bluuebunny/crossref_metadata_2025_split huggingface dataset:
The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis
Authors: Hu Lisong , Xu Zhongping , Wang Maojun , Fan Rui , Yuan Daojun , Wu Baoduo , Wu Huasong , Qin Xiaowei , Yan Lin , Tan Lehe , Sim Soonliang , Li Wen , Saski Christopher A , Daniell Henry , Wendel Jonathan F. , Lindsey Keith , Zhang Xianlong , Hao Chaoyun , Jin Shuangxia 
Published: October 2019

AbstractBlack pepper (Piper nigrum), dubbed the ‘King of Spices’ and ‘Black Gold’, is one of the most widely used spices. Here, we present its reference genome assembly by integrating PacBio, 10x Chromium, BioNano DLS optical mapping, and Hi-C mapping technologies. The 761.2 Mb sequences (45 scaffolds with an N50 of 29.8 Mb) are assembled into 26 pseudochromosomes. A phylogenomic analysis of representative plant genomes places magnoliids as sister to the monocots-eudicots clade and indicates that black pepper has diverged from the shared Laurales-Magnoliales lineage approximately 180 million years ago. Comparative genomic analyses reveal specific gene expansions in the glycosyltransferase, cytochrome P450, shikimate hydroxycinnamoyl transferase, lysine decarboxylase, and acyltransferase gene families. Comparative transcriptomic analyses disclose berry-specific upregulated expression in representative genes in each of these gene families. These data provide an evolutionary perspective and shed light on the metabolic processes relevant to the molecular basis of species-specific piperine biosynthesis.
Bypassing stroke-damaged neural pathways via a neural interface induces targeted cortical adaptation
Authors: Kato Kenji , Sawada Masahiro , Nishimura Yukio 
Published: October 2019

AbstractRegaining the function of an impaired limb is highly desirable in paralyzed individuals. One possible avenue to achieve this goal is to bridge the interrupted pathway between preserved neural structures and muscles using a brain–computer interface. Here, we demonstrate that monkeys with subcortical stroke were able to learn to use an artificial cortico-muscular connection (ACMC), which transforms cortical activity into electrical stimulation to the hand muscles, to regain volitional control of a paralysed hand. The ACMC induced an adaptive change of cortical activities throughout an extensive cortical area. In a targeted manner, modulating high-gamma activity became localized around an arbitrarily-selected cortical site controlling stimulation to the muscles. This adaptive change could be reset and localized rapidly to a new cortical site. Thus, the ACMC imparts new function for muscle control to connected cortical sites and triggers cortical adaptation to regain impaired motor function after stroke.
Super-resolution imaging of fluorescent dipoles via polarized structured illumination microscopy
Authors: Zhanghao Karl , Chen Xingye , Liu Wenhui , Li Meiqi , Liu Yiqiong , Wang Yiming , Luo Sha , Wang Xiao , Shan Chunyan , Xie Hao , Gao Juntao , Chen Xiaowei , Jin Dayong , Li Xiangdong , Zhang Yan , Dai Qionghai , Xi Peng 
Published: October 2019

AbstractFluorescence polarization microscopy images both the intensity and orientation of fluorescent dipoles and plays a vital role in studying molecular structures and dynamics of bio-complexes. However, current techniques remain difficult to resolve the dipole assemblies on subcellular structures and their dynamics in living cells at super-resolution level. Here we report polarized structured illumination microscopy (pSIM), which achieves super-resolution imaging of dipoles by interpreting the dipoles in spatio-angular hyperspace. We demonstrate the application of pSIM on a series of biological filamentous systems, such as cytoskeleton networks and λ-DNA, and report the dynamics of short actin sliding across a myosin-coated surface. Further, pSIM reveals the side-by-side organization of the actin ring structures in the membrane-associated periodic skeleton of hippocampal neurons and images the dipole dynamics of green fluorescent protein-labeled microtubules in live U2OS cells. pSIM applies directly to a large variety of commercial and home-built SIM systems with various imaging modality.
Cetylpyridinium chloride produces increased zeta-potential on Salmonella Typhimurium cells, a mechanism of the pathogen’s inactivation
Authors: Yegin Yagmur , Oh Jun K. , Akbulut Mustafa , Taylor Thomas 
Published: October 2019

