Book reviews

Teaching/Communication/Extension/Profession,

Arabidopsis nucleolar protein database (AtNoPDB)

The Arabidopsis Nucleolar Protein Database (http://bioinf.scri.sari.ac.uk/cgi-bin/atnopdb/home) provides information on 217 proteins identified in a proteomic analysis of nucleoli isolated from Arabidopsis cell culture. The database is organized on the basis of the Arabidopsis gene identifier number. The information provided includes protein description, protein class, whether or not the plant protein has a homologue in the most recent human nucleolar proteome and the results of reciprocal BLAST analysis of the human proteome. In addition, for one-third of the 217 Arabidopsis nucleolar proteins, localization images are available from analysis of full-length cDNA–green fluorescent protein (GFP) fusions and the strength of signal in different parts of the cell—nucleolus, nucleolus-associated structures, nucleoplasm, nuclear bodies and extra-nuclear—is provided. For each protein, the most likely human and yeast orthologues, where identifiable through BLASTX analysis, are given with links to relevant information sources

The use of hydrazine-based derivatization reagents for improved sensitivity and detection of carbonyl containing compounds using MALDI-MSI

Hydrazine-based derivatization reagents have been used to detect the presence of the carbonyl containing glucocorticoid fluticasone proprionate in rat lung tissue by MALDI-MSI. Such reagents also act as a matrix for analysis by MALDI-MS and have been termed “reactive matrices”. Cryosections of rat lung tissue (12 μm), spotted with a range of concentrations of fluticasone proprionate, were derivatized in situ with 2,4-dinitrophenylhydrazine (DNPH) and 4-dimethylamino-6-(4-methoxy-1-naphthyl)-1,3,5-triazine-2-hydrazine (DMNTH) by the use of an acoustic reagent spotter. It has been demonstrated that DMNTH gave superior results compared to DNPH and that analysis of samples immediately after application of DMNTH resulted in the detection of the protonated hydrazone derivative ([MD + H]+) of fluticasone propionate at a concentration of 500 ng/μL. It has been further shown that a prolonged reaction time (~48 h) improves the detection limit of the protonated hydrazone derivative to 50 ng/μL and that improvements in sensitivity and limits of detection are obtained when a conventional MALDI matrix CHCA is employed in conjunction with the DNPH/DMNTH reactive matrix

Petion for a Writ of Certiorari. Knight v. Thompson, 136 S.Ct. 2534 (2016) (No. 15-999), 2016 U.S. S. Ct. Briefs LEXIS 542, 2016 WL 447654

QUESTION PRESENTED In Holt v. Hobbs, 135 S.Ct. 853 (2015), this Court held that the Religious Land Use and Institutionalized Persons Act of 2000 (“RLUIPA”), renders unlawful an absolute ban on inmates\u27 wearing a beard for religious reasons. The Eleventh Circuit, subsequent to and despite this Court\u27s decision in Holt, rejected a RLUIPA challenge to Alabama\u27s similarly inflexible policy prohibiting all male inmates from wearing long hair for religious reasons. A vast majority of states, the District of Columbia, and all federal prisons accommodate inmates whose religious practices include wearing beards or long hair. The Question Presented is: Whether Alabama\u27s grooming policy violates RLUIPA, 42 U.S.C. § 2000cc, et seq., to the extent that it prohibits Petitioners from wearing unshorn hair in accordance with their sincerely held religious beliefs

Reply Brief of Petitioners. Knight v. Thompson, 136 S.Ct. 2534 (2016) (No. 15-999), 2016 U.S. S. Ct. Briefs LEXIS 1645, 2016 WL 1555013+A12

QUESTION PRESENTED Section 3 of the Religious Land Use and Institutionalized Persons Act of 2000 ( RLUIPA ) prohibits state and local governments from imposing a substantial burden on the religious exercise of a person residing in or confined to an institution . . . unless the government demonstrates that imposition of the burden on that person : (1) is in furtherance of a compelling governmental interest, and (2) is the least restrictive means of furthering that compelling governmental interest. 42 U.S.C. § 2000cc-l(a). The Question Presented is: Whether RLUIPA requires that prison officials actually consider and demonstrate a sufficient basis for rejecting widely accepted accommodations to traditional religious practices as part of their burden of proving that they have chosen the least restrictive means of furthering their asserted governmental interests

A non-invasive method for measuring preimplantation embryo physiology

Author Posting. © Cambridge University Press, 2000. This article is posted here by permission of Cambridge University Press for personal use, not for redistribution. The definitive version was published in Zygote 8 (2000): 15-24, doi:10.1017/S0967199400000782.The physiology of the early embryo may be indicative of embryo vitality and therefore methods for non-invasively monitoring physiological parameters from embryos could improve preimplantation diagnoses. The self-referencing electrophysiological technique is capable of non-invasive measurement of the physiology of individual cells by monitoring the movement of ions and molecules between the cell and the surrounding media. Here we use this technique to monitor gradients of calcium, potassium, oxygen and hydrogen peroxide around individual mouse preimplantation embryos. The calcium-sensitive electrode in self-referencing mode identified a region of elevated calcium concentration ([similar]0.25 pmol) surrounding each embryo. The calcium gradient surrounding embryos was relatively steep, such that the region of elevated calcium extended into the medium only 4 [mu]m from the embryo. By contrast, using an oxygen-sensitive electrode an extensive gradient of reduced dissolved oxygen concentration was measured surrounding the embryo and extended tens of micrometres into the medium. A gradient of neither potassium nor hydrogen peroxide was observed around unperturbed embryos. We also demonstrate that monitoring the physiology of embryos using the self-referencing technique does not compromise their subsequent development. Blastocysts studied with the self-referencing technique implanted and developed to term at the same frequency as did unexamined, control embryos. Therefore, the self-referencing electrode provides a valuable non-invasive technique for studying the physiology and pathophysiology of individual embryos without hindering their subsequent development.A portion of this work was funded by an NIH R21 #RR 12718–02 to D.L.K. and P.J.S.S., KO81099 to D.L.K. and NIH P41 RR01395 to P.J.S.S

Performance of PCA3 and TMPRSS2:ERG urinary biomarkers in prediction of biopsy outcome in the Canary Prostate Active Surveillance Study (PASS).

