Discussion on “Instrumented difference-in-differences” by Ye,Ertefaie, Flory,Hennessy, Small

Ye, Ertefaie, Flory, Hennessy, and Small (YEFHS) proposed a new method, instrumented difference-in-differences, for dealing with unmeasured confounding. In this note, I connect and compare assumptions and identifications in instrumental variable (IV) and difference-in-differences (DID) methods with those in YEFHS, derive new identification results, and discuss different choices when extending such results to adjust for covariates.     

Reliability of Analyses of Hg,Fe, Ca,K, P,pH, Alkalinity,Conductivity, Hardness and Colour from Lakes

The aim of this report has been to present results concerning analytical quality controls of Hg analysis of fish and sediment, analyses of Fe, Ca, total-P, K, pH, alkalinity, conductivity, colour and hardness (Ca + Mg) of lake water samples. Despite the fact that these are standard parameters in many regular water control programs, there are major differences in the reliability with which these parameters can be determined. The focus here is on an overall inter-laboratory comparison between the parameters. Six laboratories have been involved in the analysis. Selected results: pH gives the lowest (average) relative standard deviation (error), about 2 %; conductivity gives an error of about 5–7 %; alkalinity yields an average error of as much as 13–25 %, which is the largest among the parameters studied here; colour also gives a high error, 9–15 %; hardness gives a relative standard deviation of about 6–7 %. Of the other parameters (i. e., Hg, Fe, Ca and P), Hg gives the best reliability and Fe and P the lowest. To have knowledge of the reliability of the analytical data is of paramount importance in most control programs and research projects.     

Functional recA, lexA, umuD, umuC, polA, and polB genes are not required for the Escherichia coli UVM response.

The Escherichia coli UVM response is a recently described phenomenon in which pretreatment of cells with DNA-damaging agents such as UV or alkylating agents significantly enhances mutation fixation at a model mutagenic lesion (3,N4-ethenocytosine; epsilon C) borne on a transfected M13 single-stranded DNA genome. Since UVM is observed in delta recA cells in which SOS induction should not occur, UVM may represent a novel, SOS-independent, inducible response. Here, we have addressed two specific hypothetical mechanisms for UVM: (i) UVM results from a recA-independent pathway for the induction of SOS genes thought to play a role in induced mutagenesis, and (ii) UVM results from a polymerase switch in which M13 replication in treated cells is carried out by DNA polymerase I (or DNA polymerase II) instead of DNA polymerase III. To address these hypotheses, E. coli cells with known defects in recA, lexA, umuDC, polA, or polB were treated with UV or 1-methyl-3-nitro-1-nitrosoguanidine before transfection of M13 single-stranded DNA bearing a site-specific ethenocytosine lesion. Survival of the transfected DNA was measured as transfection efficiency, and mutagenesis at the epsilon C residue was analyzed by a quantitative multiplex DNA sequencing technology. Our results show that UVM is observable in delta recA cells, in lexA3 (noninducible SOS repressor) cells, in LexA-overproducing cells, and in delta umuDC cells. Furthermore, our data show that UVM induction occurs in the absence of detectable induction of dinD, an SOS gene. These results make it unlikely that UVM results from a recA-independent alternative induction pathway for SOS gene.     

Cover Image,Volume 116, Number 3, March 2019

Transglutaminase (TGase) induces the cross-linking of proteins by catalyzing an acyl transfer reaction. TGase is a zymogen, activated by the removal of its pro-region. Because the pro-region is crucial for folding and inhibition of the TGase activity, the recombinant expression of the mature TGase (mTGase) without the pro-region, usually results in inactive inclusion bodies or low protein yield. Here, Streptomyces netropsis TGase was fused with Escherichia coli lysyl-tRNA synthetase (LysRS), as a module with chaperoning activity in an RNA dependent manner (chaperna). The TGase activity from purified fusion protein induced via the removal of LysRS by tev protease in vitro. Moreover, active mTGase was produced in E. coli via an intracellular cleavage system, wherein LysRS-mTGase was cleaved by the coexpressed tev protease in vivo. The results suggest that LysRS essentially mimics pro-region, which exerts a dual function—folding of TGase into active conformation and keeping it as dormant state—in an RNA-dependent manner. Thus, trans-acting RNAs, prompt the cis-acting chaperone function of LysRS, while being mechanistically similar to the intramolecular chaperone function of the pro-region. These results could be implemented and extended for the folding of “difficult-to-express” recombinant proteins, by harnessing the chaperna function.     

