High Degree Of Repetition Research Articles

Whole-Genome Resequencing and Evolutionary Analysis of Wild Morel Mushroom Morchella sp.

Morels (Morchella sp.) are important edible fungi cultivated mainly in China. Although the relevant culture technology for Morchella is now fundamentally mature, it is limited to the Elata and Rufobrunnea clades, and the artificial culture technology for the Esculenta clade, which also has economic value, has not been extensively studied. In this study, we selected a wild morel belonging to the Esculenta clade as the research material and performed de novo sequencing and assembly of the Morchella sp. (Mosp) genome using second- and third-generation sequencing. The whole-genome size of Mosp was 55.17 Mb with a contig N50 of 1.89 Mb, and the GC content was 47.49%. A total of 10,896 protein-coding genes were identified. The non-coding RNA prediction results showed that there were 329 tRNAs, 65 rRNAs, and 37 snRNAs in the Mosp genome. The functional annotation of the Mosp genes showed that most of the genes were related to the reproductive and metabolic processes of the cells and participated in nutrient digestion, absorption, utilization, and catabolism in morels. There was a high degree of repetition (21.58%) in the Mosp genome, and the sizes of the DNA transposons and the long terminal repeats were 0.55 Mb and 5.85 Mb, respectively. The phylogeny analysis showed that Mosp clusters together with four other Morchella species: Morchella importuna, Morchella conica, Morchella sextelata, and Morchella snyderi. Molecular dating indicated that the differentiation of Mosp and the black morels group occurred about 147.0 million years ago (MYA). In addition, the evolutionary analysis showed that 296 gene families were contracted and 96 gene families were expanded in Mosp versus the related morel species. The results of this study provide new insights into the genome evolution of Mosp and lay the foundation for future in-depth research into the molecular biology and breeding of the genus Morchella.

Whole-genome sequencing and evolutionary analysis of the wild edible mushroom, Morchella eohespera.

Morels (Morchella, Ascomycota) are an extremely desired group of edible mushrooms with worldwide distribution. Morchella eohespera is a typical black morel species, belonging to the Elata clade of Morchella species. The biological and genetic studies of this mushroom are rare, largely hindering the studies of molecular breeding and evolutionary aspects. In this study, we performed de novo sequencing and assembly of the M. eohespera strain m200 genome using the third-generation nanopore sequencing platform. The whole-genome size of M. eohespera was 53.81 Mb with a contig N50 of 1.93 Mb, and the GC content was 47.70%. A total of 9,189 protein-coding genes were annotated. Molecular dating showed that M. eohespera differentiated from its relative M. conica at ~19.03 Mya (million years ago) in Burdigalian. Evolutionary analysis showed that 657 gene families were contracted and 244 gene families expanded in M. eohespera versus the related morel species. The non-coding RNA prediction results showed that there were 336 tRNAs, 76 rRNAs, and 45 snRNAs in the M. eohespera genome. Interestingly, there was a high degree of repetition (20.93%) in the M. eohespera genome, and the sizes of long interspersed nuclear elements, short interspersed nuclear elements, and long terminal repeats were 0.83 Mb, 0.009 Mb, and 4.56 Mb, respectively. Additionally, selection pressure analysis identified that a total of 492 genes in the M. eohespera genome have undergone signatures of positive selection. The results of this study provide new insights into the genome evolution of M. eohespera and lay the foundation for in-depth research into the molecular biology of the genus Morchella in the future.

Morphological function of toe fringe in the sand lizard Phrynocephalus mystaceus

Toe fringe is the most typical morphological feature of lizards adapted to sandy environments, and it is simple in shape, can evolve repeatedly, and has a high degree of repetition; therefore, this feature is suitable for testing the adaptive convergence suggested by form-environment correlations. Phrynocephalus mystaceus mainly lives in dune habitats, has a developed bilateral toe fringe, and exhibits fast sand-burying behavior for predator avoidance. We tested the effects of resecting the medial and bilateral toe fringes on the locomotor performance and sand-burying performance of P. mystaceus. The results showed that the maximum sprint speed and acceleration on sand substrate did not significantly differ under different conditions (P > 0.05). Sand-burying performance scores of the unresected individuals were significantly greater than those of the resected individuals (P < 0.05). A partial least squares (PLS) regression analysis showed that the relative area of toe fringe was the main factor affecting the sand-burying performance of unresected P. mystaceus. For lizards without fringe, the PLS regression showed that the swinging index of the hind-limb was the main factor affecting the sand-burying performance of the lizard. A comparison of the swinging indexes of the hind-limb of the lizard under three states revealed that under the unresected states, the frequency of the swinging of the hind-limb was significantly higher than those of lizards with resected bilateral fringes, further indicating that the lizards compensated for the loss of fringe by increasing the time and frequency of swinging of the hind-limb. A path analysis also showed that the fringe affected the sand-burying performance of P. mystaceus not only directly but also indirectly by affecting the frequency of the swinging of the hind-limb. After the bilateral toe fringe was removed, a significant negative correlation between locomotor and sand-burying performance was observed (P < 0.05). Taken together, these results provide experimental evidence that toe fringe is positively associated with the sand-burying performance of P. mystaceus.

