Brief original report: Does smoking status provide information relevant to screening for other substance use among US adults?

We assessed whether tobacco screening provides clinically meaningful information about other substance use, including alcohol and other drug use, potentially facilitating targeting of screening for substance use. Using data from the Veterans Aging Cohort Study survey sample (VACS; N = 7510), we calculated test performance characteristics of tobacco use screening results for identification of other substance use including sensitivity, specificity, positive-likelihood-ratio (+LR = [sensitivity/(1-specificity)]: increase in odds of substance use informed by a positive tobacco screen), and negative-likelihood-ratio (-LR: [(1-sensitivity)/specificity]: reduction in odds of substance use informed by a negative tobacco screen). The sample was 95% male, 75% minority, and 43% were current and 33% were former smokers. Never smoking, versus any history, indicated an approximate four-fold decrease in the odds of injection drug use (-LR = 0.26), an approximate 2.5-fold decrease in crack/cocaine (-LR = 0.35) and unhealthy alcohol use (-LR = 0.40), an approximate two-fold decrease in marijuana (-LR = 0.51) and illicit opioid use (-LR = 0.48), and an approximate 30% decrease in non-crack/cocaine stimulant use (-LR = 0.75). Never smoking yielded more information than current non-smoking (never/former smoking). Positive results on tobacco screening were less informative than negative results; current smoking, versus former/never smoking, provided more information than lifetime smoking and was associated with a 40% increase in the odds of non-crack/cocaine stimulant use (+LR = 1.40) and opioid use (+LR = 1.44), 50% increase in marijuana use (+LR = 1.52) and injection drug use (+LR = 1.55), and an 80-90% increase in crack/cocaine use (+LR = 1.93) and unhealthy alcohol use (+LR = 1.75). When comprehensive screening for substance use is not possible, tobacco screening may inform decisions about targeting substance use screening.

Lifetime Burden of Incarceration and Violence, Internalized Homophobia, and HIV/STI Risk Among Black Men Who Have Sex with Men in the HPTN 061 Study

Black men who have sex with men (BMSM) have disproportionate HIV/STI acquisition risk. Incarceration may increase exposure to violence and exacerbate psychosocial vulnerabilities, including internalized homophobia, which are associated with HIV/STI acquisition risk. Using data from HIV Prevention Trials Network 061 (N = 1553), we estimated adjusted prevalence ratios (APR) and 95% confidence intervals (CIs) for associations between lifetime burden of incarceration and HIV/STI risk outcomes. We measured associations between incarceration and HIV/STI risk outcomes with hypothesized mediators of recent violence victimization and internalized homophobia. Compared to those never incarcerated, those with 3-9 or ≥ 10 incarcerations had approximately 10% higher prevalence of multiple partnerships. Incarceration burden was associated with selling sex (1-2 incarcerations: APR: 1.52, 95% CI 1.14-2.03; 3-9: APR: 1.77, 95% CI 1.35-2.33; ≥ 10: APR: 1.85, 95% CI 1.37-2.51) and buying sex (≥ 10 incarcerations APR: 1.80, 95% CI 1.18-2.75). Compared to never incarcerated, 1-2 incarcerations appeared to be associated with current chlamydia (APR: 1.47, 95% CI 0.98-2.20) and 3-9 incarcerations appeared to be associated with current syphilis (APR: 1.46, 95% CI 0.92-2.30). Incarceration was independently associated with violence, which in turn was a correlate of transactional sex. Longitudinal research is warranted to clarify the role of incarceration in violence and HIV/STI risk in this population.

Longitudinal Associations between Police Harassment and Experiences of Violence among Black Men Who Have Sex with Men in Six US Cities: the HPTN 061 Study

Interactions with the police may result in police brutality, particularly for people of color. Black men who have sex with men (BMSM) face disproportionate risk of police contact and may experience elevated violence risk. We measured longitudinal associations between discriminatory police harassment (DPH) and subsequent risk of a range of interpersonal violence experiences, including intimate partner violence (IPV). In this study, we estimated associations between DPH motivated by racism, homophobia, or both, and subsequent violent experiences (being physically harassed, hit, threatened with weapons, and intimate partner violence) among BMSM. Bivariate and multivariable regression analyses were used to control for demographic and behavioral factors. Among 1160 BMSM included at 12-month follow-up, experiencing DPH motivated by racism and homophobia was associated with over four times the odds of being threatened with violence (AOR 4.85, 95% CI 3.20, 7.33), four times the odds of or experiencing violence defined as being punched, kicked, or beaten, or having an object thrown at them (AOR 4.51, 95% CI 2.82, 7.19), and nearly three times the odds of physical partner abuse (AOR 3.49, 95% CI 1.69, 7.19). Findings suggest that for BMSM, DPH is associated with the threat and experience of violence, with a dose-response relationship between DPH motivated by one or more causes. Given that BMSM are a population particularly vulnerable to both police harassment related to race and sexual orientation and violence coupled with stigma, additional research evaluating mechanisms linking these associations is needed in order to develop additional supportive interventions.

