bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rebound of Cotton leaf curl Multan virus and its exclusive detection in cotton leaf curl disease outbreak, Punjab (India), 2015
Authors: Datta Sibnarayan , Budhauliya Raghvendra , Das Bidisha , Gopalakrishnan Reji , Sharma Sonika , Chatterjee Soumya , Vanlalhmuaka  , Raju P. Srinivas , Veer Vijay 
Published: December 2017

AbstractCotton leaf curl disease (CLCuD) outbreaks caused by CLCuD associated begomoviruses (CABs) significantly constrain cotton production in India and Pakistan. In comparison to the CABs circulating in Pakistan, molecular epidemiology, evolution and recombination patterns of CABs circulating in India are less studied. In this work, we characterized CAB complex sequences obtained from the most recent outbreak (Punjab, India, 2015), and rigorously analyzed them with reference to GenBank sequences, submitted from India, Pakistan and other neighbouring countries, using contemporary bioinformatics approaches. In this manuscript, we illustrate the detection of a recombinant, phylogenetically distinct clade of Cotton leaf curl Multan virus (CLCuMuV), suggesting rebound of CLCuMuV in this region. Interestingly, we could not detect Cotton leaf curl Kokhran virus-Burewala strain (CLCuKoV-Bu), which was prevalent in this region, until now. Our study thus indicates substitution of the ‘virulent resistance breaking’ CLCuKoV-Bu by the re-emerging CLCuMuV recombinants. Our findings corroborate with that of a very recent study from Pakistan and we here discuss epidemiological links between the CAB complexes reported in these two studies. Taken together, these observations signify a shifting epidemiology of CABs, and seem to correlate with the recent prediction of the ‘third epidemic’ of CLCuD in the Indian subcontinent.
The Human DNA glycosylases NEIL1 and NEIL3 Excise Psoralen-Induced DNA-DNA Cross-Links in a Four-Stranded DNA Structure
Authors: Martin Peter R. , Couvé Sophie , Zutterling Caroline , Albelazi Mustafa S. , Groisman Regina , Matkarimov Bakhyt T. , Parsons Jason L. , Elder Rhoderick H. , Saparbaev Murat K. 
Published: December 2017

AbstractInterstrand cross-links (ICLs) are highly cytotoxic DNA lesions that block DNA replication and transcription by preventing strand separation. Previously, we demonstrated that the bacterial and human DNA glycosylases Nei and NEIL1 excise unhooked psoralen-derived ICLs in three-stranded DNA via hydrolysis of the glycosidic bond between the crosslinked base and deoxyribose sugar. Furthermore, NEIL3 from Xenopus laevis has been shown to cleave psoralen- and abasic site-induced ICLs in Xenopus egg extracts. Here we report that human NEIL3 cleaves psoralen-induced DNA-DNA cross-links in three-stranded and four-stranded DNA substrates to generate unhooked DNA fragments containing either an abasic site or a psoralen-thymine monoadduct. Furthermore, while Nei and NEIL1 also cleave a psoralen-induced four-stranded DNA substrate to generate two unhooked DNA duplexes with a nick, NEIL3 targets both DNA strands in the ICL without generating single-strand breaks. The DNA substrate specificities of these Nei-like enzymes imply the occurrence of long uninterrupted three- and four-stranded crosslinked DNA-DNA structures that may originate in vivo from DNA replication fork bypass of an ICL. In conclusion, the Nei-like DNA glycosylases unhook psoralen-derived ICLs in various DNA structures via a genuine repair mechanism in which complex DNA lesions can be removed without generation of highly toxic double-strand breaks.
Probing the requirement for CD38 in retinoic acid-induced HL-60 cell differentiation with a small molecule dimerizer and genetic knockout
Authors: MacDonald Robert J. , Shrimp Jonathan H. , Jiang Hong , Zhang Lu , Lin Hening , Yen Andrew 
Published: December 2017

