Bacterial communities in the digester bed and liquid effluent of a microflush composting toilet system
Lack of access to clean water and sanitation is a major factor impacting public health in communities worldwide. To address this, the S-Lab at Providence College and the Global Sustainable Aid Project developed a microflush composting toilet system to isolate and treat human waste. Solid waste is composted within a filter-digester bed via an aerobic process involving microbes and invertebrates. Liquid waste may be sanitized by solar disinfection (SODIS) or slow sand filtration (SSF). Here, we used 16S rRNA amplicon sequencing of samples from a scaled-down test version of the system to better understand the bacterial component of the toilet system. Immediately after fecal matter was deposited in the test system, the bacterial community of the filter-digester bed at the site of deposition resembled that of the human gut at both the phylum and genus level, which was expected. Genus-level analysis of filter-digester bed samples collected over the next 30 days from the site of deposition showed reduced or undetectable levels of fecal-associated taxa, with the exception of Clostridium XI, which persisted at low abundance throughout the sampling period. Starting with the sample collected on day 4, the bacterial community of the filter-digester bed at the site of deposition was dominated by bacterial taxa commonly associated with environmental sources, reflecting a major shift in bacterial community composition. These data support the toilet system’s capacity for processing solid human waste. We also analyzed how SODIS and SSF sanitization methods affected the bacterial community composition of liquid effluent collected on day 15 from the test system. Untreated and treated liquid effluent samples were dominated by Proteobacteria. At the genus level, the bacterial community of the untreated effluent included taxa commonly associated with environmental sources. In the SODIS-treated effluent, these genera increased in abundance, whereas in the SSF-treated effluent, they were greatly reduced or undetectable. By analyzing operational taxonomic units that were unclassified at the genus level, we observed that SSF appears to introduce new taxa into the treated effluent, likely from the biological film of microbes and small animals that constitutes the key element of SSF. These data will inform continued development of liquid waste handling strategies for the toilet system. Using the test system as an indicator of the performance of the full-scale version, we have shown the effectiveness of the microflush composting toilet system for containing and eliminating gut-associated bacteria, thereby improving sanitation and contributing to better public health in rural and peri-urban communities.
Environmental Contamination and Remediation
Williams et al. (2018) Bacterial communities in the digester bed and liquid effluent of a microflush composting toilet system. PeerJ 6:e6077 https://doi.org/10.7717/peerj.6077
Modelling of the SDF-1/CXCR4 regulated in vivo homing of therapeutic mesenchymal stem/stromal cells in mice
Background Mesenchymal stem/stromal cells (MSCs) are a promising tool for cell-based therapies in the treatment of tissue injury. The stromal cell-derived factor-1 (SDF-1)/CXC chemokine receptor 4 (CXCR4) axis plays a significant role in directing MSC homing to sites of injury. However in vivo MSC distribution following intravenous transplantation remains poorly understood, potentially hampering the precise prediction and evaluation of therapeutic efficacy. Methods A murine model of partial ischemia/reperfusion (I/R) is used to induce liver injury, increase the hepatic levels of SDF-1, and study in vivo MSC distribution. Hypoxia-preconditioning increases the expression of CXCR4 in human bone marrow-derived MSCs. Quantitative assays for human DNA using droplet digital PCR (ddPCR) allow us to examine the in vivo kinetics of intravenously infused human MSCs in mouse blood and liver. A mathematical model-based system is developed to characterize in vivo homing of human MSCs in mouse models with SDF-1 levels in liver and CXCR4 expression on the transfused MSCs. The model is calibrated to experimental data to provide novel estimates of relevant parameter values. Results Images of immunohistochemistry for SDF-1 in the mouse liver with I/R injury show a significantly higher SDF-1 level in the I/R injured liver than that in the control. Correspondingly, the ddPCR results illustrate a higher MSC concentration in the I/R injured liver than the normal liver. CXCR4 is overexpressed in hypoxia-preconditioned MSCs. An increased number of hypoxia-preconditioned MSCs in the I/R injured liver is observed from the ddPCR results. The model simulations align with the experimental data of control and hypoxia-preconditioned human MSC distribution in normal and injured mouse livers, and accurately predict the experimental outcomes with different MSC doses. Discussion The modelling results suggest that SDF-1 in organs is an effective in vivo attractant for MSCs through the SDF-1/CXCR4 axis and reveal the significance of the SDF-1/CXCR4 chemotaxis on in vivo homing of MSCs. This in vivo modelling approach allows qualitative characterization and prediction of the MSC homing to normal and injured organs on the basis of clinically accessible variables, such as the MSC dose and SDF-1 concentration in blood. This model could also be adapted to abnormal conditions and/or other types of circulating cells to predict in vivo homing patterns.
