Parkinson's Disease: Advances in Treatment and the Syntheses of Various Classes of Pharmaceutical Drug Substances.

An overview of Parkinson's disease (PD) prevalence, diagnosis, and currently available treatment options is provided. A comprehensive list of different classes of marketed pharmaceutical drug products and the syntheses of various drug substances are summarized based on published literature.

Human neutrophil IL1ß directs intestinal epithelial cell extrusion during Salmonella infection.

Infection of the human gut by Salmonella enterica Typhimurium (STM) results in a localized inflammatory disease that is not mimicked in murine infections. To determine mechanisms by which neutrophils, as early responders to bacterial challenge, direct inflammatory programming of human intestinal epithelium, we established a multi-component human intestinal organoid (HIO) model of STM infection. HIOs were micro-injected with STM and seeded with primary human polymorphonuclear leukocytes (PMN-HIOs). PMNs did not significantly alter luminal colonization of Salmonella, but their presence reduced intraepithelial bacterial burden. Adding PMNs to infected HIOs resulted in substantial accumulation of shed TUNEL+ epithelial cells that was driven by PMN Caspase-1 activity. Inhibition of Caspases-1, -3 or -4 abrogated epithelial cell death and extrusion in the infected PMN-HIOs but only Caspase-1 inhibition significantly increased bacterial burden in the PMN-HIO epithelium. Thus, PMNs promote cell death in human intestinal epithelial cells through multiple caspases as a protective response to infection. IL-1ß was necessary and sufficient to induce cell shedding in the infected HIOs. These data support a critical innate immune function for human neutrophils in amplifying cell death and extrusion of human epithelial cells from the Salmonella-infected intestinal monolayer.

Human milk oligosaccharides reduce necrotizing enterocolitis-induced neuroinflammation and cognitive impairment in mice.

Necrotizing enterocolitis (NEC) is the leading cause of morbidity and mortality in premature infants. One of the most devastating complications of NEC is the development of NEC-induced brain injury, which manifests as impaired cognition that persists beyond infancy and which represents a proinflammatory activation of the gut-brain axis. Given that oral administration of the human milk oligosaccharides (HMOs) 2'-fucosyllactose (2'-FL) and 6'-sialyslactose (6'-SL) significantly reduced intestinal inflammation in mice, we hypothesized that oral administration of these HMOs would reduce NEC-induced brain injury and sought to determine the mechanisms involved. We now show that the administration of either 2'-FL or 6'-SL significantly attenuated NEC-induced brain injury, reversed myelin loss in the corpus callosum and midbrain of newborn mice, and prevented the impaired cognition observed in mice with NEC-induced brain injury. In seeking to define the mechanisms involved, 2'-FL or 6'-SL administration resulted in a restoration of the blood-brain barrier in newborn mice and also had a direct anti-inflammatory effect on the brain as revealed through the study of brain organoids. Metabolites of 2'-FL were detected in the infant mouse brain by nuclear magnetic resonance (NMR), whereas intact 2'-FL was not. Strikingly, the beneficial effects of 2'-FL or 6'-SL against NEC-induced brain injury required the release of the neurotrophic factor brain-derived neurotrophic factor (BDNF), as mice lacking BDNF were not protected by these HMOs from the development of NEC-induced brain injury. Taken in aggregate, these findings reveal that the HMOs 2'-FL and 6'-SL interrupt the gut-brain inflammatory axis and reduce the risk of NEC-induced brain injury.NEW & NOTEWORTHY This study reveals that the administration of human milk oligosaccharides, which are present in human breast milk, can interfere with the proinflammatory gut-brain axis and prevent neuroinflammation in the setting of necrotizing enterocolitis, a major intestinal disorder seen in premature infants.

Comparative transcriptional profiling of the early host response to infection by typhoidal and non-typhoidal Salmonella serovars in human intestinal organoids.

