bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of a novel starfish neuropeptide that acts as a muscle relaxant
Authors: Kim Chan‐Hee , Kim Eun Jung , Go Hye‐Jin , Oh Hye Young , Lin Ming , Elphick Maurice R. , Park Nam Gyu
Published: January 2016

Neuropeptides that act as muscle relaxants have been identified in chordates and protostomian invertebrates but little is known about the molecular identity of neuropeptides that act as muscle relaxants in deuterostomian invertebrates (e.g. echinoderms) that are ‘evolutionary intermediates’ of chordates and protostomes. Here, we have used the apical muscle of the starfish Patiria pectinifera to assay for myorelaxants in extracts of this species. A hexadecapeptide with the amino acid sequence Phe‐Gly‐Lys‐Gly‐Gly‐Ala‐Tyr‐Asp‐Pro‐Leu‐Ser‐Ala‐Gly‐Phe‐Thr‐Asp was identified and designated starfish myorelaxant peptide (SMP). Cloning and sequencing of a cDNA encoding the SMP precursor protein revealed that it comprises 12 copies of SMP as well as 3 peptides (7 copies in total) that are structurally related to SMP. Analysis of the expression of SMP precursor transcripts in P. pectinifera using qPCR revealed the highest expression in the radial nerve cords and lower expression levels in a range of neuromuscular tissues, including the apical muscle, tube feet and cardiac stomach. Consistent with these findings, SMP also caused relaxation of tube foot and cardiac stomach preparations. Furthermore, SMP caused relaxation of apical muscle preparations from another starfish species – Asterias amurensis. Collectively, these data indicate that SMP has a general physiological role as a muscle relaxant in starfish. Interestingly, comparison of the sequence of the SMP precursor with known neuropeptide precursors revealed that SMP belongs to a bilaterian family of neuropeptides that include molluscan pedal peptides (PP) and arthropodan orcokinins (OK). This is the first study to determine the function of a PP/OK‐type peptide in a deuterostome.

image

Pedal peptide/orcokinin (PP/OK)‐type peptides are a family of structurally related neuropeptides that were first identified and functionally characterised in protostomian invertebrates. Here, we report the discovery of starfish myorelaxant peptide (SMP), a novel member of the PP/OK‐type neuropeptide identified in the starfish Patiria pectinifera (phylum Echinodermata). SMP is the first PP/OK‐type neuropeptide to be functionally characterised in a deuterostome.
2‐Methylcitric acid impairs glutamate metabolism and induces permeability transition in brain mitochondria
Authors: Amaral Alexandre Umpierrez , Cecatto Cristiane , Castilho Roger Frigério , Wajner Moacir
Published: January 2016

Accumulation of 2‐methylcitric acid (2MCA) is observed in methylmalonic and propionic acidemias, which are clinically characterized by severe neurological symptoms. The exact pathogenetic mechanisms of brain abnormalities in these diseases are poorly established and very little has been reported on the role of 2MCA. In the present work we found that 2MCA markedly inhibited ADP‐stimulated and uncoupled respiration in mitochondria supported by glutamate, with a less significant inhibition in pyruvate plus malate respiring mitochondria. However, no alterations occurred when α‐ketoglutarate or succinate was used as respiratory substrates, suggesting a defect on glutamate oxidative metabolism. It was also observed that 2MCA decreased ATP formation in glutamate plus malate or pyruvate plus malate‐supported mitochondria. Furthermore, 2MCA inhibited glutamate dehydrogenase activity at concentrations as low as 0.5 mM. Kinetic studies revealed that this inhibitory effect was competitive in relation to glutamate. In contrast, assays of osmotic swelling in non‐respiring mitochondria suggested that 2MCA did not significantly impair mitochondrial glutamate transport. Finally, 2MCA provoked a significant decrease in mitochondrial membrane potential and induced swelling in Ca2+‐loaded mitochondria supported by different substrates. These effects were totally prevented by cyclosporine A plus ADP or ruthenium red, indicating induction of mitochondrial permeability transition. Taken together, our data strongly indicate that 2MCA behaves as a potent inhibitor of glutamate oxidation by inhibiting glutamate dehydrogenase activity and as a permeability transition inducer, disturbing mitochondrial energy homeostasis. We presume that 2MCA‐induced mitochondrial deleterious effects may contribute to the pathogenesis of brain damage in patients affected by methylmalonic and propionic acidemias.

image

We propose that brain glutamate oxidation is disturbed by 2‐methylcitric acid (2MCA), which accumulates in tissues from patients with propionic and methylmalonic acidemias because of a competitive inhibition of glutamate dehydrogenase (GDH) activity. 2MCA also induced mitochondrial permeability transition (PT) and decreased ATP generation in brain mitochondria. We believe that these pathomechanisms may be involved in the neurological dysfunction of these diseases.
Hypothalamic Wnt Signalling and its Role in Energy Balance Regulation
Authors: Helfer G. , Tups A.
Published: January 2016