Jin et al. (2018) Modelling of the SDF-1/CXCR4 regulated in vivo homing of therapeutic mesenchymal stem/stromal cells in mice. PeerJ 6:e6072 https://doi.org/10.7717/peerj.6072
Conservation implications of primate trade in China over 18 years based on web news reports of confiscations
Primate species have been increasingly threatened by legal and illegal trade in China, mainly for biomedical research or as pets and traditional medicine, yet most reports on trade from China regard international trade. To assess a proxy for amount of national primate trades, we quantified the number of reports of native primate species featuring in unique web news reports from 2000 to 2017, including accuracy of their identification, location where they were confiscated or rescued, and their condition upon rescue. To measure temporal trends across these categories, the time span was divided into three sections: 2000–2005, 2006–2011 and 2012–2017. A total of 735 individuals of 14 species were reported in 372 news reports, mostly rhesus macaques (n = 165, 22.5%, Macaca mulatta) and two species of slow lorises (n = 487, 66.3%, Nycticebus spp.). During the same period, live individuals of rhesus macaques were recorded 206 times (70,949 individuals) in the Convention on International Trade in Endangered Species of Wild Fauna and Flora Trade Database, whereas slow lorises were only recorded four times (nine individuals), indicating that the species originated illegally from China or were illegally imported into China. Due to their rescued locations in residential areas (n = 211, 56.7%), most primates appeared to be housed privately as pets. A higher proportion of ‘market’ rescues during 2006–2011 (χ2 = 8.485, df = 2, p = 0.014), could be partly attributed to an intensive management on wildlife markets since the outbreak of severe acute respiratory syndrome (SARS) in 2003. More than half (68.3%, 502 individuals) of the primate individuals were unhealthy, injured or dead when rescued. Thus, identification and welfare training and capacity-building should be provided to husbandry and veterinary professionals, as well as education to the public through awareness initiatives. The increase in presence of some species, especially slow lorises, with a declining population in restricted areas, also suggests the urgent need for public awareness about the illegal nature of keeping these taxa as pets.
Ni et al. (2018) Conservation implications of primate trade in China over 18 years based on web news reports of confiscations. PeerJ 6:e6069 https://doi.org/10.7717/peerj.6069
Association of urinary activity of MMP-9 with renal impairment in Mexican patients with type 2 diabetes mellitus
Background Diabetic kidney disease is the most common cause of chronic kidney disease (CKD). An early event in diabetic kidney disease is alteration of the glomerular basement membrane and the mesangial expansion. Matrix metalloproteinases (MMP) are a family of endopeptidases responsible for controlling the pathophysiological remodeling of tissues, including renal tissues. MMP-9 in human urine has been proposed as a marker of diabetic nephropathy and urinary tract infections (UTI). Methods A cross-sectional study was conducted in type 2 diabetes mellitus (T2DM) patients who receive first level medical attention in Mexico. We used ELISA to measure MMP-9 levels in the urine of subjects with T2DM ≥ 18 years of age, who fulfilled the clinical requirements for calculation of glomerular filtration rate (GFR), according to the K/DOQI guide, in an attempt to identify whether MMP-9 levels in T2DM differ in patients with and without renal impairment. Univariate and multivariable analyses were performed in order to identify the association between MMP-9 and renal impairment. Results Included in the study were 34 (45%) subjects with renal impairment and 42 (55%) without. In the group with renal impairment, 10 subjects corresponded to stages 1–2 and 24 subjects corresponded to stage 3, according to their values of GFR and urinary albumin, following that proposed by the K/DOQI. No differences were found relating to sex, age, having or not having a partner, education, being able to read and write a message and duration of T2DM. Moreover, no differences were found between the groups in terms of weight, height, body mass index, waist size in general and frequency of UTI. In contrast, serum creatinine and urinary albumin were higher in the group with renal impairment, while GFR was greater in the group without renal impairment. Levels of MMP-9 were greater in women compared to men. Through univariate analysis in the general population, the presence of MMP-9 and that of its percentile 90 (P90) P90 were associated with the renal impairment group; however, in patients without UTI, only the presence of MMP-9 was associated with the renal impairment group, and no association was found with its P90. Multivariate analysis revealed an association between MMP-9 and its P90 with renal impairment. Discussion It is necessary to validate sensitive and non-invasive biological markers of CKD. We demonstrate that the presence and P90 of urinary MMP-9 are associated with renal impairment in Mexican patients with T2DM. While high levels of MMP-9 were associated to females and UTI, the presence of UTI was not associated with the incidence of renal impairment.
