Miracle-dz/UniFAR-FTUs huggingface dataset:
An Animal-Like Cryptochrome Controls the Chlamydomonas Sexual Cycle1

The animal-like cryptochrome, which accumulates and is located differentially during the Chlamydomonas life cycle, controls germination in a positive and gametogenesis in a negative manner. Cryptochromes are known as flavin-binding blue light receptors in bacteria, fungi, plants, and insects. The animal-like cryptochrome (aCRY) of the green alga Chlamydomonas reinhardtii has extended our view on cryptochromes, because it responds also to other wavelengths of the visible spectrum, including red light. Here, we have investigated if aCRY is involved in the regulation of the sexual life cycle of C. reinhardtii, which is controlled by blue and red light at the steps of gametogenesis along with its restoration and germination. We show that aCRY is differentially expressed not only during the life cycle but also within the cell as part of the soluble and/or membrane-associated protein fraction. Moreover, localization of aCRY within the algal cell body varies between vegetative cells and the different cell types of gametogenesis. aCRY is significantly (early day) or to a small extent (late night) enriched in the nucleus in vegetative cells. In pregametes, gametes and dark-inactivated gametes, aCRY is localized over the cell body. aCRY plays an important role in the sexual life cycle of C. reinhardtii: It controls the germination of the alga, under which the zygote undergoes meiosis, in a positive manner, similar to the regulation by the blue light receptors phototropin and plant cryptochrome (pCRY). However, aCRY acts in combination with pCRY as a negative regulator for mating ability as well as for mating maintenance, opposite to the function of phototropin in these processes.
Die Diagnose des Phäochromozytoms und Paraganglioms

Zusammenfassung Hintergrund: Stark erhöhte Plasma-Metanephrinkonzentrationen weisen auf ein Phäochromozytom/Paragangliom (P/PGL) hin. Im Gegensatz dazu besteht bei leicht erhöhten Werten erhebliche diagnostische Unsicherheit. In der vorliegenden Arbeit wurde untersucht, ob der Clonidin-Suppressionstest (CST) in diesen Fällen zum Tumornachweis oder -ausschluss beitragen kann. Patienten und Methoden: 24 Patienten mit grenzwertiger Erhöhung der freien Metanephrine und/oder Katecholamine im Plasma wurden in die Studie aufgenommen. Blutproben wurden unmittelbar vor und 3 Stunden nach oraler Gabe von Clonidin entnommen und die Plasmakonzentrationen der freien Metanephrine und Katecholamine bestimmt. Ein negatives Testergebnis wurde definiert als Abfall der Normetanephrin- bzw. Noradrenalinkonzentration unter die oberen Grenzwerte der Referenzintervalle oder um mehr als 40 % bzw. 50 % des Ausgangswerts. Ergebnisse: Bei 9 Patienten wurde ein P/PGL nachgewiesen, bei 15 durch unabhängige Untersuchungen ausgeschlossen. Bei über der Hälfte der Patienten ohne P/PGL wurde unmittelbar vor Clonidingabe gegenüber dem Studieneinschluss eine normale Normetanephrinkonzentration gemessen. 3 Stunden nach Clonidingabe waren bei allen Patienten ohne P/PGL die Normetanephrin- und Noradrenalinkonzentration um den definierten Betrag gefallen oder lagen innerhalb des Referenzintervalls, entsprechend einer diagnostischen Spezifität des CST von 100 % (KI 78–100 %). Bei P/PGL war die diagnostische Sensitivität des Tests mit Normetanephrin 100 % (KI 66–100 %), mit Noradrenalin nur 22 % (KI 2,8–60 %). Folgerung: Die Ergebnisse sind vereinbar mit einer hohen diagnostischen Aussagefähigkeit des CST in Verbindung mit der Bestimmung des freien Normetanephrins bei grenzwertig erhöhter Normetanephrinplasmakonzentration und vermutetem P/PGL. Durch standardisierte Blutentnahmen im Liegen kann der CST häufig vermieden werden.
The Conserved and Unique Genetic Architecture of Kernel Size and Weight in Maize and Rice1[OPEN]

