Quantitative and correlation analysis of the DNA methylation and expression of DAPK in breast cancer
Background Death-associated protein kinase 1 (DAPK) is an important tumor suppressor kinase involved in the regulation of multiple cellular activities such as apoptosis and autophagy. DNA methylation of DAPK gene was found in various types of cancers and often correlated with the clinicopathological characteristics. However, the mRNA and protein expression of DAPK in the same sample was rarely measured. Thus, it was unclear if the correlation between DAPK gene methylation and clinicopathological parameters was due to the loss of DAPK expression. Methods In this study, the DNA methylation rate, mRNA and protein expression of DAPK was quantitatively detected in 15 pairs of breast cancer patient samples including tumor (T) and adjacent non-tumor (N) tissues. Results The correlation between DNA methylation rate and mRNA expression, together with the correlation between mRNA and protein expression, was calculated. No correlation was observed between any levels using either the measurement value of each sample or the T/N ratio of each pair. Discussion These data suggested that the DNA methylation status of DAPK did not correlate well with its mRNA or protein expression. Extra caution is needed when interpreting the DNA methylation data of DAPK gene in clinical studies.
Zhu et al. (2017) Quantitative and correlation analysis of the DNA methylation and expression of DAPK in breast cancer. PeerJ 5:e3084 https://doi.org/10.7717/peerj.3084
Comparison of methods of alert acknowledgement by critical care clinicians in the ICU setting
Background Electronic Health Record (EHR)-based sepsis alert systems have failed to demonstrate improvements in clinically meaningful endpoints. However, the effect of implementation barriers on the success of new sepsis alert systems is rarely explored. Objective To test the hypothesis time to severe sepsis alert acknowledgement by critical care clinicians in the ICU setting would be reduced using an EHR-based alert acknowledgement system compared to a text paging-based system. Study Design In one arm of this simulation study, real alerts for patients in the medical ICU were delivered to critical care clinicians through the EHR. In the other arm, simulated alerts were delivered through text paging. The primary outcome was time to alert acknowledgement. The secondary outcomes were a structured, mixed quantitative/qualitative survey and informal group interview. Results The alert acknowledgement rate from the severe sepsis alert system was 3% (N = 148) and 51% (N = 156) from simulated severe sepsis alerts through traditional text paging. Time to alert acknowledgement from the severe sepsis alert system was median 274 min (N = 5) and median 2 min (N = 80) from text paging. The response rate from the EHR-based alert system was insufficient to compare primary measures. However, secondary measures revealed important barriers. Conclusion Alert fatigue, interruption, human error, and information overload are barriers to alert and simulation studies in the ICU setting.
Harrison et al. (2017) Comparison of methods of alert acknowledgement by critical care clinicians in the ICU setting. PeerJ 5:e3083 https://doi.org/10.7717/peerj.3083
The Neotropical land snails (Mollusca, Gastropoda) collected by the ‘Comisión Científica del Pacífico’
The land snails collected by the ‘Comisión Científica del Pacifíco’ (CCP), a Spanish expedition to South and Central America from 1862–1866, are restudied and revised. The historical context of the expedition and the study of its collected material are described. Biographical data is given for the main persons involved. The land snails were previously studied by Joaquin Hidalgo between 1867 and 1893. A total of 3,470 specimens belonging to 211 species are treated in this paper. Of 34 species mentioned by Hidalgo is his catalogue, the corresponding material could not be located. Bulimus visendus Hidalgo, 1869 is now placed in the genus Synapterpes Pilsbry, 1896, a new combination.
