Sequence S1 Research Articles

Selecting vertex disjoint paths in plane graphs

We study variants of the vertex disjoint paths problem in plane graphs where paths have to be selected from given sets of paths. We investigate the problem as a decision, maximization, and routing-in-rounds problem. Although all considered variants are NP-hard in planar graphs, restrictions on the locations of the terminals on the outer face of the given planar embedding of the graph lead to polynomially solvable cases for the decision and maximization versions of the problem. For the routing-in-rounds problem, we obtain a p-approximation algorithm, where p is the maximum number of alternative paths for a terminal pair, when restricting the locations of the terminals to the outer face such that they appear in a counterclockwise traversal of the boundary as a sequence s1,s2,',sk,tπ1,tπ2,',tπk for some permutation π. © 2015 Wiley Periodicals, Inc.NETWORKS, Vol. 662, 136-144 2015

A note on the longest common substring with k-mismatches problem

The recently introduced longest common substring with k-mismatches (k-LCF) problem is to find, given two sequences S1 and S2 of length n each, a longest substring A1 of S1 and A2 of S2 such that the Hamming distance between A1 and A2 is at most k. So far, the only subquadratic time result for this problem was known for k=1[5]. We present two output-dependent algorithms solving the k-LCF problem and show that for k=O(log1−ε⁡n), where ε>0, at least one of them works in subquadratic time, using O(n) words of space. The choice of one of these two algorithms to be applied for a given input can be done after linear time and space preprocessing.

Sulfono-γ-AApeptides as a new class of nonnatural helical foldamer.

Foldamers offer an attractive opportunity for the design of novel molecules that mimic the structures and functions of proteins and enzymes including biocatalysis and biomolecular recognition. Herein we report a new class of nonnatural helical sulfono-γ-AApeptide foldamers of varying lengths. The crystal structure of the sulfono-γ-AApeptide monomer S6 illustrates the intrinsic folding propensity of sulfono-γ-AApeptides, which likely originates from the bulkiness of tertiary sulfonamide moiety. The two-dimensional solution NMR spectroscopy data for the longest sequence S1 demonstrates a 10/16 right-handed helical structure. Optical analysis using circular dichroism further supports well- defined helical conformation of sulfono-γ-AApeptides in solution containing as few as five building blocks. Future development of sulfono-γ-AApeptides may lead to new foldamers with discrete functions, enabling expanded application in chemical biology and biomedical sciences.

Sequence stratigraphy and paleogeography of the Middle Jurassic coal measures in the Yuqia coalfield, northern Qaidam Basin, northwestern China

Detailed stratigraphic and paleogeographic analyses of data from 72 boreholes for the Middle Jurassic intermontane fluvial-lacustrine coal-bearing sequences were conducted in the Yuqia coalfield of the northern Qaidam Basin, northwestern China. Three third-order sequences lasting in total ca. 10.6 m.y., and an internal lowstand systems tract (LST), transgressive systems tract (TST), highstand systems tract (HST), and falling-stage systems tract (FSST) have been identified. A series of sequence-specific paleogeographic maps have been constructed based on the contours of lithological parameters. The paleogeographic units include alluvial fan-braided (meandering) fluvial plain, upper delta plain, lower delta plain, subaqueous delta, shore-shallow lake, and deep lake. The preferred sites of coal accumulation are interdelta bays, upper delta plains, lower delta plains, and fluvial back swamps. The sequence stratigraphic and sedimentological analysis of the Middle Jurassic coal-bearing measures of the Yuqia coalfield provides a basis for a comprehensive coal accumulation model that involves a six-period evolution from the LST, early TST, late TST, early HST, late HST to FSST. The major coal seams were accumulated in the early and late TST of the sequences S1 and S2. These results are of practical significance for coal resources exploration and enhance geological effects of prospecting engineering in the northern Qaidam Basin.

