bluuebunny/crossref_metadata_2025 huggingface dataset:
ZmCCT9
enhances maize adaptation to higher latitudes
Authors: Huang Cheng , Sun Huayue , Xu Dingyi , Chen Qiuyue , Liang Yameng , Wang Xufeng , Xu Guanghui , Tian Jinge , Wang Chenglong , Li Dan , Wu Lishuan , Yang Xiaohong , Jin Weiwei , Doebley John F. , Tian Feng
Published: December 2017

Significance

Flowering time is a critical determinant of crop adaptation to local environments. As a result of natural and artificial selection, maize has evolved a reduced photoperiod sensitivity to adapt to regions over 90° of latitude in the Americas. Here we show that a distant Harbinger-like transposon acts as a
cis
-regulatory element to repress
ZmCCT9
expression to promote flowering under the long days of higher latitudes. The transposon at
ZmCCT9
and another functional transposon at a second flowering-time gene,
ZmCCT10
, arose sequentially following domestication and were targeted by selection as maize spread from the tropics to higher latitudes. Our results demonstrate that new functional variation created by transposon insertions helped maize to spread over a broad range of latitudes rapidly.
Structural and molecular basis of mismatch correction and ribavirin excision from coronavirus RNA
Authors: Ferron François , Subissi Lorenzo , Silveira De Morais Ana Theresa , Le Nhung Thi Tuyet , Sevajol Marion , Gluais Laure , Decroly Etienne , Vonrhein Clemens , Bricogne Gérard , Canard Bruno , Imbert Isabelle
Published: December 2017

Significance

Emerging coronaviruses (CoVs; severe acute respiratory syndrome-CoV and Middle East respiratory syndrome-CoV) pose serious health threats globally, with no specific antiviral treatments available. These viruses are able to faithfully synthesize their large genomic RNA. We report, however, that their main RNA polymerase, nsp12, is not accurate. To achieve accuracy, CoVs have acquired nsp14, a bifunctional enzyme able to methylate the viral RNA cap [methyltransferase (MTase)] and excise erroneous mutagenic nucleotides inserted by nsp12. Strikingly, ribavirin can be excised from the viral genome, thus showing no antiviral activity. The crystal structure of nsp14 shows that it is unique, having been replaced by other MTase types during evolution. This unprecedented RNA correction machinery has allowed RNA genome size expansion, but also provided potential nucleoside drug resistance to these deadly pathogens.
Structure–function insights into direct lipid transfer between membranes by Mmm1–Mdm12 of ERMES
Authors: Kawano Shin , Tamura Yasushi , Kojima Rieko , Bala Siqin , Asai Eri , Michel Agnès H. , Kornmann Benoît , Riezman Isabelle , Riezman Howard , Sakae Yoshitake , Okamoto Yuko , Endo Toshiya
Published: December 2017

The endoplasmic reticulum (ER)–mitochondrial encounter structure (ERMES) physically links the membranes of the ER and mitochondria in yeast. Although the ER and mitochondria cooperate to synthesize glycerophospholipids, whether ERMES directly facilitates the lipid exchange between the two organelles remains controversial. Here, we compared the x-ray structures of an ERMES subunit Mdm12 from Kluyveromyces lactis with that of Mdm12 from Saccharomyces cerevisiae and found that both Mdm12 proteins possess a hydrophobic pocket for phospholipid binding. However in vitro lipid transfer assays showed that Mdm12 alone or an Mmm1 (another ERMES subunit) fusion protein exhibited only a weak lipid transfer activity between liposomes. In contrast, Mdm12 in a complex with Mmm1 mediated efficient lipid transfer between liposomes. Mutations in Mmm1 or Mdm12 impaired the lipid transfer activities of the Mdm12–Mmm1 complex and furthermore caused defective phosphatidylserine transport from the ER to mitochondrial membranes via ERMES in vitro. Therefore, the Mmm1–Mdm12 complex functions as a minimal unit that mediates lipid transfer between membranes.
Breastfeeding and Maternal Hypertension
Authors: Park Sangshin , Choi Nam-Kyong
Published: December 2017

BACKGROUND

Little is known about the relationship between breastfeeding and hypertension. We performed this study to identify whether breastfeeding itself influenced maternal hypertension and whether degree of obesity or insulin sensitivity would contribute to the relationship between breastfeeding and hypertension in postmenopausal women.

METHODS

Our study population comprised 3,119 nonsmoking postmenopausal women aged 50 years or above in the 2010–2011 Korea National Health and Nutrition Examination Survey. We performed logistic regression analyses to examine the relationship between breastfeeding and hypertension and mediation analyses to examine the contributions of obesity and insulin sensitivity to the breastfeeding-hypertension relationship.

RESULTS

The odds ratios, with 95% confidence intervals, for hypertension among the highest quintile of number of breastfed children (5–11) and the highest quintile of duration of breastfeeding (96–324 months) were 0.49 (0.31–0.75) and 0.55 (0.37–0.82), respectively, compared to each of lowest quintile groups. The population attributable fractions of hypertension caused by breastfeeding 3 or fewer children and breastfeeding for 56 months or less were 10.2% (P < 0.001) and 6.5% (P = 0.017), respectively. In the mediation analysis, unexpectedly, increased insulin resistance significantly attenuated the protective effect on hypertension of having breastfed more children; additionally, greater obesity and insulin resistance significantly attenuated the protective effects on hypertension of having breastfed for longer.