Does Reducing Drinking in Patients with Unhealthy Alcohol Use Improve Pain Interference, Use of Other Substances, and Psychiatric Symptoms?

BACKGROUND

We aimed to investigate the impact of reducing drinking in patients with unhealthy alcohol use on improvement of chronic pain interference, substance use, and psychiatric symptoms.

METHODS

We analyzed longitudinal data from 2003 to 2015 in the Veterans Aging Cohort Study, a prospective, multisite observational study of US veterans, by emulating a hypothetical randomized trial (a target trial). Alcohol use was assessed using the Alcohol Use Disorders Identification Test (AUDIT) questionnaire, and outcome conditions were assessed via validated survey items. Individuals were followed from the first time their AUDIT score was ≥ 8 (baseline), a threshold consistent with unhealthy alcohol use. We compared individuals who reduced drinking (AUDIT < 8) at the next follow-up visit with individuals who did not (AUDIT ≥ 8). We fit separate logistic regression models to estimate odds ratios for improvement of each condition 2 years postbaseline among individuals who had that condition at baseline: moderate or severe pain interference symptoms, tobacco smoking, cannabis use, cocaine use, depressive symptoms, and anxiety symptoms. Inverse probability weighting was used to account for potential selection bias and confounding.

RESULTS

Adjusted 2-year odds ratios (95% confidence intervals) for associations between reducing drinking and improvement or resolution of each condition were as follows: 1.49 (0.91, 2.42) for pain interference symptoms, 1.57 (0.93, 2.63) for tobacco smoking, 1.65 (0.92, 2.95) for cannabis use, 1.83 (1.03, 3.27) for cocaine use, 1.11 (0.64, 1.92) for depressive symptoms, and 1.33 (0.80, 2.22) for anxiety symptoms.

CONCLUSIONS

We found some evidence for improvement of pain interference symptoms and substance use after reducing drinking among US veterans with unhealthy alcohol use, but confidence intervals were wide.

Insights Provided by Depression Screening Regarding Pain, Anxiety, and Substance use in a Veteran Population

Objective:

We sought to quantify the extent to which a depression screening instrument commonly used in primary care settings provides additional information regarding pain interference symptoms, anxiety, and substance use.

Methods:

Veterans Aging Cohort Study (VACS) data collected from 2003 through 2015 was used to calculate odds ratios (OR) for associations between positive depression screening result cutoffs and clustering conditions. We assessed the test performance characteristics (likelihood ratio value, positive predictive value, and the percentage of individuals correctly classified) of a positive Patient Health Questionnaire (PHQ-9 & PHQ-2) depression screen for the identification of pain interference symptoms, anxiety, and substance use.

Results:

A total 7731 participants were included in the analyses. The median age was 50 years. The PHQ-9 threshold of ≥20 was strongly associated with pain interference symptoms (OR 21.6, 95% CI 17.5-26.7) and anxiety (OR 72.1, 95% CI 52.8-99.0) and yielded likelihood ratio values of 7.5 for pain interference symptoms and 21.8 for anxiety and positive predictive values (PPV) of 84% and 95%, respectively. A PHQ-9 score of ≥10 still showed significant associations with pain interference symptoms (OR 6.1, 95% CI 5.4-6.9) and symptoms of anxiety (OR 11.3, 95% CI 9.7-13.1) and yet yielded lower likelihood ratio values (4.36 & 8.24, respectively). The PHQ-9 was less strongly associated with various forms of substance use.

Conclusion:

Depression screening provides substantial additional information regarding the likelihood of pain interference symptoms and anxiety and should trigger diagnostic assessments for these other conditions.

Association of Alcohol Screening Scores With Adverse Mental Health Conditions and Substance Use Among US Adults

IMPORTANCE

Alcohol screening may be associated with health outcomes that cluster with alcohol use (ie, alcohol-clustering conditions), including depression, anxiety, and use of tobacco, marijuana, and illicit drugs.

OBJECTIVE

To quantify the extent to which alcohol screening provides additional information regarding alcohol-clustering conditions and to compare 2 alcohol use screening tools commonly used for this purpose.

DESIGN, SETTING, AND PARTICIPANTS

This longitudinal cohort study used data from the Veterans Aging Cohort Study. Data were collected at 8 Veterans Health Administration facilities from 2003 through 2012. A total of 7510 participants were enrolled, completed a baseline survey, and were followed up. Veterans with HIV were matched with controls without HIV by age, race, sex, and site of care. Data were analyzed from January 2019 to December 2019.

EXPOSURES

The Alcohol Use Disorders Identification Test (AUDIT) and Alcohol Use Disorders Identification Test-Consumption (AUDIT-C) were used to assess alcohol use, with 4 risk groups delineated for each test: score 0 to 7 (reference), score 8 to 15, score 16 to 19, and score 20 to 40 (maximum score) for the full AUDIT and score 0 to 3 (reference), score 4 to 5, score 6 to 7, and score 8 to 12 (maximum score) for the AUDIT-C.

