bluuebunny/crossref_metadata_2025 huggingface dataset:
Design of a unidirectional water valve in Tillandsia
Authors: Raux Pascal S. , Gravelle Simon , Dumais Jacques
Published: January 2020

The bromeliad Tillandsia landbeckii thrives in the Atacama desert of Chile using the fog captured by specialized leaf trichomes to satisfy its water needs. However, it is still unclear how the trichome of T. landbeckii and other Tillandsia species is able to absorb fine water droplets during intermittent fog events while also preventing evaporation when the plant is exposed to the desert’s hyperarid conditions. Here, we explain how a 5800-fold asymmetry in water conductance arises from a clever juxtaposition of a thick hygroscopic wall and a semipermeable membrane. While absorption is achieved by osmosis of liquid water, evaporation under dry external conditions shifts the liquid-gas interface forcing water to diffuse through the thick trichome wall in the vapor phase. We confirm this mechanism by fabricating artificial composite membranes mimicking the trichome structure. The reliance on intrinsic material properties instead of moving parts makes the trichome a promising basis for the development of microfluidics valves.
Mutational signatures in tumours induced by high and low energy radiation in Trp53 deficient mice
Authors: Rose Li Yun , Halliwill Kyle D. , Adams Cassandra J. , Iyer Vivek , Riva Laura , Mamunur Rashid , Jen Kuang-Yu , del Rosario Reyno , Fredlund Erik , Hirst Gillian , Alexandrov Ludmil B. , Adams David , Balmain Allan
Published: January 2020

Ionising radiation (IR) is a recognised carcinogen responsible for cancer development in patients previously treated using radiotherapy, and in individuals exposed as a result of accidents at nuclear energy plants. However, the mutational signatures induced by distinct types and doses of radiation are unknown. Here, we analyse the genetic architecture of mammary tumours, lymphomas and sarcomas induced by high (56Fe-ions) or low (gamma) energy radiation in mice carrying Trp53 loss of function alleles. In mammary tumours, high-energy radiation is associated with induction of focal structural variants, leading to genomic instability and Met amplification. Gamma-radiation is linked to large-scale structural variants and a point mutation signature associated with oxidative stress. The genomic architecture of carcinomas, sarcomas and lymphomas arising in the same animals are significantly different. Our study illustrates the complex interactions between radiation quality, germline Trp53 deficiency and tissue/cell of origin in shaping the genomic landscape of IR-induced tumours.
Nickel-catalyzed allylic carbonylative coupling of alkyl zinc reagents with tert-butyl isocyanide
Authors: Weng Yangyang , Zhang Chenhuan , Tang Zaiquan , Shrestha Mohini , Huang Wenyi , Qu Jingping , Chen Yifeng
Published: January 2020

Transition metal-catalyzed carbonylation with carbon nucleophiles is one of the most prominent methods to construct ketones, which are highly versatile motifs prevalent in a variety of organic compounds. In comparison to the well-established palladium catalytic system, the nickel-catalyzed carbonylative coupling is much underdeveloped due to the strong binding affinity of CO to nickel. By leveraging easily accessible tert-butyl isocyanide as the CO surrogate, we present a nickel-catalyzed allylic carbonylative coupling with alkyl zinc reagent, allowing for the practical and straightforward preparation of synthetically important β,γ-unsaturated ketones in a linear-selective fashion with excellent trans-selectivity under mild conditions. Moreover, the undesired polycarbonylation process which is often encountered in palladium chemistry could be completely suppressed. This nickel-based method features excellent functional group tolerance, even including the active aryl iodide functionality to allow the orthogonal derivatization of β,γ-unsaturated ketones. Preliminary mechanistic studies suggest that the reaction proceeds via a π-allylnickel intermediate.
Extending the coherence of a quantum dot hybrid qubit
Authors: Thorgrimsson Brandur , Kim Dohun , Yang Yuan-Chi , Smith L. W. , Simmons C. B. , Ward Daniel R. , Foote Ryan H. , Corrigan J. , Savage D. E. , Lagally M. G. , Friesen Mark , Coppersmith S. N. , Eriksson M. A.
Published: January 2020

Identifying and ameliorating dominant sources of decoherence are important steps in understanding and improving quantum systems. Here, we show that the free induction decay time ($$T_2^*$$T2*) and the Rabi decay rate (ΓRabi) of the quantum dot hybrid qubit can be increased by more than an order of magnitude by appropriate tuning of the qubit parameters and operating points. By operating in the spin-like regime of this qubit, and choosing parameters that increase the qubit’s resilience to charge noise (which we show is presently the limiting noise source for this qubit), we achieve a Ramsey decay time $$T_2^*$$T2* of 177 ns and a Rabi decay time 1/ΓRabi exceeding 1 μs. We find that the slowest ΓRabi is limited by fluctuations in the Rabi frequency induced by charge noise and not by fluctuations in the qubit energy itself.
An Optimised Protocol Harnessing Laser Capture Microdissection for Transcriptomic Analysis on Matched Primary and Metastatic Colorectal Tumours
Authors: Ong Chin-Ann J. , Tan Qiu Xuan , Lim Hui Jun , Shannon Nicholas B. , Lim Weng Khong , Hendrikson Josephine , Ng Wai Har , Tan Joey W. S. , Koh Kelvin K. N. , Wasudevan Seettha D. , Ng Cedric C. Y. , Rajasegaran Vikneswari , Lim Tony Kiat Hon , Ong Choon Kiat , Kon Oi Lian , Teh Bin Tean , Tan Grace H. C. , Chia Claramae Shulyn , Soo Khee Chee , Teo Melissa C. C.
Published: January 2020

