Amniotes co-opt intrinsic genetic instability to protect germ-line genome integrity

Unlike PIWI-interacting RNA (piRNA) in other species that mostly target transposable elements (TEs), >80% of piRNAs in adult mammalian testes lack obvious targets. However, mammalian piRNA sequences and piRNA-producing loci evolve more rapidly than the rest of the genome for unknown reasons. Here, through comparative studies of chickens, ducks, mice, and humans, as well as long-read nanopore sequencing on diverse chicken breeds, we find that piRNA loci across amniotes experience: (1) a high local mutation rate of structural variations (SVs, mutations ≥ 50 bp in size); (2) positive selection to suppress young and actively mobilizing TEs commencing at the pachytene stage of meiosis during germ cell development; and (3) negative selection to purge deleterious SV hotspots. Our results indicate that genetic instability at pachytene piRNA loci, while producing certain pathogenic SVs, also protects genome integrity against TE mobilization by driving the formation of rapid-evolving piRNA sequences.

Determination of Glyphosate and AMPA in Blood Can Predict the Severity of Acute Glyphosate Herbicide Poisoning

OBJECTIVE

To evaluate a potential association between blood and urine concentration of glyphosate and its metabolite, aminomethylphosphonic acid (AMPA), with severity of acute glyphosate (herbicide) poisoning.

METHODS

In our retrospective study of acute glyphosate poisoning, we examined records from the French National Database of Poisonings, dated between January 1, 2004, and December 31, 2016. We compared the severity of poisoning among case individuals using the Fisher exact test and Wilcoxon test. Also, we calculated ROC curves to determine the cutoff for blood and urine concentration.

RESULTS

A total of 17 plasma glyphosate, 11 urine glyphosate, 13 plasma AMPA, and 10 urine AMPA specimens were included in our study, with collection dates ranging from January 1, 2004, through December 31, 2016.

CONCLUSION

The optimal cutoff we discovered for blood concentration of AMPA was 0.88 mg/L; for glyphosate, it was 600 mg/L. The cutoff plasma concentration of AMPA has never been described in the literature, to our knowledge.

geoPIPE: Geospatial Pipeline for Enhancing Open Data for Substance Use Disorders Research

We present our open-source pipeline for quickly enhancing open data sets with research-focused expansions and show its effectiveness on a cornerstone open data set released by the Cook County government in Illinois. The City of Chicago and Cook County were both early adopters of open data portals and have made a wide variety of data available to the public; we focus on the medical examiner case archive which provides information about deaths recorded by Cook County's Office of the Medical Examiner, including overdoses invaluable to substance use disorder research. Our pipeline derives key variables from open data and links to other publicly available data sets in support of accelerating translational research on substance use disorders. Our methods apply to location-based analyses of overdoses in general and, as an example, we highlight their impact on opioid research. We provide our pipeline as open-source software to act as open infrastructure for open data to help fill the gap between data release and data use.

Social media attention and citations of published outputs from re-use of clinical trial data: a matched comparison with articles published in the same journals

BACKGROUND

Data-sharing policies in randomized clinical trials (RCTs) should have an evaluation component. The main objective of this case-control study was to assess the impact of published re-uses of RCT data in terms of media attention (Altmetric) and citation rates.

METHODS

Re-uses of RCT data published up to December 2019 (cases) were searched for by two reviewers on 3 repositories (CSDR, YODA project, and Vivli) and matched to control papers published in the same journal. The Altmetric Attention Score (primary outcome), components of this score (e.g. mention of policy sources, media attention) and the total number of citations were compared between these two groups.

RESULTS

89 re-uses were identified: 48 (53.9%) secondary analyses, 34 (38.2%) meta-analyses, 4 (4.5%) methodological analyses and 3 (3.4%) re-analyses. The median (interquartile range) Altmetric Attention Scores were 5.9 (1.3-22.2) for re-use and 2.8 (0.3-12.3) for controls (p = 0.14). No statistical difference was found on any of the components of in the Altmetric Attention Score. The median (interquartile range) numbers of citations were 3 (1-8) for reuses and 4 (1 - 11.5) for controls (p = 0.30). Only 6/89 re-uses (6.7%) were cited in a policy source.

