Learning from Instructional Explanations: Effects of Prompts Based on the Active-Constructive-Interactive Framework

Although instructional explanations are commonly provided when learners are introduced to new content, they often fail because they are not integrated into effective learning activities. The recently introduced active-constructive-interactive framework posits an effectiveness hierarchy in which interactive learning activities are at the top; these are then followed by constructive and active learning activities, respectively. Against this background, we combined instructional explanations with different types of prompts that were designed to elicit these learning activities and tested the central predictions of the active-constructive-interactive framework. In Experiment 1, N = 83 students were randomly assigned to one of four combinations of instructional explanations and prompts. To test the active < constructive learning hypothesis, the learners received either (1) complete explanations and engaging prompts designed to elicit active activities or (2) explanations that were reduced by inferences and inference prompts designed to engage learners in constructing the withheld information. Furthermore, in order to explore how interactive learning activities can be elicited, we gave the learners who had difficulties in constructing the prompted inferences adapted remedial explanations with either (3) unspecific engaging prompts or (4) revision prompts. In support of the active < constructive learning hypothesis, we found that the learners who received reduced explanations and inference prompts outperformed the learners who received complete explanations and engaging prompts. Moreover, revision prompts were more effective in eliciting interactive learning activities than engaging prompts. In Experiment 2, N = 40 students were randomly assigned to either (1) a reduced explanations and inference prompts or (2) a reduced explanations and inference prompts plus adapted remedial explanations and revision prompts condition. In support of the constructive < interactive learning hypothesis, the learners who received adapted remedial explanations and revision prompts as add-ons to reduced explanations and inference prompts acquired more conceptual knowledge.     

Role of individual phosphorylation sites in inactivation of pyruvate dehydrogenase complex in rat heart mitochondria

1. A method is described using trypsin/formic acid cleavage for unambiguously measuring occupancies of phosphorylation sites in rat heart pyruvate dehydrogenase [³²P]phosphate complexes. 2. In mitochondria oxidizing 2-oxoglutarate+l-malate relative initial rates of phosphorylation were site 1>site 2>site 3. 3. Dephosphorylation and reactivation of fully phosphorylated complex was initiated in mitochondria by inhibiting the kinase reaction. Using dichloroacetate relative rates of dephosphorylation were site 2>(1=3). Using sodium dithionite or sodium pyruvate or uncouplers+sodium arsenite or steady state turnover (³¹P replacing ³²P in inactive complex) relative rates were site 2>site 1>site 3. With dithionite reactivation was faster than site 3 dephosphorylation, i.e. site 3 is apparently not inactivating. 4. The steady state proportion of inactive complex was varied (92–48%) in mitochondria oxidizing 2-oxoglutarate/l-malate by increasing extramitochondrial Ca²⁺ (0–2.6μm). This action of Ca²⁺ induced dephosphorylation (site 3>site 2>site 1). These experiments enable prediction of site occupancies in vivo for given steady state proportions of inactive complexes. 5. The proportion of inactive complex was related linearly to occupancy of site 1. 6. Sodium dithionite (10mm) and Ca²⁺ (0.5μm) together resulted in faster dephosphorylations of each site than either agent alone; relative rates were site 2>(1=3). 7. Dephosphorylation and possibly phosphorylation of sites 1 and 2 was not purely sequential as shown by detection of complexes phosphorylated in site 2 but not in site 1. Estimates of the contribution of site 2 phosphorylation to inactivation ranged from 0.7 to 6.4%. 8. It is concluded that the primary function of site 1 phosphorylation is inactivation, phosphorylation of site 2 is not primarily concerned with inactivation and that phosphorylation of site 3 is non-inactivating.     

