Utilization of Immunization Information Systems (IIS) among independently owned community pharmacies: A national survey

BACKGROUND/OBJECTIVE

Immunization information systems (IIS) consolidate provider-submitted immunization information. We reassessed independently owned community pharmacies' IIS enrollment, verification of immunizations needs via IIS records retrieval, and immunization records reporting to IISs following post-pandemic shifts in community pharmacy operations.

METHODS

A cross-sectional online survey of National Community Pharmacists Association pharmacist, pharmacy owner, and pharmacy technician members was conducted in Fall 2022.

RESULTS

202 complete responses were analyzed. Margin of error was an estimated 7 %. Respondents were: 53.2 % female, ∼87 % White, 69.8 % managers, and 86.1 % practicing in standalone community pharmacies. Almost all (91.6 %) were enrolled in IIS. About two-thirds frequently or always utilized IIS to retrieve immunization records prior to immunization. On average, 81.2 % of influenza and 83.5 % of non-COVID/non-influenza vaccination records were submitted.

CONCLUSIONS

Enrollment rates are high among studied pharmacies, as are records reporting rates. However, records retrieval rates are suboptimal. Future work should focus on addressing suboptimal retrieval rates within immunization-providing pharmacies.

Immune-inflammatory-nutritional status predicts oncologic outcomes after radical cystectomy for urothelial carcinoma of bladder

OBJECTIVE

To perform the first investigation of the role of immune-inflammatory-nutritional status (INS) on oncological outcomes in patients undergoing open radical cystectomy (ORC) for urothelial carcinoma (UC).

MATERIALS AND METHODS

The records of consecutive patients who underwent ORC for non-metastatic bladder cancer between 2009 and 2020 were retrospectively analyzed. Neoadjuvant chemotherapy, non-urothelial tumor biology, and absence of oncological follow-up were exclusion criteria. Systemic immune-inflammatory index (SII) and Prognostic Nutritional Index (PNI) values were calculated and optimal cut-off values for these were used to designate four subgroups: "high SII-high PNI", "low SII-high PNI", "low SII-low PNI", and "high SII-low PNI". The Low SII-high PNI INS group had best overall survival (OS) rate while the remainder were included in non-favorable INS group. Survival curves were constructed, and a multivariate Cox regression model was used for OS and recurrence-free survival (RFS).

RESULTS

After exclusions, the final cohort size was 173 patients. The mean age was 64.31 ± 8.35 and median follow-up was 21 (IQR: 9-58) months. Optimal cut-off values for SII and PNI were 1216 and 47, respectively. The favorable INS group (low SII-high PNI, n = 89) had the best OS rate (62.9%). Multivariate Cox regression analysis indicated that non-favorable INS (n = 84) was a worse independent prognostic factor for OS (HR: 1.509, 95%CI: 1.104-3.145, p = 0.001) and RFS (HR: 1.285; 95%CI: 1.009-1.636, p = 0.042).

CONCLUSION

Preoperative assessment of INS may be a useful prognostic panel for OS and RFS in patients who had ORC for UC.

Devo-Aging: Intersections Between Development and Aging

There are two fundamental questions in developmental biology. How does a single fertilized cell give rise to a whole body? and how does this body later produce progeny? Synchronization of these embryonic and postembryonic developments ensures continuity of life from one generation to the next. An enormous amount of work has been done to unravel the molecular mechanisms behind these processes, but more recently, modern developmental biology has been expanded to study development in wider contexts, including regeneration, environment, disease, and even aging. However, we have just started to understand how the mechanisms that govern development also regulate aging. This review discusses examples of signaling pathways involved in development to elucidate how their regulation influences healthspan and lifespan. Therefore, a better knowledge of developmental signaling pathways stresses the possibility of using them as innovative biomarkers and targets for aging and age-related diseases.

The Janus-Faced Role of Lipid Droplets in Aging: Insights from the Cellular Perspective

It is widely accepted that nine hallmarks-including mitochondrial dysfunction, epigenetic alterations, and loss of proteostasis-exist that describe the cellular aging process. Adding to this, a well-described cell organelle in the metabolic context, namely, lipid droplets, also accumulates with increasing age, which can be regarded as a further aging-associated process. Independently of their essential role as fat stores, lipid droplets are also able to control cell integrity by mitigating lipotoxic and proteotoxic insults. As we will show in this review, numerous longevity interventions (such as mTOR inhibition) also lead to strong accumulation of lipid droplets in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and mammalian cells, just to name a few examples. In mammals, due to the variety of different cell types and tissues, the role of lipid droplets during the aging process is much more complex. Using selected diseases associated with aging, such as Alzheimer's disease, Parkinson's disease, type II diabetes, and cardiovascular disease, we show that lipid droplets are "Janus"-faced. In an early phase of the disease, lipid droplets mitigate the toxicity of lipid peroxidation and protein aggregates, but in a later phase of the disease, a strong accumulation of lipid droplets can cause problems for cells and tissues.

