bluuebunny/crossref_metadata_2025_split huggingface dataset:
Health and safety considerations and guidelines.
Authors: Nur F. , Forster B. P. , Osei S. A. , Amiteye S. , Ciomas J. , Hoeman S. , Jankuloski L. 
Published: September 2018

Abstract

Mutation induction is the most hazardous part of mutation breeding. The application of physical or chemical mutagens as well as the general handling of mutant materials in mutation breeding has associated high health and safety risks. Poor practice can be hazardous, resulting in minor or serious personal injuries, and even fatal accidents. Therefore, the use of standard health and safety protocols as guides in mutation induction activities is an absolute necessity. It is important to abide by the rules and regulations of mutation induction in order to avoid, or reduce to the barest minimum, injuries and accidents, as well as associated financial costs. With respect to chemical mutagens, these need specialist waste disposal systems after use. It is essential that mutation induction is carried out by specially trained personnel, and it is recommended that this is done in specialized institutes, or at least laboratories. International, regional and national service facilities are available (Chapter 6 of this manual). Certain rules and regulations constituting the operation guidelines may be generally applicable; however, depending on local requirements, some rules and regulations may be specific to a particular region or country. In certain jurisdictions, negligence in the strict adherence to health and safety protocols may incur sanctions such as fines, jail terms, or an embargo on field and laboratory research or commercial operations. This chapter highlights the standard operating protocols on health and safety issues relating to mutation induction for breeding in oil palm. Once mutation treatment has been carried out, subsequent steps (mutation detection, mutant line development and breeding) are relatively safe, but adherence to good laboratory, glasshouse and field practices is essential.
Options for mutation breeding in oil palm.
Authors: Nur F. , Forster B. P. , Osei S. A. , Amiteye S. , Ciomas J. , Hoeman S. , Jankuloski L. 
Published: September 2018

Abstract

Theoretical and practical options for mutation breeding in oil palm are discussed. In theory, haploids are considered the ideal targets, as the induced mutation can be fixed instantly on conversion to doubled haploids. However, haploid/doubled haploid technology is in its infancy in oil palm and therefore other practical targets need to be considered. The two obvious targets are pollen and seed, as these are produced in large numbers in breeding and commercial seed production. Schemes for pollen and seed irradiation and subsequent mutant population development are compared. The irradiation of germinated seed is currently considered to be the better approach in terms of convenience and time. A major constraint in mutation breeding in oil palm is the long life cycle. Oil palm has a long juvenile stage, and it takes 4-5 years from sowing a seed to getting seed of the next generation. Traditionally, mutant selection has relied on phenotypic selection, which can only take place in the second mutant generation (M2) due to the presence of physiological disorders and chimeras in the M1. However, now that the oil palm genome has been sequenced, it is feasible to select for mutants genotypically in the M1. Early detection of mutants is extremely valuable in oil palm, as it saves space in growing up only selected mutants in the field. Mutation breeding is a non-GM technique that has been used for over nine decades. New methods in genetic manipulation include gene editing, which has huge potential for the future but is currently still under debate as to whether it is considered a GM method and is subject to restrictive regulations.
Protocol for developing mutant generations for mutant selection.
Authors: Nur F. , Forster B. P. , Osei S. A. , Amiteye S. , Ciomas J. , Hoeman S. , Jankuloski L. 
Published: September 2018

Abstract

A practical step-by-step protocol is presented for mutation induction and mutation detection in oil palm. Germinated seed is chosen as the target material for mutation induction, as this provides the quickest development of mutant populations (as discussed in Chapters 3 and 4 of this manual). The protocol adopts gamma irradiation as this is a proven effective mutagen for mutation breeding. Genotyping is deployed in the M1 to select for mutants in target genes. These selections, plus a random selection of M1 plants, are then advanced from nursery to field conditions to produce mature palms, which may be self-pollinated to produce the M2 generation. The M2 generation is subject to phenotypic screening at all stages in plant development, from seed, germination, seedling, juvenile to adult palms. A list of target genes and traits for mutation is given. As discussed in Chapter 4 of this manual, there are two practical targets for mutation induction in oil palm: pollen and seed. The seed option is the more favoured, as it takes less time and involves only one pollination/seed production stage, thus saving time and labour. A step-by-step guide is provided in generating the M1 and M2 populations for mutant detection.
Applied strategies for the control of coccidiosis in poultry.
Authors: Chapman H. D. 
Published: September 2018

