Structure of the PII signal transduction protein of Neisseria meningitidis at 1.85 Ȃ resolution

Copyright @ 2006 International Union of CrystallographyThe PII signal transduction proteins GlnB and GlnK are implicated in the regulation of nitrogen assimilation in Escherichia coli and other enteric bacteria. PII-like proteins are widely distributed in bacteria, archaea and plants. In contrast to other bacteria, Neisseria are limited to a single PII protein (NMB 1995), which shows a high level of sequence identity to GlnB and GlnK from Escherichia coli (73 and 62%, respectively). The structure of the PII protein from N. meningitidis (serotype B) has been solved by molecular replacement to a resolution of 1.85 Ȃ. Comparison of the structure with those of other PII proteins shows that the overall fold is tightly conserved across the whole population of related proteins, in particular the positions of the residues implicated in ATP binding. It is proposed that the Neisseria PII protein shares functions with GlnB/GlnK of enteric bacteria.This study is funded by the Medical Research Council UK and Europe (SPINE) consortium (European Commission Grant No. QLG2-CT-2002-00988)

Contaminated Confessions Revisited

A second wave of false confessions is cresting. In the first twenty-one years of post-conviction DNA testing, 250 innocent people were exonerated, forty of which had falsely confessed. Those false confessions attracted sustained public attention from judges, law enforcement, policymakers, and the media. Those exonerations not only showed that false confessions can happen, but did more by shedding light on the problem of confession contamination, in which details of the crime are disclosed to suspects during the interrogation process. As a result, false confessions can appear deceptively rich, detailed, and accurate. In just the last five years, there has been a new surge in false confessions — a set of twenty-six more false confessions among DNA exonerations. All but two of these most recent confessions included crime scene details corroborated by crime scene information. Illustrating the power of contaminated false confessions, in nine of the cases, defendants were convicted despite DNA tests that excluded them at the time. As a result, this second wave of false confessions should cause even more alarm than the first. In the vast majority of cases there is no evidence to test using DNA. Unless a scientific framework is adopted to regulate interrogations, including by requiring recording of entire interrogations, overhauling interrogation methods, providing for judicial review of reliability at trial, and informing jurors with expert testimony, the insidious problems of confession contamination will persist

Invalid Forensic Science Testimony and Wrongful Convictions

This is the first study to explore the forensic science testimony by prosecution experts in the trials of innocent persons, all convicted of serious crimes, who were later exonerated by post-conviction DNA testing. Trial transcripts were sought for all 156 exonerees identified as having trial testimony by forensic analysts, of which 137 were located and reviewed. These trials most commonly included testimony concerning serological analysis and microscopic hair comparison, but some included bite mark, shoe print, soil, fiber, and fingerprint comparisons, and several included DNA testing. This study found that in the bulk of these trials of innocent defendants - 82 cases or 60% - forensic analysts called by the prosecution provided invalid testimony at trial - that is, testimony with conclusions misstating empirical data or wholly unsupported by empirical data. This was not the testimony of a mere handful of analysts: this set of trials included invalid testimony by 72 forensic analysts called by the prosecution and employed by 52 laboratories, practices, or hospitals from 25 states. Unfortunately, the adversarial process largely failed to police this invalid testimony. Defense counsel rarely cross-examined analysts concerning invalid testimony and rarely obtained experts of their own. In the few cases in which invalid forensic science was challenged, judges seldom provided relief. This evidence supports efforts to create scientific oversight mechanisms for reviewing forensic testimony and to develop clear scientific standards for written reports and testimony. The scientific community can through an official government entity promulgate standards to ensure the valid presentation of forensic science in criminal cases and thus the integrity and fairness of the criminal process

Contaminated Confessions Revisited

A second wave of false confessions is cresting. In the first twenty-one years of post-conviction DNA testing, 250 innocent people were exonerated, forty of which had falsely confessed. Those false confessions attracted sustained public attention from judges, law enforcement, policymakers, and the media. Those exonerations not only showed that false confessions can happen, but did more by shedding light on the problem of confession contamination, in which details of the crime are disclosed to suspects during the interrogation process. As a result, false confessions can appear deceptively rich, detailed, and accurate. In just the last five years, there has been a new surge in false confessions — a set of twenty-six more false confessions among DNA exonerations. All but two of these most recent confessions included crime scene details corroborated by crime scene information. Illustrating the power of contaminated false confessions, in nine of the cases, defendants were convicted despite DNA tests that excluded them at the time. As a result, this second wave of false confessions should cause even more alarm than the first. In the vast majority of cases there is no evidence to test using DNA. Unless a scientific framework is adopted to regulate interrogations, including by requiring recording of entire interrogations, overhauling interrogation methods, providing for judicial review of reliability at trial, and informing jurors with expert testimony, the insidious problems of confession contamination will persist

Invalid Forensic Science Testimony and Wrongful Convictions

This is the first study to explore the forensic science testimony by prosecution experts in the trials of innocent persons, all convicted of serious crimes, who were later exonerated by post-conviction DNA testing. Trial transcripts were sought for all 156 exonerees identified as having trial testimony by forensic analysts, of which 137 were located and reviewed. These trials most commonly included testimony concerning serological analysis and microscopic hair comparison, but some included bite mark, shoe print, soil, fiber, and fingerprint comparisons, and several included DNA testing. This study found that in the bulk of these trials of innocent defendants - 82 cases or 60% - forensic analysts called by the prosecution provided invalid testimony at trial - that is, testimony with conclusions misstating empirical data or wholly unsupported by empirical data. This was not the testimony of a mere handful of analysts: this set of trials included invalid testimony by 72 forensic analysts called by the prosecution and employed by 52 laboratories, practices, or hospitals from 25 states. Unfortunately, the adversarial process largely failed to police this invalid testimony. Defense counsel rarely cross-examined analysts concerning invalid testimony and rarely obtained experts of their own. In the few cases in which invalid forensic science was challenged, judges seldom provided relief. This evidence supports efforts to create scientific oversight mechanisms for reviewing forensic testimony and to develop clear scientific standards for written reports and testimony. The scientific community can through an official government entity promulgate standards to ensure the valid presentation of forensic science in criminal cases and thus the integrity and fairness of the criminal process

