bluuebunny/crossref_metadata_2025 huggingface dataset:
Bayesian estimation of the global biogeographical history of the Solanaceae
Authors: Dupin Julia , Matzke Nicholas J. , Särkinen Tiina , Knapp Sandra , Olmstead Richard G. , Bohs Lynn , Smith Stacey D.
Published: November 2016

Aim

The tomato family Solanaceae is distributed on all major continents except Antarctica and has its centre of diversity in South America. Its worldwide distribution suggests multiple long‐distance dispersals within and between the New and Old Worlds. Here, we apply maximum likelihood (ML) methods and newly developed biogeographical stochastic mapping (BSM) to infer the ancestral range of the family and to estimate the frequency of dispersal and vicariance events resulting in its present‐day distribution.

Location

Worldwide.

Methods

Building on a recently inferred megaphylogeny of Solanaceae, we conducted ML model fitting of a range of biogeographical models with the program ‘BioGeoBEARS’. We used the parameters from the best fitting model to estimate ancestral range probabilities and conduct stochastic mapping, from which we estimated the number and type of biogeographical events.

Results

Our best model supported South America as the ancestral area for the Solanaceae and its major clades. The BSM analyses showed that dispersal events, particularly range expansions, are the principal mode by which members of the family have spread beyond South America.

Main conclusions

For Solanaceae, South America is not only the family's current centre of diversity but also its ancestral range, and dispersal was the principal driver of range evolution. The most common dispersal patterns involved range expansions from South America into North and Central America, while dispersal in the reverse direction was less common. This directionality may be due to the early build‐up of species richness in South America, resulting in large pool of potential migrants. These results demonstrate the utility of BSM not only for estimating ancestral ranges but also in inferring the frequency, direction and timing of biogeographical events in a statistically rigorous framework.
Undercarboxylated osteocalcin can predict insulin secretion ability in type 2 diabetes
Authors: Takashi Yuichi , Koga Minae , Matsuzawa Yoko , Saito Jun , Omura Masao , Nishikawa Tetsuo
Published: November 2016

It has been reported that there is an intimate relationship between diabetes and bone metabolism including undercarboxylated osteocalcin (ucOC). In contrast, data on the relationship between ucOC and glucose metabolism are limited in type 2 diabetes. We recruited 50 Japanese patients with type 2 diabetes, and examined the association with ucOC on the insulin secretion, evaluated by both glucagon loading test and meal tolerance test. UcOC was shown to correlate positively with the change in C‐peptide response in the glucagon loading test and C‐peptide response after eating a meal (P = 0.025, P = 0.047). Therefore, ucOC reflects the reserve capacity of β‐cell function, such as the bolus insulin secretion ability in patients with type 2 diabetes.
Long‐term progression of viral load and serum markers of fibrosis among treated and untreated patients with chronic hepatitis B
Authors: Li Jia , Gordon Stuart C , Rupp Loralee B , Zhang Talan , Trudeau Sheri , Holmberg Scott D , Moorman Anne C , Spradling Philip R , Teshale Eyasu H , Boscarino Joseph A , Daida Yihe G , Schmidt Mark A , Lu Mei ,   for the CHeCS Investigators
Published: November 2016

Background and Aims

Antiviral therapy for patients with hepatitis B (HBV) infection is generally deferred for “immune inactive” patients, although longitudinal changes in viral load and liver fibrosis remain understudied in this population. Likewise, in treated patients, the temporal relationship between changes in viral load and liver fibrosis is not well characterized. Using data from the chronic hepatitis cohort study, the study investigated viral load and the Fibrosis‐4 index (FIB4, a serum‐based marker of liver fibrosis) trajectories in both untreated and treated HBV patients.

Materials and Methods

We applied a bivariate, piecewise, linear spline, mixed‐effects modeling approach to data from 766 HBV patients (342 untreated, 424 treated). Treatment selection bias was adjusted using propensity scores. Multiple sensitivity analyses were used to confirm results in untreated patients.

Results

Among all untreated patients, FIB4 began to increase by 0.9% per month (11% per year; P < 0.05) at 28 months post‐index date, suggesting fibrosis progression. Significant FIB4 progression was also observed in a subgroup analysis of “immune inactive” untreated patients. In treated patients, viral load declined 31.8% per month (P < 0.05) for the first 5 months after treatment initiation, and 1.4–1.7% per month (P < 0.05) thereafter. At 5 months after treatment initiation, FIB4 began to decline 0.5% per month (P < 0.05), stabilizing at 28 months.

Conclusion

Among untreated HBV patients, FIB4 gradually increases over time, suggesting fibrosis progression, even in those patients designated as immune inactive. In treated patients, antiviral therapy results in a rapid decline in viral load followed by a delayed decline in markers of liver fibrosis.
Self‐Reported Masticatory Dysfunction and Mortality in Community Dwelling Elderly Adults: A 9‐Year Follow‐Up
Authors: Laudisio Alice , Gemma Antonella , Fontana Davide O. , Rivera Chiara , Bandinelli Stefania , Ferrucci Luigi , Incalzi Raffaele Antonelli
Published: November 2016

Objectives

To evaluate the association, if any, between masticatory dysfunction (MD) and mortality in older adults.

Design

The Invecchiare in Chianti (InCHIANTI) Study, a cohort study with 9‐year follow‐up.

Setting

Tuscany, Italy.

Participants

Individuals aged 65 and older (N = 1,155).

