title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1816 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Familiar face + novel face = familiar face? Representational bias in the perception of morphed faces in chimpanzees link: https://peerj.com/articles/2304 last-modified: 2016-08-04 description: Highly social animals possess a well-developed ability to distinguish the faces of familiar from novel conspecifics to induce distinct behaviors for maintaining society. However, the behaviors of animals when they encounter ambiguous faces of familiar yet novel conspecifics, e.g., strangers with faces resembling known individuals, have not been well characterised. Using a morphing technique and preferential-looking paradigm, we address this question via the chimpanzee’s facial–recognition abilities. We presented eight subjects with three types of stimuli: (1) familiar faces, (2) novel faces and (3) intermediate morphed faces that were 50% familiar and 50% novel faces of conspecifics. We found that chimpanzees spent more time looking at novel faces and scanned novel faces more extensively than familiar or intermediate faces. Interestingly, chimpanzees looked at intermediate faces in a manner similar to familiar faces with regards to the fixation duration, fixation count, and saccade length for facial scanning, even though the participant was encountering the intermediate faces for the first time. We excluded the possibility that subjects merely detected and avoided traces of morphing in the intermediate faces. These findings suggest a bias for a feeling-of-familiarity that chimpanzees perceive familiarity with an intermediate face by detecting traces of a known individual, as 50% alternation is sufficient to perceive familiarity. creator: Yoshi-Taka Matsuda creator: Masako Myowa-Yamakoshi creator: Satoshi Hirata uri: https://doi.org/10.7717/peerj.2304 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Matsuda et al. title: Novel fermented chickpea milk with enhanced level of γ-aminobutyric acid and neuroprotective effect on PC12 cells link: https://peerj.com/articles/2292 last-modified: 2016-08-04 description: In this study, novel fermented chickpea milk with high γ -aminobutyric acid (GABA) content and potential neuroprotective activity was developed. Fermentation starter that can produce GABA was selected from 377 strains of lactic acid bacteria isolated from traditional Chinese fermented foods. Among the screened strains, strain M-6 showed the highest GABA-producing capacity in De Man–Rogosa and Sharp (MRS) broth and chickpea milk. M-6 was identified as Lactobacillus plantarum based on Gram staining, API carbohydrate fermentation pattern testing, and 16s rDNA sequencing. The complete gene encoding glutamate decarboxylase was cloned to confirm the presence of the gene in L. plantarum M-6. The fermentation condition was optimized by response surface methodology. Results demonstrated that L. plantarum M-6 produced the highest GABA content of 537.23 mg/L. The optimal condition included an inoculum concentration of 7%, presence of 0.2% (m/v) monosodium glutamate and 55 µ M pyridoxal-5-phosphate, incubation temperature of 39 °C and fermentation time of 48 h . GABA-enriched chickpea milk exerted protective effects on PC12 cells against MnCl2 -induced injury. GABA-enriched chickpea milk improved cell viability and markedly attenuated the release of lactate dehydrogenase compared with the impaired cells. creator: Wen Li creator: Mingming Wei creator: Junjun Wu creator: Xin Rui creator: Mingsheng Dong uri: https://doi.org/10.7717/peerj.2292 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Li et al. title: Use of the melting curve assay as a means for high-throughput quantification of Illumina sequencing libraries link: https://peerj.com/articles/2281 last-modified: 2016-08-04 description: Background. Multiplexed sequencing is commonly performed on massively parallel short-read sequencing platforms such as Illumina, and the efficiency of library normalisation can affect the quality of the output dataset. Although several library normalisation approaches have been established, none are ideal for highly multiplexed sequencing due to issues of cost and/or processing time.Methods. An inexpensive and high-throughput library quantification method has been developed, based on an adaptation of the melting curve assay. Sequencing libraries were subjected to the assay using the Bio-Rad Laboratories CFX ConnectTM Real-Time PCR Detection System. The library quantity was calculated through summation of reduction of relative fluorescence units between 86 and 95 °C.Results.PCR-enriched sequencing libraries are