Heterogeneous expression patterns and separate roles of the SEPALLATA gene LEAFY HULL STERILE1 in grasses

SEPALLATA (SEP) genes exhibit distinct patterns of expression and function in the grass species rice (Oryza sativa) and maize (Zea mays), suggesting that the role of the genes has changed during the evolution of the family. Here, we examine expression of the SEP-like gene LEAFY HULL STERILE1 (LHS1) in phylogenetically disparate grasses, reconstruct the pattern of gene expression evolution within the family, and then use the expression patterns to test hypotheses of gene function. Our data support a general role for LHS1 in specifying determinacy of the spikelet meristem and also in determining the identity of lemmas and paleas; these two functions are separable, as is the role of the gene in specifying floret meristems. We find no evidence that LHS1 determines flower number; it is strongly expressed in all spikelet meristems even as they are producing flowers, and expression is not correlated with eventual flower number. LHS1 expression in only the upper flowers of the spikelet appears to be the ancestral state; expression in all flowers is derived in subfamily Pooideae. LHS1 expression in pistils, stamens, and lodicules varies among the cereals. We hypothesize that LHS1 may have affected morphological diversification of grass inflorescences by mediating the expression of different floral identity genes in different regions of the floret and spikelet.     

Book Reviews

Unearthing Garden Mysteries: Experiments For Kids. Ellen Talmage. Golden, Colo.: Fulcrum Publishing. 2000. 90 pp. $17.95 (paperback). ISBN: 1-55591-993-6.

Greening School Grounds: Creating Habitats For Learning. Tim Grant and Gail Littlejohn (eds.). Gabriola Island, BC, Canada: New Society Publishers. 2001. 136 pp. $16.95 (paperback). ISBN: 0-86571-436-3.

Science Projects About Sound. Robert Gardner. Berkeley Heights, N.J.: Enslow. 2000. 112 pp. $19.95 (hardcover). ISBN: 0-7660-1166-6.

The Science of Sound and Music. Shar Levine and Leslie Johnstone. New York: Sterling Publishing. 2000. 80 pp. $19.95 (hardcover). ISBN: 0-8069-7183-5.

Elephants and Their Young. Great Explorations in Mathematics and Science (GEMS). Berkeley, Calif.: University of California, Lawrence Hall of Science. 2001. 100 pp. $18 (paperback). ISBN: 0-924886-55-2.

Mia2: Romaine's New Hat. Montreal, Quebec, Canada: Kotoka Kids Interactive. ($19.99 from Amazon.com).

System Requirements: PC. O/S: Windows 95 or better, CPU: Pentium 166MMX, RAM: 32 MB (64MB recommended), Video: 640 × 480 (256 colors), Sound: 16-bit Sound Blaster or 100% compatible, CD-ROM: 6X, 40 MB of hard drive disk space.

Macintosh: O/S: Systems 8.1 or better (System 9 requires 64 MB of Ram), CPU: PowerPC 275mhz, G3 233mhz, iMac, RAM: 32 MB (64 MB recommended), Video: 640 × 480 (256 colors), Sound: Standard Macintosh, CD-ROM: 6X, 40 MB of hard drive disk space.     

Are extraversion and openness indicators of a slow life history strategy?