CONCLUSIONS

More children breastfed and longer duration of breastfeeding were associated with lower risk of hypertension in postmenopausal women, and degree of obesity and insulin resistance moderated the breastfeeding-hypertension association.
Stereotyped high-frequency oscillations discriminate seizure onset zones and critical functional cortex in focal epilepsy
Authors: Liu Su , Gurses Candan , Sha Zhiyi , Quach Michael M , Sencer Altay , Bebek Nerses , Curry Daniel J , Prabhu Sujit , Tummala Sudhakar , Henry Thomas R , Ince Nuri F
Published: December 2017

High-frequency oscillations in local field potentials recorded with intracranial EEG are putative biomarkers of seizure onset zones in epileptic brain. However, localized 80–500 Hz oscillations can also be recorded from normal and non-epileptic cerebral structures. When defined only by rate or frequency, physiological high-frequency oscillations are indistinguishable from pathological ones, which limit their application in epilepsy presurgical planning. We hypothesized that pathological high-frequency oscillations occur in a repetitive fashion with a similar waveform morphology that specifically indicates seizure onset zones. We investigated the waveform patterns of automatically detected high-frequency oscillations in 13 epilepsy patients and five control subjects, with an average of 73 subdural and intracerebral electrodes recorded per patient. The repetitive oscillatory waveforms were identified by using a pipeline of unsupervised machine learning techniques and were then correlated with independently clinician-defined seizure onset zones. Consistently in all patients, the stereotypical high-frequency oscillations with the highest degree of waveform similarity were localized within the seizure onset zones only, whereas the channels generating high-frequency oscillations embedded in random waveforms were found in the functional regions independent from the epileptogenic locations. The repetitive waveform pattern was more evident in fast ripples compared to ripples, suggesting a potential association between waveform repetition and the underlying pathological network. Our findings provided a new tool for the interpretation of pathological high-frequency oscillations that can be efficiently applied to distinguish seizure onset zones from functionally important sites, which is a critical step towards the translation of these signature events into valid clinical biomarkers.

5721572971001 awx374media1 5721572971001
Meaningful use’s benefits and burdens for US family physicians
Authors: Holman G Talley , Waldren Steven E , Beasley John W , Cohen Deborah J , Dardick Lawrence D , Fox Chester H , Marquard Jenna , Mullins Ryan , North Charles Q , Rafalski Matt , Rivera A Joy , Wetterneck Tosha B
Published: December 2017

Objective

The federal meaningful use (MU) program was aimed at improving adoption and use of electronic health records, but practicing physicians have criticized it. This study was aimed at quantifying the benefits (ie, usefulness) and burdens (ie, workload) of the MU program for practicing family physicians.

Materials and Methods

An interdisciplinary national panel of experts (physicians and engineers) identified the work associated with MU criteria during patient encounters. They conducted a national survey to assess each criterion’s level of patient benefit and compliance burden.

Results

In 2015, 480 US family physicians responded to the survey. Their demographics were comparable to US norms. Eighteen of 31 MU criteria were perceived as useful for more than half of patient encounters, with 13 of those being useful for more than two-thirds. Thirteen criteria were useful for less than half of patient encounters. Four useful criteria were reported as having a high compliance burden.

Discussion

There was high variability in physicians’ perceived benefits and burdens of MU criteria. MU Stage 1 criteria, which are more related to basic/routine care, were perceived as beneficial by most physicians. Stage 2 criteria, which are more related to complex and population care, were perceived as less beneficial and more burdensome to comply with.

Conclusion

MU was discontinued, but the merit-based incentive payment system within the Medicare Access and CHIP Reauthorization Act of 2015 adopted its criteria. For many physicians, MU created a significant practice burden without clear benefits to patient care. This study suggests that policymakers should not assess MU in aggregate, but as individual criteria for open discussion.
Clinical Use of Cerebrovascular Compliance Imaging to Evaluate Revascularization in Patients With Moyamoya
Authors: Watchmaker Jennifer M , Frederick Blaise deB , Fusco Matthew R , Davis Larry T , Juttukonda Meher R , Lants Sarah K , Kirshner Howard S , Donahue Manus J
Published: December 2017

BACKGROUND

Surgical revascularization is often performed in patients with moyamoya, however routine tools for efficacy evaluation are underdeveloped. The gold standard is digital subtraction angiography (DSA); however, DSA requires ionizing radiation and procedural risk, and therefore is suboptimal for routine surveillance of parenchymal health.

OBJECTIVE

To determine whether parenchymal vascular compliance measures, obtained noninvasively using magnetic resonance imaging (MRI), provide surrogates to revascularization success by comparing measures with DSA before and after surgical revascularization.

METHODS

Twenty surgical hemispheres with DSA and MRI performed before and after revascularization were evaluated. Cerebrovascular reactivity (CVR)-weighted images were acquired using hypercapnic 3-Tesla gradient echo blood oxygenation level-dependent MRI. Standard and novel analysis algorithms were applied (i) to quantify relative CVR (rCVRRAW), and decompose this response into (ii) relative maximum CVR (rCVRMAX) and (iii) a surrogate measure of the time for parenchyma to respond maximally to the stimulus, CVRDELAY. Measures between time points in patients with good and poor surgical outcomes based on DSA-visualized neoangiogenesis were contrasted (signed-rank test; significance: 2-sided P < .050).