MAIN OUTCOMES AND MEASURES

Alcohol-clustering conditions, including self-reported symptoms of depression and anxiety and use of tobacco, marijuana, cocaine, other stimulants, opioids, and injection drugs.

RESULTS

A total of 6431 US patients (6104 [95%] men; median age during survey years 2003-2004, 50 years [range, 28-86 years; interquartile range, 44-55 years]) receiving care in the Veterans Health Administration completed 1 or more follow-up surveys when the AUDIT was administered and were included in the present analyses. Of the male participants, 4271 (66%) were African American, 1498 (24%) were white, and 590 (9%) were Hispanic. The AUDIT and AUDIT-C scores were associated with each alcohol-clustering condition. In particular, an AUDIT score of 20 or higher (vs <8, the reference) was associated with symptoms of depression (odds ratio [OR], 8.37; 95% CI, 6.20-11.29) and anxiety (OR, 8.98; 95% CI, 6.39-12.60) and with self-reported use of tobacco (OR, 14.64; 95% CI, 8.94-23.98), marijuana (OR, 12.41; 95% CI, 8.61-17.90), crack or cocaine (OR, 39.47; 95% CI, 27.38-56.90), other stimulants (OR, 21.31; 95% CI, 12.73-35.67), and injection drugs (OR, 8.67; 95% CI, 5.32-14.13). An AUDIT score of 20 or higher yielded likelihood ratio (sensitivity / 1 - specificity) values greater than 3.5 for depression, anxiety, crack or cocaine use, and other stimulant use. Associations between AUDIT-C scores and alcohol-clustering conditions were more modest.

CONCLUSIONS AND RELEVANCE

Alcohol screening can inform decisions about further screening and diagnostic assessment for alcohol-clustering conditions, particularly for depression, anxiety, crack or cocaine use, and other stimulant use. Future studies using clinical diagnoses rather than screening tools to assess alcohol-clustering conditions may be warranted.

Childhood Traumatic Experiences and Receptive Anal Intercourse Among Women

CONTEXT

Receptive anal intercourse (RAI), which has become increasingly common among U.S. heterosexual women, is associated with STDs, including HIV, when it is unprotected and coercive. Childhood traumatic experiences may increase sexual risk behavior, but the relationship between childhood trauma and RAI among women has not been examined.

METHODS

Data from 4,876 female participants in Waves 1 (1994-1995), 3 (2001-2002) and 4 (2007-2008) of the National Longitudinal Study of Adolescent to Adult Health were used to examine associations between nine self-reported childhood traumas (neglect; emotional, physical and sexual abuse; parental binge drinking and incarceration; and witnessing, being threatened with and experiencing violence) and RAI during adulthood using modified Poisson regression analysis. Whether depression, low self-esteem, drug use, relationship characteristics or sex trade involvement mediated the relationship between trauma and RAI was also explored.

RESULTS

Forty percent of the sample reported having engaged in receptive anal intercourse. After adjustment for sociodemographic characteristics, eight of the nine childhood traumas were associated with increased risk of RAI (adjusted prevalence ratios, 1.2-1.5); the strongest association was with experience of violence. Each unit increase in the number of traumas yielded a 16% increase in RAI prevalence. In mediation analyses, only drug use and relationship factors slightly attenuated the association between childhood trauma and RAI (1.2 for each).

CONCLUSIONS

Women with a history of childhood trauma may be at increased risk of engaging in RAI, highlighting the importance of screening and trauma-informed education in sexual health settings. Pathways linking childhood trauma and RAI among women are complex and warrant further research.

Evaluation of anthelmintic activity in captive wild ruminants by fecal egg reduction tests and a larval development assay

The effectiveness of anthelmintics was evaluated in four herds of captive ruminants, wapiti (Cervus elaphus), Armenian red sheep (Ovis orientalis), giraffe (Giraffa camelopardalis), and pronghorn (Antilocapra americana), by the use of fecal egg reduction tests (FERTs) and a commercial larval development assay (LDA) designed to evaluate susceptibility or resistance of nematodes to anthelmintics. Haemonchus sp. was the predominant nematode in the red sheep, giraffe, and pronghorn herds, whereas Ostertagia sp. and Trichostrongylus sp. were predominant in the wapiti. The LDA data indicated susceptibility by the worms to benzimidazoles except in the red sheep flock, which showed a high level of resistance. High levels of resistance to levamisole were seen in the worm populations from the wapiti and red sheep, moderate resistance in the pronghorn herd, and susceptibility in the giraffe herd. Worms were susceptible in all four herds to a combination of benzimidazole/levamisole. There was suspected avermectin resistance by Trichostrongylus sp. in the wapiti herd and by Haemonchus sp. in the giraffe. The FERTs agreed with the LDA in showing the Haemonchus in the giraffe was susceptible to fenbendazole and had suspected resistance to ivermectin, whereas Haemonchus in the red sheep and pronghorn were susceptible to ivermectin. There was correlation between the tests evaluating anthelmintics. The LDA is useful as a screening test in the selection of an anthelmintic for use in grazing ruminants, but the effectiveness of a drug in a host species may depend as much on the dose used, and the method of administration, as it does on the parasite's sensitivity to the anthelmintic.