Developmental Eye Movement (DEM) Test Norms for Mandarin Chinese-Speaking Chinese Children

The Developmental Eye Movement (DEM) test is commonly used as a clinical visual-verbal ocular motor assessment tool to screen and diagnose reading problems at the onset. No established norm exists for using the DEM test with Mandarin Chinese-speaking Chinese children. This study aims to establish the normative values of the DEM test for the Mandarin Chinese-speaking population in China; it also aims to compare the values with three other published norms for English-, Spanish-, and Cantonese-speaking Chinese children. A random stratified sampling method was used to recruit children from eight kindergartens and eight primary schools in the main urban and suburban areas of Nanjing. A total of 1,425 Mandarin Chinese-speaking children aged 5 to 12 years took the DEM test in Mandarin Chinese. A digital recorder was used to record the process. All of the subjects completed a symptomatology survey, and their DEM scores were determined by a trained tester. The scores were computed using the formula in the DEM manual, except that the “vertical scores” were adjusted by taking the vertical errors into consideration. The results were compared with the three other published norms. In our subjects, a general decrease with age was observed for the four eye movement indexes: vertical score, adjusted horizontal score, ratio, and total error. For both the vertical and adjusted horizontal scores, the Mandarin Chinese-speaking children completed the tests much more quickly than the norms for English- and Spanish-speaking children. However, the same group completed the test slightly more slowly than the norms for Cantonese-speaking children. The differences in the means were significant (P<0.001) in all age groups. For several ages, the scores obtained in this study were significantly different from the reported scores of Cantonese-speaking Chinese children (P<0.005). Compared with English-speaking children, only the vertical score of the 6-year-old group, the vertical-horizontal time ratio of the 8-year-old group and the errors of 9-year-old group had no significant difference (P>0.05); compared with Spanish-speaking children, the scores were statistically significant (P<0.001) for the total error scores of the age groups, except the 6-, 9-, 10-, and 11-year-old age groups (P>0.05). DEM norms may be affected by differences in language, cultural, and educational systems among various ethnicities. The norms of the DEM test are proposed for use with Mandarin Chinese-speaking children in Nanjing and will be proposed for children throughout China.     

Zur Androeciumanlage und Antherenentwicklung beiCaloncoba echinata (Flacourtiaceae)

The polyandrous androecium ofCaloncoba echinata (Oliv.)Gilg initially consists of a flat, ring-like mound. On it stamen primordia arise almost simultaneously and in somewhat irregular (neither clearly centrifugal nor centripetal) sequence. This fits the development reported for other members of theGuttiferales-Violales group. The anther loculi are transversely septate as in someAnnonaceae and a few other Angiosperm families. This character does not appear to be phylogenetically primitive.     

EFFECTS OF HYDROXYL ON NEGATIVE AND POSITIVE CELLS OF NITELLA

Remarkable changes are brought about by KOH in transforming negative cells of Nitella (showing dilute solution negative with KOH) to positive cells (showing dilute solution positive with KOH). NaOH is less effective as a transforming agent. This might be explained on the ground that the protoplasm contains an acid (possibly a fatty acid) which makes the cell negative and which is dissolved out more rapidly by KOH than by NaOH, as happens with the fatty acids in ordinary soaps. Part of a negative cell can be changed to positive by exposure to KOH while the untreated portion remains negative. After exposure to KOH the potential the protoplasm has when in contact with NaCl may increase. At the same time there may be an increase in the potassium effect; i.e., in the change of P.D. in a positive direction observed when 0.01 M KCl is replaced by 0.01 M NaCl. In some cases the order of ionic mobilities is u _K > v _OH > u _Na. This shows that the protoplasmic surface cannot be a pore system: for in such a system all cations must have greater mobilities than all anions or vice versa.     

Masked Syllable Priming Effects in Word and Picture Naming in Chinese

Four experiments investigated the role of the syllable in Chinese spoken word production. Chen, Chen and Ferrand (2003) reported a syllable priming effect when primes and targets shared the first syllable using a masked priming paradigm in Chinese. Our Experiment 1 was a direct replication of Chen et al.’s (2003) Experiment 3 employing CV (e.g., 拔营,/ba2.ying2/, strike camp) and CVG (e.g., 白首,/bai2.shou3/, white haired) syllable types. Experiment 2 tested the syllable priming effect using different syllable types: e.g., CV (气球,/qi4.qiu2/, balloon) and CVN (蜻蜓,/qing1.ting2/, dragonfly). Experiment 3 investigated this issue further using line drawings of common objects as targets that were preceded either by a CV (e.g., 企,/qi3/, attempt), or a CVN (e.g., 情,/qing2/, affection) prime. Experiment 4 further examined the priming effect by a comparison between CV or CVN priming and an unrelated priming condition using CV-NX (e.g., 迷你,/mi2.ni3/, mini) and CVN-CX (e.g., 民居,/min2.ju1/, dwellings) as target words. These four experiments consistently found that CV targets were named faster when preceded by CV primes than when they were preceded by CVG, CVN or unrelated primes, whereas CVG or CVN targets showed the reverse pattern. These results indicate that the priming effect critically depends on the match between the structure of the prime and that of the first syllable of the target. The effect obtained in this study was consistent across different stimuli and different tasks (word and picture naming), and provides more conclusive and consistent data regarding the role of the syllable in Chinese speech production.     