AbstractCetylpyridinium chloride (CPC) is a quaternary ammonium sanitizer approved for fresh poultry animal carcass sanitization from microbial human pathogens, such as Salmonella enterica. Nonetheless, the interactions of CPC with Salmonella cells, and the mechanism of the sanitizer’s neutralization by lecithin remains largely unknown. This study aimed to investigate the interaction of CPC with lecithin and Salmonella Typhimurium to determine the interactions of the sanitizer and neutralizer impacting the bacterium’s survival. Application of 0.8% CPC is proposed to produce loss of microbial membrane integrity with loss of electrostatic repulsion between individual cells, resulting in the eventual emulsification of membrane lipids with cytoplasmic contents leakage. Our findings point to a two-phase interaction between CPC and lecithin impacting S. Typhimurium survival. The first consists of electrostatic attraction and charge neutralization between oppositely charged components of pathogen cell and CPC. The second involves formation of aggregates between sanitizer and pathogen, or between sanitizer, pathogen membrane lipids, and lecithin.
Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials
Authors: Högfors-Rönnholm Eva , Lopez-Fernandez Margarita , Christel Stephan , Brambilla Diego , Huntemann Marcel , Clum Alicia , Foster Brian , Foster Bryce , Roux Simon , Palaniappan Krishnaveni , Varghese Neha , Mukherjee Supratim , Reddy T. B. K. , Daum Chris , Copeland Alex , Chen I-Min A. , Ivanova Natalia N. , Kyrpides Nikos C. , Harmon-Smith Miranda , Eloe-Fadrosh Emiley A. , Lundin Daniel , Engblom Sten , Dopson Mark 
Published: October 2019

AbstractNatural sulfide rich deposits are common in coastal areas worldwide, including along the Baltic Sea coast. When artificial drainage exposes these deposits to atmospheric oxygen, iron sulfide minerals in the soils are rapidly oxidized. This process turns the potential acid sulfate soils into actual acid sulfate soils and mobilizes large quantities of acidity and leachable toxic metals that cause severe environmental problems. It is known that acidophilic microorganisms living in acid sulfate soils catalyze iron sulfide mineral oxidation. However, only a few studies regarding these communities have been published. In this study, we sampled the oxidized actual acid sulfate soil, the transition zone where oxidation is actively taking place, and the deepest un-oxidized potential acid sulfate soil. Nucleic acids were extracted and 16S rRNA gene amplicons, metagenomes, and metatranscriptomes generated to gain a detailed insight into the communities and their activities. The project will be of great use to microbiologists, environmental biologists, geochemists, and geologists as there is hydrological and geochemical monitoring from the site stretching back for many years.
Dual-defect-modified graphitic carbon nitride with boosted photocatalytic activity under visible light
Authors: Katsumata Hideyuki , Higashi Fumiya , Kobayashi Yuya , Tateishi Ikki , Furukawa Mai , Kaneco Satoshi 
Published: October 2019

AbstractThe development of photocatalysts that efficiently degrade organic pollutants is an important environmental-remediation objective. To that end, we report a strategy for the ready fabrication of oxygen-doped graphitic carbon nitride (CN) with engendered nitrogen deficiencies. The addition of KOH and oxalic acid during the thermal condensation of urea led to a material that exhibits a significantly higher pseudo-first-order rate constant for the degradation of bisphenol A (BPA) (0.0225 min−1) compared to that of CN (0.00222 min−1). The enhanced photocatalytic activity for the degradation of BPA exhibited by the dual-defect-modified CN (Bt-OA-CN) is ascribable to a considerable red-shift in its light absorption compared to that of CN, as well as its modulated energy band structure and more-efficient charge separation. Furthermore, we confirmed that the in-situ-formed cyano groups in the Bt-OA-CN photocatalyst act as strong electron-withdrawing groups that efficiently separate and transfer photo-generated charge carriers to the surface of the photocatalyst. This study provides novel insight into the in-situ dual-defect strategy for g-C3N4, which is extendable to the modification of other photocatalysts; it also introduces Bt-OA-CN as a potential highly efficient visible-light-responsive photocatalyst for use in environmental-remediation applications.
Localized Mechanical Actuation using pn Junctions
Authors: Kanygin Mikhail , Joy Abbin Perunnilathil , Bahreyni Behraad 
Published: October 2019

