Herbarium specimen sequencing allows precise dating of Xanthomonas citri pv. citri diversification history

Herbarium collections are an important source of dated, identified and preserved DNA, whose use in comparative genomics and phylogeography can shed light on the emergence and evolutionary history of plant pathogens. Here, we reconstruct 13 historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri (Xci) from infected Citrus herbarium specimens. Following authentication based on ancient DNA damage patterns, we compare them with a large set of modern genomes to estimate their phylogenetic relationships, pathogenicity-associated gene content and several evolutionary parameters. Our results indicate that Xci originated in Southern Asia ~11,500 years ago (perhaps in relation to Neolithic climate change and the development of agriculture) and diversified during the beginning of the 13th century, after Citrus diversification and before spreading to the rest of the world (probably via human-driven expansion of citriculture through early East-West trade and colonization).

Genome-wide association study for resistance in bread wheat (Triticum aestivum L.) to stripe rust (Puccinia striiformis f. sp. tritici) races in Argentina

BACKGROUND

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases of the wheat crop. It causes significant reductions in both grain yield and grain quality. In recent years, new and more virulent races have overcome many of the known resistance genes in Argentinian germplasm. In order to identify loci conferring resistance to the local races of Pst for effective utilization in future breeding programs, a genome-wide association study (GWAS) was performed using a collection of 245 bread wheat lines genotyped with 90 K SNPs.

RESULTS

To search for adult plant resistance (APR) the panel was evaluated for disease severity (DS) and area under disease progress curve (AUDPC) in field trials during two years under natural infection conditions. To look for seedling or all-stage resistance (ASR) the panel was evaluated to determine infection type (IT) under greenhouse conditions against two prevalent races in Argentina. The phenotypic data showed that the panel possessed enough genetic variability for searching for sources of resistance to Pst. Significant correlations between years were observed for Pst response in the field and high heritability values were found for DS (H² = 0.89) and AUDPC (H² = 0.93). Based on GWAS, eight markers associated with Pst resistance (FDR < 0.01) were identified, of these, five were associated with ASR (on chromosomes 1B, 2A, 3A and 5B) and three with APR (on chromosomes 3B and 7A). These markers explained between 2% and 32.62% of the phenotypic variation. Five of the markers corresponded with previously reported Yr genes/QTL, while the other three (QYr.Bce.1B.sd.1, QYr.Bce.3A.sd and QYr.Bce.3B.APR.2) might be novel resistance loci.

CONCLUSION

Our results revealed high genetic variation for resistance to Argentinian stripe rust races in the germplasm used here. It constitutes a very promising step towards the improvement of Pst resistance of bread wheat in Argentina. Also, the identification of new resistance loci would represent a substantial advance for diversifying the current set of resistance genes and to advance in the improvement of the durable resistance to the disease.

First historical genome of a crop bacterial pathogen from herbarium specimen: Insights into citrus canker emergence

Over the past decade, ancient genomics has been used in the study of various pathogens. In this context, herbarium specimens provide a precious source of dated and preserved DNA material, enabling a better understanding of plant disease emergences and pathogen evolutionary history. We report here the first historical genome of a crop bacterial pathogen, Xanthomonas citri pv. citri (Xci), obtained from an infected herbarium specimen dating back to 1937. Comparing the 1937 genome within a large set of modern genomes, we reconstructed their phylogenetic relationships and estimated evolutionary parameters using Bayesian tip-calibration inferences. The arrival of Xci in the South West Indian Ocean islands was dated to the 19th century, probably linked to human migrations following slavery abolishment. We also assessed the metagenomic community of the herbarium specimen, showed its authenticity using DNA damage patterns, and investigated its genomic features including functional SNPs and gene content, with a focus on virulence factors.