The Binaural Masking-Level Difference of Mandarin Tone Detection and the Binaural Intelligibility-Level Difference of Mandarin Tone Recognition in the Presence of Speech-Spectrum Noise

Binaural hearing involves using information relating to the differences between the signals that arrive at the two ears, and it can make it easier to detect and recognize signals in a noisy environment. This phenomenon of binaural hearing is quantified in laboratory studies as the binaural masking-level difference (BMLD). Mandarin is one of the most commonly used languages, but there are no publication values of BMLD or BILD based on Mandarin tones. Therefore, this study investigated the BMLD and BILD of Mandarin tones. The BMLDs of Mandarin tone detection were measured based on the detection threshold differences for the four tones of the voiced vowels /i/ (i.e., /i1/, /i2/, /i3/, and /i4/) and /u/ (i.e., /u1/, /u2/, /u3/, and /u4/) in the presence of speech-spectrum noise when presented interaurally in phase (S₀N₀) and interaurally in antiphase (S_πN₀). The BILDs of Mandarin tone recognition in speech-spectrum noise were determined as the differences in the target-to-masker ratio (TMR) required for 50% correct tone recognitions between the S₀N₀ and S_πN₀ conditions. The detection thresholds for the four tones of /i/ and /u/ differed significantly (p<0.001) between the S₀N₀ and S_πN₀ conditions. The average detection thresholds of Mandarin tones were all lower in the S_πN₀ condition than in the S₀N₀ condition, and the BMLDs ranged from 7.3 to 11.5 dB. The TMR for 50% correct Mandarin tone recognitions differed significantly (p<0.001) between the S₀N₀ and S_πN₀ conditions, at –13.4 and –18.0 dB, respectively, with a mean BILD of 4.6 dB. The study showed that the thresholds of Mandarin tone detection and recognition in the presence of speech-spectrum noise are improved when phase inversion is applied to the target speech. The average BILDs of Mandarin tones are smaller than the average BMLDs of Mandarin tones.     

Implicit Value Updating Explains Transitive Inference Performance: The Betasort Model

Transitive inference (the ability to infer that B > D given that B > C and C > D) is a widespread characteristic of serial learning, observed in dozens of species. Despite these robust behavioral effects, reinforcement learning models reliant on reward prediction error or associative strength routinely fail to perform these inferences. We propose an algorithm called betasort, inspired by cognitive processes, which performs transitive inference at low computational cost. This is accomplished by (1) representing stimulus positions along a unit span using beta distributions, (2) treating positive and negative feedback asymmetrically, and (3) updating the position of every stimulus during every trial, whether that stimulus was visible or not. Performance was compared for rhesus macaques, humans, and the betasort algorithm, as well as Q-learning, an established reward-prediction error (RPE) model. Of these, only Q-learning failed to respond above chance during critical test trials. Betasort’s success (when compared to RPE models) and its computational efficiency (when compared to full Markov decision process implementations) suggests that the study of reinforcement learning in organisms will be best served by a feature-driven approach to comparing formal models.     

Imaging atherosclerotic plaque composition with intracoronary optical coherence tomography

Optical coherence tomography (OCT) allows highly accurate diagnosis of atherosclerotic plaques, including measurement of the thickness of fibrous caps, permitting an assessment of the risk of rupture. While the OCT image presents morphological information in highly resolved detail, it relies on interpretation by trained readers for the identification of tissue type. We developed a method for quantitative classification of atherosclerotic plaque constituents. The optical attenuation coefficient μ_t distinguishes different tissue types: necrotic core and macrophage infiltration exhibit strong attenuation, μ_t≥10 mm⁻¹, while calcific and fibrous tissue have a lower μ_t≈2–5 mm⁻¹. (Neth Heart J 2009;17:448-50.)     