AbstractWe are reporting on the fabrication and characterization of microscale electromechanical actuators driven by the internal forces induced within the depletion region of a typical pn junction. Depletion region actuators operate based on the modulation of the interactions of the internal electric field and the net space charge within the depletion region of a pn junction by an external potential. In terms of performance, depletion region actuators fall between electrostatic actuators, where a physical gap separates the charges on two electrodes, and piezoelectric actuators, where the separation between the charges is on the order of lattice constants of the material. An analytic model of depletion region actuator response to an applied potential is developed and verified experimentally. The prototype micro-mechanical device utilized the local stresses produced by the depletion region actuators to generate mechanical vibrations at frequencies far below the resonance frequencies of the structure. A laser Doppler vibrometer was used to measure and compare the displacements and vibration patterns caused by the depletion region and electrostatic actuators. Utilizing depletion region actuators neither requires etching of narrow gaps, which is technically challenging nor is there a need for introducing piezoelectric materials into the fabrication process flow. The simple operating principle and the possibility of exploiting the technique for various optimized linear or nonlinear actuation at small scales provide opportunities for precise electro-mechanical transduction for micro- and nano-mechanical devices. These actuators are therefore suited for the co-fabrication of micro- and nano-mechanical systems and microelectronic circuits. Additionally, the produced strains depend only on the depletion region specifications and the excitation voltage and do not scale with device dimensions. As such, depletion region actuators can be candidates for efficient nanoscale electromechanical actuation.
Isolation and characterization of an atypical LEA gene (IpLEA) from Ipomoea pes-caprae conferring salt/drought and oxidative stress tolerance
Authors: Zheng Jiexuan , Su Huaxiang , Lin Ruoyi , Zhang Hui , Xia Kuaifei , Jian Shuguang , Zhang Mei 
Published: October 2019

AbstractLate embryogenesis abundant (LEA) proteins belong to a large family that exists widely in plants and is mainly involved in desiccation processes during plant development or in the response to abiotic stresses. Here, we reported on an atypical LEA gene (IpLEA) related to salt tolerance from Ipomoea pes-caprae L. (Convolvulaceae). Sequence analysis revealed that IpLEA belongs to the LEA_2 (PF03168) group. IpLEA was shown to have a cytoplasmic localization pattern. Quantitative reverse transcription PCR analysis showed that IpLEA was widely expressed in different organs of the I. pes-caprae plants, and the expression levels increased following salt, osmotic, oxidative, freezing, and abscisic acid treatments. Analysis of the 1,495 bp promoter of IpLEA identified distinct cis-acting regulatory elements involved in abiotic stress. Induction of IpLEA improved Escherichia coli growth performance compared with the control under abiotic stresses. To further assess the function of IpLEA in plants, transgenic Arabidopsis plants overexpressing IpLEA were generated. The IpLEA-overexpressing Arabidopsis seedlings and adult plants showed higher tolerance to salt and drought stress than the wild-type. The transgenic plants also showed higher oxidative stress tolerance than the wild-type Arabidopsis. Furthermore, the expression patterns of a series of stress-responsive genes were affected. The results indicate that IpLEA is involved in the plant response to salt and drought, probably by mediating water homeostasis or by acting as a reactive oxygen species scavenger, thereby influencing physiological processes under various abiotic stresses in microorganisms and plants.
Pentagamavunon-1 (PGV-1) inhibits ROS metabolic enzymes and suppresses tumor cell growth by inducing M phase (prometaphase) arrest and cell senescence
Authors: Lestari Beni , Nakamae Ikuko , Yoneda-Kato Noriko , Morimoto Tsumoru , Kanaya Shigehiko , Yokoyama Takashi , Shionyu Masafumi , Shirai Tsuyoshi , Meiyanto Edy , Kato Jun-ya 
Published: October 2019

