Misdiagnosis in multiple sclerosis in a Brazilian reference center: Clinical, radiological, laboratory profile and failures in the diagnostic process-Cohort study.

BACKGROUND: Multiple sclerosis misdiagnosis remains a problem despite the well-validated McDonald 2017. For proper evaluation of errors in the diagnostic process that lead to misdiagnosis, it is adequate to incorporate patients who are already under regular follow-up at reference centers of demyelinating diseases. OBJECTIVES: To evaluate multiple sclerosis misdiagnosis in patients who are on follow-up at a reference center of demyelinating diseases in Brazil. METHODS: We designed an observational study including patients in regular follow-up, who were diagnosed with multiple sclerosis at our specialized outpatient clinic in the Hospital of Clinics in the University of Sao Paulo, from 1996 to 2021, and were reassessed for misdiagnosis in 2022. We evaluated demographic information, clinical profile, and complementary exams and classified participants as "established multiple sclerosis," "non-multiple sclerosis, diagnosed," and "non-multiple sclerosis, undiagnosed." Failures in the diagnostic process were assessed by the modified Diagnostic Error Evaluation and Research tool. RESULTS: A total of 201 patients were included. After analysis, 191/201 (95.02%) participants were confirmed as "established multiple sclerosis," 5/201 (2.49%) were defined as "non-multiple sclerosis, diagnosed," and 5/201 (2.49%) were defined as "non-multiple sclerosis, undiagnosed." CONCLUSIONS: Multiple sclerosis misdiagnosis persists in reference centers, emphasizing the need for careful interpretation of clinical findings to prevent errors.

Arginine Residues Modulate the Membrane Interactions of pHLIP Peptides.

Most processes at the water-membrane interface often involve protonation events in proteins or peptides that trigger important biological functions and events. This is the working principle behind the pHLIP peptide technology. A key titrating aspartate (Asp14 in wt) is required to protonate to induce the insertion process, increase its thermodynamic stability when membrane-embedded, and trigger the peptide's overall clinical functionality. At the core of pHLIP properties, the aspartate pKa and protonation are a consequence of the residue side chain sensing the changing surrounding environment. In this work, we characterized how the microenvironment of the key aspartate residue (Asp13 in the investigated pHLIP variants) can be modulated by a simple point mutation of a cationic residue (ArgX) at distinct sequence positions (R10, R14, R15, and R17). We carried out a multidisciplinary study using pHRE simulations and experimental measurements. Fluorescence and circular dichroism measurements were carried out to establish the stability of pHLIP variants in state III and establish the kinetics of the insertion and exit of the peptide from the membrane. We estimated the contribution of the arginine to the local electrostatic microenvironment, which promotes or hinders other electrostatic players from coexisting in the Asp interaction shell. Our data indicate that the stability and kinetics of the peptide insertion and exit from the membrane are altered when Arg is topologically available for a direct salt-bridge formation with Asp13. Hence, the position of arginine contributes to fine-tuning the pH responses of pHLIP peptides, which finds wide applications in clinics.

Biomechanical testing of osteosynthetic locking plates for proximal humeral shaft fractures - a systematic literature review.

Proximal humeral shaft fractures can be treated with helically deformed bone plates to reduce the risk of iatrogenic nerve lesion. Controversially to this common surgical technique that was first established in 1999, no biomechanical investigation on humeral helical plating is recorded by other reviews, which focus on proximal fractures exclusively. Does an additional scope for shaft fractures reveal findings of helical testing? The present systematic literature review was performed based on guidelines by Kitchenham et al. to systematically search and synthesize literature regarding biomechanical testing of osteosynthetic systems for proximal humeral shaft fractures. Therefore, a systematic approach to search and screen literature was defined beforehand and applied on the findings of the database PubMed®. Synthesized information of the included literature was categorized, summarized and analyzed via descriptive statistics. Out of 192 findings, 22 publications were included for qualitative synthesis. A wide range of different test methods was identified, leading to a suboptimal comparability of specific results between studies. Overall, 54 biomechanical test scenarios were identified and compared. Physiological based boundary conditions (PB-BC) were referenced in 7 publications only. One study of testing straight and helical dynamic compression plates without PB-BCs was identified, showing significant differences under compressional loading. The absence of test standards of specific fields like humeral fractures lead to a high variance in biomechanical testing of osteosynthetic locking plates for proximal humeral shaft fractures. Physiological approaches offer realistic test scenarios but need to be uniformed for enhanced comparability between studies. The impact of helically deformed locking plates under PB-BC was not identified in literature.