RESULTS

rCVRRAW increases (P = .010) and CVRDELAY decreases (P = .001) were observed pre- vs post-revascularization in hemispheres with DSA-confirmed collateral formation; no difference was found pre- vs post-revascularization in hemispheres with poor revascularization. No significant change in rCVRMAX post-revascularization was observed in either group, or between any of the MRI measures, in the nonsurgical hemisphere.

CONCLUSION

Improvement in parenchymal compliance measures post-revascularization, primarily attributed to reductions in microvascular response time, is concurrent with collateral formation visualized on DSA, and may be useful for longitudinal monitoring of surgical outcomes.
Trigeminal Nerve Compression Without Trigeminal Neuralgia: Intraoperative vs Imaging Evidence
Authors: Jani Ronak H , Hughes Marion A , Gold Michael S , Branstetter Barton F , Ligus Zachary E , Sekula Raymond F
Published: December 2017

BACKGROUND

While high-resolution imaging is increasingly used in guiding decisions about surgical interventions for the treatment of trigeminal neuralgia, direct assessment of the extent of vascular contact of the trigeminal nerve is still considered the gold standard for the determination of whether nerve decompression is warranted.

OBJECTIVE

To compare intraoperative and magnetic resonance imaging (MRI) findings of the prevalence and severity of vascular compression of the trigeminal nerve in patients without classical trigeminal neuralgia.

METHODS

We prospectively recruited 27 patients without facial pain who were undergoing microvascular decompression for hemifacial spasm and had undergone high-resolution preoperative MRI. Neurovascular contact/compression (NVC/C) by artery or vein was assessed both intraoperatively and by MRI, and was stratified into 3 types: simple contact, compression (indentation of the surface of the nerve), and deformity (deviation or distortion of the nerve).

RESULTS

Intraoperative evidence of NVC/C was detected in 23 patients. MRI evidence of NVC/C was detected in 18 patients, all of whom had intraoperative evidence of NVC/C. Thus, there were 5, or 28% more patients in whom NVC/C was detected intraoperatively than with MRI (Kappa = 0.52); contact was observed in 4 of these patients and compression in 1 patient. In patients where NVC/C was observed by both methods, there was agreement regarding the severity of contact/compression in 83% (15/18) of patients (Kappa = 0.47). No patients exhibited deformity of the nerve by imaging or intraoperatively.

CONCLUSION

There was moderate agreement between imaging and operative findings with respect to both the presence and severity of NVC/C.
A Functional General Stress Response of Bradyrhizobium diazoefficiens Is Required for Early Stages of Host Plant Infection
Authors: Ledermann Raphael , Bartsch Ilka , Müller Barbara , Wülser Janine , Fischer Hans-Martin
Published: December 2017

Phylogenetically diverse bacteria respond to various stress conditions by mounting a general stress response (GSR) resulting in the induction of protection or damage repair functions. In α-proteobacteria, the GSR is induced by a regulatory cascade consisting of the extracytoplasmic function (ECF) σ factor σEcfG, its anti-σ factor NepR, and the anti-anti-σ factor PhyR. We have reported previously that σEcfG and PhyR of Bradyrhizobium diazoefficiens (formerly named Bradyrhizobium japonicum), the nitrogen-fixing root nodule symbiont of soybean and related legumes, are required for efficient symbiosis; however, the precise role of the GSR remained undefined. Here, we analyze the symbiotic defects of a B. diazoefficiens mutant lacking σEcfG by comparing distinct infection stages of enzymatically or fluorescently tagged wild-type and mutant bacteria. Although root colonization and root hair curling were indistinguishable, the mutant was not competitive, and showed delayed development of emerging nodules and only a few infection threads. Consequently, many of the mutant-induced nodules were aborted, empty, or partially colonized. Congruent with these results, we found that σEcfG was active in bacteria present in root-hair-entrapped microcolonies and infection threads but not in root-associated bacteria and nitrogen-fixing bacteroids. We conclude that GSR-controlled functions are crucial for synchronization of infection thread formation, colonization, and nodule development.
Liquid crystalline tactoids: ordered structure, defective coalescence and evolution in confined geometries
Authors: Wang Pei-Xi , MacLachlan Mark J.
Published: December 2017

Tactoids are liquid crystalline microdroplets that spontaneously nucleate from isotropic dispersions, and transform into macroscopic anisotropic phases. These intermediate structures have been found in a range of molecular, polymeric and colloidal liquid crystals. Typically only studied by polarized optical microscopy, these ordered but easily deformable microdroplets are now emerging as interesting components for structural investigations and developing new materials. In this review, we highlight the structure, property and transformation of tactoids in different compositions, but especially cellulose nanocrystals. We have selected references that illustrate the diversity and most exciting developments in tactoid research, while capturing the historical development of this field.

