bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kinematic analysis deconstructs the evolved loss of schooling behavior in cavefish
Authors: Patch Adam , Paz Alexandra , Holt Karla , Duboue Erik , Kowalko Johanna E. , Keene Alex C. , Fily Yaouen 
Published: February 2020

AbstractFish display a remarkable diversity of social behaviors, from highly social to largely solitary. While social behaviors are likely critical for survival, surprisingly little is known about how they evolve in response to changing environmental pressures. With its highly social surface form and multiple populations of a largely asocial, blind, cave-dwelling form, the Mexican tetra,Astyanax mexicanus, provides a powerful model to study the evolution of social behavior. Given numerous morphological and behavioral differences between the surface and cave forms, a primary impediment to understanding how this behavior evolved is a lack of computational and statistical approaches that can precisely identify independent aspects of social behavior. Here, we use motion tracking and kinematic analysis to quantify social swimming patterns and argue that the absence of schooling in cavefish is not merely a consequence of their inability to see but rather a genuine behavioral adaptation that impacts the way they explore their cave environment. Surface fish school, maintaining both close proximity and alignment with each other. In the dark, surface fish no longer school, but we show that they still attempt to align and maintain proximity when they find themselves near another fish. Conversely, cavefish exhibit little preference for proximity or alignment, instead actively avoiding each other. Cavefish also slow down when more fish are present in the tank, which neither surface fish in the light or in the dark do. Using data-driven computer simulations, we show that those two traits – active avoidance and collective slowdown – are sufficient to shift the exploration strategy of cavefish from mostly-following-the-walls to exploring-the-entire-tank. Finally, we find that those differences in collective swimming patterns are largely consistent across independently-evolved cave populations, revealing an evolutionary convergence on this emergent social behavior.Author SummaryThe Mexican tetra fish offers a fascinating window into the evolution of schooling behavior. Its ancestral-like surface form is found in the rivers and lakes of Mexico and Texas and is highly social. Over the last million years,A. mexicanusrepeatedly evolved a second, largely asocial cave form after colonizing a series of dark, underground caves. Here we use motion tracking technology to compare the collective displacement patterns of four populations and present evidence that the loss of schooling in cave populations (i) is a genuine example of parallel behavioral evolution rather than a mere consequence of not being able to see in the dark and (ii) could constitute a cave-specific exploration strategy.
Klp2 and Ase1 synergize to maintain meiotic spindle stability during metaphase I
Authors: Zheng Fan , Dong Fenfen , Yu Shuo , Li Tianpeng , Jian Yanze , Nie Lingyun , Fu Chuanhai 
Published: February 2020

ABSTRACTThe spindle apparatus segregates bi-oriented sister chromatids during mitosis but mono-oriented homologous chromosomes during meiosis I. It has remained unclear if similar molecular mechanisms operate to regulate spindle dynamics during mitosis and meiosis I. Here, we employed live-cell microscopy to compare the spindle dynamics of mitosis and meiosis I in fission yeast cells and demonstrated that the conserved kinesin-14 motor Klp2 plays a specific role in maintaining metaphase spindle length during meiosis I, but not during mitosis. Moreover, the maintenance of metaphase spindle stability during meiosis I requires the synergism between Klp2 and the conserved microtubule crosslinker Ase1 as the absence of both proteins causes exacerbated defects in metaphase spindle stability. The synergism is not necessary for regulating mitotic spindle dynamics. Hence, our work reveals a new molecular mechanism underlying meiotic spindle dynamics and provides insights into understanding differential regulation of meiotic and mitotic events.
Cross-feeding betweenThauera aminoaromaticaandRhodococcus pyridinivoransdrove quinoline biodegradation in a denitrifying bioreactor
Authors: Wu Xinxin , Wu Xiaogang , Li Ji , Wu Qiaoyu , Ma Yiming , Sui Weikang , Zhao Liping , Zhang Xiaojun 
Published: February 2020

