KAUST Metagenomic Analysis Platform (KMAP), enabling access to massive analytics of re-annotated metagenomic data.

Exponential rise of metagenomics sequencing is delivering massive functional environmental genomics data. However, this also generates a procedural bottleneck for on-going re-analysis as reference databases grow and methods improve, and analyses need be updated for consistency, which require acceess to increasingly demanding bioinformatic and computational resources. Here, we present the KAUST Metagenomic Analysis Platform (KMAP), a new integrated open web-based tool for the comprehensive exploration of shotgun metagenomic data. We illustrate the capacities KMAP provides through the re-assembly of ~ 27,000 public metagenomic samples captured in ~ 450 studies sampled across ~ 77 diverse habitats. A small subset of these metagenomic assemblies is used in this pilot study grouped into 36 new habitat-specific gene catalogs, all based on full-length (complete) genes. Extensive taxonomic and gene annotations are stored in Gene Information Tables (GITs), a simple tractable data integration format useful for analysis through command line or for database management. KMAP pilot study provides the exploration and comparison of microbial GITs across different habitats with over 275 million genes. KMAP access to data and analyses is available at https://www.cbrc.kaust.edu.sa/aamg/kmap.start .

DDIEM: drug database for inborn errors of metabolism.

BACKGROUND: Inborn errors of metabolism (IEM) represent a subclass of rare inherited diseases caused by a wide range of defects in metabolic enzymes or their regulation. Of over a thousand characterized IEMs, only about half are understood at the molecular level, and overall the development of treatment and management strategies has proved challenging. An overview of the changing landscape of therapeutic approaches is helpful in assessing strategic patterns in the approach to therapy, but the information is scattered throughout the literature and public data resources. RESULTS: We gathered data on therapeutic strategies for 300 diseases into the Drug Database for Inborn Errors of Metabolism (DDIEM). Therapeutic approaches, including both successful and ineffective treatments, were manually classified by their mechanisms of action using a new ontology. CONCLUSIONS: We present a manually curated, ontologically formalized knowledgebase of drugs, therapeutic procedures, and mitigated phenotypes. DDIEM is freely available through a web interface and for download at http://ddiem.phenomebrowser.net.

Genome sequence analysis of Zooshikella ganghwensis strain VG4 and its potential for the synthesis of antimicrobial metabolites.

With antimicrobial resistance on the rise, the discovery of new compounds with novel structural scaffolds exhibiting antimicrobial properties has become an important area of research. Such compounds can serve as starting points for the development of new antimicrobials. In this report, we present the draft genome sequence of the Zooshikella ganghwensis strain VG4, isolated from Red Sea sediments, that produces metabolites with antimicrobial properties. A genomic analysis reveals that it carries at least five gene clusters that have the potential to direct biosynthesis of bioactive secondary metabolites such as polyketides and nonribosomal peptides. By using in-silico approaches, we predict the structure of these metabolites.

Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs.

The OM43 clade within the family Methylophilaceae of Betaproteobacteria represents a group of methylotrophs that play important roles in the metabolism of C1 compounds in marine environments and other aquatic environments around the globe. Using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (here designated MBRS-H7) from the ultraoligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species that forms a distinct cluster together with isolate KB13 from Hawaii (Hawaii-Red Sea [H-RS] cluster) that is separate from the cluster represented by strain HTCC2181 (from the Oregon coast). Phylogenetic analyses using the robust 16S-23S internal transcribed spacer revealed a potential ecotype separation of the marine OM43 clade members, which was further confirmed by metagenomic fragment recruitment analyses that showed trends of higher abundance in low-chlorophyll and/or high-temperature provinces for the H-RS cluster but a preference for colder, highly productive waters for the HTCC2181 cluster. This potential environmentally driven niche differentiation is also reflected in the metabolic gene inventories, which in the case of the H-RS cluster include those conferring resistance to high levels of UV irradiation, temperature, and salinity. Interestingly, we also found different energy conservation modules between these OM43 subclades, namely, the existence of the NADH:quinone oxidoreductase complex I (NUO) system in the H-RS cluster and the nonhomologous NADH:quinone oxidoreductase (NQR) system in the HTCC2181 cluster, which might have implications for their overall energetic yields.