Salmonella enterica represents over 2500 serovars associated with a wide-ranging spectrum of disease; from self-limiting gastroenteritis to invasive infections caused by non-typhoidal serovars (NTS) and typhoidal serovars, respectively. Host factors strongly influence infection outcome as malnourished or immunocompromised individuals can develop invasive infections from NTS, however, comparative analyses of serovar-specific host responses have been constrained by reliance on limited model systems. Here we used human intestinal organoids (HIOs), a three-dimensional "gut-like" in vitro system derived from human embryonic stem cells, to elucidate similarities and differences in host responses to NTS and typhoidal serovars. HIOs discriminated between the two most prevalent NTS, Salmonella enterica serovar Typhimurium (STM) and Salmonella enterica serovar Enteritidis (SE), and typhoidal serovar Salmonella enterica serovar Typhi (ST) in epithelial cell invasion, replication and transcriptional responses. Pro-inflammatory signaling and cytokine output was reduced in ST-infected HIOs compared to NTS infections, consistent with early stages of NTS and typhoidal diseases. While we predicted that ST would induce a distinct transcriptional profile from the NTS strains, more nuanced expression profiles emerged. Notably, pathways involved in cell cycle, metabolism and mitochondrial functions were downregulated in STM-infected HIOs and upregulated in SE-infected HIOs. These results correlated with suppression of cellular proliferation and induction of host cell death in STM-infected HIOs and in contrast, elevated levels of reactive oxygen species production in SE-infected HIOs. Collectively, these results suggest that the HIO model is well suited to reveal host transcriptional programming specific to infection by individual Salmonella serovars, and that individual NTS may provoke unique host epithelial responses during intestinal stages of infection.

Extraction and Characterization of Bioactive Compounds from Diverse Marine Microalgae and Their Potential Antioxidant Activities.

This study compared free and bound phenolic compounds in various marine microalgae species. It assessed total phenolic content (TPC), total flavonoid content (TFC) and total condensed tannin content (TCT) and their antioxidant capacities using 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay, 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS⋅+ ) radical cation-based assay and ferric ion reducing antioxidant power assay. Liquid chromatography-mass spectrometry (LC-MS) was also employed to characterize the phenolic profiling. Results showed that free phenolic compounds ranged from 1.83-6.45 mg GAE/g d. w., while bound phenolic compounds ranged from 4.03-26.03 mg GAE/g d. w., indicating significant differences. These variations were consistent across assays, highlining unique profiles in different species. A total 10 phenolics were found in these seven microalgae, including 1 phenolic acid, 6 flavonoids, 1 other polyphenol and 2 lignans. 4'-O-methyl-(-)-epigallocatechin 7-O-glucuronide and chrysoeriol 7-O-glucoside in microalgae were firstly reported in microalgal samples. These findings have implications for future applications in industries.

Scalable Asymmetric Syntheses of Foslevodopa and Foscarbidopa Drug Substances for the Treatment of Parkinson's Disease.

Foslevodopa (FLD, levodopa 4'-monophosphate, 3) and foscarbidopa (FCD, carbidopa 4'-monophosphate, 4) were identified as water-soluble prodrugs of levodopa (LD, 1) and carbidopa (CD, 2), respectively, which are useful for the treatment of Parkinson's disease. Herein, we describe asymmetric syntheses of FLD (3) and FCD (4) drug substances and their manufacture at pilot scale. The synthesis of FLD (3) employs a Horner-Wadsworth-Emmons olefination reaction followed by enantioselective hydrogenation of the double bond as key steps to introduce the α-amino acid moiety with the desired stereochemistry. The synthesis of FCD (4) features a Mizoroki-Heck reaction followed by enantioselective hydrazination to install the quaternary chiral center bearing a hydrazine moiety.

Experiences of adolescent pregnancy among Maasai in Kenya: Implications for prevention.

Adolescent fertility rates are high in Kenya and increase the likelihood of maternal and infant morbidity and mortality. The objectives were to (1) explore the prevalence of unintended pregnancy among Maasai adolescent mothers, (2) understand the context in which pregnancy is occurring, and (3) suggest community-based strategies to prevent adolescent pregnancy. In in-depth, individual, qualitative interviews with Maasai females that gave birth during adolescence, pregnancy was unintended in 100% of cases. Our results suggest a desire among this population to prevent pregnancy and the need for contraception. Our recommendations include comprehensive sex education that targets very young adolescents, implementation of mechanisms to strive toward universal primary education, and the provision of resources and skills to adolescents that they need to practice safer sex.

