Anomalies in natural populations of amphibians: Methodology for field studies

To be really efficient and conclusive, studies on the anomalies in natural populations of amphibians must be carried out in a perspective clearly centered on this topic rather than being a side product of works dealing with other questions. Recommendations are offered here on the methodology for such studies

Anomalies in Natural Populations of Amphibians: Methodology for Laboratory Studies

Recommendations are offered for the laboratory study of anomalies found in natural populations of amphibians to elucidate their causes. Various methods are mentioned, particularly breeding experiments, experimental gynogenesis and regeneration experiments

SSMART: Sequence-structure motif identification for RNA-binding proteins

MOTIVATION: RNA-binding proteins (RBPs) regulate every aspect of RNA metabolism and function. There are hundreds of RBPs encoded in the eukaryotic genomes, and each recognize its RNA targets through a specific mixture of RNA sequence and structure properties. For most RBPs, however, only a primary sequence motif has been determined, while the structure of the binding sites is uncharacterized. RESULTS: We developed SSMART, an RNA motif finder that simultaneously models the primary sequence and the structural properties of the RNA targets sites. The sequence-structure motifs are represented as consensus strings over a degenerate alphabet, extending the IUPAC codes for nucleotides to account for secondary structure preferences. Evaluation on synthetic data showed that SSMART is able to recover both sequence and structure motifs implanted into 3'UTR-like sequences, for various degrees of structured/unstructured binding sites. In addition, we successfully used SSMART on high-throughput in vivo and in vitro data, showing that we not only recover the known sequence motif, but also gain insight into the structural preferences of the RBP. AVAILABILITY: SSMART is freely available at https://ohlerlab.mdc-berlin.de/software/SSMART 137

COUGER-co-factors associated with uniquely-bound genomic regions

Most transcription factors (TFs) belong to protein families that share a common DNA binding domain and have very similar DNA binding preferences. However, many paralogous TFs (i.e. members of the same TF family) perform different regulatory functions and interact with different genomic regions in the cell. A potential mechanism for achieving this differential in vivo specificity is through interactions with protein co-factors. Computational tools for studying the genomic binding profiles of paralogous TFs and identifying their putative co-factors are currently lacking. Here, we present an interactive web implementation of COUGER, a classification-based framework for identifying protein co-factors that might provide specificity to paralogous TFs. COUGER takes as input two sets of genomic regions bound by paralogous TFs, and it identifies a small set of putative co-factors that best distinguish the two sets of sequences. To achieve this task, COUGER uses a classification approach, with features that reflect the DNA-binding specificities of the putative co-factors. The identified co-factors are presented in a user-friendly output page, together with information that allows the user to understand and to explore the contributions of individual co-factor features. COUGER can be run as a stand-alone tool or through a web interface: http://couger.oit.duke.edu

Designation of a Neotype for \u3cem\u3eLeptodactylus gracilis\u3c/em\u3e (Duméril and Bibron, 1840) (Amphibia: Leptodactylidae)

The examination of the preserved specimens in the herpetological collection of the Museum National d\u27Histoire Naturelle, along with a review of the original literature, indicates that no extant specimen can be undoubtedly identified as the holotype of Leptodactylus gracilis (DumCri.l and Bibron, 1840). Furthermore, it revealed that the type locality recently assigned to this taxon is in error

Designation of a Neotype for \u3cem\u3eLeptodactylus gracilis\u3c/em\u3e (Duméril and Bibron, 1840) (Amphibia: Leptodactylidae)

The examination of the preserved specimens in the herpetological collection of the Museum National d\u27Histoire Naturelle, along with a review of the original literature, indicates that no extant specimen can be undoubtedly identified as the holotype of Leptodactylus gracilis (DumCri.l and Bibron, 1840). Furthermore, it revealed that the type locality recently assigned to this taxon is in error

What You Need to Know About Moving Collections and Acquisitions Into an E‐Dominant Model!

Two different University of Maryland Libraries discuss how they have moved to an e‐dominant model, the reasons why, and the new acquisitions strategies libraries can use in crafting an e‐dominant collection. Whether your organization is a large ARL library like University of Maryland, College Park (UMD) Libraries or a nontraditional online library like the University of Maryland University College (UMUC) Library, there are many strategies for taking advantage of the new acquisitions environment and rethinking how to build collections in an e‐dominant world. At UMD, adopting an e‐dominant model has been a gradual change over time, allowing the library staff to develop new ideas about collection development and experiment with new tools and techniques for acquiring and managing the libraries’ collection. As these changes have unfolded over time, staff began to develop a more comprehensive and holistic picture, becoming more aware of how their own work with e‐resources impacts our colleagues, our patrons, and the wider library community. At the UMUC Library, the electronic resources management staff developed an e‐model initiative that represents a fundamental shift for electronic resources management at UMUC. Electronic resources have become a critical, important, and fully integrated component in course development for the university and this is driving the direction of collection development for the Library. The main thrust of this shift has been the establishment of an E‐Resources Initiative to replace the use of textbooks in print with e‐resources, primarily open access, embedded within the learning management system (LMS) course modules