Experts\u27 Advice to Information Systems Doctoral Students

This paper summarizes the results of a panel discussion offering advice to doctoral students in advancing through their programs and getting a start on their career. The panel was held at the 2003 Annual Conference of the Southern Association for Information Systems, and panelists included five senior MIS faculty members who, combined, have chaired over 80 dissertations. Topics included choosing a dissertation topic, dealing with the dissertation committee, completing the dissertation, the job hunt, marketability, building a publication record, and advice for new faculty

CRISPR/Cas9 DNA cleavage at SNP-derived PAM enables both in vitro and in vivo KRT12 mutation-specific targeting

CRISPR/Cas9-based therapeutics hold the possibility for permanent treatment of genetic disease. The potency and specificity of this system has been used to target dominantly inherited conditions caused by heterozygous missense mutations through inclusion of the mutated base in the short-guide RNA (sgRNA) sequence. This research evaluates a novel approach for targeting heterozygous single-nucleotide polymorphisms (SNPs) using CRISPR/Cas9. We determined that a mutation within KRT12, which causes Meesmann's epithelial corneal dystrophy (MECD), leads to the occurrence of a novel protospacer adjacent motif (PAM). We designed an sgRNA complementary to the sequence adjacent to this SNP-derived PAM and evaluated its potency and allele specificity both in vitro and in vivo. This sgRNA was found to be highly effective at reducing the expression of mutant KRT12 mRNA and protein in vitro. To assess its activity in vivo we injected a combined Cas9/sgRNA expression construct into the corneal stroma of a humanized MECD mouse model. Sequence analysis of corneal genomic DNA revealed non-homologous end-joining repair resulting in frame-shifting deletions within the mutant KRT12 allele. This study is the first to demonstrate in vivo gene editing of a heterozygous disease-causing SNP that results in a novel PAM, further highlighting the potential for CRISPR/Cas9-based therapeutics

CRISPR/Cas9 DNA cleavage at SNP-derived PAM enables both in vitro and in vivo KRT12 mutation-specific targeting

CRISPR/Cas9-based therapeutics hold the possibility for permanent treatment of genetic disease. The potency and specificity of this system has been used to target dominantly inherited conditions caused by heterozygous missense mutations through inclusion of the mutated base in the short-guide RNA (sgRNA) sequence. This research evaluates a novel approach for targeting heterozygous single-nucleotide polymorphisms (SNPs) using CRISPR/Cas9. We determined that a mutation within KRT12, which causes Meesmann's epithelial corneal dystrophy (MECD), leads to the occurrence of a novel protospacer adjacent motif (PAM). We designed an sgRNA complementary to the sequence adjacent to this SNP-derived PAM and evaluated its potency and allele specificity both in vitro and in vivo. This sgRNA was found to be highly effective at reducing the expression of mutant KRT12 mRNA and protein in vitro. To assess its activity in vivo we injected a combined Cas9/sgRNA expression construct into the corneal stroma of a humanized MECD mouse model. Sequence analysis of corneal genomic DNA revealed non-homologous end-joining repair resulting in frame-shifting deletions within the mutant KRT12 allele. This study is the first to demonstrate in vivo gene editing of a heterozygous disease-causing SNP that results in a novel PAM, further highlighting the potential for CRISPR/Cas9-based therapeutics

Keratin 12 missense mutation induces the unfolded protein response and apoptosis in meesmann epithelial corneal dystrophy

Meesmann epithelial corneal dystrophy (MECD) is a rare autosomal dominant disorder caused by dominant-negative mutations within the KRT3 or KRT12 genes, which encode the cytoskeletal protein keratins K3 and K12, respectively. To investigate the pathomechanism of this disease, we generated and phenotypically characterized a novel knock-in humanized mouse model carrying the severe, MECD-associated, K12-Leu132Pro mutation. Although no overt changes in corneal opacity were detected by slit-lamp examination, the corneas of homozygous mutant mice exhibited histological and ultrastructural epithelial cell fragility phenotypes. An altered keratin expression profile was observed in the cornea of mutant mice, confirmed by western blot, RNA-seq and quantitative real-time polymerase chain reaction. Mass spectrometry (MS) and immunohistochemistry demonstrated a similarly altered keratin profile in corneal tissue from a K12-Leu132Pro MECD patient. The K12-Leu132Pro mutation results in cytoplasmic keratin aggregates. RNA-seq analysis revealed increased chaperone gene expression, and apoptotic unfolded protein response (UPR) markers, CHOP and Caspase 12, were also increased in the MECD mice. Corneal epithelial cell apoptosis was increased 17-fold in the mutant cornea, compared with the wild-type (P < 0.001). This elevation of UPR marker expression was also observed in the human MECD cornea. This is the first reporting of a mouse model for MECD that recapitulates the human disease and is a valuable resource in understanding the pathomechanism of the disease. Although the most severe phenotype is observed in the homozygous mice, this model will still provide a test-bed for therapies not only for corneal dystrophies but also for other keratinopathies caused by similar mutations