Measurements

MD was self‐reported; Cox regression was used to assess the association between self‐reported MD and 9‐year all‐cause mortality. This association was also evaluated after stratifying according to use of dentures. Analyses were adjusted for potential confounders, including demographic characteristics, lifestyle habits, comorbidities, nutrient intake, medications, and objective parameters.

Results

Four hundred five (35%) participants reported MD. Over the 9‐year follow‐up, 475 (41%) subjects died. According to Cox regression analysis, self‐reported MD was associated with higher mortality (relative risk (RR) = 1.23, 95% confidence interval (CI) = 1.02–1.48), after adjusting for potential confounders. In participants with self‐reported MD, uncorrected edentulism was the condition associated with the greatest risk of mortality (RR = 2.10, 95% CI = 1.07–4.14); use of dentures seemed to blunt this association (RR = 1.12, 95% CI = 0.87–1.44).

Conclusion

Self‐reported MD, chiefly when due to uncorrected edentulism, is associated with 9‐year all‐cause mortality in community‐dwelling elderly adults. Further studies are needed to evaluate whether the timely correction of MD using adequate dentures can increase the survival of older adults.
Interventions for the Management of Denture Stomatitis: A Systematic Review and Meta‐Analysis
Authors: Hilgert Juliana Balbinot , Giordani Jessye Melgarejo do Amaral , de Souza Raphael Freitas , Wendland Eliana Márcia Da Ros , D'Avila Otavio Pereira , Hugo Fernando Neves
Published: November 2016

Objectives

To assess the effectiveness of different interventions for treating or preventing denture stomatitis (DS).

Design

Systematic review.

Setting

Randomized controlled trials (RCTs) comparing any agent or procedure prescribed to treat or prevent DS in adults.

Participants

Older adults with denture stomatitis.

Measurements

There were two main outcomes reported in the trials included in this review: clinical signs of DS and remaining presence of yeast. There were no restrictions regarding language or date of publication. The search period was up to February 2016.

Results

Thirty‐five studies were included in the systematic review, with 32 judged as having high risk of bias. Three RCTs compared nystatin with placebo and found a significant effect on the reduction of clinical signs of stomatitis (risk ratio (RR) = 0.51, 95% confidence interval (CI) = 0.36–0.72), four RCTs compared nystatin with placebo and found a significant effect on mycological assessment (RR = 0.61, 95% CI = 0.46–0.80). Five studies of disinfectant agents also showed a significant effect in comparison with an inactive agent (RR = 0.52, 95% CI = 0.30–0.92) in clinical assessment. No evidence was found of an effect of miconazole, amphotericin, or imidazolic drugs. No RCT evaluated the effectiveness of preventive approaches.

Conclusion

The results are supportive of the use of nystatin and disinfecting agents in the treatment of DS, but clinicians need to be aware that individual studies had high risk of bias and that the overall quality of the individual reports was judged to be low.
Sp2 is the only glutamine‐rich specificity protein with minor impact on development and differentiation in myelinating glia
Authors: Wegener Amélie , Küspert Melanie , Sock Elisabeth , Philipsen Sjaak , Suske Guntram , Wegner Michael
Published: November 2016

Oligodendrocytes and Schwann cells are the myelinating glia of the vertebrate nervous system and by generation of myelin sheaths allow rapid saltatory conduction. Previous in vitro work had pointed to a role of the zinc finger containing specificity proteins Sp1 and Sp3 as major regulators of glial differentiation and myelination. Here, we asked whether such a role is also evident in vivo using mice with specific deletions of Sp1 or Sp3 in myelinating glia. We also studied glia‐specific conditional Sp2‐ and constitutive Sp4‐deficient mice to include all related glutamine‐rich Sp factors into our analysis. Surprisingly, we did not detect developmental Schwann cell abnormalities in any of the mutant mice. Oligodendrocyte development and differentiation was also not fundamentally affected as oligodendrocytes were present in all mouse mutants and retained their ability to differentiate and initiate myelin gene expression. The most severe defect we observed was a 50% reduction in Mbp‐ and proteolipid protein 1 (Plp1)‐positive differentiating oligodendrocytes in Sp2 mutants at birth. Unexpectedly, glial development appeared undisturbed even in the joint absence of Sp1 and Sp3. We conclude that Sp2 has a minor effect on the differentiation of myelinating glia, and that glutamine‐rich Sp proteins are not essential regulators of the process.

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The neuronal insulin receptor in its environment
Authors: Gralle Matthias
Published: November 2016

Insulin is known mainly for its effects in peripheral tissues, such as the liver, skeletal muscles and adipose tissue, where the activation of the insulin receptor (IR) has both short‐term and long‐term effects. Insulin and the IR are also present in the brain, and since there is evidence that neuronal insulin signaling regulates synaptic plasticity and that it is impaired in disease, this pathway might be the key to protection or reversal of symptoms, especially in Alzheimer's disease. However, there are controversies about the importance of the neuronal IR, partly because biophysical data on its activation and signaling are much less complete than for the peripheral IR. This review briefly summarizes the neuronal IR signaling in health and disease, and then focuses on known differences between the neuronal and peripheral IR with regard to alternative splicing and glycosylation, and lack of data with respect to phosphorylation and membrane subdomain localization. Particularities in the neuronal IR itself and its environment may have consequences for downstream signaling and impact synaptic plasticity. Furthermore, establishing the relative importance of insulin signaling through IR or through hybrids with its homolog, the insulin‐like growth factor 1 receptor, is crucial for evaluating the consequences of brain IR activation. An improved biophysical understanding of the neuronal IR may help predict the consequences of insulin‐targeted interventions.