Morphology Control and Stabilization in Immiscible Polypropylene and Polyamide 6 Blends with Organoclay

Abstract In the current study, 70/30 (w/w) polypropylene (PP)/polyamide 6 (PA6)/organoclay ternary blends were prepared by melt mixing in three different blending sequences, i. e., organoclay premixed with PA6 and then mixed with PP (S1 blending sequence), organoclay premixed with PP and then mixed with PA6 (S2 blending sequence), and organoclay, PA6 and PP mixed simultaneously (S3 blending sequence). The effects of organoclay on the phase morphologies, rheological properties and mechanical properties of the blends are examined to reveal the role of organoclay in these immiscible blends. First of all, the dispersion and distribution of organoclay is investigated using XRD and TEM techniques. The organoclay is exfoliated and distributed in the dispersed PA6 phase as well as at the interface between PA6 and PP. Interestingly, more organoclay sheets are observed at the interface when the S2 or S3 blending sequences are utilized. From the SEM images, it is clear that the domain size of the PA6 phase decreases remarkably after introducing organoclay into the PP/PA6 blends. Two different rheological protocols are applied to probe the effect of organoclay on the morphology of the blend by in-situ monitoring the morphological evolution. The rheological results reveal that the phase morphology of the PP/PA6 blends remains relatively stable during shear for a wide range of shear rates when 1.0 wt% organoclay has been added. For the blends with a relatively high clay loading (5.0 wt%), a characteristic and pronounced “plateau” is observed in the low frequency range of the G′-ω curves, which indicates the presence of a percolating network of clay nanosheets. From the mechanical measurements, we find that the tensile strength of the blends increases slightly first and then declines dramatically with increasing organoclay content. Moreover, the elongation at break drops sharply as the organoclay content increases. In summary, it is clear that the organoclay can effectively reduce the domain size of the dispersed PA6 phase and stabilize the phase morphology in shear flow. However, the mechanical properties of the blends are not really improved by clay addition, even though a cocontinuous morphology with a percolated clay network was generated.

Efficient heart sound segmentation and extraction using ensemble empirical mode decomposition and kurtosis features.

An efficient heart sound segmentation (HSS) method that automatically detects the location of first ( S1) and second ( S2) heart sound and extracts them from heart auscultatory raw data is presented here. The heart phonocardiogram is analyzed by employing ensemble empirical mode decomposition (EEMD) combined with kurtosis features to locate the presence of S1, S2, and extract them from the recorded data, forming the proposed HSS scheme, namely HSS-EEMD/K. Its performance is evaluated on an experimental dataset of 43 heart sound recordings performed in a real clinical environment, drawn from 11 normal subjects, 16 patients with aortic stenosis, and 16 ones with mitral regurgitation of different degrees of severity, producing 2608 S1 and S2 sequences without and with murmurs, respectively. Experimental results have shown that, overall, the HSS-EEMD/K approach determines the heart sound locations in a percentage of 94.56% and segments heart cycles correctly for the 83.05% of the cases. Moreover, results from a noise stress test with additive Gaussian noise and respiratory noises justify the noise robustness of the HSS-EEMD/K. When compared with four other efficient methods that mainly employ wavelet transform, energy, simplicity, and frequency measures, respectively, using the same experimental database, the HSS-EEMD/K scheme exhibits increased accuracy and prediction power over all others at the level of 7-19% and 4-9%, respectively, both in controls and pathological cases. The promising performance of the HSS-EEMD/K paves the way for further exploitation of the diagnostic value of heart sounds in everyday clinical practice.

Physical modelling of large-scale deformational systems in the South Polar Layered Deposits (Promethei Lingula, Mars): new geological constraints and climatic implications

