Prospects for dedicated energy crop production and attitudes towards agricultural straw use: The case of livestock farmers.

Second generation biofuels utilising agricultural by-products (e.g. straw), or dedicated energy crops (DECs) produced on 'marginal' land, have been called for. A structured telephone survey of 263 livestock farmers, predominantly located in the west or 'marginal' upland areas of England captured data on attitudes towards straw use and DECs. Combined with farm physical and business data, the survey results show that 7.2% and 6.3% of farmers would respectively consider growing SRC and miscanthus, producing respective maximum potential English crop areas of 54,603 ha and 43,859 ha. If higher market prices for straw occurred, most livestock farmers would continue to buy straw. Reasons for not being willing to consider growing DECs include concerns over land quality, committing land for a long time period, lack of appropriate machinery, profitability, and time to financial return; a range of moral, land quality, production conflict and lack of crop knowledge factors were also cited. Results demonstrate limited potential for the production of DECs on livestock farms in England. Changes in policy support to address farmer concerns with respect to DECs will be required to incentivise farmers to increase energy crop production. Policy support for DEC production must be cognisant of farm-level economic, tenancy and personal objectives.

Barriers and incentives to the production of bioethanol from cereal straw: A farm business perspective.

The EU renewable energy directive stipulates a requirement for 10% of transport fuels to be derived from renewable sources by 2020. Second generation biofuels offer potential to contribute towards this target with cereal straw representing a potentially large feedstock source. From an on-farm survey of 240 arable farmers, timeliness of crop establishment and benefits of nutrient retention from straw incorporation were cited as reasons for straw incorporation. However, two-thirds (one-third) of farmers would supply wheat (barley) straw for bioenergy. The most popular contract length and continuous length of straw supply was either 1 or 3 years. Contracts stipulating a fixed area of straw supply for a fixed price were the most frequently cited preferences, with £50 t-1 the most frequently cited minimum contract price that farmers would find acceptable. Arable farmers in England would be willing to sell 2.52 Mt of cereal straw for bioenergy purposes nationally and 1.65 Mt in the main cereal growing areas of Eastern England. Cereal straw would be diverted from current markets or on-farm uses and from straw currently incorporated into soil. Policy interventions may be required to incentivise farmers to engage in this market, but food and fuel policies must increasingly be integrated to meet societal goals.

Farm systems assessment of bioenergy feedstock production: Integrating bio-economic models and life cycle analysis approaches.

Climate change and energy security concerns have driven the development of policies that encourage bioenergy production. Meeting EU targets for the consumption of transport fuels from bioenergy by 2020 will require a large increase in the production of bioenergy feedstock. Initially an increase in 'first generation' biofuels was observed, however 'food competition' concerns have generated interest in second generation biofuels (SGBs). These SGBs can be produced from co-products (e.g. cereal straw) or energy crops (e.g. miscanthus), with the former largely negating food competition concerns. In order to assess the sustainability of feedstock supply for SGBs, the financial, environmental and energy costs and benefits of the farm system must be quantified. Previous research has captured financial costs and benefits through linear programming (LP) approaches, whilst environmental and energy metrics have been largely been undertaken within life cycle analysis (LCA) frameworks. Assessing aspects of the financial, environmental and energy sustainability of supplying co-product second generation biofuel (CPSGB) feedstocks at the farm level requires a framework that permits the trade-offs between these objectives to be quantified and understood. The development of a modelling framework for Managing Energy and Emissions Trade-Offs in Agriculture (MEETA Model) that combines bio-economic process modelling and LCA is presented together with input data parameters obtained from literature and industry sources. The MEETA model quantifies arable farm inputs and outputs in terms of financial, energy and emissions results. The model explicitly captures fertiliser: crop-yield relationships, plus the incorporation of straw or removal for sale, with associated nutrient impacts of incorporation/removal on the following crop in the rotation. Key results of crop-mix, machinery use, greenhouse gas (GHG) emissions per kg of crop product and energy use per hectare are in line with previous research and industry survey findings. Results show that the gross margin - energy trade-off is £36 GJ-1, representing the gross margin forgone by maximising net farm energy cf. maximising farm gross margin. The gross margin-GHG emission trade-off is £0.15 kg-1 CO2 eq, representing the gross margin forgone per kg of CO2 eq reduced when GHG emissions are minimised cf. maximising farm gross margin. The energy-GHG emission trade-off is 0.03 GJ kg-1 CO2 eq quantifying the reduction in net energy from the farm system per kg of CO2 eq reduced when minimising GHG emissions cf. maximising net farm energy. When both farm gross margin and net farm energy are maximised all the cereal straw is baled for sale. Sensitivity analysis of the model in relation to different prices of cereal straw shows that it becomes financially optimal to incorporate wheat straw at price of £11 t-1 for this co-product. Local market conditions for straw and farmer attitudes towards incorporation or sale of straw will impact on the straw price at which farmers will supply this potential bioenergy feedstock and represent important areas for future research.

