide, it has benefited some aspects of air quality in most countries including Nigeria. This indicates that anthropogenic activities may be managed to reduce air pollution and positively impact the health of human beings.
Olusola et al. (2021) The impact of COVID-19 pandemic on nitrogen dioxide levels in Nigeria. PeerJ 9:e11387 https://doi.org/10.7717/peerj.11387
Effects of education methods on self-efficacy of smoking cessation counseling among medical students
Background Medical students need to receive training in providing smoking cessation counseling to provide effective smoking cessation interventions to smokers when they become doctors. This study examined the smoking cessation education curricula and factors affecting counseling self-efficacy (CSE) in smoking cessation treatment among medical students. Methods In a multicenter cross-sectional study, we obtained demographic information, personal history of tobacco use and intention to quit smoking, exposure to secondhand smoke in the school premises during the past week, the experience of learning about tobacco in each medical school, tobacco-related medical knowledge, and self-efficacy in smoking cessation counseling on medical students of four Korean medical schools. Results Among 1,416 medical students eligible, 313 (22.1%) students completed a self-administered questionnaire. Only 20.3% of the students reported positive CSE on smoking cessation. The factors affecting positive CSE were scores of ≥ 60 on tobacco-related medical knowledge, smoking experience, and blended learning (p = 0.014, 0.005, and 0.015, respectively). Conclusion This study shows that high scores in tobacco-related medical knowledge and blended learning are correlated with positive CSE for smoking cessation counseling.
Cho et al. (2021) Effects of education methods on self-efficacy of smoking cessation counseling among medical students. PeerJ 9:e11408 https://doi.org/10.7717/peerj.11408
Competing endogenous RNA network identifies mRNA biomarkers for overall survival of lung adenocarcinoma: two novel on-line precision medicine predictive tools
Background Individual mortality risk predicted curve at the individual level can provide valuable information for directing individual treatment decision. The present study attempted to explore potential post-transcriptional biological regulatory mechanism related with overall survival of lung adenocarcinoma (LUAD) patients through competitive endogenous RNA (ceRNA) network and develop two precision medicine predictive tools for predicting the individual mortality risk curves for overall survival of LUAD patients. Methods Multivariable Cox regression analyses were performed to explore the potential prognostic indicators, which were used to construct a prognostic model for overall survival of LUAD patients. Time-dependent receiver operating characteristic (ROC) curves were used to assess the predictive performance of prognostic model. Results There were 494 LUAD patients in model cohort and 233 LUAD patients in validation cohort. Differentially expressed mRNAs, miRNAs, and lncRNAs were identified between LUAD tissues and normal tissues. A ceRNA regulatory network was constructed on previous differentially expressed mRNAs, miRNAs, and lncRNAs. Fourteen mRNA biomarkers were identified as independent risk factors by multivariate Cox regression and used to develop a prognostic model for overall survival of LUAD patients. The C-indexes of prognostic model in model group were 0.786 (95% CI [0.744–0.828]), 0.736 (95% CI [0.694–0.778]) and 0.766 (95% CI [0.724–0.808]) for one year, two year and three year overall survival respectively. Two precision medicine predicted tools were developed for predicting individual mortality risk curves for LUAD patients. Conclusion The current study explored potential post-transcriptional biological regulatory mechanism and prognostic biomarkers for overall survival of LUAD patients. Two on-line precision medicine predictive tools were helpful to predict the individual mortality risk predicted curves for overall survival of LUAD patients. Smart Cancer Survival Predictive System could be used at https://zhangzhiqiao2.shinyapps.io/Smart_cancer_predictive_system_9_LUAD_E1002/.
Lin et al. (2021) Competing endogenous RNA network identifies mRNA biomarkers for overall survival of lung adenocarcinoma: two novel on-line precision medicine predictive tools. PeerJ 9:e11412 https://doi.org/10.7717/peerj.11412
Cranial anatomy of Besanosaurus leptorhynchus Dal Sasso & Pinna, 1996 (Reptilia: Ichthyosauria) from the Middle Triassic Besano Formation of Monte San Giorgio, Italy/Switzerland: taxonomic and palaeobiological implications
Besanosaurus leptorhynchus Dal Sasso & Pinna, 1996 was described on the basis of a single fossil excavated near Besano (Italy) nearly three decades ago. Here, we re-examine its cranial osteology and assign five additional specimens to B. leptorhynchus, four of which were so far undescribed. All of the referred specimens were collected from the Middle Triassic outcrops of the Monte San Giorgio area (Italy/Switzerland) and are housed in various museum collections in Europe. The revised diagnosis of the taxon includes the following combination of cranial characters: extreme longirostry; an elongate frontal not participating in the supratemporal fenestra; a prominent ‘triangular process’ of the quadrate; a caudoventral exposure of the postorbital on the skull roof; a prominent coronoid (preglenoid) process of the surangular; tiny conical teeth with coarsely-striated crown surfaces and deeply-grooved roots; mesial maxillary teeth set in sockets; distal maxillary teeth set in a short groove. All these characters are shared with the holotype of Mikadocephalus gracilirostris Maisch & Matzke, 1997, which we consider as a junior synonym of B. leptorhynchus. An updated phylogenetic analysis, which includes revised scores for B. leptorhynchus and several other shastasaurids, recovers B. leptorhynchus as a basal merriamosaurian, but it is unclear if Shastasauridae form a clade, or represent a paraphyletic group. The inferred body length of the examined specimens ranges from 1 m to about 8 m. The extreme longirostry suggests that B. leptorhynchus primarily fed on small and elusive prey, feeding lower in the food web than an apex predator: a novel ecological specialisation never reported before the Anisian in a large diapsid. This specialization might have triggered an increase of body size and helped to maintain low competition among the diverse ichthyosaur fauna of the Besano Formation.
Bindellini et al. (2021) Cranial anatomy of Besanosaurus leptorhynchus Dal Sasso & Pinna, 1996 (Reptilia: Ichthyosauria) from the Middle Triassic Besano Formation of Monte San Giorgio, Italy/Switzerland: taxonomic and palaeobiological implications. PeerJ 9:e11179 https://doi.org/10.7717/peerj.11179