Abstract Deformation systems (DSs) locally affect the South Polar Layered Deposits (SPLDs) along the margins of the Promethei Lingula ice sheet (part of the southern Martian ice-dome). One example is the ‘S 2 ’ deformation system, characterized by a complex pattern of brittle and brittle–ductile structures related to kilometre-scale shear zones that deform the sequence. Moreover, soft-sediment structures affect one layer located at the base of the S 2 . An earlier structural analysis suggested that: (1) two deformation stages (D 1 , in which the shear zones developed, and D 2 , in which the D 1 structures were reactivated by deep-seated gravitational slope deformation) occurred, driven by gravity; and (2) there are variations in the bulk composition of the SPLD (which is inferred to be mainly composed of water ice plus basaltic dust). This work supports these structural results through thermal and mechanical modelling of the S 2 sequence. Our modelling results suggest that several layers within the S 2 system are probably composed of, or are mixed with, CO 2 ice, and that the development of the observed deformation is inconsistent with present-day physical conditions. Soft-sediment structures probably formed under warmer surface temperatures during the past, with those warmer temperatures favouring or even triggering ice flow/basal sliding of the Promethei Lingula. Supplementary material: The complete description of the stratigraphy of the analysed S 2 sequence (in table format) is available at http://www.geolsoc.org.uk/SUP18746 .

Techniques for Understanding User Usage Behavior on the Internet

Techniques for Understanding User Usage Behavior on the Internet

Phylogenetic Evidence of Long Distance Dispersal and Transmission of Piscine Reovirus (PRV) between Farmed and Wild Atlantic Salmon

The extent and effect of disease interaction and pathogen exchange between wild and farmed fish populations is an ongoing debate and an area of research that is difficult to explore. The objective of this study was to investigate pathogen transmission between farmed and wild Atlantic salmon (Salmo salar L.) populations in Norway by means of molecular epidemiology. Piscine reovirus (PRV) was selected as the model organism as it is widely distributed in both farmed and wild Atlantic salmon in Norway, and because infection not necessarily will lead to mortality through development of disease. A matrix comprised of PRV protein coding sequences S1, S2 and S4 from wild, hatchery-reared and farmed Atlantic salmon in addition to one sea-trout (Salmo trutta L.) was examined. Phylogenetic analyses based on maximum likelihood and Bayesian inference indicate long distance transport of PRV and exchange of virus between populations. The results are discussed in the context of Atlantic salmon ecology and the structure of the Norwegian salmon industry. We conclude that the lack of a geographical pattern in the phylogenetic trees is caused by extensive exchange of PRV. In addition, the detailed topography of the trees indicates long distance transportation of PRV. Through its size, structure and infection status, the Atlantic salmon farming industry has the capacity to play a central role in both long distance transportation and transmission of pathogens. Despite extensive migration, wild salmon probably play a minor role as they are fewer in numbers, appear at lower densities and are less likely to be infected. An open question is the relationship between the PRV sequences found in marine fish and those originating from salmon.

English

A field experiment was conducted at Agronomy farm of Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar during 2008-2009 and 2009-10 on silty clay loam soil with neutral PH. The experiment comprising of three factors viz., cropping sequences S1 , S2, S3 and S4, three farm yard manure (FYM) rates R1 , R2 and R3 and three frequencies F1, F2 and F3 was laid out in a split plot design (cropping sequences in main plot and FYM rates and frequencies in sub plot) replicated thrice. The results showed that during 2009-10, the cropping sequences S1 and S4 recorded significantly higher growth characters, yield attributes and yield of maize than S2 and S3. the FYM rates increased the growth characters up to 30t ha⁻¹ and yield attributes up to 20t ha⁻¹. the grain yield of maize showed significant improvement with FYM application up to 20t ha⁻¹ while stover yield increased significantly up to 30 t ha⁻¹ FYM frequencies F1 and F2 recorded significantly higher growth characters, yield attributes and grain and stover yield of maize over F3. Highest net returns and benefit cost ratio were realized from the treatment combination S2R1F1. Key words: Maize, cropping sequence, farm yard manure (FYM), frequency

Improved Three-Party Quantum Secret Sharing Based on Bell States

Hwang et al. (Phys. Scr. 83:045004, 2011) proposed a high efficient multiparty quantum secret sharing by using Greenberger-Horne-Zeilinger (GHZ) states. But Liu et al. (Phys. Scr. 84:045015, 2011) analyzed the security of Hwang et al.’s protocol and found that it was insecure for Charlie who might obtain half of information about the dealer’s secret directly. They put forward an improved protocol by adding operation on photons in sequence S3. However, we point out Liu et al.’s protocol is not secure too if a dishonest participant Charlie carries out intercept-resend attack. And a further improved quantum secret sharing protocol is proposed based on Bell states in this paper. Our newly proposed protocol can stand against participant attack, provide a higher efficiency in transmission and reduce the complexity of implementation.

