CSEF: An internship program at community arts organizations for Honors College students

CSEF (the “Creative and Social Entrepreneurship Fellowship”) runs from August 2013 through May 2014 as part of the Creative Economy Initiative, funded by the UMass President’s Office. CSEF aims to provides students the opportunity to intern at a community arts organization, and provides local organizations the opportunity to work closely with UMass Boston students & faculty. Three intern teams immersed themselves in issues their sites were facing, proposed potential solutions, and are now using a $4000 mini-grant to implement those solutions at their partner sites

Phenotypic diversity of the threespine stickleback Gasterosteus aculeatus (Teleostei: Gasterosteidae) in the Mediterranean Sea

Gasterosteus aculeatus tritt im Mittelmeer nur in isolierten, küstennahen Populationen auf. Während des Pleistozäns war das Adria Becken wiederholt durch schwankende Meeresspiegel Niveaus starken Veränderungen unterworfen. Daher sind die Süßwasserpopulationen des dreistachligen Stichlings in der Nordadria zumindest seit der Maximalphase der letzten Eiszeit isoliert. Das Neretva System und der Fluss Isonzo stellen die extremsten Punkte dieser Region dar, nämlich jeweils die erste beziehungsweise die letzte isolierte Population. Aus diesen zwei Systemen, gemeinsam mit Referenz-Populationen vom Iznik See in der Türkei und Mulargia auf Sardinien, wurden insgesamt 208 G. aculeatus Individuen mit Methoden der geometrischen Morphometrie untersucht um die Varianz der Gestalt des Körpers zu untersuchen, sowohl zwischen Population als auch innerhalb einer Population, dem Neretva System. Die Populationen wurden sowohl mit Relative Warp Analysen als auch mit Canonical Variate Analysen untersucht. Auch wurde der Grad des Sexualdimorphismus in der Körpergestalt festgestellt, wie auch den Befall mit dem Parasiten Schistocephalus solidus und dessen Auswirkung auf die Körpergestalt. Ebenso wurde untersucht, inwieweit das Verhältnis von zwei Distanzen (Distanz zwischen ersten/zweiten und dritten Dorsalstachel, Länge der Rückenflosse) verwendbar ist um das Geschlecht zu bestimmen. Die Unterschiede in der Körpergestalt sind nicht so sehr zwischen den Populationen zu finden, sondern eher innerhalb des Neretva Systems. Sexualdimorphismus in der Körpergestalt, besonders am Kopf, stellt die größte Variation dar und findet sich in allen Populationen. Nur eine Population des Neretva Systems war stark vom Parasit Schistocephalus solidus befallen, wodurch die Körpergestalt der befallenen Individuen eine Mittelform zwischen nicht befallenen Männchen und Weibchen annahm. Es ist nicht ratsam nur ein Merkmal, wie zum Beispiel das Verhältnis zweier Distanzen, zu verwenden um das Geschlecht eines Individuums zu bestimmen, da der Sexualdimorphismus der Körpergestalt aus vielen einzelnen Merkmalen zusammengesetzt ist. Die Ergebnisse dieser Studie spiegeln die Ergebnisse bereits existierender genetischer Studien wieder, wodurch das Bild der Populationen des Adria Eizugsgebietes ergänzt wird.Gasterosteus aculeatus occurs in the Mediterranean Sea only in isolated coastal populations. During the Pleistocene the Adriatic Basin was affected repeatedly by changing sea levels. Thus Northern Adriatic freshwater populations of the threespine stickleback were isolated since at least the last glacial maximum. From these populations the Neretva System and Isonzo River form the most extreme points being the first and last isolated populations respectively. From these two systems, together with reference populations from Iznik Lake in Turkey and Mulargia in Sardinia, a total of 208 G. aculeatus specimens were examined with geometric morphometric methods to analyse variation of body shapes between populations as well as within one freshwater system, the Neretva System. The populations were analysed with relative warp analyses as well as with canonical variate analyses. Also the extent of sexual dimorphism on body shape and the state of parasitism with Schiostocephalus solidus and its influence on body shape is noted. Further the usage of a ratio of two distances (distance between the first/second and third dorsal spine, length of the dorsal fin) for sex determination is investigated. Body shape differences are not so much found between the Adria populations but mostly found within the Neretva System. Sexual dimorphism in body shape, especially in head morphology, is the highest source of variation and found in all populations. Only one population within the Neretva System is highly parasited and the body shape of these specimens is intermediate to not parasited males and females. The usage of one trait like a ratio of two distances to classify specimen as male or female is not advisable since sex dimorphism in body shape is comprised of many single small traits. The results of this study are mirrored by already existing genetic studies, thus complementing the picture of the populations of the Adriatic Drainage System

