title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1289
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Bridging the TB data gap: in silico extraction of rifampicin-resistant tuberculosis diagnostic test results from whole genome sequence data
link: https://peerj.com/articles/7564
last-modified: 2019-08-26
description: BackgroundMycobacterium tuberculosis rapid diagnostic tests (RDTs) are widely employed in routine laboratories and national surveys for detection of rifampicin-resistant (RR)-TB. However, as next-generation sequencing technologies have become more commonplace in research and surveillance programs, RDTs are being increasingly complemented by whole genome sequencing (WGS). While comparison between RDTs is difficult, all RDT results can be derived from WGS data. This can facilitate continuous analysis of RR-TB burden regardless of the data generation technology employed. By converting WGS to RDT results, we enable comparison of data with different formats and sources particularly for low- and middle-income high TB-burden countries that employ different diagnostic algorithms for drug resistance surveys. This allows national TB control programs (NTPs) and epidemiologists to utilize all available data in the setting for improved RR-TB surveillance.MethodsWe developed the Python-based MycTB Genome to Test (MTBGT) tool that transforms WGS-derived data into laboratory-validated results of the primary RDTs—Xpert MTB/RIF, XpertMTB/RIF Ultra, GenoType MDRTBplus v2.0, and GenoscholarNTM+MDRTB II. The tool was validated through RDT results of RR-TB strains with diverse resistance patterns and geographic origins and applied on routine-derived WGS data.ResultsThe MTBGT tool correctly transformed the single nucleotide polymorphism (SNP) data into the RDT results and generated tabulated frequencies of the RDT probes as well as rifampicin-susceptible cases. The tool supplemented the RDT probe reactions output with the RR-conferring mutation based on identified SNPs. The MTBGT tool facilitated continuous analysis of RR-TB and Xpert probe reactions from different platforms and collection periods in Rwanda.ConclusionOverall, the MTBGT tool allows low- and middle-income countries to make sense of the increasingly generated WGS in light of the readily available RDT results, and assess whether currently implemented RDTs adequately detect RR-TB in their setting. With its feature to transform WGS to RDT results and facilitate continuous RR-TB data analysis, the MTBGT tool may bridge the gap between and among data from periodic surveys, continuous surveillance, research, and routine tests, and may be integrated within the national information system for use by the NTP and epidemiologists to improve setting-specific RR-TB control. The MTBGT source code and accompanying documentation are available at https://github.com/KamelaNg/MTBGT.
creator: Kamela C. S. Ng
creator: Jean Claude S. Ngabonziza
creator: Pauline Lempens
creator: Bouke C. de Jong
creator: Frank van Leth
creator: Conor J. Meehan
uri: https://doi.org/10.7717/peerj.7564
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2019 Ng et al.

title: The association between evidence of a predator threat and responsiveness to alarm calls in Western Australian magpies (Cracticus tibicen dorsalis)
link: https://peerj.com/articles/7572
last-modified: 2019-08-26
description: Alarm calls are a widespread form of antipredator defence and being alerted to the presence of predators by the alarm calls of conspecifics is considered one of the benefits of group living. However, while social information can allow an individual to gain additional information, it can also at times be inaccurate or irrelevant. Such variation in the accuracy of social information is predicted to select for receivers to discriminate between sources of social information. In this study, we used playback experiments to determine whether Western Australian magpies (Cracticus tibicen dorsalis) respond to the predator information associated with alarm calls. Magpies were exposed to the alarm calls of two group members that differed in the threat associated with the alarm call: one call was played in the presence of a predator model while the other was not—in order to establish differences in the predator information provided by each caller. We then played back the alarm calls of the same group members in the absence of the predator model to determine whether magpies responded differently to signallers in response to the previous association between the alarm call and a predator threat. We found that receivers showed significantly greater levels of responsiveness to signallers that previously gave alarm calls in the appropriate context. Thus, the accuracy of threat-based information influenced subsequent receiver response.
creator: Annabel Silvestri
creator: Kate Morgan
creator: Amanda R. Ridley
uri: https://doi.org/10.7717/peerj.7572
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2019 Silvestri et al.