Continuous real-time biofeedback in orthosis improves partial weight bearing on stairs.

INTRODUCTION: Climbing up and down stairs with crutches is a particular challenge. The current study evaluates a commercially available insole orthosis device for weighing an affected limb and for biofeedback training of gait. This study was done on healthy, asymptomatic individuals before applying to the intended postoperative patient. The outcomes should demonstrate whether a continuous real-time biofeedback (BF) system is more effective on stairs than the current protocol involving a bathroom scale. MATERIALS AND METHODS: 59 healthy test subjects received both crutches and an orthosis and learned to apply a 3-point gait with a partial load of 20 kg using a bathroom scale. Thereafter, the participants were asked to complete an up-and-down course, first without (control group) and then with (test group) an audio-visual real-time biofeedback (BF). Compliance was evaluated using an insole pressure measurement system. RESULTS: Using the conventional therapy technique, 36.6% of the steps up and 39.1% of the steps down in the control group were loaded with < 20 kg. By activating continuous biofeedback, steps with < 20 kg could be increased significantly to 61.1% upstairs (p < 0.001) and 66.1% downstairs (p < 0.001). All subgroups profited from the BF system, independent of age, gender, side relieved, dominant or non-dominant side. CONCLUSIONS: Traditional training without biofeedback led to poor performance for partial weight bearing on stairs, even among young and healthy individuals. However, continuous real-time biofeedback clearly improved compliance, indicating its potential to enhance training and support future research in patient populations.

Supplementation of feedlot lambs with cactus cladodes as strategy to improve testicular function.

The aim of this study was to evaluate the effects of diets containing cactus cladodes genotypes on plasma testosterone levels, testicular histopathological and histomorphometric parameters, and oxidative stress markers in lambs. Thirty-six male, intact Santa Inês lambs (22.0 ± 2.9 kg initial body weight), were to feedlot for 86 days. A completely randomized design was used with three dietary treatments (control diet with Tifton-85 hay as the only roughage; and two more diets with Miúda or OEM cactus cladodes partially replacing hay) and twelve replicates. There was no influence of the diets on the testicular weight (P = 0.414) and gonadosomatic index (P = 0.384) of lambs. The testosterone serum concentrations were almost twice as higher in lambs fed Miúda cactus cladodes compared to control treatment. There was greater incidence and severity of lesions in the testicular parenchyma of animals that received control diet: loosening of germ cell epithelium, germ cell desquamation and vacuolization of Sertoli cells. The seminiferous tubule diameter and height of the seminiferous epithelium were higher in lambs fed OEM cactus cladodes (P = 0.003). The tubular volume and Leydig cells volume were higher in animals fed with cactus cladodes (P < 0.05). The levels of malondialdehyde were higher in the lambs of control group compared to OEM group (P = 0.039) and the testicular concentration of nitric oxide was higher in control group (P = 0.009). The diet containing OEM cactus cladodes increased the levels of superoxide dismutase. Our results indicate that diets containing cactus cladodes promote antioxidant protection to the testicular parenchyma and preserve the spermatogenic process of lambs.

Can elderly individuals perform partial weight bearing on their lower limbs? A prospective cohort study using ambulatory real-time biofeedback.

