Assuring Access: One Library\u27s Journey from Print to Electronic Only Subscriptions

The migration of library collections from print to electronic formats has been a priority for many institutions during the last ten years and has played a key role in the transformation of the modern academic library. Not surprisingly, this process has been labor-intensive, costly, and occasionally frustrating to those involved in the transformation. This article recounts the challenges that the Central Michigan University Libraries faced and the measures it established to overcome these challenges as it undertook the process of successfully moving from a print-based to a predominately electronic only subscription collection

Identifying transgene insertions in Caenorhabditis elegans genomes with Oxford Nanopore sequencing.

Genetically modified organisms are commonly used in disease research and agriculture but the precise genomic alterations underlying transgenic mutations are often unknown. The position and characteristics of transgenes, including the number of independent insertions, influences the expression of both transgenic and wild-type sequences. We used long-read, Oxford Nanopore Technologies (ONT) to sequence and assemble two transgenic strains of Caenorhabditis elegans commonly used in the research of neurodegenerative diseases: BY250 (pPdat-1::GFP) and UA44 (GFP and human α-synuclein), a model for Parkinson's research. After scaffolding to the reference, the final assembled sequences were ∼102 Mb with N50s of 17.9 Mb and 18.0 Mb, respectively, and L90s of six contiguous sequences, representing chromosome-level assemblies. Each of the assembled sequences contained more than 99.2% of the Nematoda BUSCO genes found in the C. elegans reference and 99.5% of the annotated C. elegans reference protein-coding genes. We identified the locations of the transgene insertions and confirmed that all transgene sequences were inserted in intergenic regions, leaving the organismal gene content intact. The transgenic C. elegans genomes presented here will be a valuable resource for Parkinson's research as well as other neurodegenerative diseases. Our work demonstrates that long-read sequencing is a fast, cost-effective way to assemble genome sequences and characterize mutant lines and strains

Paleozoic Geology and Structure of the Northern Rowland Quadrangle, Northern Elko County, Nevada

Throughout the early Paleozoic, sedimentation along the passive western margin of North America was characterized by deposition of shallow-water carbonate rocks on the continental shelf, which graded westward into siliceous basinal rocks. This passive margin was interrupted by two collisional tectonic episodes: the Late Devonian-Early Mississippian Antler orogeny, and the Late Permian-Early Triassic Sonoma orogeny. The Antler orogeny is characterized by the eastward thrust fault emplacement of the Roberts Mountains allochthon onto the miogeoclinal shelf edge. The Golconda allochthon was a similar thrust sheet of oceanic lithologies which was structurally emplaced on top of the Roberts Mountains allochthon. The structural fabric of both allochthons is characteristically asymmetric, east-directed folds and thrust faults. As previously mapped, the Rowland quadrangle of northernmost Elko County, Nevada, contains the northernmost exposure of the Roberts Mountains allochthon in Nevada; north of this, Tertiary volcanic rocks cover the Paleozoic strata. The supposed Roberts Mountains allochthon here is composed of the Middle Ordovician Valmy Formation and possibly the Lower-Middle Ordovician Tennessee Mountain Formation, and is unconformably overlain by Mississippian-Permian rocks of the overlap assemblage. The basal Roberts Mountains thrust fault is not exposed in the study area. Emplacement of the Roberts Mountain allochthon elsewhere in Nevada is characterized by imbricate thrust faulting and contemporaneous folding. If the Ordovician strata in the Rowland quadrangle are indeed part of the Roberts Mountains allochthon, then they should exhibit a structural style similar to that of the allochthon elsewhere. In addition, the Ordovician strata should be more deformed than the post orogenic Antler overlap assemblage. Paleozoic strata of the study area were mapped and structural data taken. Folds are present in all of the Paleozoic strata, and range from microscopic to macroscopic scale. No significant difference in structural style was observed between Ordovician strata and Mississippian-Permian strata, suggesting that folding postdates Permian strata. Also, all of the strata are offset by a post-Permian, pre-Miocene high-angle fault which divides the study area into two structural domains. Thus, three possibilities exist regarding the Antler orogeny in the study area. First, the Roberts Mountains allochthon was emplaced along a thrust fault, not exposed in the area, with little internal deformation. Second, the Roberts Mountains allochthon has been eroded away, exposing rocks of the autochthonous or parautochthonous miogeocline in the study area. Finally, the Antler orogeny may not have been widespread enough to affect this region of northeastern Nevada, or may have exhibited a significantly different tectonic style than elsewhere in Nevada. This study indicates that all deformation recognized in the Rowland quadrangle is post-Antler in age, because Ordovician strata and Mississippian-Permian strata appear to be similarly deformed

