Whitepaper on design and collaborative practices

Coming to a large state university, many students have not yet mastered how to effectively learn and study. Creating a freshman learning strategy website would be a step in the right direction to guide and inform students on topics such as time management, writing tips, and study strategies

Epigenetic inheritance of an inducibly nucleosome-depleted promoter and its associated transcriptional state in the apparent absence of transcriptional activators

<p>Abstract</p> <p>Background</p> <p>Dynamic changes to the chromatin structure play a critical role in transcriptional regulation. This is exemplified by the Spt6-mediated histone deposition on to histone-depleted promoters that results in displacement of the general transcriptional machinery during transcriptional repression.</p> <p>Results</p> <p>Using the yeast <it>PHO5 </it>promoter as a model, we have previously shown that blocking Spt6-mediated histone deposition on to the promoter leads to persistent transcription in the apparent absence of transcriptional activators <it>in vivo</it>. We now show that the nucleosome-depleted <it>PHO5 </it>promoter and its associated transcriptionally active state can be inherited through DNA replication even in the absence of transcriptional activators. Transcriptional reinitiation from the nucleosome-depleted <it>PHO5 </it>promoter in the apparent absence of activators <it>in vivo </it>does not require Mediator. Notably, the epigenetic inheritance of the nucleosome-depleted <it>PHO5 </it>promoter through DNA replication does not require ongoing transcription.</p> <p>Conclusion</p> <p>Our results suggest that there may be a memory or an epigenetic mark on the nucleosome-depleted <it>PHO5 </it>promoter that is independent of the transcription apparatus and maintains the promoter in a nucleosome-depleted state through DNA replication.</p

Respondent-Driven Sampling: An Overview in the Context of Human Trafficking

Respondent-driven sampling (RDS) is both a sampling strategy and an estimation method. It is commonly used to study individuals that are difficult to access with standard sampling techniques. As with any sampling strategy, RDS has advantages and challenges. This article examines recent work using RDS in the context of human trafficking. We begin with an overview of the RDS process and methodology, then discuss RDS in the particular context of trafficking. We end with a description of recent work and potential future directions

Characterisation of the DNA Binding Domain of the Transcriptional Regulator Encoded by VZV Gene 62

