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The nematode Caenorhabditis elegans is a research model organism particularly suited to the mechanistic understanding of synapse genesis in the nervous system. Armed with powerful genetics, knowledge of complete connectomics, and modern genomics, studies using C. elegans have unveiled multiple key regulators in the formation of a functional synapse. Importantly, many signaling networks display remarkable conservation throughout animals, underscoring the contributions of C. elegans research to advance the understanding of our brain. In this chapter, we will review up-to-date information of the contribution of C. elegans to the understanding of chemical synapses, from structure to molecules and to synaptic remodeling., Competing Interests: Conflicts of interest: None declared., (© The Author(s) 2023. Published by Oxford University Press on behalf of the Genetics Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Background: Total pancreatectomy is required to completely clear tumours that are locally advanced or located in the centre of the pancreas. However, reports describing clinical outcomes after total pancreatectomy are rare. The aim of this retrospective observational study was to assess clinical outcomes following total pancreatectomy using a nationwide registry and to create a risk model for severe postoperative complications., Methods: Patients who underwent total pancreatectomy from 2013 to 2017, and who were recorded in the Japan Society of Gastroenterological Surgery and Japanese Society of Hepato-Biliary-Pancreatic Surgery database, were included. Severe complications at 30 days were defined as those with a Clavien-Dindo grade III needing reoperation, or grade IV-V. Occurrence of severe complications was modelled using data from patients treated from 2013 to 2016, and the accuracy of the model tested among patients from 2017 using c-statistics and a calibration plot., Results: A total of 2167 patients undergoing total pancreatectomy were included. Postoperative 30-day and in-hospital mortality rates were 1·0 per cent (22 of 2167 patients) and 2·7 per cent (58 of 167) respectively, and severe complications developed in 6·0 per cent (131 of 2167). Factors showing a strong positive association with outcome in this risk model were the ASA performance status grade and combined arterial resection. In the test cohort, the c-statistic of the model was 0·70 (95 per cent c.i. 0·59 to 0·81)., Conclusion: The risk model may be used to predict severe complications after total pancreatectomy., (© 2020 BJS Society Ltd Published by John Wiley & Sons Ltd.)

A large body of epidemiologic research has concentrated on the 1918 influenza pandemic, but more work is needed to understand spatial variation in pandemic mortality and its effects on natality. We collected and analyzed 35,151 death records from Arizona for 1915-1921 and 21,334 birth records from Maricopa county for 1915-1925. We estimated the number of excess deaths and births before, during, and after the pandemic period, and we found a significant decline in the number of births occurring 9-11 months after peak pandemic mortality. Moreover, excess mortality rates were highest in northern Arizona counties, where Native Americans were historically concentrated, suggesting a link between ethnic and/or sociodemographic factors and risk of pandemic-related death. The relationship between birth patterns and pandemic mortality risk should be further studied at different spatial scales and in different ethnic groups.

The radiosensitizing effects of PR-350, a nitroimidazole derivative, were examined concerning the cell killing of human pancreatic cancer cell lines exposed to high doses of gamma-ray irradiation in vitro. The percentages of dead cells were analyzed with a multiwell plate reader to measure the fluorescence intensity of propidium iodide before and after a digitonin treatment. The sensitizing effect of PR-350 on cell killing by high-dose irradiation was confirmed by time-course, dose-dependency, and microscopic observations. In five of seven pancreatic cancer cell lines in which the number of dead cells was determined 5 days after 30 Gy irradiation in the presence of PR-350, the number was significantly increased under hypoxic conditions, but not under aerobic conditions. The selective radiosensitive effect of PR-350 on hypoxic cells was also confirmed by flow cytometry. The results indicate that PR-350 can enhance the killing of pancreatic cancer cells by high-dose irradiation under hypoxia, which supports its clinical radiosensitizing effects when administered during intraoperative irradiation to pancreatic cancer.

