title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1462
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Effect of operational parameters, characterization and antibacterial studies of green synthesis of silver nanoparticles using Tithonia diversifolia
link: https://peerj.com/articles/5865
last-modified: 2018-10-30
description: BackgroundThere is a growing interest in the green synthesis of silver nanoparticles (AgNPs) using plant extract because the technique is cost effective, eco-friendly and environmentally benign. This is phasing out the use of toxic and hazardous chemical earlier reported. Tithonia diversifolia is a wild sunflower that grows widely in the western part of Nigeria with a proven medicinal benefit. However, several studies carried out have left doubts on the basic operational parameters needed for the green synthesis of AgNPs. The objective of this work was to carry out green synthesis of AgNPs using T. diversifolia extract via an eco-friendly route through optimization of various operational parameters, characterization, and antimicrobial studies.MethodGreen synthesis of TD-AgNPs was done via bottom-up approach through wet chemistry technique using environmentally benign T. diversifolia plant extract as both reducing and stabilizing agent. Phytochemical Screening of the TD plant extract was carried out. Experimental optimization of various operational parameters—reaction time, concentration, volume ratio, and temperature was investigated. TD-AgNPs were characterized by UV–Vis spectroscopy, FTIR Spectroscopy, SEM/energy-dispersive X-ray spectroscopy (EDX), X-ray diffraction (XRD), and transmission electron microscopy (TEM). Antimicrobial studies against multi drug resistant microorganisms (MDRM) were studied using the agar well diffusion method.ResultsThis study reveals the importance of various operational parameters in the synthesis of TD-AgNPs. Excellent surface plasmon resonance peaks (SPR) were obtained at optimum experimental factors of 90 min reaction time under room temperature at 0.001M concentration with the volume ratio of 1:9 (TD extract:Ag ion solution). The synthesis was monitored using UV–Vis and maximum wavelength obtained at 430 nm was due to SPR. The morphology and elemental constituents obtained by TEM, SEM, and EDX results revealed a spherical shape of AgNPs with prominent peak of Ag at 3.0 kV in EDX spectrum. The crystallinity nature was confirmed by XRD studies. FTIR analysis proved presence of biomolecules functioning as reducing, stabilizing, and capping agents. These biomolecules were confirmed to be flavonoid, triterpenes, and saponin from phytochemical screening. The antimicrobial studies of TD-AgNPs were tested against MDRM—Escherichia coli, Salmonella typhi, Salmonella enterica, and Bacillus subtilis.DiscussionThe variation of reaction time, temperature, concentration, and volume ratio played substantive and fundamental roles in the synthesis of TD-AgNPs. A good dispersion of small spherical size between 10 and 26 nm was confirmed by TEM and SEM. A dual action mechanism of anti-microbial effects was provided by TD-AgNPs which are bactericidal and membrane-disruption. Based on the antimicrobial activity, the synthesized TD-AgNPs could find good application in medicine, pharmaceutical, biotechnology, and food science.
creator: Adewumi O. Dada
creator: Adejumoke A. Inyinbor
creator: Ebiega I. Idu
creator: Oluwasesan M. Bello
creator: Abimbola P. Oluyori
creator: Tabitha A. Adelani-Akande
creator: Abiodun A. Okunola
creator: Olarewaju Dada
uri: https://doi.org/10.7717/peerj.5865
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2018 Dada et al.

