Comparative functional analysis of proteins containing low-complexity predicted amyloid regions
Background In both prokaryotic and eukaryotic proteins, repeated occurrence of a single or a group of few amino acids are found. These regions are termed as low complexity regions (LCRs). It has been observed that amino acid bias in LCR is directly linked to their uncontrolled expansion and amyloid formation. But a comparative analysis of the behavior of LCR based on their constituent amino acids and their association with amyloidogenic propensity is not available. Methods Firstly we grouped all LCRs on the basis of their composition: homo-polymers, positively charged amino acids, negatively charged amino acids, polar amino acids and hydrophobic amino acids. We analyzed the compositional pattern of LCRs in each group and their propensity to form amyloids. The functional characteristics of proteins containing different groups of LCRs were explored using DAVID. In addition, we also analyzed the classes, pathways and functions of human proteins that form amyloids in LCRs. Results Among homopolymeric LCRs, the most common was Gln repeats. LCRs composed of repeats of Met and aromatic amino acids were amongst the least occurring. The results revealed that LCRs composed of negatively charged and polar amino acids were more common in comparison to LCRs formed by positively charged and hydrophobic amino acids. We also noted that generally proteins with LCRs were involved in transcription but those with Gly repeats were associated to translational activities. Our analysis suggests that proteins in which LCR is composed of hydrophobic residues are more prone toward amyloid formation. We also found that the human proteins with amyloid forming LCRs were generally involved in binding and catalytic activity. Discussion The presented analysis summarizes the most common and least occurring LCRs in proteins. Our results show that though repeats of Gln are the most abundant but Asn repeats make longest stretch of low complexity. The results showed that potential of LCRs to form amyloids varies with their amino acid composition.
Kumari et al. (2018) Comparative functional analysis of proteins containing low-complexity predicted amyloid regions. PeerJ 6:e5823 https://doi.org/10.7717/peerj.5823
Uncovering full-length transcript isoforms of sugarcane cultivar Khon Kaen 3 using single-molecule long-read sequencing
Background Sugarcane is an important global food crop and energy resource. To facilitate the sugarcane improvement program, genome and gene information are important for studying traits at the molecular level. Most currently available transcriptome data for sugarcane were generated using second-generation sequencing platforms, which provide short reads. The de novo assembled transcripts from these data are limited in length, and hence may be incomplete and inaccurate, especially for long RNAs. Methods We generated a transcriptome dataset of leaf tissue from a commercial Thai sugarcane cultivar Khon Kaen 3 (KK3) using PacBio RS II single-molecule long-read sequencing by the Iso-Seq method. Short-read RNA-Seq data were generated from the same RNA sample using the Ion Proton platform for reducing base calling errors. Results A total of 119,339 error-corrected transcripts were generated with the N50 length of 3,611 bp, which is on average longer than any previously reported sugarcane transcriptome dataset. 110,253 sequences (92.4%) contain an open reading frame (ORF) of at least 300 bp long with ORF N50 of 1,416 bp. The mean lengths of 5′ and 3′ untranslated regions in 73,795 sequences with complete ORFs are 1,249 and 1,187 bp, respectively. 4,774 transcripts are putatively novel full-length transcripts which do not match with a previous Iso-Seq study of sugarcane. We annotated the functions of 68,962 putative full-length transcripts with at least 90% coverage when compared with homologous protein coding sequences in other plants. Discussion The new catalog of transcripts will be useful for genome annotation, identification of splicing variants, SNP identification, and other research pertaining to the sugarcane improvement program. The putatively novel transcripts suggest unique features of KK3, although more data from different tissues and stages of development are needed to establish a reference transcriptome of this cultivar.
Piriyapongsa et al. (2018) Uncovering full-length transcript isoforms of sugarcane cultivar Khon Kaen 3 using single-molecule long-read sequencing. PeerJ 6:e5818 https://doi.org/10.7717/peerj.5818
Adipose tissues of MPC1± mice display altered lipid metabolism-related enzyme expression levels
Mitochondrial pyruvate carrier 1 (MPC1) is a component of the MPC1/MPC2 heterodimer that facilitates the transport of pyruvate into mitochondria. Pyruvate plays a central role in carbohydrate, fatty, and amino acid catabolism. The present study examined epididymal white adipose tissue (eWAT) and intrascapular brown adipose tissue (iBAT) from MPC1± mice following 24 weeks of feeding, which indicated low energy accumulation as evidenced by low body and eWAT weight and adipocyte volume. To characterize molecular changes in energy metabolism, we analyzed the transcriptomes of the adipose tissues using RNA-Sequencing (RNA-Seq). The results showed that the fatty acid oxidation pathway was activated and several genes involved in this pathway were upregulated. Furthermore, qPCR and western blotting indicated that numerous genes and proteins that participate in lipolysis were also upregulated. Based on these findings, we propose that the energy deficiency caused by reduced MPC1 activity can be alleviated by activating the lipolytic pathway.