title: Cell proliferation controls body size growth, tentacle morphogenesis, and regeneration in hydrozoan jellyfish Cladonema pacificum
link: https://peerj.com/articles/7579
last-modified: 2019-08-26
description: Jellyfish have existed on the earth for around 600 million years and have evolved in response to environmental changes. Hydrozoan jellyfish, members of phylum Cnidaria, exist in multiple life stages, including planula larvae, vegetatively-propagating polyps, and sexually-reproducing medusae. Although free-swimming medusae display complex morphology and exhibit increase in body size and regenerative ability, their underlying cellular mechanisms are poorly understood. Here, we investigate the roles of cell proliferation in body-size growth, appendage morphogenesis, and regeneration using Cladonema pacificum as a hydrozoan jellyfish model. By examining the distribution of S phase cells and mitotic cells, we revealed spatially distinct proliferating cell populations in medusae, uniform cell proliferation in the umbrella, and clustered cell proliferation in tentacles. Blocking cell proliferation by hydroxyurea caused inhibition of body size growth and defects in tentacle branching, nematocyte differentiation, and regeneration. Local cell proliferation in tentacle bulbs is observed in medusae of two other hydrozoan species, Cytaeis uchidae and Rathkea octopunctata, indicating that it may be a conserved feature among hydrozoan jellyfish. Altogether, our results suggest that hydrozoan medusae possess actively proliferating cells and provide experimental evidence regarding the role of cell proliferation in body-size control, tentacle morphogenesis, and regeneration.
creator: Sosuke Fujita
creator: Erina Kuranaga
creator: Yu-ichiro Nakajima
uri: https://doi.org/10.7717/peerj.7579
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2019 Fujita et al.

title: Transgenerational effects of UV-B radiation on egg size, fertilization, hatching and larval size of sea urchins Strongylocentrotus intermedius
link: https://peerj.com/articles/7598
last-modified: 2019-08-26
description: Transgenerational effects are important for phenotypic plasticity and adaptation of marine invertebrates in the changing ocean. Ultraviolet-B (UV-B) radiation is an increasing threat to marine invertebrates. For the first time, we reported positive and negative transgenerational effects of UV-B radiation on egg size, fertilization, hatchability and larval size of a marine invertebrate. Strongylocentrotus intermedius exposed to UV-B radiation showed positive transgenerational effects and adaptation on egg size, hatching rate and post-oral arm length of larvae. Negative transgenerational effects were found in body length, stomach length and stomach width of larvae whose parents were exposed to UV-B radiation. Sires probably play important roles in transgenerational effects of UV-B. The present study provides valuable information into transgenerational effects of UV-B radiation on fitness related traits of sea urchins (at least Strongylocentrotus intermedius).
creator: Jingyun Ding
creator: Lingling Zhang
creator: Jiangnan Sun
creator: Dongtao Shi
creator: Xiaomei Chi
creator: Mingfang Yang
creator: Yaqing Chang
creator: Chong Zhao
uri: https://doi.org/10.7717/peerj.7598
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2019 Ding et al.