AbstractCD38 is an ectoenzyme and receptor with key physiological roles. It metabolizes NAD+to adenosine diphosphate ribose (ADPR) and cyclic ADPR, regulating several processes including calcium signalling. CD38 is both a positive and negative prognostic indicator in leukaemia. In all-transretinoic acid (RA)-induced differentiation of acute promyelocytic leukaemia and HL-60 cells, CD38 is one of the earliest and most prominently upregulated proteins known. CD38 overexpression enhances differentiation, while morpholino- and siRNA-induced knockdown diminishes it. CD38, via Src family kinases and adapters, interacts with a MAPK signalling axis that propels differentiation. Motivated by evidence suggesting the importance of CD38, we sought to determine whether it functions via dimerization. We created a linker based on the suicide substrate arabinosyl-2′-fluoro-2′-deoxy NAD+(F-araNAD+), dimeric F-araNAD+, to induce homodimerization. CD38 homodimerization did not affect RA-induced differentiation. Probing the importance of CD38 further, we created HL-60 cell lines with CRISPR/Cas9-mediated CD38 truncations. Deletion of its enzymatic domain did not affect differentiation. Apart from increased RA-induced CD11b expression, ablation of all but the first six amino acids of CD38 affected neither RA-induced differentiation nor associated signalling. Although we cannot discount the importance of this peptide, our study indicates that CD38 is not necessary for RA-induced differentiation.
Enclaves of genetic diversity resisted Inca impacts on population history
Authors: Barbieri Chiara , Sandoval José R. , Valqui Jairo , Shimelman Aviva , Ziemendorff Stefan , Schröder Roland , Geppert Maria , Roewer Lutz , Gray Russell , Stoneking Mark , Fujita Ricardo , Heggarty Paul 
Published: December 2017

AbstractThe Inca Empire is claimed to have driven massive population movements in western South America, and to have spread Quechua, the most widely-spoken language family of the indigenous Americas. A test-case is the Chachapoyas region of northern Peru, reported as a focal point of Inca population displacements. Chachapoyas also spans the environmental, cultural and demographic divides between Amazonia and the Andes, and stands along the lowest-altitude corridor from the rainforest to the Pacific coast. Following a sampling strategy informed by linguistic data, we collected 119 samples, analysed for full mtDNA genomes and Y-chromosome STRs. We report a high indigenous component, which stands apart from the network of intense genetic exchange in the core central zone of Andean civilization, and is also distinct from neighbouring populations. This unique genetic profile challenges the routine assumption of large-scale population relocations by the Incas. Furthermore, speakers of Chachapoyas Quechua are found to share no particular genetic similarity or gene-flow with Quechua speakers elsewhere, suggesting that here the language spread primarily by cultural diffusion, not migration. Our results demonstrate how population genetics, when fully guided by the archaeological, historical and linguistic records, can inform multiple disciplines within anthropology.
High flux water purification using aluminium hydroxide hydrate gels
Authors: Malekizadeh Ali , Schenk Peer M. 
Published: December 2017

AbstractFiltration of aqueous liquids has wide implications, for example for provision of clean drinking water. Nevertheless, many people still lack access to safe water and suffer from preventable water-borne microbial diseases. This study reports a new ultrafiltration-range separation technology using a gelatinous layer of aluminium hydroxide polyhydrate as a secondary membrane on a retaining fabric that enables simple and cost-effective production of filtered water. Properties include at least 4-fold higher flux rates than currently available membranes, pressure-resistance, impenetrability to filtered particles, easy cleaning by backwashing and simple, cost-effective replacement by gel injection. Depending on the substrate, filtration is achieved through a packed bed of 1–2 nm hydrate gel globules, partly by mechanical straining with a size exclusion of approx. 10 nm and partly by physical adsorption. As a result, filtration of water (e.g. turbid river water) contaminated with colloids and microorganisms, including viruses, yields clear water that is free of measurable particles or detectable microorganisms. However, small water-soluble molecules (salts, sugars, proteins) remain in the filtrate. The findings demonstrate the potential for wide applicability of hydrate gels in high-flux and low-cost water purification devices.
Nonvolatile Bio-Memristor Based on Silkworm Hemolymph Proteins
Authors: Wang Lu , Wen Dianzhong 
Published: December 2017