Wnt signalling and its downstream effectors are well known for their roles in embryogenesis and tumourigenesis, including the regulation of cell proliferation, survival and differentiation. In the nervous system, Wnt signalling has been described mainly during embryonic development, although accumulating evidence suggests that it also plays a major role in adult brain morphogenesis and function. Studies have predominantly concentrated on memory formation in the hippocampus, although recent data indicate that Wnt signalling is also critical for neuroendocrine control of the developed hypothalamus, a brain centre that is key in energy balance regulation and whose dysfunction is implicated in metabolic disorders such as type 2 diabetes and obesity. Based on scattered findings that report the presence of Wnt molecules in the tanycytes and ependymal cells lining the third ventricle and arcuate nucleus neurones of the hypothalamus, their potential importance in key regions of food intake and body weight regulation has been investigated in recent studies. The present review brings together current knowledge on Wnt signalling in the hypothalamus of adult animals and discusses the evidence suggesting a key role for members of the Wnt signalling family in glucose and energy balance regulation in the hypothalamus in diet‐induced and genetically obese (leptin deficient) mice. Aspects of Wnt signalling in seasonal (photoperiod sensitive) rodents are also highlighted, given the recent evidence indicating that the Wnt pathway in the hypothalamus is not only regulated by diet and leptin, but also by photoperiod in seasonal animals, which is connected to natural adaptive changes in food intake and body weight. Thus, Wnt signalling appears to be critical as a modulator for normal functioning of the physiological state in the healthy adult brain, and is also crucial for normal glucose and energy homeostasis where its dysregulation can lead to a range of metabolic disorders.
MFN2‐related genetic and clinical features in a cohort of Chinese CMT2 patients
Authors: Xie Yongzhi , Li Xiaobo , Liu Lei , Hu Zhengmao , Huang Shunxiang , Zhan Yajin , Zi Xiaohong , Xia Kun , Tang Beisha , Zhang Ruxu
Published: January 2016

Charcot‐Marie‐Tooth disease 2A (CMT2A), caused by mutations in the mitofusin 2 gene (MFN2), is the most common CMT2 subtype. The aim of our study is to assess the frequency and summarize the genetic and clinical characteristics of Chinese CMT2A patients. A total of 17 coding exons of MFN2 were detected by direct sequencing in 82 unrelated Chinese families diagnosed as CMT2. Clinical evaluations were analyzed among CMT2A patients. We identified 14 missense variants in 9 sporadic and 6 familial cases, including four novel mutations (T129A, S249F, Q367P, and Q674L), 4 known mutations (R94W, R94Q, T105M, C132Y, M376V and Q751X), and 4 rare missense variants (K120E, C217F, K307E and T356S). A total of 23 patients had early‐onset phenotype. Two patients had a CMTNS score of 0 to 10; 16 had a score of 11 to 20; and 7 had a score greater than 20. Five patients were confirmed a de novo origin. Six of 14 variants were located or closed to the GTPase domain. We report four novel mutations and four rare missense variants. MFN2 mutations account for 18% of CMT2 families in mainland China. The common characteristics of Chinese pedigree are early disease onset and moderate phenotypes.
X‐linked Charcot‐Marie‐Tooth disease type 6 (CMTX6) patients with a p.R158H mutation in the pyruvate dehydrogenase kinase isoenzyme 3 gene
Authors: Kennerson Marina L. , Kim Eun J. , Siddell Anna , Kidambi Aditi , Kim Sung M. , Hong Young B. , Hwang Sun H. , Chung Ki W. , Choi Byung‐Ok
Published: January 2016

Charcot‐Marie‐Tooth disease (CMT) is the most common inherited peripheral neuropathy. Mutations in the pyruvate dehydrogenase kinase isoenzyme 3 (PDK3) gene have been found to cause X‐linked dominant CMT type 6 (CMTX6). This study identified the p.R158H PDK3 mutation after screening 67 probable X‐linked CMT families. The mutation fully segregated with the phenotype, and genotyping the family indicated the mutation arose on a different haplotype compared with the original Australian CMTX6 family. Results of bisulphite sequencing suggest that methylated deamination of a CpG dinucleotide may cause the recurrent p.R158H mutation. The frequency of the p.R158H PDK3 mutation in Koreans is very rare. Magnetic resonance imaging revealed fatty infiltration involving distal muscles in the lower extremities. In addition, fatty infiltrations were predominantly observed in the soleus muscles, with a lesser extent in tibialis anterior muscles. This differs from demyelinating CMT1A patients and is similar to axonal CMT2A patients. The clinical, neuroimaging, and electrophysiological findings from a second CMTX6 family with the p.R158H PDK3 mutation were similar to the axonal neuropathy reported in the Australian family.
Effect of Integration Patterns Around Implant Neck on Stress Distribution in Peri‐Implant Bone: A Finite Element Analysis
Authors: Han Jingyun , Sun Yuchun , Wang Chao
Published: January 2016

Purpose

To investigate the biomechanical performance of different osseointegration patterns between cortical bone and implants using finite element analysis.

Materials and Methods

Fifteen finite element models were constructed of the mandibular fixed prosthesis supported by implants. Masticatory loads (200 N axial, 100 N oblique, 40 N horizontal) were applied. The cortical bone/implant interface was divided equally into four layers: upper, upper‐middle, lower‐middle, and lower. The bone stress and implant displacement were calculated for 5 degrees of uniform integration (0, 20%, 40%, 60%, and 100%) and 10 integration patterns.

Results

The stress was concentrated in the bone margin and gradually decreased as osseointegration progressed, when the integrated and nonintegrated areas were alternated on the bone‐implant surface. Compared with full integration, the integration of only the lower‐middle layer or lower half layers significantly decreased von Mises, tensile, and compressive stresses in cortical bone under oblique and horizontal loads, and these patterns did not induce higher stress in the cancellous bone. For the integration of only the upper or upper‐middle layer, stress in the cortical and cancellous bones significantly increased and was considerably higher than in the case of nonintegration. In addition, the maximum stress in the cortical bone was sensitive to the quantity of integrated nodes at the bone margin; lower quantity was associated with higher stress. There was no significant difference in the displacement of implants among 15 models.

