Aligning Library Strategy and Structure With the Campus Academic Plan: A Case Study

Colleges and universities’ missions are typically comprised of educating students, training professionals, engaging in scholarship and research, promoting creative activity, improving healthcare, and providing public service. Academic libraries exist to support these core functions, yet most academic libraries are organized based on library functions rather than the primary missions of their college or university. This paper describes one academic library’s attempt to align library strategy and structure with its university’s academic plan.

Ontogeny and regulation of interleukin-7 expressing thymic epithelial cells

T cell development is a multistage process of differentiation that depends on proper thymocyte-thymic epithelial cell (TEC) interactions. Epithelial cells in the thymus are organized in a three-dimensional network that provides support and signals for thymocyte maturation. Concurrently, proper TEC differentiation in the adult thymus relies on thymocyte-derived signals. TECs produce interleukin-7 (IL-7), a non-redundant cytokine that promotes the survival, differentiation, and proliferation of thymocytes. We have identified IL-7 expressing TECs throughout ontogeny and in the adult thymus by in situ hybridization analysis. IL-7 expression is initiated in the thymic fated domain of the thymic primordium by embryonic day 11.5, in a Foxn1 independent pathway. Marked changes occur in the localization and regulation of IL-7 expressing TECs during development. Whereas IL-7 expressing TECs are present throughout the early thymic rudiment, the majority of IL-7 producing TECs are concentrated in the adult thymic medulla. By analyzing mouse strains that sustain blocks at different stages of thymocyte development, we show that IL-7 expression is initiated independently of hematopoietic-derived signals during thymic organogenesis. However, thymocyte-derived signals play an essential role in regulating IL-7 expression in the adult TEC compartment. Furthermore, distinct thymocyte subsets regulate the expression of IL-7 and keratin 5 in adult cortical epithelium. Intraperitoneal injection of Recombination Activating Gene deficient mice (RAG-2−/−) with anti-CD3ϵ monoclonal antibody (mAb) induces CD4− 8− double negative thymocytes to undergo β-selection and differentiate into CD4+8+ cells. Analysis of the thymic stromal compartment reveals that progression through β-selection renders thymocytes competent to alter the pattern of IL-7 expression in the cortical TEC compartment. RAG-2−/− mice do not generate mature T cells and therefore the RAG-2−/− thymus is devoid of organized medullary regions. Histological examination of RAG-2−/− thymus following anti-CD3ϵ stimulation reveals the emergence of mature thymic medullary regions, as assessed by H & E staining and expression of thymic stromal medullary markers. Stromal medullary reorganization occurs in the absence of T cell receptor αβ expression, suggesting that activation of RAG-2−/− thymocytes by CD3ϵ ligation generates thymocyte-derived signals that induce thymic epithelial reorganization, generating a mature medullary compartment. This model provides a tool to assess the mechanisms underlying thymic medullary development. ^

T cell adhesion regulation from clustering GM1 lipid rafts

Lipid rafts are small laterally mobile cell membrane structures that are highly enriched in lymphocyte signaling molecules. Lipid rafts can form from the assembly of specialized lipids and proteins through hydrophobic associations from saturated acyl chains. GM1 gangliosides are a common lipid raft component and have been shown to be essential in many T cell functions. Current lipid raft theory hypothesizes that certain aspects of T cell signaling can be initiated from the coalescence of these signaling-enriched lipid rafts to sites of receptor engagement. We have described how the specific aggregation of GM1 lipid rafts can cause a reorganization of cell surface molecular associations which include dynamic associations of β1 integrins with GM1 lipid rafts. These associations had pronounced effects on T cell adhesive and migratory states. We show that GM1 lipid raft aggregation can dramatically inhibit T cell migration and chemotaxis on the extracellular matrix constituent fibronectin. This inhibition of migration function was shown to be dependent on the src kinase Lck and PKC-regulated F-actin polymerization to extending pseudopods. Furthermore, GM1 lipid raft clustering could activate T cell adhesion-strengthening mechanisms. These include an increase in cellular rigidity, the creation of polymerized cortical F-actin structures, the induction of high affinity integrin states, an increase in surface area and symmetry of the contact plane, and resistance to shear flow detachment while adherent to fibronectin. This indicates that GM1 lipid raft aggregation defines a novel stimulus to regulate lymphocyte motility and cellular adhesion which could have important implications in T cell homing mechanisms. ^