Zou et al. (2018) Adipose tissues of MPC1± mice display altered lipid metabolism-related enzyme expression levels. PeerJ 6:e5799 https://doi.org/10.7717/peerj.5799
From the cage to the wild: introductions of Psittaciformes to Puerto Rico
Introduced psittacine birds can become highly invasive. In this study, we assessed invasions of Psittaciformes in Puerto Rico. We reviewed the literature, public databases, citizen science records, and performed in situ population surveys across the island to determine the historical and current status and distribution of psittacine species. We used count data from Ebird to determine population trends. For species whose populations were increasing, we modelled their potential distribution using niche modeling techniques. We found 46 Psittaciformes in Puerto Rico, of which 26% are only present as pets, at least 29 species have been reported in the wild, and of those, there is evidence that at least 12 species are breeding. Our results indicate that most introduced species which have been detected as established still persist, although mostly in localized areas and small populations. Clear evidence of invasiveness was found for Brotogeris versicolurus and Myiopsitta monachus, which have greatly expanded their range in recent years. Psittacara erythrogenys and Eupsittacula canicularis also showed population increases, although to a lesser degree. The niche models predicted suitable areas for the four species, and also indicate the potential for range expansion. We discuss the factors leading to invasion success, assess the potential impacts, and we discuss possible management strategies and research prospects.
Falcón et al. (2018) From the cage to the wild: introductions of Psittaciformes to Puerto Rico. PeerJ 6:e5669 https://doi.org/10.7717/peerj.5669
Using the validated Reflective Functioning Questionnaire to investigate mentalizing in individuals presenting with eating disorders with and without self-harm
Background The present study builds on previous research which explored the relationship between mentalizing and eating disorders (ED) in a subgroup of patients with comorbid self-harm (SH). Whereas previous literature had linked this comorbidity to impulse-control difficulties, more recent advances have suggested that a lack of a mentalizing stance might be responsible for a more treatment-resistant and severe symptomatology in this subgroup of clients. Methods A cross-sectional, quasi-experimental, questionnaire-based, between-groups design was employed and a measure of mentalizing was compared in individuals presenting with ED only, individuals presenting with ED and concurrent SH and a control group. Results Individuals with ED with concurrent SH reported significantly more mentalizing ability impairment than individuals without concurrent SH. In addition, both groups differed significantly from the control group. Opposite scoring patterns were identified in hypo- and hypermentalizing with the comorbid group reporting the lowest scores in hypermentalizing and the highest scores in hypomentalizing. Conclusions The current findings confirm that individuals with concurrent ED and SH report more severe impairments in mentalizing ability. Such impairments entail difficulties in symbolic capacity and abstract thinking and a concretisation of inner life, exemplified by a rigid, often inflexible focus on the physical world. The clinical implications that a lack of a mentalizing stance can have on individuals’ ability to engage with the therapeutic process and to initiate change are reflected upon.