Serious fungal infections in Peru

Epidemiological data about mycotic diseases are limited in Peru and estimation of the fungal burden has not been previously attempted. Data were obtained from the Peruvian National Institute of Statistics and Informatics, UNAIDS and from the Ministry of Health's publications. We also searched the bibliography for Peruvian data on mycotic diseases, asthma, COPD, cancer and transplants. Incidence or prevalence for each fungal disease were estimated in specific populations at risk. The Peruvian population for 2015 was 31,151,543. In 2014, the estimated number of HIV/AIDS and pulmonary tuberculosis cases was 88,625, 38,581 of them not on ART, and 22,027, respectively. A total of 581,174 cases of fungal diseases were estimated, representing approximately 1.9% of the Peruvian population. This figure includes 498,606, 17,361 and 4,431 vulvovaginal, oral and esophageal candidiasis, respectively, 1,557 candidemia cases, 3,593 CPA, 1,621 invasive aspergillosis, 22,453 allergic bronchopulmonary aspergilllosis, 29,638 severe asthma with fungal sensitization, and 1,447 Pneumocystis pneumonia. This first attempt to assess the fungal burden in Peru needs to be refined. We believe the figure obtained is an underestimation, because of under diagnosis, non-mandatory reporting and lack of a surveillance system and of good data about the size of populations at risk.

Treatment of cryptococcal meningitis in Peruvian AIDS patients using amphotericin B and fluconazole

OBJECTIVES

To describe the mycologic and clinical outcomes and factors associated with failure in Peruvian patients with AIDS-associated cryptococcal meningitis (CM) treated with amphotericin B deoxycholate (Amph B) followed by fluconazole.

METHODS

Patients were treated with intravenous Amph B 0.7 mg/kg/day for 2 or 3 weeks followed by oral fluconazole 400mg/day for 7 or 8 weeks. Clinical and laboratory evaluations including cerebrospinal fluid (CSF) studies were performed at baseline and at weeks 2 and 10.

RESULTS

The CSF cultures were negative in 25% and 68% of 47 patients at weeks 2 and 10, respectively. In the univariate analysis, baseline low body mass index (BMI), hyponatremia, low serum albumin, positive blood culture and CSF antigen titers >or=1024 were associated with a positive CSF culture at week 2. Baseline positive urine culture, positive blood culture, any positive extraneural culture and CSF opening pressure at week 2 >or=300 mm H2O were associated with a positive CSF culture at week 10. In the multivariate analysis no association was found.

CONCLUSIONS

Therapy with Amph B and fluconazole, combined with aggressive management of elevated intracranial pressure (ICP), results in low CSF sterilization rates at week 2 and acceptable CSF sterilization rates at week 10 when compared with other series.

Utility of the Determine Syphilis TP rapid test in commercial sex venues in Peru

OBJECTIVES

This study sought to evaluate the utility of the Determine Syphilis TP test performed in Peruvian commercial sex venues for the detection of active syphilis; and determine the feasibility of integrating rapid syphilis testing for female sex workers (FSW) into existing health outreach services.

METHODS

We tested 3586 female sex workers for syphilis by Determine in the field using whole blood fingerstick, and by rapid plasma reagin (RPR) and Treponema pallidum haemagglutination assay (TPHA) in a central laboratory in Lima using sera.

RESULTS

97.4% of the FSW offered rapid syphilis testing participated; and among those who tested positive, 87% visited the local health centre for treatment. More than twice as many specimens were RPR reactive using serum in Lima (5.7%) than tested positive by whole blood Determine in the field (2.8%), and although most were confirmed by TPHA, only a small proportion (0.7%) were RPR reactive at >or=1:8 dilutions, and likely indicating active syphilis. Sensitivity, specificity and positive predictive value of the Determine Syphilis TP test in whole blood when compared to serum RPR reactivity at any dilution confirmed by TPHA as the gold standard were 39.3%, 99.2% and 71.4%, respectively. Sensitivity improved to 64.0% when using serum RPR >or=1:8 confirmed by TPHA. Invalid tests were rare (0.3%).