Breure et al. (2017) The Neotropical land snails (Mollusca, Gastropoda) collected by the ‘Comisión Científica del Pacífico’. PeerJ 5:e3065 https://doi.org/10.7717/peerj.3065
Middle Pleistocene protein sequences from the rhinoceros genus Stephanorhinus and the phylogeny of extant and extinct Middle/Late Pleistocene Rhinocerotidae
Background Ancient protein sequences are increasingly used to elucidate the phylogenetic relationships between extinct and extant mammalian taxa. Here, we apply these recent developments to Middle Pleistocene bone specimens of the rhinoceros genus Stephanorhinus. No biomolecular sequence data is currently available for this genus, leaving phylogenetic hypotheses on its evolutionary relationships to extant and extinct rhinoceroses untested. Furthermore, recent phylogenies based on Rhinocerotidae (partial or complete) mitochondrial DNA sequences differ in the placement of the Sumatran rhinoceros (Dicerorhinus sumatrensis). Therefore, studies utilising ancient protein sequences from Middle Pleistocene contexts have the potential to provide further insights into the phylogenetic relationships between extant and extinct species, including Stephanorhinus and Dicerorhinus. Methods ZooMS screening (zooarchaeology by mass spectrometry) was performed on several Late and Middle Pleistocene specimens from the genus Stephanorhinus, subsequently followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) to obtain ancient protein sequences from a Middle Pleistocene Stephanorhinus specimen. We performed parallel analysis on a Late Pleistocene woolly rhinoceros specimen and extant species of rhinoceroses, resulting in the availability of protein sequence data for five extant species and two extinct genera. Phylogenetic analysis additionally included all extant Perissodactyla genera (Equus, Tapirus), and was conducted using Bayesian (MrBayes) and maximum-likelihood (RAxML) methods. Results Various ancient proteins were identified in both the Middle and Late Pleistocene rhinoceros samples. Protein degradation and proteome complexity are consistent with an endogenous origin of the identified proteins. Phylogenetic analysis of informative proteins resolved the Perissodactyla phylogeny in agreement with previous studies in regards to the placement of the families Equidae, Tapiridae, and Rhinocerotidae. Stephanorhinus is shown to be most closely related to the genera Coelodonta and Dicerorhinus. The protein sequence data further places the Sumatran rhino in a clade together with the genus Rhinoceros, opposed to forming a clade with the black and white rhinoceros species. Discussion The first biomolecular dataset available for Stephanorhinus places this genus together with the extinct genus Coelodonta and the extant genus Dicerorhinus. This is in agreement with morphological studies, although we are unable to resolve the order of divergence between these genera based on the protein sequences available. Our data supports the placement of the genus Dicerorhinus in a clade together with extant Rhinoceros species. Finally, the availability of protein sequence data for both extinct European rhinoceros genera allows future investigations into their geographic distribution and extinction chronologies.
Welker et al. (2017) Middle Pleistocene protein sequences from the rhinoceros genus Stephanorhinus and the phylogeny of extant and extinct Middle/Late Pleistocene Rhinocerotidae. PeerJ 5:e3033 https://doi.org/10.7717/peerj.3033
Occurrence of concurrent infections with multiple serotypes of dengue viruses during 2013–2015 in northern Kerala, India
Background Dengue is a global human public health threat, causing severe morbidity and mortality. The occurrence of sequential infection by more than one serotype of dengue virus (DENV) is a major contributing factor for the induction of Dengue Hemorrhagic Fever (DHF) and Dengue Shock Syndrome (DSS), two major medical conditions caused by DENV infection. However, there is no specific drug or vaccine available against dengue infection. There are reports indicating the increased incidence of concurrent infection of dengue in several tropical and subtropical regions. Recently, increasing number of DHF and DSS cases were reported in India indicating potential enhancement of concurrent DENV infections. Therefore, accurate determination of the occurrence of DENV serotype co-infections needs to be conducted in various DENV prone parts of India. In this context, the present study was conducted to analyse the magnitude of concurrent infection in northern Kerala, a southwest state of India, during three consecutive years from 2013 to 2015. Methods A total of 120 serum samples were collected from the suspected dengue patients. The serum samples were diagnosed for the presence of dengue NS1 antigen followed by the isolation of dengue genome from NS1 positive samples. The isolated dengue genome was further subjected to RTPCR based molecular serotyping. The phylogenetic tree was constructed based on the sequence of PCR amplified products. Results Out of the total number of samples collected, 100 samples were positive for dengue specific antigen (NS1) and 26 of them contained the dengue genome. The RTPCR based molecular serotyping of the dengue genome revealed the presence of all four serotypes with different combinations. However, serotypes 1 and 3 were predominant combinations of concurrent infection. Interestingly, there were two samples with all four serotypes concurrently infected in 2013. Discussion All samples containing dengue genome showed the presence of more than one serotype, indicating 100% concurrent infection. However, the combination of serotypes 1 and 3 was predominant. To the best of our knowledge, this is the first report indicating the concurrent infection of dengue in the northern Kerala, India. The phylogenetic analysis of dengue serotype 1 identified in this study shows a close relationship with the strain isolated in Delhi and South Korea during the 2006 and 2015 epidemics respectively. Similarly this study indicates that the phylogeny of dengue serotype 3 of northern Kerala is more closely related to dengue isolate of Rajasthan state, India. The geographical and climatic conditions of Kerala favours the breeding of both the mosquito vectors of dengue (Aedes albopictus and Aedes aegypti), which may enhance the severity of dengue in the future. Therefore, the study provides an alarming message for the urgent need of an antiviral strategy or other health management systems to curb the spread of dengue infection.
