The Definition of Open Reading Frame Revisited.

The term open reading frame (ORF) is of central importance to gene finding. Surprisingly, at least three definitions are in use. We discuss several molecular biological and bioinformatics aspects, and we recommend using the definition in which an ORF is bounded by stop codons.

Trends in mathematical modeling of host-pathogen interactions.

Pathogenic microorganisms entail enormous problems for humans, livestock, and crop plants. A better understanding of the different infection strategies of the pathogens enables us to derive optimal treatments to mitigate infectious diseases or develop vaccinations preventing the occurrence of infections altogether. In this review, we highlight the current trends in mathematical modeling approaches and related methods used for understanding host-pathogen interactions. Since these interactions can be described on vastly different temporal and spatial scales as well as abstraction levels, a variety of computational and mathematical approaches are presented. Particular emphasis is placed on dynamic optimization, game theory, and spatial modeling, as they are attracting more and more interest in systems biology. Furthermore, these approaches are often combined to illuminate the complexities of the interactions between pathogens and their host. We also discuss the phenomena of molecular mimicry and crypsis as well as the interplay between defense and counter defense. As a conclusion, we provide an overview of method characteristics to assist non-experts in their decision for modeling approaches and interdisciplinary understanding.

From Bedside to Bench: The Effect of Muscular Denervation on Fat Grafting to the Breast by Comparing Take Rate, Quality, and Longevity.

BACKGROUND: Autologous fat grafting (AFG) to the breast is a frequent procedure in aesthetic and reconstructive surgery. Despite pure volume gain, questions remain regarding the engraftment rate, quality, and longevity. Little is known about the role of recipient tissue or innervation of the grafted area. OBJECTIVES: The goal of this study was to determine the optimal recipient layer and muscular pretreatment of AFG. METHODS: Fat was grafted to the breast, pectoralis muscle, or adjacent subcutaneous tissue of 42 rats. Nerve treatment included excision of a nerve segment, botulinum toxin (BTX) injection, or no treatment. Magnetic resonance imaging (MRI) and histological workup were carried out after 2 and 6 weeks. RESULTS: Six weeks after AFG, the proportion of viable fat cells within the grafted fat stayed high (median, [IQR]: 81% [72% to 85%]). The signs of inflammation decreased over time. Intramuscular grafting with intact nerves had a decreasing effect on the viability of the grafted cells compared with subcutaneous treatment (-10.21%; 95% confidence interval [-21.1 to 0.68]). CONCLUSIONS: If utilized on an intact nerve, intramuscular injection may lead to inferior results. If the nerve was cut or treated with BTX; however, intramuscular injection tends to be superior. These findings may prove interesting for future studies and eventual clinical application.

Defining the transcriptomic landscape of Candida glabrata by RNA-Seq.

Candida glabrata is the second most common pathogenic Candida species and has emerged as a leading cause of nosocomial fungal infections. Its reduced susceptibility to antifungal drugs and its close relationship to Saccharomyces cerevisiae make it an interesting research focus. Although its genome sequence was published in 2004, little is known about its transcriptional dynamics. Here, we provide a detailed RNA-Seq-based analysis of the transcriptomic landscape of C. glabrata in nutrient-rich media, as well as under nitrosative stress and during pH shift. Using RNA-Seq data together with state-of-the-art gene prediction tools, we refined the annotation of the C. glabrata genome and predicted 49 novel protein-coding genes. Of these novel genes, 14 have homologs in S. cerevisiae and six are shared with other Candida species. We experimentally validated four novel protein-coding genes of which two are differentially regulated during pH shift and interaction with human neutrophils, indicating a potential role in host-pathogen interaction. Furthermore, we identified 58 novel non-protein-coding genes, 38 new introns and condition-specific alternative splicing. Finally, our data suggest different patterns of adaptation to pH shift and nitrosative stress in C. glabrata, Candida albicans and S. cerevisiae and thus further underline a distinct evolution of virulence in yeast.

Robustness during Aging-Molecular Biological and Physiological Aspects.

Understanding the process of aging is still an important challenge to enable healthy aging and to prevent age-related diseases. Most studies in age research investigate the decline in organ functionality and gene activity with age. The focus on decline can even be considered a paradigm in that field. However, there are certain aspects that remain surprisingly stable and keep the organism robust. Here, we present and discuss various properties of robust behavior during human and animal aging, including physiological and molecular biological features, such as the hematocrit, body temperature, immunity against infectious diseases and others. We examine, in the context of robustness, the different theories of how aging occurs. We regard the role of aging in the light of evolution.

Proteome analysis of bronchoalveolar lavage fluids reveals host and fungal proteins highly expressed during invasive pulmonary aspergillosis in mice and humans.

