Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Many protein-protein interactions involve the binding of short protein segments to peptide-binding domains. Usually, such interactions require the recognition of linear motifs with variable conservation. The combination of highly conserved and more variable regions in the same ligands often contributes to the multispecificity of binding, a common property of enzymes and cell signaling proteins. Characterization of amino acid preferences of peptide-binding domains is important for the design of mediators of protein-protein interactions (PPIs). Computational methods are an efficient alternative to the often costly and cumbersome experimental techniques, enabling the design of potential mediators that can be later validated in downstream experiments. Here, we described a methodology using the Pepspec application of the Rosetta molecular modeling package to predict the amino acid preferences of peptide-binding domains. This methodology is useful when the structure of the receptor protein and the nature of the peptide ligand are both known or can be inferred. The methodology starts with a well-characterized anchor from the ligand, which is extended by randomly adding amino acid residues. The binding affinity of peptides generated this way is then evaluated by flexible-backbone peptide docking in order to select the peptides with the best predicted binding scores. These peptides are then used to calculate amino acid preferences and to optionally compute a position-weight matrix (PWM) that can be used in further studies. To illustrate the application of this methodology, we used the interaction between subunits of human interferon regulatory factor 5 (IRF5), previously known to be multispecific but globally guided by a short conserved motif called pLxIS. The estimated amino acid preferences were consistent with previous knowledge about the IRF5 binding surface. Positions occupied by phosphorylatable serine residues exhibited a high frequency of aspartate and glutamate, likely because their negatively charged side chains are similar to phosphoserine.

Revisiting MOMS criteria for prenatal repair of spina bifida: upper gestational-age limit should be raised and assessment of prenatal motor function rather than anatomical level improves prediction of postnatal function

OBJECTIVES

To determine if the lower-extremity neurological motor function level in fetuses with open spina bifida deteriorates within the 4-week interval between a first prenatal motor assessment at around 22 weeks of gestation and a second evaluation, prior to 'late' prenatal surgery, defined as surgery at 26-28 weeks and, in certain situations, up to 30 weeks, and to assess the association between prenatal presurgical motor-function level, anatomical level of the lesion and postnatal motor-function level.

METHODS

This was a two-center cohort study of 94 singleton fetuses with open spina bifida which underwent percutaneous repair using the skin-over-biocellulose for antenatal fetoscopic repair (SAFER) technique between December 2016 and January 2022. All women underwent two prenatal systematic ultrasound evaluations, approximately 4 weeks apart, with the second one being performed less than 1 week before surgery, and one postnatal evaluation via physical examination within 2 months of birth. Motor-function classification was from spinal level T12 to S1, according to key muscle function. Each leg was analyzed separately; in case of discrepancy between the two legs, the worst motor-function level was considered for analysis. Motor-function-level evaluations were compared with each other and with the anatomical level as observed on ultrasound. Independent predictors of a postnatal reduction in motor-function level were assessed using a logistic regression model.

RESULTS

Prenatal motor-function level was assessed at a median gestational age of 22.5 (interquartile range (IQR), 20.7-24.3) and 26.7 (IQR, 25.4-27.3) weeks, with a median interval of 4.0 (IQR, 2.4-6.0) weeks. The median gestational age at surgery was 27.0 (IQR, 25.9-27.6) weeks and the postnatal examination was at median age of 0.8 (IQR, 0.3-5.4) months. There was no significant difference in motor-function level between the two prenatal evaluations (P = 0.861). We therefore decided to use the second prenatal evaluation for comparison with postnatal motor function and anatomical level. Overall, prenatal and postnatal motor function evaluations were significantly different from the anatomical level (preoperative assessment, P = 0.0015; postnatal assessment, P = 0.0333). Comparing prenatal with postnatal motor-function level, we found that 87.2% of babies had similar or improved motor function compared with that prior to prenatal surgery. On logistic regression analysis, lower anatomical level of defect and greater difference between anatomical level and prenatal motor-function level were identified as independent predictors of postnatal motor function (odds ratio, 0.237 (95% CI, 0.095-0.588) (P = 0.002) and 3.44 (95% CI, 1.738-6.813) (P < 0.001), respectively).

CONCLUSIONS

During a 4-week interval between first ultrasound evaluation and late fetal surgical repair of open spina bifida, motor function does not change significantly, suggesting that late repair, ≥ 26 weeks, does not impact negatively on motor-function outcome. Compared with the anatomical level of the lesion, preoperative neurological motor-function assessment via ultrasound is more predictive of postnatal motor function, and should be included in preoperative counseling. © 2023 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.

Building Programs to Eradicate Toxoplasmosis Part III: Epidemiology and Risk Factors

Purpose of Review

Review comprehensive data on rates of toxoplasmosis in Panama and Colombia.

Recent Findings

Samples and data sets from Panama and Colombia, that facilitated estimates regarding seroprevalence of antibodies to Toxoplasma and risk factors, were reviewed.