Parasite diversity and anthelmintic resistance in two herds of horses

Diversity of parasite populations was compared between two herds of horses, one a regularly treated herd the other a feral herd which has bad no anthelmintic treatment for at least 25 years. Eggs obtained from fecal samples of both herds were tested for anthelmintic resistance by use of an in-vitro larval hatch/development assay (LDA), DrenchRite. A fecal egg reduction test was also performed with the domesticated herd using fenbendazole, pyrantel pamoate and ivermectin. Cyathostomes were the predominant group of worms present in both herds. Trichostrongylus axei was seen in both herds, but Strongylus equinus, Strongylus vulgaris, Gyalocephalus capitatus, Poteriostomum spp. and Strongyloides westeri were only found in the feral horses. Larvae of Strongylus edentatus were found in a single domesticated horse. Fecal egg reduction tests with the domesticated herd showed a 32% egg count reduction for fenbendazole, a 93% reduction with pyrantel, and a 99% reduction with ivermectin. From the LDA, anthelmintic resistance was evaluated by determining the resistance ratio of the domesticated herd compared with the feral herd. For benzimidazoles in the domesticated herd, 45% of the cyathostome population was 9.4 times more tolerant than the feral herd's parasite population. The parasite population in the domesticated herd was 1.5 times more tolerant to Levamisole, and 1.7 times more tolerant to the benzimidazole/levamisole combination than the parasite population within the feral herd. 9% of the parasite population in the domesticated herd was 90 times more tolerant to avermectins than the feral herd's parasite population, even though a subpopulation of worms in the feral herd were tolerant to low concentrations of avermectins despite never being previously exposed to this class of anthelmintic.

Teratogen-mediated inhibition of target tissue response to Shh signaling

Veratrum alkaloids and distal inhibitors of cholesterol biosynthesis have been studied for more than 30 years as potent teratogens capable of inducing cyclopia and other birth defects. Here, it is shown that these compounds specifically block the Sonic hedgehog (Shh) signaling pathway. These teratogens did not prevent the sterol modification of Shh during autoprocessing but rather inhibited the response of target tissues to Shh, possibly acting through the sterol sensing domain within the Patched protein regulator of Shh response.

Crystal structure of a Hedgehog autoprocessing domain: homology between Hedgehog and self-splicing proteins

The approximately 25 kDa carboxy-terminal domain of Drosophila Hedgehog protein (Hh-C) possesses an autoprocessing activity that results in an intramolecular cleavage of full-length Hedgehog protein and covalent attachment of a cholesterol moiety to the newly generated amino-terminal fragment. We have identified a 17 kDa fragment of Hh-C (Hh-C17) active in the initiation of autoprocessing and report here its crystal structure. The Hh-C17 structure comprises two homologous subdomains that appear to have arisen from tandem duplication of a primordial gene. Residues in the Hh-C17 active site have been identified, and their role in Hedgehog autoprocessing probed by site-directed mutagenesis. Aspects of sequence, structure, and reaction mechanism are conserved between Hh-C17 and the self-splicing regions of inteins, permitting reconstruction of a plausible evolutionary history of Hh-C and the inteins.

Cholesterol modification of hedgehog signaling proteins in animal development

Hedgehog (Hh) proteins comprise a family of secreted signaling molecules essential for patterning a variety of structures in animal embryogenesis. During biosynthesis, Hh undergoes an autocleavage reaction, mediated by its carboxyl-terminal domain, that produces a lipid-modified amino-terminal fragment responsible for all known Hh signaling activity. Here it is reported that cholesterol is the lipophilic moiety covalently attached to the amino-terminal signaling domain during autoprocessing and that the carboxyl-terminal domain acts as an intramolecular cholesterol transferase. This use of cholesterol to modify embryonic signaling proteins may account for some of the effects of perturbed cholesterol biosynthesis on animal development.

Cyclopia and defective axial patterning in mice lacking Sonic hedgehog gene function

Targeted gene disruption in the mouse shows that the Sonic hedgehog (Shh) gene plays a critical role in patterning of vertebrate embryonic tissues, including the brain and spinal cord, the axial skeleton and the limbs. Early defects are observed in the establishment or maintenance of midline structures, such as the notochord and the floorplate, and later defects include absence of distal limb structures, cyclopia, absence of ventral cell types within the neural tube, and absence of the spinal column and most of the ribs. Defects in all tissues extend beyond the normal sites of Shh transcription, confirming the proposed role of Shh proteins as an extracellular signal required for the tissue-organizing properties of several vertebrate patterning centres.