Abstract

Apicomplexan parasites of the genus
Eimeria
are widespread in poultry flocks and if present in sufficient numbers can cause the intestinal disease coccidiosis. For many years, the disease has been controlled either by incorporating drugs in the feed (prophylaxis) or by immunization with live parasites (vaccination). Efficacy of anticoccidial drugs has been compromised by the acquisition of resistance which has been documented for all drugs introduced including those most widely used, the ionophorous antibiotics. A consequence of limited efficacy is that these drugs permit some parasite development thus allowing the acquisition of immunity. Combined with improvements in management, this may explain the continued use of drugs for the control of coccidiosis in broiler and turkey production. In recent years vaccination, utilizing live attenuated or non-attenuated parasites has made a significant contribution to the control of coccidiosis in chickens. Vaccines are administered on a single occasion by a variety of methods to newly hatched chicks and initiate an immune response in the bird. Full protective immunity requires secondary exposure to vaccinal oocysts in the litter, an aspect of vaccination over which the producer has little control. Exposure to wild-type parasites already present in the litter may cause clinical coccidiosis, as evident by characteristic intestinal lesions in birds, before protective immunity has time to fully develop. Several vaccines comprise parasites that have never been exposed to anticoccidial drugs and it has been shown that their use in a commercial setting may replace drug-resistant organisms resulting in a restoration of drug-sensitivity. Programs involving alternation of chemotherapy and vaccination have been introduced with the objective of prolonging the life of anticoccidial drugs that have been compromised by drug-resistance. This is the only known example of restoration of drug sensitivity in veterinary parasitology. So-called 'natural' products that include herbs, herbal and fungal extracts, and probiotics are claimed to alleviate
Eimeria
infections in poultry, but few have been thoroughly investigated. Advances have been made in our knowledge of the structure of proteins released during parasite invasion of host cells and may eventually result in novel vaccines based upon molecular technology. Hens immunized with proteins isolated from gametocyte stages of the life cycle of one species of
Eimeria
pass antibodies to developing embryos and this may provide short-term passive protection to young chickens' post-hatch. As with other approaches to vaccination, protection is dependent upon exposure to wild-type parasites present in the environment.
FA02.07: BARRIER STRUCTURE AND FUNCTION OF THE NEO-SQUAMOUS EPITHELIUM FOLLOWING SUCCESSFUL BARRETT’S ENDOTHERAPY IS IMPAIRED
Authors: Ravindran Adharsh , Blevins Christopher , Johnson Michele , Lansing Ramona , Wang Kenneth , Katzka David , Iyer Prasad 
Published: September 2018

Abstract

Background
The neo-squamous epithelium that replaces columnar epithelium after successful endoscopic ablation of Barrett's esophagus (BE) has not been fully characterized in regard to its structural and functional integrity. Intercellular space is a surrogate marker for epithelial structural integrity and mucosal impedance (MI) is a surrogate for transepithelial resistance and thus epithelial functional integrity. Impairment of the structural and functional integrity may influence recurrence following successful ablation. We aimed to measure the esophageal epithelial intercellular space diameter and MI in the neo-squamous and normal squamous epithelium of patients who underwent successful radiofrequency ablation for dysplastic BE.

Methods
Forty patients with complete remission of intestinal metaplasia (CRIM) (defined as two negative surveillance endoscopies for intestinal metaplasia) were prospectively recruited. Patients were excluded if they had endoscopic evidence of esophagitis. MI measurements were taken at 1 cm above the GE junction and 2 cm above the prior BE segment (targeting uninvolved squamous epithelium), using a novel through the scope MI probe. Endoscopic biopsies were also taken at these corresponding sites to assess intercellular space diameter using transmission electron microscopy (TEM) using standard techniques.

Results
80% of patients were male with a mean age of 69 years. Mean follow since achieving CRIM was 30 months. 39 patients underwent RFA for dysplasia. The mean intercellular space diameter was higher in the neo-squamous epithelium (1.01 μm) when compared to the untreated native squamous epithelium (0.96 μm) [Difference of 0.056 μm, 95% CI of -0.036 to 0.148, P = 0.228]. The mean MI was significantly lower in the neosquamous epithelium (4001.3 Ω) when compared to the untreated native epithelium (5168.1 Ω) [Difference of 1166.7 Ω, 95% CI 418.8 to 1914.6, P = 0.003].