Summary

Screening maps, seroprevalence maps, and risk factor mathematical models were devised based on these data. Studies in Ciudad de Panamá estimated seroprevalence at between 22 and 44%. Consistent relationships were found between higher prevalence rates and factors such as poverty and proximity to water sources. Prenatal screening rates for anti-Toxoplasma antibodies were variable, despite existence of a screening law. Heat maps showed a correlation between proximity to bodies of water and overall Toxoplasma seroprevalence. Spatial epidemiological maps and mathematical models identify specific regions that could most benefit from comprehensive, preventive healthcare campaigns related to congenital toxoplasmosis and Toxoplasma infection.

Genomic diversity and genetic variation of Leishmania panamensis within its endemic range

Species belonging to the Leishmania (Viannia) subgenus are important causative agents of cutaneous and mucocutaneous leishmaniasis in Central and South America. These parasites possess several distinctive biological features that are influenced by their genetics, population structure, and genome instability. To date, several studies have revealed varying degrees of genetic diversity within Leishmania species. Particularly, in species of the L. (Viannia) subgenus, a generalized high intraspecific genetic diversity has been reported, although, conflicting conclusions have been drawn using different molecular techniques. Despite being the most common Leishmania species circulating in Panama and Colombia, few studies have analyzed clinical samples of Leishmania panamensis using whole-genome sequencing, and their restricted number of samples has limited the information they can provide to understand the population structure of L. panamensis. Here, we used next generation sequencing (NGS) to explore the genetic diversity of L. panamensis within its endemic range, analyzing data from 43 isolates of Colombian and Panamanian origin. Our results show the occurrence of three well-defined geographically correlated groups, and suggests the possible occurrence of additional phylogeographic groups. Furthermore, these results support the existence of a mixed mode of reproduction in L. panamensis, with varying frequencies of events of genetic recombination occurring primarily within subpopulations of closely related strains. This study offers important insights into the population genetics and reproduction mode of L. panamensis, paving the way to better understand their population structure and the emergence and maintenance of key eco-epidemiological traits.

Building Programs to Eradicate Toxoplasmosis Part II: Education

Purpose of Review

Review work to create and evaluate educational materials that could serve as a primary prevention strategy to help both providers and patients in Panama, Colombia, and the USA reduce disease burden of Toxoplasma infections.

Recent Findings

Educational programs had not been evaluated for efficacy in Panama, USA, or Colombia.

Summary

Educational programs for high school students, pregnant women, medical students and professionals, scientists, and lay personnel were created. In most settings, short-term effects were evaluated. In Panama, Colombia, and USA, all materials showed short-term utility in transmitting information to learners. These educational materials can serve as a component of larger public health programs to lower disease burden from congenital toxoplasmosis. Future priorities include conducting robust longitudinal studies of whether education correlates with reduced adverse disease outcomes, modifying educational materials as new information regarding region-specific risk factors is discovered, and ensuring materials are widely accessible.

Epidemiological Aspects of Maternal and Congenital Toxoplasmosis in Panama

In Panama, epidemiological data on congenital toxoplasmosis are limited, making it difficult to understand the scope of clinical manifestations in the population and factors that may increase the risk of infection. This study provides insight into the epidemiological situation of maternal and congenital toxoplasmosis in Panama and contributing information on the burden of this disease in Central America. Blood samples were collected from 2326 pregnant women and used for the detection of anti-T. gondii antibodies. A high seroprevalence (44.41%) was observed for T. gondii infection in pregnant women from different regions of Panama, with an estimated incidence rate of congenital toxoplasmosis of 3.8 cases per 1000 live births. The main risk factors associated with T. gondii infection using bivariate statistical analysis were an elementary level education and maternal age range of 34-45 years. Multivariate statistical analyses revealed that in some regions (San Miguelito, North and West regions), the number of positive cases correlated with the presence of pets, stray dogs and the consumption of poultry. In other regions (East and Metropolitan regions), the absence of pets was considered a protective factor associated with negative cases, while the presence of stray cats and the age range of 25-34 years did not represent any risk in these regions.

Gene expression patterns associated with Leishmania panamensis infection in macrophages from BALB/c and C57BL/6 mice

Leishmania parasites can trigger different host immune responses that result in varying levels of disease severity. The C57BL/6 and BALB/c mouse strains are among the host models commonly used for characterizing the immunopathogenesis of Leishmania species and the possible antileishmanial effect of novel drug candidates. C57BL/6 mice tend to be resistant to Leishmania infections, whereas BALB/c mice display a susceptible phenotype. Studying species-specific interactions between Leishmania parasites and different host systems is a key step to characterize and validate these models for in vivo studies. Here, we use RNA-Seq and differential expression analysis to characterize the transcriptomic profiles of C57BL/6 and BALB/c peritoneal-derived macrophages in response to Leishmania panamensis infection. We observed differences between BALB/c and C57BL/6 macrophages regarding pathways associated with lysosomal degradation, arginine metabolism and the regulation of cell cycle. We also observed differences in the expression of chemokine and cytokine genes associated with regulation of immune responses. In conclusion, infection with L. panamensis induced an inflammatory gene expression pattern in C57BL/6 macrophages that is more consistently associated with a classic macrophage M1 activation, whereas in BALB/c macrophages a gene expression pattern consistent with an intermediate inflammatory response was observed.

