bluuebunny/crossref_metadata_2025_split huggingface dataset:
The first next-generation sequencing approach to the mitochondrial phylogeny of African monogenean parasites (Platyhelminthes: Gyrodactylidae and Dactylogyridae)
Authors: Vanhove Maarten P.M. , Briscoe Andrew G. , Jorissen Michiel W.P. , Littlewood D. Tim J. , Huyse Tine 
Published: March 2018

AbstractBackgroundMonogenean flatworms are the main ectoparasites of fishes. Representatives of the species-rich families Gyrodactylidae and Dactylogyridae, especially those infecting cichlid fishes and clariid catfishes, are important parasites in African aquaculture, even more so due to the massive anthropogenic translocation of their hosts worldwide. Several questions on their evolution, such as the phylogenetic position ofMacrogyrodactylusand the highly specioseGyrodactylus, remain unresolved with available molecular markers. Also, diagnostics and population-level research would benefit from the development of higher-resolution genetic markers. We aim to advance genetic work on African monogeneans by providing mitogenomic data of four species (two each belonging to the Gyrodactylidae and Dactylogyridae), and analysing their gene sequences and gene order from a phylogenetic perspective.ResultsBased on Illumina technology, the first four mitochondrial genomes of African monogeneans were assembled and annotated for the cichlid parasitesGyrodactylus nyanzae,Cichlidogyrus halli,Cichlidogyrus mbirizei(near-complete mitogenome) and the catfish parasiteMacrogyrodactylus karibae(near-complete mitogenome). The start codon TTG is new forGyrodactylusand for the Dactylogyridae, as is the incomplete stop codon TA for the Dactylogyridae. The most variable markers arenadgenes and these are under relaxed selection. Especiallynad2 is promising for primer development. Gene order was identical for protein-coding genes and differed between the African representatives of these families only in a tRNA gene transposition. A mitochondrial phylogeny based on an alignment of nearly 12,500 bp including 12 protein-coding and two ribosomal RNA genes confirms that the Neotropical oviparousAglaiogyrodactylus forficulatustakes a sister group position with respect to the other gyrodactylids, rather than the supposedly ‘primitive’ AfricanMacrogyrodactylus. Inclusion of the AfricanGyrodactylus nyanzaeconfirms the paraphyly ofGyrodactylus. The position of the African dactylogyridCichlidogyrusis unresolved, although gene order suggests it is closely related to marine ancyrocephalines.ConclusionsThe amount of mitogenomic data available for gyrodactylids and dactylogyrids is increased by roughly one-third. Our study underscores the potential of mitochondrial genes and gene order in flatworm phylogenetics, and of next-generation sequencing for marker development for these non-model helminths for which few primers are available while they constitute a risk to tropical aquaculture.
Conformational footprinting of proteins using a combination of top-down electron transfer dissociation and ion mobility
Authors: Konijnenberg Albert , Li Jinyu , Habchi Johny , Dosnon Marion , Rossetti Giulia , Grandori Rita , Longhi Sonia , Carloni Paolo , Sobott Frank 
Published: March 2018

AbstractIn recent years native mass spectrometry has been increasingly employed to study protein structure. As such a thorough understanding of the effect of the gas-phase on protein structure is becoming increasingly important. We show how a combination of top-down ETD and ion mobility can be used to probe the gas-phase structure of heterogeneous protein ensembles. By applying collisional activation to the non-covalently bound ETD products after IM separation, the peptide fragments can be released while maintaining the conformational information of the protein ion. We studied the unknown gas-phase structures of the measles virus (MeV) phosphoprotein X domain (PXD), which shows a wide range of different conformations in the gas-phase. We then generated structural models by state-of-the-art gas-phase steered molecular dynamics, which we verified using restraints from ion mobility and the fragment patterns observed. Our findings illustrate the applicability of ETD for obtaining conformational specific structural information on heterogeneous protein ensembles.
Genome-wide fitness assessment during diurnal growth reveals an expanded role of the cyanobacterial circadian clock protein KaiA
Authors: Welkie David G. , Rubin Benjamin E. , Chang Yong-Gang , Diamond Spencer , Rifkin Scott A. , LiWang Andy , Golden Susan S. 
Published: March 2018

