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Background and aims Monogenic forms of inflammatory bowel disease (IBD) illustrate the essential roles of individual genes in pathways and networks safeguarding immune tolerance and gut homeostasis. Methods To build a taxonomy model we assessed 165 disorders. Genes were prioritized based on penetrance of IBD and disease phenotypes were integrated with multi-omics datasets. Monogenic IBD genes were classified by: (1) overlapping syndromic features; (2) response to hematopoietic stem cell transplantation; (3) bulk RNA-seq of 32 tissues; (4) single-cell RNA-seq of >50 cell subsets from the intestine of healthy individuals and IBD patients (pediatric and adult), and (5) proteomes of 43 immune subsets. The model was validated by addition of newly identified monogenic IBD defects. As a proof-of-concept, we explore the intersection between immunometabolism and antimicrobial activity for a group of disorders (G6PC3/SLC37A4). Results Our quantitative integrated taxonomy defines the cellular landscape of monogenic IBD gene expression across 102 genes with high and moderate penetrance (81 in the model set and 21 genes in the validation set). We illustrate distinct cellular networks, highlight expression profiles across understudied cell types (e.g., CD8+ T cells, neutrophils, epithelial subsets and endothelial cells) and define genotype-phenotype associations (perianal disease and defective antimicrobial activity). We illustrate processes and pathways shared across cellular compartments and phenotypic groups and highlight cellular immunometabolism with mTOR activation as one of the converging pathways. There is an overlap of genes and enriched cell-specific expression between monogenic and polygenic IBD. Conclusion Our taxonomy integrates genetic, clinical and multi-omic data; providing a basis for genomic diagnostics and testable hypotheses for disease functions and treatment responses.

In some patients with extreme phenotypes of inflammatory bowel disease (IBD; in particular in those with infantile or very early onset IBD with

Publisher Summary Careful and thorough assessment of data quality is a key step that must be undertaken prior to testing for disease associations. Due to the large number of markers and individuals, many quality control (QC) procedures can be implemented to reduce the rate of false-positive and false-negative findings. This chapter outlines several procedures to identify and remove poorly genotyped markers and individuals. These procedures include the identification of poorly genotyped individuals and SNPs, the detection of individuals with discordant ancestry, the elucidation of duplicate and related pairs of individuals, and the exposure of plate-effects. Methods for the identification and removal of confounding variables such as plate-effects and divergent population ancestry are also discussed. QC procedures for both case-control and family-based association studies are highlighted. These QC procedures are seen to produce high-quality data that leads to the identification of novel susceptibility loci for many common human diseases and complex traits. Further, details of several software packages that can be used for GWAS QC are also provided.

Publisher Summary This chapter introduces the key issues involved in the design of sludge pumping systems. The key to pumping sludge is to use a pump properly sized to develop sufficient head and a smooth pipe sized to produce the proper velocity without constrictions or projections and with as few bends as possible. The most important criterion for design is the ability to transfer the necessary quantity of various solids within the required time interval. In most treatment plant sludge pumping, the consistency of the sludge changes during pumping. At first, the most concentrated sludge at the bottom of the basin is pumped. After most of that sludge is removed, a more dilute sludge with characteristics ranging from semisolids to essentially liquid is pumped. The design procedure for positive-displacement pumps involves determining the maximum pumping capacity required at the minimum sludge solids concentration; determining which combinations of simplex, duplex, and triplex pumps are feasible using the capacities found for each type of pump in a manufacturer's catalog; and plotting the sludge system head curve for the maximum percentage of dry solids sludge concentration. Due to the nature of sludge, the requirements of sludge piping systems differ in many ways from those of water piping systems. The most common pipe materials for sludge piping systems are ductile iron and steel. The most common lining for ductile iron and steel pipe is cement mortar, but an even smoother lining, such as glass, is desirable.

Publisher Summary This chapter focuses on several factors that need to be considered during the selection of valves and actuators. One of the factors is that a valve satisfactory in one location might not be satisfactory in another location even if conditions are only slightly different. Other factors include that manufacturers of several styles of valves might make some good ones and some poor ones, models are changed from time to time and a valve, once poor, might now be good, and, finally, it is extremely difficult to write specifications to comply with the law, allow competitive bidding, and still obtain a satisfactory valve. Valves require the incorporation of safety features to prevent damage from malfunctioning equipment that ensures the completion of an automatic control system. These safety features could be arranged to prevent the operation of an unprimed pump, to prevent the operation of a pump against a closed control valve that does not open on schedule, or to limit excessive pumping when discharging to a broken pipe. Isolation valves are either fully closed or fully opened. Valves that remain in one position for extended periods become difficult to operate unless they are “exercised” from time to time. Valves should be exercised at least once each year (more often if the water is corrosive or dirty), and the required exercise. A check valve is usually (but not always) required to prevent reverse flow and prevent runaway reverse pump speeds when the pump is shut off, keep the pipeline full of water to prevent the entrance of air, and minimize water hammer and surges for pump start-up and shut-down.