Generation of large amounts of genomic data is now feasible and cost-effective with improvements in next generation sequencing (NGS) technology. Ribonucleic acid sequencing (RNA-Seq) is becoming the preferred method for comprehensively characterising global transcriptome activity. Unique to cytoreductive surgery (CRS), multiple spatially discrete tumour specimens could be systematically harvested for genomic analysis. To facilitate such downstream analyses, laser capture microdissection (LCM) could be utilized to obtain pure cell populations. The aim of this protocol study was to develop a methodology to obtain high-quality expression data from matched primary tumours and metastases by utilizing LCM to isolate pure cellular populations. We demonstrate an optimized LCM protocol which reproducibly delivered intact RNA used for RNA sequencing and quantitative polymerase chain reaction (qPCR). After pathologic annotation of normal epithelial, tumour and stromal components, LCM coupled with cDNA library generation provided for successful RNA sequencing. To illustrate our framework’s potential to identify targets that would otherwise be missed with conventional bulk tumour sequencing, we performed qPCR and immunohistochemical technical validation to show that the genes identified were truly expressed only in certain sub-components. This study suggests that the combination of matched tissue specimens with tissue microdissection and NGS provides a viable platform to unmask hidden biomarkers and provides insight into tumour biology at a higher resolution.
Synchronization of the Normal Human Peripheral Immune System: A Comprehensive Circadian Systems Immunology Analysis
Authors: Beam Craig A. , Wasserfall Clive , Woodwyk Alyssa , Akers McKenzie , Rauch Heather , Blok Thomas , Mason Patrice , Vos Duncan , Perry Daniel , Brusko Todd , Peakman Mark , Atkinson Mark
Published: January 2020

In this study, we sought to fill an important gap in fundamental immunology research by conducting a comprehensive systems immunology analysis of daily variation in the normal human peripheral immune system. Although variation due to circadian rhythmicity was not a significant source of variation in daily B-cell levels or any CD4+ functional subset, it accounted for more than 25% of CD4+ regulatory T-cell variation and over 50% of CD8+ central memory variation. Circadian rhythmicity demonstrated phase alignment within functional phenotypes. In addition, we observed that previously-described mechanistic relationships can also appear in the peripheral system as phase shifting in rhythmic patterns. We identified a set of immune factors which are ubiquitously correlated with other factors and further analysis also identified a tightly-correlated “core” set whose relational structure persisted after analytically removing circadian-related variation. This core set consisted of CD8+ and its subpopulations and the NK population. In sum, the peripheral immune system can be conceptualized as a dynamic, interconnected wave-field repeating its pattern on a daily basis. Our data provide a comprehensive inventory of synchronization and correlation within this wave-field and we encourage use of our data to discover unknown mechanistic relationships which can then be tested in the laboratory.
Adverse events associated with peanut oral immunotherapy in children – a systematic review and meta-analysis
Authors: Grzeskowiak Luke E. , Tao Billy , Knight Emma , Cohen-Woods Sarah , Chataway Timothy
Published: January 2020

While peanut oral immunotherapy (POIT) represents a promising treatment for peanut allergies in children, safety concerns remain a common barrier to widespread adoption. We aimed to systematically assess available evidence to determine the risk and frequency of adverse events occurring during POIT, and examine study-level characteristics associated with their occurrence and severity. A systematic search of MEDLINE, EMBASE, and Web of Science was conducted through April 2019. Controlled and non-controlled studies evaluating POIT were eligible. Twenty-seven studies, involving 1488 subjects, were included. Adverse events to POIT were common and led to treatment discontinuation in 6.6% of children (95% CI 4.4–9.0; 27 studies, I2 = 48.7%). Adverse events requiring treatment with epinephrine occurred among 7.6% (4.5–11.4; 26 studies, I2 = 75.5%) of participants, at a rate of 2.0 per 10,000 doses (0.8–3.7; 15 studies, I2 = 64.4). Use of a rush treatment phase and targeting a higher maintenance dose were associated with a higher risk and frequency of epinephrine use, while using co-treatments in addition to POIT was associated with a lower risk of treatment discontinuation due to adverse events. While adverse events to POIT are common, this study provides promising explorative evidence that certain modifications to existing treatment protocols could significantly improve treatment outcomes.
Small temperature variations are a key regulator of reproductive growth and assimilate storage in oil palm (Elaeis guineensis)
Authors: Tani Naoki , Abdul Hamid Zubaidah Aimi , Joseph Natra , Sulaiman Othman , Hashim Rokiah , Arai Takamitsu , Satake Akiko , Kondo Toshiaki , Kosugi Akihiko
Published: January 2020