title: Habitat fragmentation is linked to cascading effects on soil functioning and CO2 emissions in Mediterranean holm-oak-forests
link: https://peerj.com/articles/5857
last-modified: 2018-10-30
description: We studied key mechanisms and drivers of soil functioning by analyzing soil respiration and enzymatic activity in Mediterranean holm oak forest fragments with different influence of the agricultural matrix. For this, structural equation models (SEM) were built including data on soil abiotic (moisture, temperature, organic matter, pH, nutrients), biotic (microbial biomass, bacterial and fungal richness), and tree-structure-related (basal area) as explanatory variables of soil enzymatic activity and respiration. Our results show that increased tree growth induced by forest fragmentation in scenarios of high agricultural matrix influence triggered a cascade of causal-effect relations, affecting soil functioning. On the one hand, soil enzymatic activity was strongly stimulated by the abiotic (changes in pH and microclimate) and biotic (microbial biomass) modifications of the soil environment arising from the increased tree size and subsequent soil organic matter accumulation. Soil CO2 emissions (soil respiration), which integrate releases from all the biological activity occurring in soils (autotrophic and heterotrophic components), were mainly affected by the abiotic (moisture, temperature) modifications of the soil environment caused by trees. These results, therefore, suggest that the increasing fragmentation of forests may profoundly impact the functioning of the plant-soil-microbial system, with important effects over soil CO2 emissions and nutrient cycling at the ecosystem level. Forest fragmentation is thus revealed as a key albeit neglected factor for accurate estimations of soil carbon dynamics under global change scenarios.
creator: Dulce Flores-Rentería
creator: Ana Rincón
creator: Teresa Morán-López
creator: Ana-Maria Hereş
creator: Leticia Pérez-Izquierdo
creator: Fernando Valladares
creator: Jorge Curiel Yuste
uri: https://doi.org/10.7717/peerj.5857
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Flores-Rentería et al.

title: HAHap: a read-based haplotyping method using hierarchical assembly
link: https://peerj.com/articles/5852
last-modified: 2018-10-30
description: BackgroundThe need for read-based phasing arises with advances in sequencing technologies. The minimum error correction (MEC) approach is the primary trend to resolve haplotypes by reducing conflicts in a single nucleotide polymorphism-fragment matrix. However, it is frequently observed that the solution with the optimal MEC might not be the real haplotypes, due to the fact that MEC methods consider all positions together and sometimes the conflicts in noisy regions might mislead the selection of corrections. To tackle this problem, we present a hierarchical assembly-based method designed to progressively resolve local conflicts.ResultsThis study presents HAHap, a new phasing algorithm based on hierarchical assembly. HAHap leverages high-confident variant pairs to build haplotypes progressively. The phasing results by HAHap on both real and simulated data, compared to other MEC-based methods, revealed better phasing error rates for constructing haplotypes using short reads from whole-genome sequencing. We compared the number of error corrections (ECs) on real data with other methods, and it reveals the ability of HAHap to predict haplotypes with a lower number of ECs. We also used simulated data to investigate the behavior of HAHap under different sequencing conditions, highlighting the applicability of HAHap in certain situations.
creator: Yu-Yu Lin
creator: Ping Chun Wu
creator: Pei-Lung Chen
creator: Yen-Jen Oyang
creator: Chien-Yu Chen
uri: https://doi.org/10.7717/peerj.5852
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2018 Lin et al.