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Deletion of the vesicular acetylcholine transporter from pedunculopontine/laterodorsal tegmental neurons modifies gait
Authors: Janickova Helena , Rosborough Kaie , Al‐Onaizi Mohammed , Kljakic Ornela , Guzman Monica S. , Gros Robert , Prado Marco A. M. , Prado Vania F.
Published: November 2016

Postural instability and gait disturbances, common disabilities in the elderly and frequently present in Parkinson's disease (PD), have been suggested to be related to dysfunctional cholinergic signaling in the brainstem. We investigated how long‐term loss of cholinergic signaling from mesopontine nuclei influence motor behaviors. We selectively eliminated the vesicular acetylcholine transporter (VAChT) in pedunculopontine and laterodorsal tegmental nuclei cholinergic neurons to generate mice with selective mesopontine cholinergic deficiency (VAChTEn1‐Cre‐flox/flox). VAChTEn1‐Cre‐flox/flox mice did not show any gross health or neuromuscular abnormality on metabolic cages, wire‐hang and grip‐force tests. Young VAChTEn1‐Cre‐flox/flox mice (2–5 months‐old) presented motor learning/coordination deficits on the rotarod; moved slower, and had smaller steps on the catwalk, but showed no difference in locomotor activity on the open field. Old VAChTEn1‐Creflox/flox mice (13–16 months‐old) showed more pronounced motor learning/balance deficits on the rotarod, and more pronounced balance deficits on the catwalk. Furthermore, old mutants moved faster than controls, but with similar step length. Additionally, old VAChT‐deficient mice were hyperactive. These results suggest that dysfunction of cholinergic neurons from mesopontine nuclei, which is commonly seen in PD, has causal roles in motor functions. Prevention of mesopontine cholinergic failure may help to prevent/improve postural instability and falls in PD patients.

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Read the Editorial Highlight for this article on page 688.
Multiregional analysis of global 5‐methylcytosine and 5‐hydroxymethylcytosine throughout the progression of Alzheimer's disease
Authors: Ellison Elizabeth M. , Abner Erin L. , Lovell Mark A.
Published: November 2016

Epigenetic modifications to cytosine are known to alter transcriptional states and deregulate gene expression in cancer, embryonic development, and most recently in neurodegeneration. To test the hypothesis that global levels of cytosine modification are altered throughout the progression of Alzheimer's disease, 5‐methylcytosine (5‐mC) and 5‐hydroxymethylcytosine (5‐hmC) were quantified using gas chromatography/mass spectrometry (GC/MS) and stable labeled internal standards of cytosine, 5‐mC, and 5‐hmC. Cytosine modifications were quantified in DNA extracted from tissue specimens of four brain regions (cerebellum, inferior parietal lobe, superior and middle temporal gyrus, and hippocampus/parahippocampal gyrus) of cognitively normal control (NC) subjects and subjects with mild cognitive impairment (MCI), preclinical Alzheimer's disease (PCAD), late onset Alzheimer's disease, frontotemporal lobar degeneration (FTLD) and dementia with Lewy bodies (DLB). Repeated measures analyses of the data show significant alterations in 5‐mC and 5‐hmC in early stages of Alzheimer's disease (PCAD and MCI), as well as FTLD and DLB subjects, across multiple regions of the brain. These data suggest alterations in epigenetic regulation of genes may play an early role in the progression of AD as well as other types of neurodegeneration.

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Constitutive regulation of the glutamate/aspartate transporter EAAT1 by Calcium‐Calmodulin‐Dependent Protein Kinase II
Authors: Chawla Aarti R. , Johnson Derrick E. , Zybura Agnes S. , Leeds Benjamin P. , Nelson Ross M. , Hudmon Andy
Published: November 2016

Glutamate clearance by astrocytes is an essential part of normal excitatory neurotransmission. Failure to adapt or maintain low levels of glutamate in the central nervous system is associated with multiple acute and chronic neurodegenerative diseases. The primary excitatory amino acid transporters in human astrocytes are EAAT1 and EAAT2 (GLAST and GLT‐1, respectively, in rodents). While the inhibition of calcium/calmodulin‐dependent kinase (CaMKII), a ubiquitously expressed serine/threonine protein kinase, results in diminished glutamate uptake in cultured primary rodent astrocytes (Ashpole et al. 2013), the molecular mechanism underlying this regulation is unknown. Here, we use a heterologous expression model to explore CaMKII regulation of EAAT1 and EAAT2. In transiently transfected HEK293T cells, pharmacological inhibition of CaMKII (using KN‐93 or tat‐CN21) reduces [3H]‐glutamate uptake in EAAT1 without altering EAAT2‐mediated glutamate uptake. While over‐expressing the Thr287Asp mutant to enhance autonomous CaMKII activity had no effect on either EAAT1 or EAAT2‐mediated glutamate uptake, over‐expressing a dominant‐negative version of CaMKII (Asp136Asn) diminished EAAT1 glutamate uptake. SPOTS peptide arrays and recombinant glutathione S‐transferase‐fusion proteins of the intracellular N‐ and C‐termini of EAAT1 identified two potential phosphorylation sites at residues Thr26 and Thr37 in the N‐terminus. Introducing an Ala (a non‐phospho mimetic) at Thr37 diminished EAAT1‐mediated glutamate uptake, suggesting that the phosphorylation state of this residue is important for constitutive EAAT1 function. Our study is the first to identify a glutamate transporter as a direct CaMKII substrate and suggests that CaMKII signaling is a critical driver of constitutive glutamate uptake by EAAT1.

