Fungi Tryptophan Synthases: What Is the Role of the Linker Connecting the α and ß Structural Domains in Hemileia vastatrix TRPS? A Molecular Dynamics Investigation.

Tryptophan synthase (TRPS) is a complex enzyme responsible for tryptophan biosynthesis. It occurs in bacteria, plants, and fungi as an αßßα heterotetramer. Although encoded by independent genes in bacteria and plants, in fungi, TRPS is generated by a single gene that concurrently expresses the α and ß entities, which are linked by an elongated peculiar segment. We conducted 1 µs all-atom molecular dynamics simulations on Hemileia vastatrix TRPS to address two questions: (i) the role of the linker segment and (ii) the comparative mode of action. Since there is not an experimental structure, we started our simulations with homology modeling. Based on the results, it seems that TRPS makes use of an already-existing tunnel that can spontaneously move the indole moiety from the α catalytic pocket to the ß one. Such behavior was completely disrupted in the simulation without the linker. In light of these results and the αß dimer's low stability, the full-working TRPS single genes might be the result of a particular evolution. Considering the significant losses that Hemileia vastatrix causes to coffee plantations, our next course of action will be to use the TRPS to look for substances that can block tryptophan production and therefore control the disease.

The Patient's Clinical Profile From a Neuro-Ophthalmology Center in Brazil: A Retrospective Study.

BACKGROUND: Neuro-ophthalmology (NO) is a subspeciality of Ophthalmology, which represents more than an intersection of Neurology and Ophthalmology. The present report highlights the increasing importance of the subspeciality in Brazil and provides a unique retrospective study of the patient's clinical profile of a NO reference center. METHODS: Our study was retrospectively planned aiming to identify all neuro-ophthalmic cases of Instituto de Olhos of the Medical School Faculdade Ciências Médicas de Minas Gerais from August 2013 to March 2022.The first clinical diagnostic impression was selected from a predetermined list of 18 neuro-ophthalmologic conditions. Some NO conditions were eventually reclassified during the follow-up as the final clinical diagnosis impression. The concordance between the first and final clinical impressions was also investigated, as well as the patient's referral source. RESULTS: The sample comprised 903 patients from which 56.4% were female. The mean age was 51.48 ± 20.93 years. Males were more frequent in lower age groups <1 year (n = 3, 100%) and 1-9 years (n = 19/37, 51.4%). An external referral source represented 23.1%, and patients referred after basic ophthalmic consultation and from glaucoma service were 30.3% and 23.2%, respectively. The most encountered first clinical diagnostic impressions were isolated optic atrophy (13.1%), non-neuro-ophthalmic disease (11.7%), optic disc abnormalities (10.4%), ischemic optic neuropathies/retinal vascular occlusions (10.2%), and other visual field defects (9.0%). The kappa concordance coefficient among the first and final clinical diagnostic impressions was 0.53 (95% CI 0.48-0.59), indicating a moderate concordance level. The concordance among the most frequent diagnoses was lower in isolated optic atrophy (33%), other visual field defects (41%), and idiopathic optic neuritis (40%). CONCLUSIONS: Due to the limited number of epidemiology studies in neuro-ophthalmology, we highlight the importance of a NO service in the public health system in Brazil. It may certainly contribute to better strategy plan assistance among professionals and health care managers. This report should seemingly stimulate other studies regarding the relevant and unique features of this subspeciality, which is undoubtedly increasing its importance among patients, and in the scientific community worldwide.

Fetal hemoglobin-boosting haplotypes of BCL11A gene and HBS1L-MYB intergenic region in the prediction of clinical and hematological outcomes in a cohort of children with sickle cell anemia.