A hybrid method for the exact planted (l, d) motif finding problem and its parallelization

BackgroundGiven a set of DNA sequences s1, ..., st, the (l, d) motif problem is to find an l-length motif sequence M , not necessary existing in any of the input sequences, such that for each sequence si, 1 ≤ i ≤ t, there is at least one subsequence differing with at most d mismatches from M. Many exact algorithms have been developed to solve the motif finding problem in the last three decades. However, the problem is still challenging and its solution is limited to small values of l and d.ResultsIn this paper we present a new efficient method to improve the performance of the exact algorithms for the motif finding problem. Our method is composed of two main steps: First, we process q ≤ t sequences to find candidate motifs. Second, the candidate motifs are searched in the remaining sequences. For both steps, we use the best available algorithms. Our method is a hybrid one, because it integrates currently existing algorithms to achieve the best running time. In this paper, we show how the optimal value of q is determined to achieve the best running time. Our experimental results show that there is about 24% speed-up achieved by our method compared to the best existing algorithm. Furthermore, we also present a parallel version of our method running on shared memory architecture. Our experiments show that the performance of our algorithm scales linearly with the number of processors. Using the parallel version, we were able to solve the (21, 8) challenging instance using 8 processors in 20.42 hours instead of 6.68 days of the serial version.ConclusionsOur method speeds up the solution of the exact motif problem. Our method is generic, because it can accommodate any new faster algorithm based on traditional methods. We expect that our method will help to discover longer motifs. The software we developed is available for free for academic research at http://www.nubios.nileu.edu.eg/tools/hymotif.

A baculovirus isolated from wild silkworm encompasses the host ranges of Bombyx mori nucleopolyhedrosis virus and Autographa californica multiple nucleopolyhedrovirus in cultured cells

A baculovirus, named BomaNPV S2, was isolated from a diseased larva of the wild silkworm, Bombyx mandarina. Notably, BomaNPV S2 exhibited a distinguishing feature in that its host range covered that of both Bombyx mori nucleopolyhedrosis virus (BmNPV) and Autographa californica multiple nucleopolyhedrovirus (AcMNPV) in cultured cells. It could replicate in cells of B. mori (Bm5 and BmN), Spodoptera frugiperda (Sf9) and Trichoplusia ni (Tn-5B1-4). However, occlusion-derived virions of BomaNPV S2 in B. mori cells contained only a single nucleocapsid, whereas they contained multiple nucleocapsids in Tn-5B1-4 cells. The complete genome sequence of BomaNPV S2, including predicted ORFs, was determined and compared with the genome sequence of its close relatives. The comparison results showed that most of the BomaNPV S2 genome sequence was shared with BmNPV (BmNPV T3) or BomaNPV S1, but several regions seemed more similar to regions of AcMNPV. This observation might explain why BomaNPV S2 covers the host ranges of BmNPV and AcMNPV. Further recombinant virus infection experiments demonstrated that GP64 plays an important role in BomaNPV S2 host-range determination.

Sedimentology, palaeoenvironments and biostratigraphy of the Pliocene–Pleistocene carbonate platform of Grande‐Terre (Guadeloupe, Lesser Antilles forearc)