Regulation of Net1A subcellular localization by the small GTPase Rac1

Activation of Rho family small G proteins is thought to be a critical event in breast cancer development and metastatic progression. Rho protein activation is stimulated by a family of enzymes known as guanine nucleotide exchange factors (Rho GEFs). The neuroepithelioma transforming gene 1 (Net1) is a Rho GEF specific for the RhoA subfamily that is overexpressed in primary breast tumors and breast cancer cell lines. Net1 isoform expression is also required for migration and invasion of breast cancer cells in vitro. These data indicate that Net1 may be a critical regulator of metastatic progression in breast cancer. Net1 activity is negatively regulated by sequestration in the nucleus, and relocalization of Net1 outside the nucleus is required to stimulate RhoA activation, actin cytoskeletal reorganization, and oncogenic transformation. However, regulatory mechanisms controlling the extranuclear localization of Net1 have not been identified. In this study, we have addressed the regulation of Net1A isoform localization by Rac1. Specifically, co-expression of constitutively active Rac1 with Net1A stimulates the relocalization of Net1A from the nucleus to the plasma membrane in breast cancer cells, and results in Net1A activation. Importantly, Net1A localization is also driven by endogenous Rac1 activity. Net1A relocalizes outside the nucleus in cells spreading on collagen, and when endogenous Rac1 expression was silenced by siRNA, Net1A remained nuclear in spreading cells. These data indicate that Rac1 controls the localization of the Net1A isoform and suggests a physiological role for Net1A in breast cancer cell adhesion and motility.

REGULATION OF ALTERNATIVE CARBON METABOLISM IN CANDIDA ALBICANS

Candida albicans is the most important fungal pathogen of humans. Transcript profiling studies show that upon phagocytosis by macrophages, C. albicans undergoes a massive metabolic reorganization activating genes involved in alternative carbon metabolism, including the glyoxylate cycle, β-oxidation and gluconeogenesis. Mutations in key enzymes such as ICL1 (glyoxylate cycle) and FOX2 (fatty acid β-oxidation) revealed that alternative carbon metabolic pathways are required for full virulence in C. albicans. These studies indicate C. albicans uses non-preferred carbon sources allowing its adaptation to microenvironments were nutrients are scarce. It has become apparent that the regulatory networks required for regulation of alternative carbon metabolism in C. albicans are considerably different from the Saccharomyces cerevisiae paradigm and appear more analogous to the Aspergillus nidulans systems. Well-characterized transcription factors in S. cerevisiae have no apparent phenotype or are missing in C. albicans. CTF1 was found to be a single functional homolog of the A. nidulans FarA/FarB proteins, which are transcription factors required for fatty acid utilization. Both FOX2 and ICL1 were found to be part of a large CTF1 regulon. To increase our understanding of how CTF1 regulates its target genes, including whether regulation is direct or indirect, the FOX2 and ICL1 promoter regions were analyzed using a combination of bioinformatics and promoter deletion analysis. To begin characterizing the FOX2 and ICL1 promoters, 5’ rapid amplification of cDNA ends (5’RACE) was used to identify two transcriptional initiation sites in FOX2 and one in ICL1. GFP reporter assays show FOX2 and ICL1 are rapidly expressed in the presence of alternative carbon sources. Both FOX2 and ICL1 harbor the CCTCGG sequence known to be bound by the Far proteins, hence rendering the motif as a putative CTF1 DNA binding element. In this study, the CCTCGG sequence was found to be essential for FOX2 regulation. However, this motif does not appear to be equally important for the regulation of ICL1. This study supports the notion that although C. albicans has diverged from the paradigms of model fungi, C. albicans has made specific adaptations to its transcription-based regulatory network that may contribute to its metabolic flexibility.