Role of Kir2.1 in human monocyte‐derived foam cell maturation

The role of K⁺ channels in macrophage immunomodulation has been well‐established. However, it remains unclear whether K⁺ channels are involved in the lipid uptake of macrophages. The expression and function of the inward rectifier potassium channel (Kir2.1, KCNJ2) in Human acute monocytic leukemia cell line (THP‐1) cells and human monocytes derived macrophages (HMDMs) were investigated using RT‐PCR and western blotting, and patch clamp technique. The expression of scavenger receptors in THP‐1–derived macrophages was detected using western blotting. Expressions of Kir2.1 mRNA and protein in HMDMs were significantly decreased by 60% (P < 0.05) and 90% (P < 0.001) on macrophage maturation, but overexpressed by approximately 1.3 (P > 0.05) and 3.8 times (P = 0.001) after foam cell formation respectively. Concurrently, the Kir2.1 peak current density in HMDMs, mature macrophages and foam cells, measured at −150 mV, were −22.61 ± 2.1 pA/pF, −7.88 ± 0.60 pA/pF and −13.39 ± 0.80 pA/pF respectively (P < 0.05). In association with an up‐regulation of Kir2.1 in foam cells, the SR‐A protein level was significantly increased by over 1.5 times compared with macrophages (P < 0.05). THP‐1 cells contained much less lipids upon Kir2.1 knockdown and cholesterol ester/total cholesterol ratio was 29.46 ± 2.01% (P < 0.05), and the SR‐BI protein level was increased by over 6.2 times, compared to that of macrophages (P < 0.001). Kir2.1 may participate in macrophage maturation and differentiation, and play a key role in lipid uptake and foam cell formation through modulating the expression of scavenger receptors.     

Novel DNA Variants and Mutation Frequencies of hMLH1 and hMSH2 Genes in Colorectal Cancer in the Northeast China Population

Research on hMLH1 and hMSH2 mutations tend to focus on Lynch syndrome (LS) and LS-like colorectal cancer (CRC). No studies to date have assessed the role of hMLH1 and hMSH2 genes in mass sporadic CRC (without preselection by MSI or early age of onset). We aimed to identify novel hMLH1 and hMSH2 DNA variants, to determine the mutation frequencies and sites in both sporadic and LS CRC and their relationships with clinicopathological characteristics of CRC in Northeast of China. 452 sporadic and 21 LS CRC patients were screened for germline and somatic mutations in hMLH1 and hMSH2 genes with PCR–SSCP sequencing. We identified 11 hMLH1 and seven hMSH2 DNA variants in our study cohort. Six of them were novel: four in hMLH1 gene (IVS8-16 A>T, c.644 GAT>GTT, c.1529 CAG>CGG and c.1831 ATT>TTT) and two in hMSH2 gene (−39 C>T, insertion AACAACA at c.1127 and deletion AAG at c.1129). In sporadic CRC, germline and somatic mutation frequencies of hMLH1/hMSH2 gene were 15.59% and 17.54%, respectively (p = 0.52). Germline mutations present in hMLH1 and hMSH2 genes were 5.28% and 10.78%, respectively (p<0.01). Somatic mutations in hMLH1 and hMSH2 genes were 6.73% and 11.70%, respectively (p = 0.02). In LS CRC, both germline and somatic mutation frequencies of hMLH1/hMSH2 gene were 28.57%. The most prevalent germline mutation site in hMSH2 gene was c.1168 CTT>TTT (3.90%), a polymorphism. Somatic mutation frequency of hMLH1/hMSH2 gene was significantly different in proximal, distal colon and rectal cancer (p = 0.03). Our findings elucidate the mutation spectrum and frequency of hMLH1 and hMSH2 genes in sporadic and LS CRC, and their relationships with clinicopathological characteristics of CRC.     