Single nucleotide polymorphisms (SNPs) of BCL11A gene and HBS1L-MYB intergenic region (named HMIP-2) affect both fetal hemoglobin (HbF) concentration and clinical outcomes in patients with sickle cell anemia (SCA). However, no previous study has examined the interaction among these SNPs in the regulation of HbF. We examined whether HbF-boosting haplotypes combining alleles of functional SNPs of BCL11A and HMIP-2 were associated with clinical outcomes and hematological parameters, and whether they interact to regulate HbF in a cohort of Brazilian children with SCA. The minor haplotype of BCL11A ("TCA", an allele combination of rs1427407, rs766432, and rs4671393) was associated with higher HbF, hemoglobin and lower reticulocytes count compared to reference haplotype "GAG". The minor haplotype of HMIP-2 ("CGC", an allele combination of rs9399137, rs4895441, and rs9494145) was associated with higher HbF and hemoglobin compared to reference haplotype "TAT". Subjects carrying minor haplotypes showed reduced rate of clinical complications compared to reference haplotypes. Non-carriers of both minor haplotypes for BCL11A and HMIP-2 showed the lowest HbF concentration. Subjects carrying only the minor haplotype of BCL11A showed significantly higher HbF concentration than non-carriers of any minor haplotype, which showed no significant difference compared to subjects carrying only the minor haplotype of HMIP-2. Interestingly, subjects carrying both minor haplotypes of BCL11A ("TCA") and HMIP-2 ("CGC") showed significantly higher HbF levels than subjects carrying only the minor haplotype of BCL11A. Our novel findings suggest that HbF-boosting haplotypes of BCL11A and HMIP-2 can predict clinical outcomes and may interact to regulate HbF in patients with SCA.

Plant Co-expression Annotation Resource: a web server for identifying targets for genetically modified crop breeding pipelines.

The development of genetically modified crops (GM) includes the discovery of candidate genes through bioinformatics analysis using genomics data, gene expression, and others. Proteins of unknown function (PUFs) are interesting targets for GM crops breeding pipelines for the novelty associated with such targets and also to avoid copyright protection. One method of inferring the putative function of PUFs is by relating them to factors of interest such as abiotic stresses using orthology and co-expression networks, in a guilt-by-association manner. In this regard, we have downloaded, analyzed, and processed genomics data of 53 angiosperms, totaling 1,862,010 genes and 2,332,974 RNA. Diamond and InterproScan were used to discover 72,266 PUFs for all organisms. RNA-seq datasets related to abiotic stresses were downloaded from NCBI/GEO. The RNA-seq data was used as input to the LSTrAP software to construct co-expression networks. LSTrAP also created clusters of transcripts with correlated expression, whose members are more probably related to the molecular mechanisms associated with abiotic stresses in the plants. Orthologous groups were created (OrhtoMCL) using all 2,332,974 proteins in order to associate PUFs to abiotic stress-related clusters of co-expression and therefore infer their function in a guilt-by-association manner. A freely available web resource named "Plant Co-expression Annotation Resource" ( https://www.machado.cnptia.embrapa.br/plantannot ), Plantannot, was created to provide indexed queries to search for PUF putatively associated with abiotic stresses. The web interface also allows browsing, querying, and retrieving of public genomics data from 53 plants. We hope Plantannot to be useful for researchers trying to obtain novel GM crops resistant to climate change hazards.

Evidence for interactions between inflammatory markers and renin-angiotensin system molecules in the occurrence of albuminuria in children with sickle cell anemia.

Sickle cell anemia (SCA) is an important cause of chronic kidney disease, but its pathophysiology is not completely understood. The aim of this study was to compare inflammatory biomarkers in urine samples of SCA children with and without albuminuria, and to explore correlations with renin-angiotensin system (RAS) molecules. A cross-sectional study of 213 children selected from the Minas Gerais state cohort were assigned to two groups: Group 1-89 children with SCA who had albuminuria; Group 2-124 children with SCA and normal albuminuria matched by age and sex with group 1. A subset of 89 children was prospectively followed for a median time of 1.1 year. Inflammatory biomarkers (chemokines and cytokines) in urine were measured using cytometric beads array, and RAS molecules were measured by ELISA. Children with albuminuria had significantly higher urinary levels of IP-10/CXCL10, MCP-1/CCL2, MIG/CXCL9, IL-8/CXCL8, IL-12p70, TNF, IL-10, and IL-6 than patients with normal albuminuria. In the correlation analysis, albumin/creatinine ratio was significantly and positively correlated with IP-10/CXCL10, MCP-1/CCL2, MIG/CXCL9, IL-8/CXCL8, TNF, IL-10, and IL-6. Significant correlations were found between inflammatory and RAS molecules. In the prospective analysis, cumulative risk of persistent albuminuria was higher for children with urinary levels of IP-10/CXCL10 or IL-6 above the 50th percentile. Our data showed that inflammatory markers and RAS molecules might contribute to the occurrence of albuminuria in children with SCA, suggesting that both pathways interact in sickle cell nephropathy.