Hedgehog patterning activity: role of a lipophilic modification mediated by the carboxy-terminal autoprocessing domain

Autocatalytic processing mediated by the carboxyterminal domain of the hedgehog (hh) protein precursor (Hh) generates an amino-terminal product that accounts for all known signaling activity. The role of autoprocessing biogenesis of the hh signal has been unclear, since a truncated unprocessed protein lacking all carboxy-terminal domain sequences retains signaling activity. Here, we present evidence that the autoprocessing reaction proceeds via an internal thioester intermediate and results in a covalent modification that increases the hydrophobic character of the signaling domain and influences its spatial and subcellular distribution. We demonstrate that truncated unprocessed amino-terminal protein causes embryonic mispatterning, even when expression is localized to cells that normally express Hh, thus suggesting a role for autoprocessing in spatial regulation of hh signaling. This type of processing also appears to operate in the biogenesis of other novel secreted proteins.

Control of Drosophila tracheal branching by the novel homeodomain gene unplugged, a regulatory target for genes of the bithorax complex

We have identified a novel Drosophila homeodomain gene, unplugged (unp), whose function is required for formation of the tracheal branches that penetrate the CNS. In unp mutant embryos the segmentally repeated ganglionic branches stall and fail to penetrate the CNS and the segment-specific cerebral branch and associated cerebral anastomosis fail to form. Expression of unp in the founder cells for the cerebral branch within the first tracheal metamere is repressed in posterior segments by Ubx and other bithorax complex genes. This pattern of expression and homeotic gene regulation is reproduced by an unusual 2.6 kb cis-regulatory sequence located downstream of the unp transcription unit. Since the unp protein is localized to the nucleus of tracheal precursor cells as they migrate and extend, unp protein appears to play a regulatory role in neural branching of the tracheae, and the segment-specific aspects of these neural branching patterns appear to be generated by homeotic regulation of unp expression.

The product of hedgehog autoproteolytic cleavage active in local and long-range signalling

The secreted protein products of the hedgehog (hh) gene family are associated with local and long-range signalling activities that are responsible for developmental patterning in multiple systems, including Drosophila embryonic and larval tissues and vertebrate neural tube, limbs and somites. In a process that is critical for full biological activity, the hedgehog protein (Hh) undergoes autoproteolysis to generate two biochemically distinct products, an 18K amino-terminal fragment, N, and a 25K carboxy-terminal fragment, C (ref. 16); mutations that block autoproteolysis impair Hh function. We have identified the site of autoproteolytic cleavage and find that it is broadly conserved throughout the hedgehog family. Knowing the site of cleavage, we were able to test the function of the N and C cleavage products in Drosophila assays. We show here that the N product is the active species in both local and long-range signalling. Consistent with this, all twelve mapped hedgehog mutations either affected the structure of the N product directly or otherwise blocked the release of N from the Hh precursor as a result of deletion or alteration of sequences in the C domain.

The novel homeodomain gene buttonless specifies differentiation and axonal guidance functions of Drosophila dorsal median cells

We have identified a novel homeodomain gene, buttonless (btn), that is specifically expressed in 20 cells of a single type during Drosophila embryonic development. These cells, the dorsal median (DM) cells, are arranged as a single pair within each segment along the dorsal midline of the CNS. Distinctive features of the DM cells include a large cell body and a long thick process extending laterally to the muscle attachment site. In the absence of btn gene function the initial commitment to the DM cell fate is made but differentiation fails to occur and the DM cells are lost. The btn mutation thus specifically eliminates the DM cells, and this genetic ablation in turn reveals a requirement for DM cells as cellular cues for axonal guidance during transverse nerve outgrowth and bifurcation of the median nerve.

The degree of variation in DNA sequence recognition among four Drosophila homeotic proteins

The homeodomain has been implicated as a major determinant of biological specificity for the homeotic selector (HOM) genes. We compare here the DNA sequence preferences of homeodomains encoded by four of the eight Drosophila HOM proteins. One of the four, Abdominal-B, binds preferentially to a sequence with an unusual 5'-T-T-A-T-3' core, whereas the other three prefer 5'-T-A-A-T-3'. Of these latter three, the Ultrabithorax and Antennapedia homeodomains display indistinguishable preferences outside the core while Deformed differs. Thus, with three distinct binding classes defined by four HOM proteins, differences in individual site recognition may account for some but not all of HOM protein functional specificity. We further show that amino acid residues within the N-terminal arm are responsible for the sequence specificity differences between the Ultrabithorax and Abdominal-B homeodomains. Similarities and differences at the corresponding positions within the N-terminal arms are conserved in the vertebrate Abdominal-B-like HOM proteins, which play critical roles in limb specifications as well as in regional specification along the anterior-posterior axis. This and other patterns of residue conservation suggest that differential DNA sequence recognition may play a role in HOM protein function in a wide range of organisms.

