Mammut pacificus sp. nov., a newly recognized species of mastodon from the Pleistocene of western North America
A new species of mastodon from the Pleistocene of western North America, Mammut pacificus sp. nov. is herein recognized, with specimens identified throughout California and from two localities in southern Idaho. This new taxon differs from the contemporaneous M. americanum in having narrower teeth, most prominently in M3/m3, as well as six sacral vertebrae, femur with a proportionally greater mid-shaft diameter, and no mandibular tusks at any growth stage. All known Pleistocene Mammut remains from California are consistent with our diagnosis of M. pacificus, which indicates that M. americanum was not present in California.
Dooley et al. (2019) Mammut pacificus sp. nov., a newly recognized species of mastodon from the Pleistocene of western North America. PeerJ 7:e6614 https://doi.org/10.7717/peerj.6614
Old wild wolves: ancient DNA survey unveils population dynamics in Late Pleistocene and Holocene Italian remains
Background The contemporary Italian wolf (Canis lupus italicus) represents a case of morphological and genetic uniqueness. Today, Italian wolves are also the only documented population to fall exclusively within the mitochondrial haplogroup 2, which was the most diffused across Eurasian and North American wolves during the Late Pleistocene. However, the dynamics leading to such distinctiveness are still debated. Methods In order to shed light on the ancient genetic variability of this wolf population and on the origin of its current diversity, we collected 19 Late Pleistocene-Holocene samples from northern Italy, which we analyzed at a short portion of the hypervariable region 1 of the mitochondrial DNA, highly informative for wolf and dog phylogenetic analyses. Results Four out of the six detected haplotypes matched the ones found in ancient wolves from northern Europe and Beringia, or in modern European and Chinese wolves, and appeared closely related to the two haplotypes currently found in Italian wolves. The haplotype of two Late Pleistocene samples matched with primitive and contemporary dog sequences from the canine mitochondrial clade A. All these haplotypes belonged to haplogroup 2. The only exception was a Holocene sample dated 3,250 years ago, affiliated to haplogroup 1. Discussion In this study we describe the genetic variability of the most ancient wolf specimens from Italy analyzed so far, providing a preliminary overview of the genetic make-up of the population that inhabited this area from the last glacial maximum to the Middle Age period. Our results endorsed that the genetic diversity carried by the Pleistocene wolves here analyzed showed a strong continuity with other northern Eurasian wolf specimens from the same chronological period. Contrarily, the Holocene samples showed a greater similarity only with modern sequences from Europe and Asia, and the occurrence of an haplogroup 1 haplotype allowed to date back previous finding about its presence in this area. Moreover, the unexpected discovery of a 24,700-year-old sample carrying a haplotype that, from the fragment here obtained, falls within the canine clade A, could represent the oldest evidence in Europe of such dog-rich clade. All these findings suggest complex population dynamics that deserve to be further investigated based on mitochondrial or whole genome sequencing.
Ciucani et al. (2019) Old wild wolves: ancient DNA survey unveils population dynamics in Late Pleistocene and Holocene Italian remains. PeerJ 7:e6424 https://doi.org/10.7717/peerj.6424
Clinicopathological characteristics, treatment and survival of pulmonary large cell neuroendocrine carcinoma: a SEER population-based study
Background This study was designed to investigate the clinicopathological characteristics, treatment and survival of patients with pulmonary large cell neuroendocrine carcinoma (LCNEC). Methods The Surveillance, Epidemiology and End Results database was utilized to identify patients diagnosed with pulmonary LCNEC between 2004 and 2013. Kaplan–Meier analysis was conducted to determine the overall survival (OS) and cancer-specific survival (CSS) rate. Univariate survival analysis along with log-rank test, and Cox proportional hazards model were employed to detect independent prognostic factors. Results Pulmonary LCNEC accounted for 0.58% (2972/510607) of the total number of lung and bronchus carcinoma. And a total of 1,530 eligible cases were identified, with the median follow-up time of 11 months. To be specific, the 3-, 5-year OS and CSS rates were 22.8%, 16.8% and 26.5%, 20.8% respectively. Generally, pulmonary LCNEC was commonly detected in the elderly (72.2%), males (55.9%), the upper lobe (62.0%) and advanced AJCC stage (65.5%). Multivariate analysis revealed that elderly [(≥60 and <80 years) HR:1.203, 95% CI [1.053–1.375], P = 0.007; (≥80 years) HR:1.530, 95% CI [1.238–1.891], P < 0.001] and advanced AJCC stage [(stage III) HR:2.606, 95% CI [2.083–3.260], P < 0.001; (stage IV) HR:4.881, 95% CI [3.923–6.072], P < 0.001] were independent unfavorable prognostic factors, and that female (HR:0.845, 95% CI [0.754–0.947], P = 0.004)), surgery [(Segmentectomy/wedge resection) HR:0.526, 95% CI [0.413–0.669], P < 0.001; (Lobectomy/Bilobectomy) HR:0.357, 95% CI [0.290–0.440], P < 0.001;(Pneumonectomy) HR:0.491, 95% CI [0.355–0.679], P < 0.001] , chemotherapy (HR:0.442, 95% CI [0.389–0.503], P < 0.001) and radiation (HR:0.837, 95% CI [0.738–0.949], P = 0.005) were independent favorable prognostic factors. Conclusion To sum up, age at diagnosis, sex, AJCC 8th edition stage, surgery, chemotherapy and radiation were significantly associated with OS of patients with pulmonary LCNEC.