Phonological Recoding in Error Detection: A Cross-sectional Study in Beginning Readers of Dutch

The present cross-sectional study investigated the development of phonological recoding in beginning readers of Dutch, using a proofreading task with pseudohomophones and control misspellings. In Experiment 1, children in grades 1 to 3 rejected fewer pseudohomophones (e.g., wein, sounding like wijn ‘wine’) as spelling errors than control misspellings (e.g., wijg). The size of this pseudohomophone effect was larger in grade 1 than in grade 2 and did not differ between grades 2 and 3. In Experiment 2, we replicated the pseudohomophone effect in beginning readers and we tested how orthographic knowledge may modulate this effect. Children in grades 2 to 4 again detected fewer pseudohomophones than control misspellings and this effect decreased between grades 2 and 3 and between grades 3 and 4. The magnitude of the pseudohomophone effect was modulated by the development of orthographic knowledge: its magnitude decreased much more between grades 2 and 3 for more advanced spellers, than for less advanced spellers. The persistence of the pseudohomophone effect across all grades illustrates the importance of phonological recoding in Dutch readers. At the same time, the decreasing pseudohomophone effect across grades indicates the increasing influence of orthographic knowledge as reading develops.     

Effect of peptide PV on the ionic permeability of lipid bilayer membranes

This paper reports the effects of peptide PV (primary structure: cyclo-(D-val-L-pro-L-val-D-pro)_δ) on the electrical properties of sheep red cell lipid bilayers. The membrane conductance (G_m) induced by PV in either Na⁺ or K⁺ medium is proportional to the concentration of PV in the aqueous phase. The PV concentration required to produce a comparable increase in G_m in K⁺ medium is about 10⁴ times greater than for its analogue, valinomycin (val). Although the selectivity sequence for PV and val is similar, K⁺ ≳ Rb⁺ > Cs⁺ > NH₄ ⁺ > TI⁺ > Na⁺ > Li⁺; the ratio of GGm in K⁺ to that in Na⁺ is about 10 for PV compared to > 10³ for val. When equal concentrations of PV are added to both sides of a bilayer, the membrane current approaches a maximum value independent of voltage when the membrane potential exceeds 100 mV. When PV is added to only one side of a bilayer separating identical salt solutions of either Na⁺ or K⁺ salts, rectification occurs such that the positive current flows more easily away rather than toward the side containing the carrier. Under these conditions, a large, stable, zero-current potential (VVm) is also observed, with the side containing PV being negative. The magnitude of this VVm is about 90 mV and relatively independent of PV concentration when the latter is larger than 2 Times; 10^–5 M. From a model which assumes that V_m equals the equilibrium potential for the PV-cation complexes (MS ⁺) and that the reaction between PV and cations is at equilibrium on the two membrane surfaces, we compute the permeability of the membrane to free PV to be about 10^–5 cm s^–1, which is about 10^–7 times the permeability of similar membranes to free val. This interpretation is supported by the fact that the observed values of V_m are in agreement with the calculated equilibrium potential for MS⁺ over a wide range of ratios of concentrations of total PV in the two bathing solutions, if the unstirred layers are taken into account in computing the MS⁺ concentrations at the membrane surfaces.     

Expression of the cancer-associated DNA polymerase ε P286R in fission yeast leads to translesion synthesis polymerase dependent hypermutation and defective DNA replication

Somatic and germline mutations in the proofreading domain of the replicative DNA polymerase ε (POLE-exonuclease domain mutations, POLE-EDMs) are frequently found in colorectal and endometrial cancers and, occasionally, in other tumours. POLE-associated cancers typically display hypermutation, and a unique mutational signature, with a predominance of C > A transversions in the context TCT and C > T transitions in the context TCG. To understand better the contribution of hypermutagenesis to tumour development, we have modelled the most recurrent POLE-EDM (POLE-P286R) in Schizosaccharomyces pombe. Whole-genome sequencing analysis revealed that the corresponding pol2-P287R allele also has a strong mutator effect in vivo, with a high frequency of base substitutions and relatively few indel mutations. The mutations are equally distributed across different genomic regions, but in the immediate vicinity there is an asymmetry in AT frequency. The most abundant base-pair changes are TCT > TAT transversions and, in contrast to human mutations, TCG > TTG transitions are not elevated, likely due to the absence of cytosine methylation in fission yeast. The pol2-P287R variant has an increased sensitivity to elevated dNTP levels and DNA damaging agents, and shows reduced viability on depletion of the Pfh1 helicase. In addition, S phase is aberrant and RPA foci are elevated, suggestive of ssDNA or DNA damage, and the pol2-P287R mutation is synthetically lethal with rad3 inactivation, indicative of checkpoint activation. Significantly, deletion of genes encoding some translesion synthesis polymerases, most notably Pol κ, partially suppresses pol2-P287R hypermutation, indicating that polymerase switching contributes to this phenotype.     