Ten segregating populations yield both conserved and species-specific genetic architecture of kernel size and weight in maize and rice. Maize (Zea mays) is a major staple crop. Maize kernel size and weight are important contributors to its yield. Here, we measured kernel length, kernel width, kernel thickness, hundred kernel weight, and kernel test weight in 10 recombinant inbred line populations and dissected their genetic architecture using three statistical models. In total, 729 quantitative trait loci (QTLs) were identified, many of which were identified in all three models, including 22 major QTLs that each can explain more than 10% of phenotypic variation. To provide candidate genes for these QTLs, we identified 30 maize genes that are orthologs of 18 rice (Oryza sativa) genes reported to affect rice seed size or weight. Interestingly, 24 of these 30 genes are located in the identified QTLs or within 1 Mb of the significant single-nucleotide polymorphisms. We further confirmed the effects of five genes on maize kernel size/weight in an independent association mapping panel with 540 lines by candidate gene association analysis. Lastly, the function of ZmINCW1, a homolog of rice GRAIN INCOMPLETE FILLING1 that affects seed size and weight, was characterized in detail. ZmINCW1 is close to QTL peaks for kernel size/weight (less than 1 Mb) and contains significant single-nucleotide polymorphisms affecting kernel size/weight in the association panel. Overexpression of this gene can rescue the reduced weight of the Arabidopsis (Arabidopsis thaliana) homozygous mutant line in the AtcwINV2 gene (Arabidopsis ortholog of ZmINCW1). These results indicate that the molecular mechanisms affecting seed development are conserved in maize, rice, and possibly Arabidopsis.
Heat Shock Factor HsfA1a Is Essential for R Gene-Mediated Nematode Resistance and Triggers H2O2 Production1

HsfA1a is essential for Mi-1.2-mediated resistance to Meloidogyne incognita and regulates Wfi1 transcription and H2O2 production. Plants generate reactive oxygen species (ROS) in the apoplast in response to pathogen attack, especially following resistance (R) gene-mediated pathogen recognition; however, the mechanisms activating ROS generation remain unknown. Here, we demonstrate that RKN (Meloidogyne incognita) infection rapidly induces ROS accumulation in the roots of tomato (Solanum lycopersicum) plants that contain the R gene Mi-1.2 but rarely induces ROS accumulation in the susceptible or Mi-1.2-silenced resistant genotypes. RNK also induces the hypersensitive response, a form of programmed cell death, in Mi-1.2 plants. RKN induces the expression of numerous class-A heat shock factor (HsfA) genes in resistant tomato plants. Silencing HsfA1a compromises Mi-1.2-mediated resistance, apoplastic H2O2 accumulation, and the transcription of whitefly induced 1 (Wfi1), which encodes a respiratory burst oxidase homolog. HsfA1a regulates Wfi1 transcription by binding to the Wfi1 promoter, and silencing of Wfi1 compromises Mi-1.2-mediated resistance. HsfA1a and Wfi1 are involved in Mi-1.2-triggered Hsp90 accumulation and basal defense in susceptible tomato. Thus, HsfA–1aWfi1-dependent ROS signaling functions as a crucial regulator of plant defense responses.
Hotelling’s T 2 multivariate proﬁling for detecting differential expression in microarrays

Summary: The most widely used statistical methods for ﬁnding differentially expressed genes (DEGs) are essentially univariate. In this study, we present a new T 2 statistic for analyzing microarray data. We implemented our method using a multiple forward search (MFS) algorithm that is designed for selecting a subset of feature vectors in high-dimensional microarray datasets. The proposed T 2 statistic is a corollary to that originally developed for multivariate analyses and possesses two prominent statistical properties. First, our method takes into account multidimensional structure of microarray data. The utilization of the information hidden in gene interactions allows for ﬁnding genes whose differential expressions are not marginally detectable in univariate testing methods. Second, the statistic has a close relationship to discriminant analyses for classiﬁcation of gene expression patterns. Our search algorithm sequentially maximizes gene expression difference/distance between two groups of genes. Including such a set of DEGs into initial feature variables may increase the power of classiﬁcation rules. We validated our method by using a spike-in HGU95 dataset from Affymetrix. The utility of the new method was demonstrated by application to the analyses of gene expression patterns in human liver cancers and breast cancers. Extensive bioinformatics analyses and cross-validation of DEGs iden-tiﬁed in the application datasets showed the signiﬁcant advantages of our new algorithm. Availability: The program for the method proposed in this article and supplementary material are available at http:
The PILNCR1-miR399 Regulatory Module Is Important for Low Phosphate Tolerance in Maize1