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Life here beyond now: Chronotopes of the ideal life among Iranian transnationals
Authors: Karimzad Farzad
Published: November 2016

I address how U.S.‐based Iranian transnationals’ migration paths affect their (re)‐construction of chronotopes of the ideal life. Adopting an ethnographically grounded, discourse‐analytic approach, I illustrate how participants with student visas and U.S. Green Cards position themselves differently relative to images of success here [in the U.S.] and lack of success there [in Iran]. I argue that the chronotopes of success here and lack of success there (re)‐constructed by non‐resident Iranian students are prompted by a large‐scale cultural chronotope which pertains to their aspiration to stay in the U.S. This chronotope of ‘life beyond’ is less about a ‘remove from homeland’ and more about an ideal future in the host country. Migrants’ desires and anxieties, I argue, can determine what receives topical prominence in migration chronotopes – as in the case of Iranian educational migrants whose future positionings make temporality topically more prominent than spatiality.

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Cans and cants: Computational potentials for multimodality with a case study in head position
Authors: Voigt Rob , Eckert Penelope , Jurafsky Dan , Podesva Robert J.
Published: November 2016

As the study of embodiment and multimodality in interaction grows in importance, there is a need for novel methodological approaches to understand how multimodal variables pattern together along social and contextual lines, and how they systematically coalesce in communicative meanings. In this work, we propose to adopt computational tools to generate replicable annotations of bodily variables: these can be examined statistically to understand their patterning with other variables across diverse speakers and interactional contexts, and can help organize qualitative analyses of large datasets. We demonstrate the possibilities thereby with a case study in head cant (side‐to‐side tilt of the head) in a dataset of video blogs and laboratory‐collected interactions, computationally extracting cant and prosody from video and audio and analyzing their interactions, looking at gender in particular. We find that head cant indexes an orientation towards the interlocutor and a sense of shared understanding, can serve a ‘bracketing’ function in interaction (for speakers to create parentheticals or asides), and has gendered associations with prosodic markers and interactional discourse particles.
Risk stratification for locally advanced hepatocellular carcinoma using pretreatment alpha‐foetoprotein and 18F‐fluoro‐2‐deoxyglucose positron emission tomography
Authors: Rhee Woo Joong , Hwang Sang Hyun , Byun Hwa Kyung , Yun Mijin , Han Kwang‐Hyub , Seong Jinsil
Published: November 2016

Background & Aims

We investigated the significance of 18F‐fluoro‐2‐deoxyglucose positron emission tomography (18F‐FDG PET) parameters and alpha‐foetoprotein (AFP) levels in patients with locally advanced hepatocellular carcinoma (LA‐HCC).

Methods

We retrospectively analysed data of 228 patients with LA‐HCC who underwent pretreatment 18F‐FDG PET between January 2003 and December 2013. All patients were treated using liver‐directed therapy involving radiotherapy. The maximum standardized uptake values (SUVs) and tumour‐to‐extratumoural liver SUV ratios were calculated, and pretreatment AFP values were obtained.

Results

Patients were divided into high and low maximum SUV (SUVmax) groups according to a SUV cut‐off of 4.825 determined via receiver‐operating characteristic analysis. High AFP level (>550 ng/mL) and high SUVmax were significant predictors of overall and progression‐free survival. Better treatment responses and longer median progression‐free and overall survival were observed in the low SUVmax group, compared to the high SUVmax group. Similar results were obtained for SUV ratio‐based (cut‐off value: 2.355) and AFP‐based analyses (cut‐off value: 550 ng/mL). Three risk groups were identified using the double biomarkers of SUVmax and AFP value as strong prognosticators predictive of survival outcomes. This risk stratification was identified as a prognosticator of survival outcomes, even after subgroup analyses. Furthermore, in high risk group, significantly high extrahepatic failure was shown while in low risk group, significantly low intrahepatic failure.

Conclusions

Clinical significance of double biomarkers, SUV and AFP, could be translated into risk stratification for LA‐HCC. It could be a valuable tool for survival outcome prediction.
Vascular cell transcriptomic changes to exercise training differ directionally along and between skeletal muscle arteriolar trees
Authors: Laughlin M. Harold , Yang Hsiao T. , Tharp Darla L. , Rector R. Scott , Padilla Jaume , Bowles Douglas K.
Published: November 2016