A Computational Approach to Explore the Interaction of Semisynthetic Nitrogenous Heterocyclic Compounds with the SARS-CoV-2 Main Protease

In the context of the ongoing coronavirus disease 2019 (COVID-19) pandemic, numerous attempts have been made to discover new potential antiviral molecules against its causative agent, SARS-CoV-2, many of which focus on its main protease (M^pro). We hereby used two approaches based on molecular docking simulation to explore the interaction of four libraries of semisynthetic nitrogenous heterocyclic compounds with M^pro. Libraries L1 and L2 contain 52 synthetic derivatives of the natural compound 2-propylquinoline, whereas libraries L3 and L4 contain 65 compounds synthesized using the natural compound physostigmine as a precursor. Validation through redocking suggested that the rigid receptor and flexible receptor approaches used for docking were suitable to model the interaction of this type of compounds with the target protein, although the flexible approach seemed to provide a more realistic representation of interactions within the active site. Using empirical energy score thresholds, we selected 58 compounds from the four libraries with the most favorable energy estimates. Globally, favorable estimates were obtained for molecules with two or more substituents, putatively accommodating in three or more subsites within the M^pro active site. Our results pave the way for further experimental evaluation of the selected compounds as potential antiviral agents against SARS-CoV-2.

HLA allele and haplotype frequencies in the Panamanian population

In this study, we report for the first time HLA allele and haplotype frequencies in the modern Panamanian population at a two-field (four digits) resolution level. Reported frequencies were calculated from genotype data for the HLA-A, -B, -C, -DPB1, -DQB1 and -DRB1 loci of 462 healthy unrelated Panamanian adults of Hispanic ethnicity. In addition to providing new insights on the allelic structure of the Panamanian population and its origin, these data are critical for better planning of healthcare strategies in the country and for future research exploring the association with certain chronic and infectious diseases.

Antileishmanial activity of a new chloroquine analog in an animal model of Leishmania panamensis infection

Leishmania panamensis is a relevant causative agent of tegumentary leishmaniasis in several Latin American countries. Available antileishmanial drugs have several limitations including relatively high toxicity, difficult administration, high production costs and the emergence of resistance in circulating strains. Therefore, the identification of new molecules as potential therapeutics for leishmaniasis is of great relevance. Here, we developed a murine model of L. panamensis infection and evaluated the effect of a new compound in vivo. After treatment of animals with the compound, we observed a significant reduction of inflammation and parasite load at the inoculation site, in a dose-dependent manner. We observed a reduction in IL-10 production by popliteal lymph nodes cells of infected mice. These results pave the way for future evaluation of this compound as a potential antileishmanial drug or as a suitable scaffold for lead optimization strategies.

Betacoronavirus Genomes: How Genomic Information has been Used to Deal with Past Outbreaks and the COVID-19 Pandemic

In the 21st century, three highly pathogenic betacoronaviruses have emerged, with an alarming rate of human morbidity and case fatality. Genomic information has been widely used to understand the pathogenesis, animal origin and mode of transmission of coronaviruses in the aftermath of the 2002-2003 severe acute respiratory syndrome (SARS) and 2012 Middle East respiratory syndrome (MERS) outbreaks. Furthermore, genome sequencing and bioinformatic analysis have had an unprecedented relevance in the battle against the 2019-2020 coronavirus disease 2019 (COVID-19) pandemic, the newest and most devastating outbreak caused by a coronavirus in the history of mankind. Here, we review how genomic information has been used to tackle outbreaks caused by emerging, highly pathogenic, betacoronavirus strains, emphasizing on SARS-CoV, MERS-CoV and SARS-CoV-2. We focus on shared genomic features of the betacoronaviruses and the application of genomic information to phylogenetic analysis, molecular epidemiology and the design of diagnostic systems, potential drugs and vaccine candidates.