Determinants to immunization information system implementation in independent community pharmacies in rural Alabama

BACKGROUND

Immunization information systems (IISs) facilitate consolidated vaccination data within each state. Many have limited pharmacy participation, especially Alabama. As pharmacists increasingly engage in delivery of vaccines recommended across the life span, it is critical to understand the barriers to IIS implementation, particularly in rural community pharmacies where access to primary care may be limited.

OBJECTIVE

The purpose of this study was to identify barriers and facilitators to IIS implementation in rural, independent community pharmacies in Alabama.

METHODS

Qualitative interviews with rural, independent community pharmacy personnel and IIS experts in both states with high IIS participation and Alabama (state with low IIS participation) were conducted. States with high participation were identified as those with ≥75% of adults recorded in their respective state IIS. Less than 25% of Alabama adults were recorded in the state IIS at the time of this study. Deductive coding using CFIR constructs was conducted with a second coder to ensure inter-rater reliability. CFIR Rating Rules were applied to the coded data to allow for identification of constructs that have the greatest impact on implementation.

RESULTS

A total of twenty-five participants (16 pharmacy personnel; 9 IIS experts) were interviewed. During interviews, 32 of 39 CFIR constructs were mentioned and 11 constructs with a strong influence (+2 or -2) were identified. These included, "adaptability", "complexity", "compatibility", "available resources", "access to knowledge and information", "needs and resources of those served by the organization", "peer pressure", "external policy and initiatives", "knowledge and beliefs about the innovation", "engaging key stakeholders", and "engaging innovation participants".

CONCLUSIONS

This qualitative study explored perceived barriers and facilitators to IIS implementation in the rural, independent community pharmacy setting from the perspectives of pharmacy personnel and IIS experts. Factors identified can be used to inform the development of resources and implementation strategies to improve IIS uptake and participation.

The Comparison of Antioxidant Performance, Immune Performance, IIS Activity and Gut Microbiota Composition between Queen and Worker Bees Revealed the Mechanism of Different Lifespan of Female Casts in the Honeybee

Queen bees and worker bees both develop from fertilized eggs, whereas queens live longer than workers. The mechanism of this phenomenon is worth exploring. Antioxidant capacity, immune and IIS are the conserved mechanisms of aging. The importance of gut bacteria for health prompted us to connect with bee aging. Therefore, the differences of antioxidant, immune, IIS and gut microflora between queen and worker bees were compared to find potential mechanisms of queens' longevity. The results showed queens had stronger antioxidant capacity and lower immune pathway and IIS activity than workers. The higher expression level of catalase and SOD1/2 in queens resulted in the stronger ROS scavenging ability, which leads to the lower ROS level and the reduced accumulation of oxidative damage products in queens. The lower IMD expression and higher antimicrobial peptides (AMPs) expressions in queens suggested that queens maintain lower immune pathway activity and stronger immune capacity than workers. Gut bacteria composition analysis indicated that queens had supernal Acetobacteraceae (notably Commensalibacter and Bombella), Lactobacillus and Bifidobacterium over workers. In conclusion, antioxidant, immune, IIS, and gut symbiotic bacteria all contribute to the longevity of queens. This study provides more insights into revealing the mechanisms of queens' longevity.

Assembly of Multiple Full-Size Genes or Genomic DNA Fragments on Human Artificial Chromosomes Using the Iterative Integration System

Human artificial chromosomes (HACs) are gene delivery vectors that have been used for decades for gene functional studies. HACs have several advantages over viral‐based gene transfer systems, including stable episomal maintenance in a single copy in the cell and the ability to carry up to megabase‐sized genomic DNA segments. We have previously developed the alphoid^tetO‐HAC, which has a single gene acceptor loxP site that allows insertion of an individual gene of interest using Chinese hamster ovary (CHO) hybrid cells. The HAC, along with a DNA segment of interest, can then be transferred from donor CHO cells to various recipient cells of interest via microcell‐mediated chromosome transfer (MMCT). Here, we detail a protocol for loading multiple genomic DNA segments or genes into the alphoid^tetO‐HAC vector using an iterative integration system (IIS) that utilizes recombinases Cre, ΦC31, and ΦBT. This IIS‐alphoid^tetO‐HAC can be used for either serially assembling genomic loci or fragments of a large gene, or for inserting multiple genes into the same artificial chromosome. The insertions are executed iteratively, whereby each round results in the insertion of a new DNA segment of interest. This is accompanied by changes of expression of marker fluorescent proteins, which simplifies screening of correct clones, and changes of selection and counterselection markers, which constitutes an error‐proofing mechanism that removes mis‐incorporated DNA segments. In addition, the IIS‐alphoid^tetO‐HAC carrying the genes can be eliminated from the cells, offering the possibility to compare the phenotypes of human cells with and without functional copies of the genes of interest. The resulting HAC molecules may be used to investigate biomedically relevant pathways or the regulation of multiple genes, and to potentially engineer synthetic chromosomes with a specific set of genes of interest. The IIS‐alphoid^tetO‐HAC system is expected to be beneficial in creating multiple‐gene humanized models with the purpose of understanding complex multi‐gene genetic disorders. Published 2021. This article is a U.S. Government work and is in the public domain in the USA. Current Protocols published by Wiley Periodicals LLC.