Conclusions

Integration patterns of cortical bone significantly affect stress distribution in peri‐implant bone. The integration of only the lower‐middle or lower half layers helps to increase the load‐bearing capacity of peri‐implant bone and decrease the risk of overloading, while upper integration may further increase the risk of bone resorption.
Prognostic significance of infections in critically ill adult patients with acute liver injury: a retrospective cohort study
Authors: Zider Alexander D. , Zopey Radhika , Garg Ronak , Wang Xiaoyan , Wang Tisha S. , Deng Jane C.
Published: January 2016

Background and Aims

Patients with acute liver failure have high rates of infections, likely from defects in immune function. Whether infections are independently associated with poor outcomes is unclear. We hypothesized that patients with acute liver injury who developed infections were at increased risk of adverse outcomes.

Methods

We conducted a retrospective analysis of 150 critically ill adult patients admitted with acute liver dysfunction at a single academic institution between 2005 and 2011. We excluded patients with immunocompromised states, patients with chronic liver disease and patients who died or were discharged within 48 h of admission. Our primary endpoint was a 30‐day event‐free survival, with events defined as either death or liver transplantation. Our secondary endpoint was length of stay. Univariate and multivariate analyses were performed to determine associations between presence of infection and our primary and secondary endpoints.

Results

Of our cohort of 150 patients, 62 (41%) were infected and 88 (59%) were not infected. Of the infected patients, 45% died or underwent transplantation, compared to 22% for the non‐infected patients (P= 0.003). Univariate and multivariate analyses demonstrated that infections in patients with acute liver dysfunction were an independent predictor of poor outcome (i.e. death or transplantation). In addition, specific types of infection, including pneumonia, independently led to a 48% increase in length of stay (P= 0.002).

Conclusions

Infections in patients with acute liver dysfunction are associated with increased risk of death or transplant and increased hospital length of stay.
The chlorine isotope composition of Martian meteorites 2. Implications for the early solar system and the formation of Mars
Authors: Sharp Zachary , Williams Jeffrey , Shearer Charles , Agee Carl , McKeegan Kevin
Published: January 2016

We determined the chlorine isotope composition of 16 Martian meteorites using gas source mass spectrometry on bulk samples and in situ secondary ion microprobe analysis on apatite grains. Measured δ37Cl values range from −3.8 to +8.6‰. The olivine‐phyric shergottites are the isotopically lightest samples, with δ37Cl mostly ranging from −4 to −2‰. Samples with evidence for a crustal component have positive δ37Cl values, with an extreme value of 8.6‰. Most of the basaltic shergottites have intermediate δ37Cl values of −1 to 0‰, except for Shergotty, which is similar to the olivine‐phyric shergottites. We interpret these data as due to mixing of a two‐component system. The first component is the mantle value of −4 to −3‰. This most likely represents the original bulk Martian Cl isotope value. The other endmember is a37Cl‐enriched crustal component. We speculate that preferential loss of35Cl to space has resulted in a high δ37Cl value for the Martian surface, similar to what is seen in other volatile systems. The basaltic shergottites are a mixture of the other two endmembers. The low δ37Cl value of primitive Mars is different from Earth and most chondrites, both of which are close to 0‰. We are not aware of any parent‐body process that could lower the δ37Cl value of the Martian mantle to −4 to −3‰. Instead, we propose that this low δ37Cl value represents the primordial bulk composition of Mars inherited during accretion. The higher δ37Cl values seen in many chondrites are explained by later incorporation of37Cl‐enrichedHCl‐hydrate.
Comparison of novel and conventional methods of trapping ixodid ticks in the southeastern U.S.A.
Authors: MAYS S. E. , HOUSTON A. E. , TROUT FRYXELL R. T.
Published: January 2016

Tick‐borne disease surveillance and research rely on resource‐effective methods for tick collection. This study compared the respective performances of several trapping methods in a mixed grassland–forest habitat in western Tennessee. To test for temporal differences in effectiveness, sites were sampled monthly (April–August 2013) using dry ice, dragging, flagging, sweep netting, carbon dioxide (CO2) dragging and CO2 flagging methods. To evaluate the effect of habitat on method effectiveness, four methods (dragging, CO2 dragging, CO2 flagging and dry ice) were compared in four habitat types (bottomland deciduous, upland deciduous, coniferous and grassland) in June 2014. In the temporal comparison, ticks were found to be most abundant in April and May, and there was a significant sampling period and method interaction, such that method effectiveness varied across sampling period. Sweep netting was significantly less effective than the other methods. In the habitat comparison, dry ice trap collections represented the most effective method in upland deciduous and coniferous habitats. Flagging using CO2 was significantly less effective than CO2 dragging and dragging in bottomland deciduous habitats. The success of the various collection methods did not differ significantly within grassland habitats. Overall, dry ice trapping and dragging were the most effective methods for tick collection across time and habitat.
Meek mothers with powerful daughters: effects of novel host environments and small trait differences on parasitoid competition
Authors: Hamerlinck Gabriela , Lemoine Nathan P. , Hood Glen R. , Abbott Karen C. , Forbes Andrew A.
Published: January 2016

