Miracle-dz/UniFAR-FTUs huggingface dataset:
An R2R3-MYB Transcription Factor Regulates Eugenol Production in Ripe Strawberry Fruit Receptacles1

A ripening-related transcription factor affects the phenylpropanoid synthesis pathway and the biosynthesis of eugenol in the strawberry fruit. Eugenol is a volatile phenylpropanoid that contributes to flower and ripe fruit scent. In ripe strawberry (Fragaria × ananassa) fruit receptacles, eugenol is biosynthesized by eugenol synthase (FaEGS2). However, the transcriptional regulation of this process is still unknown. We have identified and functionally characterized an R2R3 MYB transcription factor (EMISSION OF BENZENOID II [FaEOBII]) that seems to be the orthologous gene of PhEOBII from Petunia hybrida, which contributes to the regulation of eugenol biosynthesis in petals. The expression of FaEOBII was ripening related and fruit receptacle specific, although high expression values were also found in petals. This expression pattern of FaEOBII correlated with eugenol content in both fruit receptacle and petals. The expression of FaEOBII was repressed by auxins and activated by abscisic acid, in parallel to the ripening process. In ripe strawberry receptacles, where the expression of FaEOBII was silenced, the expression of CINNAMYL ALCOHOL DEHYDROGENASE1 and FaEGS2, two structural genes involved in eugenol production, was down-regulated. A subsequent decrease in eugenol content in ripe receptacles was also observed, confirming the involvement of FaEOBII in eugenol metabolism. Additionally, the expression of FaEOBII was under the control of FaMYB10, another R2R3 MYB transcription factor that regulates the early and late biosynthetic genes from the flavonoid/phenylpropanoid pathway. In parallel, the amount of eugenol in FaMYB10-silenced receptacles was also diminished. Taken together, these data indicate that FaEOBII plays a regulating role in the volatile phenylpropanoid pathway gene expression that gives rise to eugenol production in ripe strawberry receptacles.
Management of Giant Omphalocele: A Case Series

Giant omphalocele (GO) is congenital abdominal wall defect measuring >6 cm and/or containing liver.1 The omphalocele sac consists of amnion and peritoneum, and is prone to rupture either in utero, during delivery or after birth. The surgical management of neonates with GO is challenging. Several operative and nonoperative strategies have been described although a traditional silo chimney with graduated visceral reduction is commonly used. In this case report, we describe four patients with GO in whom postnatal management was highly problematic. We used an acellular biological xenograft called Surgisis Biodesign (Cook Ltd.) to repair the GO.2 Surgisis Biodesign is derived from porcine small intestine submucosa and consists of an extracellular matrix containing collagens, glycoproteins glycosaminoglycans, proteoglycans, and growth factors.2Once implanted into tissue it provides a scaffold for epithelialization.
Reduced Lateral Root Branching Density Improves Drought Tolerance in Maize1[OPEN]

Maize genotypes with reduced lateral root branching density have superior water capture, growth, and yield under drought. An emerging paradigm is that root traits that reduce the metabolic costs of soil exploration improve the acquisition of limiting soil resources. Here, we test the hypothesis that reduced lateral root branching density will improve drought tolerance in maize (Zea mays) by reducing the metabolic costs of soil exploration, permitting greater axial root elongation, greater rooting depth, and thereby greater water acquisition from drying soil. Maize recombinant inbred lines with contrasting lateral root number and length (few but long [FL] and many but short [MS]) were grown under water stress in greenhouse mesocosms, in field rainout shelters, and in a second field environment with natural drought. Under water stress in mesocosms, lines with the FL phenotype had substantially less lateral root respiration per unit of axial root length, deeper rooting, greater leaf relative water content, greater stomatal conductance, and 50% greater shoot biomass than lines with the MS phenotype. Under water stress in the two field sites, lines with the FL phenotype had deeper rooting, much lighter stem water isotopic signature, signifying deeper water capture, 51% to 67% greater shoot biomass at flowering, and 144% greater yield than lines with the MS phenotype. These results entirely support the hypothesis that reduced lateral root branching density improves drought tolerance. The FL lateral root phenotype merits consideration as a selection target to improve the drought tolerance of maize and possibly other cereal crops.
Subunit Q Is Required to Stabilize the Large Complex of NADPH Dehydrogenase in Synechocystis sp. Strain PCC 68031

