Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteome Analysis of Cytoplasmatic and Plastidic β-Carotene Lipid Droplets in Dunaliella bardawil1[OPEN]

Proteome analysis of two types of lipid droplets in Dunaliella bardawil uncovers enzymes involved in β-carotene biosynthesis and lipid droplet biogenesis. The halotolerant green alga Dunaliella bardawil is unique in that it accumulates under stress two types of lipid droplets: cytoplasmatic lipid droplets (CLD) and β-carotene-rich (βC) plastoglobuli. Recently, we isolated and analyzed the lipid and pigment compositions of these lipid droplets. Here, we describe their proteome analysis. A contamination filter and an enrichment filter were utilized to define core proteins. A proteome database of Dunaliella salina/D. bardawil was constructed to aid the identification of lipid droplet proteins. A total of 124 and 42 core proteins were identified in βC-plastoglobuli and CLD, respectively, with only eight common proteins. Dunaliella spp. CLD resemble cytoplasmic droplets from Chlamydomonas reinhardtii and contain major lipid droplet-associated protein and enzymes involved in lipid and sterol metabolism. The βC-plastoglobuli proteome resembles the C. reinhardtii eyespot and Arabidopsis (Arabidopsis thaliana) plastoglobule proteomes and contains carotene-globule-associated protein, plastid-lipid-associated protein-fibrillins, SOUL heme-binding proteins, phytyl ester synthases, β-carotene biosynthesis enzymes, and proteins involved in membrane remodeling/lipid droplet biogenesis: VESICLE-INDUCING PLASTID PROTEIN1, synaptotagmin, and the eyespot assembly proteins EYE3 and SOUL3. Based on these and previous results, we propose models for the biogenesis of βC-plastoglobuli and the biosynthesis of β-carotene within βC-plastoglobuli and hypothesize that βC-plastoglobuli evolved from eyespot lipid droplets.
Insights into Conifer Giga-Genomes1

The sequenced genomes of three conifer species provide the first assemblies of gymnosperm genomes and perspectives on the largest plant genomes sequenced to date. Insights from sequenced genomes of major land plant lineages have advanced research in almost every aspect of plant biology. Until recently, however, assembled genome sequences of gymnosperms have been missing from this picture. Conifers of the pine family (Pinaceae) are a group of gymnosperms that dominate large parts of the world’s forests. Despite their ecological and economic importance, conifers seemed long out of reach for complete genome sequencing, due in part to their enormous genome size (20–30 Gb) and the highly repetitive nature of their genomes. Technological advances in genome sequencing and assembly enabled the recent publication of three conifer genomes: white spruce (Picea glauca), Norway spruce (Picea abies), and loblolly pine (Pinus taeda). These genome sequences revealed distinctive features compared with other plant genomes and may represent a window into the past of seed plant genomes. This Update highlights recent advances, remaining challenges, and opportunities in light of the publication of the first conifer and gymnosperm genomes.
Atrial Fibrillation in Athletes

Abstract Many studies have shown a relationship between long-term endurance sport practice and atrial fibrillation. Inflammation, anatomic remodelling, alterations in the autonomic system and neurohormonal activation are all possible explanations for the increased prevalence of this arrhythmia in athletes. Atrial fibrillation may determine disabling symptoms like palpitations and impaired physical performance, compromising eligibility for competitive activities, but exclusion from sport is not necessary for all athletes. Limited data are available on drug therapy and recently ablation resulted to be a particularly attractive option for young athletes with paroxysmal atrial fibrillation. The purpose of this review is to discuss mechanisms, clinical features, management of atrial fibrillation in competitive athletes, including criteria for eligibility and disqualification in sport practice.
Regulation of Specialized Metabolism by WRKY Transcription Factors