How do men in the United Kingdom decide to dispose of banked sperm following cancer treatment?

Current policy in the UK recommends that men bank sperm prior to cancer treatment, but very few return to use it for reproductive purposes or agree to elective disposal even when their fertility recovers and their families are complete. We assessed the demographic, medical and psychological variables that influence the decision to dispose by contacting men (n = 499) who banked sperm more than five years previously, and asked them to complete questionnaires about their views on sperm banking, fertility and disposal. From 193 responses (38.7% response rate), 19 men (9.8%) requested disposal within four months of completing the questionnaire. Compared with men who wanted their sperm to remain in storage, they were significantly more confident that their fertility had recovered (OR = 1.78, 95% CI = 1.05-3.03, p = 0.034), saw fertility monitoring (semen analysis) as less important (OR = 0.61, 95% CI = 0.39-0.94, p = 0.026), held more positive attitudes to disposal (OR = 5.71, 95% CI = 2.89-11.27, p < 0.001), were more likely to have experienced adverse treatment side-effects (OR = 4.37, CI = 1.61-11.85, p = 0.004) and had less desire for children in the future (OR = 0.41, 95% CI = 0.26-0.64, p < 0.001). Information about men's reasons to dispose of banked sperm may be helpful in devising new strategies to encourage men to engage with sperm banking clinics and make timely decisions about the fate of their samples.

The importance of fertility preservation in cancer patients.

The potential risks of anti-cancer therapy for male and female fertility are well understood, yet evidence suggests that fewer patients than predicted actually preserve their fertility before therapy begins. Studies of post-pubertal males and females suggest that the approach of health professionals in oncology is vital in facilitating successful sperm and egg banking. For men, this seems to be compounded by a general lack of understanding about their personal risk of infertility. Those involved in delivering anticancer therapy therefore have a vital role to play in providing timely information and facilitating efficient referral to fertility services. In the future, this is likely to become more important if new fertility preservation strategies such as ovarian and testicular tissue banking become more routinely used, with implications for both pre- and post-pubertal individuals.

INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles.

BACKGROUND: The next generation sequencing technologies substantially increased the throughput of microbial genome sequencing. To functionally annotate newly sequenced microbial genomes, a variety of experimental and computational methods are used. Integration of information from different sources is a powerful approach to enhance such annotation. Functional analysis of microbial genomes, necessary for downstream experiments, crucially depends on this annotation but it is hampered by the current lack of suitable information integration and exploration systems for microbial genomes. RESULTS: We developed a data warehouse system (INDIGO) that enables the integration of annotations for exploration and analysis of newly sequenced microbial genomes. INDIGO offers an opportunity to construct complex queries and combine annotations from multiple sources starting from genomic sequence to protein domain, gene ontology and pathway levels. This data warehouse is aimed at being populated with information from genomes of pure cultures and uncultured single cells of Red Sea bacteria and Archaea. Currently, INDIGO contains information from Salinisphaera shabanensis, Haloplasma contractile, and Halorhabdus tiamatea - extremophiles isolated from deep-sea anoxic brine lakes of the Red Sea. We provide examples of utilizing the system to gain new insights into specific aspects on the unique lifestyle and adaptations of these organisms to extreme environments. CONCLUSIONS: We developed a data warehouse system, INDIGO, which enables comprehensive integration of information from various resources to be used for annotation, exploration and analysis of microbial genomes. It will be regularly updated and extended with new genomes. It is aimed to serve as a resource dedicated to the Red Sea microbes. In addition, through INDIGO, we provide our Automatic Annotation of Microbial Genomes (AAMG) pipeline. The INDIGO web server is freely available at http://www.cbrc.kaust.edu.sa/indigo.

Real-time polymerase chain reaction shows that density centrifugation does not always remove Chlamydia trachomatis from human semen.