AbstractThis paper reports the first successful fabrication of an ITO/silkworm hemolymph/Al bio-memristor using silkworm hemolymph as the active layer. Experiments demonstrate that the silkworm hemolymph bio-memristor is a nonvolatile rewritable bipolar memory device with a current switching ratio exceeding 103. The state of the bio-memristor can be retained for more than 104 seconds and remains stable for at least 500 cycles. Tests of 1/f noise have shown that the resistance switching characteristics of the silkworm hemolymph bio-memristor are related to the formation and breaking of conductive filaments, which result from the migration of oxygen ions and the oxidation and reduction of metal cations in the silkworm hemolymph film. The naturally non-toxic silkworm hemolymph offers advantages for human health, environmental protection, and biocompatibility. The proposed nonvolatile rewritable bio-memristor based on silkworm hemolymph possesses great application potential.
Baseline Chloride Levels are Associated with the Incidence of Contrast-Associated Acute Kidney Injury
Authors: Oh Hyung Jung , Kim Sungwon , Park Jung Tak , Kim Sang-Joon , Han Seung Hyeok , Yoo Tae-Hyun , Ryu Dong-Ryeol , Kang Shin-Wook , Chung Yong Eun 
Published: December 2017

AbstractAlthough hypo- and hyperchloremia have been associated with worsening renal outcomes, there has been no study that correlates hypo- and hyperchloremia and the incidence of contrast-associated acute kidney injury (CA-AKI). A total of 13,088 patients with less than 2.0 mg/dL of serum creatinine (Cr) who underwent contrast-enhanced abdominal CT (CECT) were included. Patients were divided into 3 groups based on Cl (the hypo-, normo- and hyperchloremia groups). Patients were also classified by baseline Cr (<1.2; the ‘Normal Cr group’ and 1.2–2.0 mg/dL; the ‘Slightly increased Cr group’). Multivariate logistic regression analysis was used to reveal the association between Cl and CA-AKI. Among patients, 2,525 (19.3%) and 241 (1.8%) patients were classified in the hypo- and hyperchloremia group. The incidence of CA-AKI was significantly lower in the normochloremia group (4.0%) compared to the hypo- (5.4%) and hyperchloremia groups (9.5%). On multivariate logistic regression, hypochloremia was significantly associated with the incidence of CA-AKI compared with normochloremia (1.382, P = 0.002). Moreover, hypochloremia was still significantly associated with the incidence of CA-AKI in ‘Normal Cr group’ compared with normochloremia (1.314, P = 0.015), while hyperchloremia did not show significant association with CA-AKI incidence. In conclusion, hypochloremia might be associated with the incidence of CA-AKI even in patients who have normal-range Cr levels.
A gene expression study of ornamental fin shape in Neolamprologus brichardi, an African cichlid species
Authors: Ahi Ehsan Pashay , Richter Florian , Sefc Kristina M. 
Published: December 2017

AbstractThe diversity of fin morphology within and across fish taxa offers great, but still largely unexplored, opportunities to investigate the proximate mechanisms underlying fin shape variation. Relying on available genetic knowledge brought forth mainly by the comprehensive study of the zebrafish caudal fin, we explored candidate molecular mechanisms for the maintenance and formation of the conspicuously elongated filaments adorning the unpaired fins of the East African “princess cichlid” Neolamprologus brichardi. Via qPCR assays, we detected expression differences of candidate genes between elongated and short regions of intact and regenerating fins. The identified genes include skeletogenic and growth factors (igf2b, fgf3, bmp2 and bmp4), components of the WNT pathway (lef1, wnt5b and wnt10) and a regulatory network determining fin ray segment size and junction (cx43, esco2 and sema3d), as well as other genes with different roles (mmp9, msxb and pea3). Interestingly, some of these genes showed fin specific expression differences which are often neglected in studies of model fish that focus on the caudal fin. Moreover, while the observed expression patterns were generally consistent with zebrafish results, we also detected deviating expression correlations and gene functions.
Epidermal cornification is preceded by the expression of a keratinocyte-specific set of pyroptosis-related genes
Authors: Lachner Julia , Mlitz Veronika , Tschachler Erwin , Eckhart Leopold 
Published: December 2017