Functional polymorphisms of BCL11A and HBS1L-MYB genes affect both fetal hemoglobin level and clinical outcomes in a cohort of children with sickle cell anemia.

Fetal hemoglobin (HbF) ameliorates clinical severity of sickle cell anemia (SCA). The major loci regulating HbF levels are HBB cluster, BCL11A, and HMIP-2 (HBS1L-MYB). However, the impact of noncoding single-nucleotide polymorphisms (SNPs) in these loci on clinical outcomes and their functional role on regulating HbF levels should be better elucidated. Therefore, we performed comprehensive association analyses of 14 noncoding SNPs in five loci with HbF levels and with clinical outcomes in a cohort of 250 children with SCA from Southeastern Brazil, and further performed functional annotation of these SNPs. We found SNPs independently associated with HbF levels: rs4671393 in BCL11A (ß-coefficient = 0.28), rs9399137 in HMIP-2A (ß-coefficient = 0.16), and rs4895441 in HMIP-2B (ß-coefficient = 0.15). Patients carrying minor (HbF-boosting) alleles for rs1427407, rs93979137, rs4895441, rs9402686, and rs9494145 showed reduced count of reticulocytes (p < 0.01), while those carrying the T allele of rs9494145 showed lower white blood cell count (p = 0.002). Carriers of the minor allele for rs9402686 showed higher peripheral saturation of oxygen (p = 0.002). Patients carrying minor alleles in BCL11A showed lower risk of transfusion incidence rate ratio (IRR ≥ 1.3; p < 0.0001). This effect was independent of HbF effect (p = 0.005). Carriers of minor alleles for rs9399137 and rs9402686 showed lower risk of acute chest syndrome (IRR > 1.3; p ≤ 0.01). Carriers of the reference allele for rs4671393 showed lower risk of infections (IRR = 1.16; p = 0.01). In conclusion, patients carrying HbF-boosting alleles of BCL11A and HMIP-2 were associated with milder clinical phenotypes. Higher HbF concentration may underlie this effect.

Novel mutations causing biotinidase deficiency in individuals identified by the newborn screening program in Minas Gerais, Brazil.

Biotinidase deficiency is an autosomal recessive inherited metabolic disorder caused by mutations in the BTD gene. Clinical manifestations can be treated and effectively prevented with pharmacological doses of biotin. Nine novel mutations in BTD are reported in 14 children diagnosed by the newborn screening program in Minas Gerais, Brazil, from June 2013 to December 2017. Serum BTD enzyme activity was determined for all cases and some parents. Two of the mutations are deletions and seven missense mutations located in the exonic region of the BTD gene, mostly in exon 4. Two newborns were profoundly biotinidase-deficient (one homozygous p.A534V [c.1601C > T] and another, double heterozygous for a novel mutation p.R211S [c.631C > A] co-inherited with an already described mutation p.T532 M [c.1595C > T]). Two mutations were associated with a partial deficiency of biotinidase (p.F361 V [c.1081 T > G] in two homozygous children, and p.S311 T [c.932G > C] in a compound heterozygous child who co-inherited a known severe mutation p.Y438X [c.1314 T > A]). The remaining five mutations were found in compound heterozygous children. Hence, a definitive conclusion about the degree of biotinidase deficiency is not possible yet. These results emphasize the importance of sequencing the BTD gene as an important tool to gain a better understanding of the correlation between biochemical phenotype and genotype.

Use of the Polymerase Chain Reaction as a Complementary Method for the Detection of Central Nervous System Involvement in Children and Adolescents with Acute Lymphoblastic Leukemia.

