title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1625 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: High-resolution modeling of thermal thresholds and environmental influences on coral bleaching for local and regional reef management link: https://peerj.com/articles/4382 last-modified: 2018-02-16 description: Coral reefs are one of the world’s most threatened ecosystems, with global and local stressors contributing to their decline. Excessive sea-surface temperatures (SSTs) can cause coral bleaching, resulting in coral death and decreases in coral cover. A SST threshold of 1 °C over the climatological maximum is widely used to predict coral bleaching. In this study, we refined thermal indices predicting coral bleaching at high-spatial resolution (1 km) by statistically optimizing thermal thresholds, as well as considering other environmental influences on bleaching such as ultraviolet (UV) radiation, water turbidity, and cooling effects. We used a coral bleaching dataset derived from the web-based monitoring system Sango Map Project, at scales appropriate for the local and regional conservation of Japanese coral reefs. We recorded coral bleaching events in the years 2004–2016 in Japan. We revealed the influence of multiple factors on the ability to predict coral bleaching, including selection of thermal indices, statistical optimization of thermal thresholds, quantification of multiple environmental influences, and use of multiple modeling methods (generalized linear models and random forests). After optimization, differences in predictive ability among thermal indices were negligible. Thermal index, UV radiation, water turbidity, and cooling effects were important predictors of the occurrence of coral bleaching. Predictions based on the best model revealed that coral reefs in Japan have experienced recent and widespread bleaching. A practical method to reduce bleaching frequency by screening UV radiation was also demonstrated in this paper. creator: Naoki H. Kumagai creator: Hiroya Yamano uri: https://doi.org/10.7717/peerj.4382 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Kumagai et al. title: Morphometric analysis of a triple negative breast cancer cell line in hydrogel and monolayer culture environments link: https://peerj.com/articles/4340 last-modified: 2018-02-16 description: Triple negative breast cancer (TNBC) is a belligerent carcinoma that is unresponsive to targeted receptor therapies. Development of new treatment strategies would benefit from an expanded repertoire of in vitro cell culture systems, such as those that support tridimensional growth in the presence of hydrogel scaffolds. To this end, we established protocols for maintenance of the TNBC cell line HCC70 in monolayer culture and in a commercially available basement membrane matrix hydrogel. We evaluated the general morphology of cells grown in both conditions with light microscopy, and examined their subcellular organization using transmission electron microscopy (TEM). Phase contrast and confocal microscopy showed the prevalence of irregularly shaped flattened cells in monolayer cultures, while cells maintained in hydrogel organized into multi-layered spheroids. A quantitative ultrastructural analysis comparing cells from the two culture conditions revealed that cells that formed spheroids comprised a greater number of mitochondria, autophagic vacuoles and intercellular junctions than their monolayer counterparts, within the equivalent area of sampled tissue. These observations suggest that triple negative breast cancer cells in culture can alter their organelle content, as well as their morphology, in response to their microenvironment. Methods presented here may be useful for those who intend to image cell cultures with TEM, and for investigators who seek to implement diverse in vitro models in the search for therapeutic molecular targets for TNBC. creator: Manasi P. Jogalekar creator: Elba E. Serrano uri: https://doi.org/10.7717/peerj.4340 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Jogalekar and Serrano title: Postnatal depression is associated with detrimental life-long and multi-generational impacts on relationship quality link: https://peerj.com/articles/4305 last-modified: 2018-02-16 description: Postnatal depression (PND) is known to be associated with a range of detrimental child and adolescent outcomes, resulting from its disruptive impact on mother-child relationship quality. However, until now little has been known about the impact of PND on the longer-term relationships between mothers and their children, and any intergenerational effects this may have. Mother-child relationship quality is of interest from an evolutionary perspective as it plays a role in the accrual of offspring embodied capital, thus affecting offspring quality and offspring’s capacity to subsequently invest in their own children. Relationships with offspring also mediate grandparent-grandchild relations; if PND negatively affects long-term