Research Needs and Learning Format Preferences of Graduate Students at a Large Public University: An Exploratory Study

This article reports on a study of research needs and learning preferences of graduate students at a public research university. A sequential exploratory mixed-method design was used, with a survey instrument developed from an initial qualitative stage. Significant differences were found between master’s and doctoral students’ and on-campus and online students’ confidence with several research skills. Graduate students overall prefer asynchronous online options and in-person workshops over synchronous online instruction and in-class presentations for learning research skills. The article concludes with a discussion of the value of the sequential exploratory mixed-method design for informing practice at an individual institution.Publisher allows immediate open acces

Spatial encoding in primate hippocampus during free navigation.

The hippocampus comprises two neural signals-place cells and θ oscillations-that contribute to facets of spatial navigation. Although their complementary relationship has been well established in rodents, their respective contributions in the primate brain during free navigation remains unclear. Here, we recorded neural activity in the hippocampus of freely moving marmosets as they naturally explored a spatial environment to more explicitly investigate this issue. We report place cells in marmoset hippocampus during free navigation that exhibit remarkable parallels to analogous neurons in other mammalian species. Although θ oscillations were prevalent in the marmoset hippocampus, the patterns of activity were notably different than in other taxa. This local field potential oscillation occurred in short bouts (approximately .4 s)-rather than continuously-and was neither significantly modulated by locomotion nor consistently coupled to place-cell activity. These findings suggest that the relationship between place-cell activity and θ oscillations in primate hippocampus during free navigation differs substantially from rodents and paint an intriguing comparative picture regarding the neural basis of spatial navigation across mammals

Intracellular \u3cem\u3eListeria monocytogenes\u3c/em\u3e Comprises a Minimal but Vital Fraction of the Intestinal Burden Following Foodborne Infection

Listeria monocytogenes is a highly adaptive bacterium that replicates as a free-living saprophyte in the environment as well as a facultative intracellular pathogen that causes invasive foodborne infections. The intracellular life cycle of L. monocytogenes is considered to be its primary virulence determinant during mammalian infection; however, the proportion of L. monocytogenes that is intracellular in vivo has not been studied extensively. In this report, we demonstrate that the majority of wild-type (strain EGDe) and mouse-adapted (InlAm-expressing) L. monocytogenes recovered from the mesenteric lymph nodes (MLN) was extracellular within the first few days after foodborne infection. In addition, significantly lower burdens of L. monocytogenes were recovered from the colon, spleen, and liver of gentamicin-treated mice than of control mice. This led us to investigate whether intracellular replication of L. monocytogenes was essential during the intestinal phase of infection. We found that lipoate protein ligase-deficient L. monocytogenes (ΔlplA1) mutants, which display impaired intracellular growth, were able to colonize the colon but did not persist efficiently and had a significant defect in spreading to the MLN, spleen, and liver. Together, these data indicate that the majority of the L. monocytogenes burden in the gastrointestinal tract is extracellular, but the small proportion of intracellular L. monocytogenes is essential for dissemination to the MLN and systemic organs

CpeT is the Phycoerythrobilin Lyase for Cys-165 on Beta-Phycoerythrin from Fremyella Diplosiphon and the Chaperone-like Protein CpeZ Greatly Improves its Activity.

Bilin lyases are enzymes which ligate linear tetrapyrrole chromophores to specific cysteine residues on light harvesting proteins present in cyanobacteria and red algae. The lyases responsible for chromophorylating the light harvesting protein phycoerythrin (PE) have not been fully characterized. In this study, we explore the role of CpeT, a putative bilin lyase, in the biosynthesis of PE in the cyanobacterium Fremyella diplosiphon. Recombinant protein studies show that CpeT alone can bind phycoerythrobilin (PEB), but CpeZ, a chaperone-like protein, is needed in order to correctly and efficiently attach PEB to the beta-subunit of PE. MS analyses of the recombinant beta-subunit of PE coexpressed with CpeT and CpeZ show that PEB is attached at Cys-165. Purified phycobilisomes from a cpeT knockout mutant and wild type (WT) samples from F. diplosiphon were analyzed and compared. The cpeT mutant contained much less PE and more phycocyanin than WT cells grown under green light, conditions which should maximize the production of PE. In addition, Northern blot analyses showed that the cpeCDESTR operon mRNAs were upregulated while the cpeBcpeA mRNAs were downregulated in the cpeT mutant strain when compared with WT, suggesting that CpeT may also play a direct or indirect regulatory role in transcription of these operons or their mRNA stability, in addition to its role as a PEB lyase for Cys-165 on beta-PE