BACKGROUND: Cytological analysis of the cerebrospinal fluid (CSF) remains the most widely used method for diagnosing central nervous system (CNS) involvement in acute lymphoblastic leukemia (ALL). This study aimed at evaluating the use of polymerase chain reaction (PCR), in comparison to other methods, for the assessment of the presence of blast cells in the CSF at the time of diagnosis of ALL. METHODS: This was a prospective, single-centre, study enrolling all patients up to the age of 18 years who were admitted to a university hospital between November 2011 and November 2014 with a diagnosis of ALL and from whom it was possible to draw a sufficient amount of CSF for analysis by conventional cytology (CT), immunophenotyping (IMP), and PCR. RESULTS: A total of 46 CSF samples from 44 ALL pediatric patients were included. CT was performed in all samples, IMP in 44, and PCR in 34. Thirteen (28.2%) samples showed positive results: two by CT, four by IMP, four by PCR, and three by both IMP and PCR. CONCLUSIONS: The results of this study showed that PCR should be considered a complementary method for the evaluation of the CSF in ALL patients at diagnosis.

Immunophenotyping of the cerebrospinal fluid as a prognostic factor at diagnosis of acute lymphoblastic leukemia in children and adolescents.

This study aimed at evaluating the use of immunophenotyping (IMP) in the identification of blast cells in the cerebrospinal fluid (CSF) of children and adolescents with acute lymphoblastic leukemia (ALL). Sixty-seven patients aged 18 years or younger were included. Fifty-five CSF samples were analyzed at initial diagnosis and 17 at the time of relapse. A cytological analysis (CA) was performed in all 72 samples, while IMP was done in 63. Blasts were identified in only three samples by CA, whereas all three samples were found negative by IMP, one of which had no isolation of nucleated cells after centrifugation. Among the samples analyzed by IMP, 11 showed a positive blast count, two of which had been inconclusive using CA. No equivalence was found between CA and IMP results (p = 0.55). CSF IMP positivity was not associated with other risk factors for ALL relapse. Among the 55 patients included at the time of diagnosis of ALL, eight relapsed during follow-up. Considering the cases of central nervous system (CNS) relapse, one of the patients belonged to the CSF IMP-positive group (11%) at diagnosis, and the other two cases, to the IMP-negative (5%) group. Detection of CSF blast cells using IMP was associated with a worse overall (p < 0.0001) and event-free survival (p < 0.0001). These results show that CSF IMP may be a useful additional method to conventional CA in the diagnosis of CNS involvement in ALL, and for the identification of high-risk subgroups that would benefit from an intensified therapy.

Prevalence and incidence of erythrovirus B19 infection in children with sickle cell disease: The impact of viral infection in acute clinical events.

B19V infection is common during childhood. It is self-limited in healthy individuals, but is often associated with transient aplastic crisis in children with sickle cell disease. The aim of this study was to estimate the prevalence and incidence of B19V infection in children with sickle cell disease screened by the Newborn Screening Program of Minas Gerais, Brazil, and followed-up at Fundação Hemominas. Serum or plasma samples from 278 patients were tested for anti-B19V IgG and IgM using commercial ELISA and for viral DNA using in-house real-time PCR assays; 127 negative-children were retested about 1 year later. The median age of children at first testing was 5.9 years (0.8-12.3). The estimated prevalence of B19V was 29.5 % (95%CI 24.1-34.9 %). The incidence of B19V in those 127 negative-children was 18.2 cases/100 patient-years. All DNA-positive samples were identified as genotype 1, except one sample, in which both genotypes 1 and 3 were identified. It was observed that the higher the child's age, the higher the probability of B19V infection. The analysis of clinical and hematological data showed a significant association of B19V infection with transient aplastic crisis and acute splenic sequestration, higher frequency of transfusions, and higher rate of hospitalization, but not with acute chest syndrome or stroke. These results emphasize the impact of B19V infection on the course of sickle cell disease. Strategies to prevent and monitor B19V infection in children with sickle cell disease should be considered to diminish its morbidity in this susceptible population.

Reticulocyte count is the most important predictor of acute cerebral ischemia and high-risk transcranial Doppler in a newborn cohort of 395 children with sickle cell anemia.

