Modeling repetitive,non‐globular proteins

While ab initio modeling of protein structures is not routine, certain types of proteins are more straightforward to model than others. Proteins with short repetitive sequences typically exhibit repetitive structures. These repetitive sequences can be more amenable to modeling if some information is known about the predominant secondary structure or other key features of the protein sequence. We have successfully built models of a number of repetitive structures with novel folds using knowledge of the consensus sequence within the sequence repeat and an understanding of the likely secondary structures that these may adopt. Our methods for achieving this success are reviewed here.     

Physical and chemical properties of primary defences in Tenebrio molitor

Prevention and reaction are the foundation for any defence system. In insects, the primary defences against pathogens and parasites limit invasion; the secondary ones (e.g. immune system) act when the cuticle and other primary defences fail. Because investment in both aspects of defence may be costly, they should be regulated in a plastic or variable way in accordance with the risk of infection. The mealworm beetle Tenebrio molitor L. changes cuticle colour and its resistance to fungal infection when subject to high population density, although such resistance is a result of the primary (cuticle) defences rather than the secondary (immunological) ones. The present study tests the hypothesis that the physical and chemical properties of the primary defences in T. molitor change with cuticular darkness. Beetles expressing black phenotypes (or with darker cuticle) have a thicker cuticle, with four well organized layers (epi‐, exo‐, endocuticle and formation zone) and more melanin than tan beetles. The cuticle properties investigated in the present study are likely to be the underlying mechanisms of pathogen resistance in black beetles, including the content of carbonylated proteins, which in black beetles was almost half that of tan beetles after exposure to ultraviolet radiation. It is proposed that, in polyphenic insects (such as mealworm beetles), primary and secondary defences are regulated pleiotropically, with the genes responsible for the expression of one defence having a positive effect on others, whereas, in polymorphic insects, there is no such link and so investment in one defence may impair others.     

On quantitative effects of RNA shape abstraction

Over the last few decades, much effort has been taken to develop approaches for identifying good predictions of RNA secondary structure. This is due to the fact that most computational prediction methods based on free energy minimization compute a number of suboptimal foldings and we have to identify the native folding among all these possible secondary structures. Using the abstract shapes approach as introduced by Giegerich et al. (Nucleic Acids Res 32(16):4843–4851, 2004), each class of similar secondary structures is represented by one shape and the native structures can be found among the top shape representatives. In this article, we derive some interesting results answering enumeration problems for abstract shapes and secondary structures of RNA. We compute precise asymptotics for the number of different shape representations of size n and for the number of different shapes showing up when abstracting from secondary structures of size n under a combinatorial point of view. A more realistic model taking primary structures into account remains an open challenge. We give some arguments why the present techniques cannot be applied in this case.     

Wall formation in the saprolegniales

Summary The primary and secondary cysts of Saprolegnia ferax and the secondary cysts of Dictyuchus sterile have a two layered wall structure, the outer layer of which bears various types of spines. These spines, and the outer wall layer are derived from preformed structures (bars) found in the cytoplasm prior to encystment. Golgi derived vesicles appear to contribute to the inner layer of the primary cyst wall of S. ferax. The outer surface of the secondary cyst walls of this species has fibrils which are not embedded in matrix material.     

桔梗根的发育解剖学研究

以桔梗(Platycodon grandiflorum A.DC)根为材料,运用石蜡切片和半薄切片法对其根的发育过程及结构进行解剖学观察,并对不同年限根的结构进行了比较。结果表明:桔梗根的结构发育过程包括原生分生组织、初生分生组织、初生生长和次生生长4个阶段。其原生分生组织由3群原始细胞组成,表现出典型分生组织的细胞学特征;初生分生组织包括根冠原、表皮原、皮层原和中柱原;初生结构由表皮、皮层和中柱组成,其中皮层薄壁细胞占主要地位,初生木质部为二原型;次生生长主要依靠维管形成层和木栓形成层的活动来完成,其次生结构从外到内由周皮和次生维管组织组成,次生维管组织占主导地位,其中以薄壁细胞为主,维管分子少量,分散在薄壁组织中。不同年限的根的结构基本相同,但它们在主根长度和直径、周皮厚度、木质部与韧皮部面积之比等方面存在差异。     

A Dual Role for the Zebrafish unplugged Gene in Motor Axon Pathfinding and Pharyngeal Development

On their way toward their synaptic targets, motor growth cones encounter multiple choice points, where they are confronted with trajectory choices. We have previously shown that the zebrafish unplugged gene acts as a somite-derived cue controlling pathway choice of primary motor axons. Here, we demonstrate that this trajectory choice is not exclusively controlled by a single unplugged-dependent process, but depends on the coordinated function of additional cues. We also show that secondary motor neurons, most similar to those in birds and mammals, depend on the unplugged gene to navigate a choice point, suggesting that primary and secondary motor neurons share common mechanisms controlling axonal path selection. Moreover, we show that the unplugged gene plays an additional role guiding secondary motor axons through a single segmental nerve. Finally, we report that unplugged larvae display a striking pharyngeal arch defect, consistent with a dual function of the unplugged gene in axonal guidance and cell motility.     