Delayed Thrombus Resolution and Fibroproliferative Vascular Wound Healing From Deficiency of Type III Collagen: a Paradoxical Mechanism for Tissue Fragility

Vascular Ehlers-Danlos syndrome is a heritable disease of connective tissue caused by mutations in COL3A1, conferring a tissue deficiency of type III collagen. Cutaneous wounds heal poorly in these patients, and they are susceptible to spontaneous and catastrophic rupture of expansible hollow organs like the gut, uterus, and medium-sized to large arteries, which leads to premature death. Although the predisposition for organ rupture is often attributed to inherent tissue fragility, investigation of arteries from a haploinsufficient Col3a1 mouse model (Col3a1+/-) demonstrates that mutant arteries withstand even supraphysiologic pressures comparably to wild-type vessels. We hypothesize that injury that elicits occlusive thrombi instead unmasks defective thrombus resolution resulting from impaired production of type III collagen, which causes deranged remodeling of matrix, persistent inflammation, and dysregulated behavior by resident myofibroblasts, culminating in the development of penetrating neovascular channels that disrupt the mechanical integrity of the arterial wall. Vascular injury and thrombus formation following ligation of the carotid artery reveals an abnormal persistence and elevated burden of occlusive thrombi at 21 post-operative days in vessels from Col3a1+/- mice, as opposed to near complete resolution and formation of a patent and mature neointima in wild-type mice. At only 14 days, both groups harbor comparable burdens of resolving thrombi, but wild-type mice increase production of type III collagen in actively resolving tissues, while mutant mice do not. Rather, thrombi in mutant mice contain higher burdens of macrophages and proliferative myofibroblasts, which persist through 21 days while wild-type thrombi, inflammatory cells, and proliferation all regress. At the same time that increased macrophage burdens were observed at 14 and 21 days post ligation, the medial layer of mutant arterial walls concurrently harbored a significantly higher incidence of penetrating neovessels compared with those in wild-type mice. To assess whether limited type III collagen production alters myofibroblast behavior, fibroblasts from vEDS patients with COL3A1 missense mutations were seeded into three-dimensional fibrin gel constructs and stimulated with transforming growth factor-β1 to initiate myofibroblast differentiation. Although early signaling events occur similarly in all cell lines, late extracellular matrix- and mechanically-regulated events like transcriptional upregulation of type I and type III collagen secretion are delayed in mutant cultures, while transcription of genes encoding intracellular contractile machinery is increased. Sophisticated imaging of collagen synthesized de novo by resident myofibroblasts visualizes complex matrix reorganization by control cells but only meager remodeling by COL3A1 mutant cells, concordant with their compensatory contraction to maintain tension in the matrix. Finally, administration of immunosuppressive rapamycin to mice following carotid ligation sufficiently halts the initial inflammatory phase of thrombus resolution and fully prevents both myofibroblast migration into the thrombus and the differential development of neovessels between mutant and wild-type mice, suggesting that pathological defects in mutant arteries develop secondarily to myofibroblast dysfunction and chronic inflammatory stimulation, rather than as a manifestation of tissue fragility. Together these data establish evidence that pathological defects in the vessel wall architecture develop in mutant arteries as sequelae to abnormal healing and remodeling responses activated by arterial injury. Thus, these data support the hypothesis that events threatening the integrity of type III collagen-deficient vessels develop not as a result of inherent tissue weakness and fragility at baseline but instead as an episodic byproduct of abnormally persistent granulation tissue and fibroproliferative intravascular remodeling.

Heregulin -beta 1 directly associates with RhoA via the immunoglobulin -like domain thereby modulating breast cancer metastasis-related properties

