bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in ambient temperature are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation
Authors: MacKinnon Kirk J‐M. , Cole Benjamin J. , Yu Chang , Coomey Joshua H. , Hartwick Nolan T. , Remigereau Marie‐Stanislas , Duffy Tomás , Michael Todd P. , Kay Steve A. , Hazen Samuel P. 
Published: February 2020

Summary

Plants are continuously exposed to diurnal fluctuations in light and temperature, and spontaneous changes in their physical or biotic environment. The circadian clock coordinates regulation of gene expression with a 24 h period, enabling the anticipation of these events.

We used RNA sequencing to characterize the Brachypodium distachyon transcriptome under light and temperature cycles, as well as under constant conditions.

Approximately 3% of the transcriptome was regulated by the circadian clock, a smaller proportion than reported in most other species. For most transcripts that were rhythmic under all conditions, including many known clock genes, the period of gene expression lengthened from 24 to 27 h in the absence of external cues. To functionally characterize the cyclic transcriptome in B. distachyon, we used Gene Ontology enrichment analysis, and found several terms significantly associated with peak expression at particular times of the day. Furthermore, we identified sequence motifs enriched in the promoters of similarly phased genes, some potentially associated with transcription factors.

When considering the overlap in rhythmic gene expression and specific pathway behavior, thermocycles was the prevailing cue that controlled diurnal gene regulation. Taken together, our characterization of the rhythmic B. distachyon transcriptome represents a foundational resource with implications in other grass species.
The functionally conserved effector Sta1 is a fungal cell wall protein required for virulence in Ustilago maydis
Authors: Tanaka Shigeyuki , Gollin Isabelle , Rössel Nicole , Kahmann Regine 
Published: February 2020

Summary

The biotrophic fungus Ustilago maydis causes the smut disease of maize. The interaction with its host and induction of characteristic tumors are governed largely by secreted effectors whose function is mostly unknown. To identify effectors with a prominent role in virulence, we used RNA sequencing and found that the gene sta1 is upregulated during early stages of infection.

We characterized Sta1 by comparative genomics, reverse genetics, protein localization, stress assays, and microscopy.

sta1 mutants show a dramatic reduction of virulence and show altered colonization of tissue neighboring the vascular bundles. Functional orthologues of Sta1 are found in related smut pathogens infecting monocot and dicot plants. Sta1 is secreted by budding cells but is attached to the cell wall of filamentous hyphae. Upon constitutive expression of Sta1, fungal filaments become susceptible to Congo red, β‐glucanase, and chitinase, suggesting that Sta1 alters the structure of the fungal cell wall. Constitutive or delayed expression of sta1 during plant colonization negatively impacts on virulence.

Our results suggest that Sta1 is a novel kind of effector, which needs to modify the hyphal cell wall to allow hyphae to be accommodated in tissue next to the vascular bundles.
The role of sensory drive in floral evolution
Authors: Koski Matthew H. 
Published: February 2020

SummarySensory drive theory posits that the evolution of communication signals is shaped by the sensory systems of receivers and the habitat conditions under which signals are received. It has inspired an enormous body of research, advancing our understanding of signal evolution and speciation in animals. In plants, the extreme diversification of floral signals has fascinated biologists for over a century. While processes involved in sensory drive probably play out in plant–pollinator communication, the theory has not been formally synthesized in this context. However, it has untapped potential to explain mechanisms underlying variation in pollinator preferences across populations, and how environmental conditions impact floral signal transmission and perception. Here I develop a framework of sensory drive for plant–pollinator interactions, identifying similarities and differences from its original conception. I then summarize studies that shed light on how the primary processes of sensory drive – habitat transmission, perceptual tuning, and signal matching – apply to the evolution of floral color and scent. Throughout, I propose research avenues and approaches to assess how sensory drive shapes floral diversity. This framework will be important for explaining patterns of extant floral diversity and examining how altered signaling conditions under global change will impact the evolutionary trajectory of floral traits.
Identification of introduced and stably inherited DNA methylation variants in soybean associated with soybean cyst nematode parasitism
Authors: Rambani Aditi , Pantalone Vince , Yang Songnan , Rice J. Hollis , Song Qijian , Mazarei Mitra , Arelli Prakash R. , Meksem Khalid , Stewart C. Neal , Hewezi Tarek 
Published: February 2020

Summary

DNA methylation is a widespread epigenetic mark that contributes to transcriptome reprogramming during plant–pathogen interactions. However, the distinct role of DNA methylation in establishing resistant and susceptible responses remains largely unexplored.