This article is part of a discussion meeting issue ‘New horizons for cellulose nanotechnology’.
Molecular interactions in nanocellulose assembly
Authors: Nishiyama Yoshiharu
Published: December 2017

The contribution of hydrogen bonds and the London dispersion force in the cohesion of cellulose is discussed in the light of the structure, spectroscopic data, empirical molecular-modelling parameters and thermodynamics data of analogue molecules. The hydrogen bond of cellulose is mainly electrostatic, and the stabilization energy in cellulose for each hydrogen bond is estimated to be between 17 and 30 kJ mol
−1
. On average, hydroxyl groups of cellulose form hydrogen bonds comparable to those of other simple alcohols. The London dispersion interaction may be estimated from empirical attraction terms in molecular modelling by simple integration over all components. Although this interaction extends to relatively large distances in colloidal systems, the short-range interaction is dominant for the cohesion of cellulose and is equivalent to a compression of 3 GPa. Trends of heat of vaporization of alkyl alcohols and alkanes suggests a stabilization by such hydroxyl group hydrogen bonding to be of the order of 24 kJ mol
−1
, whereas the London dispersion force contributes about 0.41 kJ mol
−1
 Da
−1
. The simple arithmetic sum of the energy is consistent with the experimental enthalpy of sublimation of small sugars, where the main part of the cohesive energy comes from hydrogen bonds. For cellulose, because of the reduced number of hydroxyl groups, the London dispersion force provides the main contribution to intermolecular cohesion.

This article is part of a discussion meeting issue ‘New horizons for cellulose nanotechnology’.
Clustering enzymes using E.coli inner cell membrane as scaffold in metabolic pathway
Authors: Wang You , Wu Yuqi , Suo Yang , Guo Huaqing , Yu Yineng , Yin Ruonan , Xi Rui , Wu Jiajie , Hua Nan , Zhang Yuehan , Zhang Shaobo , Jin Zhenming , Wang Yushu , He Lin , Ma Gang
Published: December 2017

Clustering enzymes in the same metabolism pathway is a natural strategy to enhance the productivity. Several systems have been designed to artificially cluster desired enzymes in the cell, such as synthetic protein scaffold and nucleic acid scaffold. However, these scaffolds require complicated construction process and have limited slots for target enzymes. Following this direction, we designed a scaffold system based on natural cell membrane. Target enzymes (FabZ, FabG, FabI and TesA’ in fatty acid synthesis II pathway) are anchored on the E.coli inner membrane, showing the enhanced metabolism flux without the requirement of the further artificial interactions to force the clustering. Furthermore, anchoring the enzymes on the membrane enhances the products exportation, which further increases the productivity. Together, the proposed system has potential applications in producing valuable biomaterials.
Genome-wide stability of the DNA replication program in single mammalian cells
Authors: Takahashi Saori , Miura Hisashi , Shibata Takahiro , Nagao Koji , Okumura Katsuzumi , Ogata Masato , Obuse Chikashi , Takebayashi Shin-ichiro , Hiratani Ichiro
Published: December 2017

Here, we report the establishment of asingle-cell DNAreplicationsequencing method, scRepli-seq, which is a simple genome-wide methodology that measures copy number differences between replicated and unreplicated DNA. Using scRepli-seq, we demonstrate that replication domain organization is conserved among individual mouse embryonic stem cells (mESCs). Differentiated mESCs exhibited distinct replication profiles, which were conserved from cell to cell. Haplotype-resolved scRepli-seq revealed similar replication timing profiles of homologous autosomes, while the inactive X chromosome was clearly replicated later than its active counterpart. However, a small degree of cell-to-cell replication timing heterogeneity was present, and we discovered that developmentally regulated domains are a source of such variability, suggesting a link between cell-to-cell heterogeneity and developmental plasticity. Together, our results form a foundation for single-cell-level understanding of DNA replication regulation and provide insights into 3D genome organization.
Caste-biased movements by termites in isolation
Authors: Hiroyuki Shimoji , Nobuaki Mizumoto , Kohei Oguchi , Shigeto Dobata
Published: December 2017

The caste system of termites is an example of phenotypic plasticity. The castes differ not only in morphology and physiology, but also in behavior. As most of their behaviors within colonies involve nestmates, it is difficult to extract innate differences among castes. In this study, we focused on movement patterns of isolated individuals ofHodotermopsis sjostedti. We observed distinct clusters in movement patterns over 30 min, which indicates that termites have multiple innate modes of movement. The use of these modes is biased among castes, among which neotenics had a caste-specific mode and soldiers moved more actively than workers or neotenics. These caste biases may reflect different adaptive responses to social isolation. Our study provides a basis for a deeper understanding of the roles of individual movements in social behaviors.