Untersuchung zur Abschätzung der Rolle der sozialen Erwünschtheit in Ernährungserhebungen

Ziel dieser Arbeit war die Untersuchung der SD bei Verzehrserhebungen. Hierfür wurde ein FFQ zur Verzehrshäufigkeit von Obst und Gemüse verwendet, da bereits in anderen Studien ein Overreporting von Obst und Gemüse aufgrund SD nachgewiesen wurde [MILLER et al., 2008]. Die Umfrage wurde von 14. Mai bis 28. Juni 2010 bei MitarbeiterInnen des Wilhelminenspitals in Wien durchgeführt. Es wurden zwei Methoden der SD-Kontrolle getestet. Die TeilnehmerInnen (n = 345) wurden nach dem Zufallsprinzip in zwei Gruppen geteilt. Eine Gruppe erhielt eine Zusatzinstruktion (n = 187), die die SD-Tendenz senken sollte, die andere fungierte als Kontrollgruppe (n = 158). Weiters enthielt der Internet-Fragebogen eine Übersetzung der SDF-Skala von WORSLEY et al. [1984], die die persönliche SD-Tendenz der TeilnehmerInnen messen sollte, was die Möglichkeit eines Ausschlusses von Personen mit hoher SD-Tendenz eröffnet. Die Zusatzinstruktion, entwickelt in Anlehnung an HOETH und KÖBLER [1967], zeigte keinen signifikanten Effekt auf den FFQ als Ganzes. Der Einfluss auf einzelne Items des FFQ dürfte unterschiedlich stark sein und war nur bei „Fruchtsaft“ und „grüner Salat“ signifikant (p ≤ 0,05). Jedoch weist die Zusatzinstruktion auf die Möglichkeit der „Beschönigung“ der Antworten hin und dürfte so die Korrelation zwischen dem SDF-Score und den Verzehrsangaben verstärkt haben, was kontraproduktiv ist. Bezüglich des Einsatzes von Zusatzinstruktionen beim FFQ zur SD-Reduktion wären weitere Untersuchungen sinnvoll. Es konnten hoch- bzw. höchstsignifikante (p ≤ 0,01 bzw. p ≤ 0,001) Zusammenhänge zwischen den Häufigkeitsangaben im FFQ und dem SDF-Score gefunden werden. Es dürfte ein Overreporting aufgrund SD stattgefunden haben, das anhand des SDF-Scores gemessen wurde. Die SDF-Skala dürfte sich sehr gut als Messinstrument für die Antworttendenz eignen. Die SD-Tendenz war bei den einzelnen Items des FFQ unterschiedlich hoch. Aufgrund der Post Hoc Tests erscheint es sinnvoll Personen mit einem SDF-Score ≥ 10 von der Auswertung auszuschließen. Da die Personenanzahl in dieser Gruppe gering war, wirkte sich dies nur geringfügig auf das Gesamtergebnis aus. Die Verzehrsangaben dieser Gruppe unterschieden sich jedoch deutlich von den Angaben der Personen mit einem SDF-Score ≤ 9. Eine generelle Umsetzung dieser Maßnahme ist überlegenswert. Weitere Untersuchungen wären jedoch zuvor notwendig, insbesondere da das Antwortverhalten bzgl. SD von verschiedenen Faktoren abhängig ist, die zwischen den einzelnen Untersuchungen variieren. Die Entwicklung eines neuen SD-Scores für Verzehrserhebungen, der mehr dem Zeitgeist entspricht, wäre vielversprechend

Characterization of two Bacillus subtilis proteins required for the initiation, restart, and control of DNA replication