AbstractThe recurrent pattern of light and darkness generated by Earth’s axial rotation has profoundly influenced the evolution of organisms, selecting for both biological mechanisms that respond acutely to environmental changes and circadian clocks that program physiology in anticipation of daily variations. The necessity to integrate environmental responsiveness and circadian programming is exemplified in photosynthetic organisms such as cyanobacteria, which depend on light-driven photochemical processes. The cyanobacteriumSynechococcus elongatusPCC 7942 is an excellent model system for dissecting these entwined mechanisms. Its core circadian oscillator, consisting of three proteins KaiA, KaiB, and KaiC, transmits time-of-day signals to clock-output proteins, which reciprocally regulate global transcription. Research performed under constant light facilitates analysis of intrinsic cycles separately from direct environmental responses, but does not provide insight into how these regulatory systems are integrated during light-dark cycles. Thus, we sought to identify genes that are specifically necessary in a day-night environment. We screened a dense bar-coded transposon library in both continuous light and daily cycling conditions and compared the fitness consequences of loss of each nonessential gene in the genome. Although the clock itself is not essential for viability in light-dark cycles, the most detrimental mutations revealed by the screen were those that disrupt KaiA. The screen broadened our understanding of light-dark survival in photosynthetic organisms, identified unforeseen clock-protein interaction dynamics, and reinforced the role of the clock as a negative regulator of a night-time metabolic program that is essential forS. elongatusto survive in the dark.SignificanceUnderstanding how photosynthetic bacteria respond to and anticipate natural light–dark cycles is necessary for predictive modeling, bioengineering, and elucidating metabolic strategies for diurnal growth. Here, we identify the genetic components that are important specifically under light-dark cycling conditions and determine how a properly functioning circadian clock prepares metabolism for darkness, a starvation period for photoautotrophs. This study establishes that the core circadian clock protein KaiA is necessary to enable rhythmic de-repression of a night-time circadian program.
Bacillus safensisFO-36b andBacillus pumilusSAFR-032: A Whole Genome Comparison of Two Spacecraft Assembly Facility Isolates
Authors: Tirumalai Madhan R , Stepanov Victor G. , Wünsche Andrea , Montazari Saied , Gonzalez Racquel O. , Venkateswaran Kasturi , Fox George. E. 
Published: March 2018

AbstractBackgroundBacillusstrains producing highly resistant spores have been isolated from cleanrooms and space craft assembly facilities. Organisms that can survive such conditions merit planetary protection concern and if that resistance can be transferred to other organisms, a health concern too. To further efforts to understand these resistances, the complete genome ofBacillus safensisstrain FO-36b, which produces spore resistant to peroxide and radiation was determined. The genome was compared to the complete genome ofB. pumilus SAFR-032, as well as draft genomes ofB. safensisJPL-MERTA-8-2 and the type strainB. pumilusATCC7061T. In addition, comparisons were made to 61 draft genomes that have been mostly identified as strains ofB. pumilusorB. safensis.ResultsThe FO-36b gene order is essentially the same as that in SAFR-032 and otherB. pumilusstrains [1]. The annotated genome has 3850 open reading frames and 40 noncoding RNAs and riboswitches. Of these, 307 are not shared by SAFR-032, and 65 are also not shared by either MERTA or ATCC7061T. The FO-36b genome was found to have ten unique reading frames and two phage-like regions, which have homology with theBacillusbacteriophage SPP1 (NC_004166) andBrevibacillusphage Jimmer1 (NC_029104). Differing remnants of the Jimmer1 phage are found in essentially allsafensis/pumilusstrains. Seven unique genes are part of these phage elements. Comparison ofgyrAsequences from FO-36b, SAFR-032, ATCC7061T, and 61 other draft genomes separate the various strains into three distinct clusters. Two of these are subgroups ofB. pumiluswhile the other houses all theB. safensisstrains.ConclusionsIt is not immediately obvious that the presence or absence of any specific gene or combination of genes is responsible for the variations in resistance seen. It is quite possible that distinctions in gene regulation can change the level of expression of key proteins thereby changing the organism’s resistance properties without gain or loss of a particular gene. What is clear is that phage elements contribute significantly to genome variability. The larger comparison of multiple strains indicates that many strains named asB. pumilusactually belong to theB. safensisgroup.
LncRNAOIP5-AS1is overexpressed in undifferentiated oral tumors and integrated analysis identifies as a downstream effector of stemness-associated transcription factors
Authors: Arunkumar Ganesan , Anand Shankar , Raksha Partha , Dhamodharan Shankar , Prasanna Srinivasa Rao Harikrishnan , Subbiah Shanmugam , Murugan Avaniyapuram Kannan , Munirajan Arasambattu Kannan 
Published: March 2018