Theory and data generally concur that a slower Life History Strategy (LHS) is associated with higher Conscientiousness, Agreeableness and Emotional Stability. Whether Extraversion and Openness are indicators of a slow LH, or whether they include both fast and slow LH components, remains unresolved. I addressed these questions in two studies: one of university students observed via periodic brief audio recordings during 72 h of their daily lives, and the second a re-analysis of data from Block and Block's (2006) longitudinal study. In both studies, I operationalized LHS as the correlation between an individual's California Q-Sort (CAQ) profile and the slow Life History (SLH) CAQ template created by Sherman et al. (2013) and Dunkel et al. (2015). I calculated Five Factor Model dimension scores using McCrae et al's (1986) method. In both samples, individuals whose CAQ profile more closely resembled the SLH template were higher in Conscientiousness, Agreeableness, and Emotional Stability than those pursuing a faster LHS. Extraversion was unrelated to LHS, while Openness in the Block and Block data set was actually associated with a faster LHS. Analysis of individual CAQ items revealed some differences between the studies. Generally, Extraversion-loading items tapping excitement-seeking and self-dramatization, and Openness-loading items tapping nonconformity, were associated with a faster LHS. Participants in the audio recording study also completed a HEXACO personality inventory and the Arizona Life History Battery. LHS as measured by the ALHB was uncorrelated with LHS as measured by the CAQ. Controlling for Extraversion yielded a significant positive relationship between the two LHS measures, suggesting that their poor convergent validity resulted from differences in their coverage of Extraversion-related content.     

GEMS: Gossip-Enabled Monitoring Service for Scalable Heterogeneous Distributed Systems

Gossip protocols have proven to be effective means by which failures can be detected in large, distributed systems in an asynchronous manner without the limitations associated with reliable multicasting for group communications. In this paper, we discuss the development and features of a Gossip-Enabled Monitoring Service (GEMS), a highly responsive and scalable resource monitoring service, to monitor health and performance information in heterogeneous distributed systems. GEMS has many novel and essential features such as detection of network partitions and dynamic insertion of new nodes into the service. Easily extensible, GEMS also incorporates facilities for distributing arbitrary system and application-specific data. We present experiments and analytical projections demonstrating scalability, fast response times and low resource utilization requirements, making GEMS a potent solution for resource monitoring in distributed computing.     

Serum miR-30c-5p is a potential biomarker for multiple system atrophy

Multiple system atrophy (MSA) is a neurodegenerative disease that belongs to the α synucleinopathies. Clinically, there is an overlap between MSA and Parkinson’s disease (PD), especially at the early disease stage. However, these two pathologies differ in terms of disease progression. Currently, no biomarker exists to differentiate MSA from PD. MicroRNAs are non-coding RNAs implicated in gene expression regulation. MiRNAs modulate cellular activity and they control a range of physiological and pathological functions. miRNAs are found in biofluids, such as blood, serum, plasma, saliva, and cerebrospinal fluid. Many groups, including ours, found that circulating miRNAs are differently expressed in blood, plasma, serum and cerebrospinal fluid of PD and MSA patients. In the present study, our primary aim was to determine if serum mir-30-5p and mir-148b-5p can be used as biomarkers for early diagnosis of PD and/or MSA. Our secondary goal was to determine if serum levels of those miRNAs can be correlated with the patients’ clinical profile. Using quantitative PCR (qPCR), we evaluated expression levels of miR-30c-5p and miR148b-5p in serum samples from PD (n?=?56), MSA (n?=?49), and healthy control (n?=?50) subjects. We have found that miR-30c-5p is significantly upregulated in MSA if compared with PD and healthy control subjects. Moreover, serum miR-30c-5p levels correlate with disease duration in both MSA and PD. No significant difference was found in miR-148b-5p among MSA, PD and healthy control subjects. Our results suggest a possible role of serum miR-30-5p as a biomarker for diagnosis and progression of MSA.

     