Outcomes of competition may depend both on subtle differences in traits relevant to fitness and on how those traits are expressed in the context of the environment. Environmental effects on traits impacting population dynamics are often overlooked in studies of parasitic wasp (parasitoid) competition. Lineages of the parasitoidDiachasma alloeum(Hymenoptera: Braconidae) differ in relative ovipositor length (a trait affecting the proportion of hosts available for parasitism). Since the size of natal hosts affects the overall body size of many adult parasitoids, outcomes of competition betweenD. alloeumlineages should be influenced by both their natal host's size and their inherited ovipositor:body size ratios. Previous genetic work showed the unexpected result that the apparently inferior competitor (the lineage with smaller ovipositors in its ancestral environment) has successfully colonized a new host. We present body size measurements and a phenomological model of competition showing that relative ovipositor sizes of the two lineages predict success of the apparently inferior wasp lineage in the new host. We present several variants of the model, including simulations: 1) wherein competitors have either ancestral trait values or trait values acquired in the novel environment; 2) that allow varying rates of constant immigration from the inferior competitor's source population; and 3) with stochastic immigration from both lineages' source populations. We show that ancestral trait differences and changes in environmentally mediated traits interact to affect outcomes of competition. Apparently inferior female parasitoids (‘meek mothers’) attacking a host in a novel environment can produce highly successful daughters if those daughters inherit large ovipositor:body size ratios and grow to a larger size in the new environment. Predictive models of parasitoid competition that consider effects of environmentally mediated trait changes may be particularly important for biocontrol programs wherein parasitoids are introduced into new environments or used to control novel hosts.
Synergy between shading and herbivory triggers macrophyte loss and regime shifts in aquatic systems
Authors: Hidding Bert , Bakker Elisabeth S. , Hootsmans Michiel J. M. , Hilt Sabine
Published: January 2016

Macrophytes play a keystone role in shallow aquatic ecosystems. In lakes, macrophytes stabilize clear‐water conditions with high biodiversity and their decline can cause a shift to a turbid state with lower biodiversity. Various mechanisms have been suggested as triggers of macrophyte collapse. Herbivory by waterfowl and fish seems to be one of the obvious factors, but the response of macrophytes to herbivory is ambiguous. We hypothesized that herbivory alone does not typically cause macrophyte collapse, but that shading from periphyton can enhance the effect of herbivores. Shading of macrophytes is supposed to increase with eutrophication due to changes in the top–down control cascading from fish via macroinvertebrates to periphyton. We elaborated on this idea by fitting a macrophyte growth model with different herbivore grazing and periphyton shading scenarios. In addition, we performed a meta‐analysis on existing experimental herbivore exclosure studies with respect to periphyton growth. The model supported our proposed hypothesis and the reviewed field studies appeared to point in the same direction. We suggest that a significant herbivore impact may indicate a reduced resilience of vegetation to eutrophication, making it an early warning signal for an imminent macrophyte collapse leading to a sudden shift of the system to turbid conditions.
A highly recombined, high‐density, eight‐founder wheat MAGIC map reveals extensive segregation distortion and genomic locations of introgression segments
Authors: Gardner Keith A. , Wittern Lukas M. , Mackay Ian J.
Published: January 2016

Multiparent Advanced Generation Intercross (MAGIC) mapping populations offer unique opportunities and challenges for marker and QTL mapping in crop species. We have constructed the first eight‐parent MAGIC genetic map for wheat, comprising 18 601 SNP markers. We validated the accuracy of our map against the wheat genome sequence and found an improvement in accuracy compared to published genetic maps. Our map shows a notable increase in precision resulting from the three generations of intercrossing required to create the population. This is most pronounced in the pericentromeric regions of the chromosomes. Sixteen percent of mapped markers exhibited segregation distortion (SD) with many occurring in long (>20 cM) blocks. Some of the longest and most distorted blocks were collinear with noncentromeric high‐marker‐density regions of the genome, suggesting they were candidates for introgression fragments introduced into the bread wheat gene pool from other grass species. We investigated two of these linkage blocks in detail and found strong evidence that one on chromosome 4AL, showing SD against the founder Robigus, is an interspecific introgression fragment. The completed map is available from http://www.niab.com/pages/id/326/Resources.
Rice endosperm is cost‐effective for the production of recombinant griffithsin with potent activity against HIV
Authors: Vamvaka Evangelia , Arcalis Elsa , Ramessar Koreen , Evans Abbey , O'Keefe Barry R. , Shattock Robin J. , Medina Vicente , Stöger Eva , Christou Paul , Capell Teresa
Published: January 2016

Protein microbicides containing neutralizing antibodies and antiviral lectins may help to reduce the rate of infection with human immunodeficiency virus (HIV) if it is possible to manufacture the components in large quantities at a cost affordable in HIV‐endemic regions such as sub‐Saharan Africa. We expressed the antiviral lectin griffithsin (GRFT), which shows potent neutralizing activity against HIV, in the endosperm of transgenic rice plants (Oryza sativa), to determine whether rice can be used to produce inexpensive GRFT as a microbicide ingredient. The yield of OSGRFT in the best‐performing plants was 223 μg/g dry seed weight. We also established a one‐step purification protocol, achieving a recovery of 74% and a purity of 80%, which potentially could be developed into a larger‐scale process to facilitate inexpensive downstream processing. OSGRFT bound to HIV glycans with similar efficiency to GRFT produced in Escherichia coli. Whole‐cell assays using purified OSGRFT and infectivity assays using crude extracts of transgenic rice endosperm confirmed that both crude and pure OSGRFT showed potent activity against HIV and the crude extracts were not toxic towards human cell lines, suggesting they could be administered as a microbicide with only minimal processing. A freedom‐to‐operate analysis confirmed that GRFT produced in rice is suitable for commercial development, and an economic evaluation suggested that 1.8 kg/ha of pure GRFT could be produced from rice seeds. Our data therefore indicate that rice could be developed as an inexpensive production platform for GRFT as a microbicide component.
Expression of a constitutively active nitrate reductase variant in tobacco reduces tobacco‐specific nitrosamine accumulation in cured leaves and cigarette smoke
Authors: Lu Jianli , Zhang Leichen , Lewis Ramsey S. , Bovet Lucien , Goepfert Simon , Jack Anne M. , Crutchfield James D. , Ji Huihua , Dewey Ralph E.
Published: January 2016

