Protein/DNA interactions in complex DNA topologies: expect the unexpected

DNA supercoiling results in compacted DNA structures that can bring distal sites into close proximity. It also changes the local structure of the DNA, which can in turn influence the way it is recognised by drugs, other nucleic acids and proteins. Here, we discuss how DNA supercoiling and the formation of complex DNA topologies can affect the thermodynamics of DNA recognition. We then speculate on the implications for transcriptional control and the three-dimensional organisation of the genetic material, using examples from our own simulations and from the literature. We introduce and discuss the concept of coupling between the multiple length-scales associated with hierarchical nuclear structural organisation through DNA supercoiling and topology

Azotobacter genomes: the genome of Azotobacter chroococcum NCIMB 8003 (ATCC 4412)

The genome of the soil-dwelling heterotrophic N2-fixing Gram-negative bacterium Azotobacter chroococcum NCIMB 8003 (ATCC 4412) (Ac-8003) has been determined. It consists of 7 circular replicons totalling 5,192,291 bp comprising a circular chromosome of 4,591,803 bp and six plasmids pAcX50a, b, c, d, e, f of 10,435 bp, 13,852, 62,783, 69,713, 132,724, and 311,724 bp respectively. The chromosome has a G+C content of 66.27% and the six plasmids have G+C contents of 58.1, 55.3, 56.7, 59.2, 61.9, and 62.6% respectively. The methylome has also been determined and 5 methylation motifs have been identified. The genome also contains a very high number of transposase/inactivated transposase genes from at least 12 of the 17 recognised insertion sequence families. The Ac-8003 genome has been compared with that of Azotobacter vinelandii ATCC BAA-1303 (Av-DJ), a derivative of strain O, the only other member of the Azotobacteraceae determined so far which has a single chromosome of 5,365,318 bp and no plasmids. The chromosomes show significant stretches of synteny throughout but also reveal a history of many deletion/insertion events. The Ac-8003 genome encodes 4628 predicted protein-encoding genes of which 568 (12.2%) are plasmid borne. 3048 (65%) of these show > 85% identity to the 5050 protein-encoding genes identified in Av-DJ, and of these 99 are plasmid-borne. The core biosynthetic and metabolic pathways and macromolecular architectures and machineries of these organisms appear largely conserved including genes for CO-dehydrogenase, formate dehydrogenase and a soluble NiFe-hydrogenase. The genetic bases for many of the detailed phenotypic differences reported for these organisms have also been identified. Also many other potential phenotypic differences have been uncovered. Properties endowed by the plasmids are described including the presence of an entire aerobic corrin synthesis pathway in pAcX50f and the presence of genes for retro-conjugation in pAcX50c. All these findings are related to the potentially different environmental niches from which these organisms were isolated and to emerging theories about how microbes contribute to their communities

A Multi-method Assessment of Risk and Protective Factors in Family Violence:Comparing Italian and Migrant Families

Child maltreatment is a major public health issue, which threatens psychophysical well-being of almost 100.000 minors in Italy. The prevalence and social burden of this issue clearly indicate the need for preventive efforts, early identification of victimized children and a rapid risk assessment of families referred to Child Protection Services (CPS). The present chapter proposes an evidence-based multi-method assessment system, specific for highlighting risk and protective factors in family functioning. The assessment system is comprised of six modules: \u2022 one in-depth protocol for identifying proximate and distal risk and protective factors of maltreatment and recidivism against children; \u2022 one explorative tool for assessing the (residual) social capital in an at-risk family \u2022 four screening surveys for assessing parenting stress, parental child abuse potential, parents\u2019 resilience, and traumatic symptoms (in children). In our proposal, distal risk factors imply a condition of vulnerability but exert an indirect influence on the child\u2019s developmental trajectory, while proximate factors (both risk and protective) exert a direct influence on the adaptation of the child. Research foundations of the assessment system lie on several research carried out from 2008 to nowadays: the chapter proposes a brief review of main outcomes, focusing especially on the Factors of the Protocol of risk and protective factors (Di Blasio, 2005). A better comprehension of risk and protective factors in family violence may inform and guide preventive interventions on primary, secondary and tertiary level. Our assessment system is meant to assist professionals in both decision-making and protection of children in all of these levels

Surgical perspectives from a prospective, nonrandomized, multicenter study of breast conserving surgery and adjuvant electronic brachytherapy for the treatment of breast cancer