Detection and Characterization of Leptospira Infection and Exposure in Rats on the Caribbean Island of Saint Kitts

In this study, we detected and characterized Leptospira infection and exposure in rats on the Caribbean island of Saint Kitts for the first time. We detected Leptospira infection in 17/29 (59%), 14/29 (48)%, and 11/29 (38)% of rats by RT-PCR, culture, and immunofluorescence assay, respectively. Whole genome sequencing (WGS) and analysis and serogrouping of 17 Leptospira strains isolated from rats revealed their close relationship with L. interrogans serogroup Icterohaemorrhagiae (n = 10) and L. borgpetersenii serogroup Ballum (n = 7). WGS, serogrouping, and additional PCR tests on rat kidneys confirmed mixed infections with L. interrogans and L. borgpetersenii in the kidneys of three rats. Microscopic agglutination test (MAT) was positive for 25/29 (87%) of the rats tested, and the response was restricted to serovars Icterohaemorrhagiae {24/29(83%)}, Mankarso {4/29(14%)}, Copenhageni {4/29(14%)}, Grippotyphosa {2/29(7%)}, and Wolffi {1/29(3%)}. Interestingly, there was no agglutinating antibody response to serovar Ballum. We observed a similar pattern in the serologic response using Leptospira isolates obtained from this study with each of the rat sera, with strong response to L. interrogans isolates but minimal reactivity to L. borgpetersenii isolates. Our findings suggest the use of multiple complementary diagnostic tests for Leptospira surveillance and diagnosis to improve the accuracy of the data.

Assessment of ovulation synchronization protocols in goats and use of pregnancy specific protein B (PSPB) enzyme linked immunsorbent assay (ELISA) to determine kid number at birth

The efficacy of several protocols for ovulation synchronization and timed artificial insemination (TAI) in goats was examined. In addition, the relationship between levels of pregnancy specific protein B (PSPB) during gestation assessed with a commercially available ELISA and the number of offspring at birth was determined. In Experiment 1, 70 does were randomized into four treatments: (1) breed by estrus [BBE], (2) 6-d treatment with a new [C6N], (3) once-used [C61], or (4) twice-used Controled Internal Drug Release (CIDR) device [C62)]. BBE does received two 15 mg doses of prostaglandin-F2α (PGF) at a 10-d interval and were bred 12 h after estrus onset. CIDR groups received a CIDR for 6 d with 15 mg PGF given at CIDR removal. TAI was performed 48 h after CIDR removal and does were given 50 μg GnRH. All does were inseminated with a single dose of frozen semen using a non-surgical, transcervical technique. Pregnancy rates for the BBE, C6N, C61 and C62 treatment groups were 39% ± 12%, 64% ± 12%, 77% ± 12% and 57% ± 12%, respectively, and did not differ. Reuse of CIDRs, even with reuse extending for a total of 21 d, was as effective as new CIDRs for synchronization of ovulation. In Experiment 2, 68 does were randomized into four treatments: (1) BBE, (2) C6N, (3) NC.Synch [NCS], (4) modified NCS [NCSM]. The BBE and C6N groups were as described for Experiment 1. The NCS and NCSM groups received 15 mg PGF on Day 1, 50 μg GnRH on Day 8 and 15 mg PGF on Day 15 (NCS) or Day 15.5 (NCSM). Does were bred by TAI at 72 h (NCS) or 60 h (NCSM) after the second PGF injection. All does in the NCS and NCSM groups received 50 μg GnRH at TAI. Pregnancy rates were 53% ± 12%, 30% ± 11%, 50% ± 11% and 41% ± 12% for does in the BBE, C6N, NCS and NCSM group, respectively, and did not differ. In Experiment 3, 62 does pregnant to TAI were bled at Days 48 and 85 post-insemination for PSPB. Data on kid numbers and birth weights were subsequently recorded. At Day 48 of gestation, PSPB levels for does birthing singletons were lower than for does birthing twins or triplets (25.0 ± 0.1^a, 28.8 ± 0.1^b and 30.7 ± 0^b ng/mL, respectively, ^abP<0.05). At Day 85 of gestation, PSPB levels were progressively greater for does birthing singletons versus twins versus triplets (27.0 ± 0.1^a, 28.5 ± 0.1^b and 31.6 ± 0^c ng/mL, ^abcP<0.05). In conclusion, PSPB concentrations detected using a commercially available ELISA at Day 48 or 85 of gestation could distinguish does carrying single versus multiple fetuses.

High sensitivity and reproducibility of in-house ELISAs using different genotypes of Trypanosoma cruzi

The adequate choice of Trypanosoma cruzi strains as antigen source for the diagnosis of Chagas disease is still controversial due to differences in terms of accuracy reported between different diagnostic tests. In this study was determined if the genetic variability between different genotypes of T. cruzi (TcI, TcII and TcIV) affect the final diagnosis of Chagas disease. The sensitivity and specificity index of in-house ELISA tests prepared with different T. cruzi strains were evaluated with chagasic and non-chagasic control sera and using the TESA-blot as a reference test. The results of this study revealed that the sensitivity index did not vary, with percentages of 100% for all strains in both tests. However, the specificity index for ELISA tests showed differences between 92% and 98%, but were reduced to 78%-89% when Leishmania-positive sera were included. All ELISAs and TESA-blot prepared with different antigens and the recombinant Wiener test were challenged in an endemic community for Chagas disease in Panama. Both ELISAs and TESA-blot recognized the same positive sera, corroborating the sensitivity indexes (100%) found with the control sera. The TESA-blot maintained the specificity index of 100% and did not display false positives. However, the recombinant Wiener test decreased its sensitivity to 81.25%.