Oil palm is an important crop for global vegetable oil production, and is widely grown in the humid tropical regions of Southeast Asia. Projected future climate change may well threaten palm oil production. However, oil palm plantations currently produce large amounts of unutilised biological waste. Oil palm stems – which comprise two-thirds of the waste - are especially relevant because they can contain high levels of non-structural carbohydrates (NSC) that can serve as feedstock for biorefineries. The NSC in stem are also considered a potent buffer to source-sink imbalances. In the present study, we monitored stem NSC levels and female reproductive growth. We then applied convergent cross mapping (CCM) to assess the causal relationship between the time-series. Mutual causal relationships between female reproductive growth and the stem NSC were detected, with the exception of a relationship between female reproductive organ growth and starch levels. The NSC levels were also influenced by long-term cumulative temperature, with the relationship showing a seven-month time lag. The dynamic between NSC levels and long-term cumulative rainfall showed a shorter time lag. The lower temperatures and higher cumulative rainfall observed from October to December identify this as a period with maximum stem NSC stocks.
Antinflammatory, antioxidant, and behavioral effects induced by administration of growth hormone-releasing hormone analogs in mice
Authors: Recinella Lucia , Chiavaroli Annalisa , Orlando Giustino , Ferrante Claudio , Marconi Guya Diletta , Gesmundo Iacopo , Granata Riccarda , Cai Renzhi , Sha Wei , Schally Andrew V. , Brunetti Luigi , Leone Sheila
Published: January 2020

Growth hormone-releasing hormone (GHRH) antagonist MIA-690 and GHRH agonist MR-409, previously synthesized and developed by us have demonstrated potent antitumor effects. However, little is known about the effects of these analogs on brain functions. We investigated the potential antinflammatory and antioxidant effects of GHRH antagonist MIA-690 and GHRH agonist MR-409, on isolated mouse prefrontal cortex specimens treated with lipopolysaccharide (LPS). Additionally, we studied their effects on emotional behavior after chronic in vivo treatment. Ex vivo, MIA-690 and MR-409 inhibited LPS-induced inflammatory and pro-oxidative markers. In vivo, both MIA-690 and MR-409 induced anxiolytic and antidepressant-like effects, increased norepinephrine and serotonin levels and decreased nuclear factor-kB, tumor necrosis factor-α and interleukin-6 gene expression in prefrontal cortex. Increased nuclear factor erythroid 2–related factor 2 expression was also found in mice treated with MIA-690 and MR-409. MIA-690 showed higher efficacy in inhibiting all tested inflammatory and oxidative markers. In addition, MR-409 induced a down regulation of the gene and protein expression of pituitary-type GHRH-receptor in prefrontal cortex of mice after 4 weeks of treatment at 5 µg/day. In conclusion, our results demonstrate anxiolytic and antidepressant-like effects of GHRH analogs that could involve modulatory effects on monoaminergic signaling, inflammatory and oxidative status.
Mass spectrometry imaging reveals differential localization of natural sunscreens in the mantle of the giant clam Tridacna crocea
Authors: Goto-Inoue Naoko , Sato Tomohiko , Morisasa Mizuki , Yamashita Hiroshi , Maruyama Tadashi , Ikeda Hiroki , Sakai Ryuichi
Published: January 2020

Giant clams have evolved to maximize sunlight utilization by their photosymbiotic partners, while affording them protection from harmful ultraviolet (UV) light. The presence of UV absorbing substances in the mantle is thought to be critical for light protection; however, the exact localization of such compounds remains unknown. Here, we applied a combination of UV liquid chromatography (LC), LC-mass spectrometry (MS), MS imaging, and UV micrography to localize UV absorbing substances in the giant clam Tridacna crocea. LC-MS analysis revealed that the animal contained three classes of mycosporines: progenitor, primary, and secondary mycosporines. MS imaging revealed that primary and secondary mycosporines were localized in the outermost layer of the mantle; whereas progenitor mycosporines were distributed throughout the mantle tissue. These findings were consistent with the results of UV micrography, which revealed that the surface layer of the mantle absorbed UV light at 320 ± 10 nm. This is the first report indicating that progenitor and primary mycosporines are metabolized to secondary mycosporines by the giant clam and that they are differentially localized in the surface layer of the mantle to protect the animal from UV light.
Multiscale bone quality analysis in osteoarthritic knee joints reveal a role of the mechanosensory osteocyte network in osteophytes
Authors: Rabelo Gustavo Davi , vom Scheidt Annika , Klebig Felix , Hemmatian Haniyeh , Citak Mustafa , Amling Michael , Busse Björn , Jähn Katharina
Published: January 2020

Osteophytes - bony outgrowths on joint structures - are found in healthy individuals but are specifically present in late osteoarthritis (OA). Osteophyte development and function is not well understood, yet biomechanical stimuli are thought to be critical. Bone adapts to mechanical forces via the cellular network of osteocytes. The involvement of osteocytes in osteophyte formation and maturation has not been unravelled. Forty-three osteophytes from tibias of 23 OA patients (65 ± 9 years) were analysed. The trabecular bone structure of osteophytes presented with fewer trabeculae of lower bone mineral density compared to subchondral bone. We identified 40% early stage and 60% late stage osteophytes that significantly differed in their trabecular bone characteristics. Osteophyte bone revealed a higher number of osteocytes and a lower number of empty osteocyte lacunae per bone area than the subchondral bone. We found that OA osteophytes consist of younger bone material comprised of woven and lamellar bone with the capacity to develop into a late stage osteophyte potentially via the involvement of the osteocyte network. Our analysis of OA osteophytes implies a transition from woven to lamellar bone as in physiological bone growth within a pathological joint. Therefore, osteophyte development and growth present a valuable research subject when aiming to investigate the osteogenic signalling cascade.
Separating the two polarities of the POLO contacts of an 26.1%-efficient IBC solar cell
Authors: Hollemann C. , Haase F. , Rienäcker M. , Barnscheidt V. , Krügener J. , Folchert N. , Brendel R. , Richter S. , Großer S. , Sauter E. , Hübner J. , Oestreich M. , Peibst R.
Published: January 2020