EXT‐induced arteriolar adaptations in skeletal muscle are heterogeneous because of spatial variations in muscle fiber type composition and fiber recruitment patterns during exercise. The purpose of this report is to summarize a series of experiments conducted to test the hypothesis that changes in vascular gene expression are signaled by alterations in shear stress resulting from increases in blood flow, muscle fiber type composition, and fiber recruitment patterns. We also report results from a follow‐up study of Ankrd23, one gene whose expression was changed by EXT. We expected to see differences in magnitude of changes in gene expression along arteriolar trees and between/among arteriolar trees but similar directional changes. However, transcriptional profiles of arterioles/arteries from OLETF rats exposed to END or SIT reveal that EXT does not lead to similar directional changes in the transcriptome among arteriolar trees of different skeletal muscles or along arteriolar trees within a particular muscle. END caused the most changes in gene expression in 2A arterioles of soleus and white gastrocnemius with little to no changes in the FAs. Ingenuity Pathway Analysis across vessels revealed significant changes in gene expression in 18 pathways. EXT increased expression of some genes (Shc1, desert hedgehog protein (Dhh), adenylate cyclase 4 (Adcy4), G protein‐binding protein, alpha (Gnat1), and Bcl2l1) in all arterioles examined, but decreased expression of ubiquitin D (Ubd) and cAMP response element modulator (Crem). Many contractile and/or structural protein genes were increased by SIT in the gastrocnemius FA, but the same genes exhibited decreased expression in red gastrocnemius arterioles. Ankrd23 mRNA levels increased with increasing branch order in the gastrocnemius arteriolar tree and were increased 19‐fold in gastrocnemius muscle FA by SIT. Follow‐up experiments indicate that Ankrd23 mRNA level was increased 14‐fold in cannulated gastrocnemius FA when intraluminal pressure was increased from 90 and 180 cm H2O for 4 hours. Also, Ankrd23−/− mice exhibit limited ability to form collateral arteries following femoral artery occlusion compared to WT mice (angioscore WT=0.18±0.03; Ankrd23−/−=0.04±0.01). Further research will be required to determine whether Ankrd23 plays an important role in mechanically induced vascular remodeling of the arterial tree in skeletal muscle.
Natural antisense transcripts are linked to the modulation of mitochondrial function and teliospore dormancy in Ustilago maydis
Authors: Ostrowski Lauren A. , Saville Barry J.
Published: November 2016

The basidiomycete smut fungus Ustilago maydis causes common smut of corn. This disease is spread through the production of teliospores, which are thick‐walled dormant structures characterized by low rates of respiration and metabolism. Teliospores are formed when the fungus grows within the plant, and the morphological steps involved in their formation have been described, but the molecular events leading to dormancy are not known. In U. maydis, natural antisense transcripts (NATs) can function to alter gene expression and many NATs have increased levels in the teliospore. One such NAT is as‐ssm1 which is complementary to the gene for the mitochondrial seryl‐tRNA synthetase (ssm1), an enzyme important to mitochondrial function. The disruption of ssm1 leads to cell lysis, indicating it is also essential for cellular viability. To assess the function of as‐ssm1, it was ectopically expressed in haploid cells, where it is not normally present. This expression led to reductions in growth rate, virulence, mitochondrial membrane potential and oxygen consumption. It also resulted in the formation of as‐ssm1/ssm1 double‐stranded RNA and increased ssm1 transcript levels, but no change in Ssm1 protein levels was detected. Together, these findings suggest a role for as‐ssm1 in facilitating teliospore dormancy through dsRNA formation and reduction of mitochondrial function.
cAMP‐independent signal pathways stimulate hyphal morphogenesis in Candida albicans
Authors: Parrino Salvatore M. , Si Haoyu , Naseem Shamoon , Groudan Kevin , Gardin Justin , Konopka James B.
Published: November 2016

The fungal pathogen Candida albicans can transition from budding to hyphal growth, which promotes biofilm formation and invasive growth into tissues. Stimulation of adenylyl cyclase to form cAMP induces hyphal morphogenesis. The failure of cells lacking adenylyl cyclase (cyr1Δ) to form hyphae has suggested that cAMP signaling is essential for hyphal growth. However, cyr1Δ mutants also grow slowly and have defects in morphogenesis, making it unclear whether hyphal inducers must stimulate cAMP, or if normal basal levels of cAMP are required to maintain cellular health needed for hyphal growth. Interestingly, supplementation of cyr1Δ cells with low levels of cAMP enabled them to form hyphae in response to the inducer N‐acetylglucosamine (GlcNAc), suggesting that a basal level of cAMP is sufficient for stimulation. Furthermore, we isolated faster‐growing cyr1Δ pseudorevertant strains that can be induced to form hyphae even though they lack cAMP. The pseudorevertant strains were not induced by CO2, consistent with reports that CO2 directly stimulates adenylyl cyclase. Mutational analysis showed that induction of hyphae in a pseudorevertant strain was independent of RAS1, but was dependent on the EFG1 transcription factor that acts downstream of protein kinase A. Thus, cAMP‐independent signals contribute to the induction of hyphal responses.
Fine‐scale habitat use in Indo‐Pacific humpback dolphins, Sousa chinensis, may be more influenced by fish rather than vessels in the Pearl River Estuary, China
Authors: Pine Matthew K. , Wang Kexiong , Wang Ding
Published: November 2016

Shifts in habitat use and distribution patterns in dolphins are often concerns that can result from habitat degradation. We investigated how potential changes to a habitat from human activity may alter dolphin distributions within Lingding Bay in the Pearl River Estuary, China, by studying the relationship between fish choruses, vessel presence and Indo‐Pacific humpback dolphin (Sousa chinensis) detection rates. Analyses revealed temporal and spatial variation within fish choruses, vessel presence and dolphin detection rates. After accounting for any temporal autocorrelation, correlations between fish choruses and dolphin detection rates were also found; however, no relationship between fish choruses and vessel presence or dolphin detection rates and vessel presence were observed. Furthermore, fewer dolphins were detected at sites where fish activity was less intense. Thus fish activity, rather than vessels, may be a key factor influencing the distribution of the dolphins within the estuary. These findings emphasize the risk of potential shifts in habitat use for Indo‐Pacific humpback dolphins due to detrimental changes to prey availability and dolphin feeding grounds from human activity, such as overfishing and coastal developments, within the estuary. This is a critical conservation issue for this dolphin population that is facing intense anthropogenic pressure.
B‐cell activating factor, a predictor of antibody mediated rejection in kidney transplantation recipients
Authors: Pongpirul Wannarat , Chancharoenthana Wiwat , Pongpirul Krit , Leelahavanichkul Asada , Kittikowit Wipawee , Jutivorakool Kamonwan , Nonthasoot Bunthoon , Avihingsanon Yingyos , Eiam‐Ong Somchai , Praditpornsilpa Kearkiat , Townamchai Natavudh
Published: November 2016

Aim

Donor‐specific antibody (DSA) is a widely‐used biomarker for antibody‐mediated rejection (ABMR) but correctly indicates only 30–40% of patients with ABMR. Additional biomarkers of ABMR in kidney transplant recipients are needed.

