Miracle-dz/UniFAR-FTUs huggingface dataset:
Consequences of frugivore‐mediated seed dispersal for the spatial and genetic structures of a neotropical palm

The idiosyncratic behaviours of seed dispersers are important contributors to plant spatial associations and genetic structures. In this study, we used a combination of field, molecular and spatial studies to examine the connections between seed dispersal and the spatial and genetic structures of a dominant neotropical palm Attalea phalerata. Field observation and genetic parentage analysis both indicated that the majority of A. phalerata seeds were dispersed locally over short distances (<30 m from the maternal tree). Spatial and genetic structures between adults and seedlings were consistent with localized and short‐distance seed dispersal. Dispersal contributed to spatial associations among maternal sibling seedlings and strong spatial and genetic structures in both seedlings dispersed near (<10 m) and away (>10 m) from maternal palms. Seedlings were also spatially aggregated with juveniles. These patterns are probably associated with the dispersal of seeds by rodents and the survival of recruits at specific microsites or neighbourhoods over successive fruiting periods. Our cross‐cohort analyses found palms in older cohorts and cohort pairs were associated with a lower proportion of offspring and sibling neighbours and exhibited weaker spatial and genetic structures. Such patterns are consistent with increased distance‐ and density‐dependent mortality over time among palms dispersed near maternal palms or siblings. The integrative approaches used for this study allowed us to infer the importance of seed dispersal activities in maintaining the aggregated distribution and significant genetic structures among A. phalerata palms. We further conclude that distance‐ and density‐dependent mortality is a key postdispersal process regulating this palm population.
A novel method of protein extraction from perennial Bupleurum root for 2‐DE

The perennial Bupleurum root is thick and woody and contains high levels of interfering compounds. Common protein extraction methods have proved refractory towards the isolation of proteins suitable for 2‐DE, due to the presence of interfering compounds. A novel method for extracting proteins suitable for 2‐DE was established to overcome these problems. The main characteristic of this protocol is the partitioning of the proteins into the aqueous (fraction A‐2), chloroform and isoamyl alcohol phases (A‐3), and the interphase (A‐1). The proteins are then extracted from each of these phases. From A‐1, 85% (extracted protein against total proteins) proteins could be extracted and purified. For fraction A‐2, a novel phenol extraction step is employed for the extraction of proteins. Based on the well‐resolved 2‐DE patterns, our protein preparation is free of interfering compounds. Using these methods (A‐1, A‐2, and A‐3‐3), a total of 3662 (1526 + 1128 + 1008) spots could be separated, and a protein yield of about 1.41 mg per 1.0 g fresh root material was obtained. To our knowledge, this is the first time that a protocol for protein extraction from perennial Bupleurum root has been reported that gives reproducible results. The protocol is expected to be applicable to other recalcitrant plant tissues as well.
Single Session of Dual-tDCS Transiently Improves Precision Grip and Dexterity of the Paretic Hand After Stroke

Background. After stroke, deregulated interhemispheric interactions influence residual paretic hand function. Anodal or cathodal transcranial direct current stimulation (tDCS) can rebalance these abnormal interhemispheric interactions and improve motor function. Objective. We explored whether dual-hemisphere tDCS (dual-tDCS) in participants with chronic stroke can improve fine hand motor function in 2 important aspects: precision grip and dexterity. Methods. In all, 19 chronic hemiparetic individuals with mild to moderate impairment participated in a double-blind, randomized trial. During 2 separate cross-over sessions (real/sham), they performed 10 precision grip movements with a manipulandum and the Purdue Pegboard Test (PPT) before, during, immediately after, and 20 minutes after dual-tDCS applied simultaneously over the ipsilesional (anodal) and contralateral (cathodal) primary motor cortices. Results. The precision grip performed with the paretic hand improved significantly 20 minutes after dual-tDCS, with reduction of the grip force/load force ratio by 7% and in the preloading phase duration by 18% when compared with sham. The dexterity of the paretic hand started improving during dual-tDCS and culminated 20 minutes after the end of dual-tDCS (PPT score +38% vs +5% after sham). The maximal improvements in precision grip and dexterity were observed 20 minutes after dual-tDCS. These improvements correlated negatively with residual hand function quantified with ABILHAND. Conclusions. One bout of dual-tDCS improved the motor control of precision grip and digital dexterity beyond the time of stimulation. These results suggest that dual-tDCS should be tested in longer protocols for neurorehabilitation and with moderate to severely impaired patients. The precise timing of stimulation after stroke onset and associated training should be defined.
Ethanol production by the hyperthermophilic archaeon Pyrococcus furiosus by expression of bacterial bifunctional alcohol dehydrogenases