Heregulins constitute a family of growth factors belonging to the epidermal growth factor (EGF) family. Breast cancers that overexpress specific members of the EGF receptor family (EGFR, ErbB2, ErbB3, ErbB4) have increased metastatic potential, and Heregulin-β1 (HRGβ1), a ligand for ErbB3 and ErbB4, has also been shown to induce metastasis-related properties in breast cancer cells in vitro. The secreted form of the HRGβ1 is composed of five distinct structural domains, including the N-terminal domain, an immunoglobulin-like domain (IgG-like), a glycosylation domain, an EGF-like domain, and a β1-specific domain. Of these, the EGF-like domain is well characterized for its function in metastasis-related properties as well as its structure. However, the contributions of the other HRGβ1 domains in breast cancer metastasis remains unclear. ^ To investigate this, HRGβ1 proteins with targeted domain deletions were purified and subjected to assays for metastasis-related properties, including aggregation, invasion, activation of EGFR family members, and motility of breast cancer cells. These assays showed that retaining the EGF-like domain of HRGβ1 is important for activation of EGFRs. Interestingly, the HRGβ1 protein lacking the IgG-like domain (NGEB) led to a decrease in breast cancer cell motility, indicating the IgG-like domain modulates cell motility, an important step in cancer metastasis. ^ To understand the underlying mechanisms, I performed protein sequence and structural analysis of HRGβ1 and identified that the IgG-like domain of HRGβ1 shares sequence homology and three-dimensional structural similarity with the IgG-like domain of TRIO. TRIO is a cytoplasmic protein that directly associates with RhoA, a GTPase involved in cell reorganization and cell motility. Therefore, I hypothesized that HRGβ1 may translocate inside the breast cancer cells through receptor mediated endocytosis and bind to RhoA via its IgG-like domain. I show wild type HRGβ1 but not NGEB binds RhoA in vitro and in vivo, leading to RhoA activation. Inhibition of HRG-β1 internalization via endocytosis disrupted HRGβ1 binding to RhoA. Additionally, breast cancer cell motility induced by HRG-β1 is reduced after treatment with inhibitors to both endocytosis and RhoA function, similar to levels seen with NGEB treatment. ^ Thus, in addition to the well-known role of HRGβ1 as an extracellular stimulator of the EGFR family members, HRGβ1 also functions within the cell as a binding partner and activator of RhoA to modulate cancer cell motility. ^

Diversity and faunal composition of benthic foraminifera in Hole 44-390A on the Blake Nose Plateau

Benthic foraminiferal assemblages are a widespread tool to understand changes in organic matter flux and bottom-water oxygenation and their relation to paleoceanographic changes in the Upper Cretaceous oceans. In this study, assemblage data (diversity, total number, and number per species and gram) from Deep Sea Drilling Project (DSDP) Site 390 (Blake Nose, western North Atlantic) were processed for the lower Maastrichtian (Globotruncana falsostuarti - Gansserina gansseri Planktic Foraminiferal Zone). These data document significant changes in nutrient flux to the sea floor as well as bottom-water oxygenation during this time interval. Parallel to the observed changes in the benthic foraminiferal assemblages the number of inoceramid shells decreases, reflecting also a significant increase in bottom-water oxygenation. We speculate, that these data could reflect the onset of a shift from warmer low-latitude to cooler high-latitude deep-water sources. This speculation will predate the major reorganization of the oceanic circulation resulting in a circulation mode similar to today at the Early/Late Maastrichtian boundary by ~1 Ma and therefore improves our understanding of Late Cretaceous paleoceanography.

Stable oxygen isotope record of Globigerinoides sacculifer and age determination of sediment cores from teh Somali Basin

This study documents the biological signatures impressed upon the sedimentary record underlying both the 5°N upwelling system of the Somali Current and the equatorial area of the Somali Basin out of the upwelling influence. The evolution of these two distinct hydrographic systems is compared for the last 160 kyr. Correspondence and cluster analyses are performed on combined radiolarian and planktonic foraminiferal quantitative data in order to study the changes of the planktonic assemblages through time and space. The Upwelling Radiolarian Index (URI) is used as a productivity proxy. The water temperature and hydrographic structure of the upper water masses appear to be the major factors controlling the distribution patterns of the fauna. The relative abundances of three groups of foraminifera, cold water form (dextral N. pachyderma), mixed layer dwellers (G. trilobus, G. ruber, G. sacculifer, G. conglobatus, and G. glutinata), and thermocline dwellers (G. menardii, G. tumida, N. dutertrei, G. crassaformis, and P. obliquiloculata), follow distinct evolutionary patterns at the two sites during the last 160 kyr. At the equatorial site (core MD 85668), downcore fluctuations in the relative abundances of the three groups are closely related to the glacial/interglacial cyclicity and provide some insights into the interpretation of hydrographic changes. The dominance of the mixed layer foraminifera at the transition intervals between isotope stages 6/5 and 2/1, combined with weak URI values, is thought to reflect the reorganization of the oceanographic circulation. These short-term events (with a duration of < 5000 year) could be related to the rapid inflow of oxygen-depleted water through the Indonesian straits as a result of sea level rise during deglaciation. Underneath the 5°N gyre (core MD 85674), the response to global climatic changes is overprinted by the regional effect of the Somalian upwelling, which has been persistent over the last 160 kyr.