Identification, isolation and characterization of human LGR5-positive colon adenoma cells.

The intestine is maintained by stem cells located at the base of crypts and distinguished by the expression of LGR5. Genetically engineered mouse models have provided a wealth of information about intestinal stem cells, whereas less is known about human intestinal stem cells owing to difficulty detecting and isolating these cells. We established an organoid repository from patient-derived adenomas, adenocarcinomas and normal colon, which we analyzed for variants in 71 colorectal cancer (CRC)-associated genes. Normal and neoplastic colon tissue organoids were analyzed by immunohistochemistry and fluorescent-activated cell sorting for LGR5. LGR5-positive cells were isolated from four adenoma organoid lines and were subjected to RNA sequencing. We found that LGR5 expression in the epithelium and stroma was associated with tumor stage, and by integrating functional experiments with LGR5-sorted cell RNA sequencing data from adenoma and normal organoids, we found correlations between LGR5 and CRC-specific genes, including dickkopf WNT signaling pathway inhibitor 4 (DKK4) and SPARC-related modular calcium binding 2 (SMOC2). Collectively, this work provides resources, methods and new markers to isolate and study stem cells in human tissue homeostasis and carcinogenesis.

Astrovirus replication in human intestinal enteroids reveals multi-cellular tropism and an intricate host innate immune landscape.

Human astroviruses (HAstV) are understudied positive-strand RNA viruses that cause gastroenteritis mostly in children and the elderly. Three clades of astroviruses, classic, MLB-type and VA-type have been reported in humans. One limitation towards a better understanding of these viruses has been the lack of a physiologically relevant cell culture model that supports growth of all clades of HAstV. Herein, we demonstrate infection of HAstV strains belonging to all three clades in epithelium-only human intestinal enteroids (HIE) isolated from biopsy-derived intestinal crypts. A detailed investigation of infection of VA1, a member of the non-canonical HAstV-VA/HMO clade, showed robust replication in HIE derived from different patients and from different intestinal regions independent of the cellular differentiation status. Flow cytometry and immunofluorescence analysis revealed that VA1 infects several cell types, including intestinal progenitor cells and mature enterocytes, in HIE cultures. RNA profiling of VA1-infected HIE uncovered that the host response to infection is dominated by interferon (IFN)-mediated innate immune responses. A comparison of the antiviral host response in non-transformed HIE and transformed human colon carcinoma Caco-2 cells highlighted significant differences between these cells, including an increased magnitude of the response in HIE. Additional studies confirmed the sensitivity of VA1 to exogenous IFNs, and indicated that the endogenous IFN response of HIE to curtail the growth of strains from all three clades. Genotypic variation in the permissiveness of different HIE lines to HAstV could be overcome by pharmacologic inhibition of JAK/STAT signaling. Collectively, our data identify HIE as a universal infection model for HAstV and an improved model of the intestinal epithelium to investigate enteric virus-host interactions.

Hair cortisol concentrations among urban and rural-dwelling mother-child dyads, La Romana, Dominican Republic.

Hair cortisol concentrations (HCC) were studied in mother-child dyads of La Romana, Dominican Republic (DR), a low-income city, and of the surrounding bateyes, sugarcane plantation villages with inhabitants frequently of Haitian descent. Populations of low socioeconomic status (SES) experience hypothalamic-pituitary-adrenal (HPA) axis dysregulation. Urban communities may be increasingly exposed to stressors such as crime and concentrated poverty whereas rural communities may be devoid of important community resources. As a result, the experience of stress in poverty may differ by place of residence. The goal of this study was to examine differences in HCC among urban and rural-dwelling mother-child dyads in socioeconomically disadvantaged communities surrounding La Romana, DR. Forty-five mother/child dyads were enrolled in La Romana and 45 at several bateyes surrounding La Romana. Mothers were ≥18 years and children were between 7 and 14 years. Mothers self-reported perceived stress and demographic factors. Hair samples were collected from mothers and children, and HCC was assessed using enzyme-linked immunosorbent assays. General linear models examined associations between socioeconomic factors and HCC, and between maternal and child HCC. HCC were measured in 88 maternal and 87 child samples (N = 175). Mothers living in a batey had higher HCC than those living in La Romana (p = 0.001). HCC was positively associated among maternal-child dyads (p = 0.001). Further, Haitian-born mothers as a population who frequently live in a rural batey experienced higher HCC (p = 0.025) that may partially be explained by discriminatory practices in the DR. This research helps to elucidate the impact of urban and rural environmental settings on HCC.Lay summaryThis study focuses on chronic stress, measured by hair cortisol levels, among a low-income population of Dominican and Haitian mother-child pairs who live in urban and rural settings. We found that Haitian-born mothers, who frequently live in a rural batey, had higher hair cortisol levels than Dominican born mothers. Hair cortisol levels between mothers and their children were positively associated. This study addresses the impact of urban and rural environments on the stress response among socioeconomically disadvantaged persons living in an upper middle income country who bear an excessive burden of psychosocial stress.