Assessing water uptake in sugar beet (Beta vulgaris) under different watering regimes

Sugar beet yield worldwide is substantially reduced as a result of drought stress. Water uptake may be limited by the plant (e.g. low root density) or by soil physical constraints. An experiment was conducted to assess the ability of sugar beet to produce roots and take up water throughout the soil profile under contrasting water regimes. Sugar beet was grown in columns, 15 cm in diameter and 1 m height in a glasshouse. In situ soil moisture was monitored hourly, and stomatal conductance was measured weekly. Root length and diameter at different depths were assessed destructively at 78 and 94 DAS. Greater water availability resulted in a higher root length and lower water use efficiency. Water uptake was initially from the upper soil layers but, as demand for water increased, there was a strong increase in root length density at depth. However, it was a further 16 days, after roots reached the deep layers, before significant water was taken up. A possible reason for the delay, between presence of roots and water uptake by roots, was the absence of secondary xylem early on, which was supported by a second root anatomy study. Sugar beet can grow roots up to 1 m deep and take up water from depth, however this did not happen until the late stages of drought stress and thus storage root dry weight had already been severely reduced, indicating that prevention of drought is necessary, early on, to minimise yield losses

Macrofossils and pollen representing forests of the pre-Taupo volcanic eruption (c. 1850 yr BP) era at Pureora and Benneydale, central North Island, New Zealand.

Micro- and macrofossil data from the remains of forests overwhelmed and buried at Pureora and Benneydale during the Taupo eruption (c. 1850 conventional radiocarbon yr BP) were compared. Classification of relative abundance data separated the techniques, rather than the locations, because the two primary clusters comprised pollen and litter/wood. This indicates that the pollen:litter/wood within-site comparisons (Pureora and Benneydale are 20 km apart) are not reliable. Plant macrofossils represented mainly local vegetation, while pollen assemblages represented a combination of local and regional vegetation. However, using ranked abundance and presence/absence data, both macrofossils and pollen at Pureora and Benneydale indicated conifer/broadleaved forest, of similar forest type and species composition at each site. This suggests that the forests destroyed by the eruption were typical of mid-altitude west Taupo forests, and that either data set (pollen or macrofossils) would have been adequate for regional forest interpretation. The representation of c. 1850 yr BP pollen from the known buried forest taxa was generally consistent with trends determined by modern comparisons between pollen and their source vegetation, but with a few exceptions. A pollen profile from between the Mamaku Tephra (c. 7250 yr BP) and the Taupo Ignimbrite indicated that the Benneydale forest had been markedly different in species dominance compared with the forest that was destroyed during the Taupo eruption. These differences probably reflect changes in drainage, and improvements in climate and/or soil fertility over the middle Holocene

Physiological differences between sugar beet varieties susceptible, tolerant or resistant to the beet cyst nematode, Heterodera schachtii (Schmidt) under uninfested conditions

The beet cyst nematode (BCN) is a problem to sugar beet growers around the world and can cause severe yield losses. Recently, varieties of sugar beet have been developed which are either tolerant to damage caused by BCN, or alternatively are resistant to BCN. Little is understood about these varieties and how they may have different physiological characteristics when compared with varieties of sugar beet that are susceptible to BCN. This study assessed a range of nine varieties, which were tolerant, susceptible or resistant to BCN, in pot and hydroponic tank investigations to measure differences in their canopy, early rooting and yield traits in the absence of BCN. Two field experiments, using four varieties which were susceptible, resistant or tolerant to BCN, then followed to test the hypothesis that increasing the plant population density (PPD) allows a BCN resistant variety to achieve a greater yield. In the pot and hydroponic experiments, it became clear that the varieties had different growth habits. The resistant variety yielded the least sugar and had the smallest canopy per plant. In the field experiments, which were not infested with BCN, in both years the resistant variety also showed a delayed canopy expansion compared to the other varieties. The rate of expansion could be increased by increasing the PPD. In 2016 this increased PPD resulted in higher yields of the resistant variety. However, due to better canopy development in the following year, a yield penalty was found in 2017 at higher PPDs. Understanding how different varieties need different PPDs may make resistant varieties a more economical option to cultivate in the future. However, the levels of impurities, particularly sodium impurities, in the resistant plants may still make them a less favourable choice to grow. The light tolerant varieties showed a distinct increased rooting and canopy expansion rate compared to the other variety types, while the tolerant varieties showed similar rooting and canopy traits to the susceptible varieties but had different yield responses to increased seed rate