Mind the gaps: evidence of bias in estimates of multiple sequence alignments

Multiple sequence alignment (MSA) is a crucial first step in the analysis of genomic and proteomic data. Commonly occurring sequence features, such as deletions and insertions, are known to affect the accuracy of MSA programs, but the extent to which alignment accuracy is affected by the positions of insertions and deletions has not been examined independently of other sources of sequence variation. We assessed the performance of 6 popular MSA programs (ClustalW, DIALIGN-T, MAFFT, MUSCLE, PROBCONS, and T-COFFEE) and one experimental program, PRANK, on amino acid sequences that differed only by short regions of deleted residues. The analysis showed that the absence of residues often led to an incorrect placement of gaps in the alignments, even though the sequences were otherwise identical. In data sets containing sequences with partially overlapping deletions, most MSA programs preferentially aligned the gaps vertically at the expense of incorrectly aligning residues in the flanking regions. Of the programs assessed, only DIALIGN-T was able to place overlapping gaps correctly relative to one another, but this was usually context dependent and was observed only in some of the data sets. In data sets containing sequences with non-overlapping deletions, both DIALIGN-T and MAFFT (G-INS-I) were able to align gaps with near-perfect accuracy, but only MAFFT produced the correct alignment consistently. The same was true for data sets that comprised isoforms of alternatively spliced gene products: both DIALIGN-T and MAFFT produced highly accurate alignments, with MAFFT being the more consistent of the 2 programs. Other programs, notably T-COFFEE and ClustalW, were less accurate. For all data sets, alignments produced by different MSA programs differed markedly, indicating that reliance on a single MSA program may give misleading results. It is therefore advisable to use more than one MSA program when dealing with sequences that may contain deletions or insertions, particularly for high-throughput and pipeline applications where manual refinement of each alignment is not practicable.     

Multiplication stimulating activity (MSA) from the BRL 3A rat liver cell line: Relation to human somatomedins and insulin

The properties of multiplication stimulating activity (MSA), an insulin-like growth factor (somatomedin) purified from culture medium conditioned by the BRL 3A rat liver cell line are summarized. The relationship of MSA to somatomedins purified from human and rat plasma are considered. MSA appears to be the predominant somatomedin in fetal rat serum, but a minor component ot adult rat somatomedin. In vitro biological effects of MSA and insulin in adipocytes, fibroblasts and chondrocytes are examined to determine whether they are mediated by insulin receptors or insulin-like growth factor receptors. The possible relationship of a primary defect of insulin receptors observed in fibroblasts from a patient with the rare genetic disorder, leprechaunism, to intrauterine growth retardation is discussed.     

The role of polyamines in somatomedin-stimulated differentiation of L6 myoblasts

The somatomedins are potent stimulators of proliferation and differentiation of cultured myoblasts. In studies on the mechanism(s) of these actions, we have measured the activities of ornithine decarboxylase (ODC), an enzyme associated with rapid cell proliferation, and creatine kinase (CK), a biochemical marker for muscle differentiation, after treatment of L6 myoblast cultures with Multiplication Stimulating Activity (MSA), a member of the somatomedin family of insulinlike growth factors. ODC levels reached a peak 24 hours after MSA addition (before any detectable differentiation of the myoblasts) and then decreased as differentiation commenced and CK activity increased. Addition of alpha-difluoromethylornithine (DFMO), an irreversible inhibitor of ODC, caused a dramatic decrease in differentiation. Measurement of 3H-thymidine incorporation, DNA content, and cell number established that the effect of DFMO on differentiation was not a simple consequence of its antiproliferative actions. Cellular levels of putrescine and spermidine (but not spermine) decreased substantially following addition of DFMO to the cultures. The inhibitory effects of DFMO were abolished upon addition of exogenous polyamines to the medium. However, addition of polyamines in the absence of MSA or DFMO did not mimic the stimulation of differentiation by MSA. We conclude that polyamines play an essential role in the stimulation of L6 myoblast differentiation by somatomedins, but they are not sufficient to effect this stimulation.     

Screening for Older Emergency Department Inpatients at Risk of Prolonged Hospital Stay: The Brief Geriatric Assessment Tool

Background

The aims of this study were 1) to confirm that combinations of brief geriatric assessment (BGA) items were significant risk factors for prolonged LHS among geriatric patients hospitalized in acute care medical units after their admission to the emergency department (ED); and 2) to determine whether these combinations of BGA items could be used as a prognostic tool of prolonged LHS.

Methods

Based on a prospective observational cohort design, 1254 inpatients (mean age ± standard deviation, 84.9±5.9 years; 59.3% female) recruited upon their admission to ED and discharged in acute care medical units of Angers University Hospital, France, were selected in this study. At baseline assessment, a BGA was performed and included the following 6 items: age ≥85years, male gender, polypharmacy (i.e., ≥5 drugs per day), use of home-help services, history of falls in previous 6 months and temporal disorientation (i.e., inability to give the month and/or year). The LHS in acute care medical units was prospectively calculated in number of days using the hospital registry.