Cucchi et al. (2018) Using the validated Reflective Functioning Questionnaire to investigate mentalizing in individuals presenting with eating disorders with and without self-harm. PeerJ 6:e5756 https://doi.org/10.7717/peerj.5756
Confidence in eating disorder knowledge does not predict actual knowledge in collegiate female athletes
Background Eating disorders are serious psychological disorders with long term health impacts. Athletic populations, tend to have higher incidences of eating disorders compared to the general population. Yet there is little known about athletes’ eating disorder knowledge and how it relates to their confidence in their knowledge. Therefore, the purpose of our study was to evaluate collegiate female athletes’ eating disorder (ED) knowledge and confidence in their knowledge. 51 participants were recruited from a National Association of Intercollegiate Athletics (NAIA) university in the mid-west and asked to complete a 30-question exam assessing one’s knowledge of five different categories related to eating disorders. Confidence in the correctness of answers was assessed with a 5-point Likert-scale (1 = very unconfident, 5 = very confident). A one-way ANOVA was used to determine differences between scores on different categories and overall scores. A simple regression analysis was used to determine if confidence or age was predictive in knowledge scores. Results The average score of participants was 69.1%, SD = 10.8% with an average confidence of 3.69/5, SD = 0.33. Athletes scored lowest with regards to Identifying Signs and Symptoms of EDs compared to other sub-scores (p < 0.05). There was no relationship between knowledge and confidence scores. Discussion There is limited ED knowledge among collegiate female athletes. This may be problematic as many athletes appear confident in the correctness of their answers despite these low scores. Coaches should be aware of this lack of knowledge and work with clinical practitioners, such as dieticians, team physicians and athletic trainers to educate and monitor their athletes on eating disorders, specifically signs and symptoms.
Rosa-Caldwell et al. (2018) Confidence in eating disorder knowledge does not predict actual knowledge in collegiate female athletes. PeerJ 6:e5868 https://doi.org/10.7717/peerj.5868
Ensemble learning for detecting gene-gene interactions in colorectal cancer
Colorectal cancer (CRC) has a high incident rate in both men and women and is affecting millions of people every year. Genome-wide association studies (GWAS) on CRC have successfully revealed common single-nucleotide polymorphisms (SNPs) associated with CRC risk. However, they can only explain a very limited fraction of the disease heritability. One reason may be the common uni-variable analyses in GWAS where genetic variants are examined one at a time. Given the complexity of cancers, the non-additive interaction effects among multiple genetic variants have a potential of explaining the missing heritability. In this study, we employed two powerful ensemble learning algorithms, random forests and gradient boosting machine (GBM), to search for SNPs that contribute to the disease risk through non-additive gene-gene interactions. We were able to find 44 possible susceptibility SNPs that were ranked most significant by both algorithms. Out of those 44 SNPs, 29 are in coding regions. The 29 genes include ARRDC5, DCC, ALK, and ITGA1, which have been found previously associated with CRC, and E2F3 and NID2, which are potentially related to CRC since they have known associations with other types of cancer. We performed pairwise and three-way interaction analysis on the 44 SNPs using information theoretical techniques and found 17 pairwise (p < 0.02) and 16 three-way (p ≤ 0.001) interactions among them. Moreover, functional enrichment analysis suggested 16 functional terms or biological pathways that may help us better understand the etiology of the disease.
Dorani et al. (2018) Ensemble learning for detecting gene-gene interactions in colorectal cancer. PeerJ 6:e5854 https://doi.org/10.7717/peerj.5854
Don’t worry, be active: how to facilitate the detection of errors in immersive virtual environments
The current research aims to study the link between the type of vision experienced in a collaborative immersive virtual environment (active vs. multiple passive), the type of error one looks for during a cooperative multi-user exploration of a design project (affordance vs. perceptual violations), and the type of setting in which multi-user perform (field in Experiment 1 vs. laboratory in Experiment 2). The relevance of this link is backed by the lack of conclusive evidence on an active vs. passive vision advantage in cooperative search tasks within software based on immersive virtual reality (IVR). Using a yoking paradigm based on the mixed usage of simultaneous active and multiple passive viewings, we found that the likelihood of error detection in a complex 3D environment was characterized by an active vs. multi-passive viewing advantage depending on: (1) the degree of knowledge dependence of the type of error the passive/active observers were looking for (low for perceptual violations, vs. high for affordance violations), as the advantage tended to manifest itself irrespectively from the setting for affordance, but not for perceptual violations; and (2) the degree of social desirability possibly induced by the setting in which the task was performed, as the advantage occurred irrespectively from the type of error in the laboratory (Experiment 2) but not in the field (Experiment 1) setting. Results are relevant to future development of cooperative software based on IVR used for supporting the design review. A multi-user design review experience in which designers, engineers and end-users all cooperate actively within the IVR wearing their own head mounted display, seems more suitable for the detection of relevant errors than standard systems characterized by a mixed usage of active and passive viewing.