AbstractThe homeostasis of the epidermis depends on keratinocyte differentiation and cornification, a mode of programmed cell death that does not elicit inflammation. Here, we report that cornification is associated with the expression of specific genes that control multiple steps of pyroptosis, another form of cell death that involves the processing and release of interleukin-1 family (IL1F) cytokines. Expression levels of pro-inflammatory IL1A and IL1B and of the pyroptotic pore-forming gasdermin (GSDM) D were downregulated during terminal differentiation of human keratinocytesin vitro. By contrast, negative regulators of IL-1 processing, including NLR family pyrin domain containing 10 (NLRP10) and pyrin domain-containing 1 (PYDC1), the anti-inflammatory IL1F members IL-37 (IL1F7) and IL-38 (IL1F10), and GSDMA, were strongly induced in differentiated keratinocytes. In human tissues, these keratinocyte differentiation-associated genes are expressed in the skin at higher levels than in any other organ, and mammalian species, that have lost the epidermal cornification program during evolution, i.e. whales and dolphins, lack homologs of these genes. Together, our results suggest that human epidermal cornification is accompanied by a tight control of pyroptosis and warrant further studies of potential defects in the balance between cornification and pyroptosis in skin pathologies.
Mechanistic Insights into the Reaction of Chlorination of Tryptophan Catalyzed by Tryptophan 7-Halogenase
Authors: Karabencheva-Christova Tatyana G. , Torras Juan , Mulholland Adrian J. , Lodola Alessio , Christov Christo Z. 
Published: December 2017

AbstractTryptophan 7-halogenase catalyzes chlorination of free tryptophan to 7-chlorotryptophan, which is the first step in the antibiotic pyrrolnitrin biosynthesis. Many biologically and pharmaceutically active natural products contain chlorine and thus, an understanding of the mechanism of its introduction into organic molecules is important. Whilst enzyme-catalyzed chlorination is accomplished with ease, it remains a difficult task for the chemists. Therefore, utilizing enzymes in the synthesis of chlorinated organic compounds is important, and providing atomistic mechanistic insights about the reaction mechanism of tryptophan 7-halogenase is vital and timely. In this work, we examined a mechanism for the reaction of tryptophan chlorination, performed by tryptophan 7-halogenase, by calculating potential energy and free energy surfaces using two different Combined Quantum Mechanical/Molecular Mechanical (QM/MM) methods both employing Density Functional Theory (DFT) for the QM region. Both computational strategies agree on the nature of the rate-limiting step and provided close results for the reaction barriers of the two reaction steps. The calculations for both the potential energy and the free energy profiles showed very similar geometric features and hydrogen bonding interactions for the characterized stationary points.
Generation and Analysis of High-Gain Orbital Angular Momentum Vortex Wave Using Circular Array and Parasitic EBG with oblique incidence
Authors: Xi Rui , Liu Haixia , Li Long 
Published: December 2017

AbstractThis paper presents an effective method for high-gain orbital angular momentum (OAM) vortex wave generation based on the integration of a circular antenna array (CAA) with a parasitic electromagnetic band gap (EBG) structure, which is referred to as the EP-CAA. The resonant height of the EBG structure at different oblique incidences is analyzed parametrically based on the defect mode transmission mechanism to achieve reasonable predictions of a consistent 3-dB gain bandwidth with optimal gain enhancement for different OAM modes. The effective radiation aperture of the EP-CAA at oblique incidence is proposed for analytical calculation of the aperture efficiency of the OAM beams (OAM-AE). A Wilkinson power divider (W-PD) is designed to extend the operating bandwidth of the EP-CAA, and the proposed W-PD arrangement is applicable for feasible OAM modes. Fabricated prototypes of the EP-CAA carrying four OAM modes operating at 10 GHz are measured to verify the effectiveness of the theoretical analysis, the maximum realized gain for different OAM modes are confirmed to be enhanced by at least 6 dB in 5% 3-dB gain bandwidth. The divergence angles of different OAM modes can be effectively concentrated using the proposed EP-CAA.
Anatomical evidence for scent guided foraging in the turkey vulture
Authors: Grigg Nathan P. , Krilow Justin M. , Gutierrez-Ibanez Cristian , Wylie Douglas R. , Graves Gary R. , Iwaniuk Andrew N. 
Published: December 2017

AbstractThe turkey vulture (Cathartes aura) is a widespread, scavenging species in the Western Hemisphere that locates carrion by smell. Scent guided foraging is associated with an expansion of the olfactory bulbs of the brain in vertebrates, but no such neuroanatomical data exists for vultures. We provide the first measurements of turkey vulture brains, including the size of their olfactory bulbs and numbers of mitral cells, which provide the primary output of the olfactory bulbs. Comparative analyses show that the turkey vulture has olfactory bulbs that are 4× larger and contain twice as many mitral cells as those of the sympatric black vulture (Coragyps atratus), despite having brains that are 20% smaller. The turkey vulture has the largest olfactory bulbs in absolute terms and adjusted for brain size among birds, but the number of mitral cells is proportional to the size of their olfactory bulbs. The combination of large olfactory bulbs, high mitral cell counts and a greatly enlarged nasal cavity likely reflects a highly sensitive olfactory system. We suggest that this sensitive sense of smell allowed the turkey vulture to colonize biomes that are suboptimal for scavenging birds and become the most widespread vulture species in the world.
All-nanotube stretchable supercapacitor with low equivalent series resistance
Authors: Gilshteyn Evgenia P. , Amanbayev Daler , Anisimov Anton S. , Kallio Tanja , Nasibulin Albert G. 
Published: December 2017

