Analysis of ThiC variants in the context of the metabolic network of Salmonella enterica.

In bacteria, the 4-amino-hydroxymethyl-2-methylpyrimidine (HMP) moiety of thiamine is synthesized from 5-aminoimidazole ribotide (AIR), a branch point metabolite of purine and thiamine biosynthesis. ThiC is a member of the radical S-adenosylmethionine (AdoMet) superfamily and catalyzes the complex chemical rearrangement of AIR to HMP-P. As reconstituted in vitro, the ThiC reaction requires AdoMet, AIR, and reductant. This study analyzed variants of ThiC in vivo and in vitro to probe the metabolic network surrounding AIR in Salmonella enterica. Several variants of ThiC that required metabolic perturbations to function in vivo were biochemically characterized in vitro. Results presented herein indicate that the subtleties of the metabolic network have not been captured in the current reconstitution of the ThiC reaction.

Closing the gap: inverting the genetics curriculum to ensure an informed public.

Over the past 20 years, the focus of national efforts to improve K-12 science education has ranged from curriculum and professional development of teachers to the adoption of science standards and high-stakes testing. In spite of this work, students in the United States continue to lag behind their peers in other countries. This underperformance is true for genetics, as well as for science and math in general, and is particularly worrisome given the accelerating need for scientists and engineers in our increasingly technology-driven economy. A scientifically literate public is essential if citizens are to engage effectively with policymakers on issues of scientific importance. Perhaps nowhere is this conjunction more personally meaningful than in human genetics and medicine. Rapid changes in our field have the potential to revolutionize healthcare, but the public is ill prepared to participate in this transformation. One potential solution is to modernize the genetics curriculum so that it matches the science of the 21(st) century. This paper highlights changes in human genetics that support a curricular reorganization, outlines the problems with current genetics instruction, and proposes a new genetics curriculum.

Glycoside hydrolases from a targeted compost metagenome, activity-screening and functional characterization.

BACKGROUND: Metagenomics approaches provide access to environmental genetic diversity for biotechnology applications, enabling the discovery of new enzymes and pathways for numerous catalytic processes. Discovery of new glycoside hydrolases with improved biocatalytic properties for the efficient conversion of lignocellulosic material to biofuels is a critical challenge in the development of economically viable routes from biomass to fuels and chemicals. RESULTS: Twenty-two putative ORFs (open reading frames) were identified from a switchgrass-adapted compost community based on sequence homology to related gene families. These ORFs were expressed in E. coli and assayed for predicted activities. Seven of the ORFs were demonstrated to encode active enzymes, encompassing five classes of hemicellulases. Four enzymes were over expressed in vivo, purified to homogeneity and subjected to detailed biochemical characterization. Their pH optima ranged between 5.5 - 7.5 and they exhibit moderate thermostability up to ~60-70°C. CONCLUSIONS: Seven active enzymes were identified from this set of ORFs comprising five different hemicellulose activities. These enzymes have been shown to have useful properties, such as moderate thermal stability and broad pH optima, and may serve as the starting points for future protein engineering towards the goal of developing efficient enzyme cocktails for biomass degradation under diverse process conditions.

Abusing science.

The perversion of science in the interest of ideology and greed is not a new phenomenon, but a public that is largely scientifically illiterate now is besieged by "alternative facts" and well-designed efforts to discredit legitimate science on topics ranging from vaccines to climate change. Here, we examine three topics rooted in biology and biomedicine-creationism, harms from tobacco, and opioid addiction-to show that those purveying misinformation employ a consistent pattern of intellectual dishonesty to delegitimize science that challenges their ideological positions. Individual scientists and the scientific community at large should confront and counter these attacks on the intellectual integrity that is at the heart of the scientific enterprise.

Perceived Gaps in Genetics Training Among Audiologists and Speech-Language Pathologists: Lessons From a National Survey.