AbstractLong non-coding RNAs (lncRNAs) play an important role in the regulation of key cellular processes in early development and in cancer. LncRNAOip5-as1facilitates stem cell self-renewal in mouse by sponging mmu-miR-7 and modulating NANOG level, yet its role in cancer is less understood. We analyzedOIP5-AS1expression in oral tumors and in TCGA datasets. We observed overexpression ofOIP5-AS1in oral tumors (P<0.001) and in tumors of epithelial origin from TCGA.OIP5-AS1expression was strongly associated with undifferentiated tumors (P=0.0038).In silicoanalysis showed miR-7 binding site is conserved in mouse and humanOIP5-AS1. However, humanNANOG3’-UTR lost the binding site for hsa-miR-7a-3. Therefore, we screened for other miRNAs that can be sponged byOIP5-AS1and identified six potential miRNAs and their downstream target genes. Expression analysis showed downregulation of miRNAs and upregulation of downstream target genes, particularly in undifferentiated tumors with high-level ofOIP5-AS1suggesting thatOIP5-AS1could post-transcriptionally modulate the downstream target genes. Further, systematic epigenomic analysis ofOIP5-AS1promoter revealed binding motifs for MYC, NANOG and KLF4 suggesting thatOIP5-AS1could be transactivated by stemness-associated transcription factors in cancer. Overexpression of OIP5-AS1 in undifferentiated oral tumors may confer poor prognosis through maintenance of cancer stemness.
Roles of Vitamin Metabolizing Genes in Multidrug-Resistant Plasmids of Superbugs
Authors: Chakraborty Asit Kumar 
Published: March 2018

AbstractSuperbug crisis has rocked this world with million deaths due to failure of potent antibiotics. Thousands mdr genes with hundreds of mutant isomers are generated. Small integrons and R-plasmids have combined with F’-plasmids creating a space for >10-20 of mdr genes that inactivate antibiotics in different mechanisms. Mdr genes are created to save bacteria from antibiotics because gut microbiota synthesize >20 vitamins and complex bio-molecules needed for >30000 biochemical reactions of human metabolosome. In other words, mdr gene creation is protected from both sides, intestinal luminal cells and gut bacteria in a tight symbiotic signalling system. We have proposed, to avert the crisis all vitamin metabolizing genes will be acquired in MDR- plasmids if we continue oral antibiotics therapy. Therefore, we have checked the plasmid databases and have detected thiamine, riboflavin, folate, cobalamine and biotin metabolizing enzymes in MDR plasmids. Thusvitgenes may mobilise recently into MDR-plasmids and are likely essential for gut microbiota protection. Analysis found thatcobandthigenes are abundant and likely very essential than other vit genes.
“It does not help to look young and dumb…”
Authors: Meinich Jenny , Sang Kate 
Published: March 2018

PurposeWhile age is receiving increased attention in the literature on workplace diversity, it remains under researched. Intergenerational contact and its relationship to ageism require further research to understand their mechanisms and impacts. The paper aims to discuss this issue.Design/methodology/approachUsing semi-structured interviews in the Norwegian technical industry, this paper explores how generations are formed and how this influences intergenerational contact.FindingsThrough the lens of ageism, the findings reveal that generational stereotypes are strongly held by respondents, and may affect how members of the generations interact in the workplace. Further, the data demonstrate that both age and generation are socially constructed, and age discrimination is perceived by both older and younger workers.Originality/valueThe study has relevance for managers who are overseeing organizations with considerable age differences.
Endogamy and income in native couples: the case of Finland
Authors: Härtull Camilla , Saarela Jan 
Published: March 2018

PurposeThe purpose of this paper is to study two native and equal population groups, Finnish speakers and Swedish speakers in Finland, to examine whether there is income variation across couples that differ on ethno-linguistic composition, and if such variation can be attributed to differences in education, educational homogamy and other observable characteristics.Design/methodology/approachUsing detailed register-based household data, the authors estimate OLS models to compare endogamous and exogamous couples with respect to income of the man, the woman, and both partners, respectively.FindingsEndogamous Swedish-speaking couples are found to have on average 25 per cent higher income than other couples. The advantage is not related to differences in educational homogamy, but primarily to man’s income, and roughly half of the income difference is explained by the higher educational level of Swedish-speaking men in endogamous couples. Although women in endogamous Swedish-speaking couples are higher educated than other women, and there is a higher degree of educational homogamy in these couples, their education has only a modest bearing on the income differential.Originality/valueIn the case of Finland, educational homogamy does not affect income variation across native couples that differ on ethno-linguistic composition. Endogamous mate selection seems to increase economic inequality, uphold gender inequality, and help the native minority group in sustaining its own community.
Managers’ retention decisions regarding young intermediate-level educated employees
Authors: Buers Corine , Karpinska Kasia , Schippers Joop 
Published: March 2018

Purpose
The purpose of this paper is to investigate the opportunities in the labour market for young employees with intermediate-level education by studying which young employees are most likely to be retained and under what conditions managers favour retention.

Design/methodology/approach
Retention decisions are examined by combining a vignette experiment and a survey study. Hypothetical profiles of 252 young employees were rated on their retention desirability by 21 managers, each working in a different organisation. Information on the managers’ characteristics and their organisations were collected in a survey.

Findings
Managers are generally not inclined to suggest retention. Their decisions are highly dependent on their own characteristics and organisational factors, even when young employees perform well and display desirable work-related behaviour.