CONCLUSIONS

Rapid syphilis testing in sex work venues proved feasible, but Determine using whole blood obtained by fingerstick was substantially less sensitive than reported in previous laboratory-based studies using serum. Although easy to perform in outreach venues, the utility of this rapid syphilis test was relatively low in settings where a large proportion of the targeted population has been previously tested and treated.

Introduction: perspectives on therapy with gay, lesbian, and bisexual clients

The approach that mental health professionals have taken in working with gay, lesbian, and bisexual (GLB) clients has changed dramatically over the past 25 years. Once viewed as being pathological in nature-either a sociopathic personality disorder or a sexual deviation-homosexuality is no long conceptualized as a "disorder" and instead is viewed within the broader context of human diversity. Even with such changes, many mental health professionals nonetheless retain subtle biases against working with gay, lesbian, and bisexual clients, and often lack the necessary information for working with them effectively. This issue of In Session provides a series of articles designed to help practicing therapists to become better aware of those clinical issues if they are to work with GLB individuals-which they are likely to do.

Endemic sporotrichosis

Although first reported more than a century ago, sporotrichosis, caused by Sporothrix schenckii, still remains a poorly studied disease. Results from recently published studies on sporotrichosis in endemic areas are summarised and assembled with previous findings, providing a comprehensive review that highlights the needs for further research.

A National, Randomized Survey of HIV/AIDS Knowledge and Attitudes Among Psychiatrists in Training

Given the broad spectrum of medical and psychiatric complications associated with HIV (human immunodeficiency virus) disease, HIV-related education is an important curriculum topic for all physicians. This study examined the HIV-related knowledge and attitudes among psychiatrists in training to evaluate their training needs. A survey instrument was developed containing 15 knowledge items, 15 attitude items, demographic items, and questions concerning how HIV/AIDS (acquired immunodeficiency syndrome) affected residency choice and self-perception of training needs. The questionnaire was mailed to 2,252 psychiatrists in training randomly selected and stratified by American Psychiatric Association district and postgraduate training year. The sample consisted of 825 respondents representing 37% of the initial pool. Knowledge was most lacking in areas dealing with HIV-related neuropsychiatric complications and issues concerning HIV/AIDS and special populations. In general, the respondents expressed positive attitudes about HIV-related issues; however, three items correctly endorsed by fewer than 75% of the sample dealt specifically with the management of neuropsychiatric complications, working with dying patients, and the range of normal sexuality. Targeted HIV-related education is needed for psychiatrists in training and particularly should encompass neuropsychiatric syndromes and issues of special populations.

Situational factors associated with AIDS risk behavior lapses and coping strategies used by gay men who successfully avoid lapses

While most gay men have reduced behavior practices at high risk for HIV infection, there is growing evidence that many also lapse to unsafe sex. This study examined situational factors related to risk behavior lapses as well as coping strategies used by men who successfully resist lapse urges. A convenience sample of 470 men patronizing gay bars or attending social organization meetings in four cities was surveyed. Forty-five percent of men were classified as "lapsers" (those who had had unprotected anal intercourse in the previous 6 months) and 24% were classified as "resisters" (those who successfully resisted urges to engage in this behavior). All provided information concerning the importance of factors related to the most recent occurrence of either unsafe sex or resisting unsafe urges. Most episodes of unsafe sex occurred outside monogamous relationships and with partners of unknown HIV serostatus, although simply inquiring about partner serostatus was relatively common. Lapsers rated affectionate feelings and wishing to please a partner as well as spontaneity of unsafe sex as the most important situational factors surrounding high-risk behavior. Resisters of unsafe sex urges reported active cognitive self-guidance, experience in safe sex, and recall of both AIDS fears and safety benefits as their most important coping strategies. Gay men who continue high-risk behavior may be overrelying on partner reports of negative serostatus. Lapse prevention approaches tailored to situations that create increased risk vulnerability must be developed. Teaching skills already used by men who successfully resist unsafe sex urges might be one approach.