By applying an interdigitated back contacted solar cell concept with poly-Si on oxide passivating contacts an efficiency of 26.1% was achieved recently. In this paper the impact of the implemented initially intrinsic poly-Si region between p-type poly-Si and n-type poly-Si regions is investigated. Two recombination paths are identified: The recombination at the interface between the initially intrinsic poly-Si and the wafer as well as the recombination across the resulting p(i)n diode on the rear side which is aimed to be reduced by introducing an initially intrinsic region. By using test structures, it is demonstrated that the width of the initially intrinsic region ((i) poly-Si region) has a strong influence on the recombination current through the p(i)n diode and that this initially intrinsic region needs to be about 30 μm wide to sufficiently reduce the recombination across the p(i)n diode. Lateral and depth-resolved time of flight secondary ion mass spectrometry analysis shows that the high-temperature annealing step causes a strong lateral inter-diffusion of donor and acceptor atoms into the initially intrinsic region. This diffusion has a positive impact on the passivation quality at the c-Si/SiOx/i poly-Si interface and is thus essential for achieving an independently confirmed efficiency of 26.1% with 30 μm-wide initially intrinsic poly-Si regions.
Lithium for schizophrenia: supporting evidence from a 12-year, nationwide health insurance database and from Akt1-deficient mouse and cellular models
Authors: Luo Da-Zhong , Chang Chia-Yuan , Huang Tsung-Ren , Studer Vincent , Wang Tsu-Wei , Lai Wen-Sung
Published: January 2020

Accumulating evidence suggests AKT1 and DRD2-AKT-GSK3 signaling involvement in schizophrenia. AKT1 activity is also required for lithium, a GSK3 inhibitor, to modulate mood-related behaviors. Notably, GSK3 inhibitor significantly alleviates behavioral deficits in Akt1−/− female mice, whereas typical/atypical antipsychotics have no effect. In agreement with adjunctive therapy with lithium in treating schizophrenia, our data mining indicated that the average utilization rates of lithium in the Taiwan National Health Insurance Research Database from 2002 to 2013 are 10.9% and 6.63% in inpatients and outpatients with schizophrenia, respectively. Given that lithium is commonly used in clinical practice, it is of great interest to evaluate the effect of lithium on alleviating Akt1-related deficits. Taking advantage of Akt1+/− mice to mimic genetic deficiency in patients, behavioral impairments were replicated in female Akt1+/− mice but were alleviated by subchronic lithium treatment for 13 days. Lithium also effectively alleviated the observed reduction in phosphorylated GSK3α/β expression in the brains of Akt1+/− mice. Furthermore, inhibition of Akt expression using an Akt1/2 inhibitor significantly reduced neurite length in P19 cells and primary hippocampal cell cultures, which was also ameliorated by lithium. Collectively, our findings implied the therapeutic potential of lithium and the importance of the AKT1-GSK3 signaling pathway.
Pediludiella daitoensis gen. et sp. nov. (Scenedesmaceae, Chlorophyceae), a large coccoid green alga isolated from a Loxodes ciliate
Authors: Hoshina Ryo , Hayakawa Masashi M. , Kobayashi Mayumi , Higuchi Rina , Suzaki Toshinobu
Published: January 2020

Freshwater protists often harbor unicellular green algae within their cells. In ciliates, possibly because of large host cell sizes and the small size of algal coccoids, a single host cell typically contains more than a hundred algal cells. While surveying such algae-bearing protists on Minami Daito Jima Island in Japan, we found a greenLoxodesciliate (Loxodida, Karyorelictea) that contained one or two dozens of very large coccoid algae. We isolated one of these algae and analyzed its characteristics in detail. A small subunit (SSU) rDNA phylogeny indicatedPseudodidymocystisspecies (Scenedesmaceae, Chlorophyceae) to be the taxon closest to the alga, although it was clearly separated from this by 39 or more different sites (inclusive of gaps). SSU rRNA structure analyses indicated that these displacements included eight compensatory base changes (CBCs) and seven hemi-CBCs. We therefore concluded that this alga belongs to a separate genus, and described it asPediludiella daitoensisgen. et sp. nov. The shape of the isolated and culturedP.daitoensiswas nearly spherical and reached up to 30 µm in diameter. Chloroplasts were arranged peripherally and often split and elongated. Cells were often vacuolated and possessed a net-like cytoplasm that resembled a football (soccer ball) in appearance, which was reflected in the genus name.
Cathepsin B overexpression induces degradation of perilipin 1 to cause lipid metabolism dysfunction in adipocytes
Authors: Mizunoe Yuhei , Kobayashi Masaki , Hoshino Shunsuke , Tagawa Ryoma , Itagawa Rei , Hoshino Ayana , Okita Naoyuki , Sudo Yuka , Nakagawa Yoshimi , Shimano Hitoshi , Higami Yoshikazu
Published: January 2020