mother–offspring relationship quality, it is also likely to negatively affect grandmaternal investment via reduced grandmother–grandchild relationship quality. Here, we use responses to a retrospective questionnaire study of postmenopausal women, largely from the UK and US, to assess the impact of PND occurring in generation 1 on mother–child relationship quality across the life course of the child (generation 2) with whom it was associated, and also on the relationship quality with grandchildren (generation 3) from that child. Average mother-child relationship quality was lower when the child’s birth was associated with PND. Multi-level regression modelling found that mother-child relationship quality decreased as PND symptom severity increased after controlling for individual effects and a variety of other factors known to influence relationship quality (individual mothers n = 296, mother-child dyads n = 646). Additionally, intergenerational relationships appear to be affected, with PND negatively associated with grandmother-grandchild relations (individual grandmothers n = 125, relations with grandchildren from n = 197 grandmother-parent dyads). That PND has long-term detrimental consequences for mother-child relationships, well beyond adolescence, highlights the need for investment in strategies to prevent PND and its cascade of negative multigenerational effects. creator: Sarah Myers creator: Sarah E. Johns uri: https://doi.org/10.7717/peerj.4305 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Myers and Johns title: Seroprevalence of hepatitis B virus in Taiwan 30 years after the commencement of the national vaccination program link: https://peerj.com/articles/4297 last-modified: 2018-02-16 description: BackgroundIn this study, the long-term efficacy of hepatitis B virus (HBV) vaccination was assessed using seroprevalence and an age–period–cohort (APC) model of HBV seromarkers among university entrants 30 years after the introduction of the national neonatal HBV vaccination program in Taiwan.MethodsIn total, data of 17,611 university entrants who underwent university entrance health examinations between 2005 and 2016 were included. The seroprevalence of the HBV surface antigen (HBsAg) and the levels of the antibody against the HBV surface antigen (anti-HBs) in each year group and sex were calculated. The levels of the antibody against the HBV core antigen were examined only for 2012 and 2016. The APC model was used to analyze the HBV carrier rates.ResultsThe chronic HBV infection (HBsAg positivity) rate decreased from 9.7% in university students born before June 1974 to <1.0% in students born after 1992. The prevalence of anti-HBs positivity declined, particularly between the 1984–1988 cohort (78.2%–53.2%) and the 1990–1994 cohort (60.6%–44.4%). Our APC model revealed that the chronic HBV carrier rate among the student population was affected significantly by age, period, and cohort (P < 0.001).ConclusionsHBV vaccination is one of the most effective strategies for preventing HBV infection. However, for complete eradication of HBV infection, the development of strategies that detect vaccination failure more effectively than current strategies do and early implementation of appropriate treatments are both necessary. creator: Yang-Cheng Hu creator: Chih-Ching Yeh creator: Ruey-Yu Chen creator: Chien-Tien Su creator: Wen-Chang Wang creator: Chyi-Huey Bai creator: Chi-Fei Chan creator: Fu Hsiung Su uri: https://doi.org/10.7717/peerj.4297 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hu et al. title: COREMIC: a web-tool to search for a niche associated CORE MICrobiome link: https://peerj.com/articles/4395 last-modified: 2018-02-15 description: Microbial diversity on earth is extraordinary, and soils alone harbor thousands of species per gram of soil. Understanding how this diversity is sorted and selected into habitat niches is a major focus of ecology and biotechnology, but remains only vaguely understood. A systems-biology approach was used to mine information from databases to show how it can be used to answer questions related to the core microbiome of habitat-microbe relationships. By making use of the burgeoning growth of information from databases, our tool “COREMIC” meets a great need in the search for understanding niche partitioning and habitat-function relationships. The work is unique, furthermore, because it provides a user-friendly statistically robust web-tool (http://coremic2.appspot.com or http://core-mic.com), developed using Google App Engine, to help in the process of database mining to identify the “core microbiome” associated with a given habitat. A case study is presented using data from 31 switchgrass rhizosphere community habitats across a diverse set of soil and sampling environments. The methodology utilizes an outgroup of 28 non-switchgrass (other grasses and forbs) to identify a core switchgrass microbiome. Even across a diverse set of soils (five environments), and conservative statistical