Spectral and polarization sensitivity of juvenile Atlantic salmon (Salmo salar): phylogenetic considerations.

We were interested in comparing the characteristics of polarization sensitivity in Atlantic salmon to those in Pacific salmon. Here we show that the common ancestor to the clade containing Salmo salar, Oncorhynchus mykiss, O. nerka, O. clarkii and Salvelinus fontinalis has the trait of ultraviolet polarization sensitivity. We examined spectral and polarization sensitivity of juvenile Atlantic salmon (Salmo salar) using both optic nerve compound action potential (CAP) and electroretinogram (ERG) recordings. Our experiments employed photic manipulation to adjust the sensitivity of the four cone mechanisms of Atlantic salmon. A spectrally broad background was used to ensure a contribution of all cone mechanisms to both spectral and polarization sensitivity. Chromatic adaptation was used to isolate the sensitivity of each of the four cone mechanisms for both spectral and polarization sensitivity. Under spectrally broad conditions, UV sensitive (UVS), mid wavelength sensitive (MWS) and long wavelength sensitive (LWS) cone mechanisms contributed to polarization sensitivity. CAP recordings produced the typical 'W' shaped polarization sensitivity curve reflecting two active polarization detectors with peaks at e-vector orientations of 0 deg, 90 deg and 180 deg, and troughs at 30 deg and 150 deg. ERG recordings produced a four-peaked polarization sensitivity curve reflecting two active polarization detectors and negative feedback activity, with peaks at e-vectors 0 deg, 45 deg, 90 deg, 135 deg and 180 deg, and troughs at 30 deg, 60 deg, 120 deg and 150 deg. Polarization-sensitivity measurements of isolated cone mechanisms revealed two orthogonal polarization detector mechanisms in Atlantic salmon, identical to that found in rainbow trout and other Pacific salmonid fishes. Moreover, under spectrally broad background conditions, CAP and ERG polarization sensitivity of Atlantic salmon did not differ significantly from that reported in Pacific salmonids.

Phenotypic and genotypic analysis of bacteria isolated from three municipal wastewater treatment plants on tetracycline-amended and ciprofloxacin-amended growth media.

AIMS: The goal of this study was to determine the antimicrobial susceptibility of bacteria isolated from three municipal wastewater treatment plants. METHODS AND RESULTS: Numerous bacterial strains were isolated from three municipal wastewater treatment facilities on tetracycline- (n=164) and ciprofloxacin-amended (n=65) growth media. These bacteria were then characterized with respect to their resistance to as many as 10 different antimicrobials, the presence of 14 common genes that encode resistance to tetracycline, the presence of integrons and/or the ability to transfer resistance via conjugation. All of the characterized strains exhibited some degree of multiple antimicrobial resistance, with nearly 50% demonstrating resistance to every antimicrobial that was tested. Genes encoding resistance to tetracycline were commonly detected among these strains, although intriguingly the frequency of detection was slightly higher for the bacteria isolated on ciprofloxacin-amended growth media (62%) compared to the bacteria isolated on tetracycline-amended growth media (53%). Class 1 integrons were also detected in 100% of the queried tetracycline-resistant bacteria and almost half of the ciprofloxacin-resistant strains. Conjugation experiments demonstrated that at least one of the tetracycline-resistant bacteria was capable of lateral gene transfer. CONCLUSIONS: Our results demonstrate that multiple antimicrobial resistance is a common trait among tetracycline-resistant and ciprofloxacin-resistant bacteria in municipal wastewater. SIGNIFICANCE AND IMPACT OF THE STUDY: These organisms are potentially important in the proliferation of antimicrobial resistance because they appear to have acquired multiple genetic determinants that confer resistance and because they have the potential to laterally transfer these genetic determinants to strains of clinical importance.

Lesion sites that predict the ability to gesture how an object is used.

