Structural analysis of peptides that interact with Newcastle disease virus

A peptide with the sequence CTLTTKLYC has previously been identified to inhibit the propagation of Newcastle disease virus (NDV) in embryonated chicken eggs and tissue culture. NDV has been classified into two main groups: the velogenic group, and mesogenic with lentogenic strains as the other group based on its dissociation constants. In this study the peptide, CTLTTKLYC, displayed on the pIII protein of a filamentous M13 phage was synthesized and mutated in order to identify the amino acid residues involved in the interactions with NDV. Mutations of C1 and K6 to A1 and A6 did not affect the binding significantly, but substitution of Y8 with A8 dramatically reduced the interaction. This suggests that Y8 plays an important role in the peptide-virus interaction. The three-dimensional structure of the peptide was determined using circular dichroism (CD), nuclear magnetic resonance (NMR), and molecular modeling. The peptide exhibited two possible conformers. One that consists of consecutive beta-turns around T2-L3-T4-T5 and K6-L7-Y8-C9. The other conformer exhibited a beta-hairpin bend type of structure with a bend around L3-T4-T5-K6.     

Genomic Analysis of Mycobacterium massiliense Strain M115, an Isolate from Human Sputum

We report the draft genome sequence of a clinical isolate, strain M115, identified as Mycobacterium massiliense, a member of the newly created taxon of Mycobacterium abscessus subspecies bolletii comb. nov.     

Diversity and population structure of northern switchgrass as revealed through exome capture sequencing

Panicum virgatum L. (switchgrass) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuel feedstock crop. Switchgrass is present primarily in two ecotypes: a northern upland ecotype, composed of tetraploid and octoploid accessions, and a southern lowland ecotype, composed of primarily tetraploid accessions. We employed high‐coverage exome capture sequencing (~2.4 Tb) to genotype 537 individuals from 45 upland and 21 lowland populations. From these data, we identified ~27 million single‐nucleotide polymorphisms (SNPs), of which 1 590 653 high‐confidence SNPs were used in downstream analyses of diversity within and between the populations. From the 66 populations, we identified five primary population groups within the upland and lowland ecotypes, a result that was further supported through genetic distance analysis. We identified conserved, ecotype‐restricted, non‐synonymous SNPs that are predicted to affect the protein function of CONSTANS (CO) and EARLY HEADING DATE 1 (EHD1), key genes involved in flowering, which may contribute to the phenotypic differences between the two ecotypes. We also identified, relative to the near‐reference Kanlow population, 17 228 genes present in more copies than in the reference genome (up‐CNVs), 112 630 genes present in fewer copies than in the reference genome (down‐CNVs) and 14 430 presence/absence variants (PAVs), affecting a total of 9979 genes, including two upland‐specific CNV clusters. In total, 45 719 genes were affected by an SNP, CNV, or PAV across the panel, providing a firm foundation to identify functional variation associated with phenotypic traits of interest for biofuel feedstock production.     

YSL3-mediated copper distribution is required for fertility,seed size and protein accumulation in Brachypodium

Addressing the looming global food security crisis requires the development of high-yielding crops. In agricultural soils, deficiency in the micronutrient copper significantly decreases grain yield in wheat (Triticum aestivum), a globally important crop. In cereals, grain yield is determined by inflorescence architecture, flower fertility, grain size, and weight. Whether copper is involved in these processes, and how it is delivered to the reproductive organs is not well understood. We show that copper deficiency alters not only the grain set but also flower development in both wheat and its recognized model, Brachypodium distachyon. We then show that the Brachypodium yellow stripe-like 3 (YSL3) transporter localizes to the phloem, transports copper in frog (Xenopus laevis) oocytes, and facilitates copper delivery to reproductive organs and grains. Failure to deliver copper, but not iron, zinc, or manganese to these structures in the ysl3 CRISPR-Cas9 mutant results in delayed flowering, altered inflorescence architecture, reduced floret fertility, grain size, weight, and protein accumulation. These defects are rescued by copper supplementation and are complemented by YSL3 cDNA. This knowledge will help to devise sustainable approaches for improving grain yield in regions where soil quality is a major obstacle for crop production. Copper distribution by a phloem-localized transporter is essential for the transition to flowering, inflorescence architecture, floret fertility, size, weight, and protein accumulation in seeds.

Copper distribution by a phloem-localized transporter is essential for the transition to flowering, inflorescence architecture, floret fertility, size, weight and protein accumulation in seeds.     

Ultrastructure of the male reproductive system and of spermatogenesis in the viviparous brittle-star,Amphipholis squamata

The fine structure of the male reproductive system of the hermaphroditic brittle-star, Amphipholis squamata, has been studied in specimens from both the Pacific coast (Washington) and the Atlantic coast (New Hampshire). Each testis is a small (100-μm) sphere and is attached to the internal wall of the bursa by peritoneal suspensor cells. Occasional flagellated cells are found on the external surface of the testis. The testicular wall of A. squamata is a multilayered structure, similar to that of other ophiuroids, but the hemal sinus is PAS negative in this species. Germinal cells are surrounded throughout their development by the filopodia of interstitial cells. Adjacent interstitial cells are interconnected, and thus form a structural network within the testis. Positionally and functionally, the interstitial cells resemble Sertoli cells; however, their origin, behavior and ultrastructure are different in many ways. Spermatogenesis includes a series of cyclical changes (aspermatogenic phase, proliferative phase, differentiative phase, and evacuative phase). Within a single testis, the resulting production of sperm is in short pulses, but if all 10 testes are taken together, sperm are produced continuously throughout the year. The events of spermiogenesis closely follow those that have been described in other echinoderms. However, we have provided new information on the release of excess cell membranes and the fusion process of mitochondria. The mature spermatozoa of A. squamata are flagellated and motile, and have “primitive” structural features, in spite of the fact that they fertilize the eggs inside the genital bursae. The spermatozoa do not, as was previously thought, enter the bursa by rupture of the adjacent walls. Instead, they are ejaculated through a gonoduct into the rapid incurrent flow of water entering the bursa. The locomotion of the spermatozoa is in eccentric spirals, due to the unusually large angle at which the flagellum is inserted into the base of the sperm.     

Histology of the pedicellariae of the Sand dollar, Dendraster excentricus (Echinodermata)

The pedicellariae in Dendraster excentricus are the bidentate type with a density of 80/cm². There are two distinct size groups; the larger ones measure 0.6 mm long while the small ones are only 0.14 mm. One interesting feature is the fluid of highly sulphated acid mucopolysaccharide in the lumen of the neck. This fluid functions as a hydroskeleton while the flexor muscle operates on it for complicated movement of the neck. The possibility that this fluid is also toxic and so acts as a defence mechanism is discussed. All the muscles involved in the movement of pedicellariae are smooth muscle fibres.