Cao et al. (2019) Clinicopathological characteristics, treatment and survival of pulmonary large cell neuroendocrine carcinoma: a SEER population-based study. PeerJ 7:e6539 https://doi.org/10.7717/peerj.6539
Associated bacteria of Botryococcus braunii (Chlorophyta)
Botryococcus braunii (Chlorophyta) is a green microalga known for producing hydrocarbons and exopolysaccharides (EPS). Improving the biomass productivity of B. braunii and hence, the productivity of the hydrocarbons and of the EPS, will make B. braunii more attractive for industries. Microalgae usually cohabit with bacteria which leads to the formation of species-specific communities with environmental and biological advantages. Bacteria have been found and identified with a few B. braunii strains, but little is known about the bacterial community across the different strains. A better knowledge of the bacterial community of B. braunii will help to optimize the biomass productivity, hydrocarbons, and EPS accumulation. To better understand the bacterial community diversity of B. braunii, we screened 12 strains from culture collections. Using 16S rRNA gene analysis by MiSeq we described the bacterial diversity across 12 B. braunii strains and identified possible shared communities. We found three bacterial families common to all strains: Rhizobiaceae, Bradyrhizobiaceae, and Comamonadaceae. Additionally, the results also suggest that each strain has its own specific bacteria that may be the result of long-term isolated culture.
Gouveia et al. (2019) Associated bacteria of Botryococcus braunii (Chlorophyta). PeerJ 7:e6610 https://doi.org/10.7717/peerj.6610
Evaluating the effects of a temporary fostering program on shelter dog welfare
One of the greatest stressors for dogs living in animal shelters is social isolation. Many studies have demonstrated that human interaction reduces cortisol in shelter dogs, with the possibility that longer periods of interaction may yield greater effects. These types of interventions are contingent upon removing the dog from the kennel and any such reductions in cortisol are often lost when the dog returns to the kennel. More recently, animal shelters are utilizing short-term fostering programs to provide relief from the perceived stresses of kennel life; however the effects of these programs are not well understood. This study assessed the impacts of one- and two-night fostering programs on the urinary cortisol levels, resting pulse rates, longest bout of uninterrupted rest, and proportion of time spent resting of dogs awaiting adoption. Five animal shelters, open and limited-admission facilities, from across the United States participated in the study. During the study, dogs’ urine was collected in the morning before, during, and after fostering stays for cortisol: creatinine analysis. Non-invasive health monitors were worn by the dogs, which collected heart rates and activity levels, in the shelter and in foster homes. In total, 207 dogs participated in the study, and 1,076 cortisol values were used in our analysis. Across all shelters, we found that dogs’ cortisol: creatinine ratios dropped significantly during their fostering stay, but returned to baseline levels after return to the shelter. However, the observed reduction in cortisol varied in magnitude across shelters. We found that dogs of greater weight, age, and average resting pulse rate had higher cortisol levels; and dogs with longer bouts of uninterrupted rest had lower cortisol levels. Dogs had their longest bouts of rest during sleepovers, followed by in the shelter after their sleepovers. Lastly, significant differences were found when comparing in-shelter cortisol values at our five shelters, differences that were in some cases greater than the impact of the fostering intervention itself. Considering the diversity of facilities that participated in this study, it is possible that as yet unstudied, shelter-specific, environmental factors could be contributing to the overall welfare of shelter dogs. Thus while a reprieve from the shelter is impactful for dogs awaiting adoption, mitigating the stressors present in kenneling conditions should also be addressed to improve the lives of shelter dogs.