We used a two stage procedure to predict which stroke patients would have chronic difficulties gesturing how to use an object when object recognition and hand movements were intact. First, we searched our PLORAS database by behavior and identified 5 patients who had chronic difficulty gesturing object use but no difficulty recognising objects, comprehending words or moving their hands. High definition lesion analyses showed that all 5 patients had damage to the white matter underlying the left ventral supramarginal gyrus, (A) close to the cortex, (B) deep towards the midline and (C) extending into the temporal lobe. In addition, 2 patients had damage to (D) the left posterior middle temporal cortex, and 3 patients had damage to (E) the left dorsal supramarginal gyrus and (F) the left premotor cortex. Second, we searched our database by lesion location for patients who had damage to any part of regions ABCDEF. The incidence of gesturing difficulties was higher in patients with damage to ABCD (7/9), ABCE (7/10) or ABCDE (10/13) than ABCF (7/13), ABC (8/16) or partial damage to ABCF (6/32). Thus behaviour was best predicted by the combination of regions that were damaged (a "network-lesion") rather than on the basis of each region alone or overall lesion size. Our results identify which parts of the temporal and parietal lobes impair the ability to gesture object use and which parts need to be intact to support it after damage. Our methods provide a framework for future studies aiming to predict the consequences of brain damage.

Congenital cataracts in females caused by BCOR mutations; report of six further families demonstrating clinical variability and diverse genetic mechanisms.

BACKGROUND: Pathogenic variants in the BCOR gene have been identified in males with X-linked recessive microphthalmia and in females with X-linked dominant oculofaciocardiodental (OFCD) syndrome. This latter condition has previously been regarded as rare but the increased availability of genetic testing in recent years has led to the identification of a greater number of patients. METHODS: We report the clinical and molecular findings in a series of 10 patients with pathogenic BCOR variants from 5 families, all seen in a single institution over a two year period. RESULTS: We emphasize the phenotypic variability in this cohort and the diverse genetic mechanisms involved which included point mutations and deletions of BCOR as well as the occurrence of gonadal and somatic mosaicism. CONCLUSION: In this report we demonstrate the novel findings of four newly identified variants in BCOR associated with an OFCD phenotype, and suggest that the frequency of this condition in females presenting with congenital cataract, including unilateral cataract, is more common than anticipated. We demonstrate the utility of screening for genetic causes of congenital cataract. Although gonadal mosaicism in OFCD had previously been reported, we demonstrate the presence of somatic mosaicism where BCOR mutations may only be detected in DNA from tissues other than blood such as buccal cells.

Clinical and biochemical effects of the E139K missense mutation in the TIMP3 gene, associated with Sorsby fundus dystrophy.

PURPOSE: To determine the phenotypic and biochemical characteristics of the p.E139K missense variant in tissue inhibitor of metalloproteinase 3 (TIMP3) associated with Sorsby fundus dystrophy (SFD). METHODS: The coding regions and adjacent intronic sequence of TIMP3 were amplified by polymerase chain reaction and then analyzed by bidirectional sequencing. Allele-specific PCR was used to determine the minimum allele frequency of the mutant allele in ethnically matched controls. Clinical examination and imaging of affected individuals with color fundus photography, scanning laser ophthalmoscope (fundal autofluorescence), and optical coherence tomography was performed. A mutant construct of the TIMP3 protein was created and expressed in human retinal pigment epithelium (ARPE19) cells, which were then assayed for oligomerization and intrinsic matrix metalloproteinase (MMP) inhibitory activity. RESULTS: Three affected individuals from a family of Welsh origin each harbored one allele of the TIMP3 missense variant c.415 G>A, (p.E139K), which was not identified in 534 ethnically matched control chromosomes and thus presumed pathogenic. The mutant protein was shown to dimerize in culture cells and retain its MMP inhibitory activity. Retinal examination was variable between eyes of affected individuals and between family members. Drusen-like deposits were common to all three affected individuals and yellow subretinal deposits, exudative maculopathy, and geographic atrophy were also observed. Optical coherence tomography (OCT) images of affected individuals demonstrated hyperreflectivity of the RPE-photoreceptor-choroid complex. CONCLUSIONS: The TIMP3 p.E139K mutation is another cause of SFD. It is the second TIMP3 sequence variant reported that does not affect the number of cysteine residues in the mutant protein yet dimerizes in vitro. The clinical presentation of this family is in keeping with previous clinical reports of this disorder.

Detection of a deletion of exons 8-16 of the UBE3A gene in familial Angelman syndrome using a semi-quantitative dosage PCR based assay.

Angelman syndrome (AS) is a neurodevelopmental disorder caused by failure of expression of the maternal copy of the imprinted UBE3A gene through a variety of mechanisms detected by methylation studies, mutation analysis of UBE3A and FISH. In 10-15% of suspected cases of AS these investigations do not reveal a genetic abnormality. We report here the development of a semi-quantitative dosage PCR technique used to identify sub-microscopic deletions involving UBE3A. Using this method we analysed a panel of 26 patients from 24 families, all fulfilling the clinical criteria for AS. We identified a deletion of UBE3A exons 8-16 in a sibling pair. Analysis of parental samples revealed the same deletion in their phenotypically normal mother. This is an inexpensive and valuable method for detecting UBE3A deletions in a small but important proportion of AS cases of unidentifiable cause.

