An endogenous retrovirus presumed to have been endogenized or relocated recently in a marsupial, the red-necked wallaby

An albino infant wallaby was born to a mother with the wild-type body color. PCR and sequencing analyses of <i>TYR</i> (encoding tyrosinase, which is essential for melanin biosynthesis) of this albino wallaby revealed a 7.1-kb-long DNA fragment inserted in the first exon. Because the fragment carried long terminal repeats, we assumed it to be a copy of an endogenous retrovirus, which we named <i>walb</i>. We cloned other <i>walb</i> copies residing in the genomes of this species and another wallaby species. The copies exhibited length variation, and the longest copy (>8.0 kb) contained open reading frames whose deduced amino acid sequences were well aligned with those of <i>gag</i>, <i>pol</i>, and <i>env</i> of retroviruses. It is not known through which of the following likely processes the walb copy was inserted into <i>TYR</i>: endogenization (infection of a germline cell by an exogenous virus), reinfection (infection by a virus produced from a previously endogenized provirus), or retrotransposition (intracellular relocation of a provirus). In any case, the insertion into <i>TYR</i> is considered to have been a recent event on an evolutionary timescale because albino mutant alleles generally do not persist for long because of their deleterious effects in wild circumstances.

A computational method for predicting nucleocapsid protein in retroviruses

Nucleocapsid protein (NC) in the group-specific antigen (gag) of retrovirus is essential in the interactions of most retroviral gag proteins with RNAs. Computational method to predict NCs would benefit subsequent structure analysis and functional study on them. However, no computational method to predict the exact locations of NCs in retroviruses has been proposed yet. The wide range of length variation of NCs also increases the difficulties. In this paper, a computational method to identify NCs in retroviruses is proposed. All available retrovirus sequences with NC annotations were collected from NCBI. Models based on random forest (RF) and weighted support vector machine (WSVM) were built to predict initiation and termination sites of NCs. Factor analysis scales of generalized amino acid information along with position weight matrix were utilized to generate the feature space. Homology based gene prediction methods were also compared and integrated to bring out better predicting performance. Candidate initiation and termination sites predicted were then combined and screened according to their intervals, decision values and alignment scores. All available gag sequences without NC annotations were scanned with the model to detect putative NCs. Geometric means of sensitivity and specificity generated from prediction of initiation and termination sites under fivefold cross-validation are 0.9900 and 0.9548 respectively. 90.91% of all the collected retrovirus sequences with NC annotations could be predicted totally correct by the model combining WSVM, RF and simple alignment. The composite model performs better than the simplex ones. 235 putative NCs in unannotated gags were detected by the model. Our prediction method performs well on NC recognition and could also be expanded to solve other gene prediction problems, especially those whose training samples have large length variations.

Mahonia vs. Berberis Unloaded: Generic Delimitation and Infrafamilial Classification of Berberidaceae Based on Plastid Phylogenomics