Methods

All 68 kidney transplanted‐recipients enrolled in this study were negative for graft rejection as determined by surveillance‐biopsy ELISA at day 7 post‐transplantation. Allograft biopsy was then performed at 6 months post‐transplantation for subclinical‐ABMR detection. Recipients were stratified by pre‐transplant DSA and BAFF at day 7 into four groups.

Results

During the study period, 13.2% of the recipients demonstrated subclinical‐ABMR at 6 months, without patient with clinical ABMR presentations. Overall mean BAFF at day 7 was 393 pg/mL (95% CI = 316–471 pg/mL). The optimal cut‐off value for low vs. high BAFF level was 573 pg/mL, with sensitivity and specificity at 77.8% and 88.1%, respectively. Fifty percent of recipients with high BAFF at day 7 (14 patients) and only 3.7% of patients with low BAFF demonstrated ABMR (P < 0.05). Indeed, ABMR was more common in patients high BAFF level (hazard ratio = 7.30; 95% CI = 3.77–14.15). The prevalence of ABMR among negative pre‐transplant DSA/low BAFF, positive DSA/low BAFF, negative DSA/high BAFF, and positive DSA/ high BAFF recipients were 4.4, 0, 37.5 and 66.7%, respectively (P < 0.05).

Conclusions

Post‐transplant ABMR can be predicted by perioperative serum BAFF level. Together with DSA testing, BAFF provides additional predictive value for ABMR.
Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice
Authors: Brozynska Marta , Copetti Dario , Furtado Agnelo , Wing Rod A. , Crayn Darren , Fox Glen , Ishikawa Ryuji , Henry Robert J.
Published: November 2016

The related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon‐like population, referred to as Taxon A, and O. meridionalis‐like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short‐ and long‐read next‐generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A (diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement.
Development and field performance of nitrogen use efficient rice lines for Africa
Authors: Selvaraj Michael Gomez , Valencia Milton Orlando , Ogawa Satoshi , Lu Yingzhi , Wu Liying , Downs Christopher , Skinner Wayne , Lu Zhongjin , Kridl Jean C. , Ishitani Manabu , van Boxtel Jos
Published: November 2016

Nitrogen (N) fertilizers are a major input cost in rice production, and its excess application leads to major environmental pollution. Development of rice varieties with improved nitrogen use efficiency (NUE) is essential for sustainable agriculture. Here, we report the results of field evaluations of marker‐free transgenic NERICA4 (New Rice for Africa 4) rice lines overexpressing barley alanine amino transferase (HvAlaAT) under the control of a rice stress‐inducible promoter (pOsAnt1). Field evaluations over three growing seasons and two rice growing ecologies (lowland and upland) revealed that grain yield of pOsAnt1:HvAlaAT transgenic events was significantly higher than sibling nulls and wild‐type controls under different N application rates. Our field results clearly demonstrated that this genetic modification can significantly increase the dry biomass and grain yield compared to controls under limited N supply. Increased yield in transgenic events was correlated with increased tiller and panicle number in the field, and evidence of early establishment of a vigorous root system in hydroponic growth. Our results suggest that expression of the HvAlaAT gene can improve NUE in rice without causing undesirable growth phenotypes. The NUE technology described in this article has the potential to significantly reduce the need for N fertilizer and simultaneously improve food security, augment farm economics and mitigate greenhouse gas emissions from the rice ecosystem.
Petal micromorphology and its relationship to pollination
Authors: Costa V. B. S. , Pimentel R. M. M. , Chagas M. G. S. , Alves G. D. , Castro C. C.
Published: November 2016

The characteristics of petal epidermal conical cells affect the quality of the signals perceived by various pollinators. This study aimed to identify variations in micromorphological characteristics of flower petals and their relationship to melittophily, ornithophily and chiropterophily pollination systems.

The petals of 11 species were analysed using scanning electron microscopy and optical microscopy and the micromorphological traits were described, measured and compared using Tukey's test, PCA and cluster analysis.

Unlike chiropterophily, all melittophilous and some ornithophilous species possessed adaxial epidermal conical cells. Cluster grouping separated chiropterophilous flowers from melittophilous and ornithophilous. PCA analysis showed that the two morphometric profile of conical cells was the attribute that most strongly influenced the grouping of species. When considering the data set of the three pollination systems, melittophilous and ornithophilous plants were more similar to each other than they were to chriopterophilous species. The distance between conical cell apices is an important parameter in interactions with pollinators.