suitable for this quantification without pre-purification of DNA. Short DNA molecules, which ideally should be eliminated from the library for subsequent processing, were differentiated from the target DNA in a mixture on the basis of differences in melting temperature. Quantification results for long sequences targeted using the melting curve assay were correlated with those from existing methods (R2 > 0.77), and that observed from MiSeq sequencing (R2 = 0.82).Discussion.The results of multiplexed sequencing suggested that the normalisation performance of the described method is equivalent to that of another recently reported high-throughput bead-based method, BeNUS. However, costs for the melting curve assay are considerably lower and processing times shorter than those of other existing methods, suggesting greater suitability for highly multiplexed sequencing applications. creator: Hiroshi Shinozuka creator: John W. Forster uri: https://doi.org/10.7717/peerj.2281 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Shinozuka and Forster title: The antioxidative properties of S-allyl cysteine not only influence somatic cells but also improve early embryo cleavage in pigs link: https://peerj.com/articles/2280 last-modified: 2016-08-04 description: In vitro cultivation systems for oocytes and embryos are characterised by increased levels of reactive oxygen species (ROS), which can be balanced by the addition of suitable antioxidants. S-allyl cysteine (SAC) is a sulfur compound naturally occurring in garlic (Allium sativum), which is responsible for its high antioxidant properties. In this study, we demonstrated the capacity of SAC (0.1, 0.5 and 1.0 mM) to reduce levels of ROS in maturing oocytes significantly after 24 (reduced by 90.33, 82.87 and 91.62%, respectively) and 48 h (reduced by 86.35, 94.42 and 99.05%, respectively) cultivation, without leading to a disturbance of the standard course of meiotic maturation. Oocytes matured in the presence of SAC furthermore maintained reduced levels of ROS even 22 h after parthenogenic activation (reduced by 66.33, 61.64 and 57.80%, respectively). In these oocytes we also demonstrated a growth of early embryo cleavage rate (increased by 33.34, 35.00 and 35.00%, respectively). SAC may be a valuable supplement to cultivation media. creator: Markéta Dvořáková creator: Ivona Heroutová creator: David Němeček creator: Kateřina Adámková creator: Tereza Krejčová creator: Jan Nevoral creator: Veronika Kučerová Chrpová creator: Jaroslav Petr creator: Markéta Sedmíková uri: https://doi.org/10.7717/peerj.2280 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Dvořáková et al. title: The pes of Australovenator wintonensis (Theropoda: Megaraptoridae): analysis of the pedal range of motion and biological restoration link: https://peerj.com/articles/2312 last-modified: 2016-08-03 description: The pedal range of motion in Australovenator wintonensis is investigated to determine what influence soft tissue had on range of motion in the foot. Fortunately, the theropod pes shares a close morphology with extant large cursorial birds. Therefore, to better understand the pedal range of motion of Australovenator, the pedal range of motion of Dromaius novaehollandiae (commonly known as the emu) was analysed with and without soft tissue. We used a variety of innovative digital techniques to analyse the range of motion and biologically restore the Australovenator pes. Computed tomography scans of Dromaius pes in fully flexed and fully extended positions provided the soft tissue range of motion limits. The bone on bone range of motion of the same specimen was replicated following the removal of soft tissue. It was identified that there was an increase in range of motion potential with the removal of soft tissue. This variation provided a guide to develop the potential range of motion of a fully fleshed Australovenator pes. Additionally, the dissection of the Dromaius pes provided a guide enabling the replication of the corresponding soft tissue and keratin sheaths of the Australovenator pes. creator: Matt A. White creator: Alex G. Cook creator: Ada J. Klinkhamer creator: David A. Elliott uri: https://doi.org/10.7717/peerj.2312 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 White et al. title: Cafeteria diet induce changes in blood flow that are more related with heat dissipation than energy accretion link: https://peerj.com/articles/2302 last-modified: 2016-08-03 description: Background. A “cafeteria” diet is a self-selected high-fat diet, providing an excess of energy, which can induce obesity. Excess of lipids in the diet hampers glucose utilization eliciting insulin