BACKGROUND: Partial weight bearing in an orthosis and with forearm crutches is a widespread and well-accepted therapeutic principle after an injury of the lower extremity during early rehabilitation. Complying may be challenging to do under these circumstances, especially for elderly people. This study compares the spatiotemporal parameters and peak loads performed by a group of older participants before and after activating real-time biofeedback (BF) to determine whether they benefit from a biofeedback. METHODS: Twenty-four healthy subjects between 61 and 80 years learned how to walk using forearm crutches in a lower leg orthosis while performing a weight of 20 kg using a bathroom scale with the aim of loading in a zone between 15 and 30 kg. After that, they completed a course that was on level ground (50 m) and another course on stairs (11 steps). They did a walk without BF first, and then with BF. Each step was given a maximum load, which was determined and statistically checked. In addition, spatiotemporal parameters were collected. RESULTS: The classical teaching method with a bathroom scale was ineffective. Only 32.3% of the loads could be adequately carried by a person on level ground in the 15-30 kg target zone. On the stairs, it was 48.2% and 34.3%, respectively. Thus, on level ground, 52.7% of loads exceeded 30 kg. Downstairs it was 46.4%, and upstairs it was 41.6%. Subjects clearly benefit from activated biofeedback. Biofeedback significantly reduced missteps > 30 kg in every course. The loads decreased significantly to 25.0% on level ground, to 23.0% upstairs, and to 24.4% downstairs. At the same time, speed and stride length decreased per course while total time increased. CONCLUSION: Partial weight bearing is more complex and difficult for the elderly. These study results may help better understand 3-point gait in older adults in an outpatient setting. When partial weight bearing is recommended, special follow-up attention must be given for this group. Age-based therapy strategies can be developed and monitored with the assistance of ambulatory biofeedback devices. Trial registration Retrospectively registered, https://www.drks.de/DRKS00031136 .

Dwarf and tall elephant grass silages: intake, nutrient digestibility, nitrogen balance, ruminal fermentation, and ingestive behavior in sheep.

The objective of this study was to evaluate the exclusive supply of dwarf or tall elephant grass silages, harvested at 60 days of growth, without wilting or the use of additives, on intake, apparent digestibility, nitrogen balance, rumen parameters, and ingestive behavior of sheep. Eight castrated male crossbred sheep (57.6 ± 5.25 kg body weight), fistulated in the rumen, were distributed in two 4 × 4 Latin squares with four treatments and eight animals per treatment and four periods. The treatments consisted of four elephant grass genotype silages (Mott, Taiwan A-146 2.37, IRI-381, or Elephant B). There was no effect of silages (P > 0.05) on dry matter, neutral detergent fiber, and total digestible nutrient intake. The dwarf-sized elephant grass silages provided higher crude protein intake (P = 0.047) and N intake (P = 0.047), while the IRI-381 genotype silage provided higher non-fibrous carbohydrate intake compared to Mott (P = 0.042), without differing from Taiwan A-146 2.37 and Elephant B silages. There were no differences (P > 0.05) among the digestibility coefficients of the evaluated silages. It was observed that silages produced with Mott and IRI-381 genotypes caused a slight decrease in ruminal pH (P = 0.013), and the propionic acid concentration was higher in the rumen fluid of the animals fed with Mott silage (P = 0.021). Therefore, dwarf or tall elephant grass silages, produced with cut genotypes at 60 days of growth and without the use of additives or wilting process, can be used in sheep feeding.

Sugarcane yeast with urea in replace of soybean meal in the diet of Murrah buffaloes does not cause metabolic, endocrine, and mineral disorders.

The aim of this study was to evaluate the effect of the replacement of soybean meal by increasing levels of sugarcane yeast and urea on the energy, enzymatic, protein, mineral, and hormonal profiles of buffalo heifers. Twenty Murrah heifers with an average body weight of 168 ± 2.0 kg and 1 year old were used in a completely randomized design. The treatments consisted of the replacement of soybean meal by increasing levels of sugarcane yeast and urea (0, 33, 67, and 100% dry matter). The animals were weighed at the beginning and end of the experimental period, and blood was collected on the final day. The replacement of soybean meal with sugarcane yeast influenced the performance and metabolic dynamics, with total weight gain (P = 0.005) and average daily gain (P = 0.015), presenting, for both variables, a quadratic effect. Considering the biochemical profile, there was an influence on the serum concentration of triglycerides (P = 0.055), the serum activities of aspartate aminotransferase, gamma-glutamyl transferase, and alkaline phosphatase (P < 0.05), in addition to the serum concentration of phosphorus (P = 0.007) and potassium (P = 0.053), which showed positive linear effects. The hormonal profile was not influenced by diets (P > 0.05). The elements copper, iron, and zinc were able to be quantified at all levels of sugarcane yeast and urea in the diets offered. The use of sugarcane yeast with urea promotes adequate metabolic response of buffalo heifers and can replace up to 100% of soybean meal in the concentrate.

