The diet of otters (Lutra lutra) on the Agri river system, one of the most important presence sites in Italy: a molecular approach
Background The Eurasian otter (Lutra lutra) underwent a strong decline in large areas of the Central-Western part of its distribution range, during the second half of the twentieth century. In Italy, only residual fragmented nuclei survive in the Central-Southern part of the peninsula. Nowadays, the otter is one of the most endangered mammals in Italy, and increasing the knowledge about the ecology of this species is a key step in defining fitting management strategies. Here we provide information about the diet of otter on the Agri river system, one of the most important presence sites in Italy, to understand both the species’ food requirements and the impact on fish communities. Methods DNA metabarcoding and High Throughput Sequencing were used on DNA extracted from spraints. We amplified DNA with a primer set for vertebrates, focusing efforts on the bulk of the otter’s diet (fishes and amphibians). Results Our findings showed that the diet of the otter was dominated by cyprinids (97.77%, and 99.14% of fishes), while amphibians represented 0.85% of the sequences analyzed. Results are in general accordance with previous studies based on morphological characterization; however, molecular analyses allow the resolving of some morphological uncertainties. Although the study area offers a very wide range of available prey, the diet of the otters shows marked selectivity. We highlighted a variation in prey consumed, in accordance with the typology of water system (i.e., river, lake, tributary). Some of the preys found in the diet were alien species introduced by man for sport fishing. Our findings could help define strategies useful for the conservation of the otter population in Southern Italy, suggesting management actions directed at avoiding fish community alterations through illegal stockings without severe controls on their taxonomic status. These introductions could result in a general reduction in the diversity of the otter’s preys, affecting its predatory behavior.
Buglione et al. (2020) The diet of otters (Lutra lutra) on the Agri river system, one of the most important presence sites in Italy: a molecular approach. PeerJ 8:e9606 https://doi.org/10.7717/peerj.9606
Metagenomic next-generation sequencing for the clinical diagnosis and prognosis of acute respiratory distress syndrome caused by severe pneumonia: a retrospective study
Background Metagenome next-generation sequencing (mNGS) is a valuable diagnostic tool that can be used for the identification of early pathogens of acute respiratory distress syndrome (ARDS) in severe pneumonia. Little is known about the use of this technology in clinical application and the evaluation of the prognostic value of ARDS. Methods We performed a retrospective cohort study of patients with ARDS caused by severe pneumonia. Samples were collected from patients in the intensive care unit (ICU) of Jiangmen Central Hospital from January 2018 to August 2019. The no-next generation sequencing (NGS) group was composed of patients given conventional microbiological tests to examine sputum, blood, or bronchoalveolar lavage fluid. The NGS group was composed of patients tested using mNGS and conventional microbiological tests. We evaluated the etiological diagnostic effect and clinical prognostic value of mNGS in patients with ARDS caused by severe pneumonia. Results The overall positive rate (91.1%) detected by the mNGS method was significantly higher than that of the culture method (62.2%, P = 0.001), and antibody plus polymerase chain reaction (28.9%, P < 0.001). Following adjustment of the treatment plan based on microbial testing results, the Acute Physiology and Chronic Health Evaluation-II (APACHE II) score of the NGS group was lower than that of the no-NGS group 7 days after treatment (P < 0.05). The 28-day mortality rate of the NGS group was significantly lower than that of the no-NGS group (P < 0.05). Longer ICU stay, higher APACHE II score and sequential organ failure assessment score were risk factors for the death of ARDS, and adjusting the medication regimen based on mNGS results was a protective factor. The detection of mNGS can significantly shorten the ICU stay of immunosuppressed patients (P < 0.01), shorten the ventilation time (P < 0.01), and reduce the ICU hospitalization cost (P < 0.05). Conclusions Metagenome next-generation sequencing is a valuable tool to determine the etiological value of ARDS caused by severe pneumonia to improve diagnostic accuracy and prognosis for this disease. For immunosuppressed patients, mNGS technology can be used in the early stage to provide more diagnostic evidence and guide medications.