AbstractPliocene and Pleistocene deposits from Grande‐Terre (Guadeloupe archipelago, French Lesser Antilles) provide a remarkable example of an isolated carbonate system built in an active margin setting, with sedimentation controlled by both rapid sea‐level changes and tectonic movements. Based on new field, sedimentological and palaeontological analyses, these deposits have been organized into four sedimentary sequences (S1 to S4) separated by three subaerial erosion surfaces (SB0, SB1 and SB2). Sequences S1 and S2 (‘Calcaires inférieurs à rhodolithes’) deposited during the Late Zanclean to Early Gelasian (planktonic foraminiferal Zones PL2 to PL5) in low subsidence conditions, on a distally steepened ramp dipping eastward. Red algal‐rich deposits, which dominate the western part of Grande‐Terre, change to planktonic foraminifer‐rich deposits eastward. Vertical movements of tens of metres were responsible for the formation of SB0 and SB1. Sequence S3 (‘Formation volcano‐sédimentaire’, ‘Calcaires supérieurs à rhodolithes’ and ‘Calcaires à Agaricia’) was deposited during the Late Piacenzian to Early Calabrian (Zones PL5 to PT1a) on a distally steepened, red algal‐dominated ramp that changes upward into a homoclinal, coral‐dominated ramp. Deposition of Sequence S3 occurred during a eustatic cycle in quiet tectonic conditions. Its uppermost boundary, the major erosion surface SB2, is related to the Cala1 eustatic sea‐level fall. Finally, Sequence S4 (‘Calcaires à Acropora’) probably formed during the Calabrian, developing as a coral‐dominated platform during a eustatic cycle in quiet tectonic conditions. The final emergence of the island could then have occurred in Late Calabrian times.

Duration problem with multiple exchanges

We treat a version of the multiple-choice secretary problem called the multiple-choice duration problem, in which the objective is to maximize the time of possession of relatively best objects. It is shown that, for the $m$--choice duration problem, there exists a sequence (s1,s2,...,sm) of critical numbers such that, whenever there remain k choices yet to be made, then the optimal strategy immediately selects a relatively best object if it appears at or after time $s_k$ ($1\leq k\leq m$). We also exhibit an equivalence between the duration problem and the classical best-choice secretary problem. A simple recursive formula is given for calculating the critical numbers when the number of objects tends to infinity. Extensions are made to models involving an acquisition or replacement cost.

New approach to nonrepetitive sequences

AbstractA sequence is nonrepetitive if it does not contain two adjacent identical blocks. The remarkable construction of Thue asserts that three symbols are enough to build an arbitrarily long nonrepetitive sequence. It is still not settled whether the following extension holds: for every sequence of three‐element sets L1,…,Ln there exists a nonrepetitive sequence s1,…,sn with si∈Li. We propose a new non‐constructive way to build long nonrepetitive sequences and provide an elementary proof that sets of size 4 suffice confirming the best known bound. The simple double counting in the heart of the argument is inspired by the recent algorithmic proof of the Lovász local lemma due to Moser and Tardos. Furthermore we apply this approach and present game‐theoretic type results on nonrepetitive sequences. Nonrepetitive game is played by two players who pick, one by one, consecutive terms of a sequence over a given set of symbols. The first player tries to avoid repetitions, while the second player, in contrast, wants to create them. Of course, by simple imitation, the second player can force lots of repetitions of size 1. However, as proved by Pegden, there is a strategy for the first player to build an arbitrarily long sequence over 37 symbols with no repetitions of size greater than 1. Our techniques allow to reduce 37–6. Another game we consider is the erase‐repetition game. Here, whenever a repetition occurs, the repeated block is immediately erased and the next player to move continues the play. We prove that there is a strategy for the first player to build an arbitrarily long nonrepetitive sequence over 8 symbols. © 2012 Wiley Periodicals, Inc. Random Struct. Alg., 2012

