Modified helix-loop-helix motifs of calmodulin: the influence of the exchange of helical regions on calcium-binding affinity

The four calcium-binding sites, called the helix-loop-helix, or the EF-hand motifs, of calmodulin differ in their ion-binding affinities; this has been thought to arise due to the variations in the sequences of the loop regions where the ion binds. We focus attention here on the role of the flanking helical regions on the calcium-binding affinities. Peptides were synthesized in a manner that simulates the E and F helical flanks of site 4 (the strongest calcium-binding site of the calmodulin) to sandwich the loop sequences of sites 1, 2, 3 and 4 so as to produce peptides named 414, 424, 434 and 444, as well as using the helical flanks of site 1 (the weakest site) to produce peptides 111, 121, 131 and 141. Calcium binding was monitored using the calcium-mimic dye Stains-all (4,4,4',5'-dibenzo-3,3'-diethyl-9-methyl-thiacarbocya-nine bromide). Binding abilities were seen to increase several-fold when the E and F helices of site 1 were replaced by those of site 4 (i.e., 111-414). In contrast, the intensity of circular dichroism induced in the absorption bands of the bound achiral dye decreased significantly when the helical flanks of site 4 were replaced with those of site 1 (i.e., 444-141). The helical flanks of site 4 impart greater binding ability to a given loop region, while the helical flanks of site 1 tend to weaken it

Genetic effects of oxidative DNA damages: comparative mutagenesis of the imidazole ring-opened formamidopyrimidines (Fapy lesions) and 8-oxo-purines in simian kidney cells

Fapy·dG and 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxo-dG) are formed in DNA by hydroxyl radical damage. In order to study replication past these lesions in cells, we constructed a single-stranded shuttle vector containing the lesion in 5′-TGT and 5′-TGA sequence contexts. Replication of the modified vector in simian kidney (COS-7) cells showed that Fapy·dG is mutagenic inducing primarily targeted Fapy·G→T transversions. In the 5′-TGT sequence mutational frequency of Fapy·dG was ∼30%, whereas in the 5′-TGA sequence it was ∼8%. In parallel studies 8-oxo-dG was found to be slightly less mutagenic than Fapy·dG, though it also exhibited a similar context effect: 4-fold G→T transversions (24% versus 6%) occurred in the 5′-TGT sequence relative to 5′-TGA. To investigate a possible structural basis for the higher G→T mutations induced by both lesions when their 3′ neighbor was T, we carried out a molecular modeling investigation in the active site of DNA polymerase β, which is known to incorporate both dCTP (no mutation) and dATP (G→T substitution) opposite 8-oxo-G. In pol β, the syn-8-oxo-G:dATP pair showed greater stacking with the 3′-T:A base pair in the 5′-TGT sequence compared with the 3′-A:T in the 5′-TGA sequence, whereas stacking for the anti-8-oxo-G:dCTP pair was similar in both 5′-TGT and 5′-TGA sequences. Similarly, syn-Fapy·G:dATP pairing showed greater stacking in the 5′-TGT sequence compared with the 5′-TGA sequence, while stacking for anti-Fapy·G:dCTP pairs was similar in the two sequences. Thus, for both lesions less efficient base stacking between the lesion:dATP pair and the 3′-A:T base pair in the 5′-TGA sequence might cause lower G→T mutational frequencies in the 5′-TGA sequence compared to 5′-TGT. The corresponding lesions derived from 2′-deoxyadenosine, Fapy·dA and 8-oxo-dA, were not detectably mutagenic in the 5′-TAT sequence, and were only weakly mutagenic (<1%) in the 5′-TAA sequence context, where both lesions induced targeted A→C transversions. To our knowledge this is the first investigation using extrachromosomal probes containing a Fapy·dG or Fapy·dA site-specifically incorporated, which showed unequivocally that in simian kidney cells Fapy·G→T substitutions occur at a higher frequency than 8-oxo-G→T and that Fapy·dA is very weakly mutagenic, as is 8-oxo-dA