WRKY transcription factors play an essential role in regulating the biosynthesis of plant-specialized metabolites. WRKY transcription factors (TFs) are well known for regulating plant abiotic and biotic stress tolerance. However, much less is known about how WRKY TFs affect plant-specialized metabolism. Analysis of WRKY TFs regulating the production of specialized metabolites emphasizes the values of the family outside of traditionally accepted roles in stress tolerance. WRKYs with conserved roles across plant species seem to be essential in regulating specialized metabolism. Overall, the WRKY family plays an essential role in regulating the biosynthesis of important pharmaceutical, aromatherapy, biofuel, and industrial components, warranting considerable attention in the forthcoming years.
The Evolution of Mechanisms Driving the Stomatal Response to Vapor Pressure Deficit1[OPEN]

The mechanism for a stomatal response to vapor pressure deficit evolved from a passive regulation in basal vascular plants to mediation by ABA in the earliest angiosperms. Stomatal responses to vapor pressure deficit (VPD) are a principal means by which vascular land plants regulate daytime transpiration. While much work has focused on characterizing and modeling this response, there remains no consensus as to the mechanism that drives it. Explanations range from passive regulation by leaf hydration to biochemical regulation by the phytohormone abscisic acid (ABA). We monitored ABA levels, leaf gas exchange, and water status in a diversity of vascular land plants exposed to a symmetrical, mild transition in VPD. The stomata in basal lineages of vascular plants, including gymnosperms, appeared to respond passively to changes in leaf water status induced by VPD perturbation, with minimal changes in foliar ABA levels and no hysteresis in stomatal action. In contrast, foliar ABA appeared to drive the stomatal response to VPD in our angiosperm samples. Increased foliar ABA level at high VPD in angiosperm species resulted in hysteresis in the recovery of stomatal conductance; this was most pronounced in herbaceous species. Increased levels of ABA in the leaf epidermis were found to originate from sites of synthesis in other parts of the leaf rather than from the guard cells themselves. The transition from a passive regulation to ABA regulation of the stomatal response to VPD in the earliest angiosperms is likely to have had critical implications for the ecological success of this lineage.
Galactose-Depleted Xyloglucan Is Dysfunctional and Leads to Dwarfism in Arabidopsis1

Depleting galactose from the cell wall polysaccharide xyloglucan leads to a disruption of diverse cellular and physiological processes involved in normal plant growth. Xyloglucan is a polysaccharide that has important roles in the formation and function of the walls that surround growing land plant cells. Many of these plants synthesize xyloglucan that contains galactose in two different side chains (L and F), which exist in distinct molecular environments. However, little is known about the contribution of these side chains to xyloglucan function. Here, we show that Arabidopsis (Arabidopsis thaliana) mutants devoid of the F side chain galactosyltransferase MURUS3 (MUR3) form xyloglucan that lacks F side chains and contains much less galactosylated xylose than its wild-type counterpart. The galactose-depleted xyloglucan is dysfunctional, as it leads to mutants that are dwarfed with curled rosette leaves, short petioles, and short inflorescence stems. Moreover, cell wall matrix polysaccharides, including xyloglucan and pectin, are not properly secreted and instead accumulate within intracellular aggregates. Near-normal growth is restored by generating mur3 mutants that produce no detectable amounts of xyloglucan. Thus, cellular processes are affected more by the presence of the dysfunctional xyloglucan than by eliminating xyloglucan altogether. To identify structural features responsible for xyloglucan dysfunction, xyloglucan structure was modified in situ by generating mur3 mutants that lack specific xyloglucan xylosyltransferases (XXTs) or that overexpress the XYLOGLUCAN L-SIDE CHAIN GALACTOSYLTRANSFERASE2 (XLT2) gene. Normal growth was restored in the mur3-3 mutant overexpressing XLT2 and in mur3-3 xxt double mutants when the dysfunctional xyloglucan was modified by doubling the amounts of galactosylated side chains. Our study assigns a role for galactosylation in normal xyloglucan function and demonstrates that altering xyloglucan side chain structure disturbs diverse cellular and physiological processes.
Vascular Compliance in Hypertension: Therapeutic Implications