Morphogenesis and maturation of the embryonic and postnatal intestine.

The intestine is a vital organ responsible for nutrient absorption, bile and waste excretion, and a major site of host immunity. In order to keep up with daily demands, the intestine has evolved a mechanism to expand the absorptive surface area by undergoing a morphogenetic process to generate finger-like units called villi. These villi house specialized cell types critical for both absorbing nutrients from food, and for protecting the host from commensal and pathogenic microbes present in the adult gut. In this review, we will discuss mechanisms that coordinate intestinal development, growth, and maturation of the small intestine, starting from the formation of the early gut tube, through villus morphogenesis and into early postnatal life when the intestine must adapt to the acquisition of nutrients through food intake, and to interactions with microbes.

Beginning reading interventions for children and adolescents with intellectual disability.

BACKGROUND: Historically, students with intellectual disability were not expected to learn to read, and thus were excluded from reading instruction. Over the past decades, societal expectations for this group of learners have changed in that children and adolescents with intellectual disability are now expected to be provided with, and benefit from, literacy instruction. This shift in societal expectations has also led to an increase in research examining effective interventions for increasing beginning reading skills for students with intellectual disability. OBJECTIVES: To assess the effectiveness of interventions for teaching beginning reading skills to children and adolescents with intellectual disability. SEARCH METHODS: We searched the following electronic databases up to October 2019: CENTRAL; MEDLINE, including Epub Ahead of Print and In-Process and Other Non-Indexed Citations, Embase, 13 other databases, and two trials registers. We contacted authors of included studies, examined reference lists, and used Google Scholar to search for additional studies. SELECTION CRITERIA: We included randomized controlled trials (including trials that use quasi-random methods of allocation such as date of birth), involving children and adolescents with intellectual disability (defined as an intelligence quotient (IQ) two standard deviations or more below the population mean) between the ages of 4 and 21 years, that evaluated the efficacy of a beginning reading intervention compared to a control intervention, including no treatment control, wait-list control, treatment as usual, attention control, or alternate non-reading instruction control. DATA COLLECTION AND ANALYSIS: Two review authors independently screened titles and abstracts yielded by the search against the inclusion criteria, and extracted data from each trial using a piloted data extraction form to collect information about the population, intervention, randomization methods, blinding, sample size, outcome measures, follow-up duration, attrition and handling of missing data, and methods of analysis. When data were missing, one review author contacted the study authors to request additional information. Two review authors assessed the risk of bias of each included study and rated the quality of the evidence using the GRADE approach (a systematic method for rating the certainty of evidence in meta-analyses). We conducted random-effect meta-analyses, with inverse-variance weighting to combine effect sizes for each of our primary and secondary outcomes. We presented effect sizes as standardized mean differences (SMD) with 95% confidence intervals (CI). MAIN RESULTS: We identified seven studies involving 352 children and adolescents with intellectual disabilities that met the inclusion criteria. All studies provided the intervention in school settings. Four studies were conducted in the USA, one in Canada, and two in the UK. Three studies were funded by grants from the US Department of Education, Institute of Education Sciences; one study by the Canadian Language and Literacy Research Network and the Nova Scotia Health Research Foundation; and three studies did not indicate a funding source. We identified some concerns with risk of bias, mainly due to the difficulty of blinding of participants and personnel, and the lack of blinding of outcome assessors. Meta-analyses of the data demonstrated small-to-moderate effects of beginning reading interventions delivered to children and adolescents with intellectual disability across four dependent variables. We found medium effect sizes in favor of the beginning reading interventions for the primary outcomes of phonologic awareness (SMD 0.55, 95% CI 0.23 to 0.86; 4 studies, 178 participants; moderate-quality evidence), word reading (SMD 0.54, 95% CI 0.05 to 1.03; 5 studies, 220 participants; moderate-quality evidence), and decoding (SMD 0.40, 95% CI 0.12 to 0.67; 5 studies, 230 participants; low-quality evidence). The studies reported no adverse events. We also found a moderate effect for the secondary outcomes of oral reading fluency (SMD 0.65, 95% CI -0.12 to 1.42; 2 studies, 84 participants; low-quality evidence) and language skills (SMD 0.28, 95% CI 0.03 to 0.54; 3 studies, 222 participants; moderate-quality evidence). AUTHORS' CONCLUSIONS: Results from this review provide evidence that beginning reading interventions that include elements of phonologic awareness, letter sound instruction, and decoding, delivered to children and adolescents with intellectual disability, are associated with small-to-moderate improvements in phonologic awareness, word reading, decoding, expressive and receptive language, and oral reading fluency. These findings are aligned with previously conducted studies that examined the effects of reading interventions for people without intellectual disability.