Summary Statement

Movement patterns of termites in isolation were described for different castes. We proposed movements as a novel caste-specific characteristics in social insects.
Epigenomic and genomic landscape ofDrosophila melanogasterheterochromatic genes
Authors: Saha Parna , Sowpati Divya Tej , Mishra Rakesh K
Published: December 2017

Heterochromatin is associated with transcriptional repression. In contrast, several genes in the pericentromeric regions ofDrosophila melanogasterare dependent on this heterochromatic environment for their expression. Heterochromatic genes encode proteins involved in various developmental processes. Several studies have shown that a variety of epigenetic modifications is associated with these genes. Here we present a comprehensive analysis of the epigenetic landscape of heterochromatic genes across all the developmental stages ofDrosophilausing the available histone modification and expression data from modENCODE. We find that heterochromatic genes exhibit combinations of active and inactive histone marks that correspond to their level of expression during development. Thus, we classified these genes into three groups based on the combinations of histone modifications present. We also looked for potential regulatory DNA sequence elements in the genomic neighborhood of these genes. Our results show that NuclearMatrixAssociatedRegions (MARs) are prominently present in the intergenic regions of heterochromatic genes during embryonic stages suggesting their plausible role in pericentromeric genome organization. We also find that the intergenic sequences in the heterochromatic regions have binding sites for transcription factors known to modulate epigenetic status. Taken together, our meta-analysis of the various genomic datasets suggest that the epigenomic and genomic landscape of the heterochromatic genes are distinct from that of euchromatic genes. These features could be contributing to the unusual regulatory status of the heterochromatic genes as opposed to the surrounding heterochromatin, which is repressive in nature.
Active learning reveals underlying decision strategies
Authors: Parpart Paula , Schulz Eric , Speekenbrink Maarten , Love Bradley C.
Published: December 2017

One key question is whether people rely on frugal heuristics orfull-informationstrategies when making preference decisions. We propose a novel method,model-based active learning, to answer whether people conform more to a rank-based heuristic (Take-The-Best) or a weight-based full-information strategy (logistic regression). Our method eclipses traditional model comparison techniques by using information theory to characterize model predictions for how decision makers should actively sample information. These analyses capture how sampling affects learning and how learning affects decisions on subsequent trials. We develop and test model-based active learning algorithms for both Take-The-Best and logistic regression. Our findings reveal that people largely follow a weight-based learning strategy rather than a rank-based strategy, even in cases where their preference decisions are better predicted by the Take-The-Best heuristic. This finding suggests that people may have more refined knowledge than is revealed by their preference decisions, but which can be revealed by their information sampling behavior. We argue that model-based active learning is an effective and sensitive method for model selection that expands the basis for model comparison.
AMBER: Assessment of Metagenome BinnERs
Authors: Meyer Fernando , Hofmann Peter , Belmann Peter , Garrido-Oter Ruben , Fritz Adrian , Sczyrba Alexander , McHardy Alice C.
Published: December 2017

Reconstructing the genomes of microbial community members is key to the interpretation of shotgun metagenome samples. Genome binning programs deconvolute reads or assembled contigs of such samples into individual bins, but assessing their quality is difficult due to the lack of evaluation software and standardized metrics. We present AMBER, an evaluation package for the comparative assessment of genome reconstructions from metagenome benchmark data sets. It calculates the performance metrics and comparative visualizations used in the first benchmarking challenge of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). As an application, we show the outputs of AMBER for ten different binnings on two CAMI benchmark data sets. AMBER is implemented in Python and available under the Apache 2.0 license on GitHub (https://github.com/CAMI-challenge/AMBER).
Rethinking dopamine as generalized prediction error
Authors: Gardner Matthew P.H. , Schoenbaum Geoffrey , Gershman Samuel J.
Published: December 2017

Midbrain dopamine neurons are commonly thought to report a reward prediction error, as hypothesized by reinforcement learning theory. While this theory has been highly successful, several lines of evidence suggest that dopamine activity also encodes sensory prediction errors unrelated to reward. Here we develop a new theory of dopamine function that embraces a broader conceptualization of prediction errors. By signaling errors in both sensory and reward predictions, dopamine supports a form of reinforcement learning that lies between model-based and model-free algorithms. This account remains consistent with current canon regarding the correspondence between dopamine transients and reward prediction errors, while also accounting for new data suggesting a role for these signals in phenomena such as sensory preconditioning and identity unblocking, which ostensibly draw upon knowledge beyond reward predictions.
Equivalent high-resolution identification of neuronal cell types with single-nucleus and single-cell RNA-sequencing
Authors: Bakken Trygve E. , Hodge Rebecca D. , Miller Jeremy M. , Yao Zizhen , Nguyen Thuc N. , Aevermann Brian , Barkan Eliza , Bertagnolli Darren , Casper Tamara , Dee Nick , Garren Emma , Goldy Jeff , Gray Lucas T. , Kroll Matthew , Lasken Roger S. , Lathia Kanan , Parry Sheana , Rimorin Christine , Scheuermann Richard H. , Schork Nicholas J. , Shehata Soraya I. , Tieu Michael , Phillips John W. , Bernard Amy , Smith Kimberly A. , Zeng Hongkui , Lein Ed S. , Tasic Bosiljka
Published: December 2017

Transcriptional profiling of complex tissues by RNA-sequencing of single nuclei presents some advantages over whole cell analysis. It enables unbiased cellular coverage, lack of cell isolation-based transcriptional effects, and application to archived frozen specimens. Using a well-matched pair of single-nucleus RNA-seq (snRNA-seq) and single-cell RNA-seq (scRNA-seq) SMART-Seq v4 datasets from mouse visual cortex, we demonstrate that similarly high-resolution clustering of closely related neuronal types can be achieved with both methods if intronic sequences are included in nuclear RNA-seq analysis. More transcripts are detected in individual whole cells (∼11,000 genes) than nuclei (∼7,000 genes), but the majority of genes have similar detection across cells and nuclei. We estimate that the nuclear proportion of total cellular mRNA varies from 20% to over 50% for large and small pyramidal neurons, respectively. Together, these results illustrate the high information content of nuclear RNA for characterization of cellular diversity in brain tissues.
Targeted Searches for Novel Peptides in Big Mass Spectrometry Data Sets
Authors: Gao Yu , Ma Jiao , Saghatelian Alan , Yates John R.
Published: December 2017