<p>Abstract</p> <p>Background</p> <p>Accelerated partial breast irradiation (APBI) may be used to deliver radiation to the tumor bed post-lumpectomy in eligible patients with breast cancer. Patient and tumor characteristics as well as the lumpectomy technique can influence patient eligibility for APBI. This report describes a lumpectomy procedure and examines patient, tumor, and surgical characteristics from a prospective, multicenter study of electronic brachytherapy.</p> <p>Methods</p> <p>The study enrolled 65 patients of age 45-84 years with ductal carcinoma or ductal carcinoma in situ, and 44 patients, who met the inclusion and exclusion criteria, were treated with APBI using the Axxent^®electronic brachytherapy system following lumpectomy. The prescription dose was 34 Gy in 10 fractions over 5 days.</p> <p>Results</p> <p>The lumpectomy technique as described herein varied by site and patient characteristics. The balloon applicator was implanted by the surgeon (91%) or a radiation oncologist (9%) during or up to 61 days post-lumpectomy (mean 22 days). A lateral approach was most commonly used (59%) for insertion of the applicator followed by an incision site approach in 27% of cases, a medial approach in 5%, and an inferior approach in 7%. A trocar was used during applicator insertion in 27% of cases. Local anesthetic, sedation, both or neither were administered in 45%, 2%, 41% and 11% of cases, respectively, during applicator placement. The prescription dose was delivered in 42 of 44 treated patients.</p> <p>Conclusions</p> <p>Early stage breast cancer can be treated with breast conserving surgery and APBI using electronic brachytherapy. Treatment was well tolerated, and these early outcomes were similar to the early outcomes with iridium-based balloon brachytherapy.</p

Conscientiousness, Career Success, and Longevity: A Lifespan Analysis

Markers of executive functioning, such as prudent planning for the future and impulse control, are related to conscientiousness and may be central to both occupational success and health outcomes. The aim of the study was to examine relations among conscientiousness, career success, and mortality risk across a 65-year period. Using data derived from 693 male participants in the Terman Life Cycle Study, we examined associations among childhood personality, midlife objective career success, and lifelong mortality risk through 2006. Conscientiousness and career success each predicted lower mortality risk (N = 693, relative hazard (rh) = 0.82 [95% confidence interval = 0.74, 0.91] and rh = 0.80 [0.71, 0.91], respectively), with both shared and unique variance. Importantly, childhood personality moderated the success–longevity link; conscientiousness was most relevant for least successful individuals. Conscientiousness and career success predicted longevity, but not in a straightforward manner. Findings highlight the importance of lifespan processes

Current drinking and health-risk behaviors among male high school students in central Thailand

<p>Abstract</p> <p>Background</p> <p>Alcohol drinking is frequently related to behavioral problems, which lead to a number of negative consequences. This study was to evaluate the characteristics of male high school students who drink, the drinking patterns among them, and the associations between current drinking and other health risk behaviors which focused on personal safety, violence-related behaviors, suicide and sexual behaviors.</p> <p>Method</p> <p>A cross-sectional study was conducted to explore current alcohol drinking and health-risk behaviors among male high school students in central Thailand. Five thousand one hundred and eighty four male students were classified into 2 groups according to drinking in the previous 30 days (yes = 631, no = 4,553). Data were collected by self-administered, anonymous questionnaire which consisted of 3 parts: socio-demographic factors, health-risk behaviors and alcohol drinking behavior during the past year from December 2007 to February 2008.</p> <p>Results</p> <p>The results showed that the percent of current drinking was 12.17. Most of them were 15-17 years (50.21%). Socio-demographic factors such as age, educational level, residence, cohabitants, grade point average (GPA), having a part time job and having family members with alcohol/drug problems were significantly associated with alcohol drinking (p < 0.05). Multiple logistic regression analysis, after adjusting for socio-demographic factors, revealed that health-risk behavioral factors were associated with current alcohol consumption: often drove after drinking alcohol (OR = 3.10, 95% CI = 1.88-5.12), often carried a weapon (OR = 3.51, 95% CI = 2.27-5.42), often got into a physical fight without injury (OR = 3.06, 95% CI = 1.99-4.70), dating violence (OR = 2.58, 95% CI = 1.79-3.71), seriously thought about suicide (OR = 2.07, 95% CI = 1.38-3.11), made a suicide plan (OR = 2.10, 95% CI = 1.43-3.08), ever had sexual intercourse (OR = 5.62, 95% CI = 4.33-7.29), alcohol or drug use before last sexual intercourse (OR = 2.55, 95% CI = 1.44-4.53), and got someone pregnant (OR = 3.99, 95% CI = 1.73-9.25).</p> <p>Conclusions</p> <p>An increased risk of health-risk behaviors, including driving vehicles after drinking, violence-related behaviors, sad feelings and attempted suicide, and sexual behaviors was higher among drinking students that led to significant health problems. Effective intervention strategies (such as a campaign mentioning the adverse health effects and social consequences to the risk groups, and encouraging parental and community efforts to prevent drinking) among adolescents should be implemented to prevent underage drinking and adverse consequences.</p