Genetic effects of oxidative DNA damages: comparative mutagenesis of the imidazole ring-opened formamidopyrimidines (Fapy lesions) and 8-oxo-purines in simian kidney cells

Fapy·dG and 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxo-dG) are formed in DNA by hydroxyl radical damage. In order to study replication past these lesions in cells, we constructed a single-stranded shuttle vector containing the lesion in 5′-TGT and 5′-TGA sequence contexts. Replication of the modified vector in simian kidney (COS-7) cells showed that Fapy·dG is mutagenic inducing primarily targeted Fapy·G→T transversions. In the 5′-TGT sequence mutational frequency of Fapy·dG was ∼30%, whereas in the 5′-TGA sequence it was ∼8%. In parallel studies 8-oxo-dG was found to be slightly less mutagenic than Fapy·dG, though it also exhibited a similar context effect: 4-fold G→T transversions (24% versus 6%) occurred in the 5′-TGT sequence relative to 5′-TGA. To investigate a possible structural basis for the higher G→T mutations induced by both lesions when their 3′ neighbor was T, we carried out a molecular modeling investigation in the active site of DNA polymerase β, which is known to incorporate both dCTP (no mutation) and dATP (G→T substitution) opposite 8-oxo-G. In pol β, the syn-8-oxo-G:dATP pair showed greater stacking with the 3′-T:A base pair in the 5′-TGT sequence compared with the 3′-A:T in the 5′-TGA sequence, whereas stacking for the anti-8-oxo-G:dCTP pair was similar in both 5′-TGT and 5′-TGA sequences. Similarly, syn-Fapy·G:dATP pairing showed greater stacking in the 5′-TGT sequence compared with the 5′-TGA sequence, while stacking for anti-Fapy·G:dCTP pairs was similar in the two sequences. Thus, for both lesions less efficient base stacking between the lesion:dATP pair and the 3′-A:T base pair in the 5′-TGA sequence might cause lower G→T mutational frequencies in the 5′-TGA sequence compared to 5′-TGT. The corresponding lesions derived from 2′-deoxyadenosine, Fapy·dA and 8-oxo-dA, were not detectably mutagenic in the 5′-TAT sequence, and were only weakly mutagenic (<1%) in the 5′-TAA sequence context, where both lesions induced targeted A→C transversions. To our knowledge this is the first investigation using extrachromosomal probes containing a Fapy·dG or Fapy·dA site-specifically incorporated, which showed unequivocally that in simian kidney cells Fapy·G→T substitutions occur at a higher frequency than 8-oxo-G→T and that Fapy·dA is very weakly mutagenic, as is 8-oxo-dA

Visualización en tres dimensiones, los mapas de amenaza volcánica educan al ciudadano común

Even the most reliable volcanic hazard map will be of little use, unless it is presented in terms that are useful&nbsp;to politics, emergency management officials and citizens. The Volcanic Hazard Map of the Nevado del Ruiz&nbsp;Volcano (Colombia), was superimposed on Landsat TM 5 data and digital elevation models, in order to&nbsp;generate perspective views for making the volcanic hazard situations comprehensible to the common people.This 3-D visualization methodology could be used with any volcanic hazard map available. The products&nbsp;generated help to improve the communication between volcanologists and people not familiar with volcanoes,&nbsp;in order to avoid confusion, misunderstanding and strained relations between scientists and persons responsible&nbsp;for the public welfare, during any volcanic emergency crisis.Hasta el mapa de amenaza volcánica más confiable, será de poca utilidad si es presentado de una forma que&nbsp;no lo haga útil para políticos, oficiales que manejan situaciones de emergencia y ciudadanos comunes. Se&nbsp;realizó la superposición del Mapa de Amenaza Volcánica del Volcán Nevado del Ruiz (Colombia), sobre&nbsp;imágenes Landsat TM y modelos digitales de elevación, para generar vistas en perspectiva que hagan&nbsp;comprensibles para el público en general, las situaciones de amenaza volcánica.Esta metodología de visualización en tres dimensiones, podría utilizarse en cualquier mapa de amenaza&nbsp;volcánica disponible. Los productos generados ayudan a mejorar la comunicación entre vulcanólogos y&nbsp;gente no familiarizada con los volcanes, para evitar confusiones, malos entendidos y malas relaciones entre&nbsp;científicos y personas a cargo de la seguridad pública, durante cualquier crisis de emergencia volcánica. &nbsp