Cooperative binding of an Ultrabithorax homeodomain protein to nearby and distant DNA sites

Cooperativity in binding of regulatory proteins to multiple DNA sites can heighten the sensitivity and specificity of the transcriptional response. We report here the cooperative DNA-binding properties of a developmentally active regulatory protein encoded by the Drosophila homeotic gene Ultrabithorax (Ubx). We show that naturally occurring binding sites for the Ubx-encoded protein contain clusters of multiple individual binding site sequences. Such sites can form complexes containing a dozen or more Ubx-encoded protein molecules, with simultaneous cooperative interactions between adjacent and distant DNA sites. The distant mode of interaction involves a DNA looping mechanism; both modes appear to enhance transcriptional activation in a simple yeast assay system. We found that cooperative binding is dependent on sequences outside the homeodomain, and we have identified regions predicted to form coiled coils carboxy terminal to the homeodomains of the Ubx-encoded protein and several other homeotic proteins. On the basis of our findings, we propose a multisite integrative model of homeotic protein action in which functional regulatory elements can be built from a few high-affinity sites, from many lower-affinity sites, or from sites of some intermediate number and affinity. An important corollary of this model is that even small differences in binding of homeotic proteins to individual sites could be summed to yield large overall differences in binding to multiple sites. This model is consistent with reports that homeodomain protein targets contain multiple individual binding site sequences distributed throughout sizable DNA regions. Also consistent is a recent report that sequences carboxy terminal to the Ubx homeodomain can contribute to segmental specificity.

Stimulation of rat spleen cells by staphylococcal enterotoxins

There is much interest in staphylococcal enterotoxins as T cell mitogens in humans, mice and rabbits. Rat spleen cells were shown to proliferate in response to staphylococcal enterotoxins A and B and toxic shock syndrome toxin-1 at concentrations (5 to 500 ng ml-1) which also stimulate mouse spleen cells. The proliferative response to all these enterotoxins was inhibited by cyclosporin A, indicating the response to be predominantly that of T cells. These results indicate that the rat provides another convenient model for the analysis of T cell responses to enterotoxins.

Infestation of northern spotted owls by hippoboscid (Diptera) flies in northwestern California

Hippoboscid flies were found on 62 (17%) of 382 northern spotted owls (Strix occidentalis caurina) captured between April and September, 1986 through 1990. Two species of hippoboscids were identified: Icosta americana and Ornithomya anchineuria. Male and female adult spotted owls had similar prevalences and relative densities of hippoboscid flies. Juvenile owls had lower prevalence and relative densities than adults. There were no significant differences in mean intensity of hippoboscids on adult male, adult female and juvenile spotted owls. Relative densities of flies infesting adult owls were significantly greater during years of increased fall temperatures, decreased winter precipitation, and decreased summer temperatures.

Insertion and excision of Bacteroides conjugative chromosomal elements

Many strains of Bacteroides harbor large chromosomal elements that can transfer themselves from the chromosome of the donor to the chromosome of the recipient. Most of them carry a tetracycline resistance (Tcr) gene and have thus been designated Tcr elements. In the present study, we have used transverse alternating field electrophoresis to show that all but one of the Tcr elements screened were approximately 70 to 80 kbp in size. The exception (Tcr Emr 12256) was 150 to 200 kbp in size and may be a hybrid element. All of the Tcr elements inserted in more than one site, but insertion was not random. The Tcr elements sometimes cotransfer unlinked chromosomal segments, or nonreplicating Bacteroides units (NBUs). Transverse alternating field electrophoresis analysis showed that insertion of NBUs was not random and that the NBUs did not insert near the Tcr element. Although attempts to clone one or both ends of a Tcr element have not been successful, ends of a cryptic element (XBU4422) were cloned previously and shown to be homologous to the ends of Tcr elements. We have obtained DNA sequences of junction regions between XBU4422 and its target from several different insertions. Comparison of junction sequences with target sequences showed that no target site duplication occurred during insertion and that XBU4422 carried 4 to 5 bp of adjacent chromosomal DNA when it excised from the chromosome and inserted in a plasmid. We identified a short region of sequence similarity between one of the ends of XBU4422 and its target site that may be important for insertion. This sequence contained an 8-bp segment that was identical to the recombinational hot spot sequence on Tn21. XBU4422 could exise itself from plasmids into which it inserted. In most cases, the excision left a single additional A behind in the target site, but precise excision was seen in one case.