Here, we developed and used a pair of near‐isogenic lines (NILs) to characterize DNA methylome landscapes of soybean roots during the susceptible and resistant interactions with soybean cyst nematode (SCN; Heterodera glycines). We also compared the methylomes of the NILs and their parents to identify introduced and stably inherited methylation variants.

The genomes of the NILs were substantially differentially methylated under uninfected conditions. This difference was associated with differential gene expression that may prime the NIL responses to SCN infection. In response to SCN infection, the susceptible line exhibited reduced global methylation levels in both protein‐coding genes and transposable elements, whereas the resistant line showed the opposite response, increased global methylation levels. Heritable and novel nonparental differentially methylated regions overlapping with genes associated with soybean response to SCN infection were identified and validated using transgenic hairy root system.

Our analyses indicate that DNA methylation patterns associated with the susceptible and resistant interactions are highly specific and that novel and stably inherited methylation variants are of biological significance.
Potential effects of antibiotic‐induced gut microbiome alteration on blood–brain barrier permeability compromise in rhesus monkeys
Authors: Wu Qiong , Zhang Yingqian , Zhang Yinbing , Xia Chunchao , Lai Qi , Dong Zaiquan , Kuang Weihong , Yang Cheng , Su Dan , Li Hongxia , Zhong Zhihui 
Published: February 2020

AbstractThe blood–brain barrier (BBB) contributes to the maintenance of brain homeostasis. Gut microbiome composition affects BBB development and expression of tight junction proteins in rodents. However, we still do not know if there is any direct effect of gut microbial composition on BBB permeability and function in normal adult animals. In the current study, we determined temporal and spatial changes in BBB permeability of rhesus monkeys receiving amoxicillin‐clavulanic acid (AC) by monitoring the cerebrospinal fluid/serum albumin ratio and the volume transfer constant (Ktrans). We showed that oral, but not intravenous, AC was associated with subsequent significant alteration in gut microbial composition and an increase in BBB permeability in all monkeys, especially in the thalamus area. Acetic and propionic acids might play a pivotal role in this newly found communication between the gut and the central nervous system. Antibiotic‐induced gut microbial composition change, especially the decrease in acetic acid– and propionic acid–producing phyla and genera, might have a potential effect on the increase in BBB permeability, which may contribute to a variety of neurological and psychological diseases.
Transgender pediatric surgical patients—Important perioperative considerations
Authors: Roque Remigio A. 
Published: February 2020

AbstractTransgender describes a variety of identities in which an individual's gender identity is different from expected based on the sex assigned at birth. In the United States, it is estimated that over 1 million adults and 150 000 youth identify as transgender, with increasing numbers being seen in healthcare and surgical settings. These numbers will continue to rise as visibility and acceptance grow. Current guidelines recommend transition‐related surgeries be reserved for older adolescents and adults. However, this is not the only circumstance in which the pediatric anesthesiologist may find themselves caring for a transgender patient. In order to provide the safest and most affirming care, it is crucial that the pediatric anesthesiologist develop a working knowledge of this unique and vulnerable population, including the potential impacts of gender‐affirming treatment on their perioperative care.
Rice yield formation under high day and night temperatures—A prerequisite to ensure future food security
Authors: Xu Jiemeng , Henry Amelia , Sreenivasulu Nese 
Published: February 2020