Gunter et al. (2019) Evaluating the effects of a temporary fostering program on shelter dog welfare. PeerJ 7:e6620 https://doi.org/10.7717/peerj.6620
Pixel: a content management platform for quantitative omics data
Background In biology, high-throughput experimental technologies, also referred as “omics” technologies, are increasingly used in research laboratories. Several thousands of gene expression measurements can be obtained in a single experiment. Researchers are routinely facing the challenge to annotate, store, explore and mine all the biological information they have at their disposal. We present here the Pixel web application (Pixel Web App), an original content management platform to help people involved in a multi-omics biological project. Methods The Pixel Web App is built with open source technologies and hosted on the collaborative development platform GitHub (https://github.com/Candihub/pixel). It is written in Python using the Django framework and stores all the data in a PostgreSQL database. It is developed in the open and licensed under the BSD 3-clause license. The Pixel Web App is also heavily tested with both unit and functional tests, a strong code coverage and continuous integration provided by CircleCI. To ease the development and the deployment of the Pixel Web App, Docker and Docker Compose are used to bundle the application as well as its dependencies. Results The Pixel Web App offers researchers an intuitive way to annotate, store, explore and mine their multi-omics results. It can be installed on a personal computer or on a server to fit the needs of many users. In addition, anyone can enhance the application to better suit their needs, either by contributing directly on GitHub (encouraged) or by extending Pixel on their own. The Pixel Web App does not provide any computational programs to analyze the data. Still, it helps to rapidly explore and mine existing results and holds a strategic position in the management of research data.
Denecker et al. (2019) Pixel: a content management platform for quantitative omics data. PeerJ 7:e6623 https://doi.org/10.7717/peerj.6623
Biodegradation of thiocyanate by a native groundwater microbial consortium
Gold ore processing typically generates large amounts of thiocyanate (SCN−)-contaminated effluent. When this effluent is stored in unlined tailings dams, contamination of the underlying aquifer can occur. The potential for bioremediation of SCN−-contaminated groundwater, either in situ or ex situ, remains largely unexplored. This study aimed to enrich and characterise SCN−-degrading microorganisms from mining-contaminated groundwater under a range of culturing conditions. Mildly acidic and suboxic groundwater, containing ∼135 mg L−1 SCN−, was collected from an aquifer below an unlined tailings dam. An SCN−-degrading consortium was enriched from contaminated groundwater using combinatory amendments of air, glucose and phosphate. Biodegradation occurred in all oxic cultures, except with the sole addition of glucose, but was inhibited by NH4+ and did not occur under anoxic conditions. The SCN−-degrading consortium was characterised using 16S and 18S rRNA gene sequencing, identifying a variety of heterotrophic taxa in addition to sulphur-oxidising bacteria. Interestingly, few recognised SCN−-degrading taxa were identified in significant abundance. These results provide both proof-of-concept and the required conditions for biostimulation of SCN− degradation in groundwater by native aquifer microorganisms.
Environmental Contamination and Remediation
Spurr et al. (2019) Biodegradation of thiocyanate by a native groundwater microbial consortium. PeerJ 7:e6498 https://doi.org/10.7717/peerj.6498
Development of polymorphic EST-SSR markers and characterization of the autotetraploid genome of sainfoin (Onobrychis viciifolia)
Background Sainfoin (Onobrychis viciifolia) is a highly nutritious, tannin-containing, and tetraploid forage legume. Due to the lack of detailed transcriptomic and genomic information on this species, genetic and breeding projects for sainfoin improvement have been significantly hindered. Methods In this study, a total of 24,630,711 clean reads were generated from 14 different sainfoin tissues using Illumina paired-end sequencing technology and deposited in the NCBI SRA database (SRX3763386). From these clean reads, 77,764 unigene sequences were obtained and 6,752 EST-SSRs were identified using de novo assembly. A total of 2,469 primer pairs were designed, and 200 primer pairs were randomly selected to analyze the polymorphism in five sainfoin wild accessions. Results Further analysis of 40 sainfoin individuals from the five wild populations using 61 EST-SSR loci showed that the number of alleles per locus ranged from 4 to 15, and the expected heterozygosity varied from 0.55 to 0.91. Additionally, by counting the EST-SSR band number and sequencing the three or four bands in one sainfoin individual, sainfoin was confirmed to be autotetraploid. This finding provides a high level of information about this plant. Discussion Through this study, 61 EST-SSR markers were successfully developed and shown to be useful for genetic studies and investigations of population genetic structures and variabilities among different sainfoin accessions.