ATP hydrolysis is required for transcriptional initiation by RNA polymerase II in vitro. Reconstituted transcription using purified initiation factors and RNA polymerase II have revealed that the step dependent on ATP hydrolysis occurs at the same time as initiation of RNA synthesis. We report here that ATP hydrolysis is also required for formation of the preinitiation complex in crude extracts. Two distinct preinitiation complexes were identified, one formed in the presence and the other in the absence of ATP. These complexes were isolated by glycerol gradient centrifugation. The preinitiation complex formed in the presence of ATP was able to synthesize transcripts with addition of only ribonucleotide triphosphates, whereas the preinitiation complex formed in the absence of ATP was inactive and required addition of protein fractions and ATP. These results suggest that the inactive preinitiation complex is activated by addition of the protein fractions and ATP hydrolysis. The active preinitiation complex sedimented at approximately 40 S in glycerol gradient centrifugation, a rate similar to that of RNA polymerase II holoenzyme reported by Maldonado et al. [ Nature (1996), 381, 86-89].

Interferon-gamma (IFN-gamma), vitamin D3 (VD), and retinoic acid (RA) induce differentiation of human monoblastic leukemia U937 cells to macrophage-like cells with potential superoxide anion-generating activity upon further stimulation. Here we report that U937 cells thus differentiated show various responses to apoptotic induction with a cytotoxic anti-Fas antibody and tumor necrosis factor (TNF). VD-or RA-treated U937 cells acquired resistance against Fas- or TNF receptor (TNFR)-mediated apoptosis, whereas apoptotic cell death was accelerated in IFN-gamma-treated cells. By flow cytometric analyses, no decrease in expression of surface Fas antigen or p55 TNFR was observed in differentiated U937 cells. Cell surface expression of CD11b was seen only when differentiation was induced with VD or RA but not with IFN-gamma. The growth of VD- or RA-treated cells was retarded but IFN-gamma-treated cells were prolific. These findings suggest that the differentiation state differs with the inducer and that the cellular response to apoptotic induction is closely related to the state including the cell cycle.

The yeast mRNA capping enzyme is composed of 52 (alpha) and 80 kDa (beta) polypeptides, which are responsible for its mRNA guanylyltransferase and RNA 5'-triphosphatase activities, respectively. We isolated the gene encoding the alpha subunit (CEG1) and showed that CEG1 is essential for yeast cell growth [Shibagaki et al., (1992) J. Biol. Chem. 267, 9521-9528]. In this study, CEG1 was expressed in Escherichia coli and the alpha subunit protein was purified to near homogeneity. A [32P]GMP-bound tryptic peptide derived from the recombinant enzyme-[32P]GMP covalent reaction intermediate was converted to a [32P]phosphoryl-peptide through periodate oxidation followed by beta-elimination. Hydrolysis of the [32P]phosphoryl-peptide with alkali resulted in [32P]N epsilon-phospholysine as the only phosphoamino acid, indicating that GMP in the enzyme-GMP complex is bound to a lysine residue via a phosphoamide linkage. Microsequencing of the [32P]GMP-peptide showed that the GMP binding site was located in the region between amino acids 60 and 75, which contained an internal trypsin-resistant lysine at position 70. CEG1 was subjected to site-directed mutagenesis and the mutant proteins were expressed in E. coli. Substitution of His or Ile for Lys70 entirely abolished the enzyme-GMP formation activity, and this mutation was lethal to yeast in vivo, supporting the notion that the active site in the alpha subunit is located at Lys70. Replacement of Lys70 with Arg reduced the ability to form the enzyme-GMP complex; however, yeast cells bearing this allele were not viable. A series of mutations, including 8 amino acid replacements and 3 insertions, near the active site (Lys70-Thr-Asp-Gly motif) were also introduced and the mutant polypeptides were examined for catalytic activity in vitro as well as yeast cell viability in vivo. There was a good correlation between the in vitro and in vivo functions of the mutant proteins, except when Asp72 was replaced with Glu, which allowed formation of the enzyme-GMP complex but failed to support cell growth. The results with Lys70 to Arg and Asp72 to Glu substitutions indicated that guanylyltransfer to RNA and/or additional roles besides cap formation per se are impaired in these mutant proteins.