Results

Area under receiver operating characteristic (ROC) curves of prolonged LHS of different combinations of BGA items ranged from 0.50 to 0.57. Cox regression models revealed that combinations defining a high risk of prolonged LHS, identified from ROC curves, were significant risk factors for prolonged LHS (hazard ratio >1.16 with P>0.010). Kaplan-Meier distributions of discharge showed that inpatients classified in high-risk group of prolonged LHS were discharged later than those in low-risk group (P<0.003). Prognostic value for prolonged LHS of all combinations was poor with sensitivity under 77%, a high variation of specificity (from 26.6 to 97.4) and a low likelihood ratio of positive test under 5.6.

Conclusion

Combinations of 6-item BGA tool were significant risk factors for prolonged LHS but their prognostic value was poor in the studied sample of older inpatients.     

Two MSA 2 peptides that bind to human red blood cells are relevant to Plasmodium falciparum merozoite invasion.

Plasmodium falciparum merozoite membrane surface antigen 2 (MSA2) has been associated with the development of protective immunity against malaria. MSA2 antibodies were able to inhibit in vitro merozoite invasion. In our search for experimental evidence concerning the participation of MSA2 in merozoite invasion, 40 peptides were synthesized according to sequences reported for the CAMP and FC27 prototype Plasmodium strains. These peptides were purified, 125I-radiolabeled and tested for their ability to bind to erythrocytes. Two MSA2 synthetic peptides with high specific binding to human erythrocytes were found. The peptide coded 4044 (KNESKYSNTFINNAYNMSIR), located in the MSA2 N-terminal conserved region, has an affinity coefficient of 72 nM and showed a positive cooperativity for the receptor-ligand interaction. The other peptide, coded 4053 (NPNHKNAETNPKGKGEVQKP) and located in the central variable region of MSA2, has an affinity coefficient of 49nM and also showed a positive cooperativity for the receptor-ligand interaction. The binding capacity of these peptides is affected by erythrocytes treated with neuraminidase and trypsin, but it is not affected by chymotrypsin. Both of these sequences inhibit in vitro erythrocyte parasite invasion by up to 95% suggesting that they have an important role in the parasite's invasion process. Furthermore, as published previously [A. Saul et al. (1992) J. Immunol., 148, 208-211], a protective B epitope is included in the 4044 peptide sequence.     

Multiple sequence alignment using partial order graphs

MOTIVATION: Progressive Multiple Sequence Alignment (MSA) methods depend on reducing an MSA to a linear profile for each alignment step. However, this leads to loss of information needed for accurate alignment, and gap scoring artifacts. RESULTS: We present a graph representation of an MSA that can itself be aligned directly by pairwise dynamic programming, eliminating the need to reduce the MSA to a profile. This enables our algorithm (Partial Order Alignment (POA)) to guarantee that the optimal alignment of each new sequence versus each sequence in the MSA will be considered. Moreover, this algorithm introduces a new edit operator, homologous recombination, important for multidomain sequences. The algorithm has improved speed (linear time complexity) over existing MSA algorithms, enabling construction of massive and complex alignments (e.g. an alignment of 5000 sequences in 4 h on a Pentium II). We demonstrate the utility of this algorithm on a family of multidomain SH2 proteins, and on EST assemblies containing alternative splicing and polymorphism. AVAILABILITY: The partial order alignment program POA is available at http://www.bioinformatics.ucla.edu/poa.     