Burley tobaccos (Nicotiana tabacum) display a nitrogen‐use‐deficiency phenotype that is associated with the accumulation of high levels of nitrate within the leaf, a trait correlated with production of a class of compounds referred to as tobacco‐specific nitrosamines (TSNAs). Two TSNA species, 4‐(methylnitrosamino)‐1‐(3‐pyridyl)‐1‐butanone (NNK) and N‐nitrosonornicotine (NNN), have been shown to be strong carcinogens in numerous animal studies. We investigated the potential of molecular genetic strategies to lower nitrate levels in burley tobaccos by overexpressing genes encoding key enzymes of the nitrogen‐assimilation pathway. Of the various constructs tested, only the expression of a constitutively active nitrate reductase (NR) dramatically decreased free nitrate levels in the leaves. Field‐grown tobacco plants expressing this NR variant exhibited greatly reduced levels of TSNAs in both cured leaves and mainstream smoke of cigarettes made from these materials. Decreasing leaf nitrate levels via expression of a constitutively active NR enzyme represents an exceptionally promising means for reducing the production of NNN and NNK, two of the most well‐documented animal carcinogens found in tobacco products.
Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes
Authors: Beier Sebastian , Himmelbach Axel , Schmutzer Thomas , Felder Marius , Taudien Stefan , Mayer Klaus F. X. , Platzer Matthias , Stein Nils , Scholz Uwe , Mascher Martin
Published: January 2016

Hierarchical shotgun sequencing remains the method of choice for assembling high‐quality reference sequences of complex plant genomes. The efficient exploitation of current high‐throughput technologies and powerful computational facilities for large‐insert clone sequencing necessitates the sequencing and assembly of a large number of clones in parallel. We developed a multiplexed pipeline for shotgun sequencing and assembling individual bacterial artificial chromosomes (BACs) using the Illumina sequencing platform. We illustrate our approach by sequencing 668 barley BACs (Hordeum vulgare L.) in a single Illumina HiSeq 2000 lane. Using a newly designed parallelized computational pipeline, we obtained sequence assemblies of individual BACs that consist, on average, of eight sequence scaffolds and represent >98% of the genomic inserts. Our BAC assemblies are clearly superior to a whole‐genome shotgun assembly regarding contiguity, completeness and the representation of the gene space. Our methods may be employed to rapidly obtain high‐quality assemblies of a large number of clones to assemble map‐based reference sequences of plant and animal species with complex genomes by sequencing along a minimum tiling path.
BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes
Authors: Staňková Helena , Hastie Alex R. , Chan Saki , Vrána Jan , Tulpová Zuzana , Kubaláková Marie , Visendi Paul , Hayashi Satomi , Luo Mingcheng , Batley Jacqueline , Edwards David , Doležel Jaroslav , Šimková Hana
Published: January 2016

The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC‐by‐BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high‐resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high‐resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome‐scale analysis of repetitive sequences and revealed a ~800‐kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone‐by‐clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC‐contig physical map and validate sequence assembly on a chromosome‐arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome‐by‐chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules.
Expression of ZmGA20ox cDNA alters plant morphology and increases biomass production of switchgrass (Panicum virgatum L.)
Authors: Do Phat T. , De Tar Joann R. , Lee Hyeyoung , Folta Michelle K. , Zhang Zhanyuan J.
Published: January 2016

Switchgrass (Panicum virgatum L.) is considered a model herbaceous energy crop for the USA, for its adaptation to marginal land, low rainfall and nutrient‐deficient soils; however, its low biomass yield is one of several constraints, and this might be rectified by modulating plant growth regulator levels. In this study, we have determined whether the expression of the Zea mays gibberellin 20‐oxidase (ZmGA20ox) cDNA in switchgrass will improve biomass production. The ZmGA20ox gene was placed under the control of constitutive CaMV35S promoter with a strong TMV omega enhancer, and introduced into switchgrass via Agrobacterium‐mediated transformation. The transgene integration and expression levels of ZmGA20ox in T0 plants were analysed using Southern blot and qRT‐PCR. Under glasshouse conditions, selected transgenic plants exhibited longer leaves, internodes and tillers, which resulted in twofold increased biomass. These phenotypic alterations correlated with the levels of transgene expression and the particular gibberellin content. Expression of ZmGA20ox also affected the expression of genes coding for key enzymes in lignin biosynthesis. Our results suggest that the employment of ectopic ZmGA20ox and selection for natural variants with high level expression of endogenous GA20ox are appropriate approaches to increase biomass production of switchgrass and other monocot biofuel crops.
Immunotherapy using algal‐produced Ara h 1 core domain suppresses peanut allergy in mice
Authors: Gregory James A. , Shepley‐McTaggart Ariel , Umpierrez Michelle , Hurlburt Barry K. , Maleki Soheila J. , Sampson Hugh A. , Mayfield Stephen P. , Berin M. Cecilia
Published: January 2016