Basic Protocol 1: Integration of the first DNA segment of interest into the IIS‐alphoid^teto‐HAC

Basic Protocol 2: Integration of a second DNA segment of interest into the IIS‐alphoid^teto‐HAC

Basic Protocol 3: Integration of a third DNA segment of interest into the IIS‐alphoid^teto‐HAC

Support Protocol: Fluorescence in situ hybridization analysis for the circular IIS‐alphoid^tetO‐HAC

Insulin-Like Peptide Receptor-Mediated Signaling Pathways Orchestrate Regulation of Growth in the Pacific Oyster (Crassostrea gigas), as Revealed by Gene Expression Profiles

The involvement of insulin/insulin-like growth factor signaling (IIS) pathways in the growth regulation of marine invertebrates remains largely unexplored. In this study, we used a fast-growing Pacific oyster (Crassostrea gigas) variety “Haida No.1” as the material with which to unravel the role of IIS systems in growth regulation in oysters. Systematic bioinformatics analyses allowed us to identify major components of the IIS signaling pathway and insulin-like peptide receptor (ILPR)-mediated signaling pathways, including PI3K-AKT, RAS-MAPK, and TOR, in C. gigas. The expression levels of the major genes in IIS and its downstream signaling pathways were significantly higher in “Haida No.1” than in wild oysters, suggesting their involvement in the growth regulation of C. gigas. The expression profiles of IIS and its downstream signaling pathway genes were significantly altered by nutrient abundance and culture temperature. These results suggest that the IIS signaling pathway coupled with the ILPR-mediated signaling pathways orchestrate the regulation of energy metabolism to control growth in Pacific oysters.

Long-term follow-up of patients with infantile idiopathic scoliosis: is the rib vertebra angle difference (RVAD) a reliable indicator of evolution?

PURPOSE

Since its original description by Mehta, the rib vertebra angle difference (RVAD) and, in particular, a threshold of 20° have become an accepted and widely utilised prognostic indicator in the assessment of patients presenting with an infantile idiopathic scoliosis (IIS). However, uncertainty in the utility of the RVAD in the prognosis of IIS remains. The aims of this study were to investigate the prognostic significance of the RVAD and to describe the changes in RVAD over long-term follow-up of patients with progressive and resolving IIS.

METHODS

This was a retrospective analysis of patients presenting with IIS at a tertiary spinal deformity unit in the UK. Serial patient radiographs were reviewed and a logistic regression model using the patients index RVAD was created to predict the likelihood of curve progression.

RESULTS

At both index presentation and over long-term follow-up, patients with a progressive curve had significantly greater mean Cobb angle and RVAD measurements than those with resolving curves. The RVAD and Cobb were found to correlate positively in both groups, reflecting the underlying costovertebral pathoanatomy. The logistic regression model demonstrated that the optimal RVAD threshold in predicting IIS progression was lower at 17.1° than the 20° cut-off previously advocated.

CONCLUSION

This study describes the utility of the RVAD in predicting IIS evolution. From this analysis, we would advise caution in predicting outcomes based on the index RVAD at presentation.

LEVEL OF EVIDENCE

II.

Insulin/IGF signaling and TORC1 promote vitellogenesis via inducing juvenile hormone biosynthesis in the American cockroach

Vitellogenesis, including vitellogenin (Vg) production in the fat body and Vg uptake by maturing oocytes, is of great importance for the successful reproduction of adult females. The endocrinal and nutritional regulation of vitellogenesis differs distinctly in insects. Here, the complex crosstalk between juvenile hormone (JH) and the two nutrient sensors insulin/IGF signaling (IIS) and target of rapamycin complex1 (TORC1), was investigated to elucidate the molecular mechanisms of vitellogenesis regulation in the American cockroach, Periplaneta americana Our data showed that a block of JH biosynthesis or JH action arrested vitellogenesis, in part by inhibiting the expression of doublesex (Dsx), a key transcription factor gene involved in the sex determination cascade. Depletion of IIS or TORC1 blocked both JH biosynthesis and vitellogenesis. Importantly, the JH analog methoprene, but not bovine insulin (to restore IIS) and amino acids (to restore TORC1 activity), restored vitellogenesis in the neck-ligated (IIS-, TORC1- and JH-deficient) and rapamycin-treated (TORC1- and JH-deficient) cockroaches. Combining classic physiology with modern molecular techniques, we have demonstrated that IIS and TORC1 promote vitellogenesis, mainly via inducing JH biosynthesis in the American cockroach.