CONCLUSIONS

Using all available re-uses of RCT data to date from major data repositories, we were not able to demonstrate that re-uses attracted more attention than a matched sample of studies published in the same journals. Small average differences are still possible, as the sample size was limited. However matching choices have some limitations so results should be interpreted very cautiously. Also, citations by policy sources for re-uses were rare.

TRIAL REGISTRATION

Registration: osf.io/fp62e.

[Prevalence and Risk Factors of Chlamydia Trachomatis Infection Among Women Consulting at the Sexually Transmitted Infection Centre in la Reunion: A Cross-Sectional Study]

Introduction

Chlamydia trachomatis (CT) infection is the commonest bacterial sexually transmitted infection (STI) in the world. Often asymptomatic, it can lead to significant complications in women. In France, since 2003, systematic screening for CT in STI center has been recommended for women aged less than 25 year. The main objective of this study was to determine CT prevalence in patients attending STI centers in Reunion Island. The second objective was to explore the determinants of this infection.

Method

A cross-sectional survey using an anonymous questionnaire was conducted among women attending STI center in two hospitals in western and southern Reunion Island during one year. All women who had performed a CT PCR, based on vaginal self-swabs, were included.

Results

Among the 620 patients tested, the prevalence of infection was 6.6% (95% CI [4.7-8.6]). By age group, the highest prevalence was between 12 and 17 years with 14.3% positive tests compared to 7.5% and 3.9% respectively in 18-24 and 25-67 year age group (p = 0.003). The risk factors for CT were a young age (p = 0.02), a first sexual intercourse between 11 and 14 years old (p = 0.01), lack of previous STI screening history (p = 0.02), and the following motives for seeking screening: "partner unfaithfulness" (p = 0.01) and "infected partner" (p = 0.02).

Conclusion

This study highlights the high prevalence of CT among Reunionese minors. A more systematic screening and a reinforcement of STI awareness among young people in Reunion Island seem to be essential.

Differential Effects of Sex and Genetics on Behavior and Stress Response of Turkeys

Three lines of turkeys were tested for response in T-maze and open-field tests during the first 8 d after hatch, and behavior was observed after catching, moving, and transport. They were also compared for corticosterone (CORT) levels and heterophil:lymphocyte ratios (H:L) at 15 wk of age in response to an Escherichia coli challenge followed by transport stress. Large commercial-(COMM) line birds were faster and more active in the T-maze at d 2 than egg-line birds. Male COMM-line birds were faster than male egg-line birds when tested in an open field at d 8. Egg-line birds had more sleeping behavior after moving to a new floor pen as compared with both an intermediate-sized line (F line) and the COMM line. Transport stress increased CORT levels in all 3 lines, and the increase was greater in males compared with females. The egg line had higher basal CORT levels (P = 0.03) and higher levels after transport (P < 0.0001). The H:L ratios were affected by both transport stress and line but not by sex. The H:L ratio was lower in the egg line as compared with both the F line and the COMM line (P < 0.0001), with the COMM line having the greatest increase in response to transport. These data, combined with those from previous studies of these lines, suggest that differences in activity of fast-growing turkeys may be used to select birds that are less susceptible to inflammatory bacterial disease and that the H:L ratio may be more useful than serum CORT in evaluating the deleterious effects of stress.

