bluuebunny/crossref_metadata_2025_split huggingface dataset:
WDR5 modulates cell motility and morphology and controls nuclear changes induced by a 3D environment
Authors: Wang Pengbo , Dreger Marcel , Madrazo Elena , Williams Craig J. , Samaniego Rafael , Hodson Nigel W. , Monroy Francisco , Baena Esther , Sánchez-Mateos Paloma , Hurlstone Adam , Redondo-Muñoz Javier 
Published: July 2018

Significance
Cells require nuclear deformation to squeeze through tissue matrices. We have discovered that WD repeat domain 5 (WDR5; an epigenetic modulator of H3K4 methylation) is fundamental for cell polarity and migration in vitro and in vivo, independent of transcription. We have uncovered that the interactions between cells and the surrounding 3D confined conditions induce the upregulation of H3K4me3. Moreover, 3D environments control the deformability and the mechanical properties of the nucleus. We have identified that loss of WDR5 abrogates the H3K4 methylation and the nuclear changes induced by 3D conditions. Mechanistically, we found that myosin light chain kinase and myosin function were required for WDR5-mediated H3K4 methylation in 3D matrices. Our findings uncover functions of the epigenetic machinery when cells move through constricted conditions.
Rhinovirus induces an anabolic reprogramming in host cell metabolism essential for viral replication
Authors: Gualdoni Guido A. , Mayer Katharina A. , Kapsch Anna-Maria , Kreuzberg Katharina , Puck Alexander , Kienzl Philip , Oberndorfer Felicitas , Frühwirth Karin , Winkler Stefan , Blaas Dieter , Zlabinger Gerhard J. , Stöckl Johannes 
Published: July 2018

Significance
Rhinovirus (RV) is the causative agent of the common cold and other respiratory tract infections. Despite the vast prevalence, effective treatment or prevention strategies are lacking. Here, we analyzed metabolic alterations in infected cells and found a pronounced reprogramming of host cell metabolism toward an anabolic state, which involved enhancement of glucose uptake and glycogenolysis. We further demonstrate that these alterations can be reverted by treatment with 2-deoxyglucose, a glycolysis inhibitor, which results in a disruption of RV replication in vitro and in vivo. Thus, we show how the specific metabolic fingerprint of viral infection can be used to generate targets for antiviral therapy.
1.1-billion-year-old porphyrins establish a marine ecosystem dominated by bacterial primary producers
Authors: Gueneli N. , McKenna A. M. , Ohkouchi N. , Boreham C. J. , Beghin J. , Javaux E. J. , Brocks J. J. 
Published: July 2018

Significance
The oceans of Earth’s middle age, 1.8–0.8 billion years ago, were devoid of animal-like life. According to one hypothesis, the emergence of large, active organisms was restrained by the limited supply of large food particles such as algae. Through the discovery of molecular fossils of the photopigment chlorophyll in 1.1-billion-year-old marine sedimentary rocks, we were able to quantify the abundance of different phototrophs. The nitrogen isotopic values of the fossil pigments showed that the oceans were dominated by cyanobacteria, while larger planktonic algae were scarce. This supports the hypothesis that small cells at the base of the food chain limited the flow of energy to higher trophic levels, potentially retarding the emergence of large and complex life.
Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations
Authors: Duren Zhana , Chen Xi , Zamanighomi Mahdi , Zeng Wanwen , Satpathy Ansuman T. , Chang Howard Y. , Wang Yong , Wong Wing Hung 
Published: July 2018

Significance
Biological samples are often heterogeneous mixtures of different types of cells. Suppose we have two single-cell datasets, each providing information on a different cellular feature and generated on a different sample from this mixture. Then, the clustering of cells in the two samples should be coupled as both clusterings are reflecting the underlying cell types in the same mixture. This “coupled clustering” problem is a new problem not covered by existing clustering methods. In this paper, we develop an approach for its solution based on the coupling of two nonnegative matrix factorizations. The method should be useful for integrative single-cell genomics analysis tasks such as the joint analysis of single-cell RNA-sequencing and single-cell ATAC-sequencing data.
Local magnetism in MnSiPt rules the chemical bond
Authors: Rosner Helge , Leithe-Jasper Andreas , Carrillo-Cabrera Wilder , Schnelle Walter , Ackerbauer Sarah V. , Gamza Monika B. , Grin Yuri 
Published: July 2018