Rotating magnetic field delays human umbilical vein endothelial cell aging and prolongs the lifespan of Caenorhabditis elegans

The biological effects of magnetic fields are a research hotspot in the field of biomedical engineering. In this study, we further investigated the effects of a rotating magnetic field (RMF; 0.2 T, 4 Hz) on the growth of human umbilical vein endothelial cells (HUVECs) and Caenorhabditis elegans. The results showed that RMF exposure prolonged the lifespan of C. elegans and slowed the aging of HUVECs. RMF treatment of HUVECs showed that activation of adenosine 5'-monophosphate (AMP)-activated protein kinase (AMPK) was associated with decreased mitochondrial membrane potential (MMP) due to increased intracellular Ca2+ concentrations induced by endoplasmic reticulum stress in anti-aging mechanisms. RMF also promoted the health status of C. elegans by improving activity, reducing age-related pigment accumulation, delaying Aβ-induced paralysis and increasing resistance to heat and oxidative stress. The prolonged lifespan of C. elegans was associated with decreased levels of daf-16 which related to the insulin/insulin-like growth factor signaling pathway (IIS) activity and reactive oxygen species (ROS), whereas the heat shock transcription factor-1 (hsf-1) pathway was not involved. Moreover, the level of autophagy was increased after RMF treatment. These findings expand our understanding of the potential mechanisms by which RMF treatment prolongs lifespan.

Assessing barriers and increasing use of immunization information systems in independent community pharmacies: Study protocol for a randomized controlled trial

BACKGROUND

As the number of providers administering vaccines increases, including pharmacists, there is a concern of fragmented immunization records in state and regional immunization information systems (IIS). In order for IIS to have complete records, it is critical that each provider administering vaccines, including pharmacists, participate and update the IIS each time a vaccine is administered to a patient. In Alabama, provider participation in the state IIS is not mandatory; as a result, less than 25% of adults over the age of 19 have immunization data recorded. IIS participation among independent pharmacies is of particular concern as approximately 40% of Alabama pharmacies are independently owned, but only 27% of these are enrolled in the IIS.

OBJECTIVE

The objective of this report is to describe a study protocol to assess the impact of an IIS training program among community pharmacies' IIS enrollment and actual participation rates.

METHODS

The research design is a randomized controlled trial. Study participants are Alabama pharmacists who work in independently owned pharmacies that currently provide at least one type of non-seasonal vaccine and are not currently enrolled in the Alabama IIS. Multiple outcomes including awareness, knowledge, attitudes, intention, IIS enrollment, and IIS participation will be compared between intervention and control groups across three time points (baseline, one-month, and three-months). Individual and organizational factors will be measured to identify any possible associations with outcomes.

IMPLICATIONS

The expected outcome is to create an effective training program that is scalable and ready for dissemination. If successful, this training program can be replicated and used to significantly impact the completeness and accuracy of IIS across the U.S., providing the potential for IIS to be used consistently in assessing immunization status and recommending additional vaccines in the pharmacy setting, thereby improving vaccination coverage and making the provision of immunizations safe and efficient.

A Model for Sustaining and Investing in Immunization Information Systems: Authors

In the past three years, Scientific Technologies Corporation electronically sent one-hundred fifty million retail pharmacy patient immunization events to state and community public health immunization information systems. Today, as a conservative estimate, over 85% of the U.S. population has an immunization record in an electronic health information system. Health technology, data exchange and increasing online patient health records offer consumers, providers and the immunization community new platforms to proactively identify vaccine coverage gaps. As the value of online immunization information increases, the cost to sustain and leverage these new technologies escalates. Online immunization records and integrated decision support tools are being used extensively from the pharmacy to the emergency room. They are moving from health data vaults with few users to more ubiquitous point of care services and direct consumer engagement. The data and the supporting technology infrastructure empower the community within the immunization ecosystem. To use this opportunity to reduce the impact of vaccine preventable disease on populations, investment in sustaining and modernizing existing immunization health technology systems suggest models to articulate their value and return on investment. This paper illustrates cost and technology drivers that impact sustainability and modernization of the immunization information system infrastructure. It provides a model to support investment priority decisions and estimate costs. It reviews the technical evolution of public health immunization registries and their current legacy state providing a pathway to migrate to opportunistic third generation technology platforms. It will answer: How much should be budgeted? What can this budget achieve over the next five years? What investments should be prioritized? Is there opportunity for public-private partnerships to support sustainment cost sharing? It shows that an investment of fifty million will modernize a quarter of the current second generation immunization systems and support the remainder over the next five years.