Incidence of insecticide resistance alleles in sexually-reproducing populations of the peach-potato aphid Myzus persicae (Hemiptera: Aphididae) from southern France

Intensive chemical treatments have led to the development of a number of insecticide resistance mechanisms in the peach-potato aphid Myzus persicae (Sulzer). Some of these mechanisms are known to be associated with negative pleiotropic effects (resistance costs). Molecular and biochemical methods were used to determine the genotypes or phenotypes associated with four insecticide resistance mechanisms in single aphids from sexually-reproducing populations in southern France. The mechanisms considered were E4 and FE4 carboxylesterase overproduction, modified acetycholinesterase, and kdr and rdl resistance-associated mutations. A new method for determining individual kdr genotypes is presented. Almost all resistant individuals overproduced FE4 carboxylesterase, whereas modified acetylcholinesterase was rare. Both the kdr and rdl resistance mutations were present at high frequencies in French sexually-reproducing populations. The frequencies of insecticide resistance genes were compared before and after sexual reproduction in one peach orchard at Avignon to evaluate the potential impact of selection on the persistence of resistance alleles in the over-wintering phase. The frequencies of the kdr and rdl mutations varied significantly between autumn and spring sampling periods. The frequency of the kdr mutation increased, probably due to pyrethroid treatments at the end of the winter. Conversely, the frequency of the rdl mutation decreased significantly during winter, probably because of a fitness cost associated with this mutation.

HIV-1 integrase inhibitors that compete with the target DNA substrate define a unique strand transfer conformation for integrase

Diketo acids such as L-731,988 are potent inhibitors of HIV-1 integrase that inhibit integration and viral replication in cells. These compounds exhibit the unique ability to inhibit the strand transfer activity of integrase in the absence of an effect on 3' end processing. To understand the reasons for this distinct inhibitory profile, we developed a scintillation proximity assay that permits analysis of radiolabeled inhibitor binding and integrase function. High-affinity binding of L-731,988 is shown to require the assembly of a specific complex on the HIV-1 long terminal repeat. The interaction of L-731,988 with the complex and the efficacy of L-731, 988 in strand transfer can be abrogated by the interaction with target substrates, suggesting competition between the inhibitor and the target DNA. The L-731,988 binding site and that of the target substrate are thus distinct from that of the donor substrate and are defined by a conformation of integrase that is only adopted after assembly with the viral end. These results elucidate the basis for diketo acid inhibition of strand transfer and have implications for integrase-directed HIV-1 drug discovery efforts.

Cyclodiene insecticide resistance: from molecular to population genetics

This review follows progress in the analysis of cyclodiene insecticide resistance from the initial isolation of the mutant, through cloning of the resistance gene, to an examination of the distribution of resistance alleles in natural populations. Emphasis is given to the use of a resistant Drosophila mutant as an entry point to cloning the associated gamma-aminobutyric acid (GABA) receptor subunit gene, Resistance to dieldrin. Resistance is associated with replacements of a single amino acid (alanine302) in the chloride ion channel pore of the protein. Replacements of alanine302 not only directly affect the drug binding site but also allosterically destabilize the drug preferred conformation of the receptor. Resistance is thus conferred by a unique dual mechanism associated with alanine302, which is the only residue replaced in a wide range of different resistant insects. The underlying mutations appear either to have arisen once, or multiply, depending on the population biology of the pest insect. Although resistance frequencies decline in the absence of selection, resistance alleles can persist at relatively high frequency and may cause problems for compounds to which cross-resistance is observed, such as the novel fipronils.

Duplication of the Rdl GABA receptor subunit gene in an insecticide-resistant aphid, Myzus persicae