Obesity, caused by the dysfunction of white adipose tissue (WAT), is reportedly accompanied by exacerbation of lipolysis. Perilipin 1 (PLIN1), which forms a coat around lipid droplets, interacts with several lipolysis proteins to regulate lipolysis. While it is known that perilipin family proteins are degraded in lysosomes, the underlying molecular mechanisms related to the downregulated expression of PLIN1 in obese WAT remain unknown. Recently, we found that lysosomal dysfunction originating from an abnormality of cathepsin B (CTSB), a lysosomal representative protease, occurs in obese WAT. Therefore, we investigated the effect of CTSB alterations on PLIN1 expression in obese WAT. PLIN1 protein disappeared and CTSB protein appeared in the cytoplasm of adipocytes in the early stage of obese WAT. Overexpression of CTSB reduced PLIN1 protein in 3T3L1 adipocytes, and treatment with a CTSB inhibitor significantly recovered this reduction. In addition, CTSB overexpression induced the dysfunction of lipolysis in 3T3L1 adipocytes. Therefore, we concluded that upregulation of CTSB induced the reduction of PLIN1 protein in obese WAT, resulting in lipolysis dysfunction. This suggests a novel pathology of lipid metabolism involving PLIN1 in adipocytes and that CTSB might be a therapeutic candidate molecule for obese WAT.
DNA epigenetic marks are linked to embryo aberrations in amphipods
Authors: Gorokhova Elena , Martella Giulia , Motwani Nisha H. , Tretyakova Natalia Y. , Sundelin Brita , Motwani Hitesh V.
Published: January 2020

Linking exposure to environmental stress factors with diseases is crucial for proposing preventive and regulatory actions. Upon exposure to anthropogenic chemicals, covalent modifications on the genome can drive developmental and reproductive disorders in wild populations, with subsequent effects on the population persistence. Hence, screening of chemical modifications on DNA can be used to provide information on the probability of such disorders in populations of concern. Using a high-resolution mass spectrometry methodology, we identified DNA nucleoside adducts in gravid females of the Baltic amphipods Monoporeia affinis, and linked the adduct profiles to the frequency of embryo malformations in the broods. Twenty-three putative nucleoside adducts were detected in the females and their embryos, and eight modifications were structurally identified using high-resolution accurate mass data. To identify which adducts were significantly associated with embryo malformations, partial least squares regression (PLSR) modelling was applied. The PLSR model yielded three adducts as the key predictors: methylation at two different positions of the DNA (5-methyl-2′-deoxycytidine and N6-methyl-2′-deoxyadenosine) representing epigenetic marks, and a structurally unidentified nucleoside adduct. These adducts predicted the elevated frequency of the malformations with a high classification accuracy (84%). To the best of our knowledge, this is the first application of DNA adductomics for identification of contaminant-induced malformations in field-collected animals. The method can be adapted for a broad range of species and evolve as a new omics tool in environmental health assessment.
The effect of oceanic mesoscale eddies on the looping path of the Kuroshio intrusion in the Luzon Strait
Authors: Yang Qian , Liu Hailong , Lin Pengfei
Published: January 2020

In this study, the effects of oceanic mesoscale eddies on the looping path of the Kuroshio intrusion (KI) were symmetrically investigated by composite analysis using merged satellite data. We found that the mesoscale eddies propagating from the east have a significant impact on the looping path over a time scale of 30–60 days. Cyclonic eddies (CEs) enhance the looping path, but anticyclonic eddies decrease it. We also found that strong eddies do not have strong effects on the looping path. For instance, strong CEs induce the strong surface intrusion of the Kuroshio, but the looping currents are weak due to the presence of the strong Luzon Cold Eddy in the South China Sea, which tends to prevent loop formation. The complicated relationship between eddies and the path of the KI results in a nonsignificant correlation coefficient between the KI and eddy activities in the western Pacific.
A multiplexed gRNA piggyBac transposon system facilitates efficient induction of CRISPRi and CRISPRa in human pluripotent stem cells
Authors: Hazelbaker Dane Z. , Beccard Amanda , Angelini Gabriella , Mazzucato Patrizia , Messana Angelica , Lam Daisy , Eggan Kevin , Barrett Lindy E.
Published: January 2020

CRISPR-Cas9-mediated gene interference (CRISPRi) and activation (CRISPRa) approaches hold promise for functional gene studies and genome-wide screens in human pluripotent stem cells (hPSCs). However, in contrast to CRISPR-Cas9 nuclease approaches, the efficiency of CRISPRi/a depends on continued expression of the dead Cas9 (dCas9) effector and guide RNA (gRNA), which can vary substantially depending on transgene design and delivery. Here, we design and generate new fluorescently labeledpiggyBac(PB) vectors to deliver uniform and sustained expression of multiplexed gRNAs. In addition, we generate hPSC lines harboring AAVS1-integrated, inducible and fluorescent dCas9-KRAB and dCas9-VPR transgenes to allow for accurate quantification and tracking of cells that express both the dCas9 effectors and gRNAs. We then employ these systems to target theTCF4gene in hPSCs and assess expression levels of the dCas9 effectors, individual gRNAs and targeted gene. We also assess the performance of our PB system for single gRNA delivery, confirming its utility for library format applications. Collectively, our results provide proof-of-principle application of a stable, multiplexed PB gRNA delivery system that can be widely exploited to further enable genome engineering studies in hPSCs. Paired with diverse CRISPR tools including our dual fluorescence CRISPRi/a cell lines, this system can facilitate functional dissection of individual genes and pathways as well as larger-scale screens for studies of development and disease.
Young cancer survivors have lower bone mineral density compared with healthy controls: a nationwide population-based study in Korea
Authors: Kim Hyoeun , Yoo Sunmi , Park Seung Guk
Published: January 2020