The understanding of gene regulation during varicella-zoster virus (VZV) infection is still rudimentary, although insight can be gained from the more extensively studied system of the genetically related herpes simplex virus type 1 (HSV-1). Upon infection, HSV-1 expresses three main classes of genes in a coordinately regulated temporal cascade; the immediate-early (IE), early (E) and late (L) genes. The product of the HSV-1 IE3 gene, Vmwl75, is considered to be the major regulatory protein of HSV-1 because functional Vmwl75 is an absolute requirement for transactivation of E and L gene expression and for the down-regulation of its own IE3 promoter. The polypeptide encoded by VZV gene 62 (VZV 140k) is the sequence homologue of HSV-1 Vmwl75. Transient transfection experiments have demonstrated that VZV 140k is a potent and promiscuous transactivator of gene expression, and that it can also negatively autoregulate its own gene 62 promoter. In addition, VZV 140k can complement HSV-1 viruses lacking functional Vmwl75. Therefore, by analogy to its HSV-1 counterpart, VZV 140k is likely to play a critical role in the regulation of VZV gene expression. The research described in this Thesis aimed to investigate the properties and activities of the DNA binding domain of the VZV 140k protein, in order to gain a better understanding of the mechanisms of 140k-mediated gene regulation during infection. The primary sequences of VZV 140k and HSV-1 Vmwl75 have been divided into five co-linear regions on the basis of the extent of their predicted amino acid identity. The region 2 sequences are particularly highly conserved between the two proteins and the regulatory functions of Vmwl75 require the integrity of region 2. Furthermore, sequences spanning HSV-1 Vmwl75 region 2 constitute a physically separable, stable DNA binding domain. Many of the experiments in this study stemmed from the initial demonstration that the corresponding region of the VZV 140k protein also yields a sequence-specific DNA binding domain when expressed as a non-fusion polypeptide in bacteria. The bacterially expressed VZV 140k DNA binding domain specifically recognised multiple DNA sequences in the vicinity of its target promoters; the 140k binding sites identified within its own VZV gene 62 promoter may have a role in the negative autoregulatory function of the 140k protein. Several of the 140k recognition sites showed sequence similarity to the Vmwl75 consensus binding sequence, although gel retardation assays with a systematically mutagenised binding site found the VZV 140k DNA binding domain peptide to be less sequence-specific than the corresponding domain of HSV-1 Vmwl75. These and further differences that have been identified between the DNA binding activities of the VZV 140k and HSV-1 Vmwl75 DNA binding domains may explain the previously reported variations between the regulatory functions of 140k and Vmwl75. The minimal region of the VZV 140k protein required for sequence-specific DNA binding has been defined by a deletion analysis to within 162 residues, essentially comprising the highly conserved region 2. However, additional sequences from the C-terminal end of region 1 were necessary for the full DNA binding interaction, as determined by DNase I footprinting analysis. As such, the DNA binding domain of VZV 140k is larger than those reported for other transcriptional regulators (which are often less than 80 amino acids) and therefore it may constitute a novel type of DNA binding structure. A short sequence that exhibits intriguing homology to the conserved DNA recognition helix of the homeodomain DNA binding motif is found at the centre of the VZV 140k DNA binding domain. The alterations to the DNA binding interaction that resulted from the substitution of single amino acids within this region indicate its probable involvement in the DNA recognition by VZV 140k. Of particular note, mutation of a single lysine residue drastically reduced the DNA binding activity and destroyed the transactivation function of VZV 140k; this result emphasises the importance of DNA binding for VZV 140k-mediated gene regulation. The highly purified VZV 140k DNA binding domain was a stable dimer in solution, as demonstrated by gel filtration, glycerol gradient centrifugation and cross-linking techniques. The fact that the VZV 140k DNA binding domain binds to DNA as a dimer was indicated by gel retardation assays that showed novel protein-DNA complexes of intermediate mobility following in vitro co-translation of pairs of VZV 140k peptides of differing sizes. In addition, the VZV 140k and HSV-1 Vmwl75 DNA binding domain peptides readily heterodimerised on co-translation, which indicated that these two related domains have similar modes of dimerisation. In vitro co-translation of a wide range of truncation and insertion mutation versions of the VZV 140k and HSV-1 Vmwl75 DNA binding domains, followed by analysis of their dimerisation by co-immunoprecipitation and their DNA binding ability by gel retardation, has indicated that the structural requirements for dimerisation are lower than for the DNA binding interaction. Finally, construction of a hybrid Vmwl75 protein with the VZV 140k DNA binding domain replacing that of HSV-1 Vmwl75 has allowed the relatedness of the two domains to be assessed directly. The hybrid protein was functional in tissue culture transient transfection assays and furthermore, supported viral growth when expressed from a recombinant HSV-1 genome. The details of the regulatory activities of the hybrid protein in the transient assays implied that the characteristic DNA binding activities of the VZV 140k DNA binding domain play an important part in determining its specific regulatory functions

The Experiences of Collegiality by Early-Career Counselor Educators

It is essential to develop a work culture that supports faculty needs, be it professional for promotion and tenure, or personal. This phenomenological study examined the lived experiences of collegiality by early-career counselor educator faculty members (CES) working in a CACREP institution. Relational support, expectations, administration, and doctoral experiences emerged as themes from these narratives. Implications for the field are discussed to address these experiences and provide recommendations to counselor education faculty and departments

Potter Road Bridge replacement

The purpose of this Environmental Impact Assessment (EIA) is to analyze and determine what effect the replacement of Potter Road Bridge will have on the environment. Potter Road Bridge is located in Whatcom County, Washington, and it crosses over the South Fork Nooksack River near the town of Van Zandt (Figures 1,2). Building on the Environmental Checklist that was prepared by Whatcom County, this EIA identifies significant impacts on both the natural and built environment. It also looks at a no-action alternative, as well as an alternative in which the bridge would be eliminated and Smith Road would be extended eastward

Maternal developmental history alters transfer of circadian clock genes to offspring in Japanese quail (Coturnix japonica)