Potassium and argon concentrations and age determination of ODP Site 125-782 and 125-786

K-Ar whole-rock ages have been obtained for 30 samples from Sites 782 and 786, Ocean Drilling Program Leg 125 in the Izu-Bonin (Ogasawara) forearc region. They form a trimodal spread of ages between 9 Ma and 44 Ma and are, with a few exceptions, consistent with the inferred lithostratigraphy. The ages have been interpreted in terms of at least two distinct episodes of magmatic and/or hydrothermal activity. A group of ten samples, including the lava flows, gave an isochron age of 41.3 ± 0.5 Ma (middle-late Eocene). This is thought to represent the age of the principal magmatic development of the volcanic forearc basement, and is comparable to published ages on equivalent rocks from other parts of the forearc basement high (e.g., the Ogasawara Islands). It may be significant that this age is slightly younger than the timing of major plate reorganization in the Western Pacific at about 43 Ma. This was followed by a minor episode of intrusive magmatism at 34.6 ± 0.7 Ma (early Oligocene) which appears to have reset the ages of some of the earlier units. This event probably corresponds to the initiation of rifting of the "proto-arc" to form the Parece Vela Basin. Boninitic samples were erupted during both episodes of magmatism, the earlier being of low-Ca boninite type and the later being of medium- and high-Ca types. It is also possible that a third episode of intrusive magmatism affected the Izu-Bonin forearc region at both Sites 782 and 786 at about 17 Ma. This would be consistent with magmatic activity elsewhere in the region during the Miocene, associated with the end of active spreading in the Parece Vela Basin and the start of arc activity in the West Mariana Ridge.

Radiocarbon, isotope, biogenic, and 230Th measurements for sediment core RC10-196

The subarctic North Pacific Ocean holds a large CO2 reservoir that is currently isolated from the atmosphere by a low-salinity layer. It has recently been hypothesized that the reorganization of these high-CO2 waters may have played a crucial role in the degassing of carbon dioxide to the atmosphere during the last deglaciation. This reorganization would leave some imprint on paleo-productivity records. Here we present 230Th-normalized biogenic fluxes from an intermediate depth sediment core in the Northwest Pacific (RC10-196, 54.7°N, 177.1°E, 1007 m) and place them within the context of a synthesis of previously-published biogenic flux data from 49 deep-sea cores north of 20°N, ranging from 420 to 3968 m water depth. The 230Th-normalized opal, carbonate, and organic carbon fluxes from RC10-196 peak approximately 13,000 calendar years BP during the Bølling/Allerød (B/A) period. Our data synthesis suggests that biogenic fluxes were in general lowest during the last glacial period, increased somewhat in the Northwest Pacific during Heinrich Event 1, and reached a maximum across the entire North Pacific during the B/A period. We evaluate several mechanisms as possible drivers of deglacial change in biogenic fluxes in the North Pacific, including changes in preservation, sediment focusing, sea ice extent, iron inputs, stratification, and circulation shifts initiated in the North Atlantic and North Pacific. Our analysis suggests that while micronutrient sources likely contributed to some of the observed changes, the heterogeneity in timing of glaciogenic retreat and sea level make these mechanisms unlikely causes of region-wide contemporaneous peaks in export production. We argue that paleo-observations are most consistent with ventilation increases in both the North Pacific (during H1) and North Atlantic (during B/A) being the primary drivers of increases in biogenic flux during the deglaciation, as respectively they were likely to bring nutrients to the surface via increased vertical mixing and shoaling of the global thermocline.

(Data S1) Palynological analysis of IODP and ODP sediment cores around the Antarctic margin

The circum-Antarctic Southern Ocean is an important region for global marine food webs and carbon cycling because of sea-ice formation and its unique plankton ecosystem. However, the mechanisms underlying the installation of this distinct ecosystem and the geological timing of its development remain unknown. Here, we show, on the basis of fossil marine dinoflagellate cyst records, that a major restructuring of the Southern Ocean plankton ecosystem occurred abruptly and concomitant with the first major Antarctic glaciation in the earliest Oligocene (~33.6 million years ago). This turnover marks a regime shift in zooplankton-phytoplankton interactions and community structure, which indicates the appearance of eutrophic and seasonally productive environments on the Antarctic margin. We conclude that earliest Oligocene cooling, ice-sheet expansion, and subsequent sea-ice formation were important drivers of biotic evolution in the Southern Ocean.

