An Analysis of Efficiency of Midwestern Agricultural Cooperatives

Agribusiness,

DNA Charge Transport within the Cell

The unique characteristics of DNA charge transport (CT) have prompted an examination of roles for this chemistry within a biological context. Not only can DNA CT facilitate long-range oxidative damage of DNA, but redox-active proteins can couple to the DNA base stack and participate in long-range redox reactions using DNA CT. DNA transcription factors with redox-active moieties such as SoxR and p53 can use DNA CT as a form of redox sensing. DNA CT chemistry also provides a means to monitor the integrity of the DNA, given the sensitivity of DNA CT to perturbations in base stacking as arise with mismatches and lesions. Enzymes that utilize this chemistry include an interesting and ever-growing class of DNA-processing enzymes involved in DNA repair, replication, and transcription that have been found to contain 4Fe-4S clusters. DNA repair enzymes containing 4Fe-4S clusters, that include endonuclease III (EndoIII), MutY, and DinG from bacteria, as well as XPD from archaea, have been shown to be redox-active when bound to DNA, share a DNA-bound redox potential, and can be reduced and oxidized at long-range via DNA CT. Interactions between DNA and these proteins in solution, in addition to genetics experiments within Escherichia coli, suggest that DNA-mediated CT can be used as a means of cooperative signaling among DNA repair proteins that contain 4Fe-4S clusters as a first step in finding DNA damage, even within cells. On the basis of these data, we can consider also how DNA-mediated CT may be used as a means of signaling to coordinate DNA processing across the genome

UvrC Coordinates an O₂-Sensitive [4Fe4S] Cofactor

Recent advances have led to numerous landmark discoveries of [4Fe4S] clusters coordinated by essential enzymes in repair, replication, and transcription across all domains of life. The cofactor has notably been challenging to observe for many nucleic acid processing enzymes due to several factors, including a weak bioinformatic signature of the coordinating cysteines and lability of the metal cofactor. To overcome these challenges, we have used sequence alignments, an anaerobic purification method, iron quantification, and UV–visible and electron paramagnetic resonance spectroscopies to investigate UvrC, the dual-incision endonuclease in the bacterial nucleotide excision repair (NER) pathway. The characteristics of UvrC are consistent with [4Fe4S] coordination with 60–70% cofactor incorporation, and additionally, we show that, bound to UvrC, the [4Fe4S] cofactor is susceptible to oxidative degradation with aggregation of apo species. Importantly, in its holo form with the cofactor bound, UvrC forms high affinity complexes with duplexed DNA substrates; the apparent dissociation constants to well-matched and damaged duplex substrates are 100 ± 20 nM and 80 ± 30 nM, respectively. This high affinity DNA binding contrasts reports made for isolated protein lacking the cofactor. Moreover, using DNA electrochemistry, we find that the cluster coordinated by UvrC is redox-active and participates in DNA-mediated charge transport chemistry with a DNA-bound midpoint potential of 90 mV vs NHE. This work highlights that the [4Fe4S] center is critical to UvrC

UvrC Coordinates an O₂-Sensitive [4Fe4S] Cofactor

Recent advances have led to numerous landmark discoveries of [4Fe4S] clusters coordinated by essential enzymes in repair, replication, and transcription across all domains of life. The cofactor has notably been challenging to observe for many nucleic acid processing enzymes due to several factors, including a weak bioinformatic signature of the coordinating cysteines and lability of the metal cofactor. To overcome these challenges, we have used sequence alignments, an anaerobic purification method, iron quantification, and UV–visible and electron paramagnetic resonance spectroscopies to investigate UvrC, the dual-incision endonuclease in the bacterial nucleotide excision repair (NER) pathway. The characteristics of UvrC are consistent with [4Fe4S] coordination with 60–70% cofactor incorporation, and additionally, we show that, bound to UvrC, the [4Fe4S] cofactor is susceptible to oxidative degradation with aggregation of apo species. Importantly, in its holo form with the cofactor bound, UvrC forms high affinity complexes with duplexed DNA substrates; the apparent dissociation constants to well-matched and damaged duplex substrates are 100 ± 20 nM and 80 ± 30 nM, respectively. This high affinity DNA binding contrasts reports made for isolated protein lacking the cofactor. Moreover, using DNA electrochemistry, we find that the cluster coordinated by UvrC is redox-active and participates in DNA-mediated charge transport chemistry with a DNA-bound midpoint potential of 90 mV vs NHE. This work highlights that the [4Fe4S] center is critical to UvrC

Label-free electrochemical detection of human methyltransferase from tumors

The role of abnormal DNA methyltransferase activity in the development and progression of cancer is an essential and rapidly growing area of research, both for improved diagnosis and treatment. However, current technologies for the assessment of methyltransferase activity, particularly from crude tumor samples, limit this work because they rely on radioactivity or fluorescence and require bulky instrumentation. Here, we report an electrochemical platform that overcomes these limitations for the label-free detection of human DNA(cytosine-5)-methyltransferase1 (DNMT1) methyltransferase activity, enabling measurements from crude cultured colorectal cancer cell lysates (HCT116) and biopsied tumor tissues. Our multiplexed detection system involving patterning and detection from a secondary electrode array combines low-density DNA monolayer patterning and electrocatalytically amplified DNA charge transport chemistry to measure selectively and sensitively DNMT1 activity within these complex and congested cellular samples. Based on differences in DNMT1 activity measured with this assay, we distinguish colorectal tumor tissue from healthy adjacent tissue, illustrating the effectiveness of this two-electrode platform for clinical applications