Assessing food-based strategies to address anaemia in pregnancy in rural plains Nepal: a mixed methods study

Anaemia in pregnancy is a persistent health problem in Nepal and could be reduced through nutrition counselling and strengthened iron folic acid supplementation programmes. We analysed 24-hour diet recall data from 846 pregnant women in rural plains Nepal, using linear programming to identify the potential for optimised food-based strategies to increase iron adequacy. We then conducted qualitative research to analyse how anaemia was defined and recognised, how families used food-based strategies to address anaemia, and the acceptability of optimised food-based strategies. We did 16 interviews of recently pregnant mothers, three focus group discussions with fathers, three focus group discussions with mothers-in-law and four interviews with key informants. Dietary analyses showed optimised diets did not achieve 100 % of recommended iron intakes, but iron intakes could be doubled by increasing intakes of green leaves, egg and meat. Families sought to address anaemia through food-based strategies but were often unable to because of the perceived expense of providing an ‘energy-giving’ diet. Some foods were avoided because of religious or cultural taboos, or because they were low status and could evoke social consequences if eaten. There is a need for counselling to offer affordable ways for families to optimise iron adequacy. The participation of communities in tailoring advice to ensure cultural relevance and alignment with local norms is necessary to enable its effectiveness

Addressing anaemia in pregnancy in rural plains Nepal: A qualitative, formative study.

Maternal anaemia prevalence in low-income countries is unacceptably high. Our research explored the individual-, family- and community-level factors affecting antenatal care uptake, iron folic acid (IFA) intake and consumption of micronutrient-rich diets among pregnant women in the plains of Nepal. We discuss how these findings informed the development of a home visit and community mobilisation intervention to reduce anaemia in pregnancy. We used a qualitative methodology informed by the socio-ecological framework, conducting semi-structured interviews with recently pregnant women and key informants, and focus group discussions with mothers-in-law and fathers. We found that harmful gender norms restricted women's access to nutrient-rich food, restricted their mobility and access to antenatal care. These norms also restricted fathers' role to that of the provider, as opposed to the caregiver. Pregnant women, mothers-in-law and fathers lacked awareness about iron-rich foods and how to manage the side effects of IFA. Fathers lacked trust in government health facilities affecting access to care and trust in the efficacy of IFA. Our research informed interventions by (1) informing the development of intervention tools and training; (2) informing the intervention focus to engaging mothers-in-law and men to enable behaviour change; and (3) demonstrating the need to work in synergy across individual, family and community levels to address power and positionality, gender norms, trust in health services and harmful norms. Participatory groups and home visits will enable the development and implementation of feasible and acceptable strategies to address family and contextual issues generating knowledge and an enabling environment for behaviour change

Comprehensive Anaemia Programme and Personalized Therapies (CAPPT): protocol for a cluster-randomised controlled trial testing the effect women's groups, home counselling and iron supplementation on haemoglobin in pregnancy in southern Nepal.