Mass accumulation rates, age, sedimentation rate and bulk density at the East Pacific Rise

The rate at which hydrothermal precipitates accumulate, as measured by the accumulation rate of manganese, can be used to identify periods of anomalous hydrothermal activity in the past. From a preliminary study of Sites 597 and 598, four periods prior to 6 Ma of anomalously high hydrothermal activity have been identified: 8.5 to 10.5 Ma, 12 to 16 Ma, 17 to 18 Ma, and 23-to-27 Ma. The 18-Ma anomaly is the largest and is associated with the jump in spreading from the fossil Mendoza Ridge to the East Pacific Rise, whereas the 23-to-27-Ma anomaly is correlated with the birth of the Galapagos Spreading Center and resultant ridge reorganization. The 12-to-16-Ma and 8.5-to-10.5-Ma anomalies are correlated with periods of anomalously high volcanism around the rim of the Pacific Basin and may be related to other periods of ridge reorganization along the East Pacific Rise. There is no apparent correlation between periods of fast spreading at 19°S and periods of high hydrothermal activity. We thus suggest that periods when hydrothermal activity and crustal alteration at mid-ocean ridges are the most pronounced may be periods of large-scale ridge reorganization.

Siliceous microfossils in middle Eocene sediments of ODP Holes 120-748B and 120-749B

The Middle Eocene Climatic Optimum (MECO) is a major transient warming event that occurred at ~ 40 Ma and reversed a long-term cooling trend through the early and middle Eocene. We report the results of a high-resolution, quantitative study of siliceous microfossils at Ocean Drilling Program Sites 748 and 749 (Southern Kerguelen Plateau, Southern Ocean, ~ 58°S) across a ~ 1.4 myr interval spanning the MECO event. At both sites, a significant increase in biosiliceous sedimentation is associated with the MECO event. Rich siliceous planktonic microfossil assemblages in this interval are unusual in that they are dominated by ebridians, with radiolarians as a secondary major component. Silicoflagellates and diatoms comprise only a minor fraction of the assemblage, in contrast to siliceous microfossil assemblages that characterize modern Southern Ocean sediments. Based on our new siliceous microfossil records, we interpret two ~ 300 kyr periods of elevated nutrient availability in Southern Ocean surface waters which span the peak warming interval of the MECO and the post-MECO cooling interval. A diverse assemblage of large silicoflagellates belonging to the Dictyocha grandis plexus is linked to the rapid rise in sea-surface temperatures immediately prior to peak warmth, and a pronounced turnover is observed in both ebridian and silicoflagellate assemblages at the onset of peak warming. The interval of peak warmth is also characterized by high abundance of cosmopolitan ebridians (e.g., Ammodochium spp.) and silicoflagellates (e.g., Naviculopsis spp.), and increased abundance of tropical and subtropical diatom genera (e.g., Asterolampra and Azpeitia). These observations confirm the relative pattern of temperature change interpreted from geochemical proxy data at multiple Southern Ocean sites. Furthermore, rapid assemblage changes in both autotrophic and heterotrophic siliceous microfossil groups indicate a reorganization of Southern Ocean plankton communities in response to greenhouse warming during the MECO event.

Stable isotope record of Maestrichtian foraminifera

A global compilation of deep-sea isotopic records suggests that Maastrichtian ocean-climate evolution was technically driven. During the early Maastrichtian the Atlantic intermediate-deep ocean was isolated from the Pacific, Indian, and Southern Oceans; deep water formed in the high-latitude North Atlantic and North Pacific. At the early/late Maastrichtian boundary a major reorganization of oceanic circulation patterns occurred, resulting in the development of a thermohaline circulation system similar to that of the modern oceans. A combination of isotopic and plate kinematic data suggests that this event was triggered by the final breaching of tectonic sills in the South Atlantic and the initiation of north-south flow of intermediate and deep water in the Atlantic. The onset of Laramide tectonism during the mid Maastrichtian led to the concurrent draining of major epicontinental seaways. Together, these events caused cooling, increased latitudinal temperature gradients, increased ventilation of the deep ocean, and affected a range of marine biota.