criteria (presence in more than 90% samples and FDR q-val <0.05% for Fisher’s exact test) a core set of bacteria associated with switchgrass was observed. These included, among others, closely related taxa from Lysobacter spp., Mesorhizobium spp, and Chitinophagaceae. These bacteria have been shown to have functions related to the production of bacterial and fungal antibiotics and plant growth promotion. COREMIC can be used as a hypothesis generating or confirmatory tool that shows great potential for identifying taxa that may be important to the functioning of a habitat (e.g. host plant). The case study, in conclusion, shows that COREMIC can identify key habitat-specific microbes across diverse samples, using currently available databases and a unique freely available software. creator: Richard R. Rodrigues creator: Nyle C. Rodgers creator: Xiaowei Wu creator: Mark A. Williams uri: https://doi.org/10.7717/peerj.4395 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Rodrigues et al. title: Identification and expression profile analysis of the sucrose phosphate synthase gene family in Litchi chinensis Sonn. link: https://peerj.com/articles/4379 last-modified: 2018-02-15 description: Sucrose phosphate synthase (SPS, EC 2.4.1.14) is a key enzyme that regulates sucrose biosynthesis in plants. SPS is encoded by different gene families which display differential expression patterns and functional divergence. Genome-wide identification and expression analyses of SPS gene families have been performed in Arabidopsis, rice, and sugarcane, but a comprehensive analysis of the SPS gene family in Litchi chinensis Sonn. has not yet been reported. In the current study, four SPS gene (LcSPS1, LcSPS2, LcSPS3, and LcSPS4) were isolated from litchi. The genomic organization analysis indicated the four litchi SPS genes have very similar exon-intron structures. Phylogenetic tree showed LcSPS1-4 were grouped into different SPS families (LcSPS1 and LcSPS2 in A family, LcSPS3 in B family, and LcSPS4 in C family). LcSPS1 and LcSPS4 were strongly expressed in the flowers, while LcSPS3 most expressed in mature leaves. RT-qPCR results showed that LcSPS genes expressed differentially during aril development between cultivars with different hexose/sucrose ratios. A higher level of expression of LcSPS genes was detected in Wuheli, which accumulates higher sucrose in the aril at mature. The tissue- and developmental stage-specific expression of LcSPS1-4 genes uncovered in this study increase our understanding of the important roles played by these genes in litchi fruits. creator: Dan Wang creator: Jietang Zhao creator: Bing Hu creator: Jiaqi Li creator: Yaqi Qin creator: Linhuan Chen creator: Yonghua Qin creator: Guibing Hu uri: https://doi.org/10.7717/peerj.4379 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wang et al. title: Optimization of antioxidative peptides from mackerel (Pneumatophorus japonicus) viscera link: https://peerj.com/articles/4373 last-modified: 2018-02-15 description: Mackerel (Pneumatophorus japonicus) viscera contain large amount of protein. We used five proteases to hydrolyze the viscera, and the hydrolysate treated by neutrase exhibited the highest nitrogen recovery (NR). Then we optimized the preparation conditions for mackerel viscera hydrolysate (MVH) by response surface methodology and investigated the antioxidant activity of MVH. The optimal conditions were as follows: enzyme concentration of 1,762.87 U/g, pH of 6.76, temperature of 43.75 °C, extraction time of 6.0 h and water/material ratio of 20.37 (v/w), and the maximum NR was 37.84%. Furthermore, the molecular weight distribution of MVH was almost below 3,000 Da determined by TSK G2000 SWXL gel filtration chromatography, and the MVH exhibited good antioxidant activities in various in vitro assays, including DPPH radical, hydroxyl radical and superoxide anion scavenging activities, reducing power and similar effectivelness as butylated hydroxytoluene and Vitamin E to inhibit lipid peroxidation. The results suggested that MVH could be used as a potential source of antioxidant peptide in food industries. creator: Xueqin Wang creator: Huahua Yu creator: Ronge Xing creator: Xiaolin Chen creator: Song Liu creator: Pengcheng Li uri: https://doi.org/10.7717/peerj.4373 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wang et al. title: Body mass index influences the plasma glucose concentration during iatrogenic hypoglycemia in people with type 2 diabetes mellitus: a cross-sectional study link: https://peerj.com/articles/4348 last-modified: 2018-02-15 description: BackgroundHypoglycemia occurs in an appreciable number of individuals with type 2 diabetes mellitus (T2DM) who are receiving glycemic therapy. Iatrogenic hypoglycemia induces not only complications but also a substantial medical expense. Intervention for relevant risk factors may help avert severe hypoglycemia and enhance quality of life in at-risk individuals. This study investigates the relationship between body