Zhang et al. (2020) Metagenomic next-generation sequencing for the clinical diagnosis and prognosis of acute respiratory distress syndrome caused by severe pneumonia: a retrospective study. PeerJ 8:e9623 https://doi.org/10.7717/peerj.9623
Spermatogenesis is normal in Tex33 knockout mice
Testis expressed gene 33 (Tex33) is a recently reported testis-specific gene and it is evolutionarily conserved in vertebrates. The Tex33 expression is found in cytoplasm of round spermatids in Mus musculus. However, the in vivo function of Tex33 remains unknown. In this study, we made a 62bp in frame deletion on Exon2 of Tex33 gene by CRISPR/Cas9 in C57B/L6 mouse, which cause frame shift mutation of Tex33 gene. Tex33-/-adult male were fertile, and there is no significant change on litter size compared with male wildtype (Tex33+/+) adult. Besides, no overt differences were found in testis/body weight ratios, testicular/epididymal tissue morphology, sperm counts, sperm morphology and spermatozoa motility in adult Tex33-/-male mice (N = 3), in comparison with Tex33+/+ adult (N = 3). TUNEL assay also indicates the germ cells apoptosis ratio was not significantly changed in adult Tex33-/- adult male mouse testis (N = 3), compared with adult Tex33+/+ male (N = 3). Importantly, the first wave of elongating spermatids formation happens in 5w old mice. We find that the first wave of spermiogenesis is not disrupted in both 5-week-old Tex33+/+ and Tex33-/-male mouse testes and three hallmarks of spermatogenesis, PLZF,γ-H2AX and TNP1, are all detectable in seminiferous tubule. All results indicate that Tex33 is a redundant gene to spermatogenesis. This study can help other researchers avoid repetitive works on redundant genes.
Zhu et al. (2020) Spermatogenesis is normal in Tex33 knockout mice. PeerJ 8:e9629 https://doi.org/10.7717/peerj.9629
Five genes influenced by obesity may contribute to the development of thyroid cancer through the regulation of insulin levels
Previous studies indicate that obesity is an important contributor to the proceeding of thyroid cancer (TC) with limited knowledge of the underlying mechanism. Here, we hypothesize that molecules affected by obesity may play roles in the development of TC. To test the hypothesis above, we first conducted a large-scale literature-based data mining to identify genes influenced by obesity and genes related to TC. Then, a mega-analysis was conducted to study the expression changes of the obesity-specific genes in the case of TC, using 16 independent TC array-expression datasets (783 TC cases and 439 healthy controls). After that, pathway analysis was performed to explore the functional profile of the selected target genes and their potential connections with TC. We identified 1,036 genes associated with TC and 534 regulated by obesity, demonstrating a significant overlap (N = 176, p-value = 4.07e−112). Five out of the 358 obesity-specific genes, FABP4, CFD, GHR, TNFRSF11B, and LTF, presented significantly decreased expression in TC patients (LFC<−1.44; and p-value < 1e−7). Multiple literature-based pathways were identified where obesity could promote the pathologic development of TC through the regulation of these five genes and INS levels. The five obesity genes uncovered could be novel genes that play roles in the etiology of TC through the modulation of INS levels.
Chen et al. (2020) Five genes influenced by obesity may contribute to the development of thyroid cancer through the regulation of insulin levels. PeerJ 8:e9302 https://doi.org/10.7717/peerj.9302
Assessment of potato peel and agro-forestry biochars supplementation on in vitro ruminal fermentation
Background The awareness of environmental and socio-economic impacts caused by greenhouse gas emissions from the livestock sector leverages the adoption of strategies to counteract it. Feed supplements can play an important role in the reduction of the main greenhouse gas produced by ruminants—methane (CH4). In this context, this study aims to assess the effect of two biochar sources and inclusion levels on rumen fermentation parameters in vitro. Methods Two sources of biochar (agro-forestry residues, AFB, and potato peel, PPB) were added at two levels (5 and 10%, dry matter (DM) basis) to two basal substrates (haylage and corn silage) and incubated 24-h with rumen inocula to assess the effects on CH4 production and main rumen fermentation parameters in vitro. Results AFB and PPB were obtained at different carbonization conditions resulting in different apparent surface areas, ash content, pH at the point of zero charge (pHpzc), and elemental analysis. Relative to control (0% biochar), biochar supplementation kept unaffected total gas production and yield (mL and mL/g DM, p = 0.140 and p = 0.240, respectively) and fermentation pH (p = 0.666), increased CH4production and yield (mL and mL/g DM, respectively, p = 0.001) and ammonia-N (NH3-N, p = 0.040), and decreased total volatile fatty acids (VFA) production (p < 0.001) and H2 generated and consumed (p ≤ 0.001). Biochar sources and inclusion levels had no negative effect on most of the fermentation parameters and efficiency. Acetic:propionic acid ratio (p = 0.048) and H2 consumed (p = 0.019) were lower with AFB inclusion when compared to PPB. Biochar inclusion at 10% reduced H2 consumed (p < 0.001) and tended to reduce total gas production (p = 0.055). Total VFA production (p = 0.019), acetic acid proportion (p = 0.011) and H2 generated (p = 0.048) were the lowest with AFB supplemented at 10%, no differences being observed among the other treatments. The basal substrate affected most fermentation parameters independently of biochar source and level used. Discussion Biochar supplementation increased NH3-N content, iso-butyric, iso-valeric and valeric acid proportions, and decreased VFA production suggesting a reduced energy supply for microbial growth, higher proteolysis and deamination of substrate N, and a decrease of NH3-N incorporation into microbial protein. No interaction was found between substrate and biochar source or level on any of the parameters measured. Although AFB and PPB had different textural and compositional characteristics, their effects on the rumen fermentation parameters were similar, the only observed effects being due to AFB included at 10%. Biochar supplementation promoted CH4 production regardless of the source and inclusion level, suggesting that there may be other effects beyond biomass and temperature of production of biochar, highlighting the need to consider other characteristics to better identify the mechanism by which biochar may influence CH4 production.