title: Metabolic alterations in pea leaves during arbuscular mycorrhiza development
link: https://peerj.com/articles/7495
last-modified: 2019-08-23
description: Arbuscular mycorrhiza (AM) is known to be a mutually beneficial plant-fungal symbiosis; however, the effect of mycorrhization is heavily dependent on multiple biotic and abiotic factors. Therefore, for the proper employment of such plant-fungal symbiotic systems in agriculture, a detailed understanding of the molecular basis of the plant developmental response to mycorrhization is needed. The aim of this work was to uncover the physiological and metabolic alterations in pea (Pisum sativum L.) leaves associated with mycorrhization at key plant developmental stages. Plants of pea cv. Finale were grown in constant environmental conditions under phosphate deficiency. The plants were analyzed at six distinct time points, which corresponded to certain developmental stages of the pea: I: 7 days post inoculation (DPI) when the second leaf is fully unfolded with one pair of leaflets and a simple tendril; II: 21 DPI at first leaf with two pairs of leaflets and a complex tendril; III: 32 DPI when the floral bud is enclosed; IV: 42 DPI at the first open flower; V: 56 DPI when the pod is filled with green seeds; and VI: 90–110 DPI at the dry harvest stage. Inoculation with Rhizophagus irregularis had no effect on the fresh or dry shoot weight, the leaf photochemical activity, accumulation of chlorophyll a, b or carotenoids. However, at stage III (corresponding to the most active phase of mycorrhiza development), the number of internodes between cotyledons and the youngest completely developed leaf was lower in the inoculated plants than in those without inoculation. Moreover, inoculation extended the vegetation period of the host plants, and resulted in increase of the average dry weight per seed at stage VI. The leaf metabolome, as analyzed with GC-MS, included about three hundred distinct metabolites and showed a strong correlation with plant age, and, to a lesser extent, was influenced by mycorrhization. Metabolic shifts influenced the levels of sugars, amino acids and other intermediates of nitrogen and phosphorus metabolism. The use of unsupervised dimension reduction methods showed that (i) at stage II, the metabolite spectra of inoculated plants were similar to those of the control, and (ii) at stages IV and V, the leaf metabolic profiles of inoculated plants shifted towards the profiles of the control plants at earlier developmental stages. At stage IV the inoculated plants exhibited a higher level of metabolism of nitrogen, organic acids, and lipophilic compounds in comparison to control plants. Thus, mycorrhization led to the retardation of plant development, which was also associated with higher seed biomass accumulation in plants with an extended vegetation period. The symbiotic crosstalk between host plant and AM fungi leads to alterations in several biochemical pathways the details of which need to be elucidated in further studies.
creator: Oksana Y. Shtark
creator: Roman K. Puzanskiy
creator: Galina S. Avdeeva
creator: Andrey P. Yurkov
creator: Galina N. Smolikova
creator: Vladislav V. Yemelyanov
creator: Marina S. Kliukova
creator: Alexey L. Shavarda
creator: Anastasiia A. Kirpichnikova
creator: Aleksandr I. Zhernakov
creator: Alexey M. Afonin
creator: Igor A. Tikhonovich
creator: Vladimir A. Zhukov
creator: Maria F. Shishova
uri: https://doi.org/10.7717/peerj.7495
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2019 Shtark et al.

title: The complete mitochondrial genome of Pyxicephalus adspersus: high gene rearrangement and phylogenetics of one of the world’s largest frogs
link: https://peerj.com/articles/7532
last-modified: 2019-08-23
description: The family Pyxicephalidae including two subfamilies (Cacosterninae and Pyxicephalinae) is an ecologically important group of frogs distributed in sub-Saharan Africa. However, its phylogenetic position among the Anura has remained uncertain. The present study determined the complete mitochondrial genome sequence of Pyxicephalus adspersus, the first representative mitochondrial genome from the Pyxicephalinae, and reconstructed the phylogenetic relationships within Ranoidae using 10 mitochondrial protein-coding genes of 59 frog species. The P. adspersus mitochondrial genome showed major gene rearrangement and an exceptionally long length that is not shared with other Ranoidae species. The genome is 24,317 bp in length, and contains 15 protein-coding genes (including extra COX3 and Cyt b genes), four rRNA genes (including extra 12S rRNA and 16S rRNA genes), 29 tRNA genes (including extra tRNALeu(UAG), tRNALeu(UUR), tRNAThr, tRNAPro, tRNAPhe, tRNAVal, tRNAGln genes) and two control regions (CRs). The Dimer-Mitogenome and Tandem duplication and random loss models were used to explain these gene arrangements. Finally, both Bayesian inference and maximum likelihood analyses supported the conclusion that Pyxicephalidae was monophyletic and that Pyxicephalidae was the sister clade of (Petropedetidae + Ptychadenidae).
creator: Yin-Yin Cai
creator: Shi-Qi Shen
creator: Li-Xu Lu
creator: Kenneth B. Storey
creator: Dan-Na Yu
creator: Jia-Yong Zhang
uri: https://doi.org/10.7717/peerj.7532
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2019 Cai et al.