Autophagy promotes visceral aging in wild-type C. elegans

A plethora of studies over several decades has demonstrated the importance of autophagy in aging and age-related neurodegenerative disease. The role of autophagy in damage clearance and cell survival is well established, and supports a prevailing view that increasing autophagic activity can be broadly beneficial, and could form the basis of anti-aging interventions. However, macroautophagy/autophagy also promotes some elements of senescence. For example, in C. elegans hermaphrodites it facilitates conversion of intestinal biomass into yolk, leading to sex-specific gut atrophy and senescent steatosis.

Opposing Post-transcriptional Control of InR by FMRP and LIN-28 Adjusts Stem Cell-Based Tissue Growth

Although the intrinsic mechanisms that control whether stem cells divide symmetrically or asymmetrically underlie tissue growth and homeostasis, they remain poorly defined. We report that the RNA-binding protein fragile X mental retardation protein (FMRP) limits the symmetric division, and resulting expansion, of the stem cell population during adaptive intestinal growth in Drosophila. The elevated insulin sensitivity that FMRP-deficient progenitor cells display contributes to their accelerated expansion, which is suppressed by the depletion of insulin-signaling components. This FMRP activity is mediated solely via a second conserved RNA-binding protein, LIN-28, known to boost insulin signaling in stem cells. Via LIN-28, FMRP controls progenitor cell behavior by post-transcriptionally repressing the level of insulin receptor (InR). This study identifies the stem cell-based mechanism by which FMRP controls tissue adaptation, and it raises the possibility that defective adaptive growth underlies the accelerated growth, gastrointestinal, and other symptoms that affect fragile X syndrome patients.

Obesity and Aging in the Drosophila Model

Being overweight increases the risk of many metabolic disorders, but how it affects lifespan is not completely clear. Not all obese people become ill, and the exact mechanism that turns excessive fat storage into a health-threatening state remains unknown. Drosophila melanogaster has served as an excellent model for many diseases, including obesity, diabetes, and hyperglycemia-associated disorders, such as cardiomyopathy or nephropathy. Here, we review the connections between fat storage and aging in different types of fly obesity. Whereas obesity induced by high-fat or high-sugar diet is associated with hyperglycemia, cardiomyopathy, and in some cases, shortening of lifespan, there are also examples in which obesity correlates with longevity. Transgenic lines with downregulations of the insulin/insulin-like growth factor (IIS) and target of rapamycin (TOR) signaling pathways, flies reared under dietary restriction, and even certain longevity selection lines are obese, yet long-lived. The mechanisms that underlie the differential lifespans in distinct types of obesity remain to be elucidated, but fat turnover, inflammatory pathways, and dysregulations of glucose metabolism may play key roles. Altogether, Drosophila is an excellent model to study the physiology of adiposity in both health and disease.

Frequency and Cost of Vaccinations Administered Outside Minimum and Maximum Recommended Ages-2014 Data From 6 Sentinel Sites of Immunization Information Systems

OBJECTIVE

To quantify vaccinations administered outside minimum and maximum recommended ages and to determine attendant costs of revaccination by analyzing immunization information system (IIS) records.

STUDY DESIGN

We analyzed deidentified records of doses administered during 2014 to persons aged <18 years within 6 IIS sentinel sites (10% of the US population). We quantified doses administered outside of recommended ages according to the Advisory Committee on Immunization Practices childhood immunization schedule and prescribing information in package inserts, and calculated revaccination costs. To minimize misreporting bias, we analyzed publicly funded doses for which reported lot numbers and vaccine types were consistent.

RESULTS

Among 3 394 047 doses with maximum age recommendations, 9755 (0.3%) were given after the maximum age. One type of maximum age violation required revaccination: 1344 (0.7%) of 194 934 doses of the 0.25-mL prefilled syringe formulation of quadrivalent inactivated influenza vaccine (Fluzone Quadrivalent, Sanofi Pasteur, Swiftwater, PA) were administered at age ≥36 months (revaccination cost, $111 964). We identified a total of 7 529 165 childhood, adolescent, and lifespan doses with minimum age recommendations, 9542 of which (0.1%) were administered before the minimum age. The most common among these violations were quadrivalent injectable influenza vaccines (3835, or 0.7% of 526 110 doses administered before age 36 months) and Kinrix (GlaxoSmithKline Biologicals, Rixensart, Belgium; DTaP-IPV) (2509, or 1.2% of 208 218 doses administered before age 48 months). The cost of revaccination for minimum age violations (where recommended) was $179 179.