A Marine Diterpenoid Modulates the Proteasome Activity in Murine Macrophages Stimulated with LPS

The proteasome is an intracellular complex that degrades damaged or unfolded proteins and participates in the regulation of several processes. The immunoproteasome is a specialized form that is expressed in response to proinflammatory signals and is particularly abundant in immune cells. In a previous work, we found an anti-inflammatory effect in a diterpenoid extracted from the octocoral Pseudopterogorgia acerosa, here called compound 1. This compound prevented the degradation of inhibitor κB α (IκBα) and the subsequent activation of nuclear factor κB (NFκB), suggesting that this effect might be due to inhibition of the ubiquitin-proteasome system. Here we show that compound 1 inhibits the proteasomal chymotrypsin-like activity (CTL) of murine macrophages in the presence of lipopolysaccharide (LPS) but not in its absence. This effect might be due to the capacity of this compound to inhibit the activity of purified immunoproteasome. The compound inhibits the cell surface expression of major histocompatibility complex (MHC)-I molecules and the production of proinflammatory cytokines induced by LPS in vitro and in vivo, respectively. Molecular docking simulations predicted that compound 1 selectively binds to the catalytic site of immunoproteasome subunits β1i and β5i, which are responsible for the CTL activity. Taken together these findings suggest that the compound could be a selective inhibitor of the immunoproteasome, and hence could pave the way for its future evaluation as a candidate for the treatment of inflammatory disorders and autoimmune diseases.

Genomic Variability among Field Isolates and Laboratory-Adapted Strains of Leptospira borgpetersenii Serovar Hardjo

Leptospira borgpetersenii serovar Hardjo colonizes cattle kidneys and may occasionally infect humans and other mammals. Strains belonging to two clonal subtypes (types A and B) with marked differences in their pathogenicity in the hamster experimental model have been described for this serovar. Such differences have been attributed to point mutations in individual genes, although those genes have not yet been characterized. In order to better understand genetic variability among L. borgpetersenii serovar Hardjo isolates, we sequenced and compared the genomes of two laboratory-adapted strains and three abattoir-derived field isolates of L. borgpetersenii serovar Hardjo. Relatively low genetic variability was observed within isolates of the same subtype, with most of the mutations of moderate or high impact found in the laboratory-adapted isolates. In contrast, several differences regarding gene content and genetic variants were observed between the two subtypes. Putative type-specific genes appear to encode proteins associated with functions that are critical for infection. Some of these genes seem to be involved in transcriptional regulation, possibly leading to a distinct regulatory pattern in each type. These results show that changes in regulatory mechanisms, previously suggested to be critical during Leptospira speciation, may occur in L. borgpetersenii. In addition, the bioinformatics methodology used in this study for variant calling can be useful to other groups working with nonmodel prokaryotic organisms such as Leptospira species.

VianniaTopes: a database of predicted immunogenic peptides for Leishmania (Viannia) species

Leishmania is a protozoan parasite causing several disease presentations collectively known as leishmaniasis. Pathogenic species of Leishmania are divided into two subgenera, L. (Leishmania) and L. (Viannia). Species belonging to the Viannia subgenus have only been reported in Central and South America. These species predominantly cause cutaneous leishmaniasis, but in some cases, parasites can migrate to the nasopharyngeal area and cause a highly disfiguring mucocutaneous presentation. Despite intensive efforts, no effective antileishmanial vaccine is available for use in humans, although a few candidates mainly designed for L. (Leishmania) species are now in clinical trials. After sequencing the genome of Leishmania panamensis, we noticed a high degree of sequence divergence among several orthologous proteins from both subgenera. Consequently, some of the previously published candidates may not work properly for species of the Viannia subgenus. To help in vaccine design, we predicted CD4+ and CD8+ T cell epitopes in the theoretical proteomes of four strains belonging to the Viannia subgenus. Prediction was performed with at least two independent bioinformatics tools, using the most frequent human major histocompatibility complex (MHC) class I and class II alleles in the affected geographic area. Although predictions resulted in millions of peptides, relatively few of them were predicted to bind to several MHC alleles and can therefore be considered promiscuous epitopes. Comparison of our results to previous applications to species of the Leishmania subgenus confirmed that approximately half of the reported candidates are not present in Viannia proteins with a threshold of 80% sequence similarity and coverage. However, our prediction methodology was able to predict 70-100% of the candidates that could be found in Viannia. All the prediction data generated in this study are publicly available in an interactive database called VianniaTopes.