Multiple activities of RNA-binding proteins S1 and Hfq

In all organisms, RNA-binding proteins participate in modulating all the steps in the life cycle of RNA, including transcription, folding, translation and turnover. In bacteria, RNA-binding proteins may be specific for a few RNA targets (e.g., several ribosomal proteins that recognize both rRNA during ribosome assembly and their own mRNAs when acting as highly specific autogenous repressors) or function as global regulators implicated in numerous regulatory networks. Some RNA-binding proteins combine all these features, and this particularly concerns the ribosomal protein S1 and the Sm-like protein Hfq. S1 is a key mRNA-binding protein in gram-negative bacteria; it recognizes mRNA leaders and provides binding of diverse mRNAs to the ribosome at the initiation step of translation. Moreover, S1 is a highly specific autogenous repressor that is able to distinguish its own mRNA from all the others. Hfq is recognized as a global regulator that facilitates small RNA-mRNA interactions in bacteria; it thereby controls the expression of many mRNAs either positively or negatively. In addition, these two proteins were reported to affect transcription, RNA degradation and other processes. Although they have no sequence specificity, Hfq and S1 preferentially bind A/U-rich single-stranded RNA regions; despite this, they nevertheless carry out very different tasks in the cell. This review is focused on the diversity of functions that can be performed by these abundant RNA-binding bacterial proteins.

Rewriting the fossil history of Cerionidae (Gastropoda: Pulmonata): new family assignment of the Brazilian Palaeocene genus Brasilennea Maury, 1935

The limestone formation of the Itaborai Basin at Sao Jose de Itaborai, Rio de Janeiro, Brazil, harbours a rich fauna of wellpreserved terrestrial pulmonates: 18 species have been described to date, mainly in Bulimulidae/Orthalicidae (Simone & Mezzalira, 1994). Following mammal correlations, the Itaborai limestones are now agreed to be of Palaeocene age (e.g. Paula Couto, 1952; Medeiros & Bergqvist, 1999) and, more precisely, the pulmonate fauna to be of Middle to Late Palaeocene age, although influential past malacological works have listed its pulmonate taxa as Miocene or Pliocene (e.g. Zilch, 1959–1960; Parodiz, 1969). Itaborai’s fossils are a valuable tool for studying the evolution of South American taxa due to their early Cenozoic age and the basin location. The genus Brasilennea Maury, 1935 is known only from the Itaborai basin. The type species (by original designation) is B. arethusae Maury, 1935, with B. minor Trindade, 1956 at first considered a variation, now considered a second sympatric species (Brito, 1967). A third Brasilennea species was recently found in museum collections (Salvador & Simone, unpubl.). Brasilennea was assigned to Streptaxidae subfamily Enneinae (1⁄4Ptychotrematinae) of the mainly Old World Streptaxoidea (Maury, 1935) on the basis of similarities with the African genus Ptychotrema Pfeiffer, 1853, in particular its subgenus Ennea Adams & Adams, 1855. This streptaxid allocation has been followed by all subsequent workers on the Itaborai fauna. Brasilennea remains the only fossil New World Enneinae streptaxid and there are no known Recent New World Enneinae (Rowson, 2010). The phylogenetic analysis of Rowson, Tattersfield & Symondson (2010) found that extant South American streptaxids belong to Streptaxinae, unrelated to genera in Enneinae, a result also supported by morphology (Rowson, 2010). They considered Brasilennea to be a Miocene genus (following Parodiz, 1969) that may have dispersed from Africa, but noted that several Cretaceous and early Cenozoic ‘streptaxid’ fossils have been shown to belong to other families (Nordsieck, 1986). As Brasilennea is distant in space and time from other Enneinae streptaxids its family assignment should be carefully examined. To do so we reviewed all existing literature on Brasilennea and examined type and abundant material from Itaborai of both species in the following museums: American Museum of Natural History, New York, USA (AMNH); Museu de Ciencias da Terra, Rio de Janeiro, Brazil (DGM); Museu Nacional, Rio de Janeiro, Brazil (MNRJ); Museu de Zoologia, Sao Paulo, Brazil (MZSP). Comparisons were made with material of extant Cerionidae and Streptaxidae taxa at MZSP and the National Museum of Wales, Cardiff, UK (NMW). The material of Brasilennea examined included: B. arethusae: AMNH 24237–24239 (holotype and 2 paratypes); DGM 4222, 4998, 5002, unregistered (18 specimens); MNRJ 3346, 3348, 4338 (9 specimens); MZSP 86321, 86322, 86324 (25 specimens). B. minor: DGM 4224 (holotype), 4999, unregistered (12 specimens); MNRJ 3346, 4338 (3 specimens); MZSP 86323 (2 specimens). The genus Brasilennea (Fig. 1A–L) is characterized as follows. Shell dextral, pupiform (cylindrical, multispiral, narrowing in both extremities, with acuminate apex), greatest width near central portion; triphasic (sensu Gould, 1989). Whorls slightly convex. Columella hollow in early whorls at least. Sutures well marked and linear, nearly perpendicular to columellar axis. Sculptured by regularly distributed, fine, raised ribs, becoming less oblique towards aperture; first two to three whorls unsculptured. Body whorl with two well-marked spiral furrows. Large ovate aperture, with rounded outer lip and straight inner lip. Peristome complete, upper lip virtually straight, doubled. Nearly median, single, strong parietal tooth/lamella reaching peristome. Columellar spiral lamella present. The genus remains known only from the type locality and stratum: Itaborai Basin, facies of grey limestone: Facies B in sequence S1 (Middle to Late Paleocene) sensu Medeiros & Bergqvist (1999). Our study leads us to argue that Brasilennea should be transferred to Cerionidae in Urocoptoidea, a revision with biogeographic and evolutionary implications [Streptaxoidea and Urocoptoidea (represented by Cerion) are very distantly related; Wade,Mordan,&Naggs, 2006]. AlthoughBrasilennea is not identical to any fossil or Recent taxon, it shows several features common inCerionidae but not Streptaxidae (we restrict ourselves to Enneinae and other pupiform streptaxids). The considerable shell thickness, sculpture, triphasic shape, acuminate apex and large number of whorls are features common among cerionids (Fig. 1M, N) and larger urocoptids, but uncommon or rare among streptaxids. The doubled peristome is very common among cerionids, but almost unknown in streptaxids (apparently present only in the tiny Gulella kimbozae Verdcourt, 2004 from Tanzania). The virtually straight parietal edge of the peristome