Vascular compliance is decreased in men with sustained essential hypertension. Reduced arterial compliance contributes to the maintenance of systolic pressure and end-systolic stress, thus participating in the development of cardiac hypertrophy. Reduced venous compliance contributes to maintaining the filling pressure of the heart in the presence of reduced intravascular volume. Reduced arterial and venous compliances are not the simple consequence of the elevated blood pressure but also reflect intrinsic alterations of the vascular wall. Thus, the blood pressure reduction due to antihypertensive agents is not constantly associated with a reversion of the decreased vascular compliance.
Management of hypoglycaemia in the newborn

Abstract Although there is no firm empirical evidence base for the management of neonatal hypoglycaemia, an understanding of the underlying physiology and pathophysiology of fuel metabolism in the newborn enables a rational approach to be taken. In this paper, we outline the process of neonatal metabolic adaptation; address the problem of measuring blood glucose and defining hypoglycaemia; consider those babies in whom measurement should be done routinely and the timing of this; and evaluate the various approaches that can be taken in the primary and secondary prevention and management of hypoglycaemia, and its investigation when appropriate.
Lateral Organ Boundaries Domain16 and 18 Act Downstream of the AUXIN1 and LIKE-AUXIN3 Auxin Influx Carriers to Control Lateral Root Development in Arabidopsis1

Two auxin influx carriers are required for auxin signaling that activates transcriptional control in lateral root development. Several members of the Lateral Organ Boundaries Domain (LBD)/Asymmetric Leaves2-Like (ASL) gene family have been identified to play important roles in Arabidopsis (Arabidopsis thaliana) lateral root (LR) development during auxin response, but their functional relationship with auxin transporters has not been established yet. Here, we show that the AUXIN1 (AUX1) and LIKE-AUXIN3 (LAX3) auxin influx carriers are required for auxin signaling that activates LBD16/ASL18 and LBD18/ASL20 to control LR development. The lax3 mutant phenotype was not significantly enhanced when combined with lbd16 or lbd18. However, LBD18 overexpression could rescue the defects in LR emergence in lax3 with concomitant expression of the LBD18 target genes. Genetic and gene expression analyses indicated that LBD16 and LBD18 act with AUX1 to regulate LR initiation and LR primordium development, and that AUX1 and LAX3 are needed for auxin-responsive expression of LBD16 and LBD18. LBD18:SUPERMAN REPRESSIVE DOMAIN X in the lbd18 mutant inhibited LR initiation and LR primordium development in response to a gravitropic stimulus and suppressed promoter activities of the cell cycle genes Cyclin-Dependent Kinase A1;1 and CYCLINB1;1. Taken together, these results suggest that LBD16 and LBD18 are important regulators of LR initiation and development downstream of AUX1 and LAX3.
The Soybean-Specific Maturity Gene E1 Family of Floral Repressors Controls Night-Break Responses through Down-Regulation of FLOWERING LOCUS T Orthologs1[OPEN]

Light-dependent phytochrome A-regulated transcription of floral repressors affects photoperiodic induction of flowering. Photoperiodism is a rhythmic change of sensitivity to light, which helps plants to adjust flowering time according to seasonal changes in daylength and to adapt to growing conditions at various latitudes. To reveal the molecular basis of photoperiodism in soybean (Glycine max), a facultative short-day plant, we analyzed the transcriptional profiles of the maturity gene E1 family and two FLOWERING LOCUS T (FT) orthologs (FT2a and FT5a). E1, a repressor for FT2a and FT5a, and its two homologs, E1-like-a (E1La) and E1Lb, exhibited two peaks of expression in long days. Using two different approaches (experiments with transition between light and dark phases and night-break experiments), we revealed that the E1 family genes were expressed only during light periods and that their induction after dawn in long days required a period of light before dusk the previous day. In the cultivar Toyomusume, which lacks the E1 gene, virus-induced silencing of E1La and E1Lb up-regulated the expression of FT2a and FT5a and led to early flowering. Therefore, E1, E1La, and E1Lb function similarly in flowering. Regulation of E1 and E1L expression by light was under the control of E3 and E4, which encode phytochrome A proteins. Our data suggest that phytochrome A-mediated transcriptional induction of E1 and its homologs by light plays a critical role in photoperiodic induction of flowering in soybean.
An update on red blood cell storage lesions, as gleaned through biochemistry and omics technologies