A single-transmembrane subunit of NADPH dehydrogenase is involved in respiration and cyclic electron transport around photosystem I but not in CO2 uptake. Two major complexes of NADPH dehydrogenase (NDH-1) have been identified in cyanobacteria. A large complex (NDH-1L) contains NdhD1, NdhF1, and NdhP, which are absent in a medium size complex (NDH-1M). They play important roles in respiration, NDH-1-dependent cyclic electron transport around photosystem I, and CO2 uptake. Two mutants sensitive to high light for growth and impaired in cyclic electron transport around photosystem I were isolated from the cyanobacterium Synechocystis sp. strain PCC 6803 transformed with a transposon-bearing library. Both mutants had a tag in an open reading frame encoding a product highly homologous to NdhQ, a single-transmembrane small subunit of the NDH-1L complex, identified in Thermosynechococcus elongatus by proteomics strategy. Deletion of ndhQ disassembled about one-half of the NDH-1L to NDH-1M and consequently impaired respiration, but not CO2 uptake. During prolonged incubation of the thylakoid membrane with n-dodecyl-β-d-maltoside at room temperature, the rest of the NDH-1L in ΔndhQ was disassembled completely to NDH-1M and was much faster than in the wild type. In the ndhP-deletion mutant (ΔndhP) background, absence of NdhQ almost completely disassembled the NDH-1L to NDH-1M, similar to the results observed in the ΔndhD1/ΔndhD2 mutant. We therefore conclude that both NdhQ and NdhP are essential to stabilize the NDH-1L complex.
The Prevention of Laparoscopic Bile Duct Injuries: An Analysis of 300 Cases of from a Human Factors and Cognitive Psychology Perspective

Application of human factors concepts to high-risk activities has facilitated reduction in human error. With introduction of laparoscopic cholecystectomy, the incidence of bile duct injury increased. Seeking ideas for prevention, we analyzed 300 laparoscopic bile duct injuries within the framework of human error analysis. The primary cause of error (97%) was a visual perceptual illusion. The laparoscopic environment contributed to 75% of injuries, poor visibility 22%. Most injuries involved deliberate major bile duct transection due to misperception of the anatomy. This illusion was so compelling that the surgeon usually did not recognize it. Even when irregular cues were detected, improper rules were employed, eliminating feedback. Since the complication-causing error occurred at few key steps during laparoscopic cholecystectomy; we instituted focused training to heighten vigilance, and have formulated specific rules to decrease the incidence of bile duct injury. In addition, factors in the laparoscopic environment contributing to this illusion are discussed.
Heat Impact of Revolving Instruments on Vital Dentin Tubules

The application of a fine stream of 100°F. water in "drilling" or grinding teeth during cavity preparation stabilizes the temperature of both dentin and revolving instruments and thereby prevents more than half the usual pain from operative treatment (fig. 1). It would seem probable that frictional heat is an important factor in operative pain.2 There is considerable literature on heat trauma, but the most comprehensive work was by Jeserich (1). He gave 1T. to 25°F. as the range of thermal increase for various revolving dental instruments and explained that the variation depended upon size, sharpness, speed, amount and type of pressure, and whether the operation is performed in a dry, moist, or wet field. Jeserich also stated ". it is possible to operate in a dry field with steel burs with slight thermal increase if" the precautions of size, sharpness, speed and pressure are exercised. It is with this latter statement especially, that this paper takes exception. Bronner reported 10°C. (18°F.) rises, but only during definite abuse (2). Bodecker (3) deplored heat from rapidly revolving instruments and connected it with pain. He produced a rise of 27°F. with a 8 in. carborundum stone used with moderate pressure, continuously for 45 seconds, prolonged grinding that could hardly be recommended. Wilson (4) confirmed Bodecker's experiments but found a rise of 5° to 60°F. depending upon the technique of cutting, the higher figures during abuse. All these and many other reports show temperature rises of less than 30°F. during normal operating, well within "the thermal tolerance zone"3 of living dentin, yet other writings link pain with frictional heat. Thomas (5) reported that the use of chilled burs (no frictional heat) diminished or eliminated pain in 76.8 per cent of his subjects. Previous heat measurements, such as Jeserich's, Bronner's Wilson's, and Bodecker's were made to determine the temperature changes of the enamel, dentin, and pulp during the grinding of tooth substance in operative treatment. Throughout this work much importance seemed to be given to the general temperature of the tooth and pulp, with pulp trauma and death as possible sequellae.
MicroRNA857 Is Involved in the Regulation of Secondary Growth of Vascular Tissues in Arabidopsis1