The early-diverging eudicot family Berberidaceae is composed of a morphologically diverse assemblage of disjunctly distributed genera long praised for their great horticultural and medicinal values. However, despite century-long studies, generic delimitation of Berberidaceae remains controversial and its tribal classification has never been formally proposed under a rigorous phylogenetic context. Currently, the number of accepted genera in Berberidaceae ranges consecutively from 13 to 19, depending on whether to define Berberis, Jeffersonia, and Podophyllum broadly, or to segregate these three genera further and recognize Alloberberis, Mahonia, and Moranothamnus, Plagiorhegma, and Dysosma, Diphylleia, and Sinopodophyllum, respectively. To resolve Berberidaceae’s taxonomic disputes, we newly assembled 23 plastomes and, together with 85 plastomes from the GenBank, completed the generic sampling of the family. With 4 problematic and 14 redundant plastome sequences excluded, robust phylogenomic relationships were reconstructed based on 93 plastomes representing all 19 genera of Berberidaceae and three outgroups. Maximum likelihood phylogenomic relationships corroborated with divergence time estimation support the recognition of three subfamilies Berberidoideae, Nandinoideae, and Podophylloideae, with tribes Berberideae and Ranzanieae, Leonticeae and Nandineae, and Podophylleae, Achlydeae, Bongardieae tr. nov., Epimedieae, and Jeffersonieae tr. nov. in the former three subfamilies, respectively. By applying specifically stated criteria, our phylogenomic data also support the classification of 19 genera, recognizing Alloberberis, Mahonia, and Moranothamnus, Plagiorhegma, and Diphylleia, Dysosma, and Sinopodophyllum that are morphologically and evolutionarily distinct from Berberis, Jeffersonia, and Podophyllum, respectively. Comparison of plastome structures across Berberidaceae confirms inverted repeat expansion in the tribe Berberideae and reveals substantial length variation in accD gene caused by repeated sequences in Berberidoideae. Comparison of plastome tree with previous studies and nuclear ribosomal DNA (nrDNA) phylogeny also reveals considerable conflicts at different phylogenetic levels, suggesting that incomplete lineage sorting and/or hybridization had occurred throughout the evolutionary history of Berberidaceae and that Alloberberis and Moranothamnus could have resulted from reciprocal hybridization between Berberis and Mahonia in ancient times prior to the radiations of the latter two genera.

Derivation of Yarn Package Radius Measuring System for Yarn Winding Machines

Decreasing waste materials through recycle has in the recent contributed to sustainable manufacturing in many textile industries for better resource utilization in textile mills. This has been given first priority in manufacturing, processing and finishing operations. Most of the time the yarn manufacturing and proper utilization of this material didn’t give attention in most companies. Especially yarn length variation of packages, weaving beams and copes have very critical impact on those companies which manufacture and utilize yarn products. This variation problem has great impact on their productivity and profitability. This paper describes the application of a new formula in the yarn packaging process and it is accomplished by derivation a new formula that can determine the radius of any package. The formula has integrated the basic characteristics of yarn and fiber including yarn diameter, yarn/ fiber density and mass of the yarn coiled on the cop. Finally we have concluded that package radius is the quadratic function of yarn density and package mass on the cope.

Syntactic complexity in Finnish-background EFL learners’ writing at CEFR levels A1–B2

The increasing importance of the Common European Framework of Reference (CEFR) has led to research on the linguistic characteristics of its levels, as this would help the application of the CEFR in the design of teaching materials, courses, and assessments. This study investigated whether CEFR levels can be distinguished with reference to syntactic complexity (SC). 14- and 17-year-old Finnish learners of English (N=397) wrote three writing tasks which were rated against the CEFR levels. The ratings were analysed with multi-facet Rasch analysis and the texts were analysed with automated tools. Findings suggest that the clearest separators at lower CEFR levels (A1–A2) were the mean sentence and T-unit length, variation in sentence length, infinitive density, clauses per sentence or T-unit, and verb phrases per T-unit. For higher levels (B1–B2) they were modifiers per noun phrase, mean clause length, complex nominals per clause, and left embeddedness. The results support previous findings that the length of and variation in the longer production units (sentences, T-units) are the SC indices that most clearly separate the lower CEFR levels, whereas the higher levels are best distinguished in terms of complexity at the clausal and phrasal levels.

Karakteristik Beton Mutu 16,9 MPa Mengunakan 1% Kawat Bendrat dengan Variasi Panjang

The research aimed to determine the characteristics of the 16.9 MPa, using steel fibers (bendrat wire) with lenght variations in the concrete mixture 1% by volume-weight of the concrete. This research is an explanatory research with research questions are: how significant is the difference, and what are the characteristics. The total population of each treatment is 12 specimens with a sample of 5 specimens for compressive strength and 4 specimens for split tensile strength for each given treatment which is a random sample, specifically: A (reference concrete); B, C, D, and E for concrete with length variation an expressed as L/D fiber ratio of 50; 62.5; 75 and 87.5. The concrete material meets the standard. At the level of significance 0,05 indicates that the test data are normal distribution and uniform and the characteristics of concrete between reference concrete and concrete fiber different variance values. The unit weight between the reference concrete and the fiber concrete is slightly identical. The slump value decreases with increasing L/D fiber ratio. The concrete characteristics increase up to an L/D fiber ratio of 75. It generates a compressive strength of 19.47% of the design and 16.60% of the reference concrete (17,316 MPa). The split tensile strength is 2,753 MPa (22.29% higher than the design 2,251 MPa) and 18.83% of the reference concrete (2,317 MPa). The flexural strength was 3.638 MPa (18.01% of the 3.083 MPa design) and 1.97% of the reference concrete (3.144 MPa).