AbstractIncreasing temperatures resulting from climate change dramatically impact rice crop production in Asia. Depending on the specific stage of rice development, heat stress reduces tiller/panicle number, decreases grain number per plant and lower grain weight, thus negatively impacting yield formation. Hence improving rice crop tolerance to heat stress in terms of sustaining yield stability under high day temperature (HDT), high night temperature (HNT), or combined high day and night temperature (HDNT) will bolster future food security. In this review article, we highlight the phenological alterations caused by heat and the underlying molecular‐physiological and genetic mechanisms operating under different types of heat conditions (HDT, HNT, and HDNT) to understand heat tolerance. Based on our synthesis of HDT, HNT, and HDNT effects on rice yield components, we outline future breeding strategies to contribute to sustained food security under climate change.
Non‐structural carbohydrate dynamics associated with antecedent stem water potential and air temperature in a dominant desert shrub
Authors: Guo Jessica S. , Gear Linnea , Hultine Kevin R. , Koch George W. , Ogle Kiona 
Published: February 2020

AbstractNon‐structural carbohydrates (NSCs) are necessary for plant growth and affected by plant water status, but the temporal dynamics of water stress impacts on NSC are not well understood. We evaluated how seasonal NSC concentrations varied with plant water status (predawn xylem water potential, Ψ) and air temperature (T) in the evergreen desert shrub Larrea tridentata. Aboveground sugar and starch concentrations were measured weekly or monthly for ~1.5 years on 6–12 shrubs simultaneously instrumented with automated stem psychrometers; leaf photosynthesis (Anet) was measured monthly for 1 year. Leaf sugar increased during the dry, premonsoon period, associated with lower Ψ (greater water stress) and high T. Leaf sugar accumulation coincided with declines in leaf starch and stem sugar, suggesting the prioritization of leaf sugar during low photosynthetic uptake. Leaf starch was strongly correlated with Anet and peaked during the spring and monsoon seasons, while stem starch remained relatively constant except for depletion during the monsoon. Recent photosynthate appeared sufficient to support spring growth, while monsoon growth required the remobilization of stem starch reserves. The coordinated responses of different NSC fractions to water status, photosynthesis, and growth demands suggest that NSCs serve multiple functions under extreme environmental conditions, including severe drought.
Early outcomes comparing induction with antithymocyte globulin vs alemtuzumab in two steroid‐avoidance protocols in pediatric renal transplantation
Authors: Puliyanda Dechu P. , Pizzo Helen , Rodig Nancy , Somers Michael J. G. 
Published: February 2020

AbstractSteroid avoidance in pediatric kidney transplants was found effective with extended daclizumab induction. Upon discontinuation of daclizumab, lymphocyte‐depleting agents became used, with little comparative data. We assessed outcomes in children undergoing low immunologic‐risk deceased donor (DD) kidney transplants using induction with antithymocyte globulin (ATG) compared to alemtuzumab. We reviewed consecutive DD kidney transplants from January 2015 to September 2017 at two pediatric centers that used different lymphocyte‐depleting agents in steroid‐avoidance protocols: ATG (Center A) and alemtuzumab (Center B), with tacrolimus and MMF as maintenance immunosuppression. Anti‐infective prophylaxis was based on center protocol. Over the first year post‐tx, there were similar rates of infections. EBV and BK viremia were comparable though Center A manifested more low‐grade CMV viremia (A 46% vs B 0%; P = .0009) at median onset 1.8 months, followed by early seroconversion. Reduction of immunosuppression did not differ between groups. DSA at 1 year was similar (A 8% vs 13%) with low rates of BPAR. Need for steroid‐based conversion was low. There were no graft losses and no differences in median eGFR at 30, 90, 180, and 365 days. (a) 1‐year graft outcomes are excellent in steroid‐avoidance regimens using ATG or alemtuzumab induction; (b) conversion to steroid‐based therapy is low; (c) alemtuzumab/high‐dose MMF is associated with lower WBC and more GCSF use; (d) alemtuzumab/higher dose MMF results in more diarrhea and azathioprine conversion than ATG/lower dose MMF; (e) CMV viremia is seen more often with ATG use with infection prophylaxis reduction; however, seroconversion occurs promptly.
Heart transplantation in an infant with Williams‐Beuren syndrome and rapidly progressive ischemic cardiomyopathy
Authors: Baez Hernandez Nathanya , Kirk Richard , Davies Ryan , Roumillat Jessica , Sutcliffe David , Bano Maria , Butts Ryan 
Published: February 2020