Impact of agricultural management on soil aggregates and associated organic carbon fractions: analysis of long-term experiments in Europe

Inversion tillage is a commonly applied soil cultivation practice in Europe, which often has been blamed for deteriorating topsoil stability and organic carbon (OC) content. In this study, the potential to reverse these negative effects in the topsoil by alternative agricultural management practices are evaluated in seven long-term experiments (running from 8 to 54 years the moment of sampling) in five European countries (Belgium, Czech Republic, Hungary, Italy and UK). Topsoil samples (0–15 cm) were collected and analysed to evaluate the effects of conservation tillage (reduced and no tillage) and increased organic inputs of different origin (farmyard manure, compost, crop residues) combined with inversion tillage on topsoil stability, soil aggregates and, within these, OC distribution using wet sieving after slaking. Effects from the treatments on the two main components of organic matter, i.e. particulate (POM) and mineral associated (MAOM), were also evaluated using dispersion and size fractionation. Reduced and no-tillage practices, as well as the additions of manure or compost, increased the aggregates mean weight diameter (MWD) (up to 49 % at the Belgian study site) and topsoil OC (up to 51 % at the Belgian study site), as well as the OC corresponding to the different aggregate size fractions. The incorporation of crop residues had a positive impact on the MWD but a less profound effect both on total OC and on OC associated with the different aggregates. A negative relationship between the mass and the OC content of the microaggregates (53–250 µm) was identified in all experiments. There was no effect on the mass of the macroaggregates and the occluded microaggregates (mM) within these macroaggregates, while the corresponding OC contents increased with less tillage and more organic inputs. Inversion tillage led to less POM within the mM, whereas the different organic inputs did not affect it. In all experiments where the total POM increased, the total soil organic carbon (SOC) was also affected positively. We concluded that the negative effects of inversion tillage on topsoil can be mitigated by reducing the tillage intensity or adding organic materials, optimally combined with non-inversion tillage methods.</p

Intake of dietary soy isoflavones in relation to perimenstrual symptoms of Korean women living in the USA

This study was conducted to identify the potential relationship between the dietary intake level of soy isoflavones and perimenstrual symptomatology. The research design was a cross-sectional study. The sample was made up of 84 Korean women living in the USA, aged 28–40 years. The Moos Menstrual Distress Questionnaire (MDQ) and the Food Frequency Questionnaire were used as measurement tools. The soy isoflavone intake was significantly correlated with MDQ scores in the menstrual phase. In conclusion, the beneficial effect of dietary soy isoflavones on certain menstrual symptoms was established, suggesting that soy isoflavones could be one of the dietary factors related to the complexity of premenstrual syndrome (PMS). The positive effect of soy isoflavones on PMS warrants further study.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72547/1/j.1442-2018.2006.00270.x.pd

Site-specific perturbations of alpha-synuclein fibril structure by the Parkinson's disease associated mutations A53T and E46K.

PMCID: PMC3591419This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Parkinson's disease (PD) is pathologically characterized by the presence of Lewy bodies (LBs) in dopaminergic neurons of the substantia nigra. These intracellular inclusions are largely composed of misfolded α-synuclein (AS), a neuronal protein that is abundant in the vertebrate brain. Point mutations in AS are associated with rare, early-onset forms of PD, although aggregation of the wild-type (WT) protein is observed in the more common sporadic forms of the disease. Here, we employed multidimensional solid-state NMR experiments to assess A53T and E46K mutant fibrils, in comparison to our recent description of WT AS fibrils. We made de novo chemical shift assignments for the mutants, and used these chemical shifts to empirically determine secondary structures. We observe significant perturbations in secondary structure throughout the fibril core for the E46K fibril, while the A53T fibril exhibits more localized perturbations near the mutation site. Overall, these results demonstrate that the secondary structure of A53T has some small differences from the WT and the secondary structure of E46K has significant differences, which may alter the overall structural arrangement of the fibrils