García-Tejeda et al. (2018) Association of urinary activity of MMP-9 with renal impairment in Mexican patients with type 2 diabetes mellitus. PeerJ 6:e6067 https://doi.org/10.7717/peerj.6067
Development and internal validation of a nine-lncRNA prognostic signature for prediction of overall survival in colorectal cancer patients
Background Colorectal cancer remains a serious public health problem due to the poor prognosis. In the present study, we attempted to develop and validate a prognostic signature to predict the individual mortality risk in colorectal cancer patients. Materials and Methods The original study datasets were downloaded from The Cancer Genome Atlas database. The present study finally included 424 colorectal cancer patients with wholly gene expression information and overall survival information. Results A nine-lncRNA prognostic signature was built through univariate and multivariate Cox proportional regression model. Time-dependent receiver operating characteristic curves in model cohort demonstrated that the Harrell’s concordance indexes of nine-lncRNA prognostic signature were 0.768 (95% CI [0.717–0.819]), 0.778 (95% CI [0.727–0.829]) and 0.870 (95% CI [0.819–0.921]) for 1-year, 3-year and 5-year overall survival respectively. In validation cohort, the Harrell’s concordance indexes of nine-lncRNA prognostic signature were 0.761 (95% CI [0.710–0.812]), 0.801 (95% CI [0.750–0.852]) and 0.883 (95% CI [0.832–0.934]) for 1-year, 3-year and 5-year overall survival respectively. According to the median of nine-lncRNA prognostic signature score in model cohort, 424 CRC patients could be stratified into high risk group (n = 212) and low risk group (n = 212). Kaplan–Meier survival curves showed that the overall survival rate of high risk group was significantly lower than that of low risk group (P < 0.001). Discussion The present study developed and validated a nine-lncRNA prognostic signature for individual mortality risk assessment in colorectal cancer patients. This nine-lncRNA prognostic signature is helpful to evaluate the individual mortality risk and to improve the decision making of individualized treatments in colorectal cancer patients.
Zhang et al. (2018) Development and internal validation of a nine-lncRNA prognostic signature for prediction of overall survival in colorectal cancer patients. PeerJ 6:e6061 https://doi.org/10.7717/peerj.6061
Diversity of social-genetic relationships in the socially monogamous pied flycatcher (Ficedula hypoleuca) breeding in Western Siberia
We explored the genetic background of social interactions in two breeding metapopulations of the pied flycatcher (Ficedula hypoleuca) in Western Siberia. In 2005, we sampled blood from birds breeding in study areas located in the city of Tomsk and in a natural forest 13 km southward of Tomsk (Western Siberia, Russia). We sampled 30 males, 46 females, 268 nestlings (46 nests) in the urban settlement of pied flycatcher, and 232 males, 250 females, 1,485 nestlings (250 nests) in the woodland plot. DNA fingerprinting was carried out using eight microsatellite loci, which were amplified by two multiplex-PCRs and analyzed by capillary electrophoresis. About 50–58% of all couples were socially and genetically monogamous in both study plots. However, almost all possible social and genetic interactions were detected for non-monogamous couples: polygamy, polyandry, helping, adoption, and egg dumping. Differences in the rate of polygyny and the rate of extra-pair paternity between both study sites could be explained by differences in environmental heterogeneity and breeding density. Our findings suggest that egg dumping, adoption, polygamy, extra pair copulation, and other types of social-genetic interactions are modifications of the monogamous social system caused by patchy environment, breeding density, and birds’ breeding status.
Grinkov et al. (2018) Diversity of social-genetic relationships in the socially monogamous pied flycatcher (Ficedula hypoleuca) breeding in Western Siberia. PeerJ 6:e6059 https://doi.org/10.7717/peerj.6059
Urbanization, environmental stabilization and temporal persistence of bird species: a view from Latin America
Background A scarcely studied consequence of urbanization is the effect of temporal stabilization of the environment on bird communities. This alteration is thought to dampen environmental variations between day and night, seasons and years, promoting a temporal persistence of bird composition in urban areas. The aim of this study was to review current evidence of temporal stabilization of biotic and abiotic factors in urban environments and the potential effects of such stabilization on temporal variation of bird species presence at different temporal scales. Methods I selected the literature by searching published articles and book chapters using Scopus and Google scholar. I only included articles that compared the temporal variation of bird composition or resources between different levels of urbanization. Results In general, there is evidence of temporal stabilization of abiotic and biotic factors at the three time scales considered. At the diurnal scale, the main factor considered was artificial light in the context of light pollution. At the seasonal and interannual scales, several case studies found a smaller temporal variation of primary productivity in urban than in natural and rural areas. Bird species composition showed more stabilization in urban environments at the three temporal scales: (1) several case studies reported bird activity at night, associated with artificial light; (2) studies in urban parks and along urbanization gradients showed smaller seasonal variation of bird composition in the more urbanized areas; and (3) in general, case studies along urbanization gradients showed smaller interannual variation of bird composition in the more urbanized areas, although some studies showed no relationships or opposite trends than expected. Discussion The published evidence suggests that urban areas dampen the natural cycles at several temporal scales. The stabilization of biotic and abiotic factors, such as light, temperature, food and habitat structure, is desynchronized from natural diurnal, seasonal and interannual cycles. However, there is a dearth of long-term comparisons of bird composition and studies that simultaneously analyze the relationship between resources and bird composition stabilization at the seasonal and interannual scales. More research is needed in the Southern hemisphere, where there is a lack of studies dealing with the seasonal and interannual variations of primary productivity along urbanization gradients and nocturnal activity of bird species. A future research agenda should include differentiation of spatial and temporal homogenization of avifaunas.