The interaction between the long non-coding RNA PILNCR1 and the microRNA miR399 is important for low Pi tolerance in maize (Zea mays). The regulation of adaptive responses to phosphorus (P) deficiency by the microRNA399 (miR399)/PHOSPHATE2 (PHO2) pathway has been well studied in Arabidopsis (Arabidopsis thaliana) but not in maize (Zea mays). Here, we show that miR399 transcripts are strongly induced in maize by phosphate (Pi) deficiency. Transgenic maize plants that overexpressed MIR399b accumulated excessive amounts of P in their shoots and displayed typical Pi-toxicity phenotypes. We reannotated ZmPHO2 with an additional 1,165 bp of the 5′ untranslated region. miR399-guided posttranscriptional repression of ZmPHO2 was mainly observed in the P-efficient lines. We identified Pi-deficiency-induced long-noncoding RNA1 (PILNCR1) from our strand-specific RNA libraries. Transient expression assays in Nicotiana benthamiana and maize leaf protoplasts demonstrated that PILNCR1 inhibits ZmmiR399-guided cleavage of ZmPHO2. The abundance of PILNCR1 was significantly higher in P-inefficient lines than in P-efficient lines, which is consistent with the abundance of ZmmiR399 transcripts. These results indicate that the interaction between PILNCR1 and miR399 is important for tolerance to low Pi in maize.
A reference database for circular dichroism spectroscopy covering fold and secondary structure space

MOTIVATION Circular Dichroism (CD) spectroscopy is a long-established technique for studying protein secondary structures in solution. Empirical analyses of CD data rely on the availability of reference datasets comprised of far-UV CD spectra of proteins whose crystal structures have been determined. This article reports on the creation of a new reference dataset which effectively covers both secondary structure and fold space, and uses the higher information content available in synchrotron radiation circular dichroism (SRCD) spectra to more accurately predict secondary structure than has been possible with existing reference datasets. It also examines the effects of wavelength range, structural redundancy and different means of categorizing secondary structures on the accuracy of the analyses. In addition, it describes a novel use of hierarchical cluster analyses to identify protein relatedness based on spectral properties alone. The databases are shown to be applicable in both conventional CD and SRCD spectroscopic analyses of proteins. Hence, by combining new bioinformatics and biophysical methods, a database has been produced that should have wide applicability as a tool for structural molecular biology.
Parallel multifactor dimensionality reduction: a tool for the large-scale analysis of gene-gene interactions

UNLABELLED Parallel multifactor dimensionality reduction is a tool for large-scale analysis of gene-gene and gene-environment interactions. The MDR algorithm was redesigned to allow an unlimited number of study subjects, total variables and variable states, and to remove restrictions on the order of interactions being analyzed. In addition, the algorithm is markedly more efficient, with approximately 150-fold decrease in runtime for equivalent analyses. To facilitate the processing of large datasets, the algorithm was made parallel. AVAILABILITY Parallel MDR is freely available for non-commercial research institutions. For full details see http://chgr.mc. vanderbilt.edu/ritchielab/pMDR. An open-source version of MDR software is available at http://www.epistasis. org.
SCAssign: a sparky extension for the NMR resonance assignment of aliphatic side-chains of uniformly 13C, 15N-labeled large proteins

UNLABELLED SCAssign (side-chain assignment) is a Sparky extension written in Python to assist the NMR resonance assignment of aliphatic side-chains of uniformly (13)C,(15)N-labeled large proteins. It is based on a general strategy recently developed in our laboratory that makes use of 4D (13)C,(15)N-edited NOESY, 3D MQ-(H)CC(m)H(m)-TOCSY, and prior backbone assignments. The program runs on all operating systems for which Sparky is available, and is easy to install, setup and use. Not only can it accelerate the assignment process, it also allows assignments of weak NOEs in 4D NOESY, which used to be very difficult with manual approach. AVAILABILITY The program, in the form of source code, is provided as free download at http://yangdw.science. nus.edu. sg/SCAssign. The website also contains installation guide, user manual and demonstrations recorded in Flash.
Impact of Preoperative and Intraoperative Factors in Cataract Surgery