Rigutti et al. (2018) Don’t worry, be active: how to facilitate the detection of errors in immersive virtual environments. PeerJ 6:e5844 https://doi.org/10.7717/peerj.5844
Association of urban forest landscape characteristics with biomass and soil carbon stocks in Harbin City, Northeastern China
Background Urban forests help in mitigating carbon emissions; however, their associations with landscape patterns are unclear. Understanding the associations would help us to evaluate urban forest ecological services and favor urban forest management via landscape regulations. We used Harbin, capital city of the northernmost province in China, as an example and hypothesized that the urban forests had different landscape metrics among different forest types, administrative districts, and urban–rural gradients, and these differences were closely associated with forest carbon sequestration in the biomass and soils. Methods We extracted the urban forest tree coverage area on the basis of 2 GF-1 remote sensing images and object-oriented based classification method. The analysis of forest landscape patterns and estimation of carbon storage were based on tree coverage data and 199 plots. We also examined the relationships between forest landscape metrics and carbon storage on the basis of forest types, administrative districts, ring roads, and history of urban settlements by using statistical methods. Results The small patches covering an area of less than 0.5 ha accounted for 72.6% of all patches (average patch size, 0.31 ha). The mean patch size (AREA_MN) and largest patch index (LPI) were the highest in the landscape and relaxation forest and Songbei District. The landscape shape index (LSI) and number of patches linearly decreased along rural-urban gradients (p < 0.05). The tree biomass carbon storage varied from less than 10 thousand tons in the urban center (first ring road region and 100-year regions) to more than 100 thousand tons in the rural regions (fourth ring road and newly urbanized regions). In the same urban–rural gradients, soil carbon storage varied from less than five thousand tons in the urban centers to 73–103 thousand tons in the rural regions. The association analysis indicated that the total forest area was the key factor that regulates total carbon storage in trees and soils. However, in the case of carbon density (ton ha−1), AREA_MN was strongly associated with tree biomass carbon, and soil carbon density was negatively related to LSI (p < 0.01) and AREA_MN (p < 0.05), but positively related to LPI (p < 0.05). Discussion The urban forests were more fragmented in Harbin than in other provincial cities in Northeastern China, as shown by the smaller patch size, more complex patch shape, and larger patch density. The decrease in LSI along the rural-urban gradients may contribute to the forest carbon sequestrations in downtown regions, particularly underground soil carbon accumulation, and the increasing patch size may benefit tree carbon sequestration. Our findings help us to understand how forest landscape metrics are associated with carbon storage function. These findings related to urban forest design may maximize forest carbon sequestration services and facilitate in precisely estimating the forest carbon sink.
Spatial and Geographic Information Science
Lv et al. (2018) Association of urban forest landscape characteristics with biomass and soil carbon stocks in Harbin City, Northeastern China. PeerJ 6:e5825 https://doi.org/10.7717/peerj.5825
Effects of agricultural management on phyllosphere fungal diversity in vineyards and the association with adjacent native forests
Agriculture is one of the main drivers of land conversion, and agriculture practices can impact on microbial diversity. Here we characterized the phyllosphere fungal diversity associated with Carménère grapevines under conventional and organic agricultural management. We also explored the fungal diversity present in the adjacent sclerophyllous forests to explore the potential role of native forest on vineyard phyllosphere. After conducting D2 and ITS2 amplicon sequencing, we found that fungal diversity indices did not change between conventional and organic vineyards, but community structure was sensitive to the agricultural management. On the other hand, we found a high proportion of shared fungal OTUs between vineyards and native forests. In addition, both habitats had similar levels of fungal diversity despite forest samples were derived from multiple plant species. In contrast, the community structure was different in both habitats. Interestingly, the native forest had more unidentified species and unique OTUs than vineyards. Forest dominant species were Aureobasidium pullulans and Endoconidioma populi, whereas Davidiella tassiana, Didymella sp., and Alternaria eichhorniae were more abundant in vineyards. Overall, this study argues that a better understanding of the relationship native forests and agroecosystems is needed for maintaining and enhancing ecosystem services provided by natural ecosystems. Finally, knowledge of microbial communities living in the Chilean Mediterranean biome is needed for appropriate conservation management of these biomes and their classification as biodiversity hotspots.
Castañeda et al. (2018) Effects of agricultural management on phyllosphere fungal diversity in vineyards and the association with adjacent native forests. PeerJ 6:e5715 https://doi.org/10.7717/peerj.5715