Subchromosome-Scale Nuclear and Complete Mitochondrial Genome Characteristics of Morchella crassipes.

Morchella crassipes (Vent.) Pers., a typical yellow morel species with high economic value, is mainly distributed in the low altitude plains of Eurasia. However, rare research has been performed on its genomics and polarity, thus limiting its research and development. Here, we reported a fine physical map of the nuclear genome at the subchromosomal-scale and the complete mitochondrial genome of M. crassipes. The complete size of the nuclear genome was 56.7 Mb, and 23 scaffolds were assembled, with eight of them being complete chromosomes. A total of 11,565 encoding proteins were predicted. The divergence time analysis showed that M. crassipes representing yellow morels differentiated with black morels at ~33.98 Mya (million years), with 150 gene families contracted and expanded in M. crassipes versus the two black morels (M. snyderi and M. importuna). Furthermore, 409 CAZYme genes were annotated in M. crassipes, containing almost all plant cell wall degrading enzymes compared with the mycorrhizal fungi (truffles). Genomic annotation of mating type loci and amplification of the mating genes in the monospore population was conducted, the results indicated that M. crassipes is a heterothallic fungus. Additionally, a complete circular mitochondrial genome of M. crassipes was assembled, the size reached as large as 531,195 bp. It can be observed that the strikingly large size was the biggest up till now, coupled with 14 core conserved mitochondrial protein-coding genes, two rRNAs, 31 tRNAs, 51 introns, and 412 ncORFs. The total length of intron sequences accounted for 53.67% of the mitochondrial genome, with 19 introns having a length over 5 kb. Particularly, 221 of 412 ncORFs were distributed within 51 introns, and the total length of the ncORFs sequence accounted for 40.83% of the mitochondrial genome, and 297 ncORFs had expression activity in the mycelium stage, suggesting their potential functions in M. crassipes. Meanwhile, there was a high degree of repetition (51.31%) in the mitochondria of M. crassipes. Thus, the large number of introns, ncORFs and internal repeat sequences may contribute jointly to the largest fungal mitochondrial genome to date. The fine physical maps of nuclear genome and mitochondrial genome obtained in this study will open a new door for better understanding of the mysterious species of M. crassipes.

Bodily synchronization and ecological validity: a relevant concern for nonlinear dynamical systems theory.

Bodily synchronization and ecological validity: a relevant concern for nonlinear dynamical systems theory.

Prevalence of low back pain and associated occupational factors among Chinese coal miners

BackgroundVery few studies have evaluated the association between occupational factors and low back pain (LBP) among miners. The epidemiological data on LBP in Chinese miners are limited. The aim of this study was to measure the prevalence of low back pain in Chinese coal miners and to investigate the role of occupational factors.MethodsA cross-sectional survey was conducted to examine 1573 coal miners in northern China. The prevalence of LBP over a 12-month period was assessed using the Nordic Musculoskeletal Questionnaire. Odds ratios were calculated to examine the association between the prevalence of LBP over a 12-month period and occupational factors using logistic regression.ResultsAmong the coal miners, 64.9% self-reported LBP in a 12-month period. Occupational factors associated with LBP were identified, including tasks with a high degree of repetitiveness (OR 1.3, 95%CI 1.0-1.6), tasks characterized by a high level of physical demand (OR 1.4, 95% CI 1.1-1.8), posture requiring extreme bending (OR 1.6, 95% CI 1.2-1.7) and insufficient recovery time (OR 1.4, 95% CI 1.0-1.8).ConclusionLow back pain is common among Chinese miners. There were strong associations with occupational factors.