Abstract Background: Cataract surgery is the most common procedure in ophthalmology. However the surgical outcome depends on various factors. The impact of preoperative and intraoperative factors on the surgical procedure were investigated. Patients and Methods: Prospective consecutive study of eyes that underwent cataract surgery. The studied parameters included: age, body mass index (BMI), medical history, type of anaesthesia, preoperative patientʼs anxiety level (scale from 0 to 10), spherical equivalent (SE), keratometry, axial length (AL), time and percentage of ultrasounds (US), intraoperative complications, duration of surgery. The eyes were separated into two groups: the “no complication group” and the “complication group”. Results: 529 eyes were included. Age averaged 75.5 years old (44; 100), mean BMI (kg/m2) was 26.3 (13.7; 45.2), patients had cardiovascular history in 61.05 % of cases, the type of anaesthesia used was topical in 93.4 %, subtenon in 4.7 % and general in 1.9 % of cases. Mean preoperative anxiety was 4.04 (0; 10), mean preoperative SE was − 0.12 (− 10; 7.5), mean keratometry (diopters) was 43.88 (39.5; 49), mean AL (mm) was 23.29 (20.91; 29.78), mean time of US (minutes) was 1.89 (0.08; 9.2), mean percentage of US was 10.5 (2; 30) and mean surgical duration (minutes) was 17.15 (5; 50). There was a statistically significant difference (p < 0.0001 in all cases) between both groups in the preoperative anxiety, the time of US and the duration of surgery. The “complication group” had higher scores in all cases as well as more proportion of patients with cardiovascular history. There was no statistically significant difference between both groups for the BMI, SE, AL, keratometry and percentage of US. Conclusions: The preoperative anxiety level and a cardiovascular medical history together with a prolonged time of US and a longer surgical duration seem to provide more complications during the surgery. The BMI, SE, AL and keratometry did not influence the surgical procedure.
Decomposition of complex microbial behaviors into resource-based stress responses

MOTIVATION Highly redundant metabolic networks and experimental data from cultures likely adapting simultaneously to multiple stresses can complicate the analysis of cellular behaviors. It is proposed that the explicit consideration of these factors is critical to understanding the competitive basis of microbial strategies. RESULTS Wide ranging, seemingly unrelated Escherichia coli physiological fluxes can be simply and accurately described as linear combinations of a few ecologically relevant stress adaptations. These strategies were identified by decomposing the central metabolism of E.coli into elementary modes (mathematically defined biochemical pathways) and assessing the resource investment cost-benefit properties for each pathway. The approach capitalizes on the inherent tradeoffs related to investing finite resources like nitrogen into different pathway enzymes when the pathways have varying metabolic efficiencies. The subset of ecologically competitive pathways represented 0.02% of the total permissible pathways. The biological relevance of the assembled strategies was tested against 10 000 randomly constructed pathway subsets. None of the randomly assembled collections were able to describe all of the considered experimental data as accurately as the cost-based subset. The results suggest these metabolic strategies are biologically significant. The current descriptions were compared with linear programming (LP)-based flux descriptions using the Euclidean distance metric. The current study's pathway subset described the experimental fluxes with better accuracy than the LP results without having to test multiple objective functions or constraints and while providing additional ecological insight into microbial behavior. The assembled pathways seem to represent a generalized set of strategies that can describe a wide range of microbial responses and hint at evolutionary processes where a handful of successful metabolic strategies are utilized simultaneously in different combinations to adapt to diverse conditions.
A web application to perform linkage disequilibrium and linkage analyses on a computational grid

MOTIVATION Unravelling the genetic architecture of complex traits requires large amounts of data, sophisticated models and large computational resources. The lack of user-friendly software incorporating all these requisites is delaying progress in the analysis of complex traits. METHODS Linkage disequilibrium and linkage analysis (LDLA) is a high-resolution gene mapping approach based on sophisticated mixed linear models, applicable to any population structure. LDLA can use population history information in addition to pedigree and molecular markers to decompose traits into genetic components. Analyses are distributed in parallel over a large public grid of computers in the UK. RESULTS We have proven the performance of LDLA with analyses of simulated data. There are real gains in statistical power to detect quantitative trait loci when using historical information compared with traditional linkage analysis. Moreover, the use of a grid of computers significantly increases computational speed, hence allowing analyses that would have been prohibitive on a single computer. AVAILABILITY The authors have implemented LDLA within the freely available GridQTL software (www.gridqtl.org.uk).
Unveiling Ontogenesis of Herbal Medicine in Plant Chemical Profiles by Infrared Macro-Fingerprinting