A microRNA regulates laccase transcription to affect the secondary growth of vascular tissues under the control of the transcription factor SQUAMOSA PROMOTER BINDING PROTEIN LIKE7. MicroRNAs (miRNAs) are endogenous small RNAs that repress target gene expression posttranscriptionally, and are critically involved in various developmental processes and responses to environmental stresses in eukaryotes. MiRNA857 is not widely distributed in plants and is encoded by a single gene, AtMIR857, in Arabidopsis (Arabidopsis thaliana). The functions of miR857 and its mechanisms in regulating plant growth and development are still unclear. Here, by means of genetic analysis coupled with cytological studies, we investigated the expression pattern and regulation mechanism of miR857 and its biological functions in Arabidopsis development. We found that miR857 regulates its target gene, Arabidopsis LACCASE7, at the transcriptional level, thereby reducing laccase activity. Using stimulated Raman scattering and x-ray microtomography three-dimensional analyses, we showed that miR857 was involved in the regulation of lignin content and consequently morphogenesis of the secondary xylem. In addition, miR857 was activated by SQUAMOSA PROMOTER BINDING PROTEIN-LIKE7 in response to low copper conditions. Collectively, these findings demonstrate the role of miR857 in the regulation of secondary growth of vascular tissues in Arabidopsis and reveal a unique control mechanism for secondary growth based on the miR857 expression in response to copper deficiency.
The Tomato MIXTA-Like Transcription Factor Coordinates Fruit Epidermis Conical Cell Development and Cuticular Lipid Biosynthesis and Assembly1

A MIXTA-like transcription factor from tomato regulates fruit cutin biosynthesis, and is part of a regulatory network linking epidermal cell development with cuticle formation. The epidermis of aerial plant organs is the primary source of building blocks forming the outer surface cuticular layer. To examine the relationship between epidermal cell development and cuticle assembly in the context of fruit surface, we investigated the tomato (Solanum lycopersicum) MIXTA-like gene. MIXTA/MIXTA-like proteins, initially described in snapdragon (Antirrhinum majus) petals, are known regulators of epidermal cell differentiation. Fruit of transgenically silenced SlMIXTA-like tomato plants displayed defects in patterning of conical epidermal cells. They also showed altered postharvest water loss and resistance to pathogens. Transcriptome and cuticular lipids profiling coupled with comprehensive microscopy revealed significant modifications to cuticle assembly and suggested SlMIXTA-like to regulate cutin biosynthesis. Candidate genes likely acting downstream of SlMIXTA-like included cytochrome P450s (CYPs) of the CYP77A and CYP86A subfamilies, LONG-CHAIN ACYL-COA SYNTHETASE2, GLYCEROL-3-PHOSPHATE SN-2-ACYLTRANSFERASE4, and the ATP-BINDING CASSETTE11 cuticular lipids transporter. As part of a larger regulatory network of epidermal cell patterning and L1-layer identity, we found that SlMIXTA-like acts downstream of SlSHINE3 and possibly cooperates with homeodomain Leu zipper IV transcription factors. Hence, SlMIXTA-like is a positive regulator of both cuticle and conical epidermal cell formation in tomato fruit, acting as a mediator of the tight association between fruit cutin polymer formation, cuticle assembly, and epidermal cell patterning.
MIST: a user-friendly metabolic simulator

The Metabolic Interactive Simulation Tool, MIST, is a software package, running under Microsoft Windows 3.1, which can be used for dynamic simulations, stoichiometric calculations and control analysis of metabolic pathways. The pathways can be of any complexity and are defined by the user in a simple, interactive way. The user-defined enzymatic rate equations can be compiled either by an external or an internal compiler. Simulations of pathways compiled by an external compiler run significantly faster, but since these compilers are commercial software, they are not distributed together with MIST. The simulations are performed by numerical integration of a set of ordinary differential equations. The integration can be done by either an explicit fourth-order Runge-Kutta algorithm or a semi-implicit third-order Runge-Kutta algorithm, both with adjustable step size. The second algorithm can be used if the set of differential equations is stiff. Vector-based drawing facilities are included in the program, with which results can be presented in graphs. Results of simulations, including graphics, can be stored in files. MIST is a very user-friendly, flexible and yet powerful program, with the mathematical details regarding models, simulations and calculations hidden from the user. This makes it suitable for scientists and students with limited computer experience.
LEAFY COTYLEDON1-CASEIN KINASE I-TCP15-PHYTOCHROME INTERACTING FACTOR4 Network Regulates Somatic Embryogenesis by Regulating Auxin Homeostasis1[OPEN]

