Morphological asymmetry and interspecific hybridization: A case study using hylid frogs

The limited studies addressing developmental stability of interspecific hybrids suggest a positive association between the level of fluctuating asymmetry and 1) the degree of divergence between parental species, and 2) the recency of the contact zone. To evaluate these associations, we examined asymmetry in a recentlyestablished hybrid population of treefrogs (Hyla cinerea and H. gratiosa) that show marked structural gene divergence. Fluctuating asymmetry (FA), directional asymmetry, and antisymmetry were assessed for eight paired osteometric traits in allozymically-defined parental and hybrid categories. FA levels varied considerably among traits. Nonetheless, for any given trait, the hybrid categories did not demonstrate elevated levels of FA compared to the parental categories, or compared to frogs from a non-hybridizing parental population. The only trait that differed statistically among categories (pterygoid length) involved a significantly lower FA value for the Fl hybrids. Thus, observed FA values do not support expectations that the hybrid categories should experience decreased developmental stability

Morphological asymmetry and interspecific hybridization: A case study using hylid frogs

The limited studies addressing developmental stability of interspecific hybrids suggest a positive association between the level of fluctuating asymmetry and 1) the degree of divergence between parental species, and 2) the recency of the contact zone. To evaluate these associations, we examined asymmetry in a recentlyestablished hybrid population of treefrogs (Hyla cinerea and H. gratiosa) that show marked structural gene divergence. Fluctuating asymmetry (FA), directional asymmetry, and antisymmetry were assessed for eight paired osteometric traits in allozymically-defined parental and hybrid categories. FA levels varied considerably among traits. Nonetheless, for any given trait, the hybrid categories did not demonstrate elevated levels of FA compared to the parental categories, or compared to frogs from a non-hybridizing parental population. The only trait that differed statistically among categories (pterygoid length) involved a significantly lower FA value for the Fl hybrids. Thus, observed FA values do not support expectations that the hybrid categories should experience decreased developmental stability

Morphological asymmetry and interspecific hybridization: A case study using hylid frogs

Abstract The limited studies addressing developmental stability of interspecific hybrids suggest a positive association between the level of fluctuating asymmetry and 1) the degree of divergence between parental species, and 2) the recency of the contact zone. To evaluate these associations, we examined asymmetry in a recentlyestablished hybrid population of treefrogs (Hyla cinerea and H. gratiosa) that show marked structural gene divergence. Fluctuating asymmetry (FA), directional asymmetry, and antisymmetry were assessed for eight paired osteometric traits in allozymically-defined parental and hybrid categories. FA levels varied considerably among traits. Nonetheless, for any given trait, the hybrid categories did not demonstrate elevated levels of FA compared to the parental categories, or compared to frogs from a non-hybridizing parental population. The only trait that differed statistically among categories (pterygoid length) involved a significantly lower FA value for the Fl hybrids. Thus, observed FA values do not support expectations that the hybrid categories should experience decreased developmental stability

Shared Governance in an Adult Education Doctoral Program: “Self-Directed Learning meets Democratic Process” – A Delicate Balance of Intent, Implementation, and Impact

This symposium explores the governance component offered within a doctoral program in which students were given the opportunity to engage in collective decision-making through democratic process. Panelists, most of whom were research participants for the dissertation upon which this exploration is based, represent cohort groups from 1996 through 2007

Influence of Corn Stover Harvest on Soil Quality Assessments at Multiple Locations Across the U.S.

Corn (Zea mays L.) stover has been identified as a biofuel feedstock due to its abundance and a perception that the residues are unused trash material. However, corn stover and other plant residues play a role in maintaining soil quality (health) and enhancing productivity, thus use of this abundant material as feedstock must be balanced with the need to protect the vital soil resource. Plant residues provide physical protection against erosion by wind and water, contribute to soil structure, nutrient cycling, and help sustain the soil microbiota. Replicated plots were established on productive soils at several locations (IA, IN, MN, NE, PA, SD, and SC) and a multi-year study was carried out to determine the amount of corn stover that can be removed while maintaining the current level of soil quality for each soil. These sites represented a range of soil types and climatic conditions, and have been ongoing for and least five years with some much longer studies. All sites had at least three levels of stover harvest: grain only (control), maximum removal (90-100%) and a mid-range removal rate (~50%). Data from 4 sites are presented (IA, IN, MN, and NE). The Soil Management Assessment Framework (SMAF) was used to score and assess changes in selected soil quality indicators. Data shows that removal at the highest rates resulted in some loss in soil quality with respect to soil organic carbon and bulk density. These sites were converted to no-till when the experiments were initiated, thus SOC accrual because of the shift in tillage management appeared to balance any losses due to feedstock harvest

Randomized trial of l-serine in patients with hereditary sensory and autonomic neuropathy type 1