Stroke is a severe clinical manifestation of sickle cell anemia (SCA). Despite the prognostic relevance of transcranial Doppler (TCD), more accurate tools to assess stroke risk in children with SCA are required. Here, we describe the effect of clinical, laboratory, and molecular features on the risk of stroke and high-risk TCD in children from the newborn cohort of Minas Gerais, Brazil. Outcomes studied were acute cerebral ischemia and high-risk TCD. Clinical and hematological data were retrieved from children's records. Genetic markers, which were known for their association with stroke risk, were genotyped by polymerase chain reaction/restriction fragment length polymorphism and sequencing. The cumulative incidence of acute cerebral ischemia by the age of 8 years was 7.4 % and that of high-risk TCD by the age of 11.5 years was 14.2 %. The final multivariate model for acute cerebral ischemia risk included high white blood cell count and reticulocyte count, acute chest syndrome rate, and the single nucleotide polymorphisms (SNPs) TEK rs489347 and TNF-α rs1800629. The model for high-risk TCD included high reticulocyte count and the SNPs TEK rs489347 and TGFBR3 rs284875. Children with risk factors should be considered for intensive risk monitoring and for intervention therapy.

Glucose-6-Phosphate Dehydrogenase Deficiency in Brazilian Children With Sickle Cell Anemia is not Associated With Clinical Ischemic Stroke or High-Risk Transcranial Doppler.

BACKGROUND: Stroke is a severe complication of sickle cell anemia (SCA). The role of glucose-6-phosphate dehydrogenase (G6PD) deficiency in the development of stroke in children with SCA is controversial. PROCEDURE: The aim of this study was to investigate the association of clinical ischemic stroke, high-risk transcranial Doppler measurements (TCD), and hematological features with molecular variants usually linked to G6PD deficiency or with the biochemical activity of G6PD in a cohort of 395 Brazilian children with SCA. G6PD activity was quantitatively determined using an enzymatic-colorimetric assay. G6PD mutations were determined by PCR-RFLP and sequencing. Clinical and hematological data were retrieved from the children's records. RESULTS: The prevalence of molecularly defined deficiency (hereafter, molecular deficiency) was 4.3% (95% confidence interval: 2.3-6.3%). The mean G6PD activity was 16.88 U/g hemoglobin (Hb) (standard error of the mean [SEM] 0.28) in the group without G6PD molecular deficiency and 8.43 (SEM 1.01) U/g Hb in the group with G6PD A(-) molecular deficiency. G6PD molecular deficiency was not associated with any hematological features. No effects of G6PD molecular deficiency on clinical ischemic stroke or high-risk TCD were detected. The mean G6PD activity was similar in children who had clinical ischemic stroke and in those without stroke. Similar results were obtained in analyses comparing children who had high-risk TCD and those without high-risk TCD. CONCLUSIONS: Our study demonstrated that G6PD molecular deficiency was not associated either with clinical ischemic stroke or high-risk TCD. Similarly, we found no associations between G6PD enzyme activity and stroke or high-risk TCD. Small sample size precludes definitive conclusions.

The Natural History of Hb S/Hereditary Persistence of Fetal Hemoglobin in 13 Children from the State of Minas Gerais, Brazil.

Children with Hb S (HBB: c.20A > T)/hereditary persistence of fetal hemoglobin (Hb S/HPFH) have a mild clinical phenotype, but some complications have been reported. The natural history of Hb S/HPFH in children from the State of Minas Gerais, Brazil newborn cohort is described. Clinical and hematological data regarding participants' phenotypes were retrieved from medical records. The HPFH-1, HPFH-2, and HPFH-3 and α-thalassemia (α-thal) deletions were detected by gap-polymerase chain reaction (gap-PCR). Thirteen children were included, nine (69.2%) had the Hb S/HPFH-2 deletion, and four (30.8%) had Hb S/HPFH-1 deletion; 11 children (84.6%) had αα/αα, and two (15.4%) carried the αα/-α(3.7) (rightward) deletion. The mean concentration of total hemoglobin (Hb) and Hb F was 12.52 ± 0.56 g/dL and 42.31% ± 1.97%, respectively. Mild microcytosis and hypochromia were observed. We found acute clinical manifestations of sickle cell disease, such as acute chest syndrome (ACS) and acute pain crisis in four children; nine (69.2%) children were completely asymptomatic during the follow-up period. All children were classified as having low-risk transcranial Doppler (TDC). In conclusion, children with Hb S/HPFH have a mild clinical phenotype of sickle cell disease, although acute clinical manifestations may occur. High Hb F levels and absence of anemia are common hematological characteristics.