Red blood cell (RBC) aging in the blood bank is characterized by the accumulation of a significant number of biochemical and morphologic alterations. Recent mass spectrometry and electron microscopy studies have provided novel insights into the molecular changes underpinning the accumulation of storage lesions to RBCs in the blood bank. Biochemical lesions include altered cation homeostasis, reprogrammed energy, and redox metabolism, which result in the impairment of enzymatic activity and progressive depletion of high‐energy phosphate compounds. These factors contribute to the progressive accumulation of oxidative stress, which in turn promotes oxidative lesions to proteins (carbonylation, fragmentation, hemoglobin glycation) and lipids (peroxidation). Biochemical lesions negatively affect RBC morphology, which is marked by progressive membrane blebbing and vesiculation. These storage lesions contribute to the altered physiology of long‐stored RBCs and promote the rapid clearance of up to one‐fourth of long‐stored RBCs from the recipient's bloodstream after 24 hours from administration. While prospective clinical evidence is accumulating, from the present review it emerges that biochemical, morphologic, and omics profiles of stored RBCs have observable changes after approximately 14 days of storage. Future studies will assess whether these in vitro observations might have clinically meaningful effects.
Genome-Wide Association Mapping and Genomic Prediction Elucidate the Genetic Architecture of Morphological Traits in Arabidopsis1

Integration of genome wide association mapping and genomic prediction increases resolution of genetic architecture and uncovers missing heritability of quantitative traits in plants. Quantitative traits in plants are controlled by a large number of genes and their interaction with the environment. To disentangle the genetic architecture of such traits, natural variation within species can be explored by studying genotype-phenotype relationships. Genome-wide association studies that link phenotypes to thousands of single nucleotide polymorphism markers are nowadays common practice for such analyses. In many cases, however, the identified individual loci cannot fully explain the heritability estimates, suggesting missing heritability. We analyzed 349 Arabidopsis accessions and found extensive variation and high heritabilities for different morphological traits. The number of significant genome-wide associations was, however, very low. The application of genomic prediction models that take into account the effects of all individual loci may greatly enhance the elucidation of the genetic architecture of quantitative traits in plants. Here, genomic prediction models revealed different genetic architectures for the morphological traits. Integrating genomic prediction and association mapping enabled the assignment of many plausible candidate genes explaining the observed variation. These genes were analyzed for functional and sequence diversity, and good indications that natural allelic variation in many of these genes contributes to phenotypic variation were obtained. For ACS11, an ethylene biosynthesis gene, haplotype differences explaining variation in the ratio of petiole and leaf length could be identified.
Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize1[OPEN]

Alternative splicing is common during development and drought, with a high degree of tissue specificity even among related tissue types. Alternative splicing plays a crucial role in plant development as well as stress responses. Although alternative splicing has been studied during development and in response to stress, the interplay between these two factors remains an open question. To assess the effects of drought stress on developmentally regulated splicing in maize (Zea mays), 94 RNA-seq libraries from ear, tassel, and leaf of the B73 public inbred line were constructed at four developmental stages under both well-watered and drought conditions. This analysis was supplemented with a publicly available series of 53 libraries from developing seed, embryo, and endosperm. More than 48,000 novel isoforms, often with stage- or condition-specific expression, were uncovered, suggesting that developmentally regulated alternative splicing occurs in thousands of genes. Drought induced large developmental splicing changes in leaf and ear but relatively few in tassel. Most developmental stage-specific splicing changes affected by drought were tissue dependent, whereas stage-independent changes frequently overlapped between leaf and ear. A linear relationship was found between gene expression changes in splicing factors and alternative spicing of other genes during development. Collectively, these results demonstrate that alternative splicing is strongly associated with tissue type, developmental stage, and stress condition.
Nosocomial infections in a neonatal intensive care unit in South Brazil