Resistance to cyclodiene insecticides is associated with replacements of a single amino acid (alanine 302) in a gamma-aminobutyric acid (GABA) receptor subunit encoded by the single-copy gene Resistance to dieldrin (Rdl). Alanine 302 is predicted to reside within the second membrane-spanning region of the Rdl receptor, a region that is thought to line the integral chloride ion channel pore. In all cyclodiene-resistant insects studied to date, this same alanine residue is replaced either by a serine, or, in some resistant strains of Drosophila simulans, a glycine residue. Therefore, individuals can carry only two different Rdl alleles. In contrast, here we report the presence of up to four different Rdl-like alleles in individual clones of the green peach aphid, Myzus persicae. In addition to the wild-type copy of Rdl gene (encoding A302 or allele A), M. persicae carries three other alleles with the following amino acid replacements: A302-->Glycine (allele G), A302-->SerineTCG (allele S) and A302-->SerineAGT (allele S'). Evidence from direct nucleotide sequencing and Single Stranded Conformational Polymorphism (SSCP) analysis shows that at least three of these different Rdl alleles (i.e. A, G and S) are commonly present in individual aphids or aphid clones. Southern analysis using allele-specific probes and analysis of sequences downstream of the exon containing the resistance-associated mutation confirm the presence of two independent Rdl-like loci in M. persicae. One locus carries the susceptible alanine (A) and/or resistant glycine (G) allele while the other carries the two serine alleles (S or S'). Whereas resistance levels are correlated with the glycine replacement, the S allele was present in all aphid clones, regardless of their resistance status. These results suggest that target site insensitivity is associated with replacements at the first (A/G) but not the second (S/S') locus. Phylogenetic analysis of nucleotide sequences indicates that both putative aphid Rdl loci are monophyletic with respect to other insect Rdl genes and may have arisen through a recent gene duplication event. The implications of this duplication with respect to insecticide resistance and insect GABA receptor subunit diversity are discussed.

Why are there so few resistance-associated mutations in insecticide target genes?

The genes encoding the three major targets of conventional insecticides are: Rdl, which encodes a gamma-aminobutyric acid receptor subunit (RDL); para, which encodes a voltage-gated sodium channel (PARA); and Ace, which encodes insect acetylcholinesterase (AChE). Interestingly, despite the complexity of the encoded receptors or enzymes, very few amino acid residues are replaced in different resistant insects: one within RDL, two within PARA and three or more within AChE. Here we examine the possible reasons underlying this extreme conservation by looking at the aspects of receptor and/or enzyme function that may constrain replacements to such a limited number of residues.

Analysis of a mosquito acetylcholinesterase gene promoter

Insect acetylcholinesterase is the target site for organophosphorus and carbamate insecticides and point mutations in the Ace gene are associated with resistance in Drosophila melanogaster and Musca domestica. However, little is known of the genetic regulation of insect Ace genes. Here we report the isolation of four different cDNAs from an Aedes Ace locus and identification of the gene promoter. Northern analysis reveals two large (>10 kb) transcripts and one smaller transcript of 4 kb. The region containing the initiation of transcription was localized by sequencing the two 5' most cDNAs and by 5' RACE. The transcription start point was subsequently identified by primer extension and is flanked by a perfect arthropod initiator consensus sequence. The promoter lacks a TATA box but contains several matches to other consensus sequences for eukaryotic transcription factors. In common with the Drosophila Ace gene, there are also multiple potential initiators of translation (ATGs) upstream of the main open reading frame. The structure of the 5' leader and promoter is compared to that found in other insect and vertebrate Ace genes and the possibility that this locus is homologous to one of two Ace loci described in another mosquito, Culex pipiens, is discussed.

Cloning, sequencing and functional expression of an acetylcholinesterase gene from the yellow fever mosquito Aedes aegypti

A degenerate PCR strategy was used to isolate a fragment of the acetylcholinesterase gene (Ace) homolog from Aedes aegypti and screen for a cDNA clone containing the complete open reading frame of the gene. The predicted amino acid sequence of the Aedes gene shares 64% identity with Ace from Drosophila and 87% identity with the acetylcholinesterase gene from another mosquito species Anopheles stephensi. High levels of expression of the Aedes gene were achieved by infection of Sf21 cells with a recombinant baculovirus containing the Aedes Ace cDNA. The catalytic properties and sensitivity of the recombinant enzyme to insecticide inhibition are described and discussed in relation to the role of insensitive AChE in conferring resistance to organophosphorus and carbamate insecticides.