SignificanceA crystal structure can be understood as a result of bonding interactions (covalent, ionic, van der Waals, etc.) between the constituting atoms. If the forces caused by these interactions are equilibrated, the so-stabilized crystal structure should have the lowest energy. In such an atomic configuration, additional weaker atomic interactions may further reduce the total energy, influencing the final atomic arrangement. Indeed, in the intermetallic compound MnSiPt, a 3D framework is formed by polar covalent bonds between Mn, Si, and Pt atoms. Without taking into account the local spin polarization of manganese atoms, they would form Mn–Mn bonds within the framework. Surprisingly, the local magnetic moments of manganese prevent the formation of Mn–Mn bonds, thus changing decisively and significantly the final atomic arrangement.
Preordering of water is not needed for ice recognition by hyperactive antifreeze proteins
Authors: Hudait Arpa , Moberg Daniel R. , Qiu Yuqing , Odendahl Nathan , Paesani Francesco , Molinero Valeria 
Published: July 2018

Significance
Antifreeze proteins have evolved to inhibit ice growth in organisms living at subfreezing temperatures; the mechanism by which these proteins recognize and bind ice is not understood. It has been proposed that antifreeze proteins recognize ice by preordering water at the ice-binding site already in solution. Here we use multiresolution molecular simulations to demonstrate that preordering of interfacial water is not needed for ice recognition by antifreeze proteins. We predict that preordering could emerge on the large ice-binding surfaces of aggregates of ice-nucleating proteins, where it may assist with ice nucleation.
The Obligatory Coding Principle in diachronic perspective
Authors: Creissels Denis 
Published: July 2018

Abstract
The Obligatory Coding Principle accounts for the
inventories of possible coding frames in languages that, according
to the current terminology, can be characterized as consistently
accusative or consistently ergative in their system of argument
coding. In coding frame inventories fully consistent with the
Obligatory Coding principle, every coding frame includes a given
type of coding, either A (in obligatory A coding
languages) or P (in obligatory P coding
languages). However, languages with coding frame
inventories violating this principle are not exceptional. This
chapter examines the types of evolutions that may result either in
global shifts affecting the Obligatory Coding Principle, in
systematic violations of the Obligatory Coding Principle, or in the
gradual spreading of non-canonical coding frames. The idea
underlying this study is that, before discussing the theoretical
status of this kind of generalization, it is crucial to clarify its
involvement in diachronic processes.
Incipient hierarchical alignment in four Central Salish languages
from the Proto-Salish middle
Authors: Zahir Zalmai 
Published: July 2018

Abstract
There are three distinct transitive constructions in four Coast
Salish languages, Squamish, Halkomelem, Klallam and Lushootseed. In
the V-tr construction, both A and P are unmarked for case;
in the V-mid construction (often considered antipassive), A
is unmarked and P marked; in the V-tr-mid construction
(often considered passive), P is unmarked and A marked.
Individually, none of these constructions is a hierarchical system,
but in combination, asymmetries in their distribution are well on
the way to creating a person-based hierarchical system. This paper
discusses the diachronic development of each of these constructions,
then describes their differential distribution into the four
functional domains: local (SAP A → SAP P), direct
(SAP → 3P), nonlocal (3A → 3P), and
inverse (3A → SAP P). While the distribution is not
identical in each of the languages, the trend is clear: the
etymologically passive V-tr-mid construction cannot occur
in the direct domain and has become the pragmatically
unmarked construction in the inverse domain, whereas the
etymologically antipassive V-mid construction cannot occur
in the inverse domain. While it only occurs in the
direct and nonlocal domains, even there it is
rare, giving the appearance that its function is still that of an
antipassive. In combination, the result is that whenever the two
core arguments of a clause are an SAP and a third person, regardless
of grammatical role the SAP participant is always an unmarked core
argument, whereas the third person is most often marked, leading to
a situation where the oblique case in these languages is beginning
to resemble the obviative case-marker of inverse languages.
Monitoring and evaluating the payment-for-performance premise of REDD+: the case of India’s ecological fiscal transfers
Authors: Busch Jonah 
Published: July 2018