AN ALGORITHM AND APPLICATIONS TO SEQUENCE ALIGNMENT WITH WEIGHTED CONSTRAINTS

Given two sequences S1, S2, and a constrained sequence C, a longest common subsequence of S1, S2 with restriction to C is called a constrained longest common subsequence of S1 and S2 with C. At the same time, an optimal alignment of S1, S2 with restriction to C is called a constrained pairwise sequence alignment of S1 and S2 with C. Previous algorithms have shown that the constrained longest common subsequence problem is a special case of the constrained pairwise sequence alignment problem, and that both of them can be solved in O(rnm) time, where r, n, and m represent the lengths of C, S1, and S2, respectively. In this paper, we extend the definition of constrained pairwise sequence alignment to a more flexible version, called weighted constrained pairwise sequence alignment, in which some constraints might be ignored. We first give an O(rnm)-time algorithm for solving the weighted constrained pairwise sequence alignment problem, then show that our extension can be adopted to solve some constraint-related problems that cannot be solved by previous algorithms for the constrained longest common subsequence problem or the constrained pairwise sequence alignment problem. Therefore, in contrast to previous results, our extension is a new and suitable model for sequence analysis.

Translational Repression of Cyclin E Prevents Precocious Mitosis and Embryonic Gene Activation during C. elegans Meiosis

Germ cells, the cells that give rise to sperm and egg, maintain the potential to recreate all cell types in a new individual. This wide developmental potential, or totipotency, is manifested in unusual tumors called teratomas, in which germ cells undergo somatic differentiation. Although recent studies have implicated RNA regulation, the mechanism that normally prevents the loss of germ cell identity remains unexplained. In C. elegans, a teratoma is induced in the absence of the conserved RNA-binding protein GLD-1. Here, we demonstrate that GLD-1 represses translation of CYE-1/cyclin E during meiotic prophase, which prevents germ cells from re-entering mitosis and inducing embryonic-like transcription. We describe a mechanism that prevents precocious mitosis in germ cells undergoing meiosis, propose that this mechanism maintains germ cell identity by delaying the onset of embryonic gene activation until after fertilization, and provide a paradigm for the possible origin of human teratomas.