Abstract Given that harvesting time has a great impact on the quality of herbal medicine, knowing the ontogenesis in the chemical profile aspect is essential to determine the optimal harvesting season. A high-throughput and versatile approach (herbal infrared macro-fingerprinting) harmonizing with the character of herbal medicine and providing the whole chemical profile (entirety), group analogues (part), and single compounds (major components) is developed to rapidly disclose the variation rule of the full chemical profile of herbal medicine over a growing season without extraction pretreatments, and thus to determine the optimal harvesting period in respect to groups of chemical compounds using Scutellaria baicalensis as a demonstration. IR macro-fingerprints of Scutellaria baicalensis harvested in the same period have a high similarity (> 0.91) despite small variations, suggesting that IR macro-fingerprinting can faithfully reflect the spectacle of “disordered order” in nature. From Year-1 spring to Year-3 autumn, general contents (%, w/w) of total flavonoids fluctuate up and down with a maximum value in Year-2 spring, and that of saccharides is relatively stable except for the attenuation from Year-2 autumn to Year-3 spring. From Year-1 autumn to Year-2 spring, flavonoid aglycones initially produced in Scutellaria baicalensis are extensively transformed to responding flavonoid glycosides. From Year-2 spring to Year-3 autumn, flavonoid glycosides are converted back to their corresponding aglycones. The best seasons for collecting Scutellaria baicalensis with a high content of flavonoid glycosides and aglycones would be Year-2 spring and Year-3 spring, respectively.
The Arabidopsis GTL1 Transcription Factor Regulates Water Use Efficiency and Drought Tolerance by Modulating Stomatal Density via Transrepression of SDD1[W][OA]

This work provides evidence that Arabidopsis GTL1 functions as a focal regulator of water use efficiency and water stress tolerance. The results establish a potential paradigm for how the environment influences stomatal development to reduce transpiration under low water availability conditions. A goal of modern agriculture is to improve plant drought tolerance and production per amount of water used, referred to as water use efficiency (WUE). Although stomatal density has been linked to WUE, the causal molecular mechanisms have yet to be determined. Arabidopsis thaliana GT-2 LIKE 1 (GTL1) loss-of-function mutations result in increased water deficit tolerance and higher integrated WUE by reducing daytime transpiration without a demonstrable reduction in biomass accumulation. gtl1 plants had higher instantaneous WUE that was attributable to ~25% lower transpiration and stomatal conductance but equivalent CO2 assimilation. Lower transpiration was associated with higher STOMATAL DENSITY AND DISTRIBUTION1 (SDD1) expression and an ~25% reduction in abaxial stomatal density. GTL1 expression occurred in abaxial epidermal cells where the protein was localized to the nucleus, and its expression was downregulated by water stress. Chromatin immunoprecipitation analysis indicated that GTL1 interacts with a region of the SDD1 promoter that contains a GT3 box. An electrophoretic mobility shift assay was used to determine that the GT3 box is necessary for the interaction between GTL1 and the SDD1 promoter. These results establish that GTL1 negatively regulates WUE by modulating stomatal density via transrepression of SDD1.
Two-Phase Resolution of Polyploidy in the Arabidopsis Metabolic Network Gives Rise to Relative and Absolute Dosage Constraints[W]

Exploring successive Arabidopsis genome duplications, this work shows that the types of surviving duplicated enzymes differ between events, suggesting roles for both relative and absolute dosage constraints. The abundance of detected ancient polyploids in extant genomes raises questions regarding evolution after whole-genome duplication (WGD). For instance, what rules govern the preservation or loss of the duplicated genes created by WGD? We explore this question by contrasting two possible preservation forces: selection on relative and absolute gene dosages. Constraints on the relative dosages of central network genes represent an important force for maintaining duplicates (the dosage balance hypothesis). However, preservation may also result from selection on the absolute abundance of certain gene products. The metabolic network of the model plant Arabidopsis thaliana is a powerful system for comparing these hypotheses. We analyzed the surviving WGD-produced duplicate genes in this network, finding evidence that the surviving duplicates from the most recent WGD (WGD-α) are clustered in the network, as predicted by the dosage balance hypothesis. A flux balance analysis suggests an association between the survival of duplicates from a more ancient WGD (WGD-β) and reactions with high metabolic flux. We argue for an interplay of relative and absolute dosage constraints, such that the relative constraints imposed by the recent WGD are still being resolved by evolution, while they have been essentially fully resolved for the ancient event.