CONCLUSION

Administration of vaccines outside recommended minimum and maximum ages is rare, reflecting a general adherence to recommendations. Error rates were higher for several vaccines, some requiring revaccination. Vaccine schedule complexity and confusion among similar products might contribute to errors. Minimization of errors reduces wastage, excess cost, and inconvenience for parents and patients.

Method to Assemble Genomic DNA Fragments or Genes on Human Artificial Chromosome with Regulated Kinetochore Using a Multi-Integrase System

The production of cells capable of carrying multiple transgenes to Mb-size genomic loci has multiple applications in biomedicine and biotechnology. In order to achieve this goal, three key steps are required: (i) cloning of large genomic segments; (ii) insertion of multiple DNA blocks at a precise location and (iii) the capability to eliminate the assembled region from cells. In this study, we designed the iterative integration system (IIS) that utilizes recombinases Cre, ΦC31 and ΦBT1, and combined it with a human artificial chromosome (HAC) possessing a regulated kinetochore (alphoid^tetO-HAC). We have demonstrated that the IIS-alphoid^tetO-HAC system is a valuable genetic tool by reassembling a functional gene from multiple segments on the HAC. IIS-alphoid^tetO-HAC has several notable advantages over other artificial chromosome-based systems. This includes the potential to assemble an unlimited number of genomic DNA segments; a DNA assembly process that leaves only a small insertion (<60 bp) scar between adjacent DNA, allowing genes reassembled from segments to be spliced correctly; a marker exchange system that also changes cell color, and counter-selection markers at each DNA insertion step, simplifying selection of correct clones; and presence of an error proofing mechanism to remove cells with misincorporated DNA segments, which improves the integrity of assembly. In addition, the IIS-alphoid^tetO-HAC carrying a locus of interest is removable, offering the unique possibility to revert the cell line to its pretransformed state and compare the phenotypes of human cells with and without a functional copy of a gene(s). Thus, IIS-alphoid^tetO-HAC allows investigation of complex biomedical pathways, gene(s) regulation, and has the potential to engineer synthetic chromosomes with a predetermined set of genes.

Detecting Pedigree Relationship Errors

Pedigree relationship errors often occur in family data collected for genetic studies, and unidentified errors can lead to either increased false positives or decreased power in both linkage and association analyses. Here, we review several allele sharing as well as likelihood-based statistics that were proposed to efficiently extract genealogical information from available genome-wide marker data, and the software package PREST that implements these methods. We provide the detailed analytical steps involved using two application examples, and we discuss various practical issues, including result interpretation.

CellNetVis: a web tool for visualization of biological networks using force-directed layout constrained by cellular components

BACKGROUND

The advent of "omics" science has brought new perspectives in contemporary biology through the high-throughput analyses of molecular interactions, providing new clues in protein/gene function and in the organization of biological pathways. Biomolecular interaction networks, or graphs, are simple abstract representations where the components of a cell (e.g. proteins, metabolites etc.) are represented by nodes and their interactions are represented by edges. An appropriate visualization of data is crucial for understanding such networks, since pathways are related to functions that occur in specific regions of the cell. The force-directed layout is an important and widely used technique to draw networks according to their topologies. Placing the networks into cellular compartments helps to quickly identify where network elements are located and, more specifically, concentrated. Currently, only a few tools provide the capability of visually organizing networks by cellular compartments. Most of them cannot handle large and dense networks. Even for small networks with hundreds of nodes the available tools are not able to reposition the network while the user is interacting, limiting the visual exploration capability.

RESULTS

Here we propose CellNetVis, a web tool to easily display biological networks in a cell diagram employing a constrained force-directed layout algorithm. The tool is freely available and open-source. It was originally designed for networks generated by the Integrated Interactome System and can be used with networks from others databases, like InnateDB.

CONCLUSIONS

CellNetVis has demonstrated to be applicable for dynamic investigation of complex networks over a consistent representation of a cell on the Web, with capabilities not matched elsewhere.

Emerging Molecular Pathways Governing Dietary Regulation of Neural Stem Cells during Aging

Aging alters cellular and molecular processes, including those of stem cells biology. In particular, changes in neural stem cells (NSCs) are linked to cognitive decline associated with aging. Recently, the systemic environment has been shown to alter both NSCs regulation and age-related cognitive decline. Interestingly, a well-documented and naturally occurring way of altering the composition of the systemic environment is through diet and nutrition. Furthermore, it is well established that the presence of specific nutrients as well as the overall increase or reduction of calorie intake can modulate conserved molecular pathways and respectively reduce or increase lifespan. In this review, we examine these pathways in relation to their function on NSCs and cognitive aging. We highlight the importance of the Sirtuin, mTOR and Insulin/Insulin like growth factor-1 pathways as well as the significant role played by epigenetics in the dietary regulation of NSCs and the need for further research to exploit nutrition as a mode of intervention to regulate NSCs aging.