Ethanol is an important target for the renewable production of liquid transportation fuels. It can be produced biologically from pyruvate, via pyruvate decarboxylase, or from acetyl‐CoA, by alcohol dehydrogenase E (AdhE). Thermophilic bacteria utilize AdhE, which is a bifunctional enzyme that contains both acetaldehyde dehydrogenase and alcohol dehydrogenase activities. Many of these organisms also contain a separate alcohol dehydrogenase (AdhA) that generates ethanol from acetaldehyde, although the role of AdhA in ethanol production is typically not clear. As acetyl‐CoA is a key central metabolite that can be generated from a wide range of substrates, AdhE can serve as a single gene fuel module to produce ethanol through primary metabolic pathways. The focus here is on the hyperthermophilic archaeon Pyrococcus furiosus, which grows by fermenting sugar to acetate, CO2 and H2. Previously, by the heterologous expression of adhA from a thermophilic bacterium, P. furiosus was shown to produce ethanol by a novel mechanism from acetate, mediated by AdhA and the native enzyme aldehyde oxidoreductase (AOR). In this study, the AOR gene was deleted from P. furiosus to evaluate ethanol production directly from acetyl‐CoA by heterologous expression of the adhE gene from eight thermophilic bacteria. Only AdhEs from two Thermoanaerobacter strains showed significant activity in cell‐free extracts of recombinant P. furiosus and supported ethanol production in vivo. In the AOR deletion background, the highest amount of ethanol (estimated 61% theoretical yield) was produced when adhE and adhA from Thermoanaerobacter were co‐expressed.
Direct Exponential Amplification and Sequencing (DEXAS) of Genomic DNA

In order to supply a sufficient amount of template molecules for DNA sequence determination, cloning into plasmids and subsequent plasmid purification, or amplification via the PCR, are generally used. Here, we present a method-'direct exponential amplification and sequencing' or 'DEXAS'-that permits direct sequence determination from whole genomic DNA and thus eliminates the need for template amplification and preparation. It relies on the simultaneous amplification of a target sequence and the determination of its sequence using dideoxyterminators in a two-step cycling reaction. DEXAS can be applied to single as well as multi-copy genomic sequences, and can easily be automated.
A trithorax-group complex purified from Saccharomyces cerevisiae is required for methylation of histone H3

Histone methylation has emerged as an important mechanism for regulating the transcriptional accessibility of chromatin. Several methyltransferases have been shown to target histone amino-terminal tails and mark nucleosomes associated with either euchromatic or heterochromatic states. However, the biochemical machinery responsible for regulating histone methylation and integrating it with other cellular events has not been well characterized. We report here the purification, molecular identification, and genetic and biochemical characterization of the Set1 protein complex that is necessary for methylation of histone H3 at lysine residue 4 in Saccharomyces cerevisiae. The seven-member 363-kDa complex contains homologs of Drosophila melanogaster proteins Ash2 and Trithorax and Caenorhabditis elegans protein DPY-30, which are implicated in the maintenance of Hox gene expression and regulation of X chromosome dosage compensation, respectively. Mutations of Set1 protein comparable to those that disrupt developmental function of its Drosophila homolog Trithorax abrogate histone methylation in yeast. These studies suggest that epigenetic regulation of developmental and sex-specific gene expression are species-specific readouts for a common chromatin remodeling machinery associated mechanistically with histone methylation.
Enantioseparation of aromatic amino acids using CEC monolith with novel chiral selector, N‐methacryloyl‐l‐histidine methyl ester