Prevalence of low back pain and associated occupational factors among Chinese coal miners

Very few studies have evaluated the association between occupational factors and low back pain (LBP) among miners. The epidemiological data on LBP in Chinese miners are limited. The aim of this study was to measure the prevalence of low back pain in Chinese coal miners and to investigate the role of occupational factors. A cross-sectional survey was conducted to examine 1573 coal miners in northern China. The prevalence of LBP over a 12-month period was assessed using the Nordic Musculoskeletal Questionnaire. Odds ratios were calculated to examine the association between the prevalence of LBP over a 12-month period and occupational factors using logistic regression. Among the coal miners, 64.9% self-reported LBP in a 12-month period. Occupational factors associated with LBP were identified, including tasks with a high degree of repetitiveness (OR 1.3, 95%CI 1.0-1.6), tasks characterized by a high level of physical demand (OR 1.4, 95% CI 1.1-1.8), posture requiring extreme bending (OR 1.6, 95% CI 1.2-1.7) and insufficient recovery time (OR 1.4, 95% CI 1.0-1.8). Low back pain is common among Chinese miners. There were strong associations with occupational factors.

Engineering of a polymeric bacterial protein as a scaffold for the multiple display of peptides.

Protein assemblies with a high degree of repetitiveness and organization are known to induce strong immune responses. For that reason they have been postulated for the design of subunit vaccines by means of protein engineering. The enzyme lumazine synthase from Brucella spp. (BLS) is highly immunogenic, presumably owing to its homodecameric arrangement and remarkable thermodynamic stability. Structural analysis has shown that it is possible to insert foreign peptides at the ten amino terminus of BLS without disrupting its general folding. These peptides would be displayed to the immune system in a highly symmetric three-dimensional array. In the present work, BLS has been used as a protein carrier of foreign peptides. We have established a modular system to produce chimeric proteins decorated with ten copies of a desired peptide as long as 27 residues and have shown that their folding and stability is similar to that of the wild-type protein. The knowledge about the mechanisms of dissociation and unfolding of BLS allowed the engineering of polyvalent chimeras displaying different predefined peptides on the same molecular scaffold. Moreover, the reassembly of mixtures of chimeras at different steps of the unfolding process was used to control the stoichiometry and spatial arrangement for the simultaneous display of different peptides on BLS. This strategy would be useful for vaccine development and other biomedical applications.

Work-related psychosocial, physical and individual factors associated with musculoskeletal symptoms in computer users

The aim of this study was to study associations between psychosocial, physical and individual factors, and musculoskeletal symptoms in the neck, shoulder and hand/wrist regions of computer users. Questionnaires were distributed to 5033 employees in 11 Danish companies; these employees all used computers for at least some of their work time. The response rate was 69% ( n = 3475). The analyses were based on employees working 32-41 h/week ( n = 2579). Symptomatic respondents reported symptoms for at least 8 days within the previous year. Multiple logistic regression analyses were used. Gender (female), age and duration of employment in the same job were associated with an increased prevalence of symptoms. High quantitative job demands and low possibilities for development at work were predictors of neck and hand/wrist symptoms. A high degree of repetitiveness and disturbing reflections on the computer screen were associated with symptoms in all three body regions. Repetitive movements were defined as the same finger, hand or arm movements performed many times per minute for at least 75% of their work time. Repetitiveness was the only factor that could partly explain associations between symptoms and duration of computer use, i.e. respondents who used the computer almost all the time at work reported more repetitive movements than those who used it less. Thus, long hours of computer use may be associated with musculoskeletal symptoms, due to physical factors such as repetitive movements, whereas psychosocial factors appeared to be associated with the symptoms independently of the duration of computer use.

Don Juan East/West: On the Problematics of Comparative Literature (review)