Rodrigues et al. (2020) Assessment of potato peel and agro-forestry biochars supplementation on in vitro ruminal fermentation. PeerJ 8:e9488 https://doi.org/10.7717/peerj.9488
Comparison of long-term changes in size and longevity of bee colonies in mid-west Japan and Maui with and without exposure to pesticide, cold winters, and mites
Four long-term field experiments in mid-west Japan (Shika) made it clear that extinction of colonies exposed to neonicotinoid was much higher than for colonies exposed to organophosphates. The incidence of hive death for of organophosphate-exposed and control (pesticide-free) colonies was similar. We conducted a field experiment in Maui for 271 days using the same pesticides (dinotefuran: 0.2 ppm, clothianidin: 0.08 ppm, fenitrothion: 1 ppm) as used in Shika with the honeybee, Apis mellifera, colonies without mites. Numbers of adult bees, capped brood, mites and other hive parameters were accurately counted on photographs of combs and on the inside of the hives. All six neonicotinoid (dinotefuran & clothianidin)-exposed colonies failed during the experiment. One of three organophosphate (fenitrothion)-exposed colonies and one of the three control colonies also failed. The findings from Maui, where colonies displayed no mites, provides evidence from Shika, with mites, that neonicotinoids are more hazardous to honeybee colonies than organophosphates. The apparent longevity of honeybee colonies on Maui was estimated by numbers of adult bees and capped brood using a mathematical model previously proposed. Seasonal changes in longevity on Maui differ greatly from changes at Shika, the latter showing distinct seasonal variation. Longevity on Maui remains nearly constant throughout the year with wide variations. At Shika, it increases drastically in winter, by six- to ten fold more than the other seasons. Differences seem to depend on the existence of cold winters and the length of flowering seasons. In a perpetually hospitable environment, small changes in conditions can be sensitively reflected in apparent longevity. Examining wide variations in apparent longevity that are seemingly incoherent, we recognized several differences in apparent longevity between neonicotinoid-exposed and organophosphate-exposed colonies: The colony that failed in after organophosphate-exposure colony group exhibited the longest apparent longevity and the fewest number of newly capped brood, as also was the case in control colonies. Extended longevity when few brood are newly produced is reasonable to maintain the colony from a physiological point of view. Extension of apparent longevity is not seen in neonicotinoid-exposed colonies when the number of newly capped brood is fewer. This finding suggests that neonicotinoid pesticides may inhibit normal apian physiology.
Yamada et al. (2020) Comparison of long-term changes in size and longevity of bee colonies in mid-west Japan and Maui with and without exposure to pesticide, cold winters, and mites. PeerJ 8:e9505 https://doi.org/10.7717/peerj.9505
Mediterranean swordfish (Xiphias gladius Linnaeus, 1758) population structure revealed by microsatellite DNA: genetic diversity masked by population mixing in shared areas
Background The Mediterranean swordfish stock is overfished and considered not correctly managed. Elucidating the patterns of the Mediterranean swordfish population structure constitutes an essential prerequisite for effective management of this fishery resource. To date, few studies have investigated intra-Mediterranean swordfish population structure, and their conclusions are controversial. Methods A panel of 20 microsatellites DNA was used to investigate fine-scale population structuring of swordfish from six main fishing areas of the Mediterranean Sea. Results This study provides evidence to reject the hypothesis of a single swordfish population within the Mediterranean Sea. DAPC analysis revealed the presence of three genetic clusters and a high level of admixture within the Mediterranean Sea. Genetic structure was supported by significant FST values while mixing was endorsed by the heterozygosity deficit observed in sampling localities indicative of a possible Wahlund effect, by sampling admixture individuals. Overall, our tests reject the hypothesis of a single swordfish population within the Mediterranean Sea. Homing towards the Mediterranean breeding areas may have generated a weak degree of genetic differentiation between populations even at the intra-basin scale.