Invasive pulmonary aspergillosis (IPA) is a severe infection that is difficult to diagnose due to the ubiquitous presence of fungal spores, the underlying diseases of risk patients, and limitations of currently available markers. In this study, we performed a comprehensive liquid chromatography tandem mass spectrometry (LC-MS/MS)-based identification of host and fungal proteins expressed during IPA in mice and humans. The proteomic analysis of bronchoalveolar lavage samples of individual IPA and control cases allowed the description of common host factors that had significantly increased abundance in both infected animals and IPA patients compared to their controls. Although increased levels of these individual host proteins might not be sufficient to distinguish bacterial from fungal infection, a combination of these markers might be beneficial to improve diagnosis. We also identified 16 fungal proteins that were specifically detected during infection and may be valuable candidates for biomarker evaluation.

Comparative Study on Alternative Splicing in Human Fungal Pathogens Suggests Its Involvement During Host Invasion.

Alternative splicing (AS) is an important regulatory mechanism in eukaryotes but only little is known about its impact in fungi. Human fungal pathogens are of high clinical interest causing recurrent or life-threatening infections. AS can be well-investigated genome-wide and quantitatively with the powerful technology of RNA-Seq. Here, we systematically studied AS in human fungal pathogens based on RNA-Seq data. To do so, we investigated its effect in seven fungi during conditions simulating ex vivo infection processes and during in vitro stress. Genes undergoing AS are species-specific and act independently from differentially expressed genes pointing to an independent mechanism to change abundance and functionality. Candida species stand out with a low number of introns with higher and more varying lengths and more alternative splice sites. Moreover, we identified a functional difference between response to host and other stress conditions: During stress, AS affects more genes and is involved in diverse regulatory functions. In contrast, during response-to-host conditions, genes undergoing AS have membrane functionalities and might be involved in the interaction with the host. We assume that AS plays a crucial regulatory role in pathogenic fungi and is important in both response to host and stress conditions.

Denervation leads to volume regression in breast cancer.

The nervous system plays a key role in controlling the dynamic functions of multicellular complex organisms. Although peripheral nerves are supposed to play a pivotal role in tumor growth and dissemination, little experimental evidence exists to date. We assessed the effect of denervation on breast cancer growth by magnetic resonance imaging (MRI) in rats. Human breast cancer cells were implanted into adipofascial flaps with intact or surgically excised supplying nerve. Tumor volumes were measured 2 and 8 weeks after implantation by in vivo MRI. Results were validated by histology. Postoperative tumor volumes at 2 and 8 weeks were reduced by 76% (95% CI: 22-93%) in the denervated groups. Tumor area as determined histologically was reduced by 70% (95% CI: 60-78%). Thus, peripheral denervation may be an effective surgical approach for the palliative treatment of locally progressing or uncontrollable breast cancer.

Epineural adipose-derived stem cell injection in a sciatic rodent model.

BACKGROUND: The aim was to evaluate the regenerative effect of epineural injection of rat ASCs (rASCs) in three different settings of acute and chronic compression in a rat sciatic nerve model. METHODS: Acute compression (60 s) with a vessel clamp over a distance of 1 mm (group 1) or 10 mm (group 2), as well as chronic compression with a permanent remaining, nonabsorbable polymeric clip over a distance of 1 mm (group 3) was performed. Depending on the group, either 5 × 106 rASCs or the same volume (25 µl) of culture medium (CM) was injected with a 30G needle in the epineurium at the time of compression. Outcome measures were functional gait evaluations, imaging analysis, histomorphometric analyses, and muscle weight. RESULTS: The rats in group 2 had a better function than those with group 1 at one and especially at 2 weeks. After 4 weeks however, almost all rats were close to a normal function. There was a similar Muscle Weight Ratio (MWR) after 2 weeks in all groups, whereas after 4 weeks, the MWR in group 3 was lower compared with group 1 and 2. Histomorphometric analysis showed a better myelination in group 1 & 2 compared to group 3 after 4 weeks. ASCs have a beneficial effect on myelin thickness (G-Ratio). CONCLUSIONS: We successfully evaluated the regenerative effect of epineural injection of rASCs in three different settings of acute and chronic compression. However, there were no significant differences in outcomes between the ASC-treated groups and control groups.

Validity and reliability of the CatWalk system as a static and dynamic gait analysis tool for the assessment of functional nerve recovery in small animal models.