resistance, which, further limits amino acid oxidation for energy.Methods. Male Wistar rats were exposed for a month to “cafeteria” diet. Rats were cannulated and fluorescent microspheres were used to determine blood flow.Results. Exposure to the cafeteria diet did not change cardiac output, but there was a marked shift in organ irrigation. Skin blood flow decreased to compensate increases in lungs and heart. Blood flow through adipose tissue tended to increase in relation to controls, but was considerably increased in brown adipose tissue (on a weight basis).Discussion. The results suggest that the cafeteria diet-induced changes were related to heat transfer and disposal. creator: David Sabater creator: Silvia Agnelli creator: Sofía Arriarán creator: María del Mar Romero creator: José Antonio Fernández-López creator: Marià Alemany creator: Xavier Remesar uri: https://doi.org/10.7717/peerj.2302 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Sabater et al. title: A multifunctional GH39 glycoside hydrolase from the anaerobic gut fungus Orpinomyces sp. strain C1A link: https://peerj.com/articles/2289 last-modified: 2016-08-03 description: Background. The anaerobic gut fungi (phylum Neocallimastigomycota) represent a promising source of novel lignocellulolytic enzymes. Here, we report on the cloning, expression, and characterization of a glycoside hydrolase family 39 (GH39) enzyme (Bgxg1) that is highly transcribed by the anaerobic fungus Orpinomycessp. strain C1A under different growth conditions. This represents the first study of a GH39-family enzyme from the anaerobic fungi.Methods. Using enzyme activity assays, we performed a biochemical characterization of Bgxg1 on a variety of substrates over a wide range of pH and temperature values to identify the optimal enzyme conditions and the specificity of the enzyme. In addition, substrate competition studies and comparative modeling efforts were completed.Results. Contrary to the narrow range of activities (β-xylosidase or α-L-iduronidase) observed in previously characterized GH39 enzymes, Bgxg1 is unique in that it is multifunctional, exhibiting strong β-xylosidase, β-glucosidase, β-galactosidase activities (11.5 ± 1.2, 73.4 ± 7.15, and 54.6 ± 2.26 U/mg, respectively) and a weak xylanase activity (10.8 ± 1.25 U/mg), as compared to previously characterized enzymes. Further, Bgxg1 possesses extremely high affinity (as evident by the lowest Km values), compared to all previously characterized β-glucosidases, β-galactosidases, and xylanases. Physiological characterization revealed that Bgxg1 is active over a wide range of pH (3–8, optimum 6) and temperatures (25–60 °C, optimum 39 °C), and possesses excellent temperature and thermal stability. Substrate competition assays suggest that all observed activities occur at a single active site. Using comparative modeling and bioinformatics approaches, we putatively identified ten amino acid differences between Bgxg1 and previously biochemically characterized GH39 β-xylosidases that we speculate could impact active site architecture, size, charge, and/or polarity.Discussion. Collectively, the unique capabilities and multi-functionality of Bgxg1 render it an excellent candidate for inclusion in enzyme cocktails mediating cellulose and hemicellulose saccharification from lignocellulosic biomass. creator: Jessica M. Morrison creator: Mostafa S. Elshahed creator: Noha Youssef uri: https://doi.org/10.7717/peerj.2289 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Morrison et al. title: Imbalance between subsets of CD8+ peripheral blood T cells in patients with chronic obstructive pulmonary disease link: https://peerj.com/articles/2301 last-modified: 2016-08-02 description: Background. CD8+ T lymphocytes are known to play a critical role in the pathogenesis of chronic obstructive pulmonary disease (COPD). However, systematic analyses of CD8+ T cell (Cytotoxic T cells, Tc) subsets in COPD patients have yet to be well conducted.Methods. The whole Tc subsets, including Tc1/2/10/17, CD8+ regulatory T cells (Tregs) and CD8+α7+ T cells, were quantified by flow cytometry in peripheral blood from 24 stable COPD subjects (SCOPD), 14 patients during acute exacerbations (AECOPD), and 14 healthy nonsmokers (HN).Results. Acute exacerbations of COPD were accompanied by elevated levels of circulating CD8+ T cells. Tc1 cells were increased in both SCOPD and AECOPD patients, whereas the percentage of Tc2 cells was decreased in SCOPD patients but remained normal in AECOPD patients. Tc17 cells were increased only in AECOPD patients, and the percentage of Tc10 cells was reduced in both SCOPD and AECOPD patients. The imbalances