Outcome of ileorectal anastomosis for Crohn's colitis

One hundred thirty-one patients underwent ileorectal anastomosis (IRA) for Crohn's colitis. Preoperatively, 84 patients (63 percent) were found to have mild or moderate proctitis and 47 (37 percent) had rectal sparing. Sixty-eight (52 percent) had associated small bowel disease, and 20 (15 percent) had perianal disease. Sixty-five IRAs were performed at the time of subtotal colectomy, while 56 were done after previous surgery. Anastomotic leaks occurred in four patients. There were no operative deaths. Thirteen patients (10 percent) with protecting stomas never underwent closure. Among the remaining 118 patients with functioning IRAs, 30 (23 percent) required later proctectomy and 16 (13 percent) required proximal diversion, with the mean period with a functioning IRA in these 46 patients being 4.1 years (range, 6.2 months–12.7 years). An additional 13 patients required preanastomotic resection and neo-IRA, and 11 required proximal small bowel resection. The mean duration of function of all 118 IRAs was 9.2 years. At the time of review, after a mean follow-up of 9.5 years, 72 patients (61 percent) retained a functioning IRA, with 44 being free of disease, while 28 were being treated with steroids or antidiarrheal medication. The mean stool frequency was 4.7 per day. In patients with Crohn's colitis, IRA should be considered as an alternative to proctocolectomy if the rectum is not severely diseased and sphincter function is not compromised.Read at the meeting of The American Society of Colon and Rectal Surgeons, Boston, Massachusetts, May 12 to 17, 1991.     

Exome Sequencing Reveals RAG1 Mutations in a Child with Autoimmunity and Sterile Chronic Multifocal Osteomyelitis Evolving into Disseminated Granulomatous Disease

We describe a boy who developed autoinflammatory (chronic sterile multifocal osteomyelitis) and autoimmune (autoimmune cytopenias; vitiligo) phenotypes who subsequently developed disseminated granulomatous disease. Whole exome sequencing revealed homozygous RAG1 mutations thus expanding the spectrum of combined immunodeficiency with autoimmunity and granuloma that can occur with RAG deficiency.     

Integrated analysis of genome‐wide copy number alterations and gene expression in microsatellite stable,CpG island methylator phenotype‐negative colon cancer

Microsatellite stable (MSS), CpG island methylator phenotype (CIMP)‐negative colorectal tumors, the most prevalent molecular subtype of colorectal cancer, are associated with extensive copy number alteration (CNA) events and aneuploidy. We report on the identification of characteristic recurrent CNA (with frequency >25%) events and associated gene expression profiles for a total of 40 paired tumor and adjacent normal colon tissues using genome‐wide microarrays. We observed recurrent CNAs, namely gains at 1q, 7p, 7q, 8p12‐11, 8q, 12p13, 13q, 20p, 20q, Xp, and Xq and losses at 1p36, 1p31, 1p21, 4p15‐12, 4q12‐35, 5q21‐22, 6q26, 8p, 14q, 15q11‐12, 17p, 18p, 18q, 21q21‐22, and 22q. Within these genomic regions we identified 356 genes with significant differential expression (P < 0.0001 and ±1.5‐fold change) in the tumor compared to adjacent normal tissue. Gene ontology and pathway analyses indicated that many of these genes were involved in functional mechanisms that regulate cell cycle, cell death, and metabolism. An amplicon present in >70% of the tumor samples at 20q11‐20q13 contained several cancer‐related genes (AHCY, POFUT1, RPN2, TH1L, and PRPF6) that were upregulated and demonstrated a significant linear correlation (P < 0.05) for gene dosage and gene expression. Copy number loss at 8p, a CNA associated with adenocarcinoma and poor prognosis, was observed in >50% of the tumor samples and demonstrated a significant linear correlation for gene dosage and gene expression for two potential tumor suppressor genes, MTUS1 (8p22) and PPP2CB (8p12). The results from our integration analysis illustrate the complex relationship between genomic alterations and gene expression in colon cancer. © 2013 Wiley Periodicals, Inc.     

Genomic sequencing.

Unique DNA sequences can be determined directly from mouse genomic DNA. A denaturing gel separates by size mixtures of unlabeled DNA fragments from complete restriction and partial chemical cleavages of the entire genome. These lanes of DNA are transferred and UV-crosslinked to nylon membranes. Hybridization with a short 32P-labeled single-stranded probe produces the image of a DNA sequence "ladder" extending from the 3' or 5' end of one restriction site in the genome. Numerous different sequences can be obtained from a single membrane by reprobing. Each band in these sequences represents 3 fg of DNA complementary to the probe. Sequence data from mouse immunoglobulin heavy chain genes from several cell types are presented. The genomic sequencing procedures are applicable to the analysis of genetic polymorphisms, DNA methylation at deoxycytidines, and nucleic acid-protein interactions at single nucleotide resolution.     

The Role of Exercise and Physical Activity in Weight Loss and Maintenance

This review explores the role of physical activity (PA) and exercise training (ET) in the prevention of weight gain, initial weight loss, weight maintenance, and the obesity paradox. In particular, we will focus the discussion on the expected initial weight loss from different ET programs, and explore intensity/volume relationships. Based on the present literature, unless the overall volume of aerobic ET is very high, clinically significant weight loss is unlikely to occur. Also, ET also has an important role in weight regain after initial weight loss. Overall, aerobic ET programs consistent with public health recommendations may promote up to modest weight loss (~ 2 kg), however the weight loss on an individual level is highly heterogeneous. Clinicians should educate their patients on reasonable expectations of weight loss based on their physical activity program and emphasize that numerous health benefits occur from PA programs in the absence of weight loss.     