AbstractThe complex bacterial community is predominated by several taxa, such asThaueraandRhodococcus, in a quinoline-degrading denitrifying bioreactor. Yet it remains unclear about how the interactions between the different bacteria mediate the quinoline metabolism in denitrifying condition. In this study, we designed a sequence-specific amplification to guide the isolation of the most predominant bacteria and obtained four strains ofThauera aminoaromatica,the representative of one key member in the bioreactor. Test on these isolates demonstrated that all of them were unable to strive on quinoline but could efficiently degrade 2-hydroxyquinoline, the hypothesized primary intermediate of quinoline catabolism, under nitrate-reducing condition. However, another isolate,Rhodococcus pyridinivoransYF3, corresponding to the second abundant taxon in the same bioreactor, was found to degrade quinoline via 2-hydroxyquinoline. The end products and removal rate of quinoline by isolate YF3 were largely varied with the quantity of available oxygen. Specifically, quinoline could only be converted into 2-hydroxyquinoline without further transformation under the condition with insufficient oxygen, e.g. less than 0.5% initial oxygen in the vials. However, if were aerobically pre-cultured in the medium with quinoline the resting cells of YF3 could anaerobically convert quinoline into 2-hydroxyquinoline. A two-strain consortium constructed with isolates fromThauera(R2) andRhodococcus(YF3) demonstrated an efficient denitrifying degradation of quinoline. Thus, we experimentally proved that the metabolism interaction based on the 2-hydroxyquinoline cross-feeding between two predominant bacteria constituted the mainstream of quinoline degradation. This work sheds light on the understanding of mechanism of quinoline removal in the denitrifying bioreactor.ImportanceWe experimentally verified the most predominantThauerasp. was indeed active degrader for the intermediate metabolites and the second abundant taxonRhodococcusexerted, however, key function for opening the food box for a complex quinoline-degrading community. An ecological guild composed of two isolates was assembled, revealing the different roles of keystone organisms in the microbial community. This study, to our best knowledge, is the first report on the cross feeding between the initial attacker with unprofitable catalysis of reluctant heterocyclic compounds and the second bacterium which then completely degrade the compound transformed by the first bacterium. These results could be a significant step forward towards elucidation of microbial mechanism for quinoline denitrifying degradation.
Carbohydrate complexity structures stable diversity in gut-derived microbial consortia under high dilution pressure
Authors: Yao Tianming , Chen Ming-Hsu , Lindemann Stephen R. 
Published: February 2020

ABSTRACTDietary fibers are major substrates for the colonic microbiota, but the structural specificity of these fibers for the diversity, structure, and function of gut microbial communities are poorly understood. Here, we employed anin vitrosequential batch fecal culture approach to determine: 1) whether the chemical complexity of a carbohydrate structure influences its ability to maintain microbial diversity in the face of high dilution pressure and 2) whether substrate structuring or obligate microbe-microbe metabolic interactions (e.g. exchange of amino acids or vitamins) exert more influence on maintained diversity. Sorghum arabinoxylan (SAX, complex polysaccharide), inulin (low-complexity oligosaccharide) and their corresponding monosaccharide controls were selected as model carbohydrates. Our results demonstrate that complex carbohydrates stably sustain diverse microbial consortia. Further, very similar final consortia were enriched on SAX from the same individual’s fecal microbiota across a one-month interval, suggesting that polysaccharide structure is more influential than stochastic alterations in microbiome composition in governing the outcomes of sequential batch cultivation experiments. SAX-consuming consortia were anchored byBacteroides ovatusand retained diverse consortia of >12 OTUs; whereas final inulin-consuming consortia were dominated either byKlebsiella pneumoniaeorBifidobacteriumsp. andEscherichia coli. Furthermore, auxotrophic interactions were less influential in structuring microbial consortia consuming SAX than the less-complex inulin. These data suggest that carbohydrate structural complexity affords independent niches that structure fermenting microbial consortia, whereas other metabolic interactions govern the composition of communities fermenting simpler carbohydrates.IMPORTANCEThe mechanisms by which gut microorganisms compete for and cooperate on human-indigestible carbohydrates of varying structural complexity remain unclear. Gaps in this understanding make it challenging to predict the effect of a particular dietary fiber’s structure on the diversity, composition, or function of gut microbiomes, especially with inter-individual variability in diets and microbiomes. Here, we demonstrate that carbohydrate structure governs the diversity of gut microbiota under high dilution pressure, suggesting that such structures may support microbial diversityin vivo. Further, we also demonstrate that carbohydrate polymers are not equivalent in the strength by which they influence community structure and function, and that metabolic interactions among members arising due to auxotrophy exert significant influence on the outcomes of these competitions for simpler polymers. Collectively, these data suggest that large, complex dietary fiber polysaccharides structure the human gut ecosystem in ways that smaller and simpler ones may not.
Entner–Doudoroff pathway and Non-OxPPP bypasses glycolysis and OxPPP inRalstonia solanacearum
Authors: Jyoti Poonam , Shree Manu , Joshi Chandrakant , Prakash Tulika , Ray Suvendra Kumar , Satapathy Siddhartha Sankar , Masakapalli Shyam Kumar 
Published: February 2020