Marijuana sensitivity and panic anxiety

The authors explore the relationship between marijuana smoking and panic anxiety by examining the effects of marijuana smoking on patients with panic anxiety compared with marijuana's effects on both patient and nonpatient controls. Patients with panic anxiety were found to be particularly likely to experience increased anxiety while smoking marijuana. The majority of panic anxiety patients spontaneously stopped using marijuana because of increased anxiety; continued marijuana smoking in these individuals was found to be infrequent. The results suggest that current marijuana use is atypical of panic anxiety patients.

The effects of timolol maleate on subjective and physiological components of air travel phobia

Twenty-one monophobic patients with moderately severe fear of flying were exposed to two 40 minute challenge flights after taking either Timolol 20 mg/day or placebo. Heart rate, blood pressure, subjective ratings of anxiety, fear and palpitation and Hamilton Anxiety Scale ratings were made at the predetermined assessment intervals. Post-treatment global ratings of improvement were provided by patients and the attending psychiatrist. Results showed that heart rate significantly increased from baseline with placebo while Timolol successfully inhibited tachycardia during the challenge flights. Subjective ratings of anxiety, fear and palpitations did not show any drug group differences. These variables, however, showed a non-significant decrease from outgoing to return flight assessments after an initial significant increase from baseline scores. Hamilton Anxiety Scale ratings showed a significant decrease from baseline to post-treatment assessments, irrespective of drug group. Global improvement ratings revealed no significant differences between drug groups. Overall ratings by the psychiatrist were generally more positive than patients' ratings, with the difference between the two sources of assessment reaching significance only in the placebo group. Disregarding group membership, heart rate was positively and significantly correlated with subjective ratings of fear, but not with palpitations or ratings of overall anxiety.

Ineffective dental and surgical treatment associated with atypical facial pain

Patients with atypical facial pain (AFP) are subject to ineffective dental and surgical procedures for their pain complaints. Twenty-one of fifty-eight patients (36.2 percent) with AFP had sixty-five dental and surgical treatments, with only one patient showing less pain as a result of the treatment. While the majority of patients (69 percent) with AFP suffered from a psychiatric illness, fourteen (24 percent) of the patients referred for AFP had a specific medical or dental disorder that was causal in their pain complaints. There is a trend for the AFP patient with a psychiatric diagnosis to receive more ineffective treatments than those AFP patients for whom a specific medical or dental diagnosis was made. Patients with AFP should receive conservative dental and medical treatment and a psychiatric assessment before dental and surgical procedures are contemplated.

Psychiatric disorders associated with atypical facial pain

Atypical facial pain (AFP) patients classically present with a chronic discomfort that is neither anatomic nor dermatomal in distribution. Neuropsychiatric assessment of 68 patients with AFP indicated that 46 (68%) had a specific psychiatric disorder by DSM-III criteria. A wide spectrum of psychiatric disorders was present. The authors emphasize that psychiatric assessment of patients with AFP should be an integral part in early assessments of this disorder, rather than relying on psychiatric opinions after extensive dental and other invasive procedures have been tried in vain and often to the detriment of the patient. Comments on the excellent prognosis in treating the psychiatric syndromes associated with AFP are made.

A comparison of the safety and efficacy of bupropion HCL and amitriptyline hcl in depressed outpatients

1. Thirty adult outpatients diagnosed with depressive illness were treated with either bupropion HCL or amitriptyline HCL. 2. Weekly ratings of efficacy and safety were undertaken using the Hamilton Depression, Hamilton Anxiety, Clinical Global Improvement, and Treatment Emergent Symptom Scales. Periodic physical investigations were also performed. 3. After 4 weeks of active treatment patients in both drug groups showed significant improvement on all rating scales. 4. The side effect profile of each drug was clinically different from one another with a notable absence of anticholinergic side effects characteristic of the bupropion group. 5. No significant laboratory or physical changes were found although slight changes in weight were noted with bupropion patients having a slight weight loss and amitriptyline patients a slight weight gain. There were no withdrawal effects from discontinuing either drug.