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Floods from failures of landslide dams can pose a hazard to people and property downstream, which have to be rapidly assessed and mitigated in order to reduce the potential risk. The Tangjiashan landslide dam induced by the Mw = 7.9 2008 Wenchuan earthquake had impounded the largest lake in the earthquake affected area with an estimated volume of 3 × 108 m3, and the potential catastrophic dam breach posed a serious threat to more than 2.5 million people in downstream towns and Mianyang city, located 85 km downstream. Chinese authorities had to evacuate parts of the city until the Tangjiashan landslide dam was artificially breached by a spillway, and the lake was drained. We propose an integrated approach to simulate the dam-breach floods for a number of possible scenarios, to evaluate the severity of the threat to Mianyang city. Firstly, the physically-based BREACH model was applied to predict the flood hydrographs at the dam location, which were calibrated with observational data of the flood resulting from the artificial breaching. The output hydrographs from this model were inputted into the 1-D–2-D SOBEK hydrodynamic model to simulate the spatial variations in flood parameters. The simulated flood hydrograph, peak discharge and peak arrival time at the downstream towns fit the observations. Thus this approach is capable of providing reliable predictions for the decision makers to determine the mitigation plans. The sensitivity analysis of the BREACH model input parameters reveals that the average grain size, the unit weight and porosity of the dam materials are the most sensitive parameters. The variability of the dam material properties causes a large uncertainty in the estimation of the peak flood discharge and peak arrival time, but has little influence on the flood inundation area and flood depth downstream. The effect of cascading breaches of smaller dams downstream of the Tangjiashan dam was insignificant, due to their rather small volumes, which were only 2% of the volume of the Tangjiashan lake. The construction of the spillway was proven to have played a crucial role in reducing the dam-breach flood, because all the other natural breach scenarios would have caused the flooding of the downstream towns and parts of Mianyang city. However, in retrospect improvements on the spillway design and the evacuation planning would have been possible. The dam-break flood risk will be better controlled by reducing the spillway channel gradient and the porosity of the coating of the channel bottom. The experience and lessons we learned from the Tangjiashan case will contribute to improving the hazard mitigation and risk management planning of similar events in future.

A novel process for preparing non-pyrogenic toxoids of pertussis toxin (PT) and filamentous hemagglutinin (FHA) is described. The process consists of chromatographies on perlite then on hydroxylapatite. Purification yields for PT and FHA are 62 and 68%, respectively. The purification process takes advantage of the novel use of perlite (a filter aid) for the simultaneous purification of PT and FHA. The hydroxylapatite, in addition to removing the remaining contaminants, also concentrates the antigens. The resulting PT and FHA are approximately 95% pure, and are non-pyrogenic as judged by the rabbit pyrogen test. The purification process is simple, inexpensive, and does not use blood components or toxic substances. The mild conditions in which the PT and FHA are purified ensure the recovery of native protein. The purified PT and FHA are detoxified in the presence of glycerol using glutaraldehyde and formaldehyde, respectively, to produce antigenic components of an acellular pertussis vaccine. The final PT and FHA toxoids are immunogenic in guinea-pigs and have been shown to be protective in the mouse intracerebral challenge test.

Proton NMR was used to study the secondary structure and melting behavior of six self-complementary oligoribonucleotide tetramers, each containing two guanosine and two cytidine residues (GGCC, CCGG, GCCG, CGGC, GCGC, and CGCG). GGCC and CCGG formed perfect duplexes containing four G.C base pairs with Tms of 54 and 47.8 degrees C, respectively; GCCG and CGGC formed staggered duplexes with two G.C base pairs and four 3' double-dangling bases, with Tms of 35.5 and 29.2 degrees C, respectively; GCGC formed a perfect duplex with a Tm of 49.9 degrees C, while CGCG formed a staggered duplex with a Tm of 36.9 degrees C. From these results, an order of stability of the cores containing two G.C base pairs was proposed: GC:GC is more stable than GG:CC which is more stable than CG:CG. The RY model for secondary structure stability prediction was applied to the above tetramers with reasonable success. Suggestions for refinements are discussed.

The stabilizing effects of dangling ends and terminal base pairs on the core helix GCGC are reported. Enthalpy and entropy changes of helix formation were measured spectrophotometrically for AGCGCU, UGCGCA, GGCGCCp, CGCGCGp, and the corresponding pentamers XGCGCp and GCGCYp containing the GCGC core plus a dangling end. Each 5' dangling end increases helix stability at 37 degrees C roughly 0.2 kcal/mol and each 3' end from 0.8 to 1.7 kcal/mol. The free energy increments for dangling ends on GCGC are similar to the corresponding increments reported for the GGCC core [Freier, S. M., Alkema, D., Sinclair, A., Neilson, T., & Turner, D. H. (1985) Biochemistry 24, 4533-4539], indicating a nearest-neighbor model is adequate for prediction of stabilization due to dangling ends. Nearest-neighbor parameters for prediction of the free energy effects of adding dangling ends and terminal base pairs next to G.C pairs are presented. Comparison of these free energy changes is used to partition the free energy of base pair formation into contributions of "stacking" and "pairing". If pairing contributions are due to hydrogen bonding, the results suggest stacking and hydrogen bonding make roughly comparable favorable contributions to the stability of a terminal base pair. The free energy increment associated with forming a hydrogen bond is estimated to be -1 kcal/mol of hydrogen bond.