Isolation and characterization of Leptospira interrogans serovar Copenhageni from a dog from Saint Kitts

Introduction. Leptospirosis is a zoonotic bacterial disease of global distribution affecting humans and animals. The initial phase of leptospirosis resembles many other febrile illness and due to its broad and biphasic clinical manifestations, selection and implementation of appropriate diagnostic tests can be challenging.

Case presentation. This report describes a case investigation of a 14 weeks old male, orphan puppy, presented with generalised jaundice, anemia, weakness, and anorexia. Clinical abnormalities included the evidence of renal and hepatic failure. Antemortem and postmortem diagnostic investigations were conducted to identify the cause of illness. PCR testing and culture of blood was positive for Leptospira sp. Necropsy followed by histopathology evaluation revealed lesions compatible with liver and kidney damage consisting of marked diffuse hepatocellular dissociation, acute renal tubular necrosis, and mild interstitial nephritis.

Conclusion. Multiple diagnostic techniques including bacterial isolation confirmed Leptospira infection in this puppy. Whole genome sequencing and analysis identified the Leptospira sp. isolated from this puppy as Leptospira interrogans serovar Copenhageni. To our knowledge, this case report describes the first isolation of Leptospira from Saint Kitts. This case highlights the usefulness of including multiple diagnostic tests for the diagnosis and epidemiological investigation of Leptospira infection. Accurate diagnosis followed by timely intervention can prevent case fatality and mortality in infected patients.

Use of AFLP for the study of eukaryotic pathogens affecting humans

Amplified fragment length polymorphism (AFLP) is a genotyping technique based on PCR amplification of specific restriction fragments from a particular genome. The methodology has been extensively used in plant biology to solve a variety of scientific questions, including taxonomy, molecular epidemiology, systematics, population genetics, among many others. The AFLP share advantages and disadvantages with other types of molecular markers, being particularly useful in organisms with no previous DNA sequence knowledge. In eukaryotic pathogens, the technique has not been extensively used, although it has the potential to solve many important issues as it allows the simultaneous examination of hundreds or even thousands of polymorphic sites in the genome of the organism. Here we describe the main applications published on the use of AFLP in eukaryotic pathogens, with emphasis in species of the groups fungi, protozoa and helminths, and discuss the role of this methodology in the context of new techniques derived from the advances of the next generation sequencing.

Whole Genome Sequencing Allows Better Understanding of the Evolutionary History of Leptospira interrogans Serovar Hardjo

The genome of a laboratory-adapted strain of Leptospira interrogans serovar Hardjo was sequenced and analyzed. Comparison of the sequenced genome with that recently published for a field isolate of the same serovar revealed relatively high sequence conservation at the nucleotide level, despite the different biological background of both samples. Conversely, comparison of both serovar Hardjo genomes with those of L. borgpetersenii serovar Hardjo showed extensive differences between the corresponding chromosomes, except for the region occupied by their rfb loci. Additionally, comparison of the serovar Hardjo genomes with those of different L. interrogans serovars allowed us to detect several genomic features that may confer an adaptive advantage to L. interrogans serovar Hardjo, including a possible integrated plasmid and an additional copy of a cluster encoding a membrane transport system known to be involved in drug resistance. A phylogenomic strategy was used to better understand the evolutionary position of the Hardjo serovar among L. interrogans serovars and other Leptospira species. The proposed phylogeny supports the hypothesis that the presence of similar rfb loci in two different species may be the result of a lateral gene transfer event.

11 COMPARISON OF CONTROLLED INTERNAL DRUG-RELEASE INSERT–BASED AND PROGESTERONE-FREE METHODS FOR OVULATION SYNCHRONIZATION AND TIMED ARTIFICIAL INSEMINATION OF GOATS