AbstractIschemic cardiomyopathy with resultant refractory HF may occur in patients with WBS, often as the result of coronary involvement with SVAS. The rapid development of arteriopathy at a young age raises concerns regarding transplant candidacy due to progressive stenoses at other arterial sites with potential detrimental impact on long‐term heart graft function. We report a 2‐month‐old male infant diagnosed with mild aortic stenosis during the neonatal period, but subsequently developed rapidly progressive supravalvar and coronary artery stenoses leading to cardiogenic shock due to myocardial ischemia. The presentation led to the diagnosis of WBS. He required prolonged CPR including ECMO therapy. He subsequently underwent LVAD implantation as bridge to transplant and 4 days later heart transplantation. His post‐operative course was complicated by prolonged mechanical ventilation and extended intensive care unit and hospital stays. However, at follow‐up 18 months post‐transplant he continues to have normal graft function with mild, non‐progressive residual coarctation of aorta and non‐progressive moderately hypoplastic pulmonary arteries.
Can standards save organic farming from conventionalisation? Dynamics of collective projects and rules in a French organic producers’ organisation
Authors: Dufeu Ivan , Le Velly Ronan , Bréchet Jean‐Pierre , Loconto Allison 
Published: February 2020

AbstractThe unintended consequences of standards and certification schemes, particularly their challenges for alternative agri‐food networks, is a core concern of rural sociology. The conventionalisation of organic agriculture is a prime example. In this article, we contribute to this debate by studying standards that organic farmers developed for themselves within a French organic producers’ organisation. We introduce a ‘regulationist theory of collective action’ and show that these farmers crafted specific rules that go beyond the EU regulation, which in turn gave life to their own alternative, collective project. We thus demonstrate that standardisation and certification do not inevitably engender conventionalisation.
Speciation in North American Junonia from a genomic perspective
Authors: Cong Qian , Zhang Jing , Shen Jinhui , Cao Xiaolong , Brévignon Christian , Grishin Nick V. 
Published: February 2020

AbstractDelineating species boundaries in phylogenetic groups undergoing recent radiation is a daunting challenge akin to discretizing continuity. Here, we propose a general approach exemplified by American butterflies from the genus Junonia Hübner notorious for the variety of similar phenotypes, ease of hybridization, and the lack of consensus about their classification. We obtain whole‐genome shotgun sequences of about 200 specimens. We reason that discreteness emerges from continuity by means of a small number of key players, and search for the proteins that diverged markedly between sympatric populations of different species, while keeping low polymorphism within these species. Being 0.25% of the total number, these three dozen ‘speciation’ proteins indeed partition pairs of Junonia populations into two clusters with a prominent break in between, while all proteins taken together fail to reveal this discontinuity. Populations with larger divergence from each other, comparable to that between two sympatric species, form the first cluster and correspond to different species. The other cluster is characterized by smaller divergence, similar to that between allopatric populations of the same species and comprise conspecific pairs. Using this method, we conclude that J. genoveva (Cramer), J. litoralis Brévignon, J. evarete (Cramer), and J. divaricata C. & R. Felder are restricted to South America. We find that six species of Junonia are present in the United States, one of which is new: Junonia stemosa Grishin, sp.n. (i), found in south Texas and phenotypically closest to J. nigrosuffusa W. Barnes & McDunnough (ii) in its dark appearance. In the pale nudum of the antennal club, these two species resemble J. zonalis C. & R. Felder (iii) from Florida and the Caribbean Islands. The pair of sister species, J. grisea Austin & J. Emmel (iv) and J. coenia Hübner (v), represent the classic west/east U.S.A. split. The mangrove feeder (as caterpillar), dark nudum J. neildi Brévignon (vi) enters south Texas as a new subspecies Junonia neildi varia Grishin ssp.n. characterized by more extensive hybridization with and introgression from J. coenia, and, as a consequence, more variable wing patterns compared with the nominal J. n. neildi in Florida. Furthermore, a new mangrove‐feeding species from the Pacific Coast of Mexico is described as Junonia pacoma Grishin sp.n. Finally, genomic analysis suggests that J. nigrosuffusa may be a hybrid species formed by the ancestors of J. grisea and J. stemosa sp.n.This published work has been registered on Zoobank, http://zoobank.org/urn:lsid:zoobank.org:act:C6E70C96‐463D‐4E6A‐95CC‐B0384B0EEEBA.
Closure of a hyperextended system in an orogenic lithospheric pop‐up, Western Pyrenees: The role of mantle buttressing and rift structural inheritance
Authors: Saspiturry Nicolas , Allanic Cécile , Razin Philippe , Issautier Benoit , Baudin Thierry , Lasseur Eric , Serrano Olivier , Leleu Sophie 
Published: February 2020