We have developed an in vitro transcription system using purified Sendai virus particles in which viral mRNA synthesis is almost entirely dependent on the addition of cellular proteins (host factors), one of which can be replaced by highly purified cellular tubulin [Mizumoto et al. (1995) J. Biochem. 117, 527-534]. In this study, to elucidate the function of host factors in transcription, we isolated an active initiation complex as a viral ribonucleoprotein, by incubating virus particles with bovine brain extract in the absence of nucleoside triphosphates, followed by ultracentrifugation. RNA products from the isolated initiation complex contained six mRNA species corresponding to all the virus-encoded genes, and most of them had a 5'-cap structure as well as a 3'-poly(A) tail. Immunoblotting showed that tubulin was specifically associated in the active complex. These data suggest that cellular tubulin, one of the host factors essential for Sendai virus transcription, interacts with the viral ribonucleoprotein to form an active complex at the initiation step.

8-Azido GTP (8-N3 GTP) was demonstrated to be polymerized into RNA by influenza virus-associated RNA polymerase at about one tenth the rate of GTP incorporation. The Km value for the azido analogue of GTP in primer-dependent RNA synthesis was 94 microM whereas Km for the natural substrate, GTP, was 6.7 microM. Upon exposure of a mixture of 8-N3 [alpha-32P]GTP and influenza virus ribonucleoprotein (RNP) complexes to ultraviolet light, the PB1 subunit of viral RNA polymerase was selectively radio-labeled. The photo-labeling of PB1 was competed strongly by GTP and to lesser extents by other nucleoside 5'-triphosphates. These results altogether support the prediction that the substrate-binding site (S site) of influenza RNA polymerase is located on the PB1 protein. In the presence of ApG primer, the 8-N3 GTP binding was reduced to about 40% level, suggesting that the GTP analogue can bind not only to the S site but also to the primer- and product-binding site (P site).

To elucidate the mechanism of transcription and replication of Sendai virus, we developed an efficient and faithful in vitro transcription system using purified virus particles. The in vitro RNA synthesis was almost entirely dependent on the addition of eukaryotic cell extracts, including those from various cultured mammalian cells, mammalian tissues, and even from plant cells. The RNA products were almost identical to authentic mRNA species synthesized in the infected cells, in their size distribution, the presence of 3'-poly(A) tail and the presence of methylated 5'-cap structure (m7GpppAm). Ribonuclease protection experiments after annealing the in vitro RNA with viral genomic RNA (vRNA) indicated that the virion-associated RNA-dependent RNA polymerase transcribes correct regions of the RNA genome in vitro. The active component(s) that is required for Sendai virus mRNA synthesis was partially purified from bovine brain and was separated into at least two complementary fractions, one of which could be replaced by highly purified cellular tubulin. When viral ribonucleoprotein complexes were used instead of virus particles in the in vitro transcription, only Sendai virus-infected cell extracts supported mRNA synthesis, and extracts from uninfected cells or cells infected with other viruses were found to be inert. These results suggest that, in addition to the general factors which are present ubiquitously in eukaryotic cells, a factor(s) specific to Sendai virus-infection is required for Sendai virus transcription.

Approximately 700 nucleotide sequences surrounding the transcription initiation site were determined with a cloned rDNA fragment of Tetrahymena pyriformis and the transcription initiation site was localized on these sequences using purified 35S pre-rRNA. A considerable portion of the 35S pre-rRNA was found to be capped in vitro. The 32P-labeled, capped 35S pre-rRNA, on nucleus P1 protection mapping, gave the protection band which is identical in size with that obtained with bulk 35S pre-rRNA. Both reverse transcription extension and nuclease P1 mapping localized the 5'-end of the 35S pre-rRNA at the same adenine nucleotide, 496 base pairs upstream from the HindIII site of the cloned rDNA fragment. Furthermore, sequencing of the 5'-terminal region of the in vitro capped 35S pre-rRNA unambiguously confirmed the above result. The strategy adopted in the present experiment could serve as a general procedure for determining the transcription initiation point even in cases where the concentration of the primary transcript is low.