A misfolded dimer of Cu/Zn‐superoxide dismutase leading to pathological oligomerization in amyotrophic lateral sclerosis

Misfolding of mutant Cu/Zn‐superoxide dismutase (SOD1) is a pathological hallmark in a familial form of amyotrophic lateral sclerosis. Pathogenic mutations have been proposed to monomerize SOD1 normally adopting a homodimeric configuration and then trigger abnormal oligomerization of SOD1 proteins. Despite this, a misfolded conformation of SOD1 leading to the oligomerization at physiological conditions still remains ambiguous. Here, we show that, around the body temperature (～37°C), mutant SOD1 maintains a dimeric configuration but lacks most of its secondary structures. Also, such an abnormal SOD1 dimer with significant structural disorder was prone to irreversibly forming the oligomers crosslinked via disulfide bonds. The disulfide‐crosslinked oligomers of SOD1 were detected in the spinal cords of the diseased mice expressing mutant SOD1. We hence propose an alternative pathway of mutant SOD1 misfolding that is responsible for oligomerization in the pathologies of the disease.     

Physical and chemical perturbations induce the formation of protein aggregates with different structural features

The in vitro aggregation of the model GST–GFP fusion protein was induced by several effectors, including those mimicking variations occurring under cell stress conditions. In particular, we examined the effects of thermal treatments, redox state and pH variations, salt addition, and freezing and thawing cycles. The resulting aggregates displayed different morphologies as seen by electron microscopy, and different secondary and tertiary structures, as indicated by Fourier transform infrared spectroscopy and fluorescence. Therefore, proteins can be forced to undergo multiple aggregation pathways that lead to assemblies with different molecular structures and, possibly, specific physiological and pathological roles.In conclusion, great caution should be taken in inferring conclusions on protein aggregation and disaggregation in vivo from results obtained using aggregates produced under non-physiological perturbations.     

Osteogenesis,homology, and function of the intercostal plates in ornithischian dinosaurs (Tetrapoda,Sauropsida)

Intercostal plates are bony structures positioned lateral to the anterior dorsal ribs in some ornithischian dinosaurs. Some propose these plates are homologous, or functionally analogous, with the uncinate processes of extant avian dinosaurs that assist in breathing, while others suggest they served a defensive function. To elucidate their osteogenesis, homology, and function, a histological survey of intercostal plates from three taxa (Hypsilophodon, Talenkauen, and Thescelosaurus) was undertaken. This study reveals that osteogenesis of intercostal plates closely resembles that of secondary centers of ossification in endochondral bone, typically present in the epiphyses of mammalian long bones. In contrast, ossification of avian uncinate processes begins at a primary ossification center via the development of a bony collar around a cartilaginous model. Based on these data, intercostal plates and avian uncinate processes are likely not evolutionary homologs. Dense packets of obliquely oriented Sharpey’s fibers within the parallel-fibered bone of somatically mature intercostal plates indicate these plates were positioned medial to at least a portion of the hypaxial musculature, which does not support their use as bony armor. Rather, we propose that intercostal plates performed some biomechanical function, either assisting in breathing in a way analogous to avian uncinate processes, or working together with the sternal ribs and sternal plates of these ornithischian taxa to provide increased rigidity to the anterior portion of the ribcage.     

Stage-dependent regulation of mammary ductal branching by heparan sulfate and HGF-cMet signaling

Specific interactions of growth factors with heparan sulfate may function as "switches" to regulate stages of branching morphogenesis in developing mammalian organs, such as breast, lung, salivary gland and kidney, but the evidence derives mostly from studies of explanted tissues or cell culture (Shah et al., 2004). We recently provided in vivo evidence that inactivation of Ndst1, the predominant N-deacetylase/N-sulfotransferase gene essential for the formation of mature heparan sulfate, results in a highly specific defect in murine lobuloalveolar development (Crawford et al., 2010). Here, we demonstrate a highly penetrant dramatic defect in primary branching by mammary epithelial-specific inactivation of Ext1, a subunit of the copolymerase complex that catalyzes the formation of the heparan sulfate chain. In contrast to Ext1 deletion, inactivation of Hs2st (which encodes an enzyme required for 2-O-sulfation of uronic acids in heparan sulfate) did not inhibit ductal formation but displayed markedly decreased secondary and ductal side-branches as well as fewer bifurcated terminal end buds. Targeted conditional deletion of c-Met, the receptor for HGF, in mammary epithelial cells showed similar defects in secondary and ductal side-branching, but did not result in any apparent defect in bifurcation of terminal end buds. Although there is published evidence indicating a role for 2-O sulfation in HGF binding, primary epithelial cells isolated from Hs2st conditional deletions were able to activate Erk in the presence of HGF and there appeared to be only a slight reduction in HGF-mediated c-Met phosphorylation in these cells compared to control. Thus, both c-Met and Hs2st play important, but partly independent, roles in secondary and ductal side-branching. When considered together with previous studies of Ndst1-deficient glands, the data presented here raise the possibility of partially-independent regulation by heparan sulfate-dependent pathways of primary ductal branching, terminal end bud bifurcation, secondary branching, ductal side-branching and lobuloalveolar formation.     