ABSTRACT

Introduction:
The central premise underlying international payments for Reducing Emissions from Deforestation and forest Degradation (REDD+) is that offering governments ex post payments for verified success in reducing emissions will motivate them to protect and restore forests. However, the extent to which performance-based payments motivate governments to protect and restore forests has yet to be evaluated quantitatively. Researchers have only quantitatively evaluated performance-based payments to non-governments for forest outcomes (e.g. payments for ecosystem services) and to governments for non-forest outcomes (e.g. results-based aid).

Methods:
We describe how researchers now have an opportunity to more easily evaluate performance-based payments to governments for forest outcomes thanks to India’s new ecological fiscal transfers (EFTs), which provide $6-12 billion per year to Indian states in proportion to their forest cover.

Discussion:
India’s EFTs differ from REDD+ programs in that they pay for states’ stock of forest area in the recent past rather than reductions in the rate of forest carbon loss in the near-future. Nevertheless, India’s EFTs focus on a single outcome and have many recipient governments, significant financial scale, lack of contemporaneous confounding policy changes, universal participation, and long-term data collection.

Conclusion:
These features make India’s EFTs especially useful for testing the payment-for-performance premise of REDD+.
Seizure burden pre- and postresection of low-grade gliomas as a predictor of tumor progression in low-grade gliomas
Authors: Santos-Pinheiro Fernando , Park Mingjeong , Liu Diane , Kwong Lawrence N , Cruz Savannah , Levine Nicholas B , O’Brien Barbara J , Chen Merry 
Published: July 2018

Abstract

Background
Low-grade gliomas (LGGs) are slow-growing, infiltrative tumors frequently associated with seizures. Predicting which patients will develop early tumor recurrence based on clinical indicators following initial surgical intervention remains a challenge. Seizure recurrence following surgery may be an early indicator of tumor recurrence, especially in patients presenting with increase in seizure frequency.

Methods
This study analyzed 148 patients meeting inclusion criteria (age >18 years, LGG diagnosis, at least 1 seizure event recorded before and after initial surgical intervention). All patients were treated at the Brain and Spine Center at The University of Texas MD Anderson Cancer Center from January 2000 to March 2013. Seizure frequency in a 6-month period before and after tumor resection was categorized as none, 1, few (2 to 3 seizures) or several (>3 seizures). Immediately postoperative seizures (up to 48 hours from surgery) were not included in the analysis.

Results
A total of 116 (78.4%) patients had seizures at initial presentation and most (95%) were started on antiepileptic drugs (AEDs). We found 2 clinical variables with a significant impact on progression-free survival (PFS): Higher seizure frequency during the 6-month postoperative period and seizure frequency increase between the 6-month pre- and the 6-month postoperative periods were both correlated to higher risk of early tumor recurrence (P = .007 and P = .004, respectively).

Conclusion
Seizure frequency following surgical resection of LGGs and the seizure frequency change between the 6-month preoperative and postoperative periods may serve as clinical predictors of early tumor recurrence in patients with LGGs who are also afflicted by seizures.
The Miniature-chemostat Aging Device: A new experimental platform facilitates assessment of the transcriptional and chromatin landscapes of replicatively aging yeast
Authors: Hendrickson David G. , Soifer Ilya , Wranik Bernd J. , Kim Griffin , Robles Michael , Gibney Patrick A. , McIsaac R. Scott 
Published: July 2018