BACKGROUND: Anaemia in pregnancy remains prevalent in Nepal and causes severe adverse health outcomes. METHODS: This non-blinded cluster-randomised controlled trial in the plains of Nepal has two study arms: (1) Control: routine antenatal care (ANC); (2) Home visiting, iron supplementation, Participatory Learning and Action (PLA) groups, plus routine ANC. Participants, including women in 54 non-contiguous clusters (mean 2582; range 1299-4865 population) in Southern Kapilbastu district, are eligible if they consent to menstrual monitoring, are resident, married, aged 13-49 years and able to respond to questions. After 1-2 missed menses and a positive pregnancy test, consenting women < 20 weeks' gestation, who plan to reside locally for most of the pregnancy, enrol into trial follow-up. Interventions comprise two home-counselling visits (at 12-21 and 22-26 weeks' gestation) with iron folic acid (IFA) supplement dosage tailored to women's haemoglobin concentration, plus monthly PLA women's group meetings using a dialogical problem-solving approach to engage pregnant women and their families. Home visits and PLA meetings will be facilitated by auxiliary nurse midwives. The hypothesis is as follows: Haemoglobin of women at 30 ± 2 weeks' gestation is ≥ 0.4 g/dL higher in the intervention arm than in the control. A sample of 842 women (421 per arm, average 15.6 per cluster) will provide 88% power, assuming SD 1.2, ICC 0.09 and CV of cluster size 0.27. Outcomes are captured at 30 ± 2 weeks gestation. Primary outcome is haemoglobin concentration (g/dL). Secondary outcomes are as follows: anaemia prevalence (%), mid-upper arm circumference (cm), mean probability of micronutrient adequacy (MPA) and number of ANC visits at a health facility. Indicators to assess pathways to impact include number of IFA tablets consumed during pregnancy, intake of energy (kcal/day) and dietary iron (mg/day), a score of bioavailability-enhancing behaviours and recall of one nutrition knowledge indicator. Costs and cost-effectiveness of the intervention will be estimated from a provider perspective. Using constrained randomisation, we allocated clusters to study arms, ensuring similarity with respect to cluster size, ethnicity, religion and distance to a health facility. Analysis is by intention-to-treat at the individual level, using mixed-effects regression. DISCUSSION: Findings will inform Nepal government policy on approaches to increase adherence to IFA, improve diets and reduce anaemia in pregnancy. TRIAL REGISTRATION: ISRCTN 12272130

The mutation V42M distorts the compact packing of the human gamma-S-crystallin molecule, resulting in congenital cataract.

BACKGROUND: Human γS-crystallin is an important component of the human eye lens nucleus and cortex. The mutation V42M in the molecule causes severe congenital cataract in children. We compare the structure of the mutant protein with that of the wild type in order to understand how structural changes in the mutant relate to the mechanism of opacification. METHODS: Both proteins were made using conventional cloning and expression procedures. Secondary and tertiary structural features of the proteins were analyzed using spectral methods. Structural stabilities of the proteins were analyzed using chemical and thermal denaturation methods. Self-aggregation was monitored using extrinsic spectral probes. Molecular modeling was used to compare the structural features of the two proteins. RESULTS: While the wild type and mutant have the same secondary structure, molecular modeling and fluorescence analysis suggest the mutant to have a more open tertiary structure, with a larger hydrophobic surface. Experiments using extrinsic probes reveal that the mutant readily self-aggregates, with the suggestion that the aggregates might be similar to amyloidogenic fibrils. Chemical denaturation indicates that while the wild type exhibits the classic two-state transition, V42M goes through an intermediate state, and has a distinctly lower stability than the wild type. The temperature of thermal unfolding of the mutant is also distinctly lower. Further, the mutant readily precipitates and scatters light more easily than the wild type. CONCLUSION: The replacement of valine in position 42 by the longer and bulkier methionine in human γS-crystallin perturbs the compact β-sheet core packing topology in the N-terminal domain of the molecule, exposes nonpolar residues thereby increasing the surface hydrophobicity and weakens the stability of the protein, thus promoting self-aggregation leading to light scattering particles. This set of changes in the properties of the mutant offers a molecular insight into the mechanism of opacification