Corrigendum to "Unveiling molecular details behind improved activity at neutral to alkaline pH of an engineered DyP-type peroxidase" Comput Struct Biotechnol J, 20 (2022), 3899-3910.

[This corrects the article DOI: 10.1016/j.csbj.2022.07.032.].

Serum concentrations of folic acid and cobalamin and energy metabolism of ewes as a function of the energy density of the diet, peripartum period, and pregnancy toxemia.

The aim of this study was to determine the serum levels of folic acid, cobalamin, and indicators of energy metabolism during the peripartum period of ewes submitted to different diets and with or without pregnancy toxemia. Forty Santa Inês ewes were divided into three groups, a group of 20 animals fed only roughage-diet with low energy density (G1), a group of 10 ewes submitted to diet containing roughage and concentrate-diet with high energy density (G2), and a group of 10 ewes with diagnosis of pregnancy toxemia (PT) (G3). In the ewes of groups G1 and G2, blood samples were collected -30, -15, -7 days pre-partum, on the day of partum, and 7, 15, and 30 days postpartum; blood samples from G3 animals were collected during the veterinary clinic care. Significant variations were observed in the plasma concentration of glucose and serum folic acid, cobalamin, fructosamine, NEFA, and ß-hydroxybutyrate in the groups fed diets with different energy levels, with and without PT (P < 0.05). A positive correlation of folic acid and cobalamin was observed with plasma glucose and serum NEFA concentrations, in addition to negative correlation of glucose with NEFA and ß-hydroxybutyrate and positive correlation between the latter biomarkers of energy metabolism. The ewes diagnosed with PT showed higher levels of folic acid, NEFA, and ß-hydroxybutyrate (P < 0.05). Ewes fed diet containing roughage and concentrate present higher serum levels of folic acid, cobalamin, and glucose, in the pre-partum period and in the lactation period. The results obtained contribute to better understanding of the application of blood concentration tests for folic acid and cobalamin in the energy metabolism and in PT in ewes.

Primary angiitis of the central nervous system as a mimic of multiple sclerosis: A case report.

BACKGROUND: Primary angiitis of the central nervous system is a rare inflammatory vasculopathy and it is a difficult diagnosis to make because of its kaleidoscopic presentation and its multiple mimics, including multiple sclerosis. CASE PRESENTATION: A 21-year-old men presented a four-year history of progressive gait deterioration. Magnetic resonance imaging of the brain and spine showed hyperintense round-shaped lesions on T2 images, many with contrast enhancement, in supra/infratentorial and spinal segments. He received treatment for multiple sclerosis but presented clinical worsening, and follow-up neuroimaging showed persistent contrast enhancement lesions and a cerebellar hematoma. Brain biopsy was performed and demonstrated inflammatory infiltrations in blood vessels. The patient received 6 monthly schedules of 5 g methylprednisolone and 1 g cyclophosphamide with clinical stabilization. DISCUSSION: Our patient presented a primary angiitis central nervous system according to the Birnbaum and Hellmann proposed criteria. This case reinforces the importance of advancing the differential diagnosis of patients that present red flags in brain neuroimaging. CONCLUSION: The presence of the micro/macrobleeds and persistent contrast enhancing lesions should raise the suspicion of vasculitis in the differential diagnosis of multiple sclerosis.

Increasing the Realism of in Silico pHLIP Peptide Models with a Novel pH Gradient CpHMD Method.

The pH-low insertion peptides (pHLIP) are pH-dependent membrane inserting peptides, whose function depends on the cell microenvironment acidity. Several peptide variants have been designed to improve upon the wt-sequence, particularly the state transition kinetics and the selectivity for tumor pH. The variant 3 (Var3) peptide is a 27 residue long peptide, with a key titrating residue (Asp-13) that, despite showing a modest performance in liposomes (pKins ∼ 5.0), excelled in tumor cell experiments. To help rationalize these results, we focused on the pH gradient in the cell membrane, which is one of the crucial properties that are not present in liposomes. We extended our CpHMD-L method and its pH replica-exchange (pHRE) implementation to include a pH gradient and mimic the pHLIP-membrane microenvironment in a cell where the internal pH is fixed (pH 7.2) and the external pH is allowed to change. We showed that, by properly modeling the pH-gradient, we can correctly predict the experimentally observed loss and gain of performance in tumor cells experiments by the wt and Var3 sequences, respectively. In sum, the pH gradient implementation allowed for more accurate and realistic pKa estimations and was a pivotal step in bridging the in silico data and the in vivo cell experiments.

