Wintering waterbird assemblages in the central part of the Gulf of Gabès in southern Tunisia

Although the Gulf of Gabès is recognised as an Important Bird Area, several aspects of the ecology of waterbirds inhabiting this area still need to be investigated. We observed how waterbird foraging guilds varied among habitats. In total, 49 species belonging to 16 families were recorded. Winter visitors accounted for 73% of counts. The avifauna was dominated by shorebirds (52% of records), followed by large wading birds (25%), open-water birds (18%) and waterfowl (5%). However, the structure of local waterbird communities and their composition in terms of foraging guilds varied according to habitat type. The bird communities of sandy beaches were dominated by open-water birds, whereas large mudflats were dominated by shorebirds, and wadi estuaries showed a more even representation of foraging guilds. Locally rare species had narrow distributions, whereas locally abundant species were found widely within the gulf. For four species the 1% population level criterion of the Ramsar Convention was exceeded. Overall, our results show that the Gulf of Gabès hosts important numbers of waterbirds with different ecological requirements, which confirms the importance of this gulf as a wintering area for Palearctic waterbirds.     

Zygotic dormancy underlies prolonged seed development in Franklinia alatamaha (Theaceae): a most unusual case of reproductive phenology in angiosperms

In Franklinia alatamaha (Theaceae) an extended period of dormancy, associated with winter, separates pollination in the late summer and autumn from observable fruit growth, which occurs during the subsequent summer season. Here, ovule and early seed development were examined to decipher the timing of reproductive events that underlie this unusual phenological pattern. Female gametophytes were found to be mature before pollination. Evidence for double fertilization was observed soon after pollination. Early endosperm development progresses for up to 3 months after fertilization but comes to a standstill at the onset of winter. The zygote becomes dormant shortly after fertilization and does not divide during the autumn or winter. At the start of the following growing season, endosperm development is reinitiated and the first events associated with the formation of an embryo occur. Seed development is completed roughly at the same time as new flowers are opening, a full year after pollination and fertilization. Dehiscence of fruits does not occur until later in autumn. The prolonged zygotic dormancy in Franklinia is exceedingly rare among angiosperms and differs markedly from patterns of delayed fertilization that typically underlie extended periods between pollination and seed maturation in other temperate, perennial species.     

Molprobity's ultimate rotamer‐library distributions for model validation

Here we describe the updated MolProbity rotamer‐library distributions derived from an order‐of‐magnitude larger and more stringently quality‐filtered dataset of about 8000 (vs. 500) protein chains, and we explain the resulting changes and improvements to model validation as seen by users. To include only side‐chains with satisfactory justification for their given conformation, we added residue‐specific filters for electron‐density value and model‐to‐density fit. The combined new protocol retains a million residues of data, while cleaning up false‐positive noise in the multi‐ datapoint distributions. It enables unambiguous characterization of conformational clusters nearly 1000‐fold less frequent than the most common ones. We describe examples of local interactions that favor these rare conformations, including the role of authentic covalent bond‐angle deviations in enabling presumably strained side‐chain conformations. Further, along with favored and outlier, an allowed category (0.3–2.0% occurrence in reference data) has been added, analogous to Ramachandran validation categories. The new rotamer distributions are used for current rotamer validation in MolProbity and PHENIX, and for rotamer choice in PHENIX model‐building and refinement. The multi‐dimensional distributions and Top8000 reference dataset are freely available on GitHub. These rotamers are termed “ultimate” because data sampling and quality are now fully adequate for this task, and also because we believe the future of conformational validation should integrate side‐chain with backbone criteria. Proteins 2016; 84:1177–1189. © 2016 Wiley Periodicals, Inc.     