Structural Constraints Identified with Covariation Analysis in Ribosomal RNA

Covariation analysis is used to identify those positions with similar patterns of sequence variation in an alignment of RNA sequences. These constraints on the evolution of two positions are usually associated with a base pair in a helix. While mutual information (MI) has been used to accurately predict an RNA secondary structure and a few of its tertiary interactions, early studies revealed that phylogenetic event counting methods are more sensitive and provide extra confidence in the prediction of base pairs. We developed a novel and powerful phylogenetic events counting method (PEC) for quantifying positional covariation with the Gutell lab’s new RNA Comparative Analysis Database (rCAD). The PEC and MI-based methods each identify unique base pairs, and jointly identify many other base pairs. In total, both methods in combination with an N-best and helix-extension strategy identify the maximal number of base pairs. While covariation methods have effectively and accurately predicted RNAs secondary structure, only a few tertiary structure base pairs have been identified. Analysis presented herein and at the Gutell lab’s Comparative RNA Web (CRW) Site reveal that the majority of these latter base pairs do not covary with one another. However, covariation analysis does reveal a weaker although significant covariation between sets of nucleotides that are in proximity in the three-dimensional RNA structure. This reveals that covariation analysis identifies other types of structural constraints beyond the two nucleotides that form a base pair

A randomized clinical trial comparing hydrocolloid, phenytoin and simple dressings for the treatment of pressure ulcers [ISRCTN33429693]

BACKGROUND: Pressure sores are important and common complications of spinal cord injury. Many preventive and therapeutic approaches have been tried and new trials are evolving. One relatively recent method is application of a hydrocolloid dressing (HD). In this study we compared the therapeutic effects of HD on pressure ulcer healing with two other topical applications, phenytoin cream (PC) and simple dressing (SD). METHODS: Ninety-one stage I and stage II pressure ulcers of 83 paraplegic male victims of the Iran-Iraq war were randomly allocated to three treatment groups. Mean age and weight of the participants were 36.64 ± 6.04 years and 61.12 ± 5.08 kg, respectively. All the patients were managed in long term care units or in their homes for 8 weeks by a team of general practitioners and nurses, and the ulcer status was recorded as "Complete healing", "Partial healing", "Without improvement" and "Worsening". RESULTS: Complete healing of ulcers, regardless of location and stage, was better in the HD group than the PC [23/31(74.19%) vs 12/30(40%); difference: 34.19%, 95% CI = 10.85–57.52, (P < 0.01)] or the SD [23/31(74.19%) vs 8/30(26.66%); difference: 47.53%, 95% CI = 25.45–69.61, (P < 0.005)] groups. Complete healing of stage I ulcers in the HD group [11/13(85%)] was better than in the SD [5/11(45%); difference: 40%, 95% CI = 4.7–75.22, (P < 0.05)] or PC [2/9 (22%); difference: 63%, 95% CI = 29.69–96.3, (P < 0.005)] groups. Complete healing of stage II ulcer in the HD group [12/18 (67%)] was better than in the SD group [3/19(16%); difference: 51%, 95% CI = 23.73–78.26, (P < 0.005)], but not significantly different from the PC group [10/21 (48%); difference: 19%, 95% CI = -11.47–49.47, (P > 0.05)]. We performed a second analysis considering only one ulcer per patient (i.e. 83 ulcers in 83 patients). This "per patient" analysis showed that complete ulcer healing in the HD group was better than in the PC [20/28(71.4%) vs 11/28 (39.3%); difference: 32.1%, 95% CI = 7.4–56.7, (P < 0.01)] or SD [20/28(71.4%) vs 8/27 (29.6%); difference: 41.8%, 95% CI = 17.7–65.8, (P < 0.005)] groups. CONCLUSION: We deduced that HD is the most effective method investigated for treating stage I and II pressure ulcers in young paraplegic men