title: Identification of a native Bacillus thuringiensis strain from Sri Lanka active against Dipel-resistant Plutella xylostella
link: https://peerj.com/articles/7535
last-modified: 2019-08-23
description: BackgroundBiopesticides based on strains of the bacterium Bacillus thuringiensis (Bt) are used globally for effective and environmentally friendly pest control. The most serious threat to the sustainable use of these microbial pesticides is the development of resistance on targeted pests. Populations of Plutella xylostella (diamondback moth) have evolved field resistance to Bt pesticides at diverse locations worldwide. Discovery of novel Bt strains with varied toxin profiles that overcome resistance is one of the strategies to increase sustainability of Bt pesticides against P. xylostella. In this study, we report isolation and characterization of a Bt strain named AB1 from Sri Lanka displaying toxicity towards larvae of P. xylostella resistant to the commercial Bt pesticide Dipel.MethodsStrains of Bt from diverse environments in Sri Lanka were evaluated for protein crystal production through Differential Interference Contrast (DIC) microscopic examination, and for insecticidal activity against P. xylostella in bioassays. The genome of the AB1 strain was sequenced by Hiseq Illumina sequencing to identify the insecticidal genes present in the genome and nano liquid chromatography followed by tandem mass spectrometry (nanoLC/MS/MS) of purified crystal proteins of AB1 was performed to identify the expressed insecticidal proteins. Multilocus sequence typing and Gyrase B gene sequence analyses were performed to identify the phylogenetic origin of the AB1 strain.ResultsThe AB1 strain was identified as producing high levels of bipyramidal crystals and displaying insecticidal activity against susceptible and Dipel-resistant strains of P. xylostella. Multilocus sequence typing and phylogenetic analysis of the Gyrase B gene identified that AB1 belongs to the B. thuringiensis subsp. aizawai serotype. Comparative analysis of genomic and proteomic data showed that among the insecticidal protein coding genes annotated from the AB1 genome (cry1Aa, cry1Ca, cry1Da, cry1Ia, cry2Ab and cry9), Cry1Ca and Cry1Da toxins represented most of the toxin fraction in parasporal crystals from AB1. Overall findings warrant further development of B. thuringiensis subsp. aizawai AB1 strain as a pesticide to control P. xylostella.
creator: Rashini Yasara Baragamaarachchi
creator: Jayanetti Koralage Ramani Radhika Samarasekera
creator: Ovitigala Vithanage Don Sisira Jagathpriya Weerasena
creator: Kurt Lamour
creator: Juan Luis Jurat-Fuentes
uri: https://doi.org/10.7717/peerj.7535
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2019 Baragamaarachchi et al.

title: RFRP3 influences basal lamina degradation, cellular death, and progesterone secretion in cultured preantral ovarian follicles from the domestic cat
link: https://peerj.com/articles/7540
last-modified: 2019-08-23
description: The hypothalamic neuropeptide RFRP3 can suppress hypothalamic GnRH neuron activation and inhibit gonadotropin release from the anterior pituitary. RFRP3 is also produced locally in the ovary and can inhibit steroidogenesis and follicle development in many vertebrates. However, almost nothing is known about the presence and regulatory action of RFRP3 in gonads of any carnivore species. Such knowledge is important for developing captive breeding programs for endangered carnivores and for inhibiting reproduction in feral species. Using the domestic cat as a model, our objectives were to (1) demonstrate the expression of feline RFRP3 (fRFRP3) and its receptor in the cat ovary and (2) assess the influence of fRFRP3 on ovarian follicle integrity, survival, and steroidogenesis in vitro. We first confirmed that fRFRP3 and its receptors (NPFFR1 and NPFFR2) were expressed in cat ovaries by sequencing PCR products from ovarian RNA. We then isolated and cultured preantral ovarian follicles in the presence of 10 or 1 µM fRFRP3 + FSH (1 µg/mL). We recorded the percentage of morphologically viable follicles (basal lamina integrity) over 8 days and calculated percentage survival of follicles on Day 8 (using fluorescent markers for cell survival and death). Last, we quantified progesterone accumulation in media. 10 µM fRFRP3 had no observable effect on viability, survival, or steroid production compared to follicles exposed to only FSH. However, 1 µM fRFRP3 decreased the percentage of morphologically viable follicles and the percentage of surviving follicles on Day 8. At the same time, 1 µM fRFRP3 increased the accumulation of progesterone in media. Our study shows, for the first time, direct action of RFRP3 on the follicle as a functional unit, and it is the first in a carnivore species. More broadly, our results support a conserved, inhibitory action of RFRP3 on ovarian follicle development and underscore the importance of comparative functional studies.
creator: Kathryn Wilsterman
creator: George E. Bentley
creator: Pierre Comizzoli
uri: https://doi.org/10.7717/peerj.7540
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2019 Wilsterman et al.