Peanut allergy is an IgE‐mediated adverse reaction to a subset of proteins found in peanuts. Immunotherapy aims to desensitize allergic patients through repeated and escalating exposures for several months to years using extracts or flours. The complex mix of proteins and variability between preparations complicates immunotherapy studies. Moreover, peanut immunotherapy is associated with frequent negative side effects and patients are often at risk of allergic reactions once immunotherapy is discontinued. Allergen‐specific approaches using recombinant proteins are an attractive alternative because they allow more precise dosing and the opportunity to engineer proteins with improved safety profiles. We tested whether Ara h 1 and Ara h 2, two major peanut allergens, could be produced using chloroplast of the unicellular eukaryotic alga, Chlamydomonas reinhardtii. C. reinhardtii is novel host for producing allergens that is genetically tractable, inexpensive and easy to grow, and is able to produce more complex proteins than bacterial hosts. Compared to the native proteins, algal‐produced Ara h 1 core domain and Ara h 2 have a reduced affinity for IgE from peanut‐allergic patients. We further found that immunotherapy using algal‐produced Ara h 1 core domain confers protection from peanut‐induced anaphylaxis in a murine model of peanut allergy.
Challenges and opportunities for hydrogen production from microalgae
Authors: Oey Melanie , Sawyer Anne Linda , Ross Ian Lawrence , Hankamer Ben
Published: January 2016

The global population is predicted to increase from ~7.3 billion to over 9 billion people by 2050. Together with rising economic growth, this is forecast to result in a 50% increase in fuel demand, which will have to be met while reducing carbon dioxide (CO2) emissions by 50–80% to maintain social, political, energy and climate security. This tension between rising fuel demand and the requirement for rapid global decarbonization highlights the need to fast‐track the coordinated development and deployment of efficient cost‐effective renewable technologies for the production of CO2 neutral energy. Currently, only 20% of global energy is provided as electricity, while 80% is provided as fuel. Hydrogen (H2) is the most advanced CO2‐free fuel and provides a ‘common’ energy currency as it can be produced via a range of renewable technologies, including photovoltaic (PV), wind, wave and biological systems such as microalgae, to power the next generation of H2 fuel cells. Microalgae production systems for carbon‐based fuel (oil and ethanol) are now at the demonstration scale. This review focuses on evaluating the potential of microalgal technologies for the commercial production of solar‐driven H2 from water. It summarizes key global technology drivers, the potential and theoretical limits of microalgal H2 production systems, emerging strategies to engineer next‐generation systems and how these fit into an evolving H2 economy.
Joint‐linkage mapping and GWAS reveal extensive genetic loci that regulate male inflorescence size in maize
Authors: Wu Xun , Li Yongxiang , Shi Yunsu , Song Yanchun , Zhang Dengfeng , Li Chunhui , Buckler Edward S. , Li Yu , Zhang Zhiwu , Wang Tianyu
Published: January 2016

Both insufficient and excessive male inflorescence size leads to a reduction in maize yield. Knowledge of the genetic architecture of male inflorescence is essential to achieve the optimum inflorescence size for maize breeding. In this study, we used approximately eight thousand inbreds, including both linkage populations and association populations, to dissect the genetic architecture of male inflorescence. The linkage populations include 25 families developed in the U.S. and 11 families developed in China. Each family contains approximately 200 recombinant inbred lines (RILs). The association populations include approximately 1000 diverse lines from the U.S. and China. All inbreds were genotyped by either sequencing or microarray. Inflorescence size was measured as the tassel primary branch number (TBN) and tassel length (TL). A total of 125 quantitative trait loci (QTLs) were identified (63 for TBN, 62 for TL) through linkage analyses. In addition, 965 quantitative trait nucleotides (QTNs) were identified through genomewide study (GWAS) at a bootstrap posterior probability (BPP) above a 5% threshold. These QTLs/QTNs include 24 known genes that were cloned using mutants, for example Ramosa3 (ra3), Thick tassel dwarf1 (td1), tasselseed2 (ts2), liguleless2 (lg2), ramosa1 (ra1), barren stalk1 (ba1), branch silkless1 (bd1) and tasselseed6 (ts6). The newly identified genes encode a zinc transporter (e.g. GRMZM5G838098 and GRMZM2G047762), the adapt in terminal region protein (e.g. GRMZM5G885628), O‐methyl‐transferase (e.g. GRMZM2G147491), helix‐loop‐helix (HLH) DNA‐binding proteins (e.g. GRMZM2G414252 and GRMZM2G042895) and an SBP‐box protein (e.g. GRMZM2G058588). These results provide extensive genetic information to dissect the genetic architecture of inflorescence size for the improvement of maize yield.
Genome‐wide dissection of AP2/ERF and HSP90 gene families in five legumes and expression profiles in chickpea and pigeonpea
Authors: Agarwal Gaurav , Garg Vanika , Kudapa Himabindu , Doddamani Dadakhalandar , Pazhamala Lekha T. , Khan Aamir W. , Thudi Mahendar , Lee Suk‐Ha , Varshney Rajeev K.
Published: January 2016