Inability of newborns' or pregnant women's monocytes to suppress pokeweed mitogen-induced responses

Although an excess of human adult blood adherent cells inhibits the pokeweed mitogen- (PWM) induced normal adult lymphocyte proliferation and B cell maturation into immunoglobulin-containing cells (ICC), adherent cells collected from newborn infants or pregnant women at time of delivery were unable to exert a similar suppressor activity. After activation by Concanavalin A (Con A), newborns' and pregnant women's adherent cells acquired a suppressor activity comparable to that of control adult adherent cells. The adherent suppressor cell was shown to be radioresistant (3000 rad), indicating its probable monocytic origin. Both monocyte-suppressor activities (MSA) observed in adulthood (spontaneously) and in the neonatal period (after activation) were dependent on prostaglandin E2 (PGE2) secretion, because they were abolished by indomethacin or a specific anti-PGE2 antiserum. Expression of MSA appeared to be under a negative regulation exerted by naturally occurring T suppressor lymphocytes present in the blood of newborns or pregnant women, because incubation of adult monocytes or Con A-activated newborn monocytes with newborns' or pregnant women's T lymphocytes resulted in a dramatic decrease of their MSA. These results strongly suggest that the lack of MSA in the neonatal period and in late pregnancy is a consequence of activation of T suppressor lymphocytes.     

A leaf-height-seed (LHS) plant ecology strategy scheme

A leaf-height-seed (LHS) plant ecology strategy scheme is proposed. The axes would be specific leaf area SLA (light-capturing area deployed per dry mass allocated), height of the plant's canopy at maturity, and seed mass. All axes would be log-scaled. The strategy of a species would be described by its position in the volume formed by the three axes.The advantages of the LHS scheme can be understood by comparing it to Grime's CSR scheme, which has Competitors, Stress-tolerators and Ruderals at the corners of a triangle. The CSR triangle is widely cited as expressing important strategic variation between species. The C–S axis reflects variation in responsiveness to opportunities for rapid growth; in the LHS scheme, SLA reflects the same type of variation. The R axis reflects coping with disturbance; in the LHS scheme, height and seed mass reflect separate aspects of coping with disturbance.A plant ecology strategy scheme that permitted any species worldwide to be readily positioned within the scheme could bring substantial benefits for improved meta-analysis of experimental results, for placing detailed ecophysiology in context, and for coping with questions posed by global change. In the CSR triangle the axes are defined by reference to concepts, there is no simple protocol for positioning species beyond the reference datasets within the scheme, and consequently benefits of worldwide comparison have not materialized. LHS does permit any vascular land plant species to be positioned within the scheme, without time-consuming measurement of metabolic rates or of field performance relative to other species. The merits of the LHS scheme reside (it is argued) in this potential for worldwide comparison, more than in superior explanatory power within any particular vegetation region.The LHS scheme avoids also two other difficulties with the CSR scheme: (a) It does not prejudge that there are no viable strategies under high stress and high disturbance (the missing quadrant in the CSR triangle compared to a two-axis rectangle); (b) It separates out two distinct aspects of the response to disturbance, height at maturity expressing the amount of growth attempted between disturbances, and seed mass (inverse of seed output per unit reproductive effort) expressing the capacity to colonize growth opportunities at a distance.The advantage of LHS axes defined through a single readily-measured variable needs to be weighed against the disadvantage that single plant traits may not capture as much strategy variation as CSR's multi-trait axes. It is argued that the benefits of potential worldwide comparison do actually outweigh any decrease in the proportion of meaningful variation between species that is captured. Further, the LHS scheme opens the path to quantifying what proportion of variation in any other ecologically-relevant trait is correlated with the LHS axes. This quantification could help us to move forward from unprofitable debates of the past 30 years, where CSR opponents have emphasized patterns that were not accommodated within the scheme, while CSR proponents have emphasized patterns that the scheme did account for.     