REVIEWS 1980s revision ofthe Purge in The War and in Jacques Derrida's defense ofPaul de Man following revelations concerning the latter's compromising contributions to the anti-Semitic and collaborationist Belgian daily Le Soir. In the final analysis Watts contends that, given its literary and historical repercussions, the Purge, perhaps more so than the Occupation itself, was the true guerrefranco-française, or Franco-French civil war. It is hard to find fault with a book as brilliantly conceived, beautifully written, and knowledgeable as Allegories ofthe Purge. It would perhaps have been interesting to see a lengthier discussion ofthe fascist "martyr" ofthe Purge, Robert Brasillach , something which, given Watts's erudition, would have been easily within his range. But the absence ofsuch a chapter in no way detracts from the argument or richness ofthe book, which clearly stands out, alongside Tony Judt's Past Imperfect , as one ofthe best and most accessible books written on postwar French culture and politics on either side ofthe Atlantic in the last ten years. For those interested in the complex relations between politics and literature in France and Europe as a whole in the wake ofWorld War II, Allegories ofthe Purge is indispensable. Richard J. GolsanTexasA&M University TAKAYUKI YOKOTA-MURAKAMI. Don Juan East/West: On the Problematics ofComparative Literature. Albany: SUNY Press, 1998. 226 pp. Takayuki Yokota-Murakami's book, Don Juan East/West: On the Problematics of Comparative Literature, is intended as a critique ofthe foundations ofcomparative literature, particularly the "American school" with its emphasis on aesthetic theory and a methodology based on the "anti-historicist 'metaphysics' " ofa transcivilizational , universal, and essential human nature (11). Such a critique is no surprise in the cultural studies landscape oftoday, nor is the persistent protest against colonialism , Western hegemonic thought which equates Western values with universal givens, or a "comparativism" that privileges identity over difference. The first chapter ("Problematizing Comparative Literature") and the last ("Politics ofComparative Literature") address this issue at great—too great—length and with a high degree ofrepetitiveness, which is more bothersome than the often stridently polemical style. With the focus on anti-Eurocentrism, some interesting points receive only passing and unfocused attention. Ofparticular importance for today's translated culture is Yokota-Murakami's problematization oftranslation, but the briefdiscussion (73f.) is cut short and leads yet again to a polemic against Eurocentrism (78). Similarly shortcut are reflections on genre issues, such as the (Eastern) novel versus the (Western) romance, or the (Western) saga versus the (Eastern) myth or legend (169ff.). Most bothersome, however, is the ahistorical perspective on (Western) comparative scholarship and literary theory in general. Yokota-Murakami's major authority on Don Juan, Gendarme de Bévotte, whose study appeared in 1906, is quoted and attacked as ifhe were our contemporary. Reflections on the seemingly endless "crisis of comparative literature" from René Etiemble (1963) to Claudio Guillen (1993) are presented without regard to the vastly different historical context and the changes within comparative scholarship over the last thirty-some years. YokotaMurakami 's representatives ofcomparative literary theory are Wellek and Warren, referenced in the bibliography in a 1985 edition, yet the first edition appeared in Vol. 24 (2000): 176 ??? COHPAnATIST 1942—more than halfa century ago. A large part ofthis book, then, is devoted to fighting old battles again, deconstructing structuralism in linguistics and literary criticism with the aid of old battle-axes such as Derrida and Foucault. The ahistorical approach is more than a bother, it is an unforgivable sin for a study based on the premise of historicity, or rather the chronotopicality of cultural and literary phenomena. If love, sexuality, and thus Don Juanism are historical constructs, as chapters 2 to 4 argue, then so are hermeneutic practices and literary theories. The discussions oftheory in chapters 1 and 5 yield the pre-established result that if there is a Don Juan West, then there cannot be a Don Juan East. The Don Juan (West) scholar will nevertheless find matters of interest in the details ofthe overall argument, i.e., in the exploration of "Don Juanism" from an outsider's perspective. Food for thought is offered in the deconstruction ofthe "transcendental signified(s)" (23) love and sexuality and in the presentation ofboth...

Calculation of symmetric multimer structures from NMR data using a priori knowledge of the monomer structure, co-monomer restraints, and interface mapping: The case of leucine zippers

NMR studies of symmetric multimers are problematic due to the difficulty in distinguishing between intra-, inter-, and co-monomer (mixed) NOE signals. Previously, one of us described a general calculation strategy called dynamic assignment by which this difficulty can be overcome [Nilges, M. (1993) Proteins, 17, 297-309]. Here we describe extensions to the method for handling many co-monomer NOEs and for taking advantege of prior knowledge of monomer structures. The new protocol was developed for the particularly difficult case of leucine zipper (LZ) homodimers, for which the previous protocol proved inefficient. In addition to the problem of dimer symmetry, LZs have a particularly high proportion of co-monomer NOE signals and a high degree of repetition in sequence and structure, leading to significant spectral overlap. Furthermore, the leucine zipper is a rather extended (as opposed to globular) protein domain; accurately determining such a structure based only on the very short distances obtainable by NMR is clearly a challenge to the NMR structure determination method. We have previously shown that, for LZ homodimers, many of the backbone-backbone NOESY cross peaks can be unambiguously assigned as intra-monomer, enabling approximate monomer structures to be calculated. Using model and experimental data sets, we verified that the new protocol converges to the correct dimer structure. The results show that short-range NMR distance data can be sufficient to define accurately the extended LZ. The protocol has been used to derive a novel solution structure of the c-Jun LZ domain. Based on these calculations, we propose the protocol as a prototype for the general case of symmetric multimers where the monomer structure is known.