Assuring Access: One Library\u27s Journey from Print to Electronic Only Subscriptions

The migration of library collections from print to electronic formats has been a priority for many institutions during the last ten years and has played a key role in the transformation of the modern academic library. Not surprisingly, this process has been labor-intensive, costly, and occasionally frustrating to those involved in the transformation. This article recounts the challenges that the Central Michigan University Libraries faced and the measures it established to overcome these challenges as it undertook the process of successfully moving from a print-based to a predominantly electronic only subscription collection

De Novo Genome Assemblies for Three North American Bumble Bee Species: Bombus bifarius, Bombus vancouverensis, and Bombus vosnesenskii

Bumble bees are ecologically and economically important insect pollinators. Three abundant and widespread species in western North America, Bombus bifarius, Bombus vancouverensis, and Bombus vosnesenskii, have been the focus of substantial research relating to diverse aspects of bumble bee ecology and evolutionary biology. We present de novo genome assemblies for each of the three species using hybrid assembly of Illumina and Oxford Nanopore Technologies sequences. All three assemblies are of high quality with large N50s (> 2.2 Mb), BUSCO scores indicating > 98% complete genes, and annotations producing 13,325 – 13,687 genes, comparing favorably with other bee genomes. Analysis of synteny against the most complete bumble bee genome, Bombus terrestris, reveals a high degree of collinearity. These genomes should provide a valuable resource for addressing questions relating to functional genomics and evolutionary biology in these species

Acetylenotrophic and Diazotrophic Bradyrhizobium sp. Strain I71 from Trichloroethylene-Contaminated Soils

Acetylene (C2H2) is a trace constituent of Earth’s modern atmosphere and is used by acetylenotrophic microorganisms as their sole carbon and energy source (Akob et al. 2018) Acetylenotrophs hydrate acetylene through a reaction catalyzed by acetylene hydratase, which is a heterogeneous class of enzymes. As of 2018, there were 15 known strains of acetylenotrophs including aerobic species affiliated with the Actinobacteria, and Firmicutes and anaerobic species affiliated with the Desulfobacterota. However, we hypothesized that there was an unknown diversity of acetylenotrophs in nature. We recently expanded the known distribution of acetylenotrophs via the isolation of the aerobic acetylenotroph, Bradyrhizobium sp. strain I71, from trichloroethylene (TCE)-contaminated soils (Akob et al. 2022). Strain I71 is a member of the class Alphaproteobacteria, and this is the first observation of an aerobic acetylenotroph in the Proteobacteria phylum. The isolate grows via heterotrophic and acetylenotrophic metabolism, and is diazotrophic, capable of nitrogen fixation. Acetylenotrophy and nitrogen fixation are the only two enzymatic reactions known to transform acetylene, and this is only the second isolate known to carry out both reactions (Akob et al. 2017, Baesman et al. 2019). Members of Bradyrhizobium are well studied for their abilities to improve plant health and increase crop yields by providing bioavailable nitrogen. The unique capability of Bradyrhizobium sp. strain I71 to utilize acetylene may increase the genus’ economic impact beyond agriculture as acetylenotrophy is closely linked to bioremediation of chlorinated contaminants (Mao et al. 2017, Gushgari-Doyle et al. 2021). Based on genome, cultivation, and protein prediction analysis, the ability to consume acetylene is likely not widespread within the genus Bradyrhizobium. These findings suggest that the suite of phenotypic capabilities of strain I71 may be unique and make it a good candidate for further study in several research avenues such as contaminant biodegradation and nutrient cycling

Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes.