Identifying Cryptic Relationships

Cryptic relationships such as first-degree relatives often appear in studies that collect population samples, including genome-wide association studies (GWAS) and next-generation sequencing (NGS) analyses. Cryptic relatedness not only increases type 1 error rate of association tests but also affects other analytical aspects of GWAS and NGS such as population stratification via principal component analysis. Here, we discuss three effective methods, as implemented in PREST, PLINK, and KING, to detect and correct for the problem of cryptic relatedness using high-throughput SNP data collected from GWAS and NGS experiments. We provide the analytical and practical details involved using three application examples.

Nuclear hormone receptor DHR96 mediates the resistance to xenobiotics but not the increased lifespan of insulin-mutant Drosophila

Lifespan of laboratory animals can be increased by genetic, pharmacological, and dietary interventions. Increased expression of genes involved in xenobiotic metabolism, together with resistance to xenobiotics, are frequent correlates of lifespan extension in the nematode worm Caenorhabditis elegans, the fruit fly Drosophila, and mice. The Green Theory of Aging suggests that this association is causal, with the ability of cells to rid themselves of lipophilic toxins limiting normal lifespan. To test this idea, we experimentally increased resistance of Drosophila to the xenobiotic dichlordiphenyltrichlorethan (DDT), by artificial selection or by transgenic expression of a gene encoding a cytochrome P450. Although both interventions increased DDT resistance, neither increased lifespan. Furthermore, dietary restriction increased lifespan without increasing xenobiotic resistance, confirming that the two traits can be uncoupled. Reduced activity of the insulin/Igf signaling (IIS) pathway increases resistance to xenobiotics and extends lifespan in Drosophila, and can also increase longevity in C. elegans, mice, and possibly humans. We identified a nuclear hormone receptor, DHR96, as an essential mediator of the increased xenobiotic resistance of IIS mutant flies. However, the IIS mutants remained long-lived in the absence of DHR96 and the xenobiotic resistance that it conferred. Thus, in Drosophila IIS mutants, increased xenobiotic resistance and enhanced longevity are not causally connected. The frequent co-occurrence of the two traits may instead have evolved because, in nature, lowered IIS can signal the presence of pathogens. It will be important to determine whether enhanced xenobiotic metabolism is also a correlated, rather than a causal, trait in long-lived mice.

Focal epileptiform activity in the prefrontal cortex is associated with long-term attention and sociability deficits

There is a well-described association between childhood epilepsy and pervasive cognitive and behavioral deficits. Often these children not only have ictal EEG events, but also frequent interictal abnormalities. The precise role of these interictal discharges in cognition remains unclear. In order to understand the relationship between frequent epileptiform discharges during neurodevelopment and cognition later in life, we developed a model of frequent focal interictal spikes (IIS). Postnatal day (p) 21 rats received injections of bicuculline methiodine into the prefrontal cortex (PFC). Injections were repeated in order to achieve 5 consecutive days of transient inhibitory/excitatory imbalance resulting in IIS. Short-term plasticity (STP) and behavioral outcomes were studied in adulthood. IIS is associated with a significant increase in STP bilaterally in the PFC. IIS rats did not show working memory deficits, but rather showed marked inattentiveness without significant alterations in motivation, anxiety or hyperactivity. Rats also demonstrated significant deficits in social behavior. We conclude that GABAergic blockade during early-life and resultant focal IIS in the PFC disrupt neural networks and are associated with long-term consequences for behavior at a time when IIS are no longer present, and thus may have important implications for ADHD and autism spectrum disorder associated with childhood epilepsy.

Local requirement of the Drosophila insulin binding protein imp-L2 in coordinating developmental progression with nutritional conditions

