Scientific Reports

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ISSN / EISSN : 2045-2322 / 2045-2322
Current Publisher: Springer Science and Business Media LLC (10.1038)
Former Publisher: , Springer Science and Business Media LLC (10.1038) , Springer Science and Business Media LLC (10.1038) , Springer Science and Business Media LLC (10.1038) , Springer Science and Business Media LLC (10.1038) Springer Science and Business Media LLC (10.1038)
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Iryna Zaytseva, Aleksander Abaloszew, Bruno C. Camargo, Yevgen Syryanyy, Marta Z. Cieplak
Scientific Reports, Volume 11, pp 1-2; doi:10.1038/s41598-021-87426-1

Abstract:
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Seema Sahay, Luis Robledo-Arratia, Katarzyna Glowacka, Meetu Gupta
Scientific Reports, Volume 11, pp 1-15; doi:10.1038/s41598-021-86401-0

Abstract:
Little is known about the interactive effects of exogenous nitric oxide (NO) and abscisic acid (ABA) on nitrogen (N) metabolism and related changes at molecular and biochemical levels under drought stress. The present study highlights the independent and combined effect of NO and ABA (grouped as “nitrate agonists”) on expression profiles of representative key genes known to be involved in N-uptake and assimilation, together with proline metabolism, N–NO metabolism enzyme’s activity and nutrient content in polyethylene glycol (PEG) treated roots of Indian mustard (B. juncea cv. Varuna). Here we report that PEG mediated drought stress negatively inhibited growth performance, as manifested by reduced biomass (fresh and dry weight) production. Total N content and other nitrogenous compounds (NO3 −, NO2 −) were decreased; however, NH4 +, NH4 +/ NO3 − ratio and total free amino acids content were increased. These results were positively correlated with the PEG induced changes in expression of genes and enzymes involved in N-uptake and assimilation. Also, PEG supply lowered the content of macro- and micro-nutrients but proline level and the activity of ∆1-pyrroline-5-carboxylate synthetase increased indicating increased oxidative stress. However, all these responses were reversed upon the exogenous application of nitrate agonists (PEG + NO, PEG + NO + ABA, and PEG + ABA) where NO containing nitrate agonist treatment i.e. PEG + NO was significantly more effective than PEG + ABA in alleviating drought stress. Further, increases in activities of L-arginine dependent NOS-like enzyme and S-nitrosoglutathione reductase were observed under nitrate agonist treatments. This indicates that the balanced endogenous change in NO and ABA levels together during synthesis and degradation of NO mitigated the oxidative stress in Indian mustard seedlings. Overall, our results reveal that NO independently or together with ABA may contribute to improved crop growth and productivity under drought stress.
Ekaterina Stansfield, Philipp Mitteroecker, Sergey Y. Vasilyev, Lauren N. Butaric
Scientific Reports, Volume 11, pp 1-13; doi:10.1038/s41598-021-86830-x

Abstract:
As our human ancestors migrated into Eurasia, they faced a considerably harsher climate, but the extent to which human cranial morphology has adapted to this climate is still debated. In particular, it remains unclear when such facial adaptations arose in human populations. Here, we explore climate-associated features of face shape in a worldwide modern human sample using 3D geometric morphometrics and a novel application of reduced rank regression. Based on these data, we assess climate adaptations in two crucial Upper Palaeolithic human fossils, Sungir and Mladeč, associated with a boreal-to-temperate climate. We found several aspects of facial shape, especially the relative dimensions of the external nose, internal nose and maxillary sinuses, that are strongly associated with temperature and humidity, even after accounting for autocorrelation due to geographical proximity of populations. For these features, both fossils revealed adaptations to a dry environment, with Sungir being strongly associated with cold temperatures and Mladeč with warm-to-hot temperatures. These results suggest relatively quick adaptative rates of facial morphology in Upper Palaeolithic Europe.
Delphine del Marmol, Susanne Holtze, Nadia Kichler, Arne Sahm, Benoit Bihin, Virginie Bourguignon, Sophie Dogné, Karol Szafranski, Thomas Bernd Hildebrandt, Bruno Flamion
Scientific Reports, Volume 11, pp 1-21; doi:10.1038/s41598-021-86967-9