A CIDR synchronization program is an important tool for facilitating ovulation synchronization and timed AI (OvSynch-TAI). The objective of this study was to test the efficacy of reusing CIDR for OvSynch-TAI compared with that for a progesterone-free OvSynch-TAI protocol (NCS) or a breed by oestrus detection (ED) control. A total of 87 does were randomised into 1 of 5 treatments: (1) ED (control, n = 18), (2) NCS (n = 18), (3) CIDR6-New (n = 17), (4) CIDR6–1X (n = 17), and (5) CIDR6–2X (n = 17). Does in the ED group received two 15-mg doses of PGF2α at a 10-d interval and were bred 12 h after the onset of oestrus following the second PGF2α injection. The NCS group received 15 mg of PGF2α on Day 0, 50 μg of gonadotropin-releasing hormone on Day 8, 15 mg of PGF2α on Day 15, and 50 μg of gonadotropin-releasing hormone on Day 18, concurrently with TAI. The CIDR groups (new, 1X-used, or 2X-used) received a P4 device for a 6-d period, and 15 mg of PGF2α was administered at CIDR removal. Does were bred 48 h after CIDR removal and were given 50 μg of gonadotropin-releasing hormone at TAI. The CIDR in the CIDR6–1X group were previously in place for 10 days before use, whereas CIDR in the CIDR6–2X group were previously in place for 16 days before use. Reused CIDR were rinsed in a diluted Nolvasan solution, followed by a clean water rinse, allowed to air dry, and stored in a refrigerator until time of use. The experiment was conducted in 2 replicates. Within each replicate, all treatments were scheduled so that does were bred during the same 2-day period, and all does were inseminated with a single dose of frozen semen using a nonsurgical (transcervical) technique. Blood samples were taken daily in all treatment groups to monitor concentrations of serum progesterone until the time of breeding. Pregnancy was determined by ultrasonography at 54 and 85 days of gestation. Data were analysed using GLM procedures of SAS (SAS Institute Inc., Cary, NC, USA). Data for pregnancy rates were analysed with a model that included effects of treatment, replicate, and their interactions. Data for serum progesterone concentrations were analysed with a model that included the effects of treatment, replicate, day, and their interactions. Means were separated by Duncan’s test. Mean progesterone differed (P < 0.001) with treatment (5.3 ± 0.8bc, 3.5 ± 0.8c, 7.0 ± 0.8ab, 7.9 ± 0.8a, 6.2 ± 0.8ab ng mL–1 for ED, NCS, CIDR6-New, CIDR6–1X, and CIDR6–2X, respectively; least squares mean ± standard error of the mean). Pregnancy rates for the ED, NCS, CIDR6-New, CIDR6–1X, and CIDR6–2X treatment groups were 39 ± 11%bc, 22 ± 11%c, 64 ± 12%ab, 77 ± 12%a, and 57 ± 12%ab, respectively. In conclusion, reused CIDR were as effective as new CIDR for attaining satisfactory pregnancy rates. Timed AI using a once-used CIDR was more effective for establishing pregnancy than ED and NCS treatments. The lower pregnancy rates in the ED and NCS groups were associated with lower mean progesterone levels during the Ovsynch treatment period before breeding. This research was supported by the North Carolina Agricultural Experiment Station.

The genome of Leishmania panamensis: insights into genomics of the L. (Viannia) subgenus

Kinetoplastid parasites of the Leishmania genus cause several forms of leishmaniasis. Leishmania species pathogenic to human are separated into two subgenera, Leishmania (Leishmania) and L. (Viannia). Species from the Viannia subgenus cause predominantly cutaneous leishmaniasis in Central and South America, occasionally leading to more severe clinical presentations. Although the genomes of several species of Leishmania have been sequenced to date, only one belongs to this rather different subgenus. Here we explore the unique features of the Viannia subgenus by sequencing and analyzing the genome of L. (Viannia) panamensis. Against a background of conservation in gene content and synteny, we found key differences at the genomic level that may explain the occurrence of molecular processes involving nucleic acid manipulation and differential modification of surface glycoconjugates. These differences may in part explain some phenotypic characteristics of the Viannia parasites, including their increased adaptive capacity and enhanced metastatic ability.

Growth responses and ion accumulation in the halophytic legume Prosopis strombulifera are determined by Na2SO4 and NaCl

Halophytes are potential gene sources for genetic manipulation of economically important crop species. This study addresses the physiological responses of a widespread halophyte, Prosopis strombulifera (Lam.) Benth to salinity. We hypothesised that increasing concentrations of the two major salts present in soils of central Argentina (Na2SO4, NaCl, or their iso-osmotic mixture) would produce distinct physiological responses. We used hydroponically grown P. strombulifera to test this hypothesis, analysing growth parameters, water relations, photosynthetic pigments, cations and anions. These plants showed a halophytic response to NaCl, but strong general inhibition of growth in response to iso-osmotic solutions containing Na2SO4. The explanation for the adaptive success of P. strombulifera in high NaCl conditions seems to be related to a delicate balance between Na(+) accumulation (and its use for osmotic adjustment) and efficient compartmentalisation in vacuoles, the ability of the whole plant to ensure sufficient K(+) supply by maintaining high K(+)/Na(+) discrimination, and maintenance of normal Ca(2+) levels in leaves. The three salt treatments had different effects on the accumulation of ions. Findings in bi-saline-treated plants were of particular interest, where most of the physiological parameters studied showed partial alleviation of SO4(2-)-induced toxicity by Cl(-). Thus, discussions on physiological responses to salinity could be further expanded in a way that more closely mimics natural salt environments.