Chatpal Chatbot dialogue data set

The scripts used in the ChatPal chatbot are freely available as an output from the ChatPal project. The datasets contain the chatbot utterances in English, Swedish, Finnish and Scottish Gaelic. Any replies collected from users through the ChatPal chatbot are not included in these data. Datasets are available in csv format and contain Unicode character encodings (UTF-8). Disclaimer: The datasets are open access, should be used appropriately and can be repurposed. However, the ChatPal project team are not responsible for how you chose to use the data or repurpose the content

IL-27 induces an IFN-like signature in murine macrophages which in turn modulate colonic epithelium

Mucosal delivery of IL-27 has been shown to have a therapeutic benefit in murine models of inflammatory bowel disease (IBD). The IL-27 effect was associated with phosphorylated STAT1 (pSTAT1), a product of IL27 receptor signaling, in bowel tissue. To determine whether IL-27 acted directly on colonic epithelium, murine colonoids and primary intact colonic crypts were shown to be unresponsive to IL-27 in vitro and to lack detectable IL-27 receptors. On the other hand, macrophages, which are present in inflamed colon tissue, were responsive to IL-27 in vitro. IL-27 induced pSTAT1 in macrophages, the transcriptome indicated an IFN-like signature, and supernatants induced pSTAT1 in colonoids. IL-27 induced anti-viral activity in macrophages and MHC Class II induction. We conclude that the effects of mucosal delivery of IL-27 in murine IBD are in part based on the known effects of IL27 inducing immunosuppression of T cells mediated by IL-10. We also conclude that IL-27 has potent effects on macrophages in inflamed colon tissue, generating mediators that in turn act on colonic epithelium

Vetting of 384 TESS Objects of Interest with TRICERATOPS and Statistical Validation of 12 Planet Candidates

We present TRICERATOPS, a new Bayesian tool that can be used to vet and validate TESS Objects of Interest (TOIs). We test the tool on 68 TOIs that have been previously confirmed as planets or rejected as astrophysical false positives. By looking in the false positive probability (FPP) -- nearby false positive probability (NFPP) plane, we define criteria that TOIs must meet to be classified as validated planets (FPP < 0.015 and NFPP < 10^-3), likely planets (FPP 10^-1). We apply this procedure on 384 unclassified TOIs and statistically validate 12, classify 125 as likely planets, and classify 52 as likely nearby false positives. Of the 12 statistically validated planets, 9 are newly validated. TRICERATOPS is currently the only TESS vetting and validation tool that models transits from nearby contaminant stars in addition to the target star. We therefore encourage use of this tool to prioritize follow-up observations that confirm bona fide planets and identify false positives originating from nearby stars.Comment: Accepted to A

Rumen biogeographical regions and their impact on microbial and metabolome variation