title: Effectiveness of telephone-based interventions for managing osteoarthritis and spinal pain: a systematic review and meta-analysis
link: https://peerj.com/articles/5846
last-modified: 2018-10-30
description: BackgroundOsteoarthritis and spinal pain are common and burdensome conditions; however, the majority of patients with these conditions do not receive care that is consistent with clinical practice guidelines. Telehealth models of care have the potential to improve care for osteoarthritis and spinal pain patients. The aim of this review was to assess the effectiveness of verbal real-time telehealth interventions, including telephone-based and videoconferencing interventions to reduce pain intensity and disability in patients with osteoarthritis of the knee or hip and spinal pain (back or neck pain).MethodsWe searched seven electronic databases from inception to May 2018. Randomised controlled trials (RCTs), cluster-RCTs, and non-randomised controlled trials were included. Two review authors independently extracted data for each included study. Primary outcomes were pain intensity and disability. We conducted primary meta-analyses combining all conditions with similar interventions and comparators. Standardised mean difference (SMD) and 95% confidence intervals (CIs) were calculated using random effects models. We used the Cochrane Risk of Bias tool to assess risk of bias, and GRADE to evaluate the quality of evidence.ResultsWe included 23 studies with 56 trial arms and 4,994 participants. All studies utilised telephone-based interventions. Only two studies used a telephone only approach and the remainder included educational materials and/or face-to-face components. We found no studies utilising videoconferencing. Meta-analysis showed telephone-based interventions (with educational materials) for osteoarthritis and spinal pain improved pain intensity (n = 5 trials, n = 1,357 participants, SMD −0.27, 95% CI [−0.53, −0.01], Tau2 = 0.06, I2 = 74%; moderate-quality evidence) and disability (n = 7 trials, n = 1,537 participants, SMD −0.21, 95% CI [−0.40, −0.02], Tau2 = 0.03, I2 = 56%; moderate-quality evidence) compared to usual care. Meta-analyses found telephone with face-to-face interventions does not improve pain and disability compared to usual care or face-to-face care alone.DiscussionWe are moderately confident that telephone-based interventions reduce pain intensity and disability in patients with osteoarthritis and spinal pain compared to usual care, but telephone plus face-to-face interventions are no more effective than usual care or face-to-face interventions alone.
creator: Kate M. O’Brien
creator: Rebecca K. Hodder
creator: John Wiggers
creator: Amanda Williams
creator: Elizabeth Campbell
creator: Luke Wolfenden
creator: Sze Lin Yoong
creator: Flora Tzelepis
creator: Steven J. Kamper
creator: Christopher M. Williams
uri: https://doi.org/10.7717/peerj.5846
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2018 O’Brien et al.

title: Using stiffness to assess injury risk: comparison of methods for quantifying stiffness and their reliability in triathletes
link: https://peerj.com/articles/5845
last-modified: 2018-10-30
description: BackgroundA review of the literature has indicated that lower body stiffness, defined as the extent to which the lower extremity joints resists deformation upon contact with the ground, may be a useful measure for assessing Achilles injury risk in triathletes. The nature of overuse injuries suggests that a variety of different movement patterns could conceivably contribute to the final injury outcome, any number and combination of which might be observed in a single individual. Measurements which incorporate both kinetics and kinematics (such as stiffness) of a movement may be better able to shed light on individuals at risk of injury, with further analysis then providing the exact mechanism of injury for the individual. Stiffness can be measured as vertical, leg or joint stiffness to model how the individual interacts with the environment upon landing. However, several issues with stiffness assessments limit the effectiveness of these measures to monitor athletes’ performance and/or injury risk. This may reflect the variety of common biomechanical stiffness calculations (dynamic, time, true leg and joint) that have been used to examine these three stiffness levels (vertical, leg and joint) across a variety of human movements (i.e. running or hopping) as well as potential issues with the reliability of these measures, especially joint stiffness. Therefore, the aims of this study were to provide a comparison of the various methods for measuring stiffness during two forms of human bouncing locomotion (running and hopping) along with the measurement reliability to determine the best methods to assess links with injury risk in triathletes.MethodsVertical, leg and joint stiffness were estimated in 12 healthy male competitive triathletes on two occasions, 7 days apart, using both running at 5.0 ms−1 and hopping (2.2 Hz) tasks.ResultsInter-day reliability was good for vertical (ICC = 0.85) and leg (ICC = 0.98) stiffness using the time method. Joint stiffness reliability was poor when assessed individually. Reliability was improved when taken as the sum of the hip, knee and ankle (ICC = 0.86). The knee and ankle combination provided the best correlation with leg stiffness during running (Pearson’s Correlation = 0.82).DiscussionThe dynamic and time methods of calculating leg stiffness had better reliability than the “true” method. The time and dynamic methods had the best correlation with the different combinations of joint stiffness, which suggests that they should be considered for biomechanical screening of triathletes. The knee and ankle combination had the best correlation with leg stiffness and is therefore proposed to provide the most information regarding lower limb mechanics during gait in triathletes.
creator: Anna V. Lorimer
creator: Justin W.L. Keogh
creator: Patria A. Hume
uri: https://doi.org/10.7717/peerj.5845
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Lorimer et al.