Reddy et al. (2017) Occurrence of concurrent infections with multiple serotypes of dengue viruses during 2013–2015 in northern Kerala, India. PeerJ 5:e2970 https://doi.org/10.7717/peerj.2970
Persistent erectile dysfunction in men exposed to the 5α-reductase inhibitors, finasteride, or dutasteride
Importance Case reports describe persistent erectile dysfunction (PED) associated with exposure to 5α-reductase inhibitors (5α-RIs). Clinical trial reports and the manufacturers’ full prescribing information (FPI) for finasteride and dutasteride state that risk of sexual adverse effects is not increased by longer duration of 5α-RI exposure and that sexual adverse effects of 5α-RIs resolve in men who discontinue exposure. Objective Our chief objective was to assess whether longer duration of 5α-RI exposure increases risk of PED, independent of age and other known risk factors. Men with shorter 5α-RI exposure served as a comparison control group for those with longer exposure. Design We used a single-group study design and classification tree analysis (CTA) to model PED (lasting ≥90 days after stopping 5α-RI). Covariates included subject attributes, diseases, and drug exposures associated with sexual dysfunction. Setting Our data source was the electronic medical record data repository for Northwestern Medicine. Subjects The analysis cohorts comprised all men exposed to finasteride or dutasteride or combination products containing one of these drugs, and the subgroup of men 16–42 years old and exposed to finasteride ≤1.25 mg/day. Main outcome and measures Our main outcome measure was diagnosis of PED beginning after first 5α-RI exposure, continuing for at least 90 days after stopping 5α-RI, and with contemporaneous treatment with a phosphodiesterase-5 inhibitor (PDE5I). Other outcome measures were erectile dysfunction (ED) and low libido. PED was determined by manual review of medical narratives for all subjects with ED. Risk of an adverse effect was expressed as number needed to harm (NNH). Results Among men with 5α-RI exposure, 167 of 11,909 (1.4%) developed PED (persistence median 1,348 days after stopping 5α-RI, interquartile range (IQR) 631.5–2320.5 days); the multivariable model predicting PED had four variables: prostate disease, duration of 5α-RI exposure, age, and nonsteroidal anti-inflammatory drug (NSAID) use. Of 530 men with new ED, 167 (31.5%) had new PED. Men without prostate disease who combined NSAID use with >208.5 days of 5α-RI exposure had 4.8-fold higher risk of PED than men with shorter exposure (NNH 59.8, all p < 0.002). Among men 16–42 years old and exposed to finasteride ≤1.25 mg/day, 34 of 4,284 (0.8%) developed PED (persistence median 1,534 days, IQR 651–2,351 days); the multivariable model predicting PED had one variable: duration of 5α-RI exposure. Of 103 young men with new ED, 34 (33%) had new PED. Young men with >205 days of finasteride exposure had 4.9-fold higher risk of PED (NNH 108.2, p < 0.004) than men with shorter exposure. Conclusion and relevance Risk of PED was higher in men with longer exposure to 5α-RIs. Among young men, longer exposure to finasteride posed a greater risk of PED than all other assessed risk factors.
Kiguradze et al. (2017) Persistent erectile dysfunction in men exposed to the 5α-reductase inhibitors, finasteride, or dutasteride. PeerJ 5:e3020 https://doi.org/10.7717/peerj.3020
Differential bicodon usage in lowly and highly abundant proteins
Degeneracy in the genetic code implies that different codons can encode the same amino acid. Usage preference of synonymous codons has been observed in all domains of life. There is much evidence suggesting that this bias has a major role on protein elongation rate, contributing to differential expression and to co-translational folding. In addition to codon usage bias, other preference variations have been observed such as codon pairs. In this paper, I report that codon pairs have significant different frequency usage for coding either lowly or highly abundant proteins. These usage preferences cannot be explained by the frequency usage of the single codons. The statistical analysis of coding sequences of nine organisms reveals that in many cases bicodon preferences are shared between related organisms. Furthermore, it is observed that misfolding in the drug-transport protein, encoded by MDR1 gene, is better explained by a big change in the pause propensity due to the synonymous bicodon variant, rather than by a relatively small change in codon usage. These findings suggest that codon pair usage can be a more powerful framework to understand translation elongation rate, protein folding efficiency, and to improve protocols to optimize heterologous gene expression.