Indoor air microbiological evaluation of offices, hospitals, industries, and shopping centers

In this study it was compared the MAS-100 and the Andersen air samplers' performances and a similar trend in both instruments was observed. It was also evaluated the microbial contamination levels in 3060 samples of offices, hospitals, industries, and shopping centers, in the period of 1998 to 2002, in Rio de Janeiro city. Considering each environment, 94.3 to 99.4% of the samples were the allowed limit in Brazil (750 CFU/m3). The industries' results showed more important similarity among fungi and total heterotrophs distributions, with the majority of the results between zero and 100 CFU/m3. The offices' results showed dispersion around 300 CFU/m3. The hospitals' results presented the same trend, with an average of 200 CFU/m3. Shopping centers' environments showed an average of 300 CFU/m3 for fungi, but presented a larger dispersion pattern for the total heterotrophs, with the highest average (1000 CFU/m3). It was also investigated the correlation of the sampling period with the number of airborne microorganisms and with the environmental parameters (temperature and air humidity) through the principal components analysis. All indoor air samples distributions were very similar. The temperature and air humidity had no significant influence on the samples dispersion patterns.     

Interaction between ATP,metal ions,glycine, and several minerals

Summary The adsorption of ATP and ADP on montmorillonite, kaolinite, and A1(OH)₃ was studied as a funtion of pH and, for montmorillonite and kaolinite, as a funtion of the ionic composition of the system. The three minerals exhibit different adsorption charcteristics. Mg²⁺- and Zn²⁺-montmorillonite adsorb ATP and ADP more than Na⁺-montmorillonite, presumably because of complex formation. In kaolinite, the effect of these divalent cations is small. Pure ATP decomposes upon heating, and the rate of the decomposition is accelerated by the presence of glycine. Drying and heating glycine to 70°C under vacuum in the presence of ATP results in abiotic peptide formation with yields up to 0.25%. This peptide formation also occurs when kaolinite or montmorillonite is added to the system. The presence of kaolinite, Mg²⁺-or Zn²⁺-koalinite, or Mg²⁺-montmorillonite results in a reduction in the rate of the ATP decomposition in the abiotic peptide synthesizing system. These results suggest that one role for clays and metal ions in chemical evolution may have been the stabilization of nucleotides during prebiotic peptide synthesis.On Leave from the Hebrew University of Jerusalem, Israel     

Hydralazine,antinuclear antibodies,and the lupus syndrome.

The incidence of patients with positive antinuclear antibody test results rose during three years of treatment with hydralazine. At the end of that period over half of the patients (both rapid and slow acetylators) had titres exceeding 1/20, but the rate of rise was faster in the slow acetylators than in the rapid. There was a significant relation between the cumulative dose of hydralazine and the proportion of patients found to have antinuclear factors. Fewer black patients had positive test results than white. Patients whose antinuclear antibody test results changed fron negative to positive during the study showed this change five to 26 months after beginning treatment. Some patients showed a substantial fall in antinuclear antibody titre even though hydralazine was continued. From these findings patients in whom test results for antinuclear antibody became positive during treatment with hydralazine need not have the drug stopped unless they have clinical features of the lupus syndrome.     

PKC-regulated myogenesis is associated with increased tyrosine phosphorylation of FAK,Cas, and paxillin,formation of Cas-CRK complex,and JNK activation

Previous reports suggest that PKC plays an important role in regulating myogenesis. However, the regulatory signaling pathways are not fully understood. We examined the effects of PKC downregulation on signaling events during skeletal muscle differentiation. We found that downregulation of PKC results in increased myogenesis in C2C12 cells as measured by creatine kinase activity and myogenin expression. We showed that, during differentiation, downregulation of PKC expression results in increased tyrosine phosphorylation of FAK, Cas, and paxillin, concomitant with enhanced Cas-CrkII complex formation, which leads to activation of JNK2. But in proliferated muscle cells, PKC inhibition results in FAK and Cas tyrosine dephosphorylation. Further, disruption of actin cytoskeleton by cytochalasin D prevents the activation of FAK and Cas as well as the formation of Cas-CrkII complex stimulated by PKC downregulation during muscle cell differentiation. Finally, we observed that PKC downregulation increases the tyrosine phosphorylation of focal adhesion associated proteins. Based on the above data, we propose that PKC downregulation results in enhanced tyrosine phosphorylation of FAK, Cas, and paxillin, thus promoting the establishment of Cas-CrkII complex, leading to activation of JNK and that these interactions are dependent upon the integrity of actin cytoskeleton during muscle cell differentiation. Data presented here significantly contribute to elucidating the regulatory role of PKC in myogenesis possibly through integrin signaling pathway.     