INTRODUCTION: A range of behavioral testing paradigms have been developed for the research of central and peripheral nerve injuries with the help of small animal models. Following any nerve repair strategy, improved functional outcome may be the most important evidence of axon regeneration. A novel automated gait analysis system, the CatWalk™, can measure dynamic as well as static gait patterns of small animals. Of most interest in detecting functional recovery are in particular dynamic gait parameters, coordination measures, and the intensity of the animals paw prints. This article is designed to lead to a more efficient choice of CatWalk parameters in future studies concerning the functional evaluation of nerve regeneration and simultaneously add to better interstudy comparability. METHODS: The aims of the present paper are threefold: (1) to describe the functional method of CatWalk gait analysis, (2) to characterize different parameters acquired by CatWalk gait analysis, and to find the most frequently used parameters as well as (3) to compare their reliability and validity throughout the different studies. RESULTS: In the reviewed articles, the most frequently used parameters were Swing Duration (30), Print Size (27), Stride Length (26), and Max Contact Area (24). Swing Duration was not only frequently used but was also the most reliable and valid parameter. Therefore, we hypothesize that Swing Duration constitutes an important parameter to be chosen for future studies, as it has the highest level of reliability and validity. CONCLUSION: In conclusion, CatWalk can be used as a complementary approach to other behavioral testing paradigms to assess clinically relevant behavioral benefits, with the main advantage that this system demonstrates both static and dynamic gait parameters at the same time. Due to limited reliability and validity of certain parameters, we recommend that only the most frequently assessed parameters should be used in the future.

Five-year results of laparoscopic sleeve gastrectomy.

BACKGROUND: Laparoscopic sleeve gastrectomy (LSG) is gaining popularity, but studies reporting long-term results are still rare. The objective of this study was to present the 5-year outcome concerning weight loss, modification of co-morbidities, and late complications. METHODS: This is a retrospective analysis of a prospective cohort with a minimal follow-up of 5 years. A total of 68 patients underwent LSG either as primary bariatric procedure (n = 41) or as redo operation after failed laparoscopic gastric banding (n = 27) between August 2004 and December 2007. At the time of LSG, the mean body mass index (BMI) was 43.0 ± 8.0 kg/m(2), the mean age 43.1 ± 10.1 years, and 78% were female. The follow-up rate was 100% at 1 year postoperatively, 97% after 2 years, and 91% after 5 years; the mean follow-up time was 5.9 ± 0.8 years. RESULTS: The average excessive BMI loss was 61.5% ± 23.4% after 1 year, 61.1% ± 23.4% after 2 years, and 57.4% ± 24.7% after 5 years. Co-morbidities improved considerably; a remission of type 2 diabetes could be reached at 85%. The following complications were observed: 1 leak (1.5%), 2 incisional hernias (2.9%), and new-onset gastroesophageal reflux in 11 patients (16.2%). Reoperation due to insufficient weight loss was necessary in 8 patients (11.8%). CONCLUSIONS: LSG was effective 5.9 years postoperatively with an excessive BMI loss of almost 60% and a considerable improvement or even remission of co-morbidities.

Intravenous bisphosphonates for postmenopausal osteoporosis: safety profiles of zoledronic acid and ibandronate in clinical practice.

BACKGROUND: Intravenous bisphosphonates are widely used for treatment of postmenopausal osteoporosis. They are associated with transient influenza-like symptoms, predominantly after the first zoledronic acid (up to 32 %) or ibandronate (up to 5 %) administration. The experience in clinical practice suggests that the incidence of post-dose symptoms is higher than has been reported in clinical trials. We assessed the safety of annual infusions of zoledronic acid and 3-monthly injections of ibandronate in women with postmenopausal osteoporosis. METHODS: In this retrospective study we analysed safety data from 272 postmenopausal women treated with zoledronic acid (n = 127; mean age 68.6 ± 9.4 years) or intravenous (IV) ibandronate (n = 145; mean age 69.1 ± 9.0 years). Safety data (including occurrence of acute-phase reactions and osteonecrosis of the jaw) were gathered in phone call interviews by using a standardized questionnaire. RESULTS: The number of patients with adverse events was significantly higher in zoledronic acid as compared to ibandronate-treated patients, primarily because of a larger number of post-dose symptoms after bisphosphonate administrations (54.3 % vs. 33.1 %, p < 0.001). Except for occurrence of fever (more common after zoledronic acid infusion), other influenza-like symptoms (myalgia, arthralgia, headache) appeared in a similar proportion of patients after IV treatment (within 24-36 h). Symptoms lasted for >3 days in approximately 50 % of patients. The incidence of symptoms decreased after subsequent infusions. The rate of influenza-like symptoms was more frequent after zoledronic acid than after IV ibandronate in bisphosphonate-naïve patients but comparable in patients pretreated with oral bisphosphonates. There were no spontaneous reports of osteonecrosis of the jaw, arrhythmia or delayed fracture healing. CONCLUSION: Although IV bisphosphonates are generally safe, the occurrence of transient influenza-like symptoms after IV bisphosphonates seems to be more frequent in clinical practice than has been reported in clinical trials.