of pro/anti-inflammatory Tc subsets observed in COPD may be caused by the lack of Tc10 cells and the impaired anti-inflammatory capacity of CD8+ Tregs.Conclusions. The imbalances between subsets of CD8+ peripheral blood T cells contribute to the immune response dysfunction in COPD pathogenesis. creator: Long Chen creator: Gang Chen creator: Ming-Qiang Zhang creator: Xian-Zhi Xiong creator: Hong-Ju Liu creator: Jian-Bao Xin creator: Jian-Chu Zhang creator: Jiang-Hua Wu creator: Zhao-Ji Meng creator: Sheng-Wen Sun uri: https://doi.org/10.7717/peerj.2301 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Chen et al. title: Bone lesions in Chinese POEMS syndrome patients: imaging characteristics and clinical implications link: https://peerj.com/articles/2294 last-modified: 2016-08-02 description: Objective. Bone lesion is crucial for diagnosing and management of polyneuropathy, organomegaly, endocrinopathy, monoclonal protein, and skin change (POEMS) syndrome, a rare plasma cell disorder. This study is to compare the effectiveness of X-ray skeletal survey (SS) and computed tomography (CT) for detecting bone lesions in Chinese POEMS syndrome patients, and to investigate the relationship between bone lesion features and serum markers.Methods. SS and chest/abdomen/pelvic CT images of 38 Chinese patients (26 males, 12 females, aged 21–70 years) with POEMS syndrome recruited at our medical center between January 2013 and January 2015 were retrospectively analyzed. Bone lesions identified by CT were further categorized according to the size (<5 mm, 5–10 mm, >10 mm) and appearance (osteosclerotic, lytic, mixed). The percentage of plasma cells in bone marrow smears, type of immunoglobulin, platelet (Plt), and levels of serum bone metabolic markers and inflammatory factors including alkaline phosphatase (ALP), calcium, phosphate, parathyroid hormone (PTH), beta-isomerized C-telopeptide (β-CTx), vascular endothelial growth factor (VEGF), and interleukin (IL)-6 levels were also recorded.Results. Of the 38 POEMS syndrome patients, the immunoglobulin heavy chain isotypes were IgA in 25 patients (65.8%; 25/38) and IgG in 13 patients (34.2%; 13/38), and the light chain isotypes were λ in 35 patients (92.1%; 35/38) and κ in 3 patients (7.9%; 3/38). There were 23 patients with thrombocytosis. More patients with bone lesions were detected by CT than by SS (97.4% vs. 86.8%). The most commonly affected location was the pelvis (89.5%), followed by the spine, clavicle/scapula/sternum/ribs, skull, and long bones. Of the 38 POEMS syndrome patients, 35 (94.6%) had osteosclerotic and 32 (86.5%) had mixed lesions. Osteosclerotic lesions were typically scattered, variable in size, and plaque-like, whereas mixed lesions were pouch-shaped or soup bubble-like with a clear sclerotic margin and were generally larger. Although the majority of bone lesions were small in size, 23 (62.2%) had at least one lesion >10 mm. There was no correlation between serum marker levels and bone lesion patterns after Bonferroni correction (all P > 0.001).Conclusions. CT is more sensitive and accurate than SS in detecting bone lesions in POEMS syndrome. creator: Fengdan Wang creator: Xufei Huang creator: Yan Zhang creator: Jian Li creator: Daobin Zhou creator: Zhengyu Jin uri: https://doi.org/10.7717/peerj.2294 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wang et al. title: Microbial production and characterization of poly-3-hydroxybutyrate by Neptunomonas antarctica link: https://peerj.com/articles/2291 last-modified: 2016-08-02 description: Considering the industrial interest of biodegradable polymer poly-3-hydroxybutyrate (PHB), the marine bacteria Neptunomonas antarctica was studied for its ability to accumulate PHB. The extracted polymer was confirmed to be PHB by nuclear magnetic resonance analysis. In shake flask cultures using natural seawater as medium components, PHB was produced up to 2.12 g/L with a yield of 0.18 g PHB/g fructose. In the presence of artificial seawater, the PHB titer and yield reached 2.13 g/L and 0.13 g PHB/g fructose, respectively. The accumulated polymer gradually decreased when fructose was exhausted, indicating that intracellular PHB was degraded by N. antarctica. The weight-average and number-average molecular weights of PHB produced within natural seawater were 2.4 × 105 g/mol and 1.7 × 105 g/mol, respectively. Our results highlight the potential of N. antarctica for PHB production with seawater as a nutrient source. creator: Xiao-Jie Liu creator: Jie Zhang creator: Peng-Hui Hong creator: Zheng-Jun Li uri: https://doi.org/10.7717/peerj.2291 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Liu et al.