AbstractReplicative aging of Saccharomyces cerevisiae is an established model system for eukaryotic cellular aging. A major limitation in yeast lifespan studies has been the difficulty of separating old cells from young cells in large quantities for in-depth comparative analyses. We engineered a new platform, the Miniature-chemostat Aging Device (MAD), that enables purification of aged cells at sufficient quantities to enable genomic and biochemical characterization of aging yeast populations. Using the MAD platform, we measured DNA accessibility (ATAC-Seq) and gene expression (RNA-Seq) changes in aging cells. Our data highlight an intimate connection between aging, growth rate, and stress, as many (but not all) genes that change with age have altered expression in cells that are subjected to stress. Stress-independent genes that change with age are highly enriched for targets of the signal recognition particle (SRP). By obtaining pure populations of old cells, we find that nucleosome occupancy does not change significantly with age; however, significant age-dependent changes in accessibility at ~12% of genomic loci reflect decreased replication and changing activities of cell cycle and metabolic regulators. Finally, ATAC-seq revealed that upregulating the proteasome by deleting UBR2 reduces rDNA instability usually observed in aging cells, demonstrating a connection between proteasome activity and genomic stability.
Heterogeneity of transposon expression and activation of the repressive network in human fetal germ cells
Authors: Reznik Boris , Cincotta Steven A. , Jaszczak Rebecca G. , Mateo Leslie J. , Shen Joel , Cao Mei , Baskin Laurence , Ye Ping , An Wenfeng , Laird Diana J. 
Published: July 2018

AbstractEpigenetic resetting in germ cells during development leads to the de-repression of transposable elements (TEs). piRNAs protect fetal germ cells from potentially harmful TEs by targeted destruction of mRNA and deposition of repressive epigenetic marks. Here we provide the first evidence for an active piRNA pathway and TE repression in germ cells of human fetal testis. We identify pre-pachytene piRNAs with features of secondary amplification that map most abundantly to L1 family TEs. We find that L1-ORF1p expression is heterogeneous in fetal germ cells, peaks at mid-gestation and declines concomitantly with increasing levels of piRNAs and H3K9me3, as well as nuclear localization of HIWI2. Surprisingly, following this decline, the same cells with accumulation of L1-ORF1p display highest levels of HIWI2 and H3K9me3, whereas L1-ORF1p low cells are also low in HIWI2 and H3K9me3. Conversely, earlier in development, the germ cells lacking L1-ORF1p express high levels of the chaperone HSP90a. We propose that a subset of HSP90a-armed germ cells resists L1 expression, whereas only those vulnerable L1-expressing germ cells activate the PIWI-piRNA repression pathway which leads to epigenetic silencing of L1 via H3K9me3.
A potential role for epigenetic processes in the acclimation response to elevated pCO2 in the model diatom Phaeodactylum tricornutum
Authors: Huang Ruiping , Ding Jiancheng , Gao Kunshan , de Carvalho Maria Helena Cruz , Tirichine Leila , Bowler Chris , Lin Xin 
Published: July 2018

AbstractUnderstanding of the molecular responses underpinning diatom responses to ocean acidification is fundamental for predicting how important primary producers will be shaped by the continuous rise in atmospheric CO2. In this study, we have analyzed global transcriptomic changes of the model diatom Phaeodactylum tricornutum following growth for 15 generations in elevated pCO2 by strand-specific RNA sequencing (ssRNA-seq). Our results indicate that no significant effects of elevated pCO2 and associated carbonate chemistry changes on the physiological performance of the cells were observed after 15 generations whereas the expression of genes encoding histones and other genes involved in chromatin structure were significantly down-regulated, while the expression of transposable elements (TEs) and genes encoding histone acetylation enzymes were significantly up-regulated. Furthermore, we identified a series of long non-protein coding RNAs (lncRNAs) specifically responsive to elevated pCO2, suggesting putative regulatory roles for these largely uncharacterized genome components. Taken together, our integrative analyses reveal that epigenetic elements such as TEs, histone modifications and lncRNAs may have important roles in the acclimation of diatoms to elevated pCO2 over short time scales and thus may influence longer term adaptive processes in response to progressive ocean acidification.
A new reporter cell line for studies with proteasome inhibitors in Trypanosoma brucei
Authors: Moura Danielle MN , de Melo Neto Osvaldo P , Carrington Mark 
Published: July 2018