Kidney changes in lambs fed cactus pear varieties resistant to Dactylopius opuntiae as the only roughage.

This study aimed to evaluate the effects of four varieties of cactus pear resistant to carmine cochineal as exclusive roughage for lambs on the biochemical, histopathological, and histomorphometric parameters of kidneys. Twenty-four castrated male crossbred lambs at eight months of age and an initial body weight of 21.0 ± 0.5 kg were distributed in a completely randomized design, with four treatments and six repetitions. The experimental treatments consisted of four diets containing Miúda cactus pear, IPA-Sertânia cactus pear, IPA-F21 cactus pear, or Orelha de Elefante Mexicana (OEM) cactus pear as the only roughage. Blood samples were collected every two weeks (14 d, 28 d, 42 d, and 56 d) to quantify serum urea and creatinine levels. After 72 days of the introduction of the tested diets, the animals were slaughtered and fragments of the kidneys were collected for histological analysis. The serum urea level was higher in animals fed a diet based on the Miúda variety (49.38 mg dL-1), and the serum creatinine levels were lower in the last two collections (P = 0.009). The most frequent histopathological findings in the kidneys were calcification, congestion, glomerular atrophy, presence of luminal cellular debris, and nephrosis, regardless of the cactus pear variety. The Miúda cactus pear and OEM cactus pear varieties caused more severe damage to the nephron components, while the varieties IPA F-21 and IPA-Sertânia caused less significant injuries. The use of IPA-Sertânia and IPA F-21 cactus pear varieties is suggested in lamb's diets, due to the lower impact on the renal parenchyma. However, there was no expressive impairment of renal function, and there was no difference between the cactus pear varieties tested in this study on the weight gain of the animals, and they can all be used to feed feedlot sheep.

Unveiling molecular details behind improved activity at neutral to alkaline pH of an engineered DyP-type peroxidase.

DyP-type peroxidases (DyPs) are microbial enzymes that catalyze the oxidation of a wide range of substrates, including synthetic dyes, lignin-derived compounds, and metals, such as Mn2+ and Fe2+, and have enormous biotechnological potential in biorefineries. However, many questions on the molecular basis of enzyme function and stability remain unanswered. In this work, high-resolution structures of PpDyP wild-type and two engineered variants (6E10 and 29E4) generated by directed evolution were obtained. The X-ray crystal structures revealed the typical ferredoxin-like folds, with three heme access pathways, two tunnels, and one cavity, limited by three long loops including catalytic residues. Variant 6E10 displays significantly increased loops' flexibility that favors function over stability: despite the considerably higher catalytic efficiency, this variant shows poorer protein stability compared to wild-type and 29E4 variants. Constant-pH MD simulations revealed a more positively charged microenvironment near the heme pocket of variant 6E10, particularly in the neutral to alkaline pH range. This microenvironment affects enzyme activity by modulating the pK a of essential residues in the heme vicinity and should account for variant 6E10 improved activity at pH 7-8 compared to the wild-type and 29E4 that show optimal enzymatic activity close to pH 4. Our findings shed light on the structure-function relationships of DyPs at the molecular level, including their pH-dependent conformational plasticity. These are essential for understanding and engineering the catalytic properties of DyPs for future biotechnological applications.

Diets containing cactus cladodes on serum and liver levels of microminerals in sheep and goats.