AbstractWe previously showed that curcumin, a phytopolyphenol found in turmeric (Curcuma longa), targets a series of enzymes in the ROS metabolic pathway, induces irreversible growth arrest, and causes apoptosis. In this study, we tested Pentagamavunon-1 (PGV-1), a molecule related to curcumin, for its inhibitory activity on tumor cells in vitro and in vivo. PGV-1 exhibited 60 times lower GI50 compared to that of curcumin in K562 cells, and inhibited the proliferation of cell lines derived from leukemia, breast adenocarcinoma, cervical cancer, uterine cancer, and pancreatic cancer. The inhibition of growth by PGV-1 remained after its removal from the medium, which suggests that PGV-1 irreversibly prevents proliferation. PGV-1 specifically induced prometaphase arrest in the M phase of the cell cycle, and efficiently induced cell senescence and cell death by increasing intracellular ROS levels through inhibition of ROS-metabolic enzymes. In a xenograft mouse model, PGV-1 had marked anti-tumor activity with little side effects by oral administration, whereas curcumin rarely inhibited tumor formation by this administration. Therefore, PGV-1 is a potential therapeutic to induce tumor cell apoptosis with few side effects and low risk of relapse.
Normal tension glaucoma-like degeneration of the visual system in aged marmosets
Authors: Noro Takahiko , Namekata Kazuhiko , Kimura Atsuko , Azuchi Yuriko , Hashimoto Nanako , Moriya-Ito Keiko , Komaki Yuji , Lee Chia-Ying , Okahara Norio , Guo Xiaoli , Harada Chikako , Kim Euido , Nakano Tadashi , Tsuneoka Hiroshi , Inoue Takashi , Sasaki Erika , Tokuno Hironobu , Harada Takayuki 
Published: October 2019

AbstractThe common marmoset (Callithrix jacchus) is a non-human primate that provides valuable models for neuroscience and aging research due to its anatomical similarities to humans and relatively short lifespan. This study was carried out to examine whether aged marmosets develop glaucoma, as seen in humans. We found that 11% of the aged marmosets presented with glaucoma-like characteristics; this incident rate is very similar to that in humans. Magnetic resonance imaging showed a significant volume loss in the visual cortex, and histological analyses confirmed the degeneration of the lateral geniculate nuclei and visual cortex in the affected marmosets. These marmosets did not have elevated intraocular pressure, but showed an increased oxidative stress level, low cerebrospinal fluid (CSF) pressure, and low brain-derived neurotrophic factor (BDNF) and TrkB expression in the retina, optic nerve head and CSF. Our findings suggest that marmosets have potential to provide useful information for the research of eye and the visual system.
Scalable Genome Assembly through Parallel de Bruijn Graph Construction for Multiple k-mers
Authors: Mahadik Kanak , Wright Christopher , Kulkarni Milind , Bagchi Saurabh , Chaterji Somali 
Published: October 2019

AbstractRemarkable advancements in high-throughput gene sequencing technologies have led to an exponential growth in the number of sequenced genomes. However, unavailability of highly parallel and scalable de novo assembly algorithms have hindered biologists attempting to swiftly assemble high-quality complex genomes. Popular de Bruijn graph assemblers, such as IDBA-UD, generate high-quality assemblies by iterating over a set of k-values used in the construction of de Bruijn graphs (DBG). However, this process of sequentially iterating from small to large k-values slows down the process of assembly. In this paper, we propose ScalaDBG, which metamorphoses this sequential process, building DBGs for each distinct k-value in parallel. We develop an innovative mechanism to “patch” a higher k-valued graph with contigs generated from a lower k-valued graph. Moreover, ScalaDBG leverages multi-level parallelism, by both scaling up on all cores of a node, and scaling out to multiple nodes simultaneously. We demonstrate that ScalaDBG completes assembling the genome faster than IDBA-UD, but with similar accuracy on a variety of datasets (6.8X faster for one of the most complex genome in our dataset).
RNA-Seq analysis of ileocecal valve and peripheral blood from Holstein cattle infected with Mycobacterium avium subsp. paratuberculosis revealed dysregulation of the CXCL8/IL8 signaling pathway
Authors: Alonso-Hearn Marta , Canive Maria , Blanco-Vazquez Cristina , Torremocha Rosana , Balseiro Ana , Amado Javier , Varela-Martinez Endika , Ramos Ricardo , Jugo Begoña M. , Casais Rosa 
Published: October 2019