This study facilitated recognition of smoothing pollinator resource access through petal micromorphological characteristics. Further research regarding the biometry of micromorphological traits related to pollination is required.
Patterns of local and global redox variability during the Cenomanian–Turonian Boundary Event (Oceanic Anoxic Event 2) recorded in carbonates and shales from central Italy
Authors: Owens Jeremy D. , Lyons Timothy W. , Hardisty Dalton S. , Lowery Chris M. , Lu Zunli , Lee Bridget , Jenkyns Hugh C.
Published: November 2016

Careful evaluation of the local geochemical conditions in past marine settings can provide a window to the average redox state of the global ocean during episodes of extensive organic carbon deposition. These comparisons aid in identifying the interplay between climate and biotic feedbacks contributing to and resulting from these events. Well‐documented examples are known from the Mesozoic Era, which is characterized by episodes of widespread organic carbon deposition known as Oceanic Anoxic Events. This organic carbon burial typically leads to coeval positive carbon‐isotope excursions. Geochemical data are presented here for several palaeoredox proxies (Cr/Ti, V, Mo, Zn, Mn, Fe speciation, I/Ca and sulphur isotopes) from a section exposed at Furlo in the Marche–Umbrian Apennines of Italy that spans the Cenomanian–Turonian boundary. Here, Oceanic Anoxic Event 2 is represented by a ca 1 m thick radiolarian‐rich millimetre‐laminated organic‐rich shale known locally as the Bonarelli Level. Iron speciation data for thin organic‐rich intervals observed below the Bonarelli Level imply a local redox shift going into the Oceanic Anoxic Event, with ferruginous conditions (i.e. anoxic with dissolved ferrous iron) transiently developed prior to the event and euxinia (i.e. anoxic and sulphidic bottom waters) throughout the event itself. Pre‐Oceanic Anoxic Event enrichments of elements sensitive to anoxic water columns were due to initial development of locally ferruginous bottom waters as a precursor to the event. However, the greater global expanse of dysoxic to euxinic conditions during the Oceanic Anoxic Event greatly reduced redox‐sensitive trace‐metal concentrations in seawater. Pyrite sulphur isotopes document a positive excursion during the Oceanic Anoxic Event. Carbonate I/Ca ratios were generally low, suggesting locally reduced bottom‐water oxygen conditions preceding the event and relatively increased oxygen concentrations post‐event. Combined, the Furlo geochemical data suggest a redox‐stratified water column with oxic surface waters and a shallow chemocline overlying locally ferruginous bottom waters preceding the event, globally widespread euxinic bottom waters during the Oceanic Anoxic Event, followed by chemocline shallowing but sustained local redox stratification following the event.
Oceanic tectonic islands
Authors: Palmiotto Camilla , Corda Laura , Bonatti Enrico
Published: November 2016

The origin of oceanic islands has been the subject of much speculation, starting with Darwin almost two centuries ago. Two classes of oceanic islands can be identified: ‘volcanic islands’, which form due to excess volcanism caused by melting anomalies in the suboceanic mantle, and ‘tectonic islands’, which form due to transpressive and/or transtensional tectonics of blocks of oceanic lithosphere along transform faults. Modern and sunken tectonic islands from the Atlantic Ocean and Indian Ocean and the Caribbean Sea and Red Sea expose mantle and lower‐crust lithologies and display an elongated narrow morphology; in contrast, volcanic islands expose basalts and have near‐circular morphology. Both are often capped by carbonate platforms. The life cycle of tectonic islands tends to be more complex than that of most volcanic islands; their elongated narrow morphology, together with their tectonic instability and high seismicity, affect the architecture of the carbonate platforms capping them, limiting coral reef development and favouring rhodalgal–foramol biota associations.
Records of palaeo‐sea level and eruption duration in a coastal tuff ring, Jeju Island, Korea
Authors: Yoon Woo Seok , Yoon Seok Hoon , Sohn Chanwoo , Sohn Young Kwan
Published: November 2016

Phreatomagmatic volcanoes and their sedimentary products can preserve high‐resolution records of earth surface processes because of their high deposition rate. Songaksan, Jeju Island, Korea, is a phreatomagmatic volcano, which erupted c. 3.7 ka BP in a coastal setting. Its tuff ring preserves a record of intertidal to supratidal facies transition in the basal part, which reveals the position of palaeo‐high‐tide level for at least 13 high‐tide events, and a record of a storm‐surge event in the middle part of the tuff ring, which lasted approximately three tidal cycles. Based on these features, the phreatomagmatic eruption of Songaksan is estimated to have taken place over a month. The sea level at the time was almost identical to that at present. This study shows that coastal phreatomagmatic volcanoes can preserve high‐resolution records of eruption duration and palaeo‐sea level, and can provide accurately levelled and dated data points to the Quaternary sea‐level curve.
Interplay between stress permutations and overpressure to cause strike‐slip faulting during tectonic inversion
Authors: Peacock David C. P. , Tavarnelli Enrico , Anderson Mark W.
Published: November 2016

Field data from an orogenic foreland and an orogenic belt (the Mesozoic rocks of southern England and the Umbria‐Marche Apennines of Italy respectively) indicate the following. Firstly, stress evolution during the tectonic cycle, between maximum compressive stress (σ1) being vertical during extension and least compressive stress (σ3) being vertical during contraction, can involve phases when the intermediate compressive stress (σ2) is vertical, promoting strike‐slip deformation. Secondly, variations in the relative magnitudes of the stress axes are caused by variations in overburden and tectonic forces. Thirdly, overpressure can develop because of compaction during burial, and, as overburden is reduced during uplift and erosion, the vertical stress (σV) reduces but fluid pressure (Pf) remains approximately constant. Brittle deformation, including transient strike‐slip faults, reverse‐reactivated normal faults and normal‐reactivated thrusts, is preferentially developed in overpressured areas because high Pf promotes faulting.
Towards a whole‐genome sequence for rye (Secale cereale L.)
Authors: Bauer Eva , Schmutzer Thomas , Barilar Ivan , Mascher Martin , Gundlach Heidrun , Martis Mihaela M. , Twardziok Sven O. , Hackauf Bernd , Gordillo Andres , Wilde Peer , Schmidt Malthe , Korzun Viktor , Mayer Klaus F.X. , Schmid Karl , Schön Chris‐Carolin , Scholz Uwe
Published: November 2016