We present Post-Acquisition Targeted Searches (PATS), an easy-to-use tool that allows the identification of novel peptide/protein sequences from existing big mass spectrometry data sets. PATS filters out the unrelated peptidome before the time-consuming database search to significantly speed up the identification. Using interactome data sets, PATS visualizes protein interaction network and helps to assign putative functions to the target protein based on the “guilt by association” concept.
Rethinking “normal”: The role of stochasticity in the phenology of a synchronously breeding seabird
Authors: Youngflesh Casey , Jenouvrier Stephanie , Hinke Jefferson T. , DuBois Lauren , St. Leger Judy , Trivelpiece Wayne Z. , Trivelpiece Susan G. , Lynch Heather J.
Published: December 2017

Phenological changes have been observed in a variety of systems over the past century. There is concern that, as a consequence, ecological interactions are becoming increasingly mismatched in time, with negative consequences for ecological function.

Significant spatial heterogeneity (inter‐site) and temporal variability (inter‐annual) can make it difficult to separate intrinsic, extrinsic and stochastic drivers of phenological variability. The goal of this study was to understand the timing and variability in breeding phenology of Adélie penguins under fixed environmental conditions and to use those data to identify a “null model” appropriate for disentangling the sources of variation in wild populations.

Data on clutch initiation were collected from both wild and captive populations of Adélie penguins. Clutch initiation in the captive population was modelled as a function of year, individual and age to better understand phenological patterns observed in the wild population.

Captive populations displayed as much inter‐annual variability in breeding phenology as wild populations, suggesting that variability in breeding phenology is the norm and thus may be an unreliable indicator of environmental forcing. The distribution of clutch initiation dates was found to be moderately asymmetric (right skewed) both in the wild and in captivity, consistent with the pattern expected under social facilitation.

The role of stochasticity in phenological processes has heretofore been largely ignored. However, these results suggest that inter‐annual variability in breeding phenology can arise independent of any environmental or demographic drivers and that synchronous breeding can enhance inherent stochasticity. This complicates efforts to relate phenological variation to environmental variability in the wild. Accordingly, we must be careful to consider random forcing in phenological processes, lest we fit models to data dominated by random noise. This is particularly true for colonial species where breeding synchrony may outweigh each individual's effort to time breeding with optimal environmental conditions. Our study highlights the importance of identifying appropriate null models for studying phenology.
Transient movements of a deep‐water flatfish in coastal waters: Implications of inshore‐offshore connectivity for fisheries management
Authors: Barkley Amanda N. , Fisk Aaron T. , Hedges Kevin J. , Treble Margaret A. , Hussey Nigel E.
Published: December 2017

Globally, small‐scale inshore fisheries are being recognized as highly beneficial for underdeveloped coastal communities since they directly contribute to local economies. Community coastal fisheries, however, may target species that are simultaneously harvested by large commercial vessels in adjacent offshore waters, creating uncertainty over stock units and connectivity that complicate management.

Greenland halibut Reinhardtius hippoglossoides, a commercially important flatfish species in the Arctic, were tagged in Scott Inlet, coastal Baffin Island, Canada, with acoustic transmitters and tracked for a 1‐year period. Our aim was to measure fish movement and connectivity between inshore habitats, where Inuit fisheries are developing, and offshore waters, where an established commercial fishery operates. Four movement metrics were established, and cluster analysis and a mixed effects model were used to define movement types and identify environmental covariates of the presence/absence within the coastal environment respectively.

Two distinct movement patterns were characterized for Greenland halibut; the majority were transients that were no longer detected inshore by the end of November (n = 47, 72%), and a smaller group of intermittently resident fish that moved into the offshore at the same time as transient fish, but returned to the coastal environment in the winter (n = 8, 12%), with the remainder being undefined. The presence of Greenland halibut in the inshore was negatively correlated with ice cover, indicating that fish moved offshore as sea ice formed.

Synthesis and applications. Greenland halibut were previously thought to be highly resident within the coastal environment of Baffin Bay; however, our data demonstrates that this is not true for all areas. In Scott Inlet and adjacent coastal regions, Greenland halibut exhibit complex inshore‐offshore connectivity, suggesting inshore and offshore fisheries require a shared quota. We recommend that in the face of developing global small‐scale coastal fisheries, improved understanding of stock connectivity between environments is required to sustainably manage commercial fish species.
Effects of small‐scale, shading‐induced seagrass loss on blue carbon storage: Implications for management of degraded seagrass ecosystems
Authors: Trevathan‐Tackett Stacey M. , Wessel Caitlin , Cebrián Just , Ralph Peter J. , Masqué Pere , Macreadie Peter I.
Published: December 2017

Seagrass meadows are important global blue carbon sinks. Despite a 30% loss of seagrasses globally during the last century, there is limited empirical research investigating the effects of disturbance and loss of seagrass on blue carbon stocks.

