The opportunity for all undergraduate (ug) geoscience students to obtain authentic research experiences and to learn effective communication of this research is a powerful means to establish deeper understanding of geoscience topics as well as to engage all students in the culture and practice of research. This experience, realized in the Mineralogy-Igneous/Metamorphic Petrology sequence at LSU, builds on opportunities and resources of the On the Cutting Edge program. Cutting Edge workshops have been and continue to be critical for expanding boundaries of the possible. In addition, Cutting-Edge on-line resources have been particularly useful both for faculty development and student learning. In the required sophomore-level Mineralogy course, crystallographic and physical properties, chemical systematics and 3-D visualization of mineral frameworks are studied. As a way for these students to explore concepts, to improve spatial mapping from different images, and to put theory into practice, the LSU electron microprobe (EMP) is used to provide a research experience in Mineralogy. In small groups, students collect data on selected minerals for their chemistry, compositional zoning, and alteration, and then calculate stoichiometry. A jig-saw method is used to combine data from different teams to calculate temperatures and pressures. This experience becomes the foundation for research in the junior-level Igneous and Metamorphic Petrology course with a full-fledged course-embedded research project, the Pet Rock Project. Students follow the steps of a practicing petrologist going from megascopic to microscopic descriptions, EMP imaging and quantitative analyses of selected minerals and interpreting data to provide evidence for a coherent story for development of the selected rock. Next, students write a professional petrology-type paper and give a talk to the class. Guidelines and rubrics for both content and writing/presentation skills are provided to students to clearly establish expectations. A measureable outcome of the course embedded research opportunities is the enhanced engagement of undergraduate students in subsequent research, measured by enrollment in research specific ug courses, with geoscience faculty i.e. beginning with 16 in 2002-2004 and expanding to 145 in 2015-2017.

Phylogenetic relationships within the green algal class Cladophorophyceae were investigated. For 37 species, representing 18 genera, the sequences of the 5′-end of the large subunit rRNA were aligned and analysed. Ulva fasciata and Acrosiphonia spinescens (Ulvophyceae) were used as outgroup taxa. The final alignment consisted of 644 positions containing 208 parsimony-informative sites. The analysis showed three lineages within the Cladophorophyceae: Cladophora horii diverged first, followed by two main lineages. The first lineage includes some Cladophora species and genera with a reduced thallus architecture. The second lineage comprises siphonocladalean taxa (excluding part of Cladophoropsis and including some Cladophora species). From this perspective the Siphonocladales forms a monophyletic group, the Cladophorales remaining paraphyletic. [ABSTRACT FROM AUTHOR]

Gorgonian octocorals lack corroborated hypotheses of phylogeny. This study reconstructs genealogical relationships among some octocoral species based on published DNA sequences from the large ribosomal subunit of the mitochondrial RNA (lsu-rRNA, 16S: 524 bp and 21 species) and the small subunit of the nuclear RNA (ssu-rRNA, 18S: 1815 bp and 13 spp) using information from insertions–deletions (INDELS) and the predicted secondary structure of the lsu-rRNA (16S). There were seven short (3–10 bp) INDELS in the 18S with consistent phylogenetic information. The INDELS in the 16S corresponded to informative signature sequences homologous to the G13 helix found in Escherichia coli. We found two main groups of gorgonian octocorals using a maximum parsimony analysis of the two genes. One group corresponds to deep-water taxa including species from the suborders Calcaxonia and Scleraxonia characterized by an enlargement of the G13 helix. The second group has species from Alcyoniina, Holaxonia and again Scleraxonia characterized by insertions in the 18S. Gorgonian corals, branching colonies with a gorgonin-containing flexible multilayered axis (Holaxonia and Calcaxonia), do not form a monophyletic group. These corroborated results from maternally inherited ( 16S) and biparentally inherited ( 18S) genes support a hypothesis of independent evolution of branching in the two octocoral clades.

The phylogenetic relationships of Tholurna dissimilis were investigated in relation to a phylogeny of twenty-three species in Caliciaceae and eighteen species from Physciaceae. ITS and LSU regions of the nuclear ribosomal DNA were used for the reconstruction of phylogenies by maximum parsimony methods. Calicium adaequatum was shown to be the closest relative of and possibly congeneric with Tholurna. Calicium is thus not monophyletic unless Tholurna is included. Calicium in the molecular phylogeny contains several distinct clades, which to some extent can be characterized morphologically. Cyphelium in a traditional sense is probably not monophyletic. Cyphelium s. str. has immersed apothecia, large smooth spores and a very thin excipulum throughout. C. inquinans and C. karelicum, which form a distinct and highly supported clade, may be accommodated in Acolium, possibly along with other Cyphelium and Calicium species. The phylogenies presented here do not support the recognition of neither Physciaceae nor Caliciaceae in a narrow sense, but they also do not exclude this. Numerous spliceosomal and unclassified insertions were found in the LSU sequences. They to some extent offered phylogenetic information both with respect to location and by their sequence similarities.

All five species in the heterotrophic micro-algal genus Prototheca and their relatives were compared for the extent of nucleotide divergence in the nuclear small-subunit (SSU) and in the 5′ end of large-subunit (LSU) ribosomal RNA genes (rDNAs). Phylogenetic analysis based on combined SSU and LSU rDNA sequence alignment was implemented with the neighbor-joining, the maximum-parsimony, and the maximum-likelihood methods. The relationships among the species of Prototheca based on this data set were largely concordant with those inferred from SSU or LSU rDNA sequences alone. The obtained phylogenetic trees indicated that P. stagnora and P. ulmea should be regarded as different species and that both of the species as well as P. moriformis were placed in a cluster represented by P. zopfii, whereas P. wickerhamii was not directly grouped together with the other members of Prototheca and was more closely related to the autotrophic alga Auxenochlorella protothecoides. Therefore, the genus Prototheca is paraphyletic in its present circumscription; and these conclusions lead us to propose the transfer of P. wickerhamii to Auxenochlorella or to a new genus. On the basis of nucleotide sequence similarities, unlike SSU rDNA, the LSU rDNA region examined in this study appeared to be variable in recognizing a heterogeneity within a single species P. zopfii, which had been shown earlier in a chemotaxonomic study.

Some, but not all, marine pennate diatoms of the genus Pseudo-nitzschia H. Peragallo are associated with the production of domoic acid, a naturally occurring amino acid responsible for amnesic shellfish poisoning. Distinguishing between potentially toxic and nontoxic representatives of this genus is time-consuming and difficult because it demands scanning electron microscopy of cleaned frustules. The objective of this work is to speed and ease identification of these organisms by using whole-cell (in situ) hybridization and species-specific large-subunit ribosomal RNA (LSU rRNA)-targeted aligonucleotide probes. Toward that end, cultures of P. australis Frenguelli, P. pungenes (Grunow) Hasle, P. multiseries (Hasle) Hasle, P. fraudulenta (P. T. Cleve) Heiden. P. heimii Mangum, P. delicatissima (P. T. Cleve) Heiden, P. pseudodelicatissima (Hasle) Hasle, and P. americana (Hastle) Fryxell were screened with a suite of 15 putative species-specific probes. Of those, a subset of eight probes was found that distinguished each species tested. In addition, Pseudo-nitzschia chloroplasts were labeled with a probe directed against a eubacterial-conserved sequence. Identification of new cultures based on their reactivity toward a set of probes agreed with species designations as defined by morphological criteria. Whole-cell hybridization is a rapid, sample, and cost-effective technique for discriminating among cultured Pseudo-nitzschia species. [ABSTRACT FROM AUTHOR]