Objective The aim of this study was to describe the incidence and epidemiology of nosocomial infection in newborns who were admitted to a neonatal intensive care unit in a hospital in south Santa Catarina, Brazil. Methods A prospective cohort study was conducted for 1 year among 239 neonates who remained as in-patients 48 hours after admission. The criteria that were used to diagnose infection were in accordance with the Centers for Disease Control and Prevention and the National Health Surveillance Agency. Results The incidence of nosocomial infection was 45.8%. The primary reasons for admission were primary bloodstream infection (80.7%) and pneumonia (6.7%). Coagulase-negative Staphylococcus was the most commonly identified agent in the blood cultures and in the hospital unit. Prematurity was the most prevalent reason for admission. The general mortality rate was 12.1%, and mortality from nosocomial infection was 33.8%. Conclusions The incidence of nosocomial infection in the hospital unit was higher than rates that have been reported in other national studies. The major types of nosocomial infection were primary bloodstream infection and pneumonia.
Which decision rules meet methodological standards in children with febrile neutropenia? Results of a systematic review and analysis

Clinical decision rules (CDRs) have sought to identify the few children with chemotherapy‐induced febrile neutropenia (FN) really at risk of severe infection to reduce the invasive procedures and costs for those at low risk. Several reports have shown that most rules do not perform well enough to be clinically useful. Our objective was to analyze the derivation methods and validation procedures of these CDRs.
Software for the analysis of DNA sequence elements of transcription

The detection of transcription control elements in DNA sequences became both more important and more complicated by the completion of the first full genome sequencing projects. Rapid evaluation of potential regulatory elements in large amounts of sequence data requires specific methods preferably available as user-friendly computer programs. However, many more algorithms and methods have been published than programs are available, creating problems for scientists who try to select an appropriate method for their needs from the literature. The Internet provides a worldwide and relatively easy access to computer software if the user knows where to look. One of the major problems remaining is how to find the appropriate software. We have compiled a guide detailing where software is available and what is to be expected in terms of interface and data compatibility with other programs. We also show results obtained with each program for several examples. The summarized features of each program should allow scientists to select quickly the method of their choice and inform them where to download the software.
A GTPase-Dependent Fine ER Is Required for Localized Secretion in Polarized Growth of Root Hairs1

An RHD3-dependent fine ER structure at the subapical zone, coordinated with dynamic microtubules, is required for localized secretion to the apical dome of root hairs in growth. The endoplasmic reticulum (ER) is a cellular network comprising membrane tubules and sheets stretching throughout the cytoplasm. Atlastin GTPases, including Atlastin-1 in mammals and RHD3 in plants, play a role in the generation of the interconnected tubular ER network by promoting the fusion of ER tubules. Root hairs in rhd3 are short and wavy, a defect reminiscent of axon growth in cells with depleted Atlastin-1. However, how a loss in the ER complexity could lead to a defective polarized cell growth of root hairs or neurons remains elusive. Using live-cell imaging techniques, we reveal that, a fine ER distribution, which is found in the subapical zone of growing root hairs of wild-type plants, is altered to thick bundles in rhd3. The localized secretion to the apical dome as well as the apical localization of root hair growth regulator ROP2 is oscillated in rhd3. Interestingly, the shift of ROP2 precedes the shift of localized secretion as well as the fine ER distribution in rhd3. Our live imaging and pharmacologic modification of root hair growth defects in rhd3 suggest that there is interplay between the ER and microtubules in the polarized cell growth of root hairs. We hypothesize that, under the guidance of ROP2, RHD3, together with the action of microtubules, is required for the formation of a fine ER structure in the subapical zone of growing root hairs. This fine ER structure is essential for the localized secretion to the apical dome in polarized cell growth.
Playing it safe

Every year over 35,000 children under 15 in the UK are admitted to hospital with injuries caused by toys. Accidents will happen, but are recent, potentially dangerous crazes such as Heelys, trampolines, scooters and even Nintendo Wiis contributing too much to the statistics? And how can we get the balance right by keeping kids safe at play without wrapping them in cotton wool and discouraging physical activity? JRSH's Mandy Murphy finds out.