AbstractA Trypanosoma brucei cell line is described that produces a visual readout of proteasome activity. The cell line contains an integrated transgene encoding an ubiquitin-green fluorescent protein (GFP) fusion polypeptide responsive to the addition of proteasome inhibitors. A modified version of T. brucei ubiquitin unable to be recognized by deubiquitinases (UbG76V) was fused to eGFP and constitutively expressed. The fusion protein is unstable but addition of the proteasome inhibitor lactacystin stabilizes it and leads to visually detectable GFP. This cell line can be widely used to monitor the efficiency of inhibitor treatment through detection of GFP accumulation in studies involving proteasome-mediated proteolysis, screening of proteasome inhibitors or other events related to the ubiquitin-proteasome pathway.
Metabolic diversity of bacteria and yeast from commercial probiotic products illustrated by phenotypic profiling
Authors: Ansari Juliana M. , Colasacco Christine , Emmanouil Elli , Kohlhepp Scott , Harriott Olivia 
Published: July 2018

AbstractThe number of probiotic products in the marketplace is on the rise, gaining momentum along with the upsurge in research on the role of the human gut microbiome in health. Although such products are considered safe for consumption, these probiotic supplements and beverages are not subject to stringent federal regulation for quality. While only certain strains of probiotic microbes have been studied for efficacy in clinical trials, the ingredient labels of commercial probiotics do not always list the strain names. In this study, we investigated the diversity of the bacteria and yeast sold in these products. From a representative selection of commercially available probiotic supplements and beverages, we cultured microbes and identified them with standard methods (16S rRNA gene sequencing, mass spectrometric identification, and Biolog phenotypic profiling), then assessed whether there were strain-specific differences in nutrient metabolism and tolerance to compounds across the isolates from different products. Bacillus coagulans, Bacillus subtilis, Lactobacillus plantarum, Lactobacillus rhamnosus, and the yeast Saccharomyces boulardii were cultured from 21 commercial probiotic products (fifteen probiotic supplements and six probiotic beverages). Phenotypic profiling revealed metabolic diversity in carbon source usage and tolerance to compounds, within species from different probiotics and from environmental isolates of strains belonging to the same species. Despite this strain level diversity, we observed that up to half of the probiotic supplements for sale in retail and drugstores only list the species, but not the specific strain, on the label. This study highlights that existing labeling conventions for probiotics are insufficient to convey the strain identity and diversity in these products, underscoring the need for clear strain identification and verification of strain-specific probiotic properties, particularly when moving toward therapeutic applications of beneficial microbes.
Mushroom body specific transcriptome analysis reveals dynamic regulation of learning and memory genes after acquisition of long-term courtship memory inDrosophila
Authors: Jones Spencer G. , Nixon Kevin C.J. , Kramer Jamie M. 
Published: July 2018

AbstractThe formation and recall of long-term memory (LTM) requires neuron activity-induced gene expression. Transcriptome analysis has been used to identify genes that have altered expression after memory acquisition, however, we still have an incomplete picture of the transcriptional changes that are required for LTM formation. The complex spatial and temporal dynamics of memory formation creates significant challenges in defining memory-relevant gene expression changes. The mushroom body (MB) is a signaling hub in the insect brain that integrates sensory information to form memories. Here, we performed transcriptome analysis in theDrosophilaMB at two time points after the acquisition of LTM: 1 hour and 24 hours. The MB transcriptome was compared to biologically paired whole head (WH) transcriptomes. In both, we identified more transcriptional changes 1 hour after memory acquisition (WH = 322, MB = 302) than at 24 hours (WH = 23, MB = 20). WH samples showed downregulation of developmental genes and upregulation of sensory response genes. In contrast, MB samples showed vastly different gene expression changes affecting biological processes that are specifically related to LTM. MB-downregulated genes were highly enriched for metabolic function, consistent with the MB-specific energy influx that occurs during LTM formation. MB-upregulated genes were highly enriched for known learning and memory processes, including calcium-mediated neurotransmitter release and cAMP signalling. The neuron activity inducible geneshr38andsrwere also specifically induced in the MB. These results highlight the importance of sampling time and cell type in capturing biologically relevant transcriptional changes involved in learning and memory. Our data suggests that MB cells transiently upregulate known memory-related pathways after memory acquisition and provides a critical frame of reference for further investigation into the role of MB-specific gene regulation in memory.