Analysis of ultradian heat production and aortic core temperature rhythms in the rat.

The rhythms of aortic core temperature and overall heat production in Wistar rats was analyzed by using long series of recordings of temperature obtained from implanted thermocouple probes and heat release values from a chamber calorimeter. There was a very high degree of repetitiveness in the presentation of actual heat rhythms, with high cross-correlation values ascertained wit paired periodograms. No differences were observed between heat production between male and female adult rats. The cross-correlation for temperature gave similar figures. The cross-correlation study between heat production and aortic core temperature in the same animals was significant and showed a displacement of about 30 minutes between heat release and aortic core temperature. The analysis of heat production showed a strong predominance of rhythms with periods of 24 hours (frequencies < 11.6 microHz) or more; other rhythms detected (of roughly the same relative importance) had periods of 8 or 2.2 hours (35 or 126 microHz, respectively). The analysis of aortic core temperature showed a smaller quantitative contribution of the 8 or 2.2 hours (35 or 126 microHz) rhythms, with other harmonic rhythms interspersed (5.1 and 4.0 hours, i.e. 54 and 69 microHz). The proportion of 'noise' or cycles lower than 30 minutes (< 550 microHz) was higher in internal temperature than in the actual release of heat. The results are in agreement with the existence of a basic period of about 130 minutes (126 microHz) of warming/cooling of the blood, with a number of other harmonic rhythms superimposed upon the basic circadian rhythm.

The occurrence of carpal tunnel syndrome in frozen food factory employees.

Two hundred and seven (207) active workers from two frozen food plants were classified according to their daily tasks and placed into three groups. Each classification was evaluated for risk factors which could lead to Carpal Tunnel Syndrome (CTS). The workers were thoroughly studied by structured interviews, neurological screening, and electrophysiological studies. Those workers who experienced little hands' local exposure to cold and low repetitive movements of the wrist (group I) served as the internal standard. In groups II (no local exposure to cold, but a high degree of repetitiveness) and III (a combination of local exposure to cold and a high degree of repetitiveness) 40.54% and 37.19%, of the workers respectively were diagnosed to have CTS by neurological studies. The risk of CTS for group II + III was 14.39 times higher than that of group I, when group I was compared with group II + III (high repetitiveness). After adjusted for sex, age, and/or the length of employment, group III still had a higher risk of CTS than group II. Repetitiveness as well as hands' local exposure to cold were found to be contributing factors in leading to CTS. Recognition, evaluation, and management of CTS in the related industries in Taiwan should be initiated to assure early diagnosis and prevention of this occupationally related syndrome.

The stress debate: symptom of impending synthesis?

Opposition to use of the word ‘stress’ and other terms of wide ambit in ecology and evolutionary biology often signifies a commitment to programmes of detailed research and narrowed focus. This approach is justified where the objective is to analyse the demographic, genetic or biochemical mechanisms of contemporary populations. However, concepts employing ‘stress’ are vital to those forms of research that seek to obtain a broader perspective by recognizing ecological and evolutionary patterns with a high degree of repetition (sensu MacArthur, 1968 in R. C. Lewontin, Population Biology & Evolution). It is argued that there are recurrent types of evolutionary response to stress and that these provide important clues to the structure and dynamics of communities and ecosystems. Such patterns can assist our understanding of phenomena as widely divergent as the decline or expansion of populations within the British flora and fauna and the persistence of radionuclides in unproductive terrestrial ecosystems.

A recursive finite element technique for acoustic fields in pipes with absorption

Finite element models of acoustic fields in lined pipes and ducts involve the simultaneous use of different material models as well as a high degree of repetition. Full continuity between the different materials is obtained by an appropriately scaled Galerkin procedure. Pipe sections are handled efficiently by partitioning into 2 m segments. These sections are then solved locally by a special elimination procedure, in which the pipe length is doubled in m steps. The method is illustrated by application to the individual parts of mufflers. Examples demonstrate the computational efficiency and show good agreement with experimental results.