AbstractInRalstonia solanacearum, a devastating phytopathogen whose metabolism is poorly understood, we observed that Entner-Doudoroff (ED) pathway and NonOxidative pentose phosphate pathway (OxPPP) bypasses glycolysis and OxPPP under glucose oxidation. Evidences derived from13C stable isotopes feeding and genome annotation based comparative metabolic network analysis supported the observations. Comparative metabolic network analysis derived from the currently available53annotatedR. solanacearumstrains also including the recently reported strain (F1C1), representing the four phylotypes confirmed the lack of key genes coding for phosphofructokinase (pfk-1) and phosphogluconate dehydrogenase (gnd) enzymes that are relevant for glycolysis and OxPPP respectively.R. solanacearumF1C1 cells fed with13C Glucose (99%[1-13C]- or 99%[1,2-13C]- or 40%[13C6]-glucose) followed by GC-MS based labelling analysis of fragments from amino acids, glycerol and ribose provided clear evidence that rather than Glycolysis and OxPPP, ED pathway and NonOxPPP are the main routes sustaining metabolism inR. solanacearum. The13C incorporation in the mass ions of alanine (m/z 260, m/z 232); valine (m/z 288, m/z 260), glycine (m/z 218), serine (m/z 390, m/z 362), histidine (m/z 440, m/z 412), tyrosine (m/z 466, m/z 438), phenylalanine (m/z 336, m/z 308), glycerol (m/z 377) and ribose (m/z 160) mapped the pathways supporting the observations. The outcomes help better defining the central carbon metabolic network ofR. solanacearumthat can be integrated with13C metabolic flux analysis as well as flux balance analysis studies for defining the metabolic phenotypes.ImportanceUnderstanding the metabolic versatility ofRalstonia solanacearumis important as it regulates the tradeoff between virulence and metabolism (1, 2) in a wide range of plant hosts. Due to a lack of clear evidence until this work, several published research papers reported on potential roles of Glycolysis and Oxidative pentose phosphate pathways (OxPPP) inR. solanacearum(3, 4). This work provided evidence from13C stable isotopes feeding and genome annotation based comparative metabolic network analysis that Entner-Doudoroff pathway and Non-OxPPP bypasses glycolysis and OxPPP during the oxidation of Glucose, one of the host xylem pool that serves as a potential carbon source (5). The outcomes help better defining the central carbon metabolic network ofR. solanacearumthat can be integrated with13C metabolic flux analysis as well as flux balance analysis studies for defining the metabolic phenotypes. The study highlights the need to critically examine phytopathogens whose metabolism is poorly understood.
Potent neutralization of 2019 novel coronavirus by recombinant ACE2-Ig
Authors: Lei Changhai , Fu Wenyan , Qian Kewen , Li Tian , Zhang Sheng , Ding Min , Hu Shi 
Published: February 2020

Abstract2019-nCoV, which is a novel coronavirus emerged in Wuhan, China, at the end of 2019, has caused at least infected 11,844 as of Feb 1, 2020. However, there is no specific antiviral treatment or vaccine currently. Very recently report had suggested that novel CoV would use the same cell entry receptor, ACE2, as the SARS-CoV. In this report, we generated a novel recombinant protein by connecting the extracellular domain of human ACE2 to the Fc region of the human immunoglobulin IgG1. An ACE2 mutant with low catalytic activity was also used in the study. The fusion proteins were then characterized. Both fusion proteins has high affinity binding to the receptor-binding domain (RBD) of SARS-CoV and 2019-nCoV and exerted desired pharmacological properties. Moreover, fusion proteins potently neutralized SARS-CoV and 2019-nCoVin vitro.As these fusion proteins exhibit cross-reactivity against coronaviruses, they could have potential applications for diagnosis, prophylaxis, and treatment of 2019-nCoV.
Macrophage Scavenger Receptor 1 mediates lipid-induced inflammation in non-alcoholic fatty liver disease
Authors: Govaere Olivier , Kragh Petersen Sine , Martinez-Lopez Nuria , Wouters Jasper , Van Haele Matthias , Mancina Rosellina M. , Jamialahmadi Oveis , Bilkei-Gorzo Orsolya , Bel Lassen Pierre , Darlay Rebecca , Peltier Julien , Palmer Jeremy M. , Younes Ramy , Tiniakos Dina , Aithal Guruprasad P. , Allison Michael , Vacca Michele , Göransson Melker , Drinnan Michael J , Yki-Järvinen Hannele , Dufour Jean-Francois , Ekstedt Mattias , Francque Sven , Petta Salvatore , Bugianesi Elisabetta , Schattenberg Jörn M , Day Christopher P. , Cordell Heather J. , Topal Baki , Clément Karine , Romeo Stefano , Ratziu Vlad , Roskams Tania , Daly Ann K. , Anstee Quentin M. , Trost Matthias , Härtlova Anetta 
Published: February 2020