Two experiments were performed to evaluate the effects of partial replacement of Tifton hay by Miúda cactus cladodes (Nopalea) or Orelha de Elefante Mexicana (O.E.M.) cactus cladodes (Opuntia) on serum and liver concentrations of iron (Fe), copper (Cu), zinc (Zn), and manganese (Mn) in feedlot small ruminants. The experiment 1 (Exp. 1) lasted 86 days, and thirty-six male Santa Inês lambs (22.0 ± 2.9 kg initial body weight-IBW) were used. In experiment 2 (Exp. 2), lasting 100 days, thirty-six male goats of undefined breed (19.0 ± 2.8 kg IBW) were used. In both studies, the animals were distributed in a completely randomized design, with three treatments (diet control-without cactus; and diets with hay partially replaced by Miúda or O.E.M. cactus cladodes) and twelve replicates. Blood samples were collected to quantify serum micromineral levels, and at the end of the feedlot periods, sheep and goats were slaughtered and liver fragments were collected for micromineral dosage. In Exp. 1, lambs fed Nopalea cactus cladodes diet showed greater hepatic Cu accumulation (441.87 mg/kg DM; P = 0.027). The diets containing cactus cladodes tended to increase serum levels of Cu (P = 0.075) and Zn (P = 0.058). In Exp. 2, goats fed diet containing Opuntia cactus cladodes presented higher serum levels of Fe (P = 0.024) and Cu (P = 0.012). In conclusion, the partial replacement of Tifton hay by cactus cladodes increases hepatic concentrations of Cu in lambs and serum levels of Fe and Cu in goats.

Protective and Risk Factors for Humerus Head Necrosis After Proximal Humerus Fracture Treated with Internal Locking Plate.

BACKGROUND: Proximal humerus fractures (PHF) are common and lead to post-traumatic humerus head necrosis (HHN) in 3-35% after ORIF with an internal locking plate. Few studies focus on this condition and risk factors remain a discussion topic. Hertel's criteria for initial head ischemia right after fracture (fracture complexity, medial hinge displacement and short metaphyseal head extension) have recently been correlated to HHN, but there is still a clear lack of evidence on the topic. Due to its anatomical similarities to the proximal femur, some authors argue that PHF may as well benefit from early surgery to avoid head necrosis. METHODS: In this 10-year retrospective study, we assessed 305 patients from a single center. All cases were treated with a PHILOS plate through a deltopectoral approach. The mean follow-up time was 467 days. The primary endpoint was HHN. RESULTS: HHN was diagnosed in 12 patients (4%), 10 of which were diagnosed within the first year and one case 4 years after surgery. A positive correlation (p < 0.04) was found between HHN and fracture type (both in AO and Neer's classification), initial neck-shaft-angle (NSA) and metaphyseal head extension (MHE). Medial hinge displacement (MHD) occurred in all HHN cases. Achieving perfect reduction (< 2 mm dislocation) was relevant to avoiding HHN (p = 0.035). Although HHN developed in 32% of the high risk cases (four-part fractures with a short MHE), it was completely avoided (0%) when perfect reduction was achieved. Time until surgery after admission was neither a protective nor a risk factor for HHN. CONCLUSION: We conclude that fracture complexity (four-part and C-fractures) as well as disruption of the medial hinge with a metaphyseal head extension smaller than 8 mm are relevant risk factors for humerus head necrosis. A combination of these criteria generated an high risk pattern with a 32% rate of HHN. Though often difficult to achieve, perfect reduction was a clear protective factor and reduced HHN to 0%. Perfect reduction may be key to inosculation and, therefore, salvage of the humerus head, especially in high risk cases. Surgery timing did not correlate with HHN. LEVEL OF EVIDENCE: Level 3, retrospective cohort study.

First Report of Diaporthe tulliensis and D. pseudomangiferae causing cacao pod rot in Puerto Rico.

