The Proteomic Code: a molecular recognition code for proteins

<p>Abstract</p> <p>Background</p> <p>The Proteomic Code is a set of rules by which information in genetic material is transferred into the physico-chemical properties of amino acids. It determines how individual amino acids interact with each other during folding and in specific protein-protein interactions. The Proteomic Code is part of the redundant Genetic Code.</p> <p>Review</p> <p>The 25-year-old history of this concept is reviewed from the first independent suggestions by Biro and Mekler, through the works of Blalock, Root-Bernstein, Siemion, Miller and others, followed by the discovery of a Common Periodic Table of Codons and Nucleic Acids in 2003 and culminating in the recent conceptualization of partial complementary coding of interacting amino acids as well as the theory of the nucleic acid-assisted protein folding.</p> <p>Methods and conclusions</p> <p>A novel cloning method for the design and production of specific, high-affinity-reacting proteins (SHARP) is presented. This method is based on the concept of proteomic codes and is suitable for large-scale, industrial production of specifically interacting peptides.</p

Split tendon transfers for the correction of spastic varus foot deformity: a case series study

<p>Abstract</p> <p>Background</p> <p>Overactivity of anterior and/or posterior tibial tendon may be a causative factor of spastic varus foot deformity. The prevalence of their dysfunction has been reported with not well defined results. Although gait analysis and dynamic electromyography provide useful information for the assessment of the patients, they are not available in every hospital. The purpose of the current study is to identify the causative muscle producing the deformity and apply the most suitable technique for its correction.</p> <p>Methods</p> <p>We retrospectively evaluated 48 consecutive ambulant patients (52 feet) with spastic paralysis due to cerebral palsy. The average age at the time of the operation was 12,4 yrs (9-18) and the mean follow-up 7,8 yrs (4-14). Eigtheen feet presented equinus hind foot deformity due to gastrocnemius and soleus shortening. According to the deformity, the feet were divided in two groups (Group I with forefoot and midfoot inversion and Group II with hindfoot varus). The deformities were flexible in all cases in both groups. Split anterior tibial tendon transfer (SPLATT) was performed in Group I (11 feet), while split posterior tibial tendon transfer (SPOTT) was performed in Group II (38 feet). In 3 feet both procedures were performed. Achilles tendon sliding lengthening (Hoke procedure) was done in 18 feet either preoperatively or concomitantly with the index procedure.</p> <p>Results</p> <p>The results in Group I, were rated according to Hoffer's clinical criteria as excellent in 8 feet and satisfactory in 3, while in Group II according to Kling's clinical criteria were rated as excellent in 20 feet, good in 14 and poor in 4. The feet with poor results presented residual varus deformity due to intraoperative technical errors.</p> <p>Conclusion</p> <p>Overactivity of the anterior tibial tendon produces inversion most prominent in the forefoot and midfoot and similarly overactivity of the posterior tibial tendon produces hindfoot varus. The deformity can be clinically unidentifiable in some cases when Achilles shortening co-exists producing foot equinus. By identifying the muscle causing the deformity and performing the appropriate technique, very satisfying results were achieved in the majority of our cases. In three feet both muscles contributed to a combined deformity and simultaneous SPLATT and SPOTT were considered necessary. For complex foot deformities where the component of cavus co-exists, supplementary procedures are required along with the index operation to obtain the best result.</p

Better Prognosis in Newborns with Trisomy 13 Who Received Intensive Treatments: A Retrospective Study of 16 Patients

Intensive treatment for newborns with trisomy 13 is controversial because of their lethal prognosis. We report the better life prognosis of patients with trisomy 13 who received intensive treatment. At our hospital, we provided an intensive management to such patients including resuscitation and surgical procedures as required. Herein, we present the results of a retrospective study (1989–2010) of 16 trisomy 13 cases who received an intensive treatment. None was diagnosed to have trisomy 13 before birth; 9 were delivered by C-section and oxygen was administered to all patients during postpartum resuscitation. Mechanical ventilation was used in 9 patients after tracheal intubation and tracheotomy was performed in 2 patients when withdrawing of extubation was difficult. Regarding prognosis, 9 patients died, 3 were referred to another hospital, and 4 were discharged from the hospital. Four and 7 patients died within 7 and 30 days after birth, respectively. Nine patients survived for >1 month, 7 for >180 days, and 5 for >3 years. Median survival for 16 patients was 733 days. The patients who received intensive treatments survived longer compared to the previous data. This study provides useful information concerning genetic counseling, especially from an ethical point of view, before providing intensive management to newborns with trisomy 13

