Comptonia peregrina (L.) J.M. Coult.

https://thekeep.eiu.edu/herbarium_specimens_byname/21504/thumbnail.jp

A Basic ddRADseq Two‐Enzyme Protocol Performs Well with Herbarium and Silica‐Dried Tissues across Four Genera

PREMISE: The ability to sequence genome-scale data from herbarium specimens would allow for the economical development of data sets with broad taxonomic and geographic sampling that would otherwise not be possible. Here, we evaluate the utility of a basic double-digest restriction site–associated DNA sequencing (ddRADseq) protocol using DNAs from four genera extracted from both silica-dried and herbarium tissue. METHODS: DNAs from Draba, Boechera, Solidago, and Ilex were processed with a ddRADseq protocol. The effects of DNA degradation, taxon, and specimen age were assessed. RESULTS: Although taxon, preservation method, and specimen age affected data recovery, large phylogenetically informative data sets were obtained from the majority of samples. DISCUSSION: These results suggest that herbarium samples can be incorporated into ddRADseq project designs, and that specimen age can be used as a rapid on-site guide for sample choice. The detailed protocol we provide will allow users to pursue herbariumbased ddRADseq projects that minimize the expenses associated with fieldwork and sample evaluation

A Basic ddRADseq Two‐Enzyme Protocol Performs Well with Herbarium and Silica‐Dried Tissues across Four Genera

PREMISE: The ability to sequence genome-scale data from herbarium specimens would allow for the economical development of data sets with broad taxonomic and geographic sampling that would otherwise not be possible. Here, we evaluate the utility of a basic double-digest restriction site–associated DNA sequencing (ddRADseq) protocol using DNAs from four genera extracted from both silica-dried and herbarium tissue. METHODS: DNAs from Draba, Boechera, Solidago, and Ilex were processed with a ddRADseq protocol. The effects of DNA degradation, taxon, and specimen age were assessed. RESULTS: Although taxon, preservation method, and specimen age affected data recovery, large phylogenetically informative data sets were obtained from the majority of samples. DISCUSSION: These results suggest that herbarium samples can be incorporated into ddRADseq project designs, and that specimen age can be used as a rapid on-site guide for sample choice. The detailed protocol we provide will allow users to pursue herbariumbased ddRADseq projects that minimize the expenses associated with fieldwork and sample evaluation

Angiosperm phylogeny: 17 genes, 640 taxa

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/1/ajb20704-sup-0010.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/2/ajb20704.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/3/ajb20704-sup-0001.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/4/ajb20704-sup-0016.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/5/ajb20704-sup-0017.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/6/ajb20704-sup-0021.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/7/ajb20704-sup-0003.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/8/ajb20704-sup-0002.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/9/ajb20704-sup-0011.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/10/ajb20704-sup-0019.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/11/ajb20704-sup-0015.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/12/ajb20704-sup-0006.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/13/ajb20704-sup-0020.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/14/ajb20704-sup-0013.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/15/ajb20704-sup-0004.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/16/ajb20704-sup-0012.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/17/ajb20704-sup-0005.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/18/ajb20704-sup-0018.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/19/ajb20704-sup-0009.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/20/ajb20704-sup-0014.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/21/ajb20704-sup-0007.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/22/ajb20704-sup-0008.pd

Angiosperm Phylogeny: 17 Genes, 640 Taxa

• Premise of the study : Recent analyses employing up to fi ve genes have provided numerous insights into angiosperm phylogeny, but many relationships have remained unresolved or poorly supported. In the hope of improving our understanding of angiosperm phylogeny, we expanded sampling of taxa and genes beyond previous analyses. • Methods : We conducted two primary analyses based on 640 species representing 330 families. The fi rst included 25 260 aligned base pairs (bp) from 17 genes (representing all three plant genomes, i.e., nucleus, plastid, and mitochondrion). The second included 19 846 aligned bp from 13 genes (representing only the nucleus and plastid). • Key results : Many important questions of deep-level relationships in the nonmonocot angiosperms have now been resolved with strong support. Amborellaceae, Nymphaeales, and Austrobaileyales are successive sisters to the remaining angiosperms ( Mesangiospermae ), which are resolved into Chloranthales + Magnoliidae as sister to Monocotyledoneae + [Ceratophyllaceae + Eudicotyledoneae ]. Eudicotyledoneae contains a basal grade subtending Gunneridae . Within Gunneridae , Gunnerales are sister to the remainder ( Pentapetalae ), which comprises (1) Superrosidae , consisting of Rosidae (including Vitaceae) and Saxifragales; and (2) Superasteridae , comprising Berberidopsidales, Santalales, Caryophyllales , Asteridae , and, based on this study, Dilleniaceae (although other recent analyses disagree with this placement). Within the major subclades of Pentapetalae , most deep-level relationships are resolved with strong support. • Conclusions : Our analyses confi rm that with large amounts of sequence data, most deep-level relationships within the angiosperms can be resolved. We anticipate that this well-resolved angiosperm tree will be of broad utility for many areas of biology, including physiology, ecology, paleobiology, and genomics