Syntheses and biological activities of deoxy-d-allose fatty acid ester analogs

We describe the syntheses of three different deoxy-D-allose analogs [2-deoxy-D-allose (2-DOAll), 1,2-dideoxy-D-allose (1,2-DOAll), and 1,2-didehydro-1,2-dideoxy-D-allose (1,2-DHAll)] and their fatty acid esters via regioselective lipase-catalyzed transesterification. Among them, 2-DOAll and its decanoate (2-DOAll-C10) showed higher inhibitory activity on plant growth, which is similar to D-allose (All) and its decanoate (All-C10). Bioassay results of deoxy-All-C10 on four plant species suggest that the hydroxy group at the C-1 position might be important showing growth inhibitory activity. In addition, co-addition of gibberellin (GA₃) with 1,2-DHAll-C10 and 2-DOAll-C10 recovered plant growth, suggesting that they might mainly inhibit biosynthesis of gibberellin.     

First report of Chilo partellus in Turkey,a new invasive maize pest for Europe

The spotted stem borer, Chilo partellus (Swinhoe, 1885) (Lepidoptera: Crambidae), an invasive pest of wild and cultivated grasses in Asia and Africa, was found for the first time during periodic surveys of maize fields in the East Mediterranean region of Turkey in September and October 2014. The pest was recorded in maize fields of three of four provinces surveyed (Adana, Hatay and Osmaniye; it was not detected in Icel province). The Mediterranean corn stalk borer, Sesamia nonagrioides Lefebvre (Lepidoptera: Noctuidae), is the dominant maize pest in the East Mediterranean region of Turkey, followed by the European corn borer, Ostrinia nubilalis (Hübner) (Lepidoptera: Crambidae). The new invasive species comprised 4.9% of the total number of collected lepidopteran pests collected from maize stems and cobs in locations infested by C. partellus. No natural enemies of the new pest were recorded during our surveys. We discuss possible interactions among these three lepidopteran pests sharing the same habitat, prospects for control of C. partellus by the control methods currently used against S. nonagrioides and O. nubilalis, and also speculate on the path of invasion taken by C. partellus into Turkey.     

Highly efficient de novo mutant identification in a Sorghum bicolor TILLING population using the ComSeq approach

Screening large populations for carriers of known or de novo rare single nucleotide polymorphisms (SNPs) is required both in Targeting induced local lesions in genomes (TILLING) experiments in plants and in screening of human populations. We previously suggested an approach that combines the mathematical field of compressed sensing with next‐generation sequencing to allow such large‐scale screening. Based on pooled measurements, this method identifies multiple carriers of heterozygous or homozygous rare alleles while using only a small fraction of resources. Its rigorous mathematical foundations allow scalable and robust detection, and provide error correction and resilience to experimental noise. Here we present a large‐scale experimental demonstration of our computational approach, in which we targeted a TILLING population of 1024 Sorghum bicolor lines to detect carriers of de novo SNPs whose frequency was less than 0.1%, using only 48 pools. Subsequent validation confirmed that all detected lines were indeed carriers of the predicted mutations. This novel approach provides a highly cost‐effective and robust tool for biologists and breeders to allow identification of novel alleles and subsequent functional analysis.     

Phylogenetic analyses and evolutionary timescale of Coleoptera based on mitochondrial sequence

Coleopteran phylogeny was analysed using mitochondrial genome (mitogenome) sequence. The optimal tree topology was given by the dataset consisted of all coding genes except for the exclusion of the 3rd codon sites (mtDNA12) using Bayesian Inference Method. This topology supports the monophyly of four suborders, and the sister group relationship between Adephaga and Myxophaga and between Polyphaga and Archostemata. In Polyphaga, Cucujiformia and Elateroidea formed independent node respectively, the remaining species grouped together except for Cyphon sp, among which, only Cucujiformia and Scarabaeiformia were supported as monophyletic group, respectively. Within Cucujiformia, the monophyly of Chrysomeloidea, Curculionoidea and Tenebrionoidea were supported respectively, among which Tenebrionoidea occupied the basal position of Cucujiformia. Cleroidea grouped together with Bothrideridae and Coccinellidae, and formed an independent node, which lead to the paraphyly of Cucujoidea. The monophyly of Elateriformia was not supported because of the division of Scirtoidea and Buprestoidea. Furthermore, using a Bayesian relaxed clock calibrated with fossil data, we estimated that most superfamilies within Polyphaga originated in the Jurassic period.