Back from a Predicted Climatic Extinction of an Island Endemic: A Future for the Corsican Nuthatch

The Corsican Nuthatch (Sitta whiteheadi) is red-listed as vulnerable to extinction by the IUCN because of its endemism, reduced population size, and recent decline. A further cause is the fragmentation and loss of its spatially-restricted favourite habitat, the Corsican pine (Pinus nigra laricio) forest. In this study, we aimed at estimating the potential impact of climate change on the distribution of the Corsican Nuthatch using species distribution models. Because this species has a strong trophic association with the Corsican and Maritime pines (P. nigra laricio and P. pinaster), we first modelled the current and future potential distribution of both pine species in order to use them as habitat variables when modelling the nuthatch distribution. However, the Corsican pine has suffered large distribution losses in the past centuries due to the development of anthropogenic activities, and is now restricted to mountainous woodland. As a consequence, its realized niche is likely significantly smaller than its fundamental niche, so that a projection of the current distribution under future climatic conditions would produce misleading results. To obtain a predicted pine distribution at closest to the geographic projection of the fundamental niche, we used available information on the current pine distribution associated to information on the persistence of isolated natural pine coppices. While common thresholds (maximizing the sum of sensitivity and specificity) predicted a potential large loss of the Corsican Nuthatch distribution by 2100, the use of more appropriate thresholds aiming at getting closer to the fundamental distribution of the Corsican pine predicted that 98% of the current presence points should remain potentially suitable for the nuthatch and its range could be 10% larger in the future. The habitat of the endemic Corsican Nuthatch is therefore more likely threatened by an increasing frequency and intensity of wildfires or anthropogenic activities than by climate change

Dinâmica populacional de Bemisia tabaci biótipo B em tomate monocultivo e consorciado com coentro sob cultivo orgânico e convencional.

A mosca-branca Bemisia tabaci Biótipo B (Hemiptera: Aleyrodidae), é um herbívoro de difícil controle devido à alta plasticidade genotípica da espécie. No tomateiro pode causar danos severos principalmente pela transmissão de diversas viroses. O manejo do sistema de produção e o consórcio de culturas podem ter um efeito direto nas populações desse herbívoro, sem que seja necessária a aplicação de inseticidas. Avaliou-se a influência dos sistemas de produção orgânico e convencional e o consórcio tomate-coentro na dinâmica populacional da mosca-branca no campo experimental da Embrapa Hortaliças, de maio a setembro/06. O monitoramento dos adultos da mosca-branca e de seus inimigos naturais foi realizado utilizando-se armadilhas adesivas amarelas fixadas nas bordas e no interior das parcelas experimentais e a amostragem de ninfas foi realizada por observação direta das folhas de tomate no campo. Embora as populações ao redor dos diferentes tratamentos fossem equivalentes, a abundância de adultos de mosca-branca foi significativamente menor nas parcelas de tomate consorciado com coentro, tanto no sistema convencional como orgânico. Apenas o consórcio tomatecoentro em sistema orgânico apresentou redução significativa na quantidade de ninfas por planta em relação aos demais tratamentos. Os inimigos naturais foram significativamente mais abundantes em sistema orgânico e foi verificada uma correlação negativa da abundância dos inimigos naturais e a quantidade de ninfas por planta. A associação tomate-coentro e o manejo orgânico do agroecossistema favoreceram ao controle biológico natural da mosca-branca

Climate change, phenological shifts, eco-evolutionary responses and population viability: toward a unifying predictive approach

The debate on emission targets of greenhouse gasses designed to limit global climate change has to take into account the ecological consequences. One of the clearest ecological consequences is shifts in phenology. Linking these shifts to changes in population viability under various greenhouse gasses emission scenarios requires a unifying framework. We propose a box-in-a-box modeling approach that couples population models to phenological change. This approach unifies population modeling with both ecological responses to climate change as well as evolutionary processes. We advocate a mechanistic embedded correlative approach, where the link from genes to population is established using a periodic matrix population model. This periodic model has several major advantages: (1) it can include complex seasonal behaviors allowing an easy link with phenological shifts; (2) it provides the structure of the population at each phase, including the distribution of genotypes and phenotypes, allowing a link with evolutionary processes; and (3) it can incorporate the effect of climate at different time periods. We believe that the way climatologists have approached the problem, using atmosphere–ocean coupled circulation models in which components are gradually included and linked to each other, can provide a valuable example to ecologists. We hope that ecologists will take up this challenge and that our preliminary modeling framework will stimulate research toward a unifying predictive model of the ecological consequences of climate change