In Drosophila, growth takes place during the larval stages until the formation of the pupa. Starvation delays pupariation to allow prolonged feeding, ensuring that the animal reaches an appropriate size to form a fertile adult. Pupariation is induced by a peak of the steroid hormone ecdysone produced by the prothoracic gland (PG) after larvae have reached a certain body mass. Local downregulation of the insulin/insulin-like growth factor signaling (IIS) activity in the PG interferes with ecdysone production, indicating that IIS activity in the PG couples the nutritional state to development. However, the underlying mechanism is not well understood. In this study we show that the secreted Imaginal morphogenesis protein-Late 2 (Imp-L2), a growth inhibitor in Drosophila, is involved in this process. Imp-L2 inhibits the activity of the Drosophila insulin-like peptides by direct binding and is expressed by specific cells in the brain, the ring gland, the gut and the fat body. We demonstrate that Imp-L2 is required to regulate and adapt developmental timing to nutritional conditions by regulating IIS activity in the PG. Increasing Imp-L2 expression at its endogenous sites using an Imp-L2-Gal4 driver delays pupariation, while Imp-L2 mutants exhibit a slight acceleration of development. These effects are strongly enhanced by starvation and are accompanied by massive alterations of ecdysone production resulting most likely from increased Imp-L2 production by neurons directly contacting the PG and not from elevated Imp-L2 levels in the hemolymph. Taken together our results suggest that Imp-L2-expressing neurons sense the nutritional state of Drosophila larvae and coordinate dietary information and ecdysone production to adjust developmental timing under starvation conditions.

Regulation of longevity and oxidative stress by nutritional interventions: role of methionine restriction

Comparative studies indicate that long-lived mammals have low rates of mitochondrial reactive oxygen species production (mtROSp) and oxidative damage in their mitochondrial DNA (mtDNA). Dietary restriction (DR), around 40%, extends the mean and maximum life span of a wide range of species and lowers mtROSp and oxidative damage to mtDNA, which supports the mitochondrial free radical theory of aging (MFRTA). Regarding the dietary factor responsible for the life extension effect of DR, neither carbohydrate nor lipid restriction seems to modify maximum longevity. However protein restriction (PR) and methionine restriction (at least 80% MetR) increase maximum lifespan in rats and mice. Interestingly, only 7weeks of 40% PR (at least in liver) or 40% MetR (in all the studied organs, heart, brain, liver or kidney) is enough to decrease mtROSp and oxidative damage to mtDNA in rats, whereas neither carbohydrate nor lipid restriction changes these parameters. In addition, old rats also conserve the capacity to respond to 7weeks of 40% MetR with these beneficial changes. Most importantly, 40% MetR, differing from what happens during both 40% DR and 80% MetR, does not decrease growth rate and body size of rats. All the available studies suggest that the decrease in methionine ingestion that occurs during DR is responsible for part of the aging-delaying effect of this intervention likely through the decrease of mtROSp and ensuing DNA damage that it exerts. We conclude that lowering mtROS generation is a conserved mechanism, shared by long-lived species and dietary, protein, and methionine restricted animals, that decreases damage to macromolecules situated near the complex I mtROS generator, especially mtDNA. This would decrease the accumulation rate of somatic mutations in mtDNA and maybe finally also in nuclear DNA.

MicroRNAs and the genetic network in aging

MicroRNAs (miRNAs) comprise a class of small RNAs important for the posttranscriptional regulation of numerous biological processes. Their combinatorial mode of function, in which an individual miRNA can target many genes and multiple miRNAs share targets, makes them especially suited for regulating processes and pathways at the "network" level. In particular, miRNAs have recently been implicated in aging, which is a complex process known to involve multiple pathways. Findings from genome-wide miRNA expression profiling studies highlight three themes in miRNA function during aging: many miRNAs are differentially expressed, many such miRNAs target known aging-associated pathways, and there are global trends in miRNA expression change over time. In addition, several miRNAs have emerged as potentially coordinating multiple pathways during aging. Elucidating the underlying network structure of genes and miRNAs involved in aging processes promises to advance our understanding of not only aging and associated pathogenesis but also how miRNAs can connect disparate pathways.

Protein damage, repair and proteolysis

Proteins are continuously affected by various intrinsic and extrinsic factors. Damaged proteins influence several intracellular pathways and result in different disorders and diseases. Aggregation of damaged proteins depends on the balance between their generation and their reversal or elimination by protein repair systems and degradation, respectively. With regard to protein repair, only few repair mechanisms have been evidenced including the reduction of methionine sulfoxide residues by the methionine sulfoxide reductases, the conversion of isoaspartyl residues to L-aspartate by L-isoaspartate methyl transferase and deglycation by phosphorylation of protein-bound fructosamine by fructosamine-3-kinase. Protein degradation is orchestrated by two major proteolytic systems, namely the lysosome and the proteasome. Alteration of the function for both systems has been involved in all aspects of cellular metabolic networks linked to either normal or pathological processes. Given the importance of protein repair and degradation, great effort has recently been made regarding the modulation of these systems in various physiological conditions such as aging, as well as in diseases. Genetic modulation has produced promising results in the area of protein repair enzymes but there are not yet any identified potent inhibitors, and, to our knowledge, only one activating compound has been reported so far. In contrast, different drugs as well as natural compounds that interfere with proteolysis have been identified and/or developed resulting in homeostatic maintenance and/or the delay of disease progression.