Compromised antioxidant status associated with ascites in broilers

Tissue infiltration by white blood cells in poultry with ascites has been reported, which could alter endogenous antioxidant status from oxidant stress. Therefore, the objective of this study was to determine the effect of ascites on ascorbic acid, tocopherol, and glutathione (GSH), which are major intracellular antioxidants. Broiler chicks (1 day) were placed in environmental chambers maintained with normal ventilation (Control) or under low ventilation, which produced a cumulative mortality of 31.3% due to ascites. At 3, 5, and 7 wk, lung and liver tissues were obtained from control birds (n = 5) and from birds in the low ventilation chamber with (ASC, n = 5) or without (NASC, n = 5) overt symptoms of ascites. There were no differences in tissue ascorbate, tocopherol, and GSH between the control and NASC groups with the exception of hepatic tocopherol at 7 wk, which was higher (P < .05) in NASC birds than in ASC and control birds. In general, lung and liver concentrations of all three antioxidants were lower (P < .05) in ASC birds than in NASC and control groups. Uric acid, a product of purine metabolism, was lower (P < .05) in liver and lung in ASC birds at 3 wk compared with control birds. However, uric acid concentrations in ASC birds were higher (P < .05) in the lung and serum at 5 wk, and in the liver at 7 wk compared with NASC and control birds.(ABSTRACT TRUNCATED AT 250 WORDS)

Simultaneous ligation of CD5 and CD28 on resting T lymphocytes induces T cell activation in the absence of T cell receptor/CD3 occupancy

The T cell surface molecules CD5 and CD28 have been shown to be receptors for accessory signals in T cell activation. We here demonstrate that in the absence of any other activating stimulus, simultaneous ligation of CD5 and CD28 by mAb induces polyclonal T cell activation. Immobilization of the anti-CD28 and anti-CD5 mAb was an essential requirement for T cell stimulation. This was done either through coating of the culture plates with goat anti-mouse Ig, or by coculture with mitomycin C-treated Fc gamma R-bearing P815 mouse mastocytoma cells. Most importantly, T cells could also be stimulated with B7, the natural ligand of CD28, and anti-CD5 presented on irradiated 3T6 mouse fibroblasts co-transfected with human Fc gamma RII and with B7. Neither immobilized mAb 9.3 (anti-CD28) nor any of four different anti-CD5 mAb were mitogenic as a sole stimulus. Immobilized mAb identifying CD4, CD7, or LFA-1 were not co-mitogenic with either mAb 9.3 or one of the anti-CD5 mAb. The T cell proliferation induced by cross-linking of CD5 and CD28 is IL-2-dependent, as was demonstrated by the cell-surface expression of the p55 chain of the IL-2R, the production of IL-2, and inhibition of the proliferative response by the anti-IL-2R mAb anti-Tac. CD5/CD28 ligation induced production of TNF-alpha, but not of IL-4, and did not induce modulation of the TCR/CD3 complex. Expression of IL-2R (p55) and of CD69 preferentially occurred on CD29-low naive cells, and indicated that about 50% of the cultured cells were activated. Cell proliferation was not increased by adding monocytes to the cultures and it was inhibited by PKC inhibitors (H7 and staurosporine) and by cyclosporine A. In conclusion, our data provide evidence for a pathway of Ag-independent T cell activation via CD5 and CD28, which preferentially stimulates native T cells.

Simultaneous ligation of CD5 and CD28 on resting T lymphocytes induces T cell activation in the absence of T cell receptor/CD3 occupancy