Evidence for distinct roles of the SEPALLATA gene LEAFY HULL STERILE1 in Eleusine indica and Megathyrsus maximus (Poaceae)

LEAFY HULL STERILE1 (LHS1) is an MIKC-type MADS-box gene in the SEPALLATA class. Expression patterns of LHS1 homologs vary among species of grasses, and may be involved in determining palea and lemma morphology, specifying the terminal floret of the spikelet, and sex determination. Here we present LHS1 expression data from Eleusine indica (subfamily Chloridoideae) and Megathyrsus maximus (subfamily Panicoideae) to provide further insights into the hypothesized roles of the gene. E. indica has spikelets with three to eight florets that mature acropetally; E. indica LHS1 (EiLHS1) is expressed in the palea and lemma of all florets. In contrast, M. maximus has spikelets with two florets that mature basipetally; M. maximus LHS1 (MmLHS1) is expressed in the palea and lemma of the distal floret only. These data are consistent with the hypothesis that LHS1 plays a role in determining palea and lemma morphology and specifies the terminal floret of basipetally maturing grass spikelets. However, LHS1 expression does not correlate with floret sex expression; MmLHS1 is restricted to the bisexual distal floret, whereas EiLHS1 is expressed in both sterile and bisexual floret meristems. Phylogenetic analyses reconstruct a complex pattern of LHS1 expression evolution in grasses. LHS1 expression within the gynoecium has apparently been lost twice, once before diversification of a major clade within tribe Paniceae, and once in subfamily Chloridoideae. These data suggest that LHS1 has multiple roles during spikelet development and may have played a role in the diversification of spikelet morphology.     

An intraspecific application of the leaf‐height‐seed ecology strategy scheme to forest herbs along a latitudinal gradient

We applied the leaf‐height‐seed (LHS) ecology strategy scheme (a combination of three ecologically important traits: specific leaf area (SLA), seed mass and plant height) intraspecifically to two widespread European forest herbs along a latitudinal gradient. The aims of this study were to quantify LHS trait variation, disentangle the environmental factors affecting these traits and compare the within‐species LHS trait relationships with latitude to previously established cross‐species comparisons. We measured LHS traits in 41 Anemone nemorosa and 44 Milium effusum populations along a 1900–2300 km latitudinal gradient from N France to N Sweden. We then applied multilevel models to identify the effects of regional (temperature, latitude) and local (soil fertility and acidity, overstorey canopy cover) environmental factors on LHS traits. Both species displayed a significant 4% increase in plant height with every degree northward shift (almost a two‐fold plant height difference between the southernmost and northernmost populations). Neither seed mass nor SLA showed a significant latitudinal cline. Temperature had a large effect on the three LHS traits of Anemone. Latitude, canopy cover and soil nutrients were related to the SLA and plant height of Milium. None of the investigated variables appeared to be related to the seed mass of Milium. The variation in LHS traits indicates that the ecological strategy determined by the position of each population in this three‐factor triangle is not constant along the latitudinal gradient. The significant increase in plant height suggests greater competitive abilities for both species in the northernmost populations. We also found that the studied environmental factors affected the LHS traits of the two species on various scales: spring‐flowering Anemone was affected more by temperature, whereas early‐summer flowering Milium was affected more by local and other latitude‐related factors. Finally, previously reported cross‐species correlations between LHS traits and latitude were generally unsupported by our within‐species approach.     

Clinical variables predicting the risk of a hospital stay for longer than 7 days in patients with severe acute exacerbations of chronic obstructive pulmonary disease: a prospective study

Background

Chronic obstructive pulmonary disease (COPD) patients may experience an acute exacerbation (AECOPD) that requires hospitalisation. The length of hospital stay (LHS) has a great economic impact on the health-care system. Knowing the predictors of prolonged LHS could help to identify possible interventions.

Methods

We performed a prospective study to identify the clinical predictors of prolonged LHS in patients hospitalised for AECOPD. We divided the study sample by LHS into normal (≤7?days) and prolonged LHS (>?7?days) groups. Outcomes were the need for non-invasive and invasive mechanical ventilation (NIMV and IMV), intensive care unit (ICU) admission, and the 3-year mortality.