Abstract:
Large amounts of ultra-high molecular weight hyaluronan (HA) have been described as the main cause of cancer resistance in naked mole-rats (Heterocephalus glaber, NMR). Our work examined HA metabolism in these rodents more closely. HA was localized and quantified using HA binding proteins. Its molecular weight was determined using size exclusion chromatography and gel electrophoresis, HA family gene expression using RNAseq analysis, and hyaluronidase activity using zymography. Guinea pigs (Cavia porcellus) and mice (Mus musculus) were used as controls for some experiments. We found that HA localization was similar in NMR, guinea pig, and mouse tissues but NMR had larger amounts and higher molecular weight (maximum, around 2.5 MDa) of HA in serum and almost all tissues tested. We could not find ultra-high molecular weight HA (≥ 4 MDa) in NMR samples, in contrast to previous descriptions. Hyaluronidase-1 had lower expression and activity in NMR than mouse lymph nodes. RNAseq results showed that, among HA family genes, Tnfaip6 and hyaluronidase-3 (Hyal3) were systematically overexpressed in NMR tissues. In conclusion, NMR samples, contrary to expectations, do not harbor ultra-high molecular weight HA, although its amount and average molecular weight are higher in NMR than in guinea pig tissues and serum. Although hyaluronidase expression and activity are lower in NMR than mouse lymph nodes, this not sufficient to explain the presence of high molecular weight HA. A different activity of the NMR HA synthases remains possible. These characteristics, together with extremely high Hyal3 and Tnfaip6 expression, may provide the NMR with a bespoke, and perhaps protective, HA metabolism.
Steven Korevaar, Ruwan Tennakoon, Mark Page, Peter Brotchie, John Thangarajah, Cosmin Florescu, Tom Sutherland, Ning Mao Kam, Alireza Bab-Hadiashar
Scientific Reports, Volume 11, pp 1-10; doi:10.1038/s41598-021-86972-y

Abstract:
Prostate cancer (PCa) is the second most frequent type of cancer found in men worldwide, with around one in nine men being diagnosed with PCa within their lifetime. PCa often shows no symptoms in its early stages and its diagnosis techniques are either invasive, resource intensive, or has low efficacy, making widespread early detection onerous. Inspired by the recent success of deep convolutional neural networks (CNN) in computer aided detection (CADe), we propose a new CNN based framework for incidental detection of clinically significant prostate cancer (csPCa) in patients who had a CT scan of the abdomen/pelvis for other reasons. While CT is generally considered insufficient to diagnose PCa due to its inferior soft tissue characterisation, our evaluations on a relatively large dataset consisting of 139 clinically significant PCa patients and 432 controls show that the proposed deep neural network pipeline can detect csPCa patients at a level that is suitable for incidental detection. The proposed pipeline achieved an area under the receiver operating characteristic curve (ROC-AUC) of 0.88 (95% Confidence Interval: 0.86–0.90) at patient level csPCa detection on CT, significantly higher than the AUCs achieved by two radiologists (0.61 and 0.70) on the same task.
Sarthok Rasique Rahman, Jonathan Cnaani, Lisa N. Kinch, Nick V. Grishin, Heather M. Hines
Scientific Reports, Volume 11, pp 1-12; doi:10.1038/s41598-021-87194-y

Abstract:
Bumble bees exhibit exceptional diversity in their segmental body coloration largely as a result of mimicry. In this study we sought to discover genes involved in this variation through studying a lab-generated mutant in bumble bee Bombus terrestris, in which the typical black coloration of the pleuron, scutellum, and first metasomal tergite is replaced by yellow, a color variant also found in sister lineages to B. terrestris. Utilizing a combination of RAD-Seq and whole-genome re-sequencing, we localized the color-generating variant to a single SNP in the protein-coding sequence of transcription factor cut. This mutation generates an amino acid change that modifies the conformation of a coiled-coil structure outside DNA-binding domains. We found that all sequenced Hymenoptera, including sister lineages, possess the non-mutant allele, indicating different mechanisms are involved in the same color transition in nature. Cut is important for multiple facets of development, yet this mutation generated no noticeable external phenotypic effects outside of setal characteristics. Reproductive capacity was reduced, however, as queens were less likely to mate and produce female offspring, exhibiting behavior similar to that of workers. Our research implicates a novel developmental player in pigmentation, and potentially caste, thus contributing to a better understanding of the evolution of diversity in both of these processes.
Sang-Hoo Cho, Hanbyeol Jang, Heungsoon Im, Donghyeon Lee, Je-Ho Lee, Kenji Watanabe, Takashi Taniguchi, Maeng-Je Seong, Byoung Hun Lee, Kayoung Lee
Scientific Reports, Volume 11, pp 1-9; doi:10.1038/s41598-021-87442-1

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Van der Waals (vdW) heterostructures, consisting of a variety of low-dimensional materials, have great potential use in the design of a wide range of functional devices thanks to their atomically thin body and strong electrostatic tunability. Here, we demonstrate multi-functional indium selenide (InSe)/black phosphorous (BP) heterostructures encapsulated by hexagonal boron nitride. At a positive drain bias (V D), applied on the BP while the InSe is grounded, our heterostructures show an intermediate gate voltage (V BG) regime where the current hardly changes, working as a ternary transistor. By contrast, at a negative V D, the device shows strong negative differential transconductance characteristics; the peak current increases up to ~5 μA and the peak-to-valley current ratio reaches 1600 at V D = −2 V. Four-terminal measurements were performed on each layer, allowing us to separate the contributions of contact resistances and channel resistance. Moreover, multiple devices with different device structures and contacts were investigated, providing insight into the operation principle and performance optimization. We systematically investigated the influence of contact resistances, heterojunction resistance, channel resistance, and the thickness of BP on the detailed operational characteristics at different V D and V BG regimes.
Smritikana Dutta, Anwesha Deb, Prasun Biswas, Sukanya Chakraborty, Suman Guha, Devrani Mitra, Birgit Geist, Anton R. Schäffner, Malay Das
Scientific Reports, Volume 11, pp 1-16; doi:10.1038/s41598-021-87491-6