Direct effects of cancer cells and various cancer treatments can cause bone loss in cancer survivors. The aim of this study was to assess the risk of bone loss in Korean cancer survivors, and the relationship between body composition and bone mineral density (BMD). We hypothesized that cancer survivors would have lower BMD than healthy people, and increased muscle mass has a protective effect on BMD. We measured BMD and body composition in 259 cancer survivors (99 men and 160 women). Subjects were selected from the Korean National Health and Nutrition Survey conducted from 2008 to 2011. Body composition and BMD were measured by dual-energy X-ray absorptiometry. We examined the linear trend of lumbar BMD according to tertiles of lean mass (LM) and fat mass (FM) by linear regression, adjusting for age, alcohol consumption, smoking, exercise, 25-hydroxyvitamin D, height, protein intake, and menopausal status. Cancer survivors under 50 years of age had lower lumbar BMD compared with healthy controls (0.93 ± 0.04 g/cm2 vs. 1.02 ± 0.01 g/cm2, p = 0.032 in males; 0.95 ± 0.02 g/cm2 vs. 0.98 ± 0.01 g/cm2, p = 0.015 in females). Lumbar BMD significantly increased from the lowest to highest tertiles of LM in male (p for trend < 0.001) and marginally significantly increased in female survivors (p for trend = 0.060). In this study of Korean cancer survivors, young survivors were at higher risk of having low lumbar BMD. Higher LM had beneficial effects on BMD in cancer survivors. To prevent osteoporosis and fractures, efforts to increase lean body mass, including bone, are needed for young cancer survivors.
Speed-dependent and mode-dependent modulations of spatiotemporal modules in human locomotion extracted via tensor decomposition
Authors: Takiyama Ken , Yokoyama Hikaru , Kaneko Naotsugu , Nakazawa Kimitaka
Published: January 2020

How the central nervous system (CNS) controls many joints and muscles is a fundamental question in motor neuroscience and related research areas. An attractive hypothesis is the module hypothesis: the CNS controls groups of joints or muscles (i.e., spatial modules) by providing time-varying motor commands (i.e., temporal modules) to the spatial modules rather than controlling each joint or muscle separately. Another fundamental question is how the CNS generates numerous repertoires of movement patterns. One hypothesis is that the CNS modulates the spatial and/or temporal modules depending on the required tasks. It is thus essential to quantify the spatial modules, the temporal modules, and the task-dependent modulation of these modules. Although previous attempts at such quantification have been made, they considered modulation either only in spatial modules or only in temporal modules. These limitations may be attributable to the constraints inherent to conventional methods for quantifying the spatial and temporal modules. Here, we demonstrate the effectiveness of tensor decomposition in quantifying the spatial modules, the temporal modules, and the task-dependent modulation of these modules without such limitations. We further demonstrate that tensor decomposition offers a new perspective on the task-dependent modulation of spatiotemporal modules: in switching from walking to running, the CNS modulates the peak timing in the temporal modules while recruiting more proximal muscles in the corresponding spatial modules.
Aneurysmal subarachnoid haemorrhage: Effect of CRHR1 genotype on mental health-related quality of life
Authors: Vetkas Artur , Prans Ele , Kõks Sulev , Rätsep Tõnu , Asser Toomas
Published: January 2020

Quality of life (QoL) disturbances are common after aneurysmal subarachnoid hemorrhage (aSAH) both in physical and mental health domains and their causes are not clearly understood. Corticotropin-releasing hormone receptor 1 (CRHR1) is involved in stress reactivity and development of mental health disturbances after negative life-events. We performed a retrospective cohort study of long-term QoL outcomes among 125 surgically treated aSAH patients (2001–2013). QoL was assessed with Short Form Health Survey (SF-36) and compared to an age and gender matched general population. Genotyping of CRHR1 single nucleotide polymorphisms was performed (Rs7209436, Rs110402, Rs242924) and their effect on QoL scores was explored. aSAH patients experienced a reduced quality of life in all domains. CRHR1 minor genotype was associated with higher SF-36 mental health (OR = 1.31–1.6, p < 0.05), role-emotional (OR = 1.57, p = 0.04) and vitality scores (OR = 1.31–1.38, p < 0.05). Association of all studied SNP’s with vitality and Rs242924 with mental health scores remained statistically significant after Bonferroni correction. Mental quality of life scores were associated with physical state of patients, antidepressant history and CRHR1 genotype. Predisposition to mental health disturbances after stressful life-events might be associated with reduced mental QoL after aSAH and selected patients could be provided advanced counselling in the recovery phase.
A novel lncRNA as a positive regulator of carotenoid biosynthesis in Fusarium
Authors: Parra-Rivero Obdulia , Pardo-Medina Javier , Gutiérrez Gabriel , Limón M. Carmen , Avalos Javier
Published: January 2020

The fungiFusarium oxysporumandFusarium fujikuroiproduce carotenoids, lipophilic terpenoid pigments of biotechnological interest, with xanthophyll neurosporaxanthin as the main end product. Their carotenoid biosynthesis is activated by light and negatively regulated by the RING-finger protein CarS. Global transcriptomic analysis identified in both species a putative 1-kb lncRNA that we callcarP, referred to asFo-carPandFf-carPin each species, upstream to the genecarSand transcribed from the same DNA strand.Fo-carPandFf-carPare poorly transcribed, but their RNA levels increase incarSmutants. The deletion ofFo-carPorFf-carPin the respective species results in albino phenotypes, with strong reductions in mRNA levels of structural genes for carotenoid biosynthesis and higher mRNA content of thecarSgene, which could explain the low accumulation of carotenoids. Upon alignment,Fo-carPandFf-carPshow 75–80% identity, with short insertions or deletions resulting in a lack of coincident ORFs. Moreover, none of the ORFs found in their sequences have indications of possible coding functions. We conclude thatFo-carPandFf-carPare regulatory lncRNAs necessary for the active expression of the carotenoid genes inFusariumthrough an unknown molecular mechanism, probably related to the control ofcarSfunction or expression.
Targeted metabolomics of pellicle and saliva in children with different caries activity
Authors: Schulz Annika , Lang Roman , Behr Jürgen , Hertel Susann , Reich Marco , Kümmerer Klaus , Hannig Matthias , Hannig Christian , Hofmann Thomas
Published: January 2020