How do we cultivate in England? Tillage practices in crop production systems.

Reducing tillage intensity offers the possibility of moving towards sustainable intensification objectives. Reduced tillage (RT) practices, where the plough is not used, can provide a number of environmental and financial benefits, particularly for soil erosion control. Based on 2010 harvest year data from the nationally stratified Farm Business Survey and drawing on a sub-sample of 249 English arable farmers, we estimate that approximately 32% of arable land was established under RT, with 46% of farms using some form of RT. Farms more likely to use some form of RT were larger, located in the East Midlands and South East of England and classified as 'Cereals' farms. Application of RT techniques was not determined by the age or education level of the farmer. Individual crops impacted the choice of land preparation, with wheat and oilseed rape being more frequently planted after RT than field beans and root crops, which were almost always planted after ploughing. This result suggests there can be limitations to the applicability of RT. Average tillage depth was only slightly shallower for RT practices than ploughing, suggesting that the predominant RT practices are quite demanding in their energy use. Policy makers seeking to increase sustainable RT uptake will need to address farm-level capital investment constraints and target policies on farms growing crops, such as wheat and oilseed rape, that are better suited to RT practices.

Angelman syndrome phenotype associated with mutations in MECP2, a gene encoding a methyl CpG binding protein.

Angelman syndrome (AS) is a neurodevelopmental disorder characterised by severe mental retardation, absent speech, ataxia, sociable affect, and dysmorphic facial features. Eighty five percent of patients with AS have an identifiable genetic abnormality of chromosome 15q11-13. Mutations within the X linked MECP2 gene have been identified in patients with Rett syndrome (RTT), a neurodevelopmental disorder which affects females almost exclusively and which shares phenotypic overlap with AS. RTT is usually associated with normal development in infancy followed by loss of acquired skills and evolution of characteristic hand wringing movements and episodes of hyperventilation.A panel of 25 female and 22 male patients with a clinical diagnosis of AS and no molecular abnormality of 15q11-13 were screened for MECP2 mutations and these were identified in four females and one male. Following the diagnosis, it was possible to elicit a history of regression in three of these patients, who by then were showing features suggestive of Rett syndrome. In the remaining two subjects the clinical phenotype was still considered to be Angelman-like. These findings illustrate the phenotypic overlap between the two conditions and suggest that screening for MECP2 mutations should be considered in AS patients without a demonstrable molecular or cytogenetic abnormality of 15q11-13. Since MECP2 mutations almost always occur de novo, their identification will substantially affect genetic counselling for the families concerned.

Characterization of gene rearrangements and gene conversion events in the 21-hydroxylase gene.

Congenital adrenal hyperplasia (CAH) is an inherited disorder of steroidogenesis with a wide spectrum of expression. In about 95% of cases, the disease is the result of 21-hydroxylase deficiency, an autosomal recessive condition that maps to the major histocompatibility complex (MHC) on 6p21.3 (1). Classical CAH results in excessive androgen production. Females with this disorder are frequently diagnosed at birth because of ambiguous development of external genitalia, whereas males may not present until age 4-7 when they begin to manifest inappropriate virilization. Approximately 30% of individuals with classical CAH have this simple virilizing form of the disease. The remaining 70% in addition manifest the potentially life-threatening salt-wasting form of classical CAH characterized by an inability to retain dietary sodium.

A mobile surgery for single homeless people in London.

Little is known about the social and medical characteristics of people who regularly sleep rough, or whether medical care can be targeted at these people. In 1987 a mobile surgery was used to provide primary health care at two sites in central London where many single homeless people sleep outdoors. One hundred and forty six patients were seen with illnesses ranging from scabies to osteomyelitis and tuberculosis. Sociodemographic data showed the patients to be generally an isolated group with deprived and unstable backgrounds, often compounded by alcohol abuse. Over a third of the patients from one site attended a drop in surgery for homeless people in Soho within a month after seeing a doctor in the mobile surgery. This suggests that the project can be a first step in integrating this isolated group with health care facilities.

Unification and classification of two-dimensional crystalline patterns using orbifolds.