Platelet hyaluronidase-2: an enzyme that translocates to the surface upon activation to function in extracellular matrix degradation.

Following injury, platelets rapidly interact with the exposed extracellular matrix (ECM) of the vessel wall and the surrounding tissues. Hyaluronan (HA) is a major glycosaminoglycan component of the ECM and plays a significant role in regulating inflammation. We have recently reported that human platelets degrade HA from the surfaces of activated endothelial cells into fragments capable of inducing immune responses by monocytes. We also showed that human platelets contain the enzyme hyaluronidase-2 (HYAL2), one of two major hyaluronidases that digest HA in somatic tissues. The deposition of HA increases in inflamed tissues in several inflammatory diseases, including inflammatory bowel disease (IBD). We therefore wanted to define the mechanism by which platelets degrade HA in the inflamed tissues. In this study, we show that human platelets degrade the proinflammatory matrix HA through the activity of HYAL2 and that platelet activation causes the immediate translocation of HYAL2 from a distinct population of α-granules to platelet surfaces where it exerts its catalytic activity. Finally, we show that patients with IBD have lower platelet HYAL2 levels and activity than healthy controls.

The human milk oligosaccharide 2'-fucosyllactose modulates CD14 expression in human enterocytes, thereby attenuating LPS-induced inflammation.

BACKGROUND: A major cause of enteric infection, Gram-negative pathogenic bacteria activate mucosal inflammation through lipopolysaccharide (LPS) binding to intestinal toll-like receptor 4 (TLR4). Breast feeding lowers risk of disease, and human milk modulates inflammation. OBJECTIVE: This study tested whether human milk oligosaccharides (HMOSs) influence pathogenic Escherichia coli-induced interleukin (IL)-8 release by intestinal epithelial cells (IECs), identified specific proinflammatory signalling molecules modulated by HMOSs, specified the active HMOS and determined its mechanism of action. METHODS: Models of inflammation were IECs invaded by type 1 pili enterotoxigenic E. coli (ETEC) in vitro: T84 modelled mature, and H4 modelled immature IECs. LPS-induced signalling molecules co-varying with IL-8 release in the presence or absence of HMOSs were identified. Knockdown and overexpression verified signalling mediators. The oligosaccharide responsible for altered signalling was identified. RESULTS: HMOSs attenuated LPS-dependent induction of IL-8 caused by ETEC, uropathogenic E. coli, and adherent-invasive E. coli (AIEC) infection, and suppressed CD14 transcription and translation. CD14 knockdown recapitulated HMOS-induced attenuation. Overexpression of CD14 increased the inflammatory response to ETEC and sensitivity to inhibition by HMOSs. 2'-fucosyllactose (2'-FL), at milk concentrations, displayed equivalent ability as total HMOSs to suppress CD14 expression, and protected AIEC-infected mice. CONCLUSIONS: HMOSs and 2'-FL directly inhibit LPS-mediated inflammation during ETEC invasion of T84 and H4 IECs through attenuation of CD14 induction. CD14 expression mediates LPS-TLR4 stimulation of portions of the 'macrophage migration inhibitory factors' inflammatory pathway via suppressors of cytokine signalling 2/signal transducer and activator of transcription 3/NF-κB. HMOS direct inhibition of inflammation supports its functioning as an innate immune system whereby the mother protects her vulnerable neonate through her milk. 2'-FL, a principal HMOS, quenches inflammatory signalling.