Association of alpha-thalassemia, TNF-alpha (-308G>A) and VCAM-1 (c.1238G>C) gene polymorphisms with cerebrovascular disease in a newborn cohort of 411 children with sickle cell anemia.

Cerebrovascular disease (CVD) is a severe complication associated with sickle cell anemia. Abnormal transcranial Doppler (TCD) identifies some children at high risk, but other markers would be helpful. This cohort study was aimed at evaluating the effects of genetic biomarkers on the risk of developing CVD in children from Minas Gerais, Brazil. Clinical and hematological data were retrieved from children's records. Outcomes studied were overt ischemic stroke and CVD (overt ischemic stroke, transient ischemic attack, abnormal TCD, or abnormal cerebral angiography). Out of 411 children, 386 (93.9%) had SS genotype, 23 (5.6%) had Sß(0)-thal and two had severe Sß(+)-thal (0.5%). Frequency of CVD was lower in Sß-thal group (p=0.05). No effect of VCAM-1 polymorphism on stroke or CVD risks was detected. Cumulative incidence of stroke was significantly higher for children with TNF-α A allele (p=0.02) and lower for children with HBA deletion (p=0.02). However, no association between CVD and TNF-α -308G>A was found. CVD cumulative incidence was significantly lower for children with HBA deletion (p=0.004). This study found no association between VCAM1 c.1238G>C and stroke. An association between stroke and TNF-α -308A allele has been suggested. Our results have confirmed the protective role of HBA deletion against stroke and CVD.

Clinical, laboratory, and molecular characteristics of a cohort of children with hemoglobinopathy S/beta-thalassemia.

INTRODUCTION: Hemoglobinopathy Sß-thalassemia (HbSß-thal) has a wide range of clinical and laboratory severity. There is limited information on the natural history of HbSß-thal and its modulating factors. We described the molecular, hematological, and clinical characteristics of a cohort of children with HbSß-thal and estimated its incidence in Minas Gerais, Brazil. METHODS: Laboratory and clinical data were retrieved from medical records. Molecular analysis was performed by HBB gene sequencing, PCR-RFLP, gap-PCR, and MLPA. RESULTS: Eighty-nine children were included in the study. Fourteen alleles of ß-thal mutations were identified. The incidence of HbSß-thal in the state was 1 per 22,250 newborns. The most common ßS-haplotypes were CAR and Benin. The most frequent ßthal-haplotypes were V, II, and I. Coexistence of 3.7 kb HBA1/HBA2 deletion was present in 21.3 % of children. ß-thalassemia mutations were associated with several clinical and laboratory features. In general, the incidence of clinical events per 100 patient-years was similar for children with HbSß0-thal, IVS-I-5 G>A, and IVS-I-110 G>A. Children with HbSß+-intermediate phenotypes had a more severe laboratory and clinical profile when compared with those with HbSß+-mild ones. ßS-haplotypes and α-thalassemia did not meaningfully influence the phenotype of children with HbSß-thal. CONCLUSION: The early identification of ß-thalassemia alleles may help the clinical management of these children.

Health-related quality of life among teenagers during cancer treatment in a developing country: patients' and proxies' reports.

Few studies have been performed during adolescents' cancer treatment to evaluate its interference on health-related quality of life (HRQL). The purpose of this prospective cohort study was to evaluate adolescents' HRQL during cancer treatment. The Health Utilities Index (HUI) was used for scoring. Forty-five individuals were questioned 1 month after the onset of treatment (T1) and at 4 or 6 months depending on disease type (T2). Median age was 14 years. Pain was the most frequent troublesome attribute referred to, but scores were significantly better from T1 to T2 for patients and proxies. A high correlation between patients' and family' HRQL scores was observed both at T1 and T2. Correlation of the general health scores between patients and their families was high at T1, but not so high at T2. Physicians' evaluation tended to underestimate HRQL of their patients. In conclusion, most patients and proxies reported a HRQL reduction during the initial phase of treatment, but HRQL was better later on. Generally, patient and proxy scores correlated well. Pain was the most frequently reported troublesome attribute. The patients' opinion concerning their own health and well-being should be of primary importance to assess QoL and determine therapeutic regimens.