Purpose The aim of this study was to assess knowledge, self-rated confidence, and perceived relevance of genetics in the clinical practice of audiologists and speech-language pathologists (SLPs) toward a better understanding of the need for genetics education, given that genetics plays a growing role in the diagnosis of hearing impairment and communication disorders. Method A survey consisting of 8 demographic items and 16 content questions was returned by 233 audiologists and 283 SLPs. Knowledge of applied genetics was queried with clinical scenarios in a multiple-choice format. Self-assessment of clinical confidence and perceived relevance of genetics in one's field was queried with questions and statements rated on 5-point Likert scales. The benefit of additional training in genetics was rated with a yes/no question, and if answered with yes, suggested topics were entered. Results A large significant gap between confidence in one's own genetics skills and the perceived relevance of genetics was evident, regardless of professional group. Over one third of the audiologists and over two thirds of the SLPs indicated low or somewhat low confidence in their own ability to implement principles of genetics, whereas over two thirds of both groups agreed that genetics is relevant for their field. Regardless of group, confidence scores were significantly and positively associated with relevance scores. Over 80% of respondents in both groups indicated that they would benefit from additional training in genetics. Most commonly suggested topics included genetic causes, general information about genetics, and making referrals. Conclusion Both audiologists and SLPs felt that genetics is relevant for their fields and that additional training in genetics would be beneficial. Future studies should evaluate the effect of genetics training on patient outcomes and the need for incorporating genetics more extensively into audiology and speech-language pathology training programs.

Challenges and Opportunities for Genomics Education: Insights from an Institute of Medicine Roundtable Activity.

Despite the growing availability of genomic tools for clinical care, many health care providers experience gaps in genomics knowledge and skills that serve as impediments to widespread and appropriate integration of genomics into routine care. A workshop recently held by the Institute of Medicine (IOM) Roundtable on Translating Genomics-Based Research for Health explored 1) the barriers that result in a perception among health care providers that the need for genomics education is not urgent and 2) the drivers that may spur a change in that attitude. This commentary promotes continuing and graduate education-informed by an awareness of barriers, drivers, and best practices-as the most effective approaches for preparing the workforce for genomic medicine and ultimately improving patient care, and argues that the time for education is now.

Toward clinical genomics in everyday medicine: perspectives and recommendations.

Precision or personalized medicine through clinical genome and exome sequencing has been described by some as a revolution that could transform healthcare delivery, yet it is currently used in only a small fraction of patients, principally for the diagnosis of suspected Mendelian conditions and for targeting cancer treatments. Given the burden of illness in our society, it is of interest to ask how clinical genome and exome sequencing can be constructively integrated more broadly into the routine practice of medicine for the betterment of public health. In November 2014, 46 experts from academia, industry, policy and patient advocacy gathered in a conference sponsored by Illumina, Inc. to discuss this question, share viewpoints and propose recommendations. This perspective summarizes that work and identifies some of the obstacles and opportunities that must be considered in translating advances in genomics more widely into the practice of medicine.

Assessing the Genetics Content in the Next Generation Science Standards.

Science standards have a long history in the United States and currently form the backbone of efforts to improve primary and secondary education in science, technology, engineering, and math (STEM). Although there has been much political controversy over the influence of standards on teacher autonomy and student performance, little light has been shed on how well standards cover science content. We assessed the coverage of genetics content in the Next Generation Science Standards (NGSS) using a consensus list of American Society of Human Genetics (ASHG) core concepts. We also compared the NGSS against state science standards. Our goals were to assess the potential of the new standards to support genetic literacy and to determine if they improve the coverage of genetics concepts relative to state standards. We found that expert reviewers cannot identify ASHG core concepts within the new standards with high reliability, suggesting that the scope of content addressed by the standards may be inconsistently interpreted. Given results that indicate that the disciplinary core ideas (DCIs) included in the NGSS documents produced by Achieve, Inc. clarify the content covered by the standards statements themselves, we recommend that the NGSS standards statements always be viewed alongside their supporting disciplinary core ideas. In addition, gaps exist in the coverage of essential genetics concepts, most worryingly concepts dealing with patterns of inheritance, both Mendelian and complex. Finally, state standards vary widely in their coverage of genetics concepts when compared with the NGSS. On average, however, the NGSS support genetic literacy better than extant state standards.

Cellulosic biomass pretreatment and sugar yields as a function of biomass particle size.