title: Gradual, temperature-induced change of secondary sexual characteristics in Trichogramma pretiosum infected with parthenogenesis-inducing Wolbachia
link: https://peerj.com/articles/7567
last-modified: 2019-08-23
description: Intersex is an intermediate stage of sexual differentiation in insects. Determining intersex morphology and the cause of its production will aid in the understanding of the mechanism of sexual differentiation in insects. In this paper, Wolbachia-infected Trichogramma pretiosum (T. preW+) that shows thelytokous parthenogenesis were used as subjects. In order to determine the causes of the T. preW+ intersex and the influence of parental generation temperature on gradual changes in secondary masculinization in intersex offspring, we examined the occurrence of intersex offspring (F1 and F2 generation) after the parental generations were treated with high temperature (27, 29, 31, and 33 °C) and described the external morphology of the intersexes. The results showed that the T. preW+ parental generation temperature is positively correlated with the probability of intersex offspring. The probability of F1 intersex is significantly higher than that of F2 intersex in different high temperature. The degree of secondary masculinization in T. preW+ intersexes increases as parental generation temperature increases. In addition, our study first identified 11 intersex types in T. preW+ and found that the primary and secondary sexual characteristics showed a regular distribution. We also found that the D type and H type of intersex have the highest frequency of appearance. The external genitalia of most intersexes were female, and only three intersex types have male external genitalia. Conclusions were ultimately obtained: Wolbachia is a direct factor that causes the occurrence of intersexes, while high temperature is an indirect factor that determines the external morphology of intersexes. The effects of high temperature on T. preW+ intersexes is passed through the parental generation to offspring, and this maternal effect weakens as the number of generations increases. In T. preW+ intersex individuals, most exhibit female primary sexual characteristics, and secondary sexual characteristics exhibit signs of masculinization.
creator: Su-fang Ning
creator: Jin-cheng Zhou
creator: Quan-quan Liu
creator: Qian Zhao
creator: Hui Dong
uri: https://doi.org/10.7717/peerj.7567
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2019 Ning et al.

title: Visual search characteristics of precise map reading by orienteers
link: https://peerj.com/articles/7592
last-modified: 2019-08-23
description: This article compares the differences in eye movements between orienteers of different skill levels on map information searches and explores the visual search patterns of orienteers during precise map reading so as to explore the cognitive characteristics of orienteers’ visual search. We recruited 44 orienteers at different skill levels (experts, advanced beginners, and novices), and recorded their behavioral responses and eye movement data when reading maps of different complexities. We found that the complexity of map (complex vs. simple) affects the quality of orienteers’ route planning during precise map reading. Specifically, when observing complex maps, orienteers of higher competency tend to have a better quality of route planning (i.e., a shorter route planning time, a longer gaze time, and a more concentrate distribution of gazes). Expert orienteers demonstrated obvious cognitive advantages in the ability to find key information. We also found that in the stage of route planning, expert orienteers and advanced beginners first pay attention to the checkpoint description table. The expert group extracted information faster, and their attention was more concentrated, whereas the novice group paid less attention to the checkpoint description table, and their gaze was scattered. We found that experts regarded the information in the checkpoint description table as the key to the problem and they give priority to this area in route decision making. These results advance our understanding of professional knowledge and problem solving in orienteering.
creator: Yang Liu
uri: https://doi.org/10.7717/peerj.7592
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2019 Liu