Mutation of Arabidopsis SPLICEOSOMAL TIMEKEEPER LOCUS1 Causes Circadian Clock Defects

The circadian clock plays a crucial role in coordinating plant metabolic and physiological functions with predictable environmental variables, such as dusk and dawn, while also modulating responses to biotic and abiotic challenges. Much of the initial characterization of the circadian system has focused on transcriptional initiation, but it is now apparent that considerable regulation is exerted after this key regulatory step. Transcript processing, protein stability, and cofactor availability have all been reported to influence circadian rhythms in a variety of species. We used a genetic screen to identify a mutation within a putative RNA binding protein (SPLICEOSOMAL TIMEKEEPER LOCUS1 [STIPL1]) that induces a long circadian period phenotype under constant conditions. STIPL1 is a homolog of the spliceosomal proteins TFP11 (Homo sapiens) and Ntr1p (Saccharomyces cerevisiae) involved in spliceosome disassembly. Analysis of general and alternative splicing using a high-resolution RT-PCR system revealed that mutation of this protein causes less efficient splicing of most but not all of the introns analyzed. In particular, the altered accumulation of circadian-associated transcripts may contribute to the observed mutant phenotype. Interestingly, mutation of a close homolog of STIPL1, STIP-LIKE2, does not cause a circadian phenotype, which suggests divergence in function between these family members. Our work highlights the importance of posttranscriptional control within the clock mechanism. © 2012 American Society of Plant Biologists. All rights reserved

Membrane proteins in the outer mebrane of plastids and mitochondria

Channels of the plastid and mitochondrial outer membranes facilitate the turnover of molecules and ions via these membranes. Although channels have been studied many questions pertaining to the whole diversity of plastid and mitochondrial channels in Arabidopsis thaliana and Pisum sativum remain unanswered. In this thesis I studied OEP16, OEP37 and VDAC families in two model plants, in Arabidopsis and pea. The Arabidopsis OEP16 family represents four channels of α-helical structure, similar to the pea OEP16 protein. These channels are suggested to transport amino acids and compounds with primary amino groups. Immunoblot analysis, GFP/RFP protein fusion expression, as well as proteomic analysis showed that AtOEP16.1, AtOEP16.2 and AtOEP16.4 are located in the outer envelope membrane of plastids, while AtOEP16.3 is in mitochondria. The gene expression and immunoblot analyses revealed that AtOEP16.1 and AtOEP16.3 proteins are highly abundant and ubiquitous; expression of AtOEP16.1 is regulated by light and cold. AtOEP16.2 is highly expressed in pollen, seeds and seedlings. AtOEP16.4 is a low expressed housekeeping protein. Single knockout mutants of AtOEP16.1, AtOEP16.2 and AtOEP16.4, and double mutants of AtOEP16 gene family did not show any remarkable phenotype. However, macroarray analysis of Atoep16.1-p T-DNA mutant revealed 10 down-regulated and 6 up-regulated genes. In contrast to the α-helical OEP16 proteins, the OEP37 and VDAC proteins are of β-barrel structure. The PsOEP37 and AtOEP37 channel proteins form a selective barrier in the outer envelope of chloroplasts. Electrophysiological studies in lipid bilayer membranes showed that the PsOEP37 channel is permeable for cations. Specific expression profiles showed that AtOEP37 and PsOEP37 are highly expressed in the entire plant. The isolated PsVDAC gene encodes a protein, which is located in mitochondria. In Arabidopsis gene database, five Arabidopsis genes, which code for VDAC-like proteins were announced. One gene was not detected, whereas four of these genes expressed in leaves, roots, flower buds and pollen

Diatoms synthesize sterols by inclusion of animal and fungal genes in the plant pathway

Diatoms are ubiquitous microalgae that have developed remarkable metabolic plasticity and gene diversification. Here we report the first elucidation of the complete biosynthesis of sterols in the lineage. The study has been carried out on the bloom-forming species Skeletonema marinoi and Cyclotella cryptica that synthesise an ensemble of sterols with chemotypes of animals (cholesterol and desmosterol), plants (dihydrobrassicasterol and 24-methylene cholesterol), algae (fucosterol) and marine invertebrates (clionasterol). In both species, sterols derive from mevalonate through cyclization of squalene to cycloartenol by cycloartenol synthase. The pathway anticipates synthesis of cholesterol by enzymes of the phytosterol route in plants, as recently reported in Solanaceae. Major divergences stem from reduction of Δ24(28) and Δ24(25) double bonds which, in diatoms, are apparently dependent on sterol reductases of fungi, algae and animals. Phylogenetic comparison revealed a good level of similarity between the sterol biosynthetic genes of S. marinoi and C. cryptica with those in the genomes of the other diatoms sequenced so far

Why Confronting the Internet’s Dark Side?

Raphael Cohen-Almagor, the author of Confronting the Internet’s Dark Side, explains his motivation for exploring the dangerous side of the world wide web. This new book is the first comprehensive book on social responsibility on the Internet