Three lignocellulosic pretreatment techniques (ammonia fiber expansion, dilute acid and ionic liquid) are compared with respect to saccharification efficiency, particle size and biomass composition. In particular, the effects of switchgrass particle size (32-200) on each pretreatment regime are examined. Physical properties of untreated and pretreated samples are characterized using crystallinity, surface accessibility measurements and scanning electron microscopy (SEM) imaging. At every particle size tested, ionic liquid (IL) pretreatment results in greater cell wall disruption, reduced crystallinity, increased accessible surface area, and higher saccharification efficiencies compared with dilute acid and AFEX pretreatments. The advantages of using IL pretreatment are greatest at larger particle sizes (>75 µm).

Directed evolution: new parts and optimized function.

Constructing novel biological systems that function in a robust and predictable manner requires better methods for discovering new functional molecules and for optimizing their assembly in novel biological contexts. By enabling functional diversification and optimization in the absence of detailed mechanistic understanding, directed evolution is a powerful complement to 'rational' engineering approaches. Aided by clever selection schemes, directed evolution has generated new parts for genetic circuits, cell-cell communication systems, and non-natural metabolic pathways in bacteria.

[Bi5(dpd)6 within CH3CN](ClO4)3.3CH3CN: a supramolecular, tetrahedral pentabismuth cluster derived from a nonabismuth oxo/hydroxide.

The novel tetrahedral [Bi(5)(dpd)(6) within CH(3)CN](ClO(4))(3).3CH(3)CN (dpd = di-2-pyridyl-gem-diolate) has been synthesized from [Bi(9)(mu(3)-O)(8)(mu(3)-OH)(6)](ClO(4))(5) and di-2-pyridyl ketone. The Bi(5) complex incorporates CH(3)CN via C-HO hydrogen bonding.

A connection between iron-sulfur cluster metabolism and the biosynthesis of 4-amino-5-hydroxymethyl-2-methylpyrimidine pyrophosphate in Salmonella enterica.

Several cellular pathways have been identified which affect the efficiency of thiamine biosynthesis in Salmonella enterica. Mutants defective in iron-sulfur (Fe-S) cluster metabolism are less efficient at synthesis of the pyrimidine moiety of thiamine. These mutants are compromised for the conversion of aminoimidazole ribotide (AIR) to 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P), not the synthesis of AIR. The gene product ThiC contains potential ligands for an Fe-S cluster that are required for function in vivo. The conversion of AIR to HMP-P is sensitive to oxidative stress, and variants of ThiC have been identified that have increased sensitivity to oxidative growth conditions. The data are consistent with ThiC or an as-yet-unidentified protein involved in HMP-P synthesis containing an Fe-S cluster required for its physiological function.

Inhibition of fructose-1,6-bisphosphatase by aminoimidazole carboxamide ribotide prevents growth of Salmonella enterica purH mutants on glycerol.

The enzyme fructose-1,6-bisphosphatase (FBP) is key regulatory point in gluconeogenesis. Mutants of Salmonella enterica lacking purH accumulate 5-amino-4-imidazole carboxamide ribotide (AICAR) and are unable to utilize glycerol as sole carbon and energy sources. The work described here demonstrates this lack of growth is due to inhibition of FBP by AICAR. Mutant alleles of fbp that restore growth on glycerol encode proteins resistant to inhibition by AICAR and the allosteric regulator AMP. This is the first report of biochemical characterization of substitutions causing AMP resistance in a bacterial FBP. Inhibition of FBP activity by AICAR occurs at physiologically relevant concentrations and may represent a form of regulation of gluconeogenic flux in Salmonella enterica.

A mutant allele of rpoD results in increased conversion of aminoimidazole ribotide to hydroxymethyl pyrimidine in Salmonella enterica.

An allele of rpoD (rpoD1181) that results in increased synthesis of the pyrimidine moiety of thiamine in Salmonella enterica was identified. The S508Y substitution caused by rpoD1181 is analogous to the S506F derivative of the Escherichia coli protein. The properties of this E. coli mutant protein have been well characterized in vitro. Identification of a metabolic phenotype caused by the rpoD1181 allele of S. enterica allows past in vitro results to be incorporated in continuing efforts to understand cellular processes that are integrated with the thiamine biosynthetic pathway.