Some aspects of the regulation of arginine biosynthesis in soybean cell cultures

The levels of the activities of argininosuccinate synthetase and argininosuccinate lyase were measured in soybean (glycine max L. var. Mandarin) cell suspension cultures grown in the presence or absence of exogenous arginine. In some experiments, actinomycin D or cycloheximide were also added to the cultures, at critical stages of their growth. The results obtained led to the conclusion that activity of argininosuccinate synthetase is subject to significant inhibition by levels of arginine similar to those found to occur within the cells. Argininosuccinate lyase activity appeared to be enhanced, when arginine levels were increased above those occurring physiologically. Both enzymes appeared to be subject to inactivation, possibly via proteolysis.     

A High Frequency of Beneficial Mutations Across Multiple Fitness Components in Saccharomyces cerevisiae

Mutation-accumulation experiments are widely used to estimate parameters of spontaneous mutations affecting fitness. In many experiments only one component of fitness is measured. In a previous study involving the diploid yeast Saccharomyces cerevisiae, we measured the growth rate of 151 mutation-accumulation lines to estimate parameters of mutation. We found that an unexpectedly high frequency of fitness-altering mutations was beneficial. Here, we build upon our previous work by examining sporulation efficiency, spore viability, and haploid growth rate and find that these components of fitness also show a high frequency of beneficial mutations. We also examine whether mutation-acycumulation (MA) lines show any evidence of pleiotropy among accumulated mutations and find that, for most, there is none. However, MA lines that have zero fitness (i.e., lethality) for any one fitness component do show evidence for pleiotropy among accumulated mutations. We also report estimates of other parameters of mutation based on each component of fitness.ADAPTATION can occur from standing genetic variation or from newly arising mutations. The relative importance of these two sources of adaptive mutations is affected by a variety of factors, including those that alter standing levels of genetic variation (see Barrett and Schluter 2008) and those that generate new mutations. Predicting how quickly a population will adapt and the type of beneficial mutations that will fuel that adaptation requires estimates of the additive genetic variance in fitness and of the beneficial mutation rate and the distribution of beneficial effects. While additive genetic variance for fitness has been estimated in a variety of organisms (Mousseau and Roff 1987), the beneficial mutation rate and the distribution of beneficial effects have only been estimated in a few studies (Shaw et al. 2002; Joseph and Hall 2004; Perfeito et al. 2007; Dickinson 2008; Hall et al. 2008). Surprisingly, these studies estimate that between 6 (Joseph and Hall 2004) and 50% (Shaw et al. 2002) of fitness-altering mutations are beneficial. In contrast, most mutation-accumulation (MA) experiments identify few, if any, beneficial mutations. Such wildly different estimates have even been generated from studies of the same species in similar environments (Zeyl and Devisser 2001; Joseph and Hall 2004; Dickinson 2008; Hall et al. 2008). If these estimates are correct, then they would suggest that the genotypes used in these experiments have vastly different evolutionary potential with respect to their capacity to exhibit rapid adaptation from new mutations.A more likely scenario is that much of the variation in estimates of the beneficial mutation rate is due to methodological differences between studies. One possibility is the fitness component being analyzed. The beneficial mutation rate may be under- or overestimated if the fitness component is under stabilizing selection or subject to antagonistic pleiotropy. Analyses of mutation-accumulation data typically assume that selection is directional. As a result, analyses of phenotypes under stabilizing selection may falsely conclude that mutations that increase a phenotype are beneficial and mutations that lower values are deleterious (see Keightley and Lynch''s 2003 criticism of Shaw et al. 2002). Alternatively, the beneficial mutation rate may be over- (or under) estimated if mutations increase fitness in regard to one component, but lower fitness in regard to lifetime fitness or another fitness component (i.e., antagonistic pleiotropy). Here, we explore these possibilities by investigating whether the high beneficial mutation rates estimated from our previous experiments are specific to the fitness component that we examined.In two previous studies we accumulated mutations in 152 yeast, MA lines and used measures of their effects on diploid growth rate to estimate parameters of beneficial and deleterious mutations. In the first study we estimated that 6% of mutations accumulated during the first 1012 generations of accumulation improved diploid growth (Joseph and Hall 2004). To determine whether this high beneficial mutation rate was due to sampling error, we passaged the lines for an additional 1050 generations and found that 13% of mutations improved diploid growth (Hall et al. 2008). Similarly, another yeast MA experiment (Dickinson 2008) estimated an uncorrected frequency of beneficial mutations of 25%, although correction for within-colony selection reduces this estimate by approximately half. Together, these studies indicate that a substantial proportion of mutations accumulated in these yeast MA lines are beneficial for a single fitness component and that this observation cannot be explained by the chance sampling of a few beneficial mutations.In this study we return to our yeast MA lines (Joseph and Hall 2004) and examine whether the high beneficial mutation rate that we estimated after 1012 generations is an artifact of the fitness component that we examined. To test this hypothesis we examined whether our MA lines carry mutations that are beneficial across multiple fitness components: diploid growth, sporulation efficiency, spore viability, and haploid growth rate. If our previous results are due to us analyzing a fitness component that is either subject to stabilizing selection or antagonistic pleiotropy, then mutations accumulated in our lines will be conditionally beneficial and analyses of additional fitness components would yield different estimates of the beneficial mutation rate. We found that three of the four fitness components yield high estimates of the beneficial mutation rate. This suggests that multiple MA lines have accumulated beneficial mutations and that the high beneficial mutation rate that we previously estimated is not an artifact of the fitness component that we examined.Measuring multiple components of fitness also allowed us to examine the pleiotropic effects of beneficial and deleterious mutations. In general, we found that mutations altering one component of fitness have little effect on other components. However, lethal mutations were typically pleiotropic.