Different sodium salts cause different solute accumulation in the halophyte Prosopis strombulifera

The success of Prosopis strombulifera in growing under high NaCl concentrations involves a carefully controlled balance among different processes, including compartmentation of Cl(-) and Na(+) in leaf vacuoles, exclusion of Na(+) in roots, osmotic adjustment and low transpiration. In contrast, Na(2) SO(4) causes growth inhibition and toxicity. We propose that protection of the cytoplasm can be achieved through production of high endogenous levels of specific compatible solutes. To test our hypothesis, we examined endogenous levels of compatible solutes in roots and leaves of 29-, 40- and 48-day-old P. strombulifera plants grown in media containing various concentrations of NaCl, Na(2) SO(4) or in mixtures of both, with osmotic potentials of -1.0,-1.9 and -2.6 MPa, as correlated with changes in hydric parameters. At 24 h after the last pulse plants grown in high NaCl concentrations had higher relative water content and relatively higher osmotic potential than plants grown in Na(2) SO(4) (at 49 days). These plants also had increased synthesis of proline, pinitol and mannitol in the cytoplasm, accompanied by normal carbon metabolism. When the sulphate anion is present in the medium, the capacities for ion compartmentalisation and osmotic adjustment are reduced, resulting in water imbalance and symptoms of toxicity due to altered carbon metabolism, e.g. synthesis of sorbitol instead of mannitol, reduced sucrose production and protein content. This inhibition was partially mitigated when both anions were present together in the solution, demonstrating a detrimental effect of the sulphate ion on plant growth.

Identification of new meningococcal serogroup B surface antigens through a systematic analysis of neisserial genomes

The difficulty of inducing an effective immune response against the Neisseria meningitidis serogroup B capsular polysaccharide has lead to the search for vaccines for this serogroup based on outer membrane proteins. The availability of the first meningococcal genome (MC58 strain) allowed the expansion of high-throughput methods to explore the protein profile displayed by N. meningitidis. By combining a pan-genome analysis with an extensive experimental validation to identify new potential vaccine candidates, genes coding for antigens likely to be exposed on the surface of the meningococcus were selected after a multistep comparative analysis of entire Neisseria genomes. Eleven novel putative ORF annotations were reported for serogroup B strain MC58. Furthermore, a total of 20 new predicted potential pan-neisserial vaccine candidates were produced as recombinant proteins and evaluated using immunological assays. Potential vaccine candidate coding genes were PCR-amplified from a panel of representative strains and their variability analyzed using maximum likelihood approaches for detecting positive selection. Finally, five proteins all capable of inducing a functional antibody response vs N. meningitidis strain CU385 were identified as new attractive vaccine candidates: NMB0606 a potential YajC orthologue, NMB0928 the neisserial NlpB (BamC), NMB0873 a LolB orthologue, NMB1163 a protein belonging to a curli-like assembly machinery, and NMB0938 (a neisserial specific antigen) with evidence of positive selection appreciated for NMB0928. The new set of vaccine candidates and the novel proposed functions will open a new wave of research in the search for the elusive neisserial vaccine.

Computational identification of beta-barrel outer-membrane proteins in Mycobacterium tuberculosis predicted proteomes as putative vaccine candidates

Mycobacterial porins and other beta-barrel outer-membrane proteins are represented by the structure of Mycobacterium smegmatis porin MspA. On the basis of existing knowledge of beta-barrel outer-membrane proteins, several state of the art prediction methods, as well as a new in-house program (PROB) were employed for the systematic exploration of Mycobacterium tuberculosis predicted proteomes for potential beta-barrel structures. PROB allowed parameter optimization while functioning with an adaptive algorithm for the detection of outer-membrane beta-barrel proteins in highly divergent proteomes. As a result of the predictions, 114 proteins in total were predicted to be beta-barrel structures; of these, 40 were PE-PPE proteins, 8 Mce proteins, 24 hypothetical, 11 probable membrane proteins, 10 transporters, 4 lipoproteins, and 14 classified as other. The congruence among three of the predictors, PROB, TMB-Hunt, and BOMP, was low with only three proteins (MT0318, MT0356, and MT2423) predicted by the three. Overall, 79 new proteins for which no previous experimental work has been performed are reported. At least 10 of these have high potential of being not only surface-exposed but also served as putative vaccine candidates as determined by in silico predictions of CD4T cell MHC-II restricted epitopes.

Identification of a pore lining segment in gap junction hemichannels

The ability of certain connexins to form open hemichannels has been exploited to study the pore structure of gap junction (hemi)channels. Cysteine scanning mutagenesis was applied to cx46 and to a chimeric connexin, cx32E(1)43, which both form patent hemichannels when expressed in Xenopus oocytes. The thiol reagent maleimido-butyryl-biocytin was used to probe 12 cysteine replacement mutants in the first transmembrane segment and two in the amino-terminal segment. Maleimido-butyryl-biocytin was found to inhibit channel activity with cysteines in two equivalent positions in both connexins: I33C and M34C in cx32E(1)43 and I34C and L35C in cx46. These two positions in the first transmembrane segment are thus accessible from the extracellular space and consequently appear to contribute to the pore lining. The data also suggest that the pore structure is complex and may involve more than one transmembrane segment.