The concept of an orbifold is particularly suited to classification and enumeration of crystalline groups in the euclidean (flat) plane and its elliptic and hyperbolic counterparts. Using Conway's orbifold naming scheme, this article explicates conventional point, frieze and plane groups, and describes the advantages of the orbifold approach, which relies on simple rules for calculating the orbifold topology. The article proposes a simple taxonomy of orbifolds into seven classes, distinguished by their underlying topological connectedness, boundedness and orientability. Simpler `crystallographic hyperbolic groups' are listed, namely groups that result from hyperbolic sponge-like sections through three-dimensional euclidean space related to all known genus-three triply periodic minimal surfaces (i.e. the P, D, Gyroid, CLP and H surfaces) as well as the genus-four I-WP surface.

Predicting IQ change from brain structure: a cross-validation study.

Procedures that can predict cognitive abilities from brain imaging data are potentially relevant to educational assessments and studies of functional anatomy in the developing brain. Our aim in this work was to quantify the degree to which IQ change in the teenage years could be predicted from structural brain changes. Two well-known k-fold cross-validation analyses were applied to data acquired from 33 healthy teenagers - each tested at Time 1 and Time 2 with a 3.5 year interval. One approach, a Leave-One-Out procedure, predicted IQ change for each subject on the basis of structural change in a brain region that was identified from all other subjects (i.e., independent data). This approach predicted 53% of verbal IQ change and 14% of performance IQ change. The other approach used half the sample, to identify regions for predicting IQ change in the other half (i.e., a Split half approach); however--unlike the Leave-One-Out procedure--regions identified using half the sample were not significant. We discuss how these out-of-sample estimates compare to in-sample estimates; and draw some recommendations for k-fold cross-validation procedures when dealing with small datasets that are typical in the neuroimaging literature.

Structural correlates for lexical efficiency and number of languages in non-native speakers of English.

We used structural magnetic resonance imaging (MRI) and voxel based morphometry (VBM) to investigate whether the efficiency of word processing in the non-native language (lexical efficiency) and the number of non-native languages spoken (2+ versus 1) were related to local differences in the brain structure of bilingual and multilingual speakers. We dissociate two different correlates for non-native language processing. Firstly, multilinguals who spoke 2 or more non-native languages had higher grey matter density in the right posterior supramarginal gyrus compared to bilinguals who only spoke one non-native language. This is interpreted in relation to previous studies that have shown that grey matter density in this region is related to the number of words learnt in bilinguals relative to monolinguals and in monolingual adolescents with high versus low vocabulary. Our second result was that, in bilinguals, grey matter density in the left pars opercularis was positively related to lexical efficiency in second language use, as measured by the speed and accuracy of lexical decisions and the number of words produced in a timed verbal fluency task. Grey matter in the same region was also negatively related to the age at which the second language was acquired. This is interpreted in terms of previous findings that associated the left pars opercularis with phonetic expertise in the native language.

[Minimal ocular findings in a patient with Best disease caused by the c.653G>A mutation in BEST1]. / Minimální nález u pacienta s Bestovou chorobou podmínenou mutací c.653G>A v genu BEST1.

PURPOSE: To describe the phenotype in an asymptomatic 64-year-old patient with family history of Best disease and to identify the disease causing variant in the BEST1 gene. METHODS: Detailed ocular examination of the proband including spectral-domain optical coherence tomography (SD-OCT), fluorescein angiography and electrooculography was performed. Direct sequencing approach was used to screen the whole coding sequence of 11 exons of BEST1. RESULTS: An early vitelliform stage of Best disease presenting as a small yellowish spot in the macula was observed in the right eye. The fundus appearance in the left eye was normal. SD-OCT of the right macula revealed hypodense space between the retinal pigment epithelium and the neuroretinal layer. Arden ratio was bilaterally mildly reduced; 1.36 in the right and 1.3 in the left eye. Molecular genetic analysis identified a heterozygous change c.653G>A (p.Arg218His) as the disease-causing variant. CONCLUSION: Here we report for the first time a phenotype-genotype correlation in a Czech patient with Best disease. SD-OCT is a fast method that may show the presence of small pathological changes. The screening of BEST1 gene enables identification of disease-causing variants in asymptomatic individuals with normal fundus appearance and thus improves counseling to the affected families.

Three-dimensional Euclidean nets from two-dimensional hyperbolic tilings: kaleidoscopic examples.

We present a method for geometric construction of periodic three-dimensional Euclidean nets by projecting two-dimensional hyperbolic tilings onto a family of triply periodic minimal surfaces (TPMSs). Our techniques extend the combinatorial tiling theory of Dress, Huson & Delgado-Friedrichs to enumerate simple reticulations of these TPMSs. We include a taxonomy of all networks arising from kaleidoscopic hyperbolic tilings with up to two distinct tile types (and their duals, with two distinct vertices), mapped to three related TPMSs, namely Schwarz's primitive (P) and diamond (D) surfaces, and Schoen's gyroid (G).