A new type of polymethacrylate‐based monolithic column with chiral stationary phase was prepared for the enantioseparation of aromatic amino acids, namely d,l‐phenylalanine, d,l‐tyrosine, and d,l‐tryptophan by CEC. The monolithic column was prepared by in situ polymerization of butyl methacrylate (BMA), N‐methacryloyl‐l‐histidine methyl ester (MAH), and ethylene dimethacrylate (EDMA) in the presence of porogens. The porogen mixture included DMF and phosphate buffer. MAH was used as a chiral selector. FTIR spectrum of the polymethacrylate‐based monolith showed that MAH was incorporated into the polymeric structure via in situ polymerization. Some experimental parameters including pH, concentration of the mobile phase, and MAH concentration with regard to the chiral CEC separation were investigated. Single enantiomers and enantiomer mixtures of the amino acids were separately injected into the monolithic column. It was observed that l‐enantiomers of aromatic amino acids migrated before d‐enantiomers. The reversal enantiomer migration order for tryptophan was observed upon changing of pH. Using the chiral monolithic column (100 μm id and 375 μm od), the best chiral separation was performed in 35:65% ACN/phosphate buffer (pH 8.0, 10 mM) with an applied voltage of 12 kV in CEC. SEM images showed that the chiral monolithic column has a continuous polymeric skeleton and large through‐pore structure.
A practical algorithm for connectivity extraction for very large VLSI layouts

Moore's law is alive and well. With designs entering the billion transistor era, there is an ever increasing demand on CAD tools to handle larger data sizes efficiently. One problem with processing large VLSI layouts is that the data to be processed is far too massive to fit into main memory. When dealing with data sets of sizes exceeding main memory, communication between the fast internal memory and the slow external memory is often the performance bottleneck and algorithms and data structures designed under the assumption of a single level of memory may not be meaningful. External memory algorithms try to optimize performance by taking into account disk accesses. One can certainly use the standard main memory algorithms for data that reside on disk but their performance is often considerably below the optimum because there is no control over how the operating system performs disk accesses. On demand thrashing can be high thus resulting in an increase in response time.
RESEARCH IN CONTEXT: PART OF A SPECIAL ISSUE ON POLLINATOR-DRIVEN SPECIATION Do specialized flowers promote reproductive isolation? Realized pollination accuracy of three sympatric Pedicularis species

W. Scott Armbruster1,2,3,*, Xiao-Qing Shi4 and Shuang-Quan Huang4 School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK, Department of Biology, NTNU, NO-7491 Trondheim, Norway, Institute of Arctic Biology, University of Alaska, Fairbanks, AK 99775, USA and State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China * For correspondence. E-mail scott.armbruster@port.ac. uk
Role of α-Helical Coiled-coil Interactions in Receptor Dimerization, Signaling, and Adaptation during Bacterial Chemotaxis*

The aspartate receptor, Tar, is a member of a large family of signal transducing membrane receptors that interact with CheA and CheW proteins to mediate the chemotactic responses of bacteria. A highly conserved cytoplasmic region, the signaling domain, is flanked by two sequences, methylated helices 1 and 2 (MH1 and MH2), that are predicted to form α-helical coiled-coils. MH1 and MH2 contain glutamine and glutamate residues that are subject to deamidation, methylation, and demethylation. We show that the signaling domain is an independently folding unit that binds CheW. When expressed in vivo the signaling domain inhibits CheA kinase activity, but if MH1 or an unrelated leucine zipper coiled-coil sequence is attached to the signaling domain, CheA is activated. A construct that contains a leucine zipper fused to MH1-signaling domain-MH2 also activates the kinase, both in vivo and in vitro, and this activation is regulated by the level of glutamate modification. These findings support a model for receptor signaling where aspartate binding controls the relative orientation of receptor monomers to favor the formation of coiled-coils between MH1 and/or MH2 between subunits. Glutamate modification may stabilize these coiled-coils by reducing electrostatic repulsion between helices.
Does the transition into daylight saving time really cause partial sleep deprivation?