BackgroundFor men on active surveillance for prostate cancer, biomarkers may improve prediction of reclassification to higher grade or volume cancer. This study examined the association of urinary PCA3 and TMPRSS2:ERG (T2:ERG) with biopsy-based reclassification.MethodsUrine was collected at baseline, 6, 12, and 24 months in the multi-institutional Canary Prostate Active Surveillance Study (PASS), and PCA3 and T2:ERG levels were quantitated. Reclassification was an increase in Gleason score or ratio of biopsy cores with cancer to ≥34%. The association of biomarker scores, adjusted for common clinical variables, with short- and long-term reclassification was evaluated. Discriminatory capacity of models with clinical variables alone or with biomarkers was assessed using receiver operating characteristic (ROC) curves and decision curve analysis (DCA).ResultsSeven hundred and eighty-two men contributed 2069 urine specimens. After adjusting for PSA, prostate size, and ratio of biopsy cores with cancer, PCA3 but not T2:ERG was associated with short-term reclassification at the first surveillance biopsy (OR = 1.3; 95% CI 1.0-1.7, p = 0.02). The addition of PCA3 to a model with clinical variables improved area under the curve from 0.743 to 0.753 and increased net benefit minimally. After adjusting for clinical variables, neither marker nor marker kinetics was associated with time to reclassification in subsequent biopsies.ConclusionsPCA3 but not T2:ERG was associated with cancer reclassification in the first surveillance biopsy but has negligible improvement over clinical variables alone in ROC or DCA analyses. Neither marker was associated with reclassification in subsequent biopsies

Interpreting Sentinel-1 SAR Backscatter Signals of Snowpack Surface Melt/Freeze, Warming, and Ripening, Through Field Measurements and Physically-Based SnowModel

The transition of a cold winter snowpack to one that is ripe and contributing to runoff is crucial to gauge for water resource management, but is highly variable in space and time. Snow surface melt/freeze cycles, associated with diurnal fluctuations in radiative inputs, are hallmarks of this transition. C-band synthetic aperture radar (SAR) reliably detects meltwater in the snowpack. Sentinel-1 (S1) C-band SAR offers consistent acquisition patterns that allow for diurnal investigations of melting snow. We used over 50 snow pit observations from 2020 in Grand Mesa, Colorado, USA, to track temperature and wetness in the snowpack as a function of depth and time during snowpack phases of warming, ripening, and runoff. We also ran the physically-based SnowModel, which provided a spatially and temporally continuous independent indication of snowpack conditions. Snowpack phases were identified and corroborated by comparing field measurements with SnowModel outputs. Knowledge of snowpack warming, ripening, and runoff phases was used to interpret diurnal changes in S1 backscatter values. Both field measurements and SnowModel simulations suggested that S1 SAR was not sensitive to the initial snowpack warming phase on Grand Mesa. In the ripening and runoff phases, the diurnal cycle in S1 SAR co-polarized backscatter was affected by both surface melt/freeze as well as the conditions of the snowpack underneath (ripening or ripe). The ripening phase was associated with significant increases in morning backscatter values, likely due to volume scattering from surface melt/freeze crusts, as well as significant decreases in evening backscatter values associated with snowmelt. During the runoff phase, both morning and evening backscatter decreased compared to reference values. These unique S1 diurnal signatures, and their interpretations using field measurements and SnowModel outputs, highlight the capacities and limitations of S1 SAR to understand snow surface states and bulk phases, which may offer runoff forecasting or energy balance model validation or parameterization, especially useful in remote or sparsely-gauged alpine basins

Use of Surface Motion Characteristics Determined by InSAR to Assess Peatland Condition

Peatland surface motion is a key property of peatland that relates to condition. However, field‐based techniques to measure surface motion are not cost‐effective over large areas and long time periods. An alternative method that can quantify peatland surface motion over large areas is interferometric synthetic aperture radar. Although field validation of the accuracy of this method is difficult, the value of InSAR as a means of quantifying peat condition can be tested. To achieve this the characteristics of InSAR time series measured over an18‐month period at 22 peatland sites in the Flow Country northern Scotland were compared to site condition assessment based on plant functional type and site management history. Sites in good condition dominated by Sphagnum display long‐term stability or growth and a seasonal cycle with maximum uplift and subsidence in Aug‐Nov and April‐June respectively. Drier and partially drained sites dominated by shrubs display long‐term subsidence with maximum uplift and subsidence in July‐Oct and Feb‐June respectively. Heavily degraded sites with large bare peat extent display subsidence with no distinct seasonal oscillations. Seasonal oscillation in surface motion at sites with a dominant non‐vascular plant community is interpreted as resulting from changes in seasonal evaporative demand. On sites with extensive vascular plants cover and falling water table, surface oscillations are interpreted as representing sustained drawdown during the growing season and subsequent recharge in late winter. This study highlights the potential to use InSAR to characterize peatland condition and provide a new view of the surface dynamics of peatland landscapes