Cover Image,Volume 87, Issue 12

CASP (critical assessment of structure prediction) assesses the state of the art in modeling protein structure from amino acid sequence. The most recent experiment (CASP13 held in 2018) saw dramatic progress in structure modeling without use of structural templates (historically “ab initio” modeling). Progress was driven by the successful application of deep learning techniques to predict inter-residue distances. In turn, these results drove dramatic improvements in three-dimensional structure accuracy: With the proviso that there are an adequate number of sequences known for the protein family, the new methods essentially solve the long-standing problem of predicting the fold topology of monomeric proteins. Further, the number of sequences required in the alignment has fallen substantially. There is also substantial improvement in the accuracy of template-based models. Other areas—model refinement, accuracy estimation, and the structure of protein assemblies—have again yielded interesting results. CASP13 placed increased emphasis on the use of sparse data together with modeling and chemical crosslinking, SAXS, and NMR all yielded more mature results. This paper summarizes the key outcomes of CASP13. The special issue of PROTEINS contains papers describing the CASP13 assessments in each modeling category and contributions from the participants.     

A revised probability matrix for the identification of gram-negative, aerobic, rod-shaped, fermentative bacteria

The results of the identification of 933 strains of Gram-negative, aerobic, rod-shaped, fermentative bacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae) by a probabilistic method, in a computer, are given. The identification rate on the matrix was 89.2%. Many of the strains were atypical and had caused difficulty in identification in medical diagnostic laboratories. The results are given for each taxon by genus and species.     

Knock-in and knock-out. Transgenes, Development and Disease: A Keystone Symposium sponsored by Genentech and Immunex, Tamarron, CO, USA, January 12-18, 1991

The meeting clearly reflected the recent rapid and staggering progress in the use of transgenic mice. Being able to manipulate single units of genetic information in their natural position in a cell genome and to examine the results of that manipulation in the background of a terminally differentiated organism has been an outstanding achievement on the road toward a deeper and generalizable understanding of complex life forms. However, there are many examples of genetic diseases in humans (for instance, Lesh-Nyhan syndrome, Duchenne muscular dystrophy, phenylketonuria) whose genotypic "equivalent" in transgenic mice results in very different phenotypes or no phenotypic changes at all. Mice are clearly not human beings. Why not? No doubt, we will find out!     

Cryptochrome, phytochrome, and anthocyanin production

Anthocyanin production in cabbage (Brassica oleracea L.) and tomato (Lycopersicon esculentum Mill.) seedlings exposed to prolonged irradiations was studied under conditions that allowed discrimination, within certain limits, between the contribution of cryptochrome and phytochrome in the photoregulation of the response. The results of the study provide confirming evidence for the involvement of cryptochrome and direct evidence for a significant contribution of cryptochrome to the fluence rate dependence of the response to blue. The results provide some preliminary, direct indication for an interaction between cryptochrome and phytochrome in the photoregulation of anthocyanin production in seedlings exposed to the prolonged irradiations required for a high level of expression of the response. The type and degree of interaction between the two photoreceptors vary significantly, depending on the species and experimental conditions.     

Cover Image,Volume 120, Number 8, August 2019

Circular RNAs (circRNAs) are novel noncoding RNAs and play crucial roles in various biological processes. However, little is known about the functions of circRNAs in osteogenic differentiation. The current study aimed to investigate the differential expression of circRNAs in rat dental follicle cells (rDFCs) during osteogenic differentiation, identified by RNA high-throughput sequencing and quantitative real-time polymerase chain reaction. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to further explore the biofunctions of circRNA biofunctions. Two hundred sixty-six differentially-expressed circRNAs that are involved in several important signaling pathways, including mitogen-activated protein kinases (MAPK) and transforming growth factor-β (TGF-β) signaling pathways were revealed. Among these, circFgfr2 and its predicted downstream targets, miR-133 and BMP6 (bone morphogenetic protein-6), were identified both in vivo and in vitro. For further validation, circFgfr2 was overexpressed in rDFCs, the results showed that the expression of miR-133 was downregulated and the expression of BMP6 was upregulated. Taken together, the results revealed the circRNA expression profiles and indicated the importance of circRNAs of rDFCs. In addition, circFgfr2 might promote osteogenesis by controlling miR-133/BMP6, which is a potential new target for the manipulation of tooth regeneration and bone formation.     