Conclusion
Neo-squamous epithelium that replaces BE epithelium following successful endoscopic therapy for BE appears to be functionally and likely structurally deficient with regards to acid reflux barrier function, when compared to native squamous esophageal epithelium. This impairment may be associated with recurrence following successful ablation.

Disclosure
All authors have declared no conflicts of interest.
RNAseq dataset describing transcriptional changes in cervical sensory ganglia after bilateral pyramidotomy and forelimb intramuscular gene therapy with AAV1 encoding human neurotrophin-3
Authors: Kathe Claudia , Moon Lawrence D F 
Published: September 2018

AbstractUnilateral or bilateral corticospinal tract injury in the pyramids of adult rats causes changes in proprioceptive axon terminal arborization in the cervical spinal cord accompanied by hyperreflexia and abnormal movements including spasms [1, 2]. Treatment of affected forelimb muscles with an Adeno-Associated Viral Vector (AAV) encoding human neurotrophin-3 (NT3) normalizes many of these anatomical, neurophysiological and behavioural changes [1]. Interestingly, in several studies, neurotrophin-3 protein accumulates in cervical dorsal root ganglia (DRG) on the side ipsilateral to AAV injection [1, 3]. We hypothesize that neurotrophin-3 induces these changes (in proprioceptive axon wiring, proprioceptive reflex neurophysiology and sensorimotor behaviors involving proprioception) by modifying gene expression in affected cervical dorsal root ganglia (DRG). As a first step in testing this hypothesis, we analyzed the transcriptomes of cervical DRGs obtained during a previous study from naïve rats and from rats after bilateral pyramidotomy (bPYX) with unilateral intramuscular injections of either AAV1-CMV-NT3 or AAV1-CMV-EGFP made 24h after injury [1]. Ten weeks after surgery, Poly(A) RNAs and small RNAs from C6 to C8 DRGs on the treated side were sequenced. We detected mRNAs or small RNAs that were significantly regulated under three conditions (bPYX+GFP vs naïve; bPYX+NT3 versus naïve; bPYX+NT3 vs bPYX+GFP). We identified mRNAs and small RNAs whose expression level was altered after pyramidotomy and normalized by neurotrophin-3 treatment. A bioinformatic analysis enabled us to identify genes that are likely to be expressed in proprioceptors after injury and which were regulated by neurotrophin-3 in the direction expected from other datasets involving knockout or overexpression of neurotrophin-3. This dataset will help us and others identify genes in sensory neurons whose expression levels are regulated by neurotrophin-3 treatment. This may help identify novel therapeutic targets to improve sensation and movement after neurological injury. Data has been deposited in the Gene Expression Omnibus (GSE82197).
VEP-G2P: A Tool for Efficient, Flexible and Scalable Diagnostic Filtering of Genomic Variants
Authors: Thormann Anja , Halachev Mihail , McLaren William , Moore David J , Svinti Victoria , Campbell Archie , Kerr Shona M , Hunt Sarah , Dunlop Malcolm G , Hurles Matthew E , Wright Caroline F , Firth Helen V , Cunningham Fiona , FitzPatrick David R 
Published: September 2018