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2004."September 2004."Includes bibliographical references.(cont.) This is consistent with an inability of dnaBS371P cells to adjust the frequency of initiation according to growth rate. I also found that cells over-producing DnaBS371P are filamentous, contain decreased DNA contents, and are hypersensitive to DNA-damaging agents. These abnormalities may result from a defect in replication restart at damaged or stalled replication forks. Thus, whereas dnaBS3 71P suppresses the defects of mutant cells that cannot initiate or restart replication, expressing DnaBS371P in wild-type cells causes defects in initiation and restart.DnaB and DnaD are essential proteins that function in the initiation and control of DNA replication in Bacillus subtilis. I found that DnaB and DnaD are required to load the replicative helicase onto chromosomal origins during replication initiation. DnaB and DnaD are also involved in loading helicase during replication restart at sites of stalled replication forks. Despite the fact that DnaB and DnaD are thought to work together to load helicase, DnaB and DnaD are found in separate subcellular compartments. I showed that DnaB is found in the membrane fraction of cells, and DnaD is found in the cytoplasmic fraction. This separation could prevent helicase loading during the majority of the cell cycle. I isolated a missense mutation in dnaB, dnaBS371P, that disrupts the spatial separation of DnaB and DnaD. I isolated dnaBS371P as a suppressor of the temperature sensitivity of dnaBts cells and dnaDts cells. dnaBS3 71P also suppresses the growth defects of ipriA cells, which cannot restart replication at stalled forks. I found that a significant fraction of DnaD is found in the membrane fraction of dnaBS371P cells. In addition, I observed a direct interaction between DnaBS371P and DnaD that is not observed between the wild-type proteins. I hypothesize that the DnaB-DnaD interaction is regulated, thereby controlling when these two proteins converge at the membrane to coordinate helicase loading. dnaBS3 71P cells lack proper control of replication, suggesting that the spatial separation of DnaB and DnaD is an important mechanism of replication control in B. subtilis. I showed that dnaBS371P cells over-initiate replication when grown slowly in minimal medium, but contain decreased DNA content when grown faster, in rich medium.by Megan E. Rokop.Ph.D

When simple sequence comparison fails: the cryptic case of the shared domains of the bacterial replication initiation proteins DnaB and DnaD

DnaD and DnaB are essential DNA-replication-initiation proteins in low-G+C content Gram-positive bacteria. Here we use sensitive Hidden Markov Model-based techniques to show that the DnaB and DnaD proteins share a common structure that is evident across all their structural domains, termed DDBH1 and DDBH2 (DnaD DnaB Homology 1 and 2). Despite strong sequence divergence, many of the DNA-binding and oligomerization properties of these domains have been conserved. Although eluding simple sequence comparisons, the DDBH2 domains share the only strong sequence motif; an extremely highly conserved YxxxIxxxW sequence that contributes to DNA binding. Sequence alignments of DnaD alone fail to identify another key part of the DNA-binding module, since it includes a poorly conserved sequence, a solvent-exposed and somewhat unstable helix and a mobile segment. We show by NMR, in vitro mutagenesis and in vivo complementation experiments that the DNA-binding module of Bacillus subtilis DnaD comprises the YxxxIxxxW motif, the unstable helix and a portion of the mobile region, the latter two being essential for viability. These structural insights lead us to a re-evaluation of the oligomerization and DNA-binding properties of the DnaD and DnaB proteins

Evaluation of the uranium double spike technique for environmental monitoring

Use of a uranium double spike in analysis of environmental samples showed that a {sup 235}U enrichment of 1% ({sup 235}U/{sup 238}U = 0.00732) can be distinguished from natural ({sup 235}U/{sup 238}U = 0.00725). Experiments performed jointly at Los Alamos National Laboratory (LANL) and Oak Ridge National Laboratory (ORNL) used a carefully calibrated double spike of {sup 233}U and {sup 236}U to obtain much better precision than is possible using conventional analytical techniques. A variety of different sampling media (vegetation and swipes) showed that, provided sufficient care is exercised in choice of sample type, relative standard deviations of less than {+-} 0.5% can be routinely obtained. This ability, unavailable without use of the double spike, has enormous potential significance in the detection of undeclared nuclear facilities

High throughput analysis of epistasis in genome-wide association studies with BiForce