The product of the human p53 tumor suppressor gene (TP53) is a 393-amino-acid polypeptide that functions as a homotetrameric transcription factor. p53 regulates the expression of genes that control cell cycle progression, the induction of apoptosis, DNA repair, and other functions involved in cellular responses to stress. Loss of p53 function, either directly through mutation or indirectly through several mechanisms, plays a central role in the development of cancer. While the p53 protein normally is short lived and is present at low levels in unstressed mammalian cells, in response to both genotoxic and nongenotoxic stresses it accumulates in the nucleus where it binds to specific DNA sequences. Genomic approaches have shown that p53 induces or inhibits the expression of more than 150 genes including p21 GADD45, MDM2, IGFBP3, and BAX, many of which mediate cell cycle arrest or apoptosis. p53 modulates DNA repair processes, and the arrest of cell cycle progression may provide time for the repair of DNA damage. This chapter highlights recent studies on the pathways that modulate p53 stability and activity in response to genotoxic and nongenotoxic stresses through covalent posttranslational modifications to p53 including the phosphorylation of serine and threonines and the acetylation of lysines.

Publisher Summary This chapter describes the preparation of a cell-free protein-synthesizing system from wheat germ. Crude extracts of commercial wheat germ are known to be capable of translating a wide variety of messenger RNAs. Most wheat germ extracts have low endogenous activity. If necessary, endogenous activity may be further reduced by a preincubation step with creatine phosphokinase or by treatment with micrococcal nuclease. Even with extracts that have a relatively high endogenous activity as determined by the incorporation of radioactive amino acids, few if any endogenous protein bands are observed on SDS-polyacrylamide gels. HEPES should be stored frozen in small aliquots; it supports microbial growth and it is not stable to autoclaving. One should also remember that the buffer supplies some potassium that has not been accounted for in the concentrations given.

Publisher Summary This chapter describes the preparation of a cell-free protein-synthesizing system from wheat germ. Crude extracts of commercial wheat germ are known to be capable of translating a wide variety of messenger RNAs. Most wheat germ extracts have low endogenous activity. If necessary, endogenous activity may be further reduced by a preincubation step with creatine phosphokinase or by treatment with micrococcal nuclease. Even with extracts that have a relatively high endogenous activity as determined by the incorporation of radioactive amino acids, few if any endogenous protein bands are observed on SDS-polyacrylamide gels. HEPES should be stored frozen in small aliquots; it supports microbial growth and it is not stable to autoclaving. One should also remember that the buffer supplies some potassium that has not been accounted for in the concentrations given.

Publisher Summary This chapter reviews that in Escherichia coli , site-specific cleavages by RNase III are the initial events in the processing of rRNAs and are also responsible for generating the individual “early” mRNAs of bacteriophages T7 and T3. Using purified E. coli RNA polymerase and RNase III, it is possible to synthesize in vitro early T7 and T3 mRNAs that are identical to those found in infected cells. RNase III cleavage of rRNA and early mRNA takes place at specific processing signals that are present in the RNA itself. It discusses that enzymes similar to E. coli RNase III might be found in other organisms. One approach to identifying a RNase-III-type enzyme in a source other than E. coli is to ask whether extracts prepared from the organism contain an activity that will faithfully process T7 and T3 early RNAs. A complementary approach would be to test a putative precursor RNA with RNase III from E. coli to see whether the RNA contains processing signals and whether specific products are generated. The chapter summarizes some aspects of T7 and T3 early RNA processing and the properties of E. coli RNase III that is useful in studies of this type.

Out of a group of 1300 photographs of cosmic-ray tracks in a vertical Wilson chamber 15 tracks were of positive particles which could not have a mass as great as that of the proton. From an examination of the energy-loss and ionization produced it is concluded that the charge is less than twice, and is probably exactly equal to, that of the proton. If these particles carry unit positive charge the curvatures and ionizations produced require the mass to be less than twenty times the electron mass. These particles will be called positrons. Because they occur in groups associated with other tracks it is concluded that they must be secondary particles ejected from atomic nuclei.

Publisher Summary This chapter describes the nature of cosmic-ray particles. Measurements of the energy loss of particles occurring in the cosmic ray showers have shown that this loss is proportional to the incident energy and is within the range of the measurements. It has been known for a long time that there exist particles of both penetrating and non-penetrating types. Crussard and Leprince–Ringuet have shown that either the absorption law changes with energy or that there is a difference in character among the particles. Independent evidence indicating the existence of particles of a new type has already been found, based on range, curvature, and ionization relations. Excellent experimental evidence showing the existence of particles less massive than protons, but more penetrating than electrons obeying the Bethe–Heitler theory, has just been reported by Street and Stevenson.

Cloud chamber photographs of cosmic-ray tracks in a magnetic field up to 17,000 gauss are shown. On the assumption that the particles producing the tracks are traveling downward through the chamber rather than upward, particles of positive charge appear as well as electrons. From the specific ionization along the track it is concluded that the positives are protons, and are not nuclei of charge greater than unity. No evidence is uncovered demanding the introduction of a neutron for cosmic-ray phenomena. Eight examples of associated tracks are shown. Energies range from below 10 6 electron-volts to values in a few cases of the order of 10 9 electron-volts. Energy values for 70 tracks are listed. The scattering of cosmic particles in traversing a 6.0 mm lead plate is measured.