AbstractPurposeWe aimed to develop an efficient, flexible, scalable and evidence-based approach to sequence-based diagnostic analysis/re-analysis of conditions with very large numbers of different causative genes. We then wished to define the expected rate of plausibly causative variants coming through strict filtering in control in comparison to disease populations to quantify background diagnostic “noise”.MethodsWe developed G2P (www.ebi.ac.uk/gene2phenotype) as an online system to facilitate the development, validation, curation and distribution of large-scale, evidence-based datasets for use in diagnostic variant filtering. Each locus-genotype-mechanism-disease-evidence thread (LGMDET) associates an allelic requirement and a mutational consequence at a defined locus with a disease entity and a confidence level and evidence links. We then developed an extension to Ensembl Variant Effect Predictor (VEP), VEP-G2P, which can filter based on G2P other widely used gene panel curation systems. We compared the output of disease-associated and control whole exome sequence (WES) using Developmental Disorders G2P (G2PDD; 2044 LGMDETs) and constitutional cancer predisposition G2P (G2PCancer; 128 LGMDETs).ResultsWe have shown a sensitivity/precision of 97.3%/33% and 81.6%/22.7% for causative de novo and inherited variants respectively using VEP-G2PDD in DDD study probands WES. Many of the apparently diagnostic genotypes “missed” are likely false-positive reports with lower minor allele frequencies and more severe predicted consequences being diagnostically-discriminative features.ConclusionCase:control comparisons using VEP-G2PDD established an observed:expected ratio of 1:30,000 plausibly causative variants in proband WES to ~1:40,000 reportable but presumed-benign variants in controls. At least half the filtered variants in probands represent background “noise”. Supporting phenotypic evidence is, therefore, necessary in genetically-heterogeneous disorders. G2P and VEP-G2P provides a practical approach to optimize disease-specific filtering parameters in diagnostic genetic research.
Dating genomic variants and shared ancestry in population-scale sequencing data
Authors: Albers Patrick K. , McVean Gil 
Published: September 2018

AbstractThe origin and fate of new mutations within species is the fundamental process underlying evolution. However, while much attention has been focused on characterizing the presence, frequency, and phenotypic impact of genetic variation, the evolutionary histories of most variants are largely unexplored. We have developed a non-parametric approach for estimating the date of origin of genetic variants in large-scale sequencing data sets. The accuracy and robustness of the approach is demonstrated through simulation. Using data from two publicly available human genomic diversity resources, we estimated the age of more than 45 million single nucleotide polymorphisms (SNPs) in the human genome and release the Atlas of Variant Age as a public online database. We characterize the relationship between variant age and frequency in different geographical regions, and demonstrate the value of age information in interpreting variants of functional and selective importance. Finally, we use allele age estimates to power a rapid approach for inferring the ancestry shared between individual genomes, to quantify genealogical relationships at different points in the past, as well as describe and explore the evolutionary history of modern human populations.
Warm Temperatures, Cool Sponges: The Effect of Increased Temperatures on the Antarctic SpongeIsodictyasp
Authors: González-Aravena M. , Kenny N.J. , Osorio M. , Font A. , Riesgo A. , Cárdenas C.A. 
Published: September 2018

AbstractAlthough the cellular and molecular responses to exposure to relatively high temperatures (acute thermal stress or heat shock) have been studied previously, only sparse empirical evidence of how it affects cold-water species is available. As climate change becomes more pronounced in areas such as the Western Antarctic Peninsula, it has become crucial to understand the capacity of these species to respond to thermal stress.Here we use the Antarctic spongeIsodictyasp. to investigate how sessile organisms (particularly Porifera) can adjust to acute short-term heat stress, by exposing this species to 3 and 5 °C for 4 hours, corresponding to predicted temperatures under high-end 2080 IPCC-SRES scenarios. Assembling ade novoreference transcriptome (90,188 contigs, >93.7% metazoan BUSCO genes) we have begun to discern the molecular componentry employed byIsodictyato adjust to environmental insult.Our initial analyses suggest that TGF-β, ubiquitin and hedgehog cascades are involved, alongside other genes. However, the degree and type of response changed little from 3 to 5 °C, suggesting that even moderate rises in temperature could cause stress at the limits of this organism’s capacity. Given the importance of sponges to Antarctic ecosystems, our findings are vital for discerning the consequences of increases in Antarctic ocean temperature on these and other species.
A stress-induced Tyrosine tRNA depletion response mediates codon-based translational repression and growth suppression
Authors: Huh Doowon , Passarelli Maria C. , Gao Jenny , Dusmatova Shahnoza N , Goin Clara , Fish Lisa , Pinzaru Alexandra M. , Molina Henrik , McMillan Elizabeth A. , Asgharian Hosseinali , Goodarzi Hani , Tavazoie Sohail F. 
Published: September 2018