Optimal DNA sequence recognition by the Ultrabithorax homeodomain of Drosophila

The 61 amino acid homeodomain is conserved among members of a family of eukaryotic DNA-binding proteins that play regulatory roles in transcription and in development. We have refined a rapid method for determining optimal DNA binding sites and have applied it to a 72 amino acid peptide containing the homeodomain of the Ultrabithorax (Ubx) homeotic gene of Drosophila. The site (5'-TTAATGG-3') is tightly bound (KD approximately 7 x 10(-11) M) by the Ubx homeodomain peptide; the four central TAAT bases of this sequence play a primary role in determining the affinity of binding, with significant secondary contributions deriving from the flanking bases. Although previously defined genomic sites contain multiple TAAT sequences with flanking bases distinct from those in the optimal binding site, we have found a new binding site with seven near-perfect repeats of the optimal sequence; this site is located in the promoter region of decapentaplegic, a probable Ubx regulatory target. The presence of a TAAT motif in the binding sites for most other homeodomain proteins suggests the existence of a conserved mechanism for recognition of this core sequence, with further specificity conferred by interactions with bases flanking this core.

Repeated DNA of the human Y chromosome

A significant fraction of the human Y chromosome is composed of DNA sequences which have homologues on the X chromosome or autosomes in humans and non-human primates. However, most human Ychromosome sequences so far examined do not have homologues on the Y chromosomes of other primates. This observation suggests that a significant proportion of the human Y chromosome is composed of sequences that have acquired their Y-chromosome association since humans diverged from other primates.

More than 50 % of the human Y chromosome is composed of a variety of repeated DNAs which, with one known exception, can be distinguished from homologues elsewhere in the genome. These include the alphoid repeats, the major human SINE (Alu repeats) and several additional families of repeats which account for the majority of Y-chromosome repeated DNA. The alphoid sequences tandemly clustered near the centromere on the Y chromosome can be distinguished from those on other chromosomes by both sequence and repeat organization, while the majority of Y-chromosome Alu repeats have little homology with genomic consensus Alu sequences. In contrast, the Y-chromosome LINE repeats cannot be distinguished from LINEs found on other chromosomes. It has been proposed that both SINE and LINE repeats have been dispersed throughout the genome by mechanisms that involve RNA intermediates. The difference in the relationship of the Y-chromosome Alu and LINE repeats to their respective family members elsewhere in the genome makes it possible that their dispersal to the Y chromosome has occurred by different mechanisms or at different rates.

In addition to the SINE and LINE repeats, the human Y chromosome contains a group of repeated DNA elements originally identified as 3·4 and 2·1 kb fragments in HaeIII digests of male genomic DNA. Although the 3·4 and 2·1 kb Y repeats do not crossreact, both exist as tandem clusters of alternating Yspecific and non-Y-specific sequences.

The 3·4 kb Y repeats contain at least three distinct sequences with autosomal homologies interspersed in various ways with a collection of several different Yspecific repeat sequences. Individual recombinant clones derived from isolated 3·4 kb HaeIII Y fragments have been identified which do not cross-react. Thus, the 3·4 kb HaeIII Y fragments are a heterogeneous mixture of sequences which have in common the regular occurrence of HaeIII restriction sites at 3·4 kb intervals and an organization as tandem clusters at various sites along the Y-long arm.

The 2·1 kb HaeIII Y fragment cross-reacts with a 1i9 kb HaeIII autosomal fragment. Both the Ychromosomal and autosomal fragments are part of tandem clusters which have a unit length of 2·4 kb. All of the 2·4 kb Y repeats are similar and contain a 1·6 kb Y-specific repeat and an 800 bp sequence which has homology with an 800 bp sequence in the autosomal 2·4 kb repeats. While this 800 bp sequence is common to both Y and autosomal 2·4 kb repeats and is associated with a single Y-specific repeat, it is associated with at least four non-cross-reacting autosome-specific sequences. Like the Y repeat, the autosomal repeats exist as tandem clusters of 2·4 kb units and are composed of an 800 bp common sequence alternating with a 1·6 kb autosome-specific sequence. Thus, in humans, the common sequence is associated with several different sequences yet always occurs as part of a tandem cluster of 2·4 kb repeats. The common and autosome-specific sequences of the 2·4 kb repeats are also present in gorillas as part of organized repeat units. However, in gorillas the two are not associated with each other.

The Y-chromosome repeats described here are a heterogeneous mixture of sequences organized into specific sets of alternating Y-specific and non-Y-specific sequences. They do not have an identified function and the mechanisms by which they are generated are unknown. Nevertheless, their marked chromosomal speciticity and the regularity of the basic repeat unit in each type of repeat seem inconsistent with stochastic mechanisms of sequence diffusion between chromosomes.

Use of repetitive DNA for diagnosis of chromosomal rearrangements

We have used two repeated DNA fragments (3.4 and 2.1 kb) released from Y chromosome DNA by digestion with the restriction endonuclease Hae III to analyze potential Y chromosome/autosome translocations. Two female patients were studied who each had an abnormal chromosome 22 with extra quinacrine fluorescent material on the short arm. The origin of the 22p+ chromosomes was uncertain after standard cytologic examinations. Analysis of one patient's DNA with the Y-specific repeated DNA probes revealed the presence of both the 3.4 and 2.1kb Y-specific fragments. Thus, in this patient, the additional material was from the Y chromosome. Analysis of the second patient's DNA for Y-specific repeated DNA was negative, indicating that the extra chromosomal segment was not from the long arm of the Y chromosome. These two cases demonstrate that repeated DNA can distinguish between similar appearing aberrant chromosomes and may be useful in karyotypic and prenatal diagnosis.