A nursery Area for Sharks and Rays in Northeastern Brazil

Synopsis Elasmobranch nurseries are habitats where females give birth to their young and juveniles spend their early life history. Hypotheses concerning nurseries suggest that these provide the young a better source of food and protection against predation, however the degree of exposure to predatory risk in nursery areas vary. According to Branstetter hypothesis, slow growing species are either born at relatively large sizes or use protected nursery grounds, whereas faster growing species tend to rely more on growth rates than others factors. Primary nurseries are habitats where parturition occurs and in which the young live for a short time and secondary nurseries are habitats in which juveniles are found after leaving the primary nursery and before reaching maturity. Rhizoprionodon porosus and Carcharhinus acronotus use coastal waters off Cai?ara do Norte as both primary and secondary nurseries, while Carcharhinus limbatus makes use of the area as a seasonal primary nursery in late spring and early summer. C. falciformis apparently makes use of the end of inner continental shelf and the outer continental shelf as a primary nursery. Gymnura micrura, Rhinobatos percellens and Narcine brasiliensis makes use of coastal and turbid waters of region as both primary and secondary nurseries throughout the year, while Dasyatis guttata utilizes the area as a primary nursery. Aetobatus narinari and Rhinoptera bonasus, although caught in lesser number, appear to use the region as both primary and secondary nurseries and only primary nursery respectively. Dasyatis marianae (endemic from Northeastern Brazil) may use coastal sandbanks as a primary nursery, while Dasyatis Americana apparently exploits waters about 10 – 20 m in depth with rocky reef substrate only as secondary nursery. There was a measurable degree of temporal and spatial separation among sharks’ species, which may effectively create separate ecological niches, whereas among rays, with the exception of the stingray D. marianae, a spatial and temporal overlaps were observed. The Branstetter’s hypothesis was supported.     

Structural and Histochemical Features of the Slow-Growing Perennial <i>Coptis chinensis</i> Franch. (Ranunculaceae)

Huanglian (Coptis chinensis Franch.) is a slow-growing perennial medicinal herb with considerable economic value. This study aimed to determine the structural characteristics and the levels of berberine deposits in the organs and tissues of Huanglian using light and epifluorescence microscopy. The adventitious roots are composed of primary and secondary structures with endodermis, exodermis, and phellem. The rhizome structures are composed of primary and secondary structures with cuticle and phellem. The leaves are composed of sclerenchymatous rings, isolateral mesophyll, and thin cuticles. We detected berberine in the xylem walls of the roots and rhizomes as well as in the sclerenchymatous rings of the petioles. We postulate that as the exodermis is developed, the deposition of berberine in the xylem closest to the root tips may affect water and nutrient absorption and transfer. Leaf blades had a thin cuticle and isolateral mesophyll, suggesting shade tolerance. These structural and histochemical features suggest that Huanglian is adapted to the slow growing nature of a shady environment.     

RNA structures with pseudo-knots: Graph-theoretical, combinatorial, and statistical properties

The secondary structures of nucleic acids form a particularly important class of contact structures. Many important RNA molecules, however, contain pseudo-knots, a structural feature that is excluded explicitly from the conventional definition of secondary structures. We propose here a generalization of secondary structures incorporating ‘non-nested’ pseudo-knots, which we call bi-secondary structures, and discuss measures for the complexity of more general contact structures based on their graph-theoretical properties. Bi-secondary structures are planar trivalent graphs that are characterized by special embedding properties. We derive exact upper bounds on their number (as a function of the chain length n) implying that there are fewer different structures than sequences. Computational results show that the number of bi-secondary structures grows approximately like 2.35ⁿ. Numerical studies based on kinetic folding and a simple extension of the standard energy model show that the global features of the sequence-structure map of RNA do not change when pseudo-knots are introduced into the secondary structure picture. We find a large fraction of neutral mutations and, in particular, networks of sequences that fold into the same shape. These neutral networks percolate through the entire sequence space.     