Motivation: Gene–gene interactions (epistasis) are thought to be important in shaping complex traits, but they have been under-explored in genome-wide association studies (GWAS) due to the computational challenge of enumerating billions of single nucleotide polymorphism (SNP) combinations. Fast screening tools are needed to make epistasis analysis routinely available in GWAS. Results: We present BiForce to support high-throughput analysis of epistasis in GWAS for either quantitative or binary disease (case–control) traits. BiForce achieves great computational efficiency by using memory efficient data structures, Boolean bitwise operations and multithreaded parallelization. It performs a full pair-wise genome scan to detect interactions involving SNPs with or without significant marginal effects using appropriate Bonferroni-corrected significance thresholds. We show that BiForce is more powerful and significantly faster than published tools for both binary and quantitative traits in a series of performance tests on simulated and real datasets. We demonstrate BiForce in analysing eight metabolic traits in a GWAS cohort (323 697 SNPs, >4500 individuals) and two disease traits in another (>340 000 SNPs, >1750 cases and 1500 controls) on a 32-node computing cluster. BiForce completed analyses of the eight metabolic traits within 1 day, identified nine epistatic pairs of SNPs in five metabolic traits and 18 SNP pairs in two disease traits. BiForce can make the analysis of epistasis a routine exercise in GWAS and thus improve our understanding of the role of epistasis in the genetic regulation of complex traits. Availability and implementation: The software is free and can be downloaded from http://bioinfo.utu.fi/BiForce/. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

Control of the replication initiator DnaA by an anti-cooperativity factor

Proper coordination of DNA replication with cell growth and division is critical for production of viable progeny. In bacteria, coordination of DNA replication with cell growth is generally achieved by controlling activity of the replication initiator DnaA and its access to the chromosomal origin of replication, oriC. Here we describe a previously unknown mechanism for regulation of DnaA. YabA, a negative regulator of replication initiation in Bacillus subtilis, interacts with DnaA and DnaN, the sliding (processivity) clamp of DNA polymerase. We found that in vivo, YabA associated with the oriC region in a DnaA-dependent manner and limited the amount of DnaA at oriC. In vitro, purified YabA altered binding of DnaA to DNA by inhibiting cooperativity. Although previously undescribed, proteins that directly inhibit cooperativity may be a common mechanism for regulating replication initiation. Conditions that cause release of DnaN from the replisome, or overproduction of DnaN, caused decreased association of YabA and increased association of DnaA with oriC. This effect of DnaN, either directly or indirectly, is likely responsible, in part, for enabling initiation of a new round of replication following completion of a previous round.United States. Public Health Service (grant GM41934)National Institutes of Health (U.S.) (NIH Kirschstein NRSA postdoctoral fellowship F32GM093408

Ordered association of helicase loader proteins with the Bacillus subtilis origin of replication in vivo

January 1, 2011The essential proteins DnaB, DnaD and DnaI of Bacillus subtilis are required for initiation, but not elongation, of DNA replication, and for replication restart at stalled forks. The interactions and functions of these proteins have largely been determined in vitro based on their roles in replication restart. During replication initiation in vivo, it is not known if these proteins, and the replication initiator DnaA, associate with oriC independently of each other by virtue of their DNA binding activities, as a (sub)complex like other loader proteins, or in a particular dependent order. We used temperature-sensitive mutants or a conditional degradation system to inactivate each protein and test for association of the other proteins with oriC in vivo. We found that there was a clear order of stable association with oriC; DnaA, DnaD, DnaB, and finally DnaI-mediated loading of helicase. The loading of helicase via stable intermediates resembles that of eukaryotes and the established hierarchy provides several potential regulatory points. The general approach described here can be used to analyse assembly of other complexes.Netherlands Organization for Scientific Research (Rubicon fellowship)National Institutes of Health (U.S.) (Public Health Service Grant GM41934

Molybdenum solar neutrino experiment

The goal of the molybdenum solar neutrino experiment is to deduce the /sup 8/B solar neutrino flux, averaged over the past several million years, from the concentration of /sup 98/Tc in a deeply buried molybdenum deposit. The experiment is important to an understanding of stellar processes because it will shed light on the reason for the discrepancy between theory and observation of the chlorine solar neutrino experiment. Possible reasons for the discrepancy may lie in the properties of neutrinos (neutrino oscillations or massive neutrinos) or in deficiencies of the standard solar model. The chlorine experiment only measures the /sup 8/B neutrino flux in current times and does not address possible temporal variations in the interior of the sun, which are also not considered in the standard model. In the molybdenum experiment, we plan to measure /sup 98/Tc (4.2 Myr), also produced by /sup 8/B neutrinos, and possibly /sup 97/Tc (2.6 Myr), produced by lower energy neutrinos