AbstractParatuberculosis is chronic granulomatous enteritis of ruminants caused by Mycobacterium avium subsp. paratuberculosis (MAP). Whole RNA-sequencing (RNA-Seq) is a promising source of novel biomarkers for early MAP infection and disease progression in cattle. Since the blood transcriptome is widely used as a source of biomarkers, we analyzed whether it recapitulates, at least in part, the transcriptome of the ileocecal valve (ICV), the primary site of MAP colonization. Total RNA was prepared from peripheral blood (PB) and ICV samples, and RNA-Seq was used to compare gene expression between animals with focal or diffuse histopathological lesions in gut tissues versus control animals with no detectable signs of infection. Our results demonstrated both shared, and PB and ICV-specific gene expression in response to a natural MAP infection. As expected, the number of differentially expressed (DE) genes was larger in the ICV than in the PB samples. Among the DE genes in the PB and ICV samples, there were some common genes irrespective of the type of lesion including the C-X-C motif chemokine ligand 8 (CXCL8/IL8), apolipoprotein L (APOLD1), and the interferon inducible protein 27 (IFI27). The biological processes (BP) enriched in the PB gene expression profiles from the cows with diffuse lesions included the killing of cells of other organism, defense response, immune response and the regulation of neutrophil chemotaxis. Two of these BP, the defense and immune response, were also enriched in the ICV from the cows with diffuse lesions. Metabolic analysis of the DE genes revealed that the N-glycan biosynthesis, bile secretion, one-carbon pool by folate and purine metabolism were significantly enriched in the ICV from the cows with focal lesions. In the ICV from cows with diffuse lesions; the valine, leucine and isoleucine degradation route, purine metabolism, vitamin digestion and absorption and the cholesterol routes were enriched. Some of the identified DE genes, BP and metabolic pathways will be studied further to develop novel diagnostic tools, vaccines and immunotherapeutics.
The effects of soil phosphorus and zinc availability on plant responses to mycorrhizal fungi: a physiological and molecular assessment
Authors: Nguyen Thi Diem , Cavagnaro Timothy R. , Watts-Williams Stephanie J. 
Published: October 2019

AbstractThe positive effects of arbuscular mycorrhizal fungi (AMF) have been demonstrated for plant biomass, and zinc (Zn) and phosphorus (P) uptake, under soil nutrient deficiency. Additionally, a number of Zn and P transporter genes are affected by mycorrhizal colonisation or implicated in the mycorrhizal pathway of uptake. However, a comprehensive study of plant physiology and gene expression simultaneously, remains to be undertaken. Medicago truncatula was grown at different soil P and Zn availabilities, with or without inoculation of Rhizophagus irregularis. Measures of biomass, shoot elemental concentrations, mycorrhizal colonisation, and expression of Zn transporter (ZIP) and phosphate transporter (PT) genes in the roots, were taken. Mycorrhizal plants had a greater tolerance of both P and Zn soil deficiency; there was also evidence of AMF protecting plants against excessive Zn accumulation at high soil Zn. The expression of all PT genes was interactive with both P availability and mycorrhizal colonisation. MtZIP5 expression was induced both by AMF and soil Zn deficiency, while MtZIP2 was down-regulated in mycorrhizal plants, and up-regulated with increasing soil Zn concentration. These findings provide the first comprehensive physiological and molecular picture of plant-mycorrhizal fungal symbiosis with regard to soil P and Zn availability. Mycorrhizal fungi conferred tolerance to soil Zn and P deficiency and this could be linked to the induction of the ZIP transporter gene MtZIP5, and the PT gene MtPT4.
MDT-28/PLIN-1 mediates lipid droplet-microtubule interaction via DLC-1 in Caenorhabditis elegans
Authors: Xie Kang , Zhang Peng , Na Huimin , Liu Yangli , Zhang Hong , Liu Pingsheng 
Published: October 2019

AbstractEctopic lipid accumulation in lipid droplets (LD) has been linked to many metabolic diseases. In this study, DHS-3::GFP was used as a LD marker in C. elegans and a forward genetic screen was carried out to find novel LD regulators. There were 140 mutant alleles identified which were divided into four phenotypic categories: enlarged, aggregated, aggregated and small, and decreased. After genetic mapping, mutations in three known LD regulatory genes (maoc-1, dhs-28, daf-22) and a peroxisome-related gene (acox-3) were found to enlarge LDs, demonstrating the reliability of using DHS-3 as a living marker. In the screen, the cytoskeleton protein C27H5.2 was found to be involved in LD aggregation, as was the LD resident/structure-like protein, MDT-28/PLIN-1. Using yeast two-hybrid screening and pull-down assays, MDT-28/PLIN-1 was found to bind to DLC-1 (dynein light chain). Fluorescence imaging confirmed that MDT-28/PLIN-1 mediated the interaction between DHS-3 labeled LDs and DLC-1 labeled microtubules. Furthermore, MDT-28/PLIN-1 was directly bound to DLC-1 through its amino acids 1–210 and 275–415. Taken together, our results suggest that MDT-28/PLIN-1 is involved in the regulation of LD distribution through its interaction with microtubule-related proteins.