title: Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management
link: https://peerj.com/articles/5826
last-modified: 2018-10-30
description: Aquaculture production of the Pacific white shrimp is the largest in the world for crustacean species. Crucial to the sustainable global production of this important seafood species is a fundamental understanding of the shrimp gut microbiota and its relationship to the microbial ecology of shrimp pond. This is especially true, given the recently recognized role of beneficial microbes in promoting shrimp nutrient intake and in conferring resistance against pathogens. Unfortunately, aquaculture-related microbiome studies are scarce in Southeast Asia countries despite the severe impact of early mortality syndrome outbreaks on shrimp production in the region. In this study, we employed the 16S rRNA amplicon (V3–V4 region) sequencing and amplicon sequence variants (ASV) method to investigate the microbial diversity of shrimp guts and pond water samples collected from aquaculture farms located in Malaysia and Vietnam. Substantial differences in the pond microbiota were observed between countries with the presence and absence of several taxa extending to the family level. Microbial diversity of the shrimp gut was found to be generally lower than that of the pond environments with a few ubiquitous genera representing a majority of the shrimp gut microbial diversity such as Vibrio and Photobacterium, indicating host-specific selection of microbial species. Given the high sequence conservation of the 16S rRNA gene, we assessed its veracity at distinguishing Vibrio species based on nucleotide alignment against type strain reference sequences and demonstrated the utility of ASV approach in uncovering a wider diversity of Vibrio species compared to the conventional OTU clustering approach.
creator: Muhammad Zarul Hanifah Md Zoqratt
creator: Wilhelm Wei Han Eng
creator: Binh Thanh Thai
creator: Christopher M. Austin
creator: Han Ming Gan
uri: https://doi.org/10.7717/peerj.5826
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Md Zoqratt et al.

title: Comparative functional analysis of proteins containing low-complexity predicted amyloid regions
link: https://peerj.com/articles/5823
last-modified: 2018-10-30
description: BackgroundIn 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.MethodsFirstly 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.ResultsAmong 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.DiscussionThe 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.
creator: Bandana Kumari
creator: Ravindra Kumar
creator: Vipin Chauhan
creator: Manish Kumar
uri: https://doi.org/10.7717/peerj.5823
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2018 Kumari et al.

title: Uncovering full-length transcript isoforms of sugarcane cultivar Khon Kaen 3 using single-molecule long-read sequencing
link: https://peerj.com/articles/5818
last-modified: 2018-10-30
description: BackgroundSugarcane 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.MethodsWe 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.ResultsA 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.DiscussionThe 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.
creator: Jittima Piriyapongsa
creator: Pavita Kaewprommal
creator: Sirintra Vaiwsri
creator: Songtham Anuntakarun
creator: Warodom Wirojsirasak
creator: Prapat Punpee
creator: Peeraya Klomsa-ard
creator: Philip J. Shaw
creator: Wirulda Pootakham
creator: Thippawan Yoocha
creator: Duangjai Sangsrakru
creator: Sithichoke Tangphatsornruang
creator: Sissades Tongsima
creator: Somvong Tragoonrung
uri: https://doi.org/10.7717/peerj.5818
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Piriyapongsa et al.

title: Adipose tissues of MPC1± mice display altered lipid metabolism-related enzyme expression levels
link: https://peerj.com/articles/5799
last-modified: 2018-10-30
description: 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.
creator: Shiying Zou
creator: Liye Zhu
creator: Kunlun Huang
creator: Haoshu Luo
creator: Wentao Xu
creator: Xiaoyun He
uri: https://doi.org/10.7717/peerj.5799
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Zou et al.

title: From the cage to the wild: introductions of Psittaciformes to Puerto Rico
link: https://peerj.com/articles/5669
last-modified: 2018-10-30
description: 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.
creator: Wilfredo Falcón
creator: Raymond L. Tremblay
uri: https://doi.org/10.7717/peerj.5669
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Falcón and Tremblay