The self-fertile nematode worms Caenorhabditis elegans, C. briggsae, and C. tropicalis evolved independently from outcrossing male-female ancestors and have genomes 20-40% smaller than closely related outcrossing relatives. This pattern of smaller genomes for selfing species and larger genomes for closely related outcrossing species is also seen in plants. We use comparative genomics, including the first high quality genome assembly for an outcrossing member of the genus (C. remanei) to test several hypotheses for the evolution of genome reduction under a change in mating system. Unlike plants, it does not appear that reductions in the number of repetitive elements, such as transposable elements, are an important contributor to the change in genome size. Instead, all functional genomic categories are lost in approximately equal proportions. Theory predicts that self-fertilization should equalize the effective population size, as well as the resulting effects of genetic drift, between the X chromosome and autosomes. Contrary to this, we find that the self-fertile C. briggsae and C. elegans have larger intergenic spaces and larger protein-coding genes on the X chromosome when compared to autosomes, while C. remanei actually has smaller introns on the X chromosome than either self-reproducing species. Rather than being driven by mutational biases and/or genetic drift caused by a reduction in effective population size under self reproduction, changes in genome size in this group of nematodes appear to be caused by genome-wide patterns of gene loss, most likely generated by genomic adaptation to self reproduction per se

Estradiol improves right ventricular function in rats with severe angioproliferative pulmonary hypertension: effects of endogenous and exogenous sex hormones

Estrogens are disease modifiers in PAH. Even though female patients exhibit better right ventricular (RV) function than men, estrogen effects on RV function (a major determinant of survival in PAH) are incompletely characterized. We sought to determine whether sex differences exist in RV function in the SuHx model of PAH, whether hormone depletion in females worsens RV function, and whether E2 repletion improves RV adaptation. Furthermore, we studied the contribution of ERs in mediating E2’s RV effects. SuHx-induced pulmonary hypertension (SuHx-PH) was induced in male and female Sprague-Dawley rats as well as OVX females with or without concomitant E2 repletion (75 μg·kg−1·day−1). Female SuHx rats exhibited superior CI than SuHx males. OVX worsened SuHx-induced decreases in CI and SuHx-induced increases in RVH and inflammation (MCP-1 and IL-6). E2 repletion in OVX rats attenuated SuHx-induced increases in RV systolic pressure (RVSP), RVH, and pulmonary artery remodeling and improved CI and exercise capacity (V̇o2max). Furthermore, E2 repletion ameliorated SuHx-induced alterations in RV glutathione activation, proapoptotic signaling, cytoplasmic glycolysis, and proinflammatory cytokine expression. Expression of ERα in RV was decreased in SuHx-OVX but was restored upon E2 repletion. RV ERα expression was inversely correlated with RVSP and RVH and positively correlated with CO and apelin RNA levels. RV-protective E2 effects observed in females were recapitulated in male SuHx rats treated with E2 or with pharmacological ERα or ERβ agonists. Our data suggest significant RV-protective ER-mediated effects of E2 in a model of severe PH

Differences in total gene size (introns and exons) versus protein coding size (exons) in <i>C. elegans</i>, <i>C. briggsae</i> and <i>C. remanei</i>.