APETALA2/ethylene response factor (AP2/ERF) and heat‐shock protein 90 (HSP90) are two significant classes of transcription factor and molecular chaperone proteins which are known to be implicated under abiotic and biotic stresses. Comprehensive survey identified a total of 147 AP2/ERF genes in chickpea, 176 in pigeonpea, 131 in Medicago, 179 in common bean and 140 in Lotus, whereas the number of HSP90 genes ranged from 5 to 7 in five legumes. Sequence alignment and phylogenetic analyses distinguished AP2, ERF, DREB, RAV and soloist proteins, while HSP90 proteins segregated on the basis of their cellular localization. Deeper insights into the gene structure allowed ERF proteins to be classified into AP2s based on DNA‐binding domains, intron arrangements and phylogenetic grouping. RNA‐seq and quantitative real‐time PCR (qRT‐PCR) analyses in heat‐stressed chickpea as well as Fusarium wilt (FW)‐ and sterility mosaic disease (SMD)‐stressed pigeonpea provided insights into the modus operandi of AP2/ERF and HSP90 genes. This study identified potential candidate genes in response to heat stress in chickpea while for FW and SMD stresses in pigeonpea. For instance, two DREB genes (Ca_02170 and Ca_16631) and three HSP90 genes (Ca_23016, Ca_09743 and Ca_25602) in chickpea can be targeted as potential candidate genes. Similarly, in pigeonpea, a HSP90 gene, C.cajan_27949, was highly responsive to SMD in the resistant genotype ICPL 20096, can be recommended for further functional validation. Also, two DREB genes, C.cajan_41905 and C.cajan_41951, were identified as leads for further investigation in response to FW stress in pigeonpea.
Haplotype hitchhiking promotes trait coselection in Brassica napus
Authors: Qian Lunwen , Qian Wei , Snowdon Rod J.
Published: January 2016

Local haplotype patterns surrounding densely spaced DNA markers with significant trait associations can reveal information on selective sweeps and genome diversity associated with important crop traits. Relationships between haplotype and phenotype diversity, coupled with analysis of gene content in conserved haplotype blocks, can provide insight into coselection for nonrelated traits. We performed genome‐wide analysis of haplotypes associated with the important physiological and agronomic traits leaf chlorophyll and seed glucosinolate content, respectively, in the major oilseed crop species Brassica napus. A locus on chromosome A01 showed opposite effects on leaf chlorophyll content and seed glucosinolate content, attributed to strong linkage disequilibrium (LD) between orthologues of the chlorophyll biosynthesis genes EARLY LIGHT‐INDUCED PROTEIN and CHLOROPHYLL SYNTHASE, and the glucosinolate synthesis gene ATP SULFURYLASE 1. Another conserved haplotype block, on chromosome A02, contained a number of chlorophyll‐related genes in LD with orthologues of the key glucosinolate biosynthesis genes METHYLTHIOALKYMALATE SYNTHASE‐LIKE 1 and 3. Multigene haplogroups were found to have a significantly greater contribution to variation for chlorophyll content than haplotypes for any single gene, suggesting positive effects of additive locus accumulation. Detailed reanalysis of population substructure revealed a clade of ten related accessions exhibiting high leaf chlorophyll and low seed glucosinolate content. These accessions each carried one of the above‐mentioned haplotypes from A01 or A02, generally in combination with further chlorophyll‐associated haplotypes from chromosomes A05 and/or C05. The phenotypic rather than pleiotropic correlations between leaf chlorophyll content index and seed GSL suggest that LD may have led to inadvertent coselection for these two traits.
Fusarium oxysporum mediates systems metabolic reprogramming of chickpea roots as revealed by a combination of proteomics and metabolomics
Authors: Kumar Yashwant , Zhang Limin , Panigrahi Priyabrata , Dholakia Bhushan B. , Dewangan Veena , Chavan Sachin G. , Kunjir Shrikant M. , Wu Xiangyu , Li Ning , Rajmohanan Pattuparambil R. , Kadoo Narendra Y. , Giri Ashok P. , Tang Huiru , Gupta Vidya S.
Published: January 2016

Molecular changes elicited by plants in response to fungal attack and how this affects plant–pathogen interaction, including susceptibility or resistance, remain elusive. We studied the dynamics in root metabolism during compatible and incompatible interactions between chickpea and Fusarium oxysporum f. sp. ciceri (Foc), using quantitative label‐free proteomics and NMR‐based metabolomics. Results demonstrated differential expression of proteins and metabolites upon Foc inoculations in the resistant plants compared with the susceptible ones. Additionally, expression analysis of candidate genes supported the proteomic and metabolic variations in the chickpea roots upon Foc inoculation. In particular, we found that the resistant plants revealed significant increase in the carbon and nitrogen metabolism; generation of reactive oxygen species (ROS), lignification and phytoalexins. The levels of some of the pathogenesis‐related proteins were significantly higher upon Foc inoculation in the resistant plant. Interestingly, results also exhibited the crucial role of altered Yang cycle, which contributed in different methylation reactions and unfolded protein response in the chickpea roots against Foc. Overall, the observed modulations in the metabolic flux as outcome of several orchestrated molecular events are determinant of plant's role in chickpea–Foc interactions.
Metabolic regulation of triacylglycerol accumulation in the green algae: identification of potential targets for engineering to improve oil yield
Authors: Goncalves Elton C. , Wilkie Ann C. , Kirst Matias , Rathinasabapathi Bala
Published: January 2016