Neural representation of reward in recovered depressed patients

These findings support the view that abnormal neural responses to reward may be an endophenotype for depression and a potential target for intervention and prevention strategies

Perlecan (HSPG2) promotes structural, contractile, and metabolic development of human cardiomyocytes

Perlecan (HSPG2), a heparan sulfate proteoglycan similar to agrin, is key for extracellular matrix (ECM) maturation and stabilization. Although crucial for cardiac development, its role remains elusive. We show that perlecan expression increases as cardiomyocytes mature in vivo and during human pluripotent stem cell differentiation to cardiomyocytes (hPSC-CMs). Perlecan-haploinsuffient hPSCs (HSPG2+/−) differentiate efficiently, but late-stage CMs have structural, contractile, metabolic, and ECM gene dysregulation. In keeping with this, late-stage HSPG2+/− hPSC-CMs have immature features, including reduced ⍺-actinin expression and increased glycolytic metabolism and proliferation. Moreover, perlecan-haploinsuffient engineered heart tissues have reduced tissue thickness and force generation. Conversely, hPSC-CMs grown on a perlecan-peptide substrate are enlarged and display increased nucleation, typical of hypertrophic growth. Together, perlecan appears to play the opposite role of agrin, promoting cellular maturation rather than hyperplasia and proliferation. Perlecan signaling is likely mediated via its binding to the dystroglycan complex. Targeting perlecan-dependent signaling may help reverse the phenotypic switch common to heart failure

Differential activation of the frontal pole to high vs low calorie foods: The neural basis of food preference in Anorexia Nervosa?

Neuroimaging studies in anorexia nervosa (AN) suggest that altered food reward processing may result from dysfunction in both limbic reward and cortical control centers of the brain. This fMRI study aimed to index the neural correlates of food reward in a subsample of individuals with restrictive AN: twelve currently ill, fourteen recovered individuals and sixteen healthy controls. Participants were shown pictures of high and low-calorie foods and asked to evaluate how much they wanted to eat each one following a four hour fast. Whole-brain task-activated analysis was followed by psychophysiological interaction analysis (PPI) of the amygdala and caudate. In the AN group, we observed a differential pattern of activation in the lateral frontal pole: increasing following presentation of high-calorie stimuli and decreasing in during presentation of low-calorie food pictures, the opposite of which was seen in the healthy control (HC) group. In addition, decreased activation to food pictures was observed in somatosensory regions in the AN group. PPI analyses suggested hypo-connectivity in reward pathways, and between the caudate and both somatosensory and visual processing regions in the AN group. No significant between-group differences were observed between the recovered group and the currently ill and healthy controls in the PPI analysis. Taken together, these findings further our understanding of the neural processes which may underpin the avoidance of high-calorie foods in those with AN and might exacerbate the development of compulsive weight-loss behavior, despite emaciation

Non-invasive multiresidue screening methods for the determination of pesticides in heritage collections

This paper describes the development of a novel non-invasive sampling and analysis method that can be used to assess the presence of volatile pesticides on objects held in heritage collections. Vapour phase sampling was conducted using sampling tubes loaded with Tenax-TA™ and trapped analytes were determined using thermal desorption-gas chromatography–mass spectrometry (TD-GC-MS). The results of this study are presented in a simple ‘decision tree’ diagram to provide the heritage sector with the best methods to identify the presence of pesticides in collections. To illustrate the use of the methodology developed, the results from two case studies in heritage institutions are presented. Attempts were made to measure a range of pesticides, known to have been used in heritage collections, in the vapour phase including aldrin, camphor, chloronaphthalene, dichlorodiphenyltrichloroethane (4,4′-DDT), dichlorvos, dieldrin, endrin, a mixture of α-, β-, γ- and δ-hexachlorocyclohexane (hereafter referred to as HCH), naphthalene, and thymol. Of the analytes included in this study, as expected 4,4′-DDT was not sufficiently volatile to be detected in the vapour phase and swab sampling (using hexane) is recommended for this analyte. After method development and validation, the air inside a display case (Swiss Cottage, Isle of Wight) was sampled. The results gave a positive identification for camphor, chloronaphthalene and naphthalene. In contrast, the air around a ceremonial dance mask from the British Museum was analysed but no volatile pesticides were identified. In this case, liquid chromatographic analysis of swab samples from the mask yielded a positive identification of dichlorvos. The proposed non-invasive sampling methods require sampling of a volume of air around an object. To be detected the pesticide must possess suitable volatility. It was demonstrated that camphor, chloronaphthalene, naphthalene and thymol could be successfully trapped onto Tenax TA™ sorbent tubes and pseudo-quantitatively analysed using TD-GC-MS. Dichlorvos, HCH, aldrin, dieldrin and endrin were also trapped onto Tenax TA™ and qualitatively detected by TD-GC-MS. Although a key objective of the developed methods was non-invasive sampling, the low volatility of 4,4′-DDT precluded it from vapour phase monitoring and hexane swabbing followed by HPLC analysis was required