Traveler's diarrhea: a clinical review.

IMPORTANCE: Acute diarrhea is the most common illness that affects travelers to low-income regions of the world. Although improved hygiene has reduced the risk of traveler's diarrhea in many destinations, the risk remains high in others. OBJECTIVE: To review the current state of knowledge on the etiology, risk factors, prevention, and management of traveler's diarrhea. EVIDENCE REVIEW: A search of the PubMed, Google Scholar, and Cochrane Library databases for the period 2012-April 2014 was performed for articles on traveler's diarrhea. The database search yielded 2976 articles, of which 37 were included in this review. These were added to 85 articles previously identified by the authors. FINDINGS: Improved hygiene has reduced the risk of traveler's diarrhea from 20% or more (for a 2-week stay) to between 8% and 20% in some parts of the world. Acquiring traveler's diarrhea causes 12% to 46% of travelers to change their travel plans. Returning travelers seeking medical care have a diagnosis of gastrointestinal disturbance in approximately one-third of all cases. Postinfectious irritable bowel syndrome may occur in 3% to 17% of patients who have had traveler's diarrhea. Prevention of traveler's diarrhea by dietary avoidance measures is often not successful. Chemoprophylaxis should be restricted to travelers who are at risk of severe complications of diarrhea. Ciprofloxacin is the standard treatment in self-therapy of traveler's diarrhea except when patients are in South or Southeast Asia, where azithromycin is preferred. CONCLUSIONS AND RELEVANCE: Diarrhea remains a common problem for international travelers. Persons intending to travel to at-risk countries should be counseled regarding prevention measures and may be given a travel pack that includes medications for self-treatment should they become ill.

Early grade curriculum-based reading measures for students with intellectual disability.

The purpose of this study was to extend previous research on the use of curriculum-based measurement (CBM) for students with intellectual disability by having 19 special education teachers monitor weekly reading progress of 38 students with intellectual disability for approximately 15 weeks and examining whether students exhibited gains on the progress monitoring measures. In addition to the weekly CBM, teachers reported the type and duration of daily reading instruction. Data were analyzed to explore relationships between CBM performance and reading instruction. Our results indicate that teachers are capable of administering and scoring CBM on a weekly basis and that CBM does capture reading growth for some students with intellectual disability. Correlations between CBM performance and a teacher report of skills taught during reading instruction indicate that teachers may be differentiating instruction based on students' reading ability. Directions for future research as well as limitations of the study are discussed.

Human milk hyaluronan enhances innate defense of the intestinal epithelium.

Breast-feeding is associated with enhanced protection from gastrointestinal disease in infants, mediated in part by an array of bioactive glycan components in milk that act through molecular mechanisms to inhibit enteric pathogen infection. Human milk contains hyaluronan (HA), a glycosaminoglycan polymer found in virtually all mammalian tissues. We have shown that synthetic HA of a specific size range promotes expression of antimicrobial peptides in intestinal epithelium. We hypothesize that hyaluronan from human milk also enhances innate antimicrobial defense. Here we define the concentration of HA in human milk during the first 6 months postpartum. Importantly, HA isolated from milk has a biological function. Treatment of HT-29 colonic epithelial cells with human milk HA at physiologic concentrations results in time- and dose-dependent induction of the antimicrobial peptide human ß-defensin 2 and is abrogated by digestion of milk HA with a specific hyaluronidase. Milk HA induction of human ß-defensin 2 expression is also reduced in the presence of a CD44-blocking antibody and is associated with a specific increase in ERK1/2 phosphorylation, suggesting a role for the HA receptor CD44. Furthermore, oral administration of human milk-derived HA to adult, wild-type mice results in induction of the murine Hß D2 ortholog in intestinal mucosa and is dependent upon both TLR4 and CD44 in vivo. Finally, treatment of cultured colonic epithelial cells with human milk HA enhances resistance to infection by the enteric pathogen Salmonella typhimurium. Together, our observations suggest that maternally provided HA stimulates protective antimicrobial defense in the newborn.