In this study, we hypothesised that seagrass loss would reduce blue carbon stocks. Using shading cloth, we simulated small‐scale die‐offs of two subtropical seagrass species, Halodule wrightii and Thalassia testudinum, in a dynamic northern Gulf of Mexico lagoon. The change in quantity and quality of sediment organic matter (OM) and organic carbon was compared among die‐off, control and bare plots before the die‐off treatment, shortly after the die‐off treatment and 11 months after the die‐off treatment. 210Pb age dating was performed on bare and Thalassia plots at 11 months to evaluate the impact of sediment erosion in the absence of vegetation.

The small‐scale die‐off led to a 50%–65% OM loss in the sediment in the top 8 cm of Halodule plots. Thalassia plots lost significant portions of OM (50%) and organic carbon (Corg; 21%–47%) in only the top 1 cm of sediment. The 210Pb profiles indicated Thalassia die‐off reduced the Corg sequestration rate by 10%, in addition to a loss of c. 1 year's worth of Corg stocks (c. 22 g/m2). Furthermore, analyses on OM/Corg quality indicated a loss of labile OM/Corg and enhanced remineralisation by microbes.

Synthesis and applications. This study provides empirical evidence that small‐scale shading‐induced seagrass die‐offs can reduce seagrass carbon sequestration capacity and trigger losses of blue carbon stocks. While the losses recorded here are modest, these losses in blue carbon storage capacity are notable due to the proximity of shading structures (e.g. boat docks) to seagrass habitats. Thus, policies to avoid or protect seagrass habitats from common small‐scale, shading disturbances are important for optimising both carbon sequestration capacity and coastline development and management.
Nutrient limitation or home field advantage: Does microbial community adaptation overcome nutrient limitation of litter decomposition in a tropical peatland?
Authors: Hoyos‐Santillan Jorge , Lomax Barry H. , Turner Benjamin L. , Sjögersten Sofie
Published: December 2017

Litter decomposition is an important control on carbon accumulation in tropical peatlands. Stoichiometric theory suggests that decomposition is regulated by elemental ratios in litter while the home field advantage (HFA) hypothesis predicts that decomposer communities are adapted to local conditions. To date, the relative importance of these contrasting theories for litter decomposition and therefore the carbon balance of tropical peatlands remain poorly understood.

We conducted two in situ litter decomposition experiments in a lowland tropical peatland. The first experiment tested the importance of the stoichiometric theory using a factorial nutrient addition experiment at two sites with contrasting vegetation (Raphia taedigera and Campnosperma panamensis) to assess how nutrient addition affected microbial enzyme activity and litter mass loss at the peat surface and at 50 cm depth. The second experiment tested the importance of HFA by reciprocal translocation of leaf litter from R. taedigera and C. panamensis forests, which differed in both litter chemistry and soil nutrient availability, to separate the influence of litter chemistry and soil/site properties on litter mass loss.

The activities of hydrolytic enzymes involved in the decomposition of large plant polymers were stimulated by nitrogen addition only where nitrogen availability was low relative to phosphorus, and were stimulated by phosphorus addition where phosphorus availability was low.

The addition of nitrogen, but not phosphorus, increased leaf litter decomposition under waterlogged conditions at 50 cm depth, but not at the peat surface.

Decomposition was greatest for autochthonous litter irrespective of site nutrient status, indicating that adaptation of the microbial community to low nutrients can partly overcome nutrient limitation, and suggesting that HFA can influence litter decomposition rates.

Synthesis. Our study shows that leaf litter decomposition and the activity of microbial enzymes in tropical peatlands are constrained in part by nutrient availability. However, such nutrient limitation of litter decomposition can be overcome by adaptation of the microbial community.
Ecosystem nitrogen retention is regulated by plant community trait interactions with nutrient status in an alpine meadow
Authors: Wang Fangping , Shi Guoxi , Nicholas Ostle , Yao Buqing , Ji Mingfei , Wang Wenying , Ma Zhen , Zhou Huakun , Zhao Xinquan
Published: December 2017

Biotic nitrogen (N) retention is an important ecosystem function in the context of ongoing land‐use intensification, N deposition and global warming. However, a paucity of experimental evidence limits understanding of how different plant community components influence N retention in terrestrial ecosystems.

In this investigation, we conducted a 15N labelling experiment to test how plant community properties, including plant species richness/diversity, dominance and functional traits, influence plant N uptake and retention under different nutrient availabilities. A 3‐year experiment examined the effects of adding N (10 g N m−2 year−1) and phosphorus (P) (5 g P m−2 year−1) to an alpine meadow on the Qinghai‐Tibetan Plateau.

Results show that 15N retention increased with the addition of N and P; the addition of P produced the largest increase of 15N retention in plant and soil N pools. Changes in soil nutrient conditions also facilitated different plant community controls on ecosystem N retention. Ecosystem 15N retention was influenced by species richness and root biomass in the control plots; whereas the N addition treatment showed an important effect of community‐weighted means (CWM) of specific leaf area, and plots with additional P recorded lower CWM of root nitrogen content (root N) and larger CWM root:shoot ratios as important determinants.