The T cell surface molecules CD5 and CD28 have been shown to be receptors for accessory signals in T cell activation. We here demonstrate that in the absence of any other activating stimulus, simultaneous ligation of CD5 and CD28 by mAb induces polyclonal T cell activation. Immobilization of the anti-CD28 and anti-CD5 mAb was an essential requirement for T cell stimulation. This was done either through coating of the culture plates with goat anti-mouse Ig, or by coculture with mitomycin C-treated Fc gamma R-bearing P815 mouse mastocytoma cells. Most importantly, T cells could also be stimulated with B7, the natural ligand of CD28, and anti-CD5 presented on irradiated 3T6 mouse fibroblasts co-transfected with human Fc gamma RII and with B7. Neither immobilized mAb 9.3 (anti-CD28) nor any of four different anti-CD5 mAb were mitogenic as a sole stimulus. Immobilized mAb identifying CD4, CD7, or LFA-1 were not co-mitogenic with either mAb 9.3 or one of the anti-CD5 mAb. The T cell proliferation induced by cross-linking of CD5 and CD28 is IL-2-dependent, as was demonstrated by the cell-surface expression of the p55 chain of the IL-2R, the production of IL-2, and inhibition of the proliferative response by the anti-IL-2R mAb anti-Tac. CD5/CD28 ligation induced production of TNF-alpha, but not of IL-4, and did not induce modulation of the TCR/CD3 complex. Expression of IL-2R (p55) and of CD69 preferentially occurred on CD29-low naive cells, and indicated that about 50% of the cultured cells were activated. Cell proliferation was not increased by adding monocytes to the cultures and it was inhibited by PKC inhibitors (H7 and staurosporine) and by cyclosporine A. In conclusion, our data provide evidence for a pathway of Ag-independent T cell activation via CD5 and CD28, which preferentially stimulates native T cells.

A longitudinal analysis of the effect of experience on the therapeutic approach: revisited

The published results of readministering the Therapist Orientation Questionnaire to a group of "low experience" therapists (N = 60) 4 years after an initial administration were recalculated due to scoring errors. Ss had been classified into Freudian, Sullivanian, and Rogerian schools. Differences present among schools on several TOQ factors were present initially and were mostly still there at the readministration. Although relative to each other the groups were stable, many scores shifted, essentially, away from a Freudian philosophy.

The state mental hospital: a local health department's role

The publicizing of the abysmal conditions in state mental institutions and the problems precipitated by their deinstitutionalization programs, have challenged local health authorities to develop effective roles in ameliorating these difficulties. Long-view State Hospital is a state mental hospital in Cincinnati, Ohio. The Cincinnati Health Department acted as a change agent to deal with the hospital's many chronic problems and the new difficulties precipitated by moving patients into the community for care. The city conducted its own evaluation of the hospital and its deinstitutionalization program and strongly advocated needed improvements. Problems were encountered in implementing this advocacy role, particularly in relation to the local health department's authority regarding this state-funded and operated institution. However, the many city recommendations that were implemented, the increased funding given the hospital and the community mental health centers, the continuing communication between city and state officials, as well as a follow-up evaluation indicated that the Cincinnati Health Department had played a positive role in the change process. (Am. J. Public Health 69:64-67, 1979.)

Immunization: public health programming through law enforcement

The pre-inoculation program review of the school immunization records in fall, 1974 found that only 60 per cent of the 63,000 children in the Cincinnati primary school system were adequately immunized. Following a program based upon their legal authority to require immunizations, the Board of Health in collaboration with the Board of Education was able to obtain in a two-year effort a 91 per cent immunization level.

Malingering as role taking

This study investigated the relationship among psychopathology, intelligence and the simulation of psychopathological roles. The 132 Ss were 48 inpatients, 48 outpatients, and 36 nonprofessional employees. Each S simulated the MMPI profile of an anxiety neurotic, psychopathic deviate, or paranoid schizophrenic. Their simulation target was dissimilar to their diagnosis and/or Personality Screening Inventory profile. The findings were: (1) the hypothesized negative relationship between psychopathology and psychopathological role-taking was not supported broadly, but was supported more with males, blacks, neurotics, and simulators of the psychopathic deviate personality; and (2) the hypothesized positive relationship between intelligence and the simulation of psychopathological roles was supported in a small but definite relationship, with greater support among the Caucasians, males, neurotics, simulators of the 2-7 and 6-8 profile patterns, and when the simulation measure emphasized scatter and elevation similarities.