Shen et al. (2019) Development of polymorphic EST-SSR markers and characterization of the autotetraploid genome of sainfoin (Onobrychis viciifolia). PeerJ 7:e6542 https://doi.org/10.7717/peerj.6542
Proteomics alterations in chicken jejunum caused by 24 h fasting
The small intestine is the longest part of the chicken (Gallus gallus) gastrointestinal system that is specialized for nutrient absorption. It is known that decrease in intestinal villi area or height in early age can cause a reduction in essential nutrient intake, which may lead to delayed growth and consequently poorer performance of broiler chickens. The small intestinal absorptive surface is known to be affected by various factors, among others things the nutritional state. In our experiment, we aimed to investigate the possible protein expression alterations that lie behind the villus area and height decrease caused by feed deprivation. A total of 24 chickens were divided into three groups, namely ad libitum fed, fasted for 24 h, fasted for 24 h then refed for 2 h. The morphometric parameters were also measured in the duodenum, jejunum and ileum tissue sections using image analysis. Differential proteome analyses from jejunum samples were performed using two-dimensional difference gel electrophoresis followed by tryptic digestion and protein identification by matrix-assisted laser desorption/ionization mass spectrometry. Overall 541 protein spots were detected after 2D. Among them, eleven showed 1.5-fold or higher significant difference in expression and were successfully identified. In response to 24 h fasting, the expression of nine proteins was higher and that of two proteins was lower compared to the ad libitum fed group. The functions of the differentially expressed proteins indicate that the 24 h fasting mainly affects the expression of structural proteins, and proteins involved in lipid transport, general stress response, and intestinal defense.
Simon et al. (2019) Proteomics alterations in chicken jejunum caused by 24 h fasting. PeerJ 7:e6588 https://doi.org/10.7717/peerj.6588
Comparative genomic analysis of the IDD genes in five Rosaceae species and expression analysis in Chinese white pear (Pyrus bretschneideri)
The INDETERMINATE DOMAIN (IDD) gene family encodes hybrid transcription factors with distinct zinc finger motifs and appears to be found in all higher plant genomes. IDD genes have been identified throughout the genomes of the model plants Arabidopsis thaliana and Oryza sativa, and the functions of many members of this gene family have been studied. However, few studies have investigated the IDD gene family in Rosaceae species (among these species, a genome-wide identification of the IDD gene family has only been completed in Malus domestica). This study focuses on a comparative genomic analysis of the IDD gene family in five Rosaceae species (Pyrus bretschneideri, Fragaria vesca, Prunus mume, Rubus occidentalis and Prunus avium). We identified a total of 68 IDD genes: 16 genes in Chinese white pear, 14 genes in F. vesca, 13 genes in Prunus mume, 14 genes in R. occidentalis and 11 genes in Prunus avium. The evolution of the IDD genes in these five Rosaceae species was revealed by constructing a phylogenetic tree, tracking gene duplication events, and performing a sliding window analysis and a conserved microsynteny analysis. The expression analysis of different organs showed that most of the pear IDD genes are found at a very high transcription level in fruits, flowers and buds. Based on our results with those obtained in previous research, we speculated that PbIDD2 and PbIDD8 might participate in flowering induction in pear. A temporal expression analysis showed that the expression patterns of PbIDD3 and PbIDD5 were completely opposite to the accumulation pattern of fruit lignin and the stone cell content. The results of the composite phylogenetic tree and expression pattern analysis indicated that PbIDD3 and PbIDD5 might be involved in the metabolism of lignin and secondary cell wall (SCW) formation. In summary, we provide basic information about the IDD genes in five Rosaceae species and thereby provide a theoretical basis for studying the function of these IDD genes.
Su et al. (2019) Comparative genomic analysis of the IDD genes in five Rosaceae species and expression analysis in Chinese white pear (Pyrus bretschneideri). PeerJ 7:e6628 https://doi.org/10.7717/peerj.6628