Abstract:
Bamboos, member of the family Poaceae, represent many interesting features with respect to their fast and extended vegetative growth, unusual, yet divergent flowering time across species, and impact of sudden, large scale flowering on forest ecology. However, not many studies have been conducted at the molecular level to characterize important genes that regulate vegetative and flowering habit in bamboo. In this study, two bamboo FD genes, BtFD1 and BtFD2, which are members of the florigen activation complex (FAC) have been identified by sequence and phylogenetic analyses. Sequence comparisons identified one important amino acid, which was located in the DNA-binding basic region and was altered between BtFD1 and BtFD2 (Ala146 of BtFD1 vs. Leu100 of BtFD2). Electrophoretic mobility shift assay revealed that this alteration had resulted into ten times higher binding efficiency of BtFD1 than BtFD2 to its target ACGT motif present at the promoter of the APETALA1 gene. Expression analyses in different tissues and seasons indicated the involvement of BtFD1 in flower and vegetative development, while BtFD2 was very lowly expressed throughout all the tissues and conditions studied. Finally, a tenfold increase of the AtAP1 transcript level by p35S::BtFD1 Arabidopsis plants compared to wild type confirms a positively regulatory role of BtFD1 towards flowering. However, constitutive expression of BtFD1 had led to dwarfisms and apparent reduction in the length of flowering stalk and numbers of flowers/plant, whereas no visible phenotype was observed for BtFD2 overexpression. This signifies that timely expression of BtFD1 may be critical to perform its programmed developmental role in planta.
Kazutoshi Yoshitake, Atushi Fujiwara, Aiko Matsuura, Masashi Sekino, Motoshige Yasuike, Yoji Nakamura, Reiichiro Nakamichi, Masaaki Kodama, Yumiko Takahama, Akinori Takasuka, et al.
Scientific Reports, Volume 11, pp 1-12; doi:10.1038/s41598-021-86190-6

Abstract:
Many studies have investigated the ability to identify species from environmental DNA (eDNA). However, even when individual species are identified, the accurate estimation of their abundances by traditional eDNA analyses has been still difficult. We previously developed a novel analytical method called HaCeD-Seq (Haplotype Count from eDNA), which focuses on the mitochondrial D-loop sequence. The D-loop is a rapidly evolving sequence and has been used to estimate the abundance of eel species in breeding water. In the current study, we have further improved this method by applying unique molecular identifier (UMI) tags, which eliminate the PCR and sequencing errors and extend the detection range by an order of magnitude. Based on this improved HaCeD-Seq pipeline, we computed the abundance of Pacific bluefin tuna (Thunnus orientalis) in aquarium tanks at the Tokyo Sea Life Park (Kasai, Tokyo, Japan). This tuna species is commercially important but is at high risk of resource depletion. With the developed UMI tag method, 90 out of 96 haplotypes (94%) were successfully detected from Pacific bluefin tuna eDNA. By contrast, only 29 out of 96 haplotypes (30%) were detected when UMI tags were not used. Our findings indicate the potential for conducting non-invasive fish stock surveys by sampling eDNA.
Scientific Reports, Volume 11, pp 1-9; doi:10.1038/s41598-021-87062-9

Abstract:
The purpose of the retrospective study was to investigate the long-term result of implant-induced injury on the adjacent tooth. The subjects of this retrospective study were patients who had received implants and had tooth injury; direct invasion of root (group I), root surface contact (group II), or < 1 mm distance of the implant from the root (group III). Clinical and pathological changes were periodically examined using radiographs and intra-oral examinations. Paired t-tests and chi-square tests were used to evaluate the implant stability quotient (ISQ) of implant and tooth complications, respectively (α = 0.05). A total of 32 implants and teeth in 28 patients were observed for average 122.7 (± 31.7, minimum 86) months. Seven teeth, three of which were subsequently extracted, needed root canal treatment. Finally, 90.6% of the injured teeth remained functional. Complications were significant and varied according to the group, with group I showing higher events than the others. The ISQs increased significantly. One implant in group I resulted in osseointegration failure. The implant survival rate was 96.9%. In conclusion, it was found even when a tooth is injured by an implant, immediate extraction is unnecessary, and the osseointegration of the invading implant is also predictable.
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