AbstractObesity-associated inflammation is a key player in the pathogenesis of non-alcoholic fatty liver disease (NAFLD). However, the exact mechanisms remain incompletely understood. Here we demonstrate that macrophage scavenger receptor 1 (MSR1, CD204) expression is associated with the occurrence of hepatic lipid-laden foamy macrophages and correlates with the degree of steatosis and steatohepatitis in a cohort of 170 NAFLD patients. Mice lacking Msr1 are protected against high fat-cholesterol diet (HFD)-induced metabolic disorder, showing fewer hepatic lipid-laden foamy macrophages, less hepatic inflammation, improved dyslipidemia and glucose tolerance, while showing a change in hepatic lipid metabolism. We show that MSR1 induces a pro-inflammatory response via the JNK signaling pathway upon triggering by saturated fatty acids.In vitroblockade of the receptor prevented the accumulation of lipids in primary macrophages which inhibited the switch towards a pro-inflammatory phenotype and the release of cytokines such as TNFa. Targeting MSR1 using monoclonal antibody therapy in an obesity-associated NAFLD mouse model andex vivohuman liver slices resulted in the prevention of foamy macrophage formation and liver inflammation. Moreover, we identified that rs41505344, a polymorphism in the upstream transcriptional region ofMSR1,was associated with altered serum triglycerides and aspartate transaminase levels in a cohort of over 400,000 patients. Taken together, our data suggest a critical role for MSR1 in lipid homeostasis and a potential therapeutic target for the treatment of NAFLD.One Sentence SummaryThe immunometabolic role of MSR1 in human NAFLD.
Scleraxis-Lineage Cell Depletion Improves Tendon Healing and Disrupts Adult Tendon Homeostasis
Authors: Best Katherine T. , Korcari Antonion , Mora Keshia E. , Knapp Emma , Buckley Mark R. , Loiselle Alayna E. 
Published: February 2020

AbstractDespite the requirement forScleraxis-lineage (ScxLin) cells during tendon development, the function of ScxLincells during adult tendon repair, post-natal growth, and adult homeostasis have not been defined. Therefore, we inducibly depleted ScxLincells (ScxLinDTR) prior to tendon injury and repair surgery and hypothesized that ScxLinDTRmice would exhibit functionally deficient healing compared to wildtype littermates. Surprisingly, depletion of ScxLincells resulted in increased biomechanical properties without impairments in gliding function at 28 days post-repair, indicative of regeneration. RNA sequencing of day 28 post-repair tendons highlighted differences in matrix-related genes, cell motility, cytoskeletal organization, and metabolism. We also utilized ScxLinDTRmice to define the effects on post-natal tendon growth and adult tendon homeostasis and discovered that adult ScxLincell depletion resulted in altered tendon collagen fibril diameter, density, and dispersion. Collectively, these findings enhance our fundamental understanding of tendon cell localization, function, and fate during healing, growth, and homeostasis.
FK506-binding protein FklB is involved in biofilm formation through its peptidyl-prolyl isomerase activity
Authors: Zografou Chrysoula , Dimou Maria , Katinakis Panagiotis 
Published: February 2020