AbstractWe report high-performance, stable, low equivalent series resistance all-nanotube stretchable supercapacitor based on single-walled carbon nanotube film electrodes and a boron nitride nanotube separator. A layer of boron nitride nanotubes, fabricated by airbrushing from isopropanol dispersion, allows avoiding problem of high internal resistance and short-circuiting of supercapacitors. The device, fabricated in a two-electrode test cell configuration, demonstrates electrochemical double layer capacitance mechanism and retains 96% of its initial capacitance after 20 000 electrochemical charging/discharging cycles with the specific capacitance value of 82 F g−1 and low equivalent series resistance of 4.6 Ω. The stretchable supercapacitor prototype withstands at least 1000 cycles of 50% strain with a slight increase in the volumetric capacitance from 0.4 to 0.5 mF cm−3 and volumetric power density from 32 mW cm−3 to 40 mW cm−3 after stretching, which is higher than reported before. Moreover, a low resistance of 250 Ω for the as-fabricated stretchable prototype was obtained, which slightly decreased with the strain applied up to 200 Ω. Simple fabrication process of such devices can be easily extended making the all-nanotube stretchable supercapacitors, presented here, promising elements in future wearable devices.
Recent spread of Varroa destructor virus-1, a honey bee pathogen, in the United States
Authors: Ryabov Eugene V. , Childers Anna K. , Chen Yanping , Madella Shayne , Nessa Ashrafun , vanEngelsdorp Dennis , Evans Jay D. 
Published: December 2017

AbstractRNA viruses impact honey bee health and contribute to elevated colony loss rates worldwide. Deformed wing virus (DWV) and the closely related Varroa destructor virus-1 (VDV1), are the most widespread honey bee viruses. VDV1 is known to cause high rates of overwintering colony losses in Europe, however it was unknown in the United States (US). Using next generation sequencing, we identified VDV1 in honey bee pupae in the US. We tested 603 apiaries the US in 2016 and found that VDV1 was present in 66.0% of them, making it the second most prevalent virus after DWV, which was present in 89.4% of the colonies. VDV1 had the highest load in infected bees (7.45*1012 ± 1.62*1012 average copy number ± standard error) compared to other tested viruses, with DWV second (1.04*1012 ± 0.53*1012). Analysis of 75 colonies sourced in 2010 revealed that VDV1 was present in only 2 colonies (2.7%), suggesting its recent spread. We also detected newly emerged recombinants between the US strains of VDV1 and DWV. The presence of these recombinants poses additional risk, because similar VDV1-DWV recombinants constitute the most virulent honeybee viruses in the UK.
The glutamic residue at position 402 in the C-terminus of Newcastle disease virus nucleoprotein is critical for the virus
Authors: Yu Xiaohui , Cheng Jinlong , He Zirong , Li Chuang , Song Yang , Xue Jia , Yang Huiming , Zhang Rui , Zhang Guozhong 
Published: December 2017

AbstractThe nucleocapsid proteins (NPs) of Newcastle disease virus (NDV) and other paramyxoviruses play an important functional role during genomic RNA replication. Our previous study showed that the NP-encoding gene significantly influenced viral replication. Here, we investigated the roles of certain amino acid residues in the NP C-terminus in viral replication and virulence. Results showed that the glutamic acid residue at position 402 (E402) in the C-terminus of the NP is critical for RNA synthesis in the NDV mini-genome system. Mutation of E402 resulted in larger viral plaques that appeared more quickly, and increased the virulence of NDV. Further study indicated that the mutant virus had increased RNA levels during the early stages of virus infection, but that RNA replication was inhibited at later time points. These findings increase our knowledge of viral replication and contribute to a more comprehensive understanding of the virulence factors associated with NDV.