Synthesis. Ecosystem N retention was influenced by conservative and exploitative plant species and/or their traits under N deficient and abundant conditions, respectively, whereas species richness and community plant biomass were most influential under middle condition. The discovery of an interaction between plant community traits and nutrient biogeochemistry as a mechanism for ecosystem N retention offers a means to predict how vegetation in alpine meadow ecosystems will respond to expected global change.
The roots of the drought: Hydrology and water uptake strategies mediate forest‐wide demographic response to precipitation
Authors: Chitra‐Tarak Rutuja , Ruiz Laurent , Dattaraja Handanakere S. , Mohan Kumar M. S. , Riotte Jean , Suresh Hebbalalu S. , McMahon Sean M. , Sukumar Raman
Published: December 2017

Drought‐induced tree mortality is expected to increase globally due to climate change, with profound implications for forest composition, function and global climate feedbacks. How drought is experienced by different species is thought to depend fundamentally on where they access water vertically below‐ground, but this remains untracked so far due to the difficulty of measuring water availability at depths at which plants access water (few to several tens of metres), the broad temporal scales at which droughts at those depths unfold (seasonal to decadal), and the difficulty in linking these patterns to forest‐wide species‐specific demographic responses.

We address this problem through a new eco‐hydrological framework: we used a hydrological model to estimate below‐ground water availability by depth over a period of two decades that included a multi‐year drought. Given this water availability scenario and 20 year long‐records of species‐specific growth patterns, we inversely estimated the relative depths at which 12 common species in the forest accessed water via a model of water stress. Finally, we tested whether our estimates of species relative uptake depths predicted mortality in the multi‐year drought.

The hydrological model revealed clear below‐ground niches as precipitation was decoupled from water availability by depth at multi‐annual scale. Species partitioned the hydrological niche by diverging in their uptake depths and so in the same forest stand, different species experienced very different drought patterns, resulting in clear differences in species‐specific growth. Finally, species relative water uptake depths predicted species mortality patterns after the multi‐year drought. Species that our method ranked as relying on deeper water were the ones that had suffered from greater mortality, as the zone from which they access water took longer to recharge after depletion.

Synthesis. This research changes our understanding of how hydrological niches operate for trees, with a trade‐off between realized growth potential and survival under drought with decadal scale return time. The eco‐hydrological framework highlights the importance of species‐specific below‐ground strategies in predicting forest response to drought. Applying this framework more broadly may help us better understand species coexistence in diverse forest communities and improve mechanistic predictions of forests productivity and compositional change under future climate.
Growing numbers, growing influence? A comparative study of policy congruence between parliaments and citizens of immigrant origin
Authors: KROEBER CORINNA
Published: December 2017

A large set of research argues that policy responsiveness towards excluded societal factions such as minorities of immigrant origin improves through the presence of group members in parliaments because they bring forward different perspectives during parliamentary debates. This article challenges the straightforwardness of this relationship by demonstrating that the ability of legislators with immigrant backgrounds to shift the parliamentary agenda closer to the ideal points of citizens of foreign descent is conditional on two factors. First, representatives of immigrant origin need incentives to cultivate a personal vote, and second, their overall proportion of parliamentary seats has to remain rather marginal to influence the policy positions of the majority of representatives. The article's findings thus stress the importance of studying the contextual factors that moderate the relationship between group belonging and the capacity to promote group interests. Empirical evidence from nine European Democracies between 2002 and 2014 substantiates this argument – so that the analysis constitutes the first cross‐country comparison in a research field that has so far been dominated by single country studies. By using policy congruence as a measure for responsiveness, this article shifts the focal point from individual representatives’ attempts to promote the interests of citizens with immigrant backgrounds towards effectiveness of these endeavours.
Biological Activities of Camelina and Sophia Seeds Phenolics: Inhibition of LDL Oxidation, DNA Damage, and Pancreatic Lipase and α‐Glucosidase Activities
Authors: Rahman Md. Jiaur , Ambigaipalan Priyatharini , Shahidi Fereidoon
Published: December 2017

The free, esterified and insoluble‐bound phenolics of defatted meals of camelina and sophia seeds were extracted using an ultrasonic‐assisted procedure and alkaline hydrolysis. The antioxidant activities of the extracts were evaluated using DPPH and hydroxyl radical scavenging assays as well as inhibition of bleaching of β‐carotene in an oil‐in‐water system. Moreover, inhibition activity against pancreatic lipase, α‐glucosidase, low density lipoprotein (LDL) oxidation and DNA damage induced by peroxyl and hydroxyl radicals were examined for all seed extracts using in vitro systems. The seed extracts of camelina and sophia not only showed significant antioxidant activity but also inhibited pancreatic lipase and α‐glucosidase activities effectively. These enzymes in the digestive tract are associated with lipid and carbohydrate digestion, respectively, and control obesity and blood glucose level in the human body. The findings of this work may provide supporting information that camelina and sophia meals may inhibit human LDL oxidation and DNA nicking caused by free radicals and upon consumption may also exert anti‐obesity and antidiabetic effects. However, further research is required to confirm these biological activities in vivo.

Practical Application

The seed phenolic extracts of camelina and sophia not only showed significant antioxidant activity but also effectively inhibited the activities of pancreatic lipase and α‐glucosidase. Thus, camelina and sophia seed meals may serve as nutritional ingredients with bioactive phenolics that show in vitro antioxidant and biological effects. However, further research is required to confirm these health effects in vivo.