<p>(a-b) Gene Size differs between autosomes and the X chromosome in <i>C. briggsae</i> (Kruskal-Wallis <i>χ</i>² = 24.63, <i>df</i> = 1, <i>p</i> < 6.96<i>x</i>10⁻⁷), <i>C. elegans</i> (Kruskal-Wallis <i>χ</i>² = 58.04, <i>df</i> = 1, <i>p</i> < 2.56<i>x</i>10⁻¹⁴) and <i>C. remanei</i> (Kruskal-Wallis <i>χ</i>² = 99.10, <i>df</i> = 1, <i>p</i> < 2<i>x</i>10⁻¹⁶) but protein size does not (<i>C. briggsae</i> Kruskal-Wallis <i>χ</i>² = 0.94, <i>df</i> = 1, <i>p</i> = 0.66; <i>C. elegans</i> Kruskal-Wallis <i>χ</i>² = 0.29, <i>df</i> = 1, <i>p</i> = 1; <i>C. remanei</i> Kruskal-Wallis <i>χ</i>² = 4.3096, <i>df</i> = 1, <i>p</i> = 0.08). Gene size differs significantly among the species on autosomes (Kruskal-Wallis <i>χ</i>² = 152.86; <i>df</i> = 2, <i>p</i> < 2<i>x</i>10⁻¹⁶; Bonferroni-adjusted Pairwise Wilcoxon Rank Sum <i>C. remanei</i>:<i>C. elegans</i><i>p</i> < 2<i>x</i>10⁻¹⁶, <i>C. remanei</i>:<i>C. briggsae</i><i>p</i> < 2<i>x</i>10⁻¹⁶; <i>C. briggsae</i>:<i>C. elegans</i><i>p</i> < 6<i>x</i>10⁻⁵) and between <i>C. remanei</i> and the self-fertile hermaprodites on the X chromsome (Kruskal-Wallis <i>χ</i>² = 64.39; <i>df</i> = 2, <i>p</i> < 1<i>x</i>10⁻¹⁴; Bonferroni-adjusted Pairwise Wilcoxon Rank Sum <i>C. remanei</i>:<i>C. elegans</i><i>p</i> < 2<i>x</i>10⁻¹⁰, <i>C. remanei</i>:<i>C. briggsae</i><i>p</i> < 1.8<i>x</i>10⁻¹¹; <i>C. briggsae</i>:<i>C.elegans</i><i>p</i> = 1). (c-d) Protein size differs significantly between <i>C. briggsae</i> and <i>C. elegans</i> and <i>C. briggsae</i> and <i>C. remanei</i> on both the autosomes (Kruskal-Wallis <i>χ</i>² = 91.32; <i>df</i> = 2, <i>p</i> < 2<i>x</i>10⁻¹⁶; Bonferroni-adjusted Pairwise Wilcoxon Rank Sum <i>C. remanei</i>:<i>C. elegans</i><i>p</i> = 1, <i>C. remanei</i>:<i>C. briggsae</i><i>p</i> < 2<i>x</i>10⁻¹⁶; <i>C. briggsae</i>:<i>C.elegans</i><i>p</i> < 1.5<i>x</i>10⁻¹¹) and X chromosome (Kruskal-Wallis <i>χ</i>² = 40.36; <i>df</i> = 2, <i>p</i> < 1.7<i>x</i>10⁻⁹; Bonferroni-adjusted Pairwise Wilcoxon Rank Sum <i>C. remanei</i>:<i>C. elegans</i><i>p</i> = 0.92, <i>C. remanei</i>:<i>C. briggsae</i><i>p</i> < 4<i>x</i>10⁻⁹; <i>C. briggsae</i>:<i>C.elegans</i><i>p</i> < 2<i>x</i>10⁻⁵).</p

Whole chromosome comparisons among <i>C. elegans</i>, <i>C. briggsae</i>, and <i>C. remanei</i>.

<p>The <i>C. remanei</i> The linkage map was sufficient to assemble and order 98.93% of the scaffolds with orthologous genes aligning to <i>C. elegans</i> chromosome X, 78.38% of the scaffolds with orthologous genes aligning to <i>C. elegans</i> chromosome II and 81.40% of the scaffolds with orthologous genes aligning to <i>C. elegans</i> chromosome IV. (a) <i>C. remanei</i> linkage groups were assigned to chromosomes based on gene orthology to <i>C. elegans</i> chromosomes. Reproductive incompatibility between the <i>C. remanei</i> strains used to construct the linkage map resulted in over-dispersion of the linkage map and 13 linkage groups instead of the 6 chromosomes expected (both <i>C. elegans</i> and <i>C. briggsae</i> have 6 chromosomes, respectively). (b) The cumulative size and orthologous gene alignments for scaffolds that were not assigned to linkage groups. c-e) Orthologous gene alignments indicated blocks of syntenic DNA between <i>C. elegans</i>, <i>C. briggsae</i>, and <i>C. remanei</i>. The panels c-e show orthologous genes on chromosomes X, II, and IV, with chromosome size scaled to linkage group size in <i>C. remanei</i> (X 18.5Mb, II 12.5Mb, IV 14.5 Mb). Orthologous genes were connected between species pairs, and grouped together if the genes were within 50,000 nucleotides of each other. Single gene translocations were excluded for clarity. Green indicates orthologs identified between <i>C. elegans</i> and <i>C. remanei</i>, blue indicates orthologs identified between <i>C. remanei</i> and <i>C. briggsae</i>, and grey indicates orthologs identified between <i>C. briggsae</i> and <i>C. elegans</i>. The outer rings are chromosomes X, II, and IV in each species. Each gray line is an orthologous gene located on the same chromosome in the other species and each black line is an orthologous gene that is located on a different chromosome in one of the other species. There are few blocks of interchromosomal translocation, and few black lines. White indicates regions of the chromosome where there were no orthologous genes identified between the species. (c) There was a large region of divergence (roughly 3.6Mb) on the <i>C. remanei</i> X; (d) Chromosome II is not completely assembled in <i>C. remanei</i>, and there were several regions of <i>C. elegans</i> and <i>C. briggsae</i> chromosome II that were not represented in <i>C. remanei</i>; (e) Chromosome IV.</p