Pellicle is the initial proteinaceous layer that is formed almost instantaneously on all solid surfaces in the oral cavity. It is of essential relevance for any interactions and metabolism on the tooth surface. Up to now, there is no information on the metabolome of this structure. Accordingly, the present study aims to characterise the metabolomic profile ofin-situpellicle in children with different caries activity for the first time in comparison to saliva. Small molecules such as carbohydrates, amino acids, organic acids, and fatty acids, putatively involved in the formation of caries were quantified using mass spectrometry (MS)-based techniques, such as (stable isotope dilution analysis)-ultra-performance liquid chromatography-tandem MS and gas chromatography/electron ionisation-MS. Pellicle and corresponding saliva samples were collected from caries-active, caries-free and caries-rehabilitated 4- to 6-year-old children. The most abundant analytes in pellicle were acetic acid (1.2–10.5 nmol/cm2), propionic acid (0.1–8.5 nmol/cm2), glycine (0.7–3.5 nmol/cm2), serine (0.08–2.3 nmol/cm2), galactose (galactose + mannose; 0.035–0.078 nmol/cm2), lactose (0.002–0.086 nmol/cm2), glucose (0.018–0.953 nmol/cm2), palmitic acid (0.26–2.03 nmol/cm2), and stearic acid (0.34–1.81 nmol/cm2). Significant differences depending on caries activity were detected neither in saliva nor in the corresponding pellicle samples.
Regrowth of zebrafish caudal fin regeneration is determined by the amputated length
Authors: Uemoto Toshiaki , Abe Gembu , Tamura Koji
Published: January 2020

Fish have a high ability to regenerate fins, including the caudal fin. After caudal fin amputation, original bi-lobed morphology is reconstructed during its rapid regrowth. It is still controversial whether positional memory in the blastema cells regulates reconstruction of fin morphology as in amphibian limb regeneration, in which limb blastema cells located at the same proximal-distal level have the same positional identity. We investigated growth period and growth rate in zebrafish caudal fin regeneration. We found that both the growth period and growth rate differed for fin rays that were amputated at the same proximal-distal level, indicating that it takes different periods of time for fin rays to restore their original lengths after straight amputation. We also show that more proximal amputation takes longer period to reconstruct the original morphology/size than more distal amputation. Statistical analysis suggested that both the growth period/rate are determined by amputated length (depth) regardless of the fin ray identity along dorsal-ventral axis. In addition, we suggest the possibility that the structural/physical condition such as width of the fin ray at the amputation site (niche at the stump) may determine the growth period/rate.
Molecular characterization of sarcomatoid clear cell renal cell carcinoma unveils new candidate oncogenic drivers
Authors: Malouf Gabriel G. , Flippot Ronan , Dong Yiyu , Dinatale Renzo G. , Chen Ying-Bei , Su Xiaoping , Compérat Eva , Rouprêt Morgan , Mano Roy , Blum Kyle A. , Yao Hui , Mouawad Roger , Spano Jean-Philippe , Khayat David , Karam Jose A. , Ho Thai H. , Tickoo Satish K. , Russo Paul , Hsieh James J. , Tannir Nizar M. , Hakimi Abraham A.
Published: January 2020

Sarcomatoid clear-cell renal cell carcinomas (sRCC) are associated with dismal prognosis. Genomic alterations associated with sarcomatoid dedifferentiation are poorly characterized. We sought to define the genomic landscape of sRCC and uncover potentially actionable therapeutic targets. We assessed the genomic landscape of sRCC using targeted panel sequencing including patients with microdissected sarcomatoid and epithelial components. Along with common genomic alterations associated with clear-cell histology, we found that Hippo was one of the most frequently altered pathways in these tumours. Hippo alterations were differentially enriched in sRCC compared to non-sRCC. Functional analysis showed that Hippo members mutations were associated with higher nuclear accumulation of YAP/TAZ, core effectors of the Hippo pathway. In a NF2-mutant sRCC model, YAP1 knockdown and NF2 reconstitution suppressed cell proliferation, tumour growth and invasion, both in vitro and in vivo. Overall, we show that Hippo pathway alterations are a feature of sRCC, and enable the exploration of the Hippo pathway as a novel potential therapeutic target.
Improved multiparametric scrape loading-dye transfer assay for a simultaneous high-throughput analysis of gap junctional intercellular communication, cell density and viability
Authors: Dydowiczová Aneta , Brózman Ondřej , Babica Pavel , Sovadinová Iva
Published: January 2020