Variable temperature 1H-nuclear magnetic resonance (NMR) has been used to study the interaction of the RNA trimer, GpCpA, with the intercalators ethidium bromide and the acridine derivatives; proflavin, 9-amino-acridine, acridine orange, acridine yellow and acriflavin. The complexes formed were studied at nucleic acid to drug ratios of 1:1 and 5:1, the latter being useful in defining the effects of structural variation in the acridine series and in determining the site of intercalation. All the intercalators greatly stabilized the oligonucleotide duplex, the average melting temperature (Tm) increasing by up to 30 degrees C. Significant changes in individual Tms and chemical shifts were observed for all the GpCpA protons. 9-Amino-acridine and acriflavin did not stabilize the GpCpA duplex as substantially as the other acridine derivatives. It is suggested that this intercalator:GpCpA system, and its associated NMR-derived Tm, is a useful physical probe for potential mutagens.

The role of stacking in terminal base-pair formation was studied by comparison of the stability increments for dangling ends to those for fully formed base pairs. Thermodynamic parameters were measured spectrophotometrically for helix formation of the hexanucleotides AGGCCUp, UGGCCAp, CGGCCGp, GCCGGCp, and UCCGGAp and for the corresponding pentanucleotides containing a 5'-dangling end on the GGCCp or CCGGp core helix. In 1 M NaCl at 1 X 10(-4) M strands, a 5'-dangling nucleotide in this series increases the duplex melting temperature (Tm) only 0-4 degrees C, about the same as adding a 5'-phosphate. In contrast, a 3'-dangling nucleotide increases the Tm at 1 X 10(-4) M strands 7-23 degrees C, depending on the sequence [Freier, S. M., Burger, B. J., Alkema, D., Neilson, T., & Turner, D. H. (1983) Biochemistry 22, 6198-6206]. These results are consistent with stacking patterns observed in A-form RNA. The stability increments from terminal A.U, C.G, or U.A base pairs on GGCC or a terminal U.A pair on CCGG are nearly equal to the sums of the stability increments from the corresponding dangling ends. This suggests stacking plays a large role in nucleic acid stability. The stability increment from the terminal base pairs in GCCGGCp, however, is about 5 times the sum of the corresponding dangling ends, suggesting hydrogen bonding can also make important contributions.

A series of pentaribonucleotides, ApGpXpGpU (where X identical to A, G, C, or U), was synthesized to investigate the effects of flanking G . C pairs on internal Watson-Crick, G . U, and nonbonded base pairs. Sequences ApGpApCpU (Tm = 26 degrees C) and ApGpCpCpU (Tm = 25 degrees C) were each found to form a duplex with non-base-paired internal residues that stacked with the rest of the sequence but were not looped out. ApGpGpCpU also forms a duplex (Tm = 30 degrees C) but with dangling terminal nonbonded adenosines rather than internal nonbonded guanosines. ApGpUpCpU prefers a stacked single-strand conformation. In addition, contribution to duplex stability from an internal A . U or G . C base pair is enhanced by 6 degrees C when flanked by G . C base pairs as compared to A . U base pairs. G . C base pairs flanking an internal G . U base pair were found to be more tolerant to the altered conformation of a G . U pair and result in an increase to stability comparable with that found for an internal A . U base pair.

A set of empirical parameters which allows the prediction of the proton NMR chemical shifts at 70 C of non-exchangeable heterobase and anomeric protons in oligoribonucleotides has been constructed. The set is based on the highly flexible nature of oligoribonucleotide single strands and the wide range of conformational states which can be populated at relatively high temperatures (70 C or greater). A pairwise subtractive procedure, using 129 ribonucleotide oligomers (all 16 dimers, all 64 trimers, 37 tetramers, and 12 pentamers), shows that significant contributions to the observed chemical shift of protons in a given nucleoside residue are made by first, second, and third neighbors on the 3' and the 5' sides. The majority of the neighbors cause shielding effects with the exception of some first neighbors on the 5' side of a given residue. The magnitude of the shielding effects is greatest for the purine heterobases and follows the order A greater than G greater than C greater than U, with first neighbors on the 3'side showing more pronounced effects than second neighbors and these in turn showing larger effects than third neighbors. Second neighbors on the 5' side showed consistently greater shieldings than first neighbors, a result attributed to the deshielding effects of the first 5' neighbor phosphate group. The parameter Tables are applied to the prediction of proton chemical shifts in one heptamer, four hexamers, and two pentamers and give average absolute differences between predicted and observed shifts less than 0.030 ppm. The parameter approach represents an excellent method of generating initial assignments of proton chemical shifts for any single strand oligoribonucleotide.

Variable temperature proton nuclear magnetic resonance spectroscopy is used to establish that both sequence and dangling bases affect stability of short RNA double helices. Tetraribonucleotides, CAUG, UGCA and AGCU form reference duplexes (Tm 25 degrees, 33 degrees, 34 degrees, respectively) which contain an equal number of G . C and A . U base pairs and which show primary sequence is important. Pentaribonucleotides GAUGA, ACAUG, UGCAA and AGCUA, form duplexes (Tm 36 degrees, 35 degrees, 46 degrees, 45 degrees, respectively) with dangling adenines. Average Tm difference from the reference is +11 degrees for two 3' or 5'-dangling adenines. Pentaribonucleotides, CAUGU and UCAUG, form duplexes (Tm both 30 degrees) with dangling uracils. Average Tm difference from the reference is +5 degrees for two 3' or 5'-dangling uracils. Fraying was detected only in duplexes from the AGCU series. Presence of a dangling adenine, in duplex, AGCUA, caused a reduction in fraying.