Funding: This work was supported by the UKRI Biotechnology and Biological Sciences Research Council (BBSRC) Eastbio Doctoral Training Programme grant number BB/M010996/1.Maternal signals shape embryonic development, and in turn post-natal phenotypes. RNA deposition is one such method of maternal signalling and circadian rhythms are one trait thought to be maternally inherited, through this mechanism. These maternal circadian gene transcripts aid development of a functioning circadian system. There is increasing evidence that maternal signals can be modified, depending on prevailing environmental conditions to optimise offspring fitness. However, currently, it is unknown if maternal circadian gene transcripts, and consequently early embryonic gene transcription, are altered by maternal developmental conditions. Here, using avian mothers who experienced either pre-natal corticosterone exposure, and/or post-natal stress as juveniles we were able to determine the effects of the timing of stress on downstream circadian RNA deposition in offspring. We demonstrated that maternal developmental history does indeed affect transfer of offspring circadian genes, but the timing of stress was important. Avian mothers who experienced stress during the first 2 weeks of post-natal life increased maternally deposited transcript levels of two core circadian clock genes, BMAL1 and PER2. These differences in transcript levels were transient and disappeared at the point of embryonic genome transcription. Pre-natal maternal stress alone was found to elicit delayed changes in circadian gene expression. After activation of the embryonic genome, both BMAL1 and PER2 expression were significantly decreased. If both pre-natal and post-natal stress occurred, then initial maternal transcript levels of BMAL1 were significantly increased. Taken together, these results suggest that developmental stress differentially produces persistent transgenerational effects on offspring circadian genes.Publisher PDFPeer reviewe

Visual perception of photographs of rotated 3D objects in goldfish (Carassius auratus)

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Wegman, J. J., Morrison, E., Wilcox, K. T., & DeLong, C. M. Visual perception of photographs of rotated 3D objects in goldfish (Carassius auratus). Animals, 12(14), (2022): 1797, https://doi.org/10.3390/ani12141797.This study examined goldfishes’ ability to recognize photographs of rotated 3D objects. Six goldfish were presented with color photographs of a plastic model turtle and frog at 0° in a two-alternative forced-choice task. Fish were tested with stimuli at 0°, 90°, 180°, and 270° rotated in the picture plane and two depth planes. All six fish performed significantly above chance at all orientations in the three rotation planes tested. There was no significant difference in performance as a function of aspect angle, which supported viewpoint independence. However, fish were significantly faster at 180° than at +/−90°, so there is also evidence for viewpoint-dependent representations. These fish subjects performed worse overall in the current study with 2D color photographs (M = 88.0%) than they did in our previous study with 3D versions of the same turtle and frog stimuli (M = 92.6%), although they performed significantly better than goldfish in our two past studies presented with black and white 2D stimuli (M = 67.6% and 69.0%). The fish may have relied on color as a salient cue. This study was a first attempt at examining picture-object recognition in fish. More work is needed to determine the conditions under which fish succeed at object constancy tasks, as well as whether they are capable of perceiving photographs as representations of real-world objectsThis work was supported with a RIT College of Liberal Arts Faculty Development Grant to CMD and the RIT Paul A. and Francena L. Miller Research Fellowship awarded to CMD from the Rochester Institute of Technology

Mediation analysis for a survival outcome with time-varying exposures, mediators, and confounders

We propose an approach to conduct mediation analysis for survival data with time-varying exposures, mediators, and confounders. We identify certain interventional direct and indirect effects through a survival mediational g-formula and describe the required assumptions. We also provide a feasible parametric approach along with an algorithm and software to estimate these effects. We apply this method to analyze the Framingham Heart Study data to investigate the causal mechanism of smoking on mortality through coronary artery disease. The risk ratio of smoking 30 cigarettes per day for ten years compared with no smoking on mortality is 2.34 (95 % CI = (1.44, 3.70)). Of the overall effect, 7.91% (95% CI: = 1.36%, 19.32%) is mediated by coronary artery disease. The survival mediational g-formula constitutes a powerful tool for conducting mediation analysis with longitudinal data