The rumen microbiome is a complex microbial network critical to the health and nutrition of its host, due to their inherent ability to convert low-quality feedstuffs into energy. In rumen microbiome studies, samples from the ventral sac are most often collected because of the ease of access and repeatability. However, anatomical musculature demarcates the rumen into five sacs (biogeographical regions), which may support distinct microbial communities. The distinction among the microbes may generate functional variation among the rumen microbiome, thus, specialized tasks within different sacs. The objective of this study was to determine the rumen liquid metabolome and epimural, planktonic, and fiber-adherent bacterial communities among each rumen biogeographical region. It was hypothesized that differences in bacterial species and metabolome would occur due to differing anatomy and physiology associated with the respective regions. To assess this variation, epithelial and content microbial-associated communities were evaluated, as well as the metabolites among various rumen biogeographical regions. A total of 17 cannulated Angus cows were utilized to examine the fiber-adherent (solid fraction), planktonic (liquid fraction), and epimural microbial communities from the cranial, dorsal, caudodorsal blind, caudoventral blind, and ventral sacs. Metagenomic DNA was extracted and sequenced from the hypervariable V4 region of the 16S rRNA gene. Reads were processed using packages ‘phyloseq’ and ‘dada2’ in R. Untargeted metabolomics were conducted on rumen liquid from each sac using UHPLC-HRMS and analyzed in MetaboAnalyst 5.0. An analysis of variance (ANOVA) revealed 13 significant differentially abundant metabolites with pairwise comparisons against the five rumen sacs (P &lt; 0.05). Within the bacterial communities, neither alpha nor beta diversity determined significance against the rumen sacs (P &gt; 0.05), although there was significance against the fraction types (P &lt; 0.05). Utilizing multivariable association analysis with MaAslin2, there were significant differential abundances found in fraction type × location (P &lt; 0.05). Knowledge of similarities among fiber-adherent microbial communities provides evidence that single sac sampling is sufficient for this fraction. However, future projects focusing on either planktonic or epimural fractions may need to consider multiple rumen sac sampling to obtain the most comprehensive analysis of the rumen. Defining these variabilities, especially among the rumen epimural microbiome, are critical to define host-microbiome interactions

Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection

Understanding the molecular basis for phenotypic differences between humans and other primates remains an outstanding challenge. Mutations in non-coding regulatory DNA that alter gene expression have been hypothesized as a key driver of these phenotypic differences. This has been supported by differential gene expression analyses in general, but not by the identification of specific regulatory elements responsible for changes in transcription and phenotype. To identify the genetic source of regulatory differences, we mapped DNaseI hypersensitive (DHS) sites, which mark all types of active gene regulatory elements, genome-wide in the same cell type isolated from human, chimpanzee, and macaque. Most DHS sites were conserved among all three species, as expected based on their central role in regulating transcription. However, we found evidence that several hundred DHS sites were gained or lost on the lineages leading to modern human and chimpanzee. Species-specific DHS site gains are enriched near differentially expressed genes, are positively correlated with increased transcription, show evidence of branch-specific positive selection, and overlap with active chromatin marks. Species-specific sequence differences in transcription factor motifs found within these DHS sites are linked with species-specific changes in chromatin accessibility. Together, these indicate that the regulatory elements identified here are genetic contributors to transcriptional and phenotypic differences among primate species

TKS X: Confirmation of TOI-1444b and a Comparative Analysis of the Ultra-short-period Planets with Hot Neptunes

We report the discovery of TOI-1444b, a 1.4-$R_\oplus$ super-Earth on a 0.47-day orbit around a Sun-like star discovered by {\it TESS}. Precise radial velocities from Keck/HIRES confirmed the planet and constrained the mass to be $3.87 \pm 0.71 M_\oplus$. The RV dataset also indicates a possible non-transiting, 16-day planet ($11.8\pm2.9M_\oplus$). We report a tentative detection of phase curve variation and secondary eclipse of TOI-1444b in the {\it TESS} bandpass. TOI-1444b joins the growing sample of 17 ultra-short-period planets with well-measured masses and sizes, most of which are compatible with an Earth-like composition. We take this opportunity to examine the expanding sample of ultra-short-period planets ($<2R_\oplus$) and contrast them with the newly discovered sub-day ultra-hot Neptunes ($>3R_\oplus$, $>2000F_\oplus$ TOI-849 b, LTT9779 b and K2-100). We find that 1) USPs have predominately Earth-like compositions with inferred iron core mass fractions of 0.32$\pm$0.04; and have masses below the threshold of runaway accretion ($\sim 10M_\oplus$), while ultra-hot Neptunes are above the threshold and have H/He or other volatile envelope. 2) USPs are almost always found in multi-planet system consistent with a secular interaction formation scenario; ultra-hot Neptunes ($P_{\rm orb} \lesssim$1 day) tend to be ``lonely' similar to longer-period hot Neptunes($P_{\rm orb}$1-10 days) and hot Jupiters. 3) USPs occur around solar-metallicity stars while hot Neptunes prefer higher metallicity hosts. 4) In all these respects, the ultra-hot Neptunes show more resemblance to hot Jupiters than the smaller USP planets, although ultra-hot Neptunes are rarer than both USP and hot Jupiters by 1-2 orders of magnitude.Comment: Accepted too AJ. 12 Figures, 4 table