Syntrophic exchange in synthetic microbial communities

Metabolic crossfeeding is an important process that can broadly shape microbial communities. However, little is known about specific crossfeeding principles that drive the formation and maintenance of individuals within a mixed population. Here, we devised a series of synthetic syntrophic communities to probe the complex interactions underlying metabolic exchange of amino acids. We experimentally analyzed multimember, multidimensional communities of Escherichia coli of increasing sophistication to assess the outcomes of synergistic crossfeeding. We find that biosynthetically costly amino acids including methionine, lysine, isoleucine, arginine, and aromatics, tend to promote stronger cooperative interactions than amino acids that are cheaper to produce. Furthermore, cells that share common intermediates along branching pathways yielded more synergistic growth, but exhibited many instances of both positive and negative epistasis when these interactions scaled to higher dimensions. In more complex communities, we find certain members exhibiting keystone species-like behavior that drastically impact the community dynamics. Based on comparative genomic analysis of >6,000 sequenced bacteria from diverse environments, we present evidence suggesting that amino acid biosynthesis has been broadly optimized to reduce individual metabolic burden in favor of enhanced crossfeeding to support synergistic growth across the biosphere. These results improve our basic understanding of microbial syntrophy while also highlighting the utility and limitations of current modeling approaches to describe the dynamic complexities underlying microbial ecosystems. This work sets the foundation for future endeavors to resolve key questions in microbial ecology and evolution, and presents a platform to develop better and more robust engineered synthetic communities for industrial biotechnology.Microbes are abundantly found in almost every part of the world, living in communities that are diverse in many facets. Although it is clear that cooperation and competition within microbial communities is central to their stability, maintenance, and longevity, there is limited knowledge about the general principles guiding the formation of these intricate systems. Understanding the underlying governing principles that shape a microbial community is key for microbial ecology but is also crucial for engineering synthetic microbiomes for various biotechnological applications (1–3). Numerous such examples have been recently described including the bioconversion of unprocessed cellulolytic feedstocks into biofuel isobutanol using fungal–bacterial communities (4) and biofuel precursor methyl halides using yeast–bacterial cocultures (5). Other emerging applications in biosensing and bioremediation against environmental toxins such as arsenic (6) and pathogens such as Pseudomonas aeruginosa and Vibrio cholerae have been demonstrated using engineered quorum-sensing Escherichia coli (7, 8). These advances paint an exciting future for the development of sophisticated multispecies microbial communities to address pressing challenges and the crucial need to understand the basic principles that enables their design and engineering.An important process that governs the growth and composition of microbial ecosystems is the exchange of essential metabolites, known as metabolic crossfeeding. Entomological studies have elucidated on a case-by-case basis the importance of amino acids in natural interkingdom and interspecies exchange networks (9–11). Recent comparative analyses of microbial genomes suggest that a significant proportion of all bacteria lack essential pathways for amino acid biosynthesis (2). These auxotrophic microbes thus require extracellular sources of amino acids for survival. Understanding amino acid exchange therefore presents an opportunity to gain new insights into basic principles in metabolic crossfeeding. Recently, several studies have used model systems of Saccharomyces cerevisiae (12), Saccharomyces enterica (13), and E. coli (14–16) to study syntrophic growth of amino acid auxotrophs in coculture environments. Numerous quantitative models have also been developed to describe the behavior of these multispecies systems, including those that integrate dynamics (17, 18), metabolism (19–21), and spatial coordination (22). Although these efforts have led to an improved understanding of the dynamics of syntrophic pairs and the energetic and benefits of cooperativity in these simple systems (23), larger more complex syntrophic systems have yet to be explored.Here, we use engineered E. coli mutants to study syntrophic crossfeeding, scaling to higher-dimensional synthetic ecosystems of increasing sophistication. We first devised pairwise syntrophic communities that show essential and interesting dynamics that can be predicted by simple kinetic models. We then increased the complexity of the interaction in three-member synthetic consortia involving crossfeeding of multiple metabolites. To further increase the complexity of our system, we devised a 14-member community to understand key drivers of population dynamics over short and evolutionary timescales. Finally, we provide evidence for widespread trends of metabolic crossfeeding based on comparative genomic analysis of amino acid biosynthesis across thousands of sequenced genomes. Our large-scale and systematic efforts represent an important foray into forward and reverse engineering synthetic microbial communities to gain key governing principles of microbial ecology and systems microbiology.     

Lead poisoning and the deceptive recovery of the critically endangered California condor

Endangered species recovery programs seek to restore populations to self-sustaining levels. Nonetheless, many recovering species require continuing management to compensate for persistent threats in their environment. Judging true recovery in the face of this management is often difficult, impeding thorough analysis of the success of conservation programs. We illustrate these challenges with a multidisciplinary study of one of the world's rarest birds-the California condor (Gymnogyps californianus). California condors were brought to the brink of extinction, in part, because of lead poisoning, and lead poisoning remains a significant threat today. We evaluated individual lead-related health effects, the efficacy of current efforts to prevent lead-caused deaths, and the consequences of any reduction in currently intensive management actions. Our results show that condors in California remain chronically exposed to harmful levels of lead; 30% of the annual blood samples collected from condors indicate lead exposure (blood lead ≥ 200 ng/mL) that causes significant subclinical health effects, measured as >60% inhibition of the heme biosynthetic enzyme δ-aminolevulinic acid dehydratase. Furthermore, each year, ～20% of free-flying birds have blood lead levels (≥450 ng/mL) that indicate the need for clinical intervention to avert morbidity and mortality. Lead isotopic analysis shows that lead-based ammunition is the principle source of lead poisoning in condors. Finally, population models based on condor demographic data show that the condor's apparent recovery is solely because of intensive ongoing management, with the only hope of achieving true recovery dependent on the elimination or substantial reduction of lead poisoning rates.