OBJECTIVE: To evaluate the efficiency of sperm washing procedures to remove Chlamydia trachomatis from semen both in clinical samples and experimental inoculations. DESIGN: Laboratory-based study. SETTING: Research laboratory in a university hospital. PATIENT(S): One hundred men attending for diagnostic semen analysis as part of infertility investigations and three sperm donors providing ejaculates for research purposes. MAIN OUTCOME MEASURE(S): Number of DNA copies of C. trachomatis, infectivity in an HeLa cell monolayer, and immunofluorescence. RESULT(S): Of the 100 semen samples examined, 13 contained detectable levels of C. trachomatis DNA (675-15,920 copies/mL) and in only 7 was this completely removed after sperm washing. In the remaining six DNA-positive samples, the number of copies in the postwash preparation ranged from 36-455 per mL. Experimental inoculations found that postwash preparations containing C. trachomatis DNA as low as 61 copies/mL were able to establish an infection in vitro. CONCLUSION(S): Undiagnosed C. trachomatis infections in men attending for assisted conception could potentially lead to infection or contamination of the IVF culture system as sperm washing methods are not 100% effective.

Intensive Short-Term Dynamic Psychotherapy of treatment-resistant depression: a pilot study.

This pilot study examined the effectiveness of Intensive Short-term Dynamic Psychotherapy (ISTDP) in treatment-resistant depression (TRD). Ten patients with TRD were provided a course of ISTDP. Clinician and patient symptom and interpersonal measures were completed every 4 weeks, at termination, and in follow-up. Medication, disability, and hospital costs were compared before and after treatment. After an average of 13.6 sessions of therapy, all mean measures reached the normal range, with effect sizes ranging from 0.87 to 3.3. Gains were maintained in follow-up assessments. Treatment costs were offset by cost reductions elsewhere in the system. This open study suggests that ISTDP may be effective with this challenging patient group. A randomized, controlled trial and qualitative research are warranted to evaluate this treatment further and to examine its possible therapeutic elements.

Reversal of cardiac dysfunction by selective ET-A receptor antagonism.

The effectiveness of a selective endothelin receptor-A (ET-A) antagonist, A-127722 (approximately 10 mg kg(-1) day(-1) as 200 mg kg(-1) powdered food), to reverse existing cardiac remodelling and prevent further remodelling was tested in deoxycorticosterone acetate (DOCA)-salt hypertensive rats. Uninephrectomised rats (UNX) administered DOCA (25 mg every fourth day s.c.) and 1% NaCl in drinking water for 28 days developed hypertension (systolic blood pressure (BP): UNX 128+/-6 mmHg, DOCA-salt 182+/-5* mmHg; *P<0.05 vs UNX), left ventricular hypertrophy (UNX 1.99+/-0.06 mg kg(-1) body wt, DOCA-salt 3.30+/-0.08* mg kg(-1) body wt), decreased left ventricular internal diameter (UNX 6.69+/-0.18 mm, DOCA-salt 5.51+/-0.37* mm), an increased left ventricular monocyte/macrophage infiltration together with an increased interstitial collagen from 2.7+/-0.3 to 11.7+/-1.3%, increased passive diastolic stiffness (UNX 21.1+/-0.5, DOCA-salt 30.1+/-1.3*), prolongation of the action potential duration at 20 and 90% of repolarisation (APD20-UNX 6.8+/-1.1, DOCA-salt 10.1+/-1.5* ms; APD90-UNX 34.4+/-3.5 ms, DOCA-salt 64.3+/-10.4* ms) and vascular dysfunctions (2.6-fold decrease in maximal contractile response to noradrenaline, 3.5-fold decrease in maximal relaxation response to acetylcholine). Administration of A-127722 for 14 days starting 14 days after surgery attenuated the increases in systolic BP (150+/-6** mmHg, **P<0.05 vs DOCA-salt), left ventricular wet weight (2.65+/-0.06** mg kg(-1) body wt) and internal diameter (6.39+/-0.31** mm), prevented left ventricular monocyte/macrophage accumulation, attenuated the increased left ventricular interstitial collagen (7.6+/-1.3%**), reversed the increased passive diastolic stiffness (22.1+/-1.2**), attenuated the action potential duration prolongation (APD20 - 7.6+/-1.4**, APD90 - 41.5+/-6.9** ms) and normalised changes in vascular function. ET-A receptor antagonism both reverses and prevents the cardiac and vascular remodelling in DOCA-salt hypertension and improves cardiovascular function.