OBJECTIVE: To evaluate the safety and efficacy of l-serine in humans with hereditary sensory autonomic neuropathy type I (HSAN1). METHODS: In this randomized, placebo-controlled, parallel-group trial with open-label extension, patients aged 18-70 years with symptomatic HSAN1 were randomized to l-serine (400 mg/kg/day) or placebo for 1 year. All participants received l-serine during the second year. The primary outcome measure was the Charcot-Marie-Tooth Neuropathy Score version 2 (CMTNS). Secondary outcomes included plasma sphingolipid levels, epidermal nerve fiber density, electrophysiologic measurements, patient-reported measures, and adverse events. RESULTS: Between August 2013 and April 2014, we enrolled and randomized 18 participants, 16 of whom completed the study. After 1 year, the l-serine group experienced improvement in CMTNS relative to the placebo group (-1.5 units, 95% CI -2.8 to -0.1, p = 0.03), with evidence of continued improvement in the second year of treatment (-0.77, 95% CI -1.67 to 0.13, p = 0.09). Concomitantly, deoxysphinganine levels dropped in l-serine-treated but not placebo-treated participants (59% decrease vs 11% increase; p \u3c 0.001). There were no serious adverse effects related to l-serine. CONCLUSION: High-dose oral l-serine supplementation appears safe in patients with HSAN1 and is potentially effective at slowing disease progression. CLINICALTRIALSGOV IDENTIFIER: NCT01733407. CLASSIFICATION OF EVIDENCE: This study provides Class I evidence that high-dose oral l-serine supplementation significantly slows disease progression in patients with HSAN1

Topologically associating domain boundaries are required for normal genome function

Topologically associating domain (TAD) boundaries partition the genome into distinct regulatory territories. Anecdotal evidence suggests that their disruption may interfere with normal gene expression and cause disease phenotypes1,2,3, but the overall extent to which this occurs remains unknown. Here we demonstrate that targeted deletions of TAD boundaries cause a range of disruptions to normal in vivo genome function and organismal development. We used CRISPR genome editing in mice to individually delete eight TAD boundaries (11–80 kb in size) from the genome. All deletions examined resulted in detectable molecular or organismal phenotypes, which included altered chromatin interactions or gene expression, reduced viability, and anatomical phenotypes. We observed changes in local 3D chromatin architecture in 7 of 8 (88%) cases, including the merging of TADs and altered contact frequencies within TADs adjacent to the deleted boundary. For 5 of 8 (63%) loci examined, boundary deletions were associated with increased embryonic lethality or other developmental phenotypes. For example, a TAD boundary deletion near Smad3/Smad6 caused complete embryonic lethality, while a deletion near Tbx5/Lhx5 resulted in a severe lung malformation. Our findings demonstrate the importance of TAD boundary sequences for in vivo genome function and reinforce the critical need to carefully consider the potential pathogenicity of noncoding deletions affecting TAD boundaries in clinical genetics screening.This work was supported by U.S. National Institutes of Health (NIH) grants to L.A.P. and A.V. (UM1HG009421). Research was conducted at the E.O. Lawrence Berkeley National Laboratory and performed under U.S. Department of Energy Contract DE-AC02-05CH11231, University of California (UC). Phenotyping performed by the UC Davis Mouse Biology Program (MBP) (www.mousebiology.org) was funded by an NIH administrative supplement to the KOMP2 grant, 3UM1OD023221-07S1, for phenotyping non-coding elements. Adyam Akeza was supported by the NIH Bridges to Baccalaureate Program Grant R25GM095401 via UC Berkeley. J.L.-R. is supported by the Spanish Ministerio de Ciencia e Innovacion (PID2020-113497GB-I00).Peer reviewe

Influence of monolayer, spheroid, and tumor growth conditions on chromosome 3 gene expression in tumorigenic epithelial ovarian cancer cell lines

<p>Abstract</p> <p>Background</p> <p>Expression microarray analyses of epithelial ovarian cancer (EOC) cell lines may be exploited to elucidate genetic and epigenetic events important in this disease. A possible variable is the influence of growth conditions on discerning candidates. The present study examined the influence of growth conditions on the expression of chromosome 3 genes in the tumorigenic EOC cell lines, OV-90, TOV-21G and TOV-112D using Affymetrix GeneChip^®HG-U133A expression microarray analysis.</p> <p>Methods</p> <p>Chromosome 3 gene expression profiles (n = 1147 probe sets, representing 735 genes) were extracted from U133A expression microarray analyses of the EOC cell lines OV-90, TOV-21G and TOV-112D that were grown as monolayers, spheroids or nude mouse xenografts and monolayers derived from these tumors. Hierarchical cluster analysis was performed to compare chromosome 3 transcriptome patterns of each growth condition. Differentially expressed genes were identified and characterized by two-way comparative analyses of fold-differences in gene expression between monolayer cultures and each of the other growth conditions, and between the maximum and minimum values of expression of all growth conditions for each EOC cell line.</p> <p>Results</p> <p>An overall high degree of similarity (> 90%) in gene expression was observed when expression values of alternative growth conditions were compared within each EOC cell line group. Two-way comparative analysis of each EOC cell line grown in an alternative condition relative to the monolayer culture showed that overall less than 15% of probe sets exhibited at least a 3-fold difference in expression profile. Less than 23% of probe sets exhibited greater than 3-fold differences in gene expression in comparisons of the maximum and minimum value of expression of all growth conditions within each EOC cell line group. The majority of these differences were less than 5-fold. There were 17 genes in common which were differentially expressed in all EOC cell lines. However, the patterns of expression of these genes were not necessarily the same for each growth condition when one cell line was compared with another.</p> <p>Conclusion</p> <p>The various alternative <it>in vivo </it>and <it>in vitro </it>growth conditions of tumorigenic EOC cell lines appeared to modestly influence the global chromosome 3 transcriptome supporting the notion that the <it>in vitro </it>cell line models are a viable option for testing gene candidates.</p