Proteolytic activity,synapse elimination,and the Hebb synapse

The Hebb synapse has been postulated to serve as a mechanism subserving both regulation of synaptic strength in the adult nervous system (long-term potentiation and depression) and developmental activity-dependent plasticity. According to this model, pre- and postsynaptic temporal concordance of activity results in strengthening of connections, while discordant activity results in synapse weakening. Evidence is presented that proteases and protease inhibitors may be involved in modification of synaptic strength. This leads to a modification of the Hebb assumptions, namely that postsynaptic activity results in protease elaboration with a consequent general reduction of synaptic connections to the active postsynaptic element. Further, presynaptic activity, if strong enough, induces local release of a protease inhibitor, such as protease nexin I, which neutralizes proteolytic activity and produces a relative preservation of the active input. This formulation produces many of the effects of the classical Hebbian construction, but the protease/inhibitor model suggests additional specific mechanistic features for activity-dependent plasticity. 1994 John Wiley & Sons, Inc.     

Amino-acid interactions in psychrophiles, mesophiles, thermophiles, and hyperthermophiles: insights from the quasi-chemical approximation

We investigate the mechanisms used by proteins to maintain thermostability throughout a wide range of temperatures. We use the quasi-chemical approximation to estimate interaction strengths for psychrophiles, mesophiles, thermophiles, and hyperthermophiles. Our results highlight the importance of core packing in thermophilic stability. Although we observed an increase in the number of charged residues, the contribution of salt bridges appears to be relatively modest by comparison. We observed results consistent with a gradual loosening of structure in psychrophiles, including a weakening of almost all types of interactions.     

Conductometric evaluation of interactions of electrolytes with D-glucitol, D-glucose, glycerol, D-mannitol, and sucrose

By measurement of the conductance of various electrolytes in solutions of D-glucitol, D-glucose, glycerol, D-mannitol, and sucrose, the hydration of the polyhydroxy compounds and their association with electrolytes have been examined. The results have been analyzed in the light of conductance equations; it was found that D-glucose and sucrose associate with electrolytes, glycerol and D-mannitol are practically inert, and D-glucitol is only rarely bound. The association constants are of the order of 10^?1 to 10^?2. The results indicate that anions guide the process, with a free-energy change of 1.5–3.0 kcal.mole^-1, the order of the energy of hydrogen bonding. In the analysis of conductance data, neglect of association may introduce hydration numbers many times greater than are usual.     

Parsimony, likelihood, and simplicity

The latest charge against parsimony in phylogenetic inference is that it involves estimating too many parameters. The charge is derived from the fact that, when each character is allowed a branch length vector of its own (instead of the homogeneous branch lengths assumed in current likelihood models), the results for likelihood and parsimony are identical. Parsimony, however, can also be derived from simpler models, involving fewer parameters. Therefore, parsimony provides (as many authors had argued before) the simplest explanation of the data, or the most realistic, depending on one's views. If (as argued by likelihoodists) phylogenetic inference is to use the simplest model that provides sufficient explanation of the data, the starting point of phylogenetic analyses should be parsimony, not maximum likelihood. If the addition of new parameters (which increase the likelihood) to a parsimony estimation is seen as desirable, this may lead to a preference for results based on current likelihood models. If the addition of parameters is continued, however, the results will eventually come back to the same place where they had started, since allowing each character a branch length of its own also produces parsimony. Parsimony can be justified by very different types of models—either very complex or very simple. This suggests that parsimony does have a unique place among methods of phylogenetic estimation.     

Photosynthesis of ATP-electrons,proton pumps,rotors, and poise

Light-driven electron transport is coupled to ATP synthesis in chloroplasts. While the nature of the coupling and the structures of key components are now known, there has long been disagreement over pathways of electron transport. Recent results now put an old idea back on the agenda-cyclic electron transport around photosystem I.     

Preconception cystic fibrosis carrier couple screening: impact,understanding, and satisfaction

The impact, understanding of test-results, and satisfaction among participating couples in a preconception cystic fibrosis (CF) carrier screening project were assessed 6 months after testing. Questionnaire data were obtained from 17/18 identified carriers, 15 partners of carriers with negative test results, and 794 (73%) other participants. None of the carriers changed their reproductive plans because of their test results. Eight participants were worried about their results, including four carriers. Those who attended a general practitioner (GP) consultation for pretest education were less worried than those who attended an educational session. Seven carriers felt less healthy. Predictors of a correct understanding of test results (correct in 62% of participants) were: positive test results, high level of knowledge of CF, high level of education, attending an educational session, and previously heard of CF. All participants who reported that they were worried, all carriers, and 95% of the other participants said that they would make the same decision to be tested again. Although couples who were educated during a GP consultation were less worried, the results of the study suggest that understanding is more correct in couples attending an educational session. The results further suggest that since satisfaction with the screening was high, worries and feeling less healthy due to the test results are probably not a great burden.