A rapid-production model incorporating the principle of selection by resistance to cytotoxicity demonstrated earlier for liver carcinogenesis in rats was established for pancreatic carcinoma development in Syrian hamsters. Adenocarcinomas were induced in 84% of treated animals by 10 weeks after initiation with 70 mg of N-nitroso-bis(2-oxopropyl)amine (BOP) per kg of body weight when augmentation pressure (choline-deficient diet combined with DL-ethionine and L-methionine and administration of 20 mg/kg BOP upon return to basal diet) was applied three times. A 52% yield of cholangiocellular tumors also resulted from this experimental protocol.

During the generation of primer for transcription initiation by endonucleolytic cleavage of capped RNA, the influenza virus-associated RNA-dependent RNA polymerase recognizes three signals of capped RNA, i.e., cap-1 structure at 5' termini, RNA sequences at the cleavage sites, and distance between these two signals (Plotch, S.J., Bouloy, M., & Krug, R.M. (1979) Proc. Natl. Acad. Sci. U.S. 76, 1618-1622; Kawakami, K., Mizumoto, K., & Ishihama, A. (1983) Nucl. Acids Res. 11, 3637-3649). The free cap-1 structure, i.e., m7GpppNm not associated with polynucleotides, stimulates the RNA synthesis as well, irrespective of the presence or absence of dinucleotide primers. Since the stimulation by m7GpppNm and ApG is additive and the free cap-1 structure is not incorporated into 5' termini of product RNA, we propose that the cap-1 structure stimulates the RNA polymerase by allosteric modulation rather than by priming the transcription initiation.

DNA fragments complementary to the Newcastle disease virus genome (strain D26) were cloned and sequenced. The sequence of 2,617 nucleotides from the 3' end of the genome was determined and an open reading frame (OP-1) consisting of 1,467 nucleotides, most likely encoding NP protein, was found in this region. This was followed by a second unfinished open reading frame (OP-2) of at least 729 nucleotides which continued beyond the 2,617th nucleotide. Another relatively short (312 nucleotides long) open reading frame (OP-2') was found overlapping with OP-2, but its significance is still unclear. The amino acid sequence deduced from the nucleotide sequence of OP-1 showed a moderate homology to that of the NP protein of Sendai virus in the central portion of the peptide. The leader sequence of 53 nucleotides was also identified. The 5' end of mRNAs synthesized in the infected cells was analyzed and found to be m7GpppA, suggesting that the transcription of viral mRNAs starts with A, but not with G residue.

An in vitro splicing system was constructed using portions of chicken delta-crystallin pre-mRNA synthesized in vitro and a HeLa nuclear extract. Analysis of the reaction products revealed that about 25% of the pre-mRNA was precisely spliced at 30 degrees C in 2 h under the standard conditions. The other major products of the reaction detected were a 5'-exon fragment and three RNA species showing unusual electrophoretic mobilities on polyacrylamide gels. Structural analyses showed that these three RNAs contain a branch (lariat) structure as seen in the in vitro splicing reactions of human beta-globin, adenovirus, and yeast pre-mRNAs. In addition, methylation at the N-7 position of the blocking guanosine of the 5'-terminal cap structure of pre-mRNA has been suggested to play an important role in the splicing reaction.

Catalytic properties of the capped RNA-specific endonuclease associated with the influenza virus RNA polymerase were analyzed with use of synthetic hetero- and homopolymers containing 32P-labeled CAP structures at their 5' termini. The endonuclease displays its intrinsic activity provided that substrate RNA contains both the CAP-1 structure (m7GpppGm) and either A or U residues at 9 to 11 nucleotides distant from the CAP structure. Independent recognition of multiple RNA signals by the endonuclease was further supported by the findings that dinucleotide ApG, free CAP structures and RNA without the CAP structure inhibited the endonuclease activity to different extents. In the presence of four species of ribonucleoside 5'-triphosphates, the endonucleolytically cleaved fragments with the CAP-1 structure were incorporated into polynucleotides, supporting the concept that they are used as the primers for the transcription. The initial nucleotide linked to the primers was a G residue, the nucleotide complementary to the second base of the 3' termini of the vRNA segments.