We report on a whole‐genome draft sequence of rye (Secale cereale L.). Rye is a diploid Triticeae species closely related to wheat and barley, and an important crop for food and feed in Central and Eastern Europe. Through whole‐genome shotgun sequencing of the 7.9‐Gbp genome of the winter rye inbred line Lo7 we obtained a de novo assembly represented by 1.29 million scaffolds covering a total length of 2.8 Gbp. Our reference sequence represents nearly the entire low‐copy portion of the rye genome. This genome assembly was used to predict 27 784 rye gene models based on homology to sequenced grass genomes. Through resequencing of 10 rye inbred lines and one accession of the wild relative S. vavilovii, we discovered more than 90 million single nucleotide variants and short insertions/deletions in the rye genome. From these variants, we developed the high‐density Rye600k genotyping array with 600 843 markers, which enabled anchoring the sequence contigs along a high‐density genetic map and establishing a synteny‐based virtual gene order. Genotyping data were used to characterize the diversity of rye breeding pools and genetic resources, and to obtain a genome‐wide map of selection signals differentiating the divergent gene pools. This rye whole‐genome sequence closes a gap in Triticeae genome research, and will be highly valuable for comparative genomics, functional studies and genome‐based breeding in rye.
Chitin receptor CERK1 links salt stress and chitin‐triggered innate immunity in Arabidopsis
Authors: Espinoza Catherine , Liang Yan , Stacey Gary
Published: November 2016

In nature, plants need to respond to multiple environmental stresses that require the involvement and fine‐tuning of different stress signaling pathways. Cross‐tolerance, in which plants pre‐treated with chitin (a fungal microbe‐associated molecular pattern) have improved salt tolerance, was observed in Arabidopsis, but is not well understood. Here, we show a unique link between chitin and salt signaling mediated by the chitin receptor CHITIN ELICITOR RECEPTOR KINASE 1 (CERK1). Transcriptome analysis revealed that salt stress‐induced genes are highly correlated with chitin‐induced genes, although this was not observed with other microbe‐associated molecular patterns (MAMPs) or with other abiotic stresses. The cerk1 mutant was more susceptible to NaCl than was the wild type. cerk1 plants had an irregular increase of cytosolic calcium ([Ca2+]cyt) after NaCl treatment. Bimolecular fluorescence complementation (BiFC) and co‐immunoprecipitation experiments indicated that CERK1 physically interacts with ANNEXIN 1 (ANN1), which was reported to form a calcium‐permeable channel that contributes to the NaCl‐induced [Ca2+]cyt signal. In turn, ann1 mutants showed elevated chitin‐induced rapid responses. In short, molecular components previously shown to function in chitin or salt signaling physically interact and intimately link the downstream responses to fungal attack and salt stress.
Differentiation of induced pluripotent stem cell–derived neutrophil granulocytes from common marmoset monkey (Callithrix jacchus)
Authors: Schrimpf Christopher , Wrede Christoph , Glage Silke , Hegermann Jan , Backhaus Samantha , Blasczyk Rainer , Heuft Hans‐Gert , Müller Thomas
Published: November 2016

BACKGROUND

Inherited and acquired marrow failure syndromes most commonly lead to defect in myeloid and/or neutrophil differentiation and/or function. Besides this, neutropenia induced by cancer‐adjusted chemotherapy is a frequent clinical problem. In both cases, cell replacement therapy is a well‐established, but due to necessity of donors limited and perilous procedure. Therefore, autologous cell replacement from patients' own marrow‐derived cells lowers risk and bares new possibilities for therapy. Since the immune system of the marmoset monkey is known to show high similarity to humans, preclinical studies with these animals bare high hopes for immunologic research and cell replacement therapy.

STUDY DESIGN AND METHODS

Marmoset‐induced pluripotent stem (iPS) cells (cj‐iPSC) were first cultivated on mouse embryonic feeder cells in medium containing recombinant human vascular endothelial growth factor. After 13 days, CD34+/vascular endothelial growth factor receptor‐2 (VEGFR2)– cells were sorted, treated with interleukin (IL‐3), thrombopoietin, and stem cell factor for 20 days and further cultivated with granulocyte–colony‐stimulating factor (G‐CSF) and IL‐3 for 10 days.

RESULTS

CD34+/VEGFR2– cells could be generated in high amounts (39.65 ± 6.01%; 2.31 × 105 cells). Afterward, these hematopoietic progenitors could be successfully differentiated into mature cj‐iPSC–derived neutrophils showing similar morphology, specific surface antigens, and neutrophil‐specific gene products and in vitro phagocytic activity.

CONCLUSION

cj‐iPSC–derived neutrophils bare high hopes in hematologic cell replacement therapy. They exhibit high morphologic similarity to native neutrophils and present neutrophil‐specific surface antigens, antimicrobial proteins, and gene products yielding an auspicious approach for continuative experiments including tests in living animals.