Abstract Aim: To identify possible changes in the sleep patterns according to chronotype in undergraduate students during the daylight saving time (DST) transition. Methods: A total of 378 students answered the Morningness-Eveningness Questionnaire (MEQ) to determine their chronotype and kept a diary about sleep–wake schedules 1 week before and after the DST transition. Oral mucosal cell samples were collected for genetic analysis. Results: After the DST transition, intermediate types (I-types) delayed bedtime and increased their time in bed and all groups delayed their wake-up time. All groups presented a shorter phase angle between sunset and the bedtime after the DST transition. On the other hand, only E-types showed a tendency to reduce the phase angle between sunrise and wake-up time, while I-types and M-types kept the same phase angles between sunrise and wake-up time after the DST transition. The polymorphisms in the human genes CLOCK and PER3 were not associated with individual differences in sleep patterns, nor were they associated with an adjustment to the DST transition. Conclusion: Under the new set of social times determined by DST, the adjustment was only partial. I-types delayed bedtime and all groups delayed their wake-up times after the beginning of DST. Consequently, the time in bed after the DST transition was not reduced; Morning (M-types) and Evening-types (E-types) kept the same time in bed and I-types showed an increase on it.
Regulated expression of 5'-deleted mouse GLUT4 minigenes in transgenic mice: effects of exercise training and high-fat diet.

Fourteen kb murine GLUT4 minigene (= -7395 GLUT4) contains DNA sequence that confers tissue specific, exercise-induced up-regulation of the GLUT4 gene in skeletal muscle and high-fat diet induced-down-regulation in white adipose tissue. To identify the DNA sequences required for regulated expression, we generated GLUT4 minigene transgenic mice harboring 3237, 2000, 1000, and 442 bp of 5'-flanking region, all exons and introns, and 1 kb of 3'-flanking sequence of the mouse GLUT4 gene. The -3237-, -2000-, and -1000-GLUT4 constructs were expressed in a tissue-specific manner identical to the endogenous GLUT4. Exercise-induced up-regulation and high-fat diet-induced down-regulation of these constructs also paralleled those of the endogenous GLUT4 gene. In contrast, the -442 GLUT4 construct was expressed substantially in skeletal muscle (gastrocnemius and quadriceps) and heart, but was only expressed very weakly in white adipose tissue and was not expressed in brown adipose tissue. Furthermore, this -442 GLUT4 construct failed to respond to exercise or a high-fat diet in either muscle or adipose tissue. These results indicate that brown and white adipocyte-specific enhancer(s) and exercise- and high-fat diet-responsive elements are located between bases -1000 and -442 of the murine GLUT4 5'-flanking region.
Polygalae Radix Extract Prevents Axonal Degeneration and Memory Deficits in a Transgenic Mouse Model of Alzheimer’s Disease

Memory impairments in Alzheimer’s disease (AD) occur due to degenerated axons and disrupted neural networks. Since only limited recovery is possible after the destruction of neural networks, preventing axonal degeneration during the early stages of disease progression is necessary to prevent AD. Polygalae Radix (roots of Polygala tenuifolia; PR) is a traditional herbal medicine used for sedation and amnesia. In this study, we aimed to clarify and analyze the preventive effects of PR against memory deficits in a transgenic AD mouse model, 5XFAD. 5XFAD mice demonstrated memory deficits at the age of 5 months. Thus, the water extract of Polygalae Radix (PR extract) was orally administered to 4-month-old 5XFAD mice that did not show signs of memory impairment. After consecutive administrations for 56 days, the PR extract prevented cognitive deficit and axon degeneration associated with the accumulation of amyloid β (Aβ) plaques in the perirhinal cortex of the 5XFAD mice. PR extract did not influence the formation of Aβ plaques in the brain of the 5XFAD mice. In cultured neurons, the PR extract prevented axonal growth cone collapse and axonal atrophy induced by Aβ. Additionally, it prevented Aβ-induced endocytosis at the growth cone of cultured neurons. Our previous study reported that endocytosis inhibition was enough to prevent Aβ-induced growth cone collapse, axonal degeneration, and memory impairments. Therefore, the PR extract possibly prevented axonal degeneration and memory impairment by inhibiting endocytosis. PR is the first preventive drug candidate for AD that inhibits endocytosis in neurons.
No Association between Serum 25-Hydroxyvitamin D3 Level and Performance on Psychometric Tests in NHANES III