A novel primary immunodeficiency with specific natural-killer cell deficiency maps to the centromeric region of chromosome 8

We describe four children with a novel primary immunodeficiency consisting of specific natural-killer (NK) cell deficiency and susceptibility to viral diseases. One child developed an Epstein-Barr virus-driven lymphoproliferative disorder; two others developed severe respiratory illnesses of probable viral etiology. The four patients are related and belong to a large inbred kindred of Irish nomadic descent, which suggests autosomal recessive inheritance of this defect. A genomewide scan identified a single 12-Mb region on chromosome 8p11.23-q11.21 that was linked to this immunodeficiency (maximum LOD score 4.51). The mapping of the disease-causing genomic region paves the way for the identification of a novel pathway governing NK cell differentiation in humans.     

注意缺陷多动障碍低觉醒模型的新证据

注意缺陷多动障碍（Attention Deficit Hyperactivity Disorder,ADHD）是儿童期常见的一种发展性的异常,其病因及发生机理至今未明。低觉醒模型是ADHD成因的一种假设。本文从睡眠障碍导致的低觉醒探讨ADHD发生机理。通过对ADHD儿童的睡眠障碍进行分析以及将ADHD外在表现与睡眠剥夺后的表现进行对比分析,得出ADHD儿童存在的低觉醒是由于外显的或内隐的睡眠障碍引起的,一方面间接证明了低觉醒模型,另一方面为ADHD的成因研究开拓了新的思路。     

Potential structure/function relationships of predicted secondary structural elements of tau

The microtubule-associated protein tau is believed to be a natively unfolded molecule with virtually no secondary structure. However, this protein self-associates into filamentous forms in various neurodegenerative diseases. Since these filamentous forms show a remarkable degree of higher order due to their regular widths and periodicity, it is widely speculated that tau does contain secondary structures that come together to form tertiary and quaternary structures in the filamentous form. The purpose of this review is to use the primary sequence of tau along with predictive methods in an effort to identify potential secondary structural elements that could be involved in its normal and pathological functions. Although there are few predicted structural elements in the tau molecule, these analyses should lead to a better understanding of the structure/function relationships that regulate the behavior of tau.     

Functional analysis of complexes with mixed primary and secondary cellulose synthases

In higher plants, cellulose is synthesized by cellulose synthase complexes, which contain multiple isoforms of cellulose synthases (CESAs). Among the total 10 CESA genes in Arabidopsis, recessive mutations at three of them cause the collapse of mature xylem cells in inflorescence stems of Arabidopsis (irx1^cesa8, irx3^cesa7 and irx5^cesa4). These CESA genes are considered secondary cell wall CESAs. The others (the function CESA10 is still unknown) are thought to be specialized for cellulose synthesis in the primary cell wall. A split-ubiquitin membrane yeast two-hybrid system was used to assess interactions among four primary CESAs (CESA1, CESA2, CESA3, CESA6) and three secondary CESAs (CESA4, CESA7, CESA8). Our results showed that primary CESAs could physically interact with secondary CESAs in a limited fashion. Analysis of transgenic lines showed that CESA1 could partially rescue irx1^cesa8 null mutants, resulting in complementation of the plant growth defect, collapsed xylem and cellulose content deficiency. These results suggest that mixed primary and secondary CESA complexes are functional using experimental set-ups.     

The values and limits of an in vitro model of Pompe disease: The best laid schemes o’ mice an’ men ……..†

In Pompe disease, a lysosomal glycogen storage disorder, cardiac and skeletal muscle abnormalities are responsible for premature death and severe weakness. Swollen glycogen-filled lysosomes, the expected pathology, are accompanied in skeletal muscle by a secondary pathology – massive accumulation of autophagic debris – that appears to contribute greatly to the weakness. We have tried to reproduce these defects in murine, Pompe myotubes derived from either primary myoblasts or myoblasts with extended proliferative capacity. The cells accumulated large lysosomes filled with glycogen, but, to our disappointment, did not have autophagic buildup even though basal autophagy was intact. When we suppressed autophagy by knocking down Atg7, we found that glycogen uptake by lysosomes was not affected, suggesting that macroautophagy is not the major pathway for glycogen delivery to lysosomes. But two apparently incidental observations – a peculiar distribution of both microinjected dextran and of small acidic structures adjacent to the interior membrane of large alkalinized glycogen-containing lysosomes – raised the possibility that glycogen traffics to the lysosomes by microautophagy or/and by the engulfment of small lysosomes by large ones. The cultured myotubes, therefore, appear to be a useful model for studying the mechanisms involved in glycogen accumulation in Pompe disease and to test substrate deprivation approaches.

^?From To a Mouse, Robert Burns, 1785