SUMMARYEukaryotic transfer RNAs can become selectively fragmented upon various stresses, generating tRNA-derived small RNA fragments. Such fragmentation has been reported to impact a small fraction of the tRNA pool and thus presumed to not directly impact translation. We report that oxidative stress can rapidly generate tyrosine tRNAGUA fragments in human cells—causing significant depletion of the precursor tRNA. Tyrosine tRNAGUA depletion impaired translation of growth and metabolic genes enriched in cognate tyrosine codons. Depletion of tyrosine tRNAGUA or its translationally regulated targets USP3 and SCD repressed proliferation—revealing a dedicated tRNA-regulated growth suppressive pathway for oxidative stress response. Tyrosine fragments are generated in a DIS3L2 exoribonuclease-dependent manner and inhibit hnRNPA1-mediated transcript destabilization. Moreover, tyrosine fragmentation is conserved in C. elegans. Thus, tRNA fragmentation can coordinately generate trans-acting small-RNAs and functionally deplete a tRNA. Our findings reveal the existence of an underlying adaptive codon-based regulatory response inherent to the genetic code.
Connexin 43 plays an important role in the transformation of human cholangiocytes upon stimulation withClonochis sinensisexcretory-secretory protein andN-nitrosodimethylamine
Authors: Kim Eun-Min , Bae Young Mee , Choi Min-Ho , Hong Sung-Tae 
Published: September 2018

AbstractBackgroundClonorchis sinensisis a group I bio-carcinogen responsible for cholangiocarcinoma (CHCA) in humans. However, the mechanism by whichC. sinensispromotes carcinogenesis is unclear.MethodologyUsing the human cholangiocyte line H69, we investigated cell proliferation and gap junction protein expression after stimulation with the hepatotoxinN-nitrosodimethylamine (NDMA) and/or excretory-secretory products (ESP) of C.sinensis, which induce inflammation. NDMA and ESP treatment increased proliferation by 146% and the proportion of cells in the G2/M phase by 37%. Moreover, the expression of the cell cycle protein E2F1 and the cell proliferation-related proteins Ki-67 and cytokeratin 19 increased in response to combined treatment with NDMA and ESP. The gap-junction proteins connexin (Cx) 43 and Cx26 also increased. In contrast, Cx32 expression decreased in cells treated with NDMA and ESP. Cox-2 was also upregulated. Silencing of Cx43 reduced cell proliferation and significantly suppressed Cx26 and Cox-2 expression.ConclusionsThese results suggest that Cx43 is an important factor in CHCA induced byC. sinensisESP and NDMA and further investigations targeting this pathway may allow prevention of this deadly disease.Author summaryClonorchis sinensis, a human fluke, resides in the liver of humans and is commonly found in the common bile duct and gall bladder. This parasite is the main cause of cholangiocarcinoma, also called bile duct cancer, in humans. Of note, the excretory-secretory products (ESP) ofC. sinensisare known to cause inflammation in the biliary epithelium, which may ultimately result in neoplasms via production of reactive oxygen species and subsequent DNA damage. Together withN-nitrosodimethylamine (NDMA), a potent hepatotoxin that can cause fibrosis and tumors in the liver, ESP led to an increase in the growth and proliferation of cholangiocytes. Our results showed that the ESPs ofC. sinensisinduced pro-inflammatory responses by increasing the levels of proinflammatory cytokines and nuclear factor kappa B (NFκB), which in turn, enhanced the production of connexin 43 (Cx43), a gap-junction protein. Therefore, Cx 43 can serve as a potential target for developing a therapeutic strategy for the treatment of cholangiocarcinoma in humans.
Understanding the trust building mechanisms in social media
Authors: Sun Yongqiang , Zhang Yan , Shen Xiao-Liang , Wang Nan , Zhang Xi , Wu Yanqiu 
Published: September 2018

Purpose
Although the impacts of trust on information disclosure have been well recognized, the trust building mechanisms in social media are still underexplored. To fill this gap, the purpose of this paper is to explore two trust building mechanisms, namely, institution-based and transference-based trust building and identify how these two mechanisms vary across gender.

Design/methodology/approach
An online survey was conducted to collect data. The partial least squares method was used to examine the relationships among regulatory effectiveness, three trusting perceptions and disclosure intention. A cross-group path coefficient comparison method was used to test gender differences.

Findings
The results suggest that regulatory effectiveness affects competence- and character-based trust and these impacts are stronger for males than for females. Both competence- and character-based trust influence general trust in members while their impacts vary. Competence-based trust is more important for males while character-based trust is more important for females.

Originality/value
This study contributes to social media literature by identifying the two trust building mechanisms with special attention to the role of regulatory effectiveness and trust transfer. Further, this study also sheds light on how these two mechanisms vary across gender.