Background: Animal studies and in vitro experiments indicate that vitamin D is involved in a diverse range of neurobiological functions. We had the opportunity to examine the relationship between serum 25-hydroxyvitamin D3 [25(OH)D] levels and performance on various cognitive tasks, based on a large, representative community sample. Methods: Three age groups were available from the population-based NHANES III survey: adolescent group (n = 1,676, age range 12–17 years), adult group (n = 4,747, 20–60 years), elderly group (n = 4,809, 60–90 years). The associations between eight psychometric measures and serum 25(OH)D were assessed. Results: In the adolescent and adult groups, none of the psychometric measures were associated with 25(OH)D levels. In the elderly group there was a significant difference between 25(OH)D quintiles performance on a learning and memory task; however, those with the highest quintile of 25(OH)D were most impaired on the task, contrary to the hypotheses. Conclusion: Lower 25(OH)D levels were not associated with impaired performance on various psychometric measures. While it remains to be seen if chronic exposure to low 25(OH)D levels alters brain function in the long term, this cross-sectional study suggests that 25(OH)D levels do not influence neurocognitive performance.
Molecular characterization of circulating pandemic strains of influenza A virus during 2012 to 2013 in Lucknow (India)

The pandemic H1N1 strain of Influenza A virus [A(H1N1)pdm09] is now well adapted in human populations. However, it is still causing sporadic outbreaks worldwide with different severity. The present study was planned to understand the genetic diversity (based on the HA1 gene) of influenza A(H1N1)pdm09 strains circulating during the post pandemic period. The HA1 gene was selected because the HA1 protein is immunogenic, functions as a receptor binding site and indirectly affects transmission and pathogenicity of virus. A total of 2,818 cases were enrolled. Nasal/throat swabs from all cases were tested by one‐step real time PCR for detection of influenza virus types and subtypes according to the CDC protocol. Of these, 134 cases were A(H1N1)pdm09 positive, 34 of which were screened for HA1 gene (position 434–905) sequencing (Big‐Dye terminator using 3130 ABI, Genetic analyzer). Molecular and phylogenetic analysis was performed using PhyML approach (v. 3.0). All A(H1N1)pdm09 positive and negative cases were clinically characterized. Phylogentically, all Lucknow strains (n = 33) except one fall with the clade seven reference strain. One strain showed 99.9% similarities with clade one reference strain A/California/07/2009. In mutational analysis, 33 strains had the S220T mutation, which is at an antigenic site and characteristic of clade seven along with few minor mutations; K180I/T/Q, V190I, S200P, S202T, A203T, A214T, S220T, V251I, and A273T. These results suggest that clade seven was the most widely circulating clade in Lucknow and A(H1N1)pdm09 cases showed mild clinical symptoms as compared to A(H3N2) or influenza B cases. J. Med. Virol. 86:2134–2141, 2014. © 2014 Wiley Periodicals, Inc.
Feasibility of home‐based dietetic intervention to improve the nutritional status of older adults post‐hospital discharge

AIM To determine if a model of home-based dietetic care improves dietary intake and weight status in a specific group of older adults post-hospitalisation. METHODS The Department of Veterans' Affairs clients aged 65 years and over were recruited from hospitals in a regional area of New South Wales, Australia (n = 32 men, n = 36 women). Nutritional status was assessed at home at baseline (within two weeks post-discharge) and three months post-discharge using a diet history, a food frequency checklist and Mini Nutritional Assessment (MNA). Personalised dietary advice was provided by a single dietitian according to participants' nutritional status. RESULTS Mean body weight improved significantly (P = 0.048), as well as mean MNA score (21.9 ± 3.5 vs 25.2 ± 3.1) (P < 0.001). Mean energy, protein and micronutrient intakes were adequate at baseline and three months, except for vitamin D. At three months, the underweight group (body mass index (BMI) < 23 kg/m2 ) had significantly higher mean protein intake per body weight (1.7 ± 0.4 g/kg) compared to those who were a desirable weight (BMI 23-27 kg/m2 ) (1.4 ± 0.3 g/kg) or overweight (BMI>27 kg/m2 ) (1.1 ± 0.3 g/kg) peers (P < 0.001). There was significant improvement in energy intake contributed from oral nutrition supplements (+95.5 ± 388.2 kJ/day) and milk (+259.6 ± 659.8 kJ/day). CONCLUSIONS Dietetic intervention improved nutritional status 3 months after hospital discharge in older adults living in the community.