mass index (BMI) and plasma glucose concentration during iatrogenic hypoglycemia in people with T2DM.MethodsEnrollment criteria were people above 20 years of age, with existing diagnosis of T2DM, a documented plasma glucose level ≤70 mg/dL, and acute cognitive impairment requiring hospitalization. Participants were classified into two groups according to their BMI. Specifically, lower BMI subgroup denotes individuals whose BMI fall within lower half of the study population, and vice versa. Plasma glucose concentration, length of hospital stay, and serum electrolyte level at hospitalization were compared between these BMI subgroups. Moreover, multivariate regression analysis was performed to identify covariates associated with plasma glucose level during iatrogenic hypoglycemia.ResultsThis study enrolled 107 participants for whom 54 were assigned to a higher BMI subgroup and the remainder to a lower BMI subgroup. People with lower BMI harbored substantially reduced plasma glucose concentration during iatrogenic hypoglycemia compared to those with higher BMI (30.1 ± 9.6 mg/dL vs. 38.4 ± 12.3 mg/dL, P < 0.001). Nonetheless, the length of stay (6.2 ± 4.6 days vs. 5.7 ± 4.0 days, P = 0.77) and serum potassium level (3.7 ± 0.9 meq/L vs. 3.9 ± 0.8 meq/L, P = 0.14) were comparable between subgroups. Multivariate regression analysis identified BMI as a determinant of plasma glucose concentration in diabetic individuals with iatrogenic hypoglycemia (β coefficient: 0.72, P = 0.008).DiscussionIn individuals with T2DM who experience severe iatrogenic hypoglycemia, BMI influences the plasma glucose level at hospitalization. People with lower BMI harbored appreciably reduced plasma glucose concentration relative to their higher BMI counterparts. In lower weight people, therefore, appropriate dosing of antidiabetic medications, frequent self-monitoring of blood glucose level and adequate nutritional support may help avert more severe hypoglycemia. Overall, BMI potentially influences the severity of iatrogenic hypoglycemia in people with T2DM. creator: Po Chung Cheng creator: Shang Ren Hsu creator: Shih Te Tu creator: Yun Chung Cheng creator: Yu Hsiu Liu uri: https://doi.org/10.7717/peerj.4348 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cheng et al. title: Vector competence of selected North American Anopheles and Culex mosquitoes for Zika virus link: https://peerj.com/articles/4324 last-modified: 2018-02-15 description: Zika virus (ZIKV) is a vector-borne flavivirus that has caused recent outbreaks associated with serious disease in infants and newborns in the Americas. Aedes mosquitoes are the primary vectors for ZIKV, but little is known about the diversity of mosquitoes that can transmit ZIKV in North America. We chose three abundant North American mosquito species (Anopheles freeborni, Anopheles quadrimaculatus, and Culex tarsalis) and one known vector species (Aedes aegypti), fed them blood meals supplemented with a recent outbreak ZIKV strain, and tested bodies, legs, and saliva for infectious ZIKV. ZIKV was able to infect, disseminate, and be transmitted by Aedes aegypti. However, Anopheles freeborni, Anopheles quadrimaculatus, and Culex tarsalis were unable to be infected. We conclude that these species are unlikely to be involved in ZIKV transmission in North America. However, we should continue to examine the ability for other mosquito species to potentially act as ZIKV vectors in North America. creator: Brittany L. Dodson creator: Sujit Pujhari creator: Jason L. Rasgon uri: https://doi.org/10.7717/peerj.4324 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Dodson et al. title: A new Python library to analyse skeleton images confirms malaria parasite remodelling of the red blood cell membrane skeleton link: https://peerj.com/articles/4312 last-modified: 2018-02-15 description: We present Skan (Skeleton analysis), a Python library for the analysis of the skeleton structures of objects. It was inspired by the “analyse skeletons” plugin for the Fiji image analysis software, but its extensive Application Programming Interface (API) allows users to examine and manipulate any intermediate data structures produced during the analysis. Further, its use of common Python data structures such as SciPy sparse matrices and pandas data frames opens the results to analysis within the extensive ecosystem of scientific libraries available in Python. We demonstrate the validity of Skan’s measurements by comparing its output to the established Analyze Skeletons Fiji plugin, and, with a new scanning electron microscopy (SEM)-based method, we confirm that the malaria parasite Plasmodium falciparum remodels the host red blood cell cytoskeleton, increasing the average distance between spectrin-actin junctions. creator: Juan Nunez-Iglesias creator: Adam J. Blanch creator: Oliver Looker creator: Matthew W. Dixon creator: Leann Tilley uri: https://doi.org/10.7717/peerj.4312 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Nunez-Iglesias et al.