Research limitations/implications
While the small scale and explorative nature of this study limit its generalisability, this paper highlights the importance of combining information on employees, the organisation and managers; when studying (early) careers and employment decisions.

Practical implications
This study suggests that job retention is only in part within an individual’s control, and the future efforts to combat youth unemployment need to account for organisational and managerial characteristics.

Originality/value
The focus on the employer’s perspective is new to research on early careers, making it a starting point for further lines of exploration. Further, this study provides a comprehensive insight into factors that influence managers’ retention decisions by combining three sets of factors in a single research design.
State dependence of labour force participation of married Australian women
Authors: Cai Lixin 
Published: March 2018

Purpose
The purpose of this paper is to enhance the understanding of labour force participation behaviour of married Australian women, with a focus on identifying the sources of observed inter-temporal labour force participation persistence.

Design/methodology/approach
A dynamic Probit model is applied to the Household, Income and Labour Dynamics in Australia (HILDA) Survey, a national representative panel survey of Australian households. The model used accounts for observed and unobserved individual heterogeneity and serially correlated transitory shocks to labour supply.

Findings
The results show that both observed and unobserved individual heterogeneity contributes to observed inter-temporal persistence of labour force participation of married Australian women, but the persistence remains even after controlling for these factors. It is also found that failing to control for serially correlated unobserved transitory shocks would lead to underestimation of genuine state dependence of labour force participation; and that state dependence of labour force participation varies with age, education, health, immigration status and the number of children under the school age.

Originality/value
This study adds to the international literature on labour force dynamics of women by providing Australian empirical evidence and through a flexible modelling framework. The result that there exists genuine positive state dependence in married Australian women’s labour force participation suggests that policy intervention that increases married women’s labour supply would have a long-lasting effect.
The impact of HR outsourcing and strategic HR integration on the HR-to-employee ratio
Authors: Szierbowski-Seibel Klaas , Kabst Ruediger 
Published: March 2018

Purpose
Two simultaneous trends have arisen in the field of HRM: the development of the human resource (HR) function toward a more strategic, value adding unit and the trend of HR outsourcing (HRO). Opinions are divided in the field of HRM research regarding the interdependences between these two trends and whether the HR function has a positive or negative effect. Therefore, the purpose of this paper is to examine the triangular relationship among strategic HR integration, the HR-to-employee ratio and HRO.

Design/methodology/approach
This study analyses data from three large evaluations conducted in 14 European countries and compares the results obtained from the 2000, 2005 and 2010 Cranet survey waves. For the hypotheses, a multilevel regression design was used.

Findings
The results allow concluding that HRO supports the professionalization of the HR function in an effort to make it a strategic asset.

Research limitations/implications
This study extends prior understandings of the theoretical perspective on HRO and its organizational impact. The sample is nested within 14 European countries and influenced by cultural aspects and institutional factors. These influences could be an exciting avenue for further research.

Practical implications
This paper includes important implications for HR practitioners. The results support a rather optimistic view of the HR function regarding its relationship with HRO and the latter’s impact on the HR-to-employee ratio and strategic HR integration.

Originality/value
The study answers the question: has HRO downsized internal HR staff over the past decade, and how is it related to the strategic integration of the HR function? In this context, this study analyses Cranet data to contribute to the discussion on the development of strategic HR integration and the impact of HRO on such efforts. Moreover, the study examines the influence of HRO on internal HR staff based on the theoretical framework of the resource-based view.
Long-term scarring effect of neither working nor studying
Authors: Andersson Fredrik W. , Gullberg Brännstrom Susanne , Mörtvik Roger 
Published: March 2018

Purpose
It is increasingly important to study labour market outcomes for people who are not in employment, education, or training (NEET). Where most studies focus solely on young people, the purpose of this paper is to include both younger and older NEETs to find out if there is any long-term scarring effect, and if the effect is different between these two groups.

Design/methodology/approach
This study uses a twin-based estimation method for the first time to measure the long-term effect of economic inactivity on income. The analysis is based on biological twins, in order to control for individuals’ unobservable heterogeneity. It is assumed that twins are similar to each other and the only unobservable heterogeneity is at the family level. Register-based data from Statistics Sweden is used.

Findings
The result indicates a significant negative income effect for those who have been in NEET, and is larger for those who have been in NEET for several consecutive periods of time. Individuals who were in NEET during 2001-2003 had on average 62 per cent lower income compared with their twin in 2011. The corresponding number for individuals who were in NEET for just one period was 33 per cent. Hence, time in NEET reduces income. The results show that the long-term scarring effect is not affected by age.

Originality/value
This study utilises for the first time a twin-based estimation method to measure the long-term effect of inactivity. Most studies focus solely on young people, but the authors also include an older group of people.