Diambra (2017) Differential bicodon usage in lowly and highly abundant proteins. PeerJ 5:e3081 https://doi.org/10.7717/peerj.3081
Frequent discordance between morphology and mitochondrial DNA in a species group of European water beetles (Coleoptera: Dytiscidae)
The Hydroporus memnonius species group includes both widespread and range restricted diving beetle taxa in the western Palaearctic, some of which have been divided into a number of geographical subspecies. Of these, Hydroporus necopinatus is distributed in the far west of Europe, from central Spain to southern Britain, and has been split into three subspecies, occurring in Iberia (necopinatus sst.), France (robertorum) and England (roni) respectively—the last of these being a rare example of an insect taxon apparently endemic to northern Europe. Here we explore inter-relationships between populations and subspecies of H. necopinatus and related members of the Hydroporus melanarius subgroup, using mitochondrial COI sequence data. We reveal widespread discordance between mitochondrial DNA sequence variation and morphology in areas where H. necopinatus and H. melanarius come into contact, consistent with historical introgressive hybridization between these taxa. In light of this discordance, the lack of clear genetic divergence between H. necopinatus subspecies, and the fact that both robertorum and roni are morphologically intermediate between H. necopinatus sstr. and H. melanarius, we suggest that these taxa may be of hybridogenic origin, rather than representing discrete evolutionary lineages.
Bilton et al. (2017) Frequent discordance between morphology and mitochondrial DNA in a species group of European water beetles (Coleoptera: Dytiscidae). PeerJ 5:e3076 https://doi.org/10.7717/peerj.3076
Diverse bacterial communities exist on canine skin and are impacted by cohabitation and time
It has previously been shown that domestic dogs and their household owners share bacterial populations, and that sharing of bacteria between humans is facilitated through the presence of dogs in the household. However, less is known regarding the bacterial communities of dogs, how these communities vary by location and over time, and how cohabitation of dogs themselves influences their bacterial community. Furthermore, the effects of factors such as breed, hair coat length, sex, shedding, and age on the canine skin microbiome is unknown. This study sampled the skin bacterial communities of 40 dogs belonging to 20 households longitudinally across three seasons (spring, summer, and winter). Significant differences in bacterial community structure between samples were identified when stratified by season, but not by dog sex, age, breed, hair type, or skin site. Cohabitating dogs were more likely to share bacteria of the skin than non-cohabitating dogs. Similar to human bacterial microbiomes, dogs’ microbiomes were more similar to their own microbiomes over time than to microbiomes of other individuals. Dogs sampled during the same season were also more similar to each other than to dogs from different seasons, irrespective of household. However, there were very few core operational taxonomic units (OTUs) identified across all dogs sampled. Taxonomic classification revealed Propionibacterium acnes and Haemophilus sp. as key members of the dog skin bacterial community, along with Corynebacterium sp. and Staphylococcus epidermidis. This study shows that the skin bacterial community structure of dogs is highly individualized, but can be shared among dogs through cohabitation.
Torres et al. (2017) Diverse bacterial communities exist on canine skin and are impacted by cohabitation and time. PeerJ 5:e3075 https://doi.org/10.7717/peerj.3075
Human head orientation and eye visibility as indicators of attention for goats (Capra hircus)
Animals domesticated for working closely with humans (e.g. dogs) have been shown to be remarkable in adjusting their behaviour to human attentional stance. However, there is little evidence for this form of information perception in species domesticated for production rather than companionship. We tested domestic ungulates (goats) for their ability to differentiate attentional states of humans. In the first experiment, we investigated the effect of body and head orientation of one human experimenter on approach behaviour by goats. Test subjects (N = 24) significantly changed their behaviour when the experimenter turned its back to the subjects, but did not take into account head orientation alone. In the second experiment, goats (N = 24) could choose to approach one of two experimenters, while only one was paying attention to them. Goats preferred to approach humans that oriented their body and head towards the subject, whereas head orientation alone had no effect on choice behaviour. In the third experiment, goats (N = 32) were transferred to a separate test arena and were rewarded for approaching two experimenters providing a food reward during training trials. In subsequent probe test trials, goats had to choose between the two experimenters differing in their attentional states. Like in Experiments 1 and 2, goats did not show a preference for the attentive person when the inattentive person turned her head away from the subject. In this last experiment, goats preferred to approach the attentive person compared to a person who closed their eyes or covered the whole face with a blind. However, goats showed no preference when one person covered only the eyes. Our results show that animals bred for production rather than companionship show differences in their approach and choice behaviour depending on human attentive state. However, our results contrast with previous findings regarding the use of the head orientation to attribute attention and show the importance of cross-validating results.
Nawroth et al. (2017) Human head orientation and eye visibility as indicators of attention for goats (Capra hircus). PeerJ 5:e3073 https://doi.org/10.7717/peerj.3073