Righi et al. (2020) Mediterranean swordfish (Xiphias gladius Linnaeus, 1758) population structure revealed by microsatellite DNA: genetic diversity masked by population mixing in shared areas. PeerJ 8:e9518 https://doi.org/10.7717/peerj.9518
Proteomic analysis of human cervical adenocarcinoma mucus to identify potential protein biomarkers
Background Cervical cancer is the most common gynecological cancer, encompassing cervical squamous cell carcinoma, adenocarcinoma, and other epithelial tumors. There are many diagnostic methods to detect cervical cancers but no precision screening tool for cervical adenocarcinoma at present. Material and methods The cervical mucus from three normal cervices (Ctrl), three endocervical adenocarcinoma (EA), and three cervical adenocarcinoma in situ (AIS) was collected for proteomic analysis. The proteins were screened using liquid chromatography-mass spectrometry analysis (LC-MS). The biological function of the differently expressed proteins were predicted by Gene Ontology (GO). Results A total of 711 proteins were identified, including 237 differently expressed proteins identified in EA/Ctrl comparison, 256 differently expressed proteins identified in AIS/Ctrl comparison, and 242 differently expressed proteins identified in AIS/EA comparison (up-regulate ≥ 1.5 or down-regulate ≤ 0.67). Functional annotation was performed using GO analysis on 1,056 differently expressed proteins to identify those that may impact cervical cancer, such as heme protein myeloperoxidase, which is involved in the immune process, and APOA1, which is associated with lipid metabolism. Conclusion We used proteomic analysis to screen out differently expressed proteins from normal cervical mucus and cervical adenocarcinoma mucus samples. These differently expressed proteins may be potential biomarkers for the diagnosis and treatment of cervical adenocarcinoma but require additional study.
Ma et al. (2020) Proteomic analysis of human cervical adenocarcinoma mucus to identify potential protein biomarkers. PeerJ 8:e9527 https://doi.org/10.7717/peerj.9527
Predatory functional response and fitness parameters of Orius strigicollis Poppius when fed Bemisia tabaci and Trialeurodes vaporariorum as determined by age-stage, two-sex life table
Background The polyphagous predatory bug O. strigicollis is an active predator used to control thrips and aphids. The whitefly species Bemisia tabaci and Trialeurodes vaporariorum are voracious pests of different economic agricultural crops and vegetables. Method In this study, the Holling disc equation and the age-stage, two-sex life table technique were used to investigate the functional response and biological traits of third instar nymphs and adult female O. strigicollis when presented third instar nymphs of both whitefly species as prey. Results The results showed a type II functional response for each life stage of O. strigicollis when fed each whitefly species. The calculated prey handling time for different O. strigicollis life stages were shorter when fed T. vaporariorum than when fed B. tabaci nymphs. In contrast, the nymphal development of O. strigicollis was significantly shorter when fed B. tabaci than T. vaporariorum nymphs. Additionally, the total pre-oviposition period of adult females was statistically shorter when fed B. tabaci nymphs than T. vaporariorum nymphs. Furthermore, the survival rates and total fecundity of O. strigicollis were higher when fed B. tabaci than T. vaporariorum. There were no significant differences in any population parameters of O. strigicollis when fed either whitefly species. These results show that O. strigicollis could survive and maintain its populations on both species of whitefly and could therefore serve as a biological control agent in integrated pest management (IPM).
Rehman et al. (2020) Predatory functional response and fitness parameters of Orius strigicollis Poppius when fed Bemisia tabaci and Trialeurodes vaporariorum as determined by age-stage, two-sex life table. PeerJ 8:e9540 https://doi.org/10.7717/peerj.9540
Comparative proteome analysis reveals VPS28 regulates milk fat synthesis through ubiquitylation in bovine mammary epithelial cells
In our previous study, we found that VPS28 (vacuolar protein sorting 28 homolog) could alter ubiquitylation level to regulate milk fat synthesis in bovine primary mammary epithelial cells (BMECs). While the information on the regulation of VPS28 on proteome of milk fat synthesis is less known, we explored its effect on milk fat synthesis using isobaric tags for relative and absolute quantitation assay after knocking down VPS28 in BMECs. A total of 2,773 proteins in three biological replicates with a false discovery rate of less than 1.2% were identified and quantified. Among them, a subset of 203 proteins were screened as significantly down-(111) and up-(92) regulated in VPS28 knockdown BMECs compared with the control groups. According to Gene Ontology analysis, the differentially expressed proteins were enriched in the “proteasome,” “ubiquitylation,” “metabolism of fatty acids,” “phosphorylation,” and “ribosome.” Meanwhile, some changes occurred in the morphology of BMECs and an accumulation of TG (triglyceride) and dysfunction of proteasome were identified, and a series of genes associated with milk fat synthesis, ubiquitylation and proteasome pathways were analyzed by quantitative real-time PCR. The results of this study suggested VPS28 regulated milk fat synthesis was mediated by ubiquitylation; it could be an important new area of study for milk fat synthesis and other milk fat content traits in bovine.
Liu et al. (2020) Comparative proteome analysis reveals VPS28 regulates milk fat synthesis through ubiquitylation in bovine mammary epithelial cells. PeerJ 8:e9542 https://doi.org/10.7717/peerj.9542