Results

We enrolled 437 patients, of which 213 and 224 had normal LHS and prolonged LHS, respectively. Patients with a prolonged LHS had more prior hospitalisations for AECOPD, a worse mMRC (modified Medical Research Council) dyspnoea score, a higher prevalence of long-term oxygen therapy and a higher rate of congestive heart disease. During the current admission, this group also tended to require NIMV, IMV and ICU admission and the mortality risks at 6?months, 1?year and 3?years were higher. In the multivariate regression analysis, an mMRC dyspnoea score?≥?2 (odds ratio-OR 2.24; 95% confidence interval-CI 1.34 to 3.74; p?=?0.002) and the presence of acute respiratory acidosis (OR 2.75; 95% CI 1.49 to 5.05; p?=?0.001) predicted a prolonged LHS at admission.

Conclusions

The presence of an mMRC ≥2 and acute respiratory acidosis at admission independently increased the risk of a prolonged LHS for AECOPD.

     

85例多系统萎缩患者预后影响因素的分析

目的:探讨多系统萎缩(multiple system atrophy,MSA)患者预后的影响因素。方法:连续收集2016年1月到2019年1月空军军医大学第一附属医院神经内科住院及门诊收治的85名临床确诊MSA患者的临床资料,每隔6月对患者进行随访记录,直至需辅助行走时间,研究时限3.5年,筛选10个可能影响MSA独立行走的危险因素,应用Cox比例风险回归模型进行单因素及多因素回归分析。结果:85例MSA患者中,很可能MSA38例(44.7%),可能MSA47例(55.3%),以帕金森表现(MSA-P)43例(50.6%),以小脑性共济失调表现(MSA-C)42例(49.4%),男性46例(54.1%),女性39例(45.9%),起病年龄54.7±8.8岁,首发运动症状30例(35.3%),首发非运动症状55例(64.7%)。起病至非运动症状合并运动症状中位时程27.9(11.5, 40.5)月。截至本研究终止,28例(32.9%)患者独立行走,57例(67.1%)患者不能独立行走,起病至辅助行走中位时程36.0(22.5, 54.0)月。Cox比例风险回归模型显示起病年龄大(HR=1.041, 95%CI 1.000-1.083, P=0.049)、HY高分期(HR=2.015,95%CI 1.031-3.938,P=0.040)、起病至非运动症状合并运动症状短时程(HR=0.980,95%CI 0.967-0.993, P=0.003)是MSA患者发展至辅助行走状态的危险因素。结论:起病年龄大、HY高分期、起病至非运动症状合并运动症状短时程是MSA患者辅助行走的不良预后因素。     

RNA secondary structure, an important bioinformatics tool to enhance multiple sequence alignment: a case study (Sordariomycetes, Fungi)

In a case study of fungi of the class Sordariomycetes, we evaluated the effect of multiple sequence alignment (MSA) on the reliability of the phylogenetic trees, topology and confidence of major phylogenetic clades. We compared two main approaches for constructing MSA based on (1) the knowledge of the secondary (2D) structure of ribosomal RNA (rRNA) genes, and (2) automatic construction of MSA by four alignment programs characterized by different algorithms and evaluation methods, CLUSTAL, MAFFT, MUSCLE, and SAM. In the primary fungal sequences of the two functional rRNA genes, the nuclear small and large ribosomal subunits (18 S and 28 S), we identified four and six, respectively, highly variable regions, which correspond mainly to hairpin loops in the 2D structure. These loops are often positioned in expansion segments, which are missing or are not completely developed in the Archaeal and Eubacterial kingdoms. Proper sorting of these sites was a key for constructing an accurate MSA. We utilized DNA sequences from 28 S as an example for one-gene analysis. Five different MSAs were created and analyzed with maximum parsimony and maximum likelihood methods. The phylogenies inferred from the alignments improved with 2D structure with identified homologous segments, and those constructed using the MAFFT alignment program, with all highly variable regions included, provided the most reliable phylograms with higher bootstrap support for the majority of clades. We illustrate and provide examples demonstrating that re-evaluating ambiguous positions in the consensus sequences using 2D structure and covariance is a promising means in order to improve the quality and reliability of sequence alignments.