Conclusions:

We find that for three of four fitness components examined, a high frequency of spontaneous, fitness-altering mutations in diploid yeast is beneficial. Further, we do not detect pleiotropy of small-effect mutations, while lethal mutations show high levels of pleiotropy. In most cases, pleiotropy is positive. Two lines show evidence of antagonistic pleiotropy, indicating trade-offs, although heterozygote advantage cannot be ruled out.     

Preserved life positions of some Jurassic bivalves

The observed life positions of 23 species of Jurassic bivalves are recorded and compared to reconstructions derived from functional interpretations of their morphology and comparisons with Recent relatives. In the majority of cases, these inferences correspond with field observations. There are, however, cases such ashognomon where likely reconstructions differ. These could easily lead to an erroneous interpretation of the autecology of some species.     

Identification of Potential Pleiotropic Genes for Immune and Skeletal Diseases Using Multivariate MetaCCA Analysis

BackgroundImmune and skeletal systems physiologically and pathologically interact with each other. Immune and skeletal diseases may share potential pleiotropic genetics factors, but the shared specific genes are largely unknown.ObjectiveThis study aimed to investigate the overlapping genetic factors between multiple diseases (including rheumatoid arthritis (RA), psoriasis, osteoporosis, osteoarthritis, sarcopenia, and fracture).MethodsThe canonical correlation analysis (metaCCA) approach was used to identify the shared genes for six diseases by integrating genome-wide association study (GWAS)-derived summary statistics. The versatile Gene-based Association Study (VEGAS2) method was further applied to refine and validate the putative pleiotropic genes identified by metaCCA.ResultsAbout 157 (p<8.19E-6), 319 (p<3.90E-6), and 77 (p<9.72E-6) potential pleiotropic genes were identified shared by two immune diseases, four skeletal diseases, and all of the six diseases, respectively. The top three significant putative pleiotropic genes shared by both immune and skeletal diseases, including HLA-B, TSBP1, and TSBP1-AS1 (p<E-300), were located in the major histocompatibility complex (MHC) region. Nineteen of 77 putative pleiotropic genes identified by metaCCA analysis were associated with at least one disease in the VEGAS2 analysis. Specifically, the majority (18) of these 19 putative validated pleiotropic genes were associated with RA.ConclusionThe metaCCA method identified some pleiotropic genes shared by the immune and skeletal diseases. These findings help to improve our understanding of the shared genetic mechanisms and signaling pathways underlying immune and skeletal diseases.