A gene network regulates auxin homeostasis, thereby affecting cell proliferation and the transition from nonembryogenic callus to somatic embryos during somatic embryogenesis. Somatic embryogenesis (SE) is an efficient tool for the propagation of plant species and also, a useful model for studying the regulatory networks in embryo development. However, the regulatory networks underlying the transition from nonembryogenic callus to somatic embryos during SE remain poorly understood. Here, we describe an upland cotton (Gossypium hirsutum) CASEIN KINASE I gene, GhCKI, which is a unique key regulatory factor that strongly affects SE. Overexpressing GhCKI halted the formation of embryoids and plant regeneration because of a block in the transition from nonembryogenic callus to somatic embryos. In contrast, defective GhCKI in plants facilitated SE. To better understand the mechanism by which GhCKI regulates SE, the regulatory network was analyzed. A direct upstream negative regulator protein, cotton LEAFY COTYLEDON1, was identified to be targeted to a cis-element, CTTTTC, in the promoter of GhCKI. Moreover, GhCKI interacted with and phosphorylated cotton CINCINNATA-like TEOSINTE BRANCHED1-CYCLOIDEA-PCF transcription factor15 by coordinately regulating the expression of cotton PHYTOCHROME INTERACTING FACTOR4, finally disrupting auxin homeostasis, which led to increased cell proliferation and aborted somatic embryo formation in GhCKI-overexpressing somatic cells. Our results show a complex process of SE that is negatively regulated by GhCKI through a complex regulatory network.
SEUSS Integrates Gibberellin Signaling with Transcriptional Inputs from the SHR-SCR-SCL3 Module to Regulate Middle Cortex Formation in the Arabidopsis Root1[OPEN]

The transcription factor SEU promotes middle cortex formation through a network of transcription factor interactions. A decade of studies on middle cortex (MC) formation in the root endodermis of Arabidopsis (Arabidopsis thaliana) have revealed a complex regulatory network that is orchestrated by several GRAS family transcription factors, including SHORT-ROOT (SHR), SCARECROW (SCR), and SCARECROW-LIKE3 (SCL3). However, how their functions are regulated remains obscure. Here we show that mutations in the SEUSS (SEU) gene led to a higher frequency of MC formation. seu mutants had strongly reduced expression of SHR, SCR, and SCL3, suggesting that SEU positively regulates these genes. Our results further indicate that SEU physically associates with upstream regulatory sequences of SHR, SCR, and SCL3; and that SEU has distinct genetic interactions with these genes in the control of MC formation, with SCL3 being epistatic to SEU. Similar to SCL3, SEU was repressed by the phytohormone GA and induced by the GA biosynthesis inhibitor paclobutrazol, suggesting that SEU acts downstream of GA signaling to regulate MC formation. Consistently, we found that SEU mediates the regulation of SCL3 by GA signaling. Together, our study identifies SEU as a new critical player that integrates GA signaling with transcriptional inputs from the SHR-SCR-SCL3 module to regulate MC formation in the Arabidopsis root.
Membrane-Induced Folding of the Plant Stress Dehydrin Lti301[OPEN]

NMR studies show at atomic resolution that the K-segment of a stress-induced dehydrin protein adapts α-helical structure when it binds membranes. Dehydrins are disordered proteins that are expressed in plants as a response to embryogenesis and water-related stress. The molecular function and structural action of the dehydrins are yet elusive, but increasing evidence points to a role in protecting the structure and functional dynamics of cell membranes. An intriguing example is the cold-induced dehydrin Lti30 that binds to membranes by its conserved K segments. Moreover, this binding can be regulated by pH and phosphorylation and shifts the membrane phase transition to lower temperatures, consistent with the protein’s postulated function in cold stress. In this study, we reveal how the Lti30-membrane interplay works structurally at atomic level resolution in Arabidopsis (Arabidopsis thaliana). Nuclear magnetic resonance analysis suggests that negatively charged lipid head groups electrostatically capture the protein’s disordered K segments, which locally fold up into α-helical segments on the membrane surface. Thus, Lti30 conforms to the general theme of structure-function relationships by folding upon binding, in spite of its disordered, atypically hydrophilic and repetitive sequence signatures. Moreover, the fixed and well-defined structure of the membrane-bound K segments suggests that dehydrins have the molecular prerequisites for higher level binding specificity and regulation, raising new questions about the complexity of their biological function.
Computer-assisted instruction for patients with traumatic brain injury: Teaching of domain-specific knowledge