Resonant cavity photon creation via the dynamical Casimir effect

Motivated by a recent proposal for an experimental verification of the dynamical Casimir effect, the macroscopic electromagnetic field within a perfect cavity containing a thin slab with a time-dependent dielectric permittivity is quantized in terms of the dual potentials. For the resonance case, the number of photons created out of the vacuum due to the dynamical Casimir effect is calculated for both polarizations (TE and TM). PACS: 42.50.Lc, 03.70.+k, 42.50.Dv, 42.60.Da.Comment: 4 pages, 1 figur

Lived experience and attitudes of people with plantar heel pain:a qualitative exploration

BACKGROUND: Plantar heel pain is a common source of pain and disability. Evidence-based treatment decisions for people with plantar heel pain should be guided by the best available evidence, expert clinical reasoning, and consider the needs of the patient. Education is a key component of care for any patient and needs to be tailored to the patient and their condition. However, no previous work has identified, far less evaluated, the approaches and content required for optimal education for people with plantar heel pain. The aim of this study was to gather the patients' perspective regarding their lived experience, attitudes and educational needs in order to inform the content and provision of meaningful education delivery approaches. METHODS: Using a qualitative descriptive design, semi-structured interviews were conducted with participants with a clinical diagnosis of plantar heel pain. A topic guide was utilised that focused on the experience of living with plantar heel pain and attitudes regarding treatment and educational needs. Interviews were audio recorded, transcribed verbatim and analysed using the Framework approach. Each transcription, and the initial findings, were reported back to participants to invite respondent validation. RESULTS: Eighteen people with plantar heel pain were interviewed. Descriptive analysis revealed eight themes including perceptions of plantar heel pain, impact on self, dealing with plantar heel pain, source of information, patient needs, patient unmet needs, advice to others and interest in online education. Participants revealed doubt about the cause, treatment and prognosis of plantar heel pain. They also expressed a desire to have their pain eliminated and education individually tailored to their condition and needs. Respondent validation revealed that the transcripts were accurate, and participants were able to recognise their own experiences in the synthesised themes. CONCLUSION: Plantar heel pain has a negative impact on health-related quality of life. Participants wanted their pain eliminated and reported that their expectations and needs were frequently unmet. Health professionals have an important role to be responsive to the needs of the patient to improve their knowledge and influence pain and behaviour. Our study informs the content needed to help educate people with plantar heel pain

Tasting Phenylthiocarbamide (PTC): A New Integrative Genetics Lab with an Old Flavor

First reported in the early 1930s, variation in the ability to taste phenylthiocarbamide (PTC) has since become one of the most widely studied of all human genetic traits. Guo and Reed (2001) provide an excellent review of work on this polymorphism prior to the identification and sequencing of the PTC gene by Kim et al. (2003), and Wooding (2006) provides a stimulating historical review of the role various scientists have played in the study of PTC taste sensitivity and the importance of these studies in relation to natural selection. Identification of the PTC gene and a number of subsequent publications (Wooding et al., 2004; Kim et al., 2005; Wooding et al., 2006) have provided the basis for a new, integrative laboratory investigation of PTC taste sensitivity. This genetics laboratory culminates in the use of the polymerase chain reaction (PCR) and restriction endonuclease digestion to determine the PTC genotype of each student. But “getting there is half the fun” and, in this case, “getting there” requires students to use not only their knowledge of molecular techniques in genetics but also their knowledge of Mendelian genetics, population genetics, probability, and pedigree analysis. The other “half the fun” in this case is that in determining their PTC phenotypes and genotypes, students are learning something about themselves

Cross-sectional and temporal relationships between bird occupancy and vegetation cover at multiple spatial scales

Scale is a key concept in ecology, but the statistically based quantification of scale effects has often proved difficult. This is exemplified by the challenges of quantifying relationships between biodiversity and vegetation cover at different spatial scales to guide restoration and conservation efforts in agricultural environments. We used data from 2002 to 2010 on 184 sites (viz., site scale) nested within 46 farms (the farm scale), nested within 23 landscapes (the landscape scale). We found cross-sectional relationships with the amount of vegetation cover that were typically positive for woodland birds and negative for open-country birds. However, for some species, relationships differed between spatial scales, suggesting differences in nesting and foraging requirements. There was a 3.5% increase in the amount of native vegetation cover in our study region between 2002 and 2010, and our analyses revealed that some open country species responded negatively to these temporal changes, typically at the farm and/or site scale, but not the landscape scale. Species generally exhibited stronger cross-sectional relationships with the amount of vegetation cover than relationships between changes in occupancy and temporal changes in vegetation cover. This unexpected result can be attributed to differences in habitat use by birds of existing vegetation cover (typically oldgrowth woodland) vs. plantings and natural regeneration, which are the main contributors to temporal increases in vegetation cover. By taking a multi-scaled empirical approach, we have identified species-specific, scale-dependent responses to vegetation cover. These findings are of considerable practical importance for understanding which species will respond to different scales of protection of existing areas of native vegetation, efforts to increase the amount of native vegetation over time, and both approaches together

Lattice Green's function approach to the solution of the spectrum of an array of quantum dots and its linear conductance

In this paper we derive general relations for the band-structure of an array of quantum dots and compute its transport properties when connected to two perfect leads. The exact lattice Green's functions for the perfect array and with an attached adatom are derived. The expressions for the linear conductance for the perfect array as well as for the array with a defect are presented. The calculations are illustrated for a dot made of three atoms. The results derived here are also the starting point to include the effect of electron-electron and electron-phonon interactions on the transport properties of quantum dot arrays. Different derivations of the exact lattice Green's functions are discussed