AbstractFklB is a member of the FK506-binding proteins (FKBPs), a family that consists of five genes inEscherichia coli. Little is known about the physiological and functional role of FklB in bacterial movement. In the present study, FklB knock-out mutant ΔfklBpresented an increased swarming and swimming motility and biofilm formation phenotype, suggesting that FklB is a negative regulator of these cellular processes. Complementation with Peptidyl-prolyl isomerase (PPIase)-deficientfklBgene(Y181A) revealed that the defects in biofilm formation were not restored byY181A, indicating that PPIase activity of FklB is modulating biofilm formation inE. coli. The mean cell length of ΔfklBswarming cells was significantly smaller as compared to the wild-type BW25113. Furthermore, the mean cell length of swarming and swimming wild-type and ΔfklBcells overexpressingfklBorY181Awas considerably larger, suggesting that PPIase activity of FklB plays a role in cell elongation and/or cell division. A multi-copy suppression assay demonstrated that defects in motility and biofilm phenotype were compensated by overexpressing sets of PPIase-encoding genes. Taken together, our data represent the first report demonstrating the involvement of FklB in cellular functions ofE. coli.
For emancipation: a Marxist critique of structure within critical realism
Authors: Andrew Jane , Baker Max 
Published: February 2020

PurposeThe authors critique Modell's proposition that critical realism is useful in elucidating and creating possibilities for emancipation.Design/methodology/approachThe authors begin by outlining Modell's conception of enabling structures. If ‘activated’ by reflexive individuals, these are theorised to be a mechanism through which agents can begin to emancipate themselves. However, the authors argue that emancipation must be contextualised within the material realities of global capitalism, paying particular attention to the shape of inequality and the subjects of exploitation. In doing this, they draw on Marx to pose an alternative view of structure.FindingsIn offering a Marxist critique of critical realism, the authors show how capitalist superstructure and base work together to reinforce inequality. In doing this, they highlight the enduring importance of collective action as the engine of emancipation. It is for this reason that they advocate for an emancipatory politics, which is collectively informed outside of, and in conflict with, the logics of capitalism.Research limitations/implicationsThe authors argue that explicit discussions of capitalism and its structures must be at the centre of critical accounting research, especially when it pertains to emancipation.Originality/valueGiven the importance of the conceptual framing of critical accounting research, this article suggests that critical realism has much to offer. That said, the authors draw on Marx to raise a number of important questions about both the nature of structure and the identity of reflexive agents within critical realism. They do this to encourage further debate about the emancipatory possibilities of the critical accounting project and the ideas proposed by Modell (2020).
An exploratory factor analysis of HONOS-LD scales
Authors: Turton Rai 
Published: February 2020

Purpose
The purpose of this study is to identify clinically meaningful groups of Health of the Nation Scales Learning Disabilities (HONOS-LD) single-item scales that might be used as short scales that are more reliable than single-item scale scores and more focused than the sum of scale scores. The single-item scales are likely to be unreliable in many applications. The sum of scale scores is a heterogeneous measure that is not a good representative of any specific difficulties that people who have intellectual disabilities may have and the effects of interventions on any specific difficulties may be masked by fluctuations in the ratings of other scales.

Design/methodology/approach
A total of 2,109 pseudonymised complete HONOS-LD ratings were factor-analysed using principal factor extraction and oblimin rotation. Three-, four- and five-factor rotated patterns were examined.

Findings
Three factors that each have three or more strong loadings (≥|0.50|) were identified that jointly included 11 single-item scales: one representing problems with cognitive competencies, one representing depressive phenomena or other mood problems and one representing problems with social competencies. A weaker factor that represents behaviour that challenges services is indicated; it includes five single-item scales. Both the cognitive competencies and social competencies groups of items were also reported in a previous study by Skelly and D’Antonio (2008) and may be stable. The present study’s factor representing behavioural difficulty has some similarity to Skelly and D’Antonio’s “functional behaviour and attachment disturbance” group. In other respects, the present study and the previous study differ.

Research limitations/implications
The outcomes of these factor analyses indicate that some of the single-item scales can be combined into groups. However, the specific groups found in this study must be regarded as possibly unstable because of the likelihood of weak inter-rater reliability in HONOS-LD data and differences between this analysis and Skelly and D’Antonio’s. Further research is needed to support or modify them.

Practical implications
The cognitive competence and social competence groups of items may be used as subscales if they are convenient. The groups representing mood and behavioural problems should be supported by further research before being used.

Originality/value
This is the second published factor analysis of the HONOS-LD and includes a much larger data set than the first. It has some similarities to and differences from the first and is a further step in the process of identifying useful groupings of HONOS-LD single-item scales.