Gap junctional intercellular communication (GJIC) is a vital cellular process required for maintenance of tissue homeostasis. In vitro assessment of GJIC represents valuable phenotypic endpoint that could be effectively utilized as an integral component in modern toxicity testing, drug screening or biomedical in vitro research. However, currently available methods for quantifying GJIC with higher-throughputs typically require specialized equipment, proprietary software and/or genetically engineered cell models. To overcome these limitations, we present here an innovative adaptation of traditional, fluorescence microscopy-based scrape loading-dye transfer (SL-DT) assay, which has been optimized to simultaneously evaluate GJIC, cell density and viability. This multiparametric method was demonstrated to be suitable for various multiwell microplate formats, which facilitates an automatized image acquisition. The assay workflow is further assisted by an open source-based software tools for batch image processing, analysis and evaluation of GJIC, cell density and viability. Our results suggest that this approach provides a simple, fast, versatile and cost effective way for in vitro high-throughput assessment of GJIC and other related phenotypic cellular events, which could be included into in vitro screening and assessment of pharmacologically and toxicologically relevant compounds.
Experimental and Numerical Sensitivity Assessment of Viscoelasticity for Polymer Composite Materials
Authors: Javidan Mohammad Mahdi , Kim Jinkoo
Published: January 2020

Viscoelastic polymer composites are widely used for vibration control in different fields of engineering like aerospace, mechanical, and structural engineering. The viscoelastic properties of these materials are strain rate-dependent and are highly related to frequency. Yet to date, less attention has been paid to quantifying the effects of these parameters and their interactions on damping properties and providing an approximation method for further applications. In the present research, a series of experimental tests was conducted on a viscoelastic material and the experimental data were numerically analyzed in detail. Sensitivity analyses are usually applied to quantify uncertainty using sampling techniques. However, in this study a method was proposed to derive a closed-form solution using the response surface function and a derivative-based global sensitivity analysis to evaluate the output contribution of each parameter. These effects were quantified and several approximation statistics were provided for future engineering implementations. The computational evaluation conducted in this study gives a detailed insight into the mechanical behavior of viscoelastic materials.
Predicting changes in bee assemblages following state transitions at North American dryland ecotones
Authors: Kazenel Melanie R. , Wright Karen W. , Bettinelli Julieta , Griswold Terry L. , Whitney Kenneth D. , Rudgers Jennifer A.
Published: January 2020

Drylands worldwide are experiencing ecosystem state transitions: the expansion of some ecosystem types at the expense of others. Bees in drylands are particularly abundant and diverse, with potential for large compositional differences and seasonal turnover across ecotones. To better understand how future ecosystem state transitions may influence bees, we compared bee assemblages and their seasonality among sites at the Sevilleta National Wildlife Refuge (NM, USA) that represent three dryland ecosystem types (and two ecotones) of the southwestern U.S. (Plains grassland, Chihuahuan Desert grassland, and Chihuahuan Desert shrubland). Using passive traps, we caught bees during two-week intervals from March–October, 2002–2014. The resulting dataset included 302 bee species and 56 genera. Bee abundance, composition, and diversity differed among ecosystems, indicating that future state transitions could alter bee assemblage composition in our system. We found strong seasonal bee species turnover, suggesting that bee phenological shifts may accompany state transitions. Common species drove the observed trends, and both specialist and generalist bee species were indicators of ecosystem types or months; these species could be sentinels of community-wide responses to future shifts. Our work suggests that predicting the consequences of global change for bee assemblages requires accounting for both within-year and among-ecosystem variation.
Wurtzite AlGaAs Nanowires
Authors: Leandro L. , Reznik R. , Clement J. D. , Repän J. , Reynolds M. , Ubyivovk E. V. , Shtrom I. V. , Cirlin G. , Akopian N.
Published: January 2020

Semiconducting nanowires, unlike bulk, can be grown in both wurtzite and zincblende crystal phases. This unique feature allows for growth and investigation of technologically important and previously unexplored materials, such as wurtzite AlGaAs. Here we grow a series of wurtzite AlGaAs nanowires with Al content varying from 0.1 to 0.6, on silicon substrates and through a comparative structural and optical analysis we experimentally derive, for the first time, the formula for the bandgap of wurtzite AlGaAs. Moreover, bright emission and short lifetime of our nanowires suggest that wurtzite AlGaAs is a direct bandgap material.
Systematic impacts of chronic unpredictable mild stress on metabolomics in rats
Authors: Geng Chunmei , Guo Yujin , Wang Changshui , Liao Dehua , Han Wenxiu , Zhang Jing , Jiang Pei
Published: January 2020

Depression is the most common disabling psychiatric disease, with a high prevalence and mortality. Chronic unpredictable mild stress (CUMS) is a well-accepted method used to mimic clinical depression. Recent evidence has consistently suggested that the cumulative effects of CUMS could lead to allostatic overload in the body, thereby inducing systemic disorders; however, there are no previous systematic metabonomics studies on the main stress-targeted tissues associated with depression. A non-targeted gas chromatography–mass spectrometry (GC–MS) approach was used to identify metabolic biomarkers in the main stress-targeted tissues (serum, heart, liver, brain, and kidney) in a CUMS model of depression. Male Sprague–Dawley rats were randomly allocated to the CUMS group (n = 8) or a control group (n = 8). Multivariate analysis was performed to identify the metabolites that were differentially expressed between the two groups. There were 10, 10, 9, 4, and 7 differentially expressed metabolites in the serum, heart, liver, brain and kidney tissues, respectively, between the control and CUMS groups. These were linked to nine different pathways related to the metabolism of amino acids, lipids, and energy. In summary, we provided a comprehensive understanding of metabolic alterations in the main stress-targeted tissues, helping to understand the potential mechanisms underlying depression.