The great need for more sustainable alternatives to fossil fuels has increased our research interests in algal biofuels. Microalgal cells, characterized by high photosynthetic efficiency and rapid cell division, are an excellent source of neutral lipids as potential fuel stocks. Various stress factors, especially nutrient‐starvation conditions, induce an increased formation of lipid bodies filled with triacylglycerol in these cells. Here we review our knowledge base on glycerolipid synthesis in the green algae with an emphasis on recent studies on carbon flux, redistribution of lipids under nutrient‐limiting conditions and its regulation. We discuss the contributions and limitations of classical and novel approaches used to elucidate the algal triacylglycerol biosynthetic pathway and its regulatory network in green algae. Also discussed are gaps in knowledge and suggestions for much needed research both on the biology of triacylglycerol accumulation and possible avenues to engineer improved algal strains.
Overexpression of MdbHLH104 gene enhances the tolerance to iron deficiency in apple
Authors: Zhao Qiang , Ren Yi‐Ran , Wang Qing‐Jie , Yao Yu‐Xin , You Chun‐Xiang , Hao Yu‐Jin
Published: January 2016

Fe deficiency is a widespread nutritional disorder in plants. The basic helix‐loop‐helix (bHLH) transcription factors (TFs), especially Ib subgroup bHLH TFs which are involved in iron uptake, have been identified. In this study, an IVc subgroup bHLH TF MdbHLH104 was identified and characterized as a key component in the response to Fe deficiency in apple. The overexpression of the MdbHLH104 gene noticeably increased the H+‐ATPase activity under iron limitation conditions and the tolerance to Fe deficiency in transgenic apple plants and calli. Further investigation showed that MdbHLH104 proteins bonded directly to the promoter of the MdAHA8 gene, thereby positively regulating its expression, the plasma membrane (PM) H+‐ATPase activity and Fe uptake. Similarly, MdbHLH104 directly modulated the expression of three Fe‐responsive bHLH genes, MdbHLH38, MdbHLH39 and MdPYE. In addition, MdbHLH104 interacted with 5 other IVc subgroup bHLH proteins to coregulate the expression of the MdAHA8 gene, the activity of PM H+‐ATPase and the content of Fe in apple calli. Therefore, MdbHLH104 acts together with other apple bHLH TFs to regulate Fe uptake by modulating the expression of the MdAHA8 gene and the activity of PM H+‐ATPase in apple.
Zebrafish Leucocyte tyrosine kinase controls iridophore establishment, proliferation and survival
Authors: Fadeev Andrey , Krauss Jana , Singh Ajeet Pratap , Nüsslein‐Volhard Christiane
Published: January 2016

The zebrafish striped pattern results from the interplay among three pigment cell types; black melanophores, yellow xanthophores and silvery iridophores, making it a valuable model to study pattern formation in vivo. It has been suggested that iridophore proliferation, dispersal and cell shape transitions play an important role during stripe formation; however, the underlying molecular mechanisms remain poorly understood. Using gain‐ and loss‐of‐function alleles ofleucocyte tyrosine kinase(ltk) and a pharmacological inhibitor approach, we show that Ltk specifically regulates iridophore establishment, proliferation and survival. Mutants inshady/ltklack iridophores and display an abnormal body stripe pattern.Moonstonemutants, ltkmne, display ectopic iridophores, suggesting hyperactivity of the mutant Ltk. The dominantltkmneallele carries a missense mutation in a conserved position of the kinase domain that highly correlates with neuroblastomas in mammals. Chimeric analysis suggests a novel physiological role of Ltk in the regulation of iridophore proliferation by homotypic competition.
Microsomal PGE2 synthase‐1 regulates melanoma cell survival and associates with melanoma disease progression
Authors: Kim Sun‐Hee , Hashimoto Yuuri , Cho Sung‐Nam , Roszik Jason , Milton Denái R. , Dal Fulya , Kim Sangwon F. , Menter David G. , Yang Peiying , Ekmekcioglu Suhendan , Grimm Elizabeth A.
Published: January 2016

COX‐2 and its product PGE2 enhance carcinogenesis and tumor progression, which has been previously reported in melanoma. As most COX inhibitors cause much toxicity, the downstream microsomal PGE2 synthase‐1 (mPGES1) is a consideration for targeting. Human melanoma TMAs were employed for testing mPGES1 protein staining intensity and percentage levels, and both increased with clinical stage; employing a different Stage III TMA, mPGES1 intensity (not percentage) associated with reduced patient survival. Our results further show that iNOS was also highly expressed in melanoma tissues with high mPGES1 levels, and iNOS‐mediated NO promoted mPGES1 expression and PGE2 production. An mPGES1‐specific inhibitor (CAY10526) as well as siRNA attenuated cell survival and increased apoptosis. CAY10526 significantly suppressed tumor growth and increased apoptosis in melanoma xenografts. Our findings support the value of a prognostic and predictive role for mPGES1, and suggest targeting this molecule in the PGE2 pathway as another avenue toward improving melanoma therapy.
Foreword: The Wounds and the Legacies of World War I
Authors: Bennett Scott H.
Published: January 2016

The articles in this special issue of Peace & Change originated as papers presented at an interdisciplinary conference on “World War I: Dissent, Activism, & Transformation.” Hosted by Georgian Court University and co‐sponsored by the Peace History Society, the conference was held on October 17‐18, 2014, in Lakewood, New Jersey. Written by the conference organizer, this Foreword explains the origins of the conference and summarizes the articles and interviews that appear in this special issue.