Leveau (2018) Urbanization, environmental stabilization and temporal persistence of bird species: a view from Latin America. PeerJ 6:e6056 https://doi.org/10.7717/peerj.6056
JacLy: a Jacobian-based method for the inference of metabolic interactions from the covariance of steady-state metabolome data
Reverse engineering metabolome data to infer metabolic interactions is a challenging research topic. Here we introduce JacLy, a Jacobian-based method to infer metabolic interactions of small networks (<20 metabolites) from the covariance of steady-state metabolome data. The approach was applied to two different in silico small-scale metabolome datasets. The power of JacLy lies on the use of steady-state metabolome data to predict the Jacobian matrix of the system, which is a source of information on structure and dynamic characteristics of the system. Besides its advantage of inferring directed interactions, its superiority over correlation-based network inference was especially clear in terms of the required number of replicates and the effect of the use of priori knowledge in the inference. Additionally, we showed the use of standard deviation of the replicate data as a suitable approximation for the magnitudes of metabolite fluctuations inherent in the system.
Khatibipour et al. (2018) JacLy: a Jacobian-based method for the inference of metabolic interactions from the covariance of steady-state metabolome data. PeerJ 6:e6034 https://doi.org/10.7717/peerj.6034
An integrative taxonomic approach reveals Octopus insularis as the dominant species in the Veracruz Reef System (southwestern Gulf of Mexico)
The common octopus of the Veracruz Reef System (VRS, southwestern Gulf of Mexico) has historically been considered as Octopus vulgaris, and yet, to date, no study including both morphological and genetic data has tested that assumption. To assess this matter, 52 octopuses were sampled in different reefs within the VRS to determine the taxonomic identity of this commercially valuable species using an integrative taxonomic approach through both morphological and genetic analyses. Morphological and genetic data confirmed that the common octopus of the VRS is not O. vulgaris and determined that it is, in fact, the recently described O. insularis. Morphological measurements, counts, indices, and other characteristics such as specific colour patterns, closely matched what had been reported for O. insularis in Brazil. In addition, sequences from cytochrome oxidase I (COI) and 16S ribosomal RNA (r16S) mitochondrial genes confirmed that the common octopus from the VRS is in the same highly supported clade as O. insularis from Brazil. Genetic distances of both mitochondrial genes as well as of cytochrome oxidase subunit III (COIII) and novel nuclear rhodopsin sequences for the species, also confirmed this finding (0–0.8%). We discuss our findings in the light of the recent reports of octopus species misidentifications involving the members of the ‘O. vulgaris species complex’ and underscore the need for more morphological studies regarding this group to properly address the management of these commercially valuable and similar taxa.
González-Gómez et al. (2018) An integrative taxonomic approach reveals Octopus insularis as the dominant species in the Veracruz Reef System (southwestern Gulf of Mexico). PeerJ 6:e6015 https://doi.org/10.7717/peerj.6015
Genetic analysis reveals Finnish Formica fennica populations do not form a separate genetic entity from F. exsecta
Coptoformica Müller, 1923 is a subgenus of Formica Linnaeus, 1758 that consists of c. a dozen species of ants that typically inhabit open grassy habitats and build small nest mounds. The most recent addition to the group is Formica fennica Seifert, 2000. The description was based on morphological characters, but the species status has not been confirmed by molecular methods. In this study, we use thirteen DNA microsatellite markers and a partial mitochondrial COI gene sequence to assess the species status of F. fennica, by comparing the genetic variation among samples identified as F. fennica and six other boreal Formica (Coptoformica) species. Most of the species studied form separate, discontinuous clusters in phylogenetic and spatial analyses with only little intraspecific genetic variation. However, both nuclear and mitochondrial markers fail to separate the species pair F. exsecta Nylander, 1846 and F. fennica despite established morphological differences. The genetic variation within the F. exsecta/fennica group is extensive, but reflects spatial rather than morphological differences. Finnish F. fennica populations studied so far should not be considered a separate species, but merely a morph of F. exsecta.
Hakala et al. (2018) Genetic analysis reveals Finnish Formica fennica populations do not form a separate genetic entity from F. exsecta. PeerJ 6:e6013 https://doi.org/10.7717/peerj.6013