An apporach to rehabilitation that uses the microcomputer to teach traumatic brain injury (TBI) patients domain-specific knowledge and skills is outlined. With a training technique called the method of vanishing cues, patients are taught information and procedures that enable them to perfrom complex functions of daily life both at home and in the workplace. Advantages of computer-based instruction are summarized, and vocational tasks that provide the best possibilities for TBI patients are suggested. Issues of transfer and generalization and ways to circumvent them are also discussed.
Habitat-Associated Life History and Stress-Tolerance Variation in Arabidopsis arenosa1[OPEN]

Plants of the usually perennial autotetraploid Arabidopsis arenosa that colonized railways became vernalization insensitive, early and perpetually flowering, and constitutively heat and cold stress tolerant. Weediness in ephemeral plants is commonly characterized by rapid cycling, prolific all-in flowering, and loss of perenniality. Many species made transitions to weediness of this sort, which can be advantageous in high-disturbance or human-associated habitats. The molecular basis of this shift, however, remains mostly mysterious. Here, we use transcriptome sequencing, genome resequencing scans for selection, and stress tolerance assays to study a weedy population of the otherwise nonweedy Arabidopsis arenosa, an obligately outbreeding relative of Arabidopsis thaliana. Although weedy A. arenosa is widespread, a single genetic lineage colonized railways throughout central and northern Europe. We show that railway plants, in contrast to plants from sheltered outcrops in hill/mountain regions, are rapid cycling, have lost the vernalization requirement, show prolific flowering, and do not return to vegetative growth. Comparing transcriptomes of railway and mountain plants across time courses with and without vernalization, we found that railway plants have sharply abrogated vernalization responsiveness and high constitutive expression of heat- and cold-responsive genes. Railway plants also have strong constitutive heat shock and freezing tolerance compared with mountain plants, where tolerance must be induced. We found 20 genes with good evidence of selection in the railway population. One of these, LATE ELONGATED HYPOCOTYL, is known in A. thaliana to regulate many stress-response genes that we found to be differentially regulated among the distinct habitats. Our data suggest that, beyond life history regulation, other traits like basal stress tolerance also are associated with the evolution of weediness in A. arenosa.
Characterization of Function of the GlgA2 Glycogen/Starch Synthase in Cyanobacterium sp. Clg1 Highlights Convergent Evolution of Glycogen Metabolism into Starch Granule Aggregation1

The GlgA2/SSIII/SSIV enzyme is mandatory to obtain polysaccharide aggregation into amylopectin. At variance with the starch-accumulating plants and most of the glycogen-accumulating cyanobacteria, Cyanobacterium sp. CLg1 synthesizes both glycogen and starch. We now report the selection of a starchless mutant of this cyanobacterium that retains wild-type amounts of glycogen. Unlike other mutants of this type found in plants and cyanobacteria, this mutant proved to be selectively defective for one of the two types of glycogen/starch synthase: GlgA2. This enzyme is phylogenetically related to the previously reported SSIII/SSIV starch synthase that is thought to be involved in starch granule seeding in plants. This suggests that, in addition to the selective polysaccharide debranching demonstrated to be responsible for starch rather than glycogen synthesis, the nature and properties of the elongation enzyme define a novel determinant of starch versus glycogen accumulation. We show that the phylogenies of GlgA2 and of 16S ribosomal RNA display significant congruence. This suggests that this enzyme evolved together with cyanobacteria when they diversified over 2 billion years ago. However, cyanobacteria can be ruled out as direct progenitors of the SSIII/SSIV ancestral gene found in Archaeplastida. Hence, both cyanobacteria and plants recruited similar enzymes independently to perform analogous tasks, further emphasizing the importance of convergent evolution in the appearance of starch from a preexisting glycogen metabolism network.