Large scale explorative oligonucleotide probe selection for thousands of genetic groups on a computing grid: application to phylogenetic probe design using a curated small subunit ribosomal RNA gene database.

Phylogenetic Oligonucleotide Arrays (POAs) were recently adapted for studying the huge microbial communities in a flexible and easy-to-use way. POA coupled with the use of explorative probes to detect the unknown part is now one of the most powerful approaches for a better understanding of microbial community functioning. However, the selection of probes remains a very difficult task. The rapid growth of environmental databases has led to an exponential increase of data to be managed for an efficient design. Consequently, the use of high performance computing facilities is mandatory. In this paper, we present an efficient parallelization method to select known and explorative oligonucleotide probes at large scale using computing grids. We implemented a software that generates and monitors thousands of jobs over the European Computing Grid Infrastructure (EGI). We also developed a new algorithm for the construction of a high-quality curated phylogenetic database to avoid erroneous design due to bad sequence affiliation. We present here the performance and statistics of our method on real biological datasets based on a phylogenetic prokaryotic database at the genus level and a complete design of about 20,000 probes for 2,069 genera of prokaryotes.

Specific-sized hyaluronan fragments promote expression of human ß-defensin 2 in intestinal epithelium.

Hyaluronan (HA) is a glycosaminoglycan polymer found in the extracellular matrix of virtually all mammalian tissues. Recent work has suggested a role for small, fragmented HA polymers in initiating innate defense responses in immune cells, endothelium, and epidermis through interaction with innate molecular pattern recognition receptors, such as TLR4. Despite these advances, little is known regarding the effect of fragmented HA at the intestinal epithelium, where numerous pattern recognition receptors act as sentinels of an innate defense response that maintains epithelial barrier integrity in the presence of abundant and diverse microbial challenges. Here we report that HA fragments promote expression of the innate antimicrobial peptide human ß-defensin 2 (HßD2) in intestinal epithelial cells. Treatment of HT-29 colonic epithelial cells with HA fragment preparations resulted in time- and dose-dependent up-regulated expression of HßD2 protein in a fragment size-specific manner, with 35-kDa HA fragment preparations emerging as the most potent inducers of intracellular HßD2. Furthermore, oral administration of specific-sized HA fragments promotes the expression of an HßD2 ortholog in the colonic epithelium of both wild-type and CD44-deficient mice but not in TLR4-deficient mice. Together, our observations suggest that a highly size-specific, TLR4-dependent, innate defense response to fragmented HA contributes to intestinal epithelium barrier defense through the induction of intracellular HßD2 protein.

A quantitative analysis of microalgal lipids for optimization of biodiesel and omega-3 production.

The lipid characteristics of microalgae are known to differ between species and change with growth conditions. This work provides a methodology for lipid characterization that enables selection of the optimal strain, cultivation conditions, and processing pathway for commercial biodiesel production from microalgae. Two different microalgal species, Nannochloropsis sp. and Chlorella sp., were cultivated under both nitrogen replete and nitrogen depleted conditions. Lipids were extracted and fractionated into three major classes and quantified gravimetrically. The fatty acid profile of each fraction was analyzed using GC-MS. The resulting quantitative lipid data for each of the cultures is discussed in the context of biodiesel and omega-3 production. This approach illustrates how the growth conditions greatly affect the distribution of fatty acid present in the major lipid classes and therefore the suitability of the lipid extracts for biodiesel and other secondary products.