Detection of North American orthopoxviruses by real time-PCR

The prevalence of North American orthopoxviruses in nature is unknown and may be more difficult to ascertain due to wide spread use of vaccinia virus recombinant vaccines in the wild. A real time PCR assay was developed to allow for highly sensitive and specific detection of North American orthopoxvirus DNA in animal tissues and bodily fluids. This method is based on the amplification of a 156 bp sequence within a myristylated protein, highly conserved within the North American orthopoxviruses but distinct from orthologous genes present in other orthopoxviruses. The analytical sensitivity was 1.1 fg for Volepox virus DNA, 1.99 fg for Skunkpox virus DNA, and 6.4 fg for Raccoonpox virus DNA with a 95% confidence interval. Our assay did not cross-react with other orthopoxviruses or ten diverse representatives of the Chordopoxvirinae subfamily. This new assay showed more sensitivity than tissue culture tests, and was capable of differentiating North American orthopoxviruses from other members of Orthopoxvirus. Thus, our assay is a promising tool for highly sensitive and specific detection of North American orthopoxviruses in the United States and abroad

Effect of Dexrazoxane and Amifostine on the Vertebral Bone Quality of Doxorubicin Treated Male Rats

Doxorubicin (DOX) is widely used in combination cocktails for treatment of childhood hematological cancers and solid tumors. A major factor limiting DOX usage is DOX-induced cardiotoxicity. However, it is not known whether protectants like dexrazoxane (DXR) and amifostine (AMF) can prevent DOX-mediated bone damage. The present study investigated whether administration of AMF alone or in combination with DXR would prevent any DOX-mediated bone damage. Male rat pups were treated with DOX, DXR, AMF, and their combinations. On neonate day 38, the bone mineral density (BMD), bone mineral content (BMC) and the micro-architecture of the lumbar vertebrae were analyzed. We have shown that when male rats are treated with DOX, DXR, DOX+DXR, AMF, DOX+AMF or DOX+DXR+AMF, there is a decrease in lumbar vertebral BMD (p<0.05). Furthermore, the relative bone volume (BV/TV) was decreased by DXR, DOX+DXR, and DOX+AMF treatments. Interestingly, DOX+AMF significantly increased BV/TV when compared to DXR treatment (p<0.04). The trabecular number (Tb.N) decreased with DXR and DOX+DXR and increased with DOX+AMF treatments. This information will be useful in designing better cancer combination therapies that do not lead to vertebrae deterioration

A Rigidity-Enhanced Antimicrobial Activity: A Case for Linear Cationic α-Helical Peptide HP(2–20) and Its Four Analogues

Linear cationic α-helical antimicrobial peptides are referred to as one of the most likely substitutes for common antibiotics, due to their relatively simple structures (≤40 residues) and various antimicrobial activities against a wide range of pathogens. Of those, HP(2–20) was isolated from Helicobacter pylori ribosomal protein. To reveal a mechanical determinant that may mediate the antimicrobial activities, we examined the mechanical properties and structural stabilities of HP(2–20) and its four analogues of same chain length by steered molecular dynamics simulation. The results indicated the following: the resistance of H-bonds to the tensile extension mediated the early extensive stage; with the loss of H-bonds, the tensile force was dispensed to prompt the conformational phase transition; and Young's moduli (N/m2) of the peptides were about 4∼8×109. These mechanical features were sensitive to the variation of the residue compositions. Furthermore, we found that the antimicrobial activity is rigidity-enhanced, that is, a harder peptide has stronger antimicrobial activity. It suggests that the molecular spring constant may be used to seek a new structure-activity relationship for different α-helical peptide groups. This exciting result was reasonably explained by a possible mechanical mechanism that regulates both the membrane pore formation and the peptide insertion

Genetic Assignment Methods for Gaining Insight into the Management of Infectious Disease by Understanding Pathogen, Vector, and Host Movement

For many pathogens with environmental stages, or those carried by vectors or intermediate hosts, disease transmission is strongly influenced by pathogen, host, and vector movements across complex landscapes, and thus quantitative measures of movement rate and direction can reveal new opportunities for disease management and intervention. Genetic assignment methods are a set of powerful statistical approaches useful for establishing population membership of individuals. Recent theoretical improvements allow these techniques to be used to cost-effectively estimate the magnitude and direction of key movements in infectious disease systems, revealing important ecological and environmental features that facilitate or limit transmission. Here, we review the theory, statistical framework, and molecular markers that underlie assignment methods, and we critically examine recent applications of assignment tests in infectious disease epidemiology. Research directions that capitalize on use of the techniques are discussed, focusing on key parameters needing study for improved understanding of patterns of disease