Dynamic Behavior Analysis and Stability Control of Tethered Satellite Formation Deployment

In recent years, Tethered Space Systems (TSSs) have received significant attention in aerospace research as a result of their significant advantages: dexterousness, long life cycles and fuel-less engines. However, configurational conversion processes of tethered satellite formation systems in a complex space environment are essentially unstable. Due to their structural peculiarities and the special environment in outer space, TSS vibrations are easily produced. These types of vibrations are extremely harmful to spacecraft. Hence, the nonlinear dynamic behavior of systems based on a simplified rigid-rod tether model is analyzed in this paper. Two stability control laws for tether release rate and tether tension are proposed in order to control tether length variation. In addition, periodic stability of time-varying control systems after deployment is analyzed by using Floquet theory, and small parameter domains of systems in asymptotically stable states are obtained. Numerical simulations show that proposed tether tension controls can suppress in-plane and out-of-plane librations of rigid tethered satellites, while spacecraft and tether stability control goals can be achieved. Most importantly, this paper provides tether release rate and tether tension control laws for suppressing wide-ranging TSS vibrations that are valuable for improving TSS attitude control accuracy and performance, specifically for TSSs that are operating in low-eccentricity orbits.

A Na+/K+ ATPase Pump Regulates Chondrocyte Differentiation and Bone Length Variation in Mice

The genetic and developmental mechanisms involved in limb formation are relatively well documented, but how these mechanisms are modulated by changes in chondrocyte physiology to produce differences in limb bone length remains unclear. Here, we used high throughput RNA sequencing (RNAseq) to probe the developmental genetic basis of variation in limb bone length in Longshanks, a mouse model of experimental evolution. We find that increased tibia length in Longshanks is associated with altered expression of a few key endochondral ossification genes such as Npr3, Dlk1, Sox9, and Sfrp1, as well reduced expression of Fxyd2, a facultative subunit of the cell membrane-bound Na+/K+ ATPase pump (NKA). Next, using murine tibia and cell cultures, we show a dynamic role for NKA in chondrocyte differentiation and in bone length regulation. Specifically, we show that pharmacological inhibition of NKA disrupts chondrocyte differentiation, by upregulating expression of mesenchymal stem cell markers (Prrx1, Serpina3n), downregulation of chondrogenesis marker Sox9, and altered expression of extracellular matrix genes (e.g., collagens) associated with proliferative and hypertrophic chondrocytes. Together, Longshanks and in vitro data suggest a broader developmental and evolutionary role of NKA in regulating limb length diversity.

The behavior of cambered belts transiting cylindrical rollers

The lateral deformations of webs in roll-to-roll process machines can affect the quality of the manufactured products. Webs with simple nonuniform length variation across their width (camber) will steer toward the long side, leading to the steady state lateral deformation and hence registration. Most previous studies have focused on a cambered web in a free span between two rollers. These studies assume some displacement and slope boundary conditions are known and seek the remaining conditions that would dictate the steady state lateral deformation of the web. This article focuses on the lateral behavior of a cambered web belt transiting between two aligned rollers as the simplest case of multiple span cambered web. Dynamic simulation has been conducted to better understand the response of a cambered web under tension that has been witnessed in tests. There are no boundary conditions enforced and no steady state deformation of the cambered webs. Thus there is no closed-form solution to the lateral movement of a cambered web transits over multiple rollers. This explained why the previous research focused more on the experimental exploration without few theoretical validations. The web travels toward the long side continually from one span to the next until a web guide attempts to return the web to an acceptable lateral location in the process machine.