Adjuvants to immunological methods for mRNA purification. Application to the isolation of mRNA for carbonic anhydrase I from rabbit reticulocytes

In order to generate the molecular probes needed to investigate the seemingly coordinate expression of carbonic anhydrase (CA I) and beta-globin within erythrocytes during human development, CA I-containing polyribosomes have been isolated from rabbit reticulocytes by reaction with purified antibodies to CA I followed by immunoadsorption of immune complexes with formalin-fixed protein A-bearing bacteria. In the course of such isolation, a series of maneuvers were seen to have a markedly favorable influence on the level of purity attained. These maneuvers include the use of 5 mg/ml of heparin concentrations to attenuate nonspecific binding and entrapment of unwanted polyribosomes, the addition of 200 units/ml of placental ribonuclease inhibitor to augment recovery in reactions which by test already appeared RNase-free, and the preadsorption of polyribosomes with formalin-fixed bacteria prior to immunological reaction so as to remove a subset of polyribosomes seemingly predisposed to nonspecific binding. In the absence of all of the maneuvers, attained purity was no greater than a few per cent. When all were employed, CA I-mRNA derived from immunopurified polyribosomes was recovered with more than 80% purity and 20% yield, as evident from both immunoassays and electrophoresis of its cell-free products.

The molecular basis of hemoglobin Grady

DNA from individuals heterozygous for the extended alpha-chain variant Hb Grady were studied by gene counting and restriction enzyme analysis. Neither method indicated the presence of an extra (fifth) alpha gene, which argues that if this variant arose by unequal crossing over, the event most likely involved mispairing between alleles rather than between the separate alpha 1 and alpha 2 loci.

Unequal crossing-over: a common basis of single alpha-globin genes in Asians and American blacks with hemoglobin-H disease

The alpha-globin genes of five black Americans, two Chinese, and five Filipinos with HbH disease (an alpha-thalassemia state in which there is a single functional alpha gene) were analyzed by restriction endonuclease techniques. All subjects were found to have one chromosome 16, lacking both alpha genes, and another containing a single alpha gene (--/-alpha). Restriction endonuclease patterns of the DNA obtained from all 12 subjects were identical and compatible with unequal crossing-over as the mechanism of origin of the single alpha gene in these individuals.

A molecular basis for hemoglobin-H disease in American blacks

We have applied gene counting and restriction endonuclease mapping techniques to the study of two American black families in which there were one or more cases of HbH disease. We found deletions of three of the four normal alpha-globin genes in individuals with HbH disease. In two of these individuals, the chromosome containing the single alpha gene could have originated by crossing over between mispaired alpha genes, resulting in a deletion of about 4.2 kilobases (kb).

Transcription of the nonrepeated fraction of "accessible" DNA in rat liver chromatin

The relationship between structure and function in eukaryotic chromatin has been studied in rat liver cells. To elucidate the functional significance of "accessible" DNA, the transcription of this DNA (prepared by titration of liver chromatin with poly-D-lysine) has been examined by RNA-DNA hybridization. The maximum extent to which nuclear RNA will hybridize to the nonrepeated fraction of "accessible" DNA has been measured and compared to the extent that whole chromatin DNA will hybridize. The results show that "accessible" DNA has the same number of sequences complementary to nuclear RNA as does total DNA. In addition DNA-DNA reassociation experiments indicate that there is only a small difference between the total unique sequence populations of "accessible" and total DNA. These results indicate that nonrepeated "accessible" DNA is not preferentially transcribed in the cell as is predicted by some models of chromatin structure.

Isolation and characterization of the DNA fraction of rat liver chromatin which binds polylysine

The structure of eukaryotic chromatin has been investigated by isolating and analyzing the "accessible" DNA fraction of rat liver chromatin. This DNA fraction has been isolated by titrating the chromatin with the protese-resistant D isomer of polylysine to bind the "accessible" DNA sites. After removal of chromosomal proteins by digestion with pronase, all DNA not protected from attack by bound polylysine was removed by digestion with DNase. Even after exhaustive treatment with pronase and DNase approximately 30% of the chromatin DNA remains resistant to nuclease attack. Analysis of the isolated DNA shows it to be mainly double-stranded with an average size of 200-250 base pairs. The DNA is slightly A-T rich and contains both repetitive and "single-copy" nuleotide sequences. The results suggest that there are extensive regions in chromatin where the DNA is not tightly complexed with protein. Furthermore, the DNA of these regions is similar in gross properties to the DNA of the total genome.