AbstractThe Early Cretaceous hyperextended Mauléon rift is localized in the north‐western Pyrenean orogen. We infer the Tertiary evolution of the Mauléon basin through the restoration of a 153‐km‐long crustal‐scale balanced cross‐section of the Pyrenean belt, which documents at least 67 km (31%) of orogenic shortening in the Western Pyrenees. Initial shortening, accommodated through inversion of inherited crustal structures, led to formation of a pop‐up structure, in which the opposite edges underwent similar shortening with different tectonic reactivation styles, localized versus. distributed. Underthrusting of the Iberian margin accommodated further convergence, forming the Axial Zone antiformal stack of crustal nappes within a lithospheric pop‐up. Thin‐skinned and thick‐skinned structures propagated outward from the heart of this pop‐up, a block of strong mantle acting as a buttress inhibiting complete inversion of the Mauléon rift basin.
Experimental model for removal of snake venom via hemoperfusion in rats
Authors: Oliveira Maximilian Estevan , Campanholi Jéssica , Cavalcante Roberta Lima , Moreno Felipe Silveira , Yoshida Edson Hideaki , Dini Murilo Melo Juste , Aranha Élvio Franco de Camargo , Cogo José Carlos , Dias Lourdes , Hyslop Stephen , Grotto Denise , Hanai‐Yoshida Valquíria Miwa , Oshima‐Franco Yoko 
Published: February 2020

AbstractObjectiveTo examine the efficiency of hemoperfusion in removing South American rattlesnake (Crotalus durissus terrificus) venom from rats compared with neutralization by antivenom.DesignAn exploratory experimental investigation in rats involving the injection of snake venom with or without subsequent hemoperfusion or antivenom administration.SettingBasic animal research laboratory in a private university.AnimalsNormal, healthy male Wistar rats (0.29‐0.40 kg, 3‐6 months old) from a commercial breeder.InterventionsFour experimental groups of randomly allocated rats (n = 3/group) were studied: Group 1: rats were injected with a single dose of venom (5 mg/kg, IM, in the right thigh) with no other treatment; blood samples were collected minutes before death to determine leukocyte, platelet, and erythrocyte counts; Group 2 (Control): rats underwent hemoperfusion alone for 60 min using a hemoperfusion cartridge designed for protein adsorption (by granulated charcoal) and protein precipitation (by tannic acid); Group 3 (Venom + antivenom): rats were injected with venom (5 mg/kg, IM) and, 10 min later, were treated with antivenom at the venom:antivenom ratio recommended by the manufacturer; Group 4 (Venom + hemoperfusion): Rats were injected with venom (5 mg/kg, IM) and, 10 min later, were hemoperfused for 60 min. In groups 2‐4, blood samples were collected for leukocyte, platelet, and erythrocyte counts 24 h after venom.Measurements and Main ResultsRats injected with venom alone (Group 1) developed signs of neurotoxicity and ataxia and died in 9.0 ± 0.43 h but showed no changes in leukocyte or erythrocyte counts. In contrast, there were no deaths in groups 2‐4. The lack of deaths in Groups 3 and 4 indicated that antivenom and hemoperfusion, respectively, protected against the lethal effects of the venom.ConclusionsHemoperfusion with a double‐action hemoperfusion cartridge capable of protein adsorption and precipitation protected rats against C. d. terrificus venom.