Worldwide cacao pod rot is a devastating disease of Theobroma cacao, infected cacao pods turn necrotic reducing yield up to 30%. From July 2020 to August 2021, a survey was conducted at the USDA-ARS cacao germplasm collection located at Mayaguez, Puerto Rico. Incidence of cacao pod rot was 73.9%, observed in 142 of the 196 accessions sampled. The disease was observed at different stages of pod development (small, green, mature pods, and dry mummified large pods). Diseased tissue from three cacao pods (1 mm2) per each cacao accession was surface disinfested by immersion in 70% ethanol for one minute, rinsed with sterile-distilled-water and plated on potato dextrose agar (PDA) amended with 250 mg/L ampicillin and 60 mg/L streptomycin. After 30 days of incubation at 25°C, seven isolates developing white fast-growing colonies with black-globose pycnidia were observed. All isolates produced hyaline, one-celled, biguttulate, and cylindrical and rounded at the apex α conidia of 5.1 to 7.3 µm × 2.5 to 3.0 µm in size and were identified as Diaporthe spp. (Gomes et al. 2013; Crous et al. 2015). To determine the species identity, seven isolates were sequenced of the internal transcribed spacer (ITS), sections of ß-tubulin (BT) and translation elongation factor 1 alpha (EF1-α) and compared using the BLASTn with Diaporthe spp. type specimens deposited in NCBI GenBank. ITS, BT and EF1-α sequences of Phomocac16, Phomcac17, Phomcac18 and Phomcac21 isolates (GenBank accession nos. OL353698 to OL353701, OL412430 to OL412433, and OL412437 to OL412440 for ITS, BT and EF1-α, respectively) were grouped to the holotype BRIP 62248a (Bootstrap BS=100) of Diaporthe tulliensis R.G. Shivas, Vawdrey & Y.P. Tan. The other three isolates (Phomcac8P1, Phomcac8P3 and Phomcac8P4) were grouped to the ex-type (CBS 101339) of Diaporthe pseudomangiferae R.R. Gomes, Glienke & Crous, ITS, BT and EF1-α sequences of (GenBank accessions nos. OL353702 to OL353704, OL412434 to OL412436, and OL412441 to OL412443, for ITS, BT and EF1-α, respectively). Pathogenicity tests were conducted using isolates Phomocac16, Phomcac17, Phomcac18 and Phomcac21 of D. tulliensis and isolates Phomcac8P1, Phomcac 8P3 and Phomcac8P4 of D. pseudomangiferae on five healthy detached green, yellow and red pods of the following cacao varieties: TARS27, ICS16, ICS1, GS29, UF601, SIAL56, Amelonado, SIAL98, EET94, ICS129 and GNV58. Cacao pods were wounded and inoculated with 5-mm mycelial disks from 8-day-old pure cultures grown on PDA of each isolate and wrapped with parafilm. Untreated controls were inoculated with PDA disks only. Fruits were kept in a humid chamber for 8 days at 25°C. Tests were repeated twice. Eight days after inoculation with D. tulliensis and D. pseudomangiferae, all cacao pods turned dark brown, untreated controls showed no symptoms of pod rot, and no fungi were isolated from tissue. Both species, D. tulliensis and D. pseudomangiferae were reisolated from their respective diseased tissues fulfilling Koch's postulates. Diaporthe tulliensis has been reported from rotted stem ends of cacao pods in Australia (Crous et al. 2015), and D. pseudomangiferae was reported in a shipment of cacao seed pods in California; however, pathogenicity tests were not conducted at either location. In California D. pseudomangiferae is considered a quarantine pathogen with a temporary Q rating (Chitambar 2017). To our knowledge, this is the first report of D. tulliensis and D. pseudomangiferae causing cacao pod rot in Puerto Rico. Knowing the identity and incidence of these new cacao pathogens is the first step for developing specific control measures and potential sources for resistance to cacao pod rot caused by Diaporthe spp. References: Chitambar J. 2017. California Pest Rating for Diaporthe pseudomangiferae R. R. Gomes, C. Glienke & Crous. https://blogs.cdfa.ca.gov/Section3162/?p=3285 Crous P.W. et al. 2015. Persoonia 35:264. https://doi.org/10.3767/003158515X690269 Gomes R.R. et al. 2013. Persoonia 31:1 http://dx.doi.org/10.3767/003158513X666844.

In Silico End-to-End Protein-Ligand Interaction Characterization Pipeline: The Case of SARS-CoV-2.

SARS-CoV-2 triggered a worldwide pandemic disease, COVID-19, for which an effective treatment has not yet been settled. Among the most promising targets to fight this disease is SARS-CoV-2 main protease (Mpro), which has been extensively studied in the last few months. There is an urgency for developing effective computational protocols that can help us tackle these key viral proteins. Hence, we have put together a robust and thorough pipeline of in silico protein-ligand characterization methods to address one of the biggest biological problems currently plaguing our world. These methodologies were used to characterize the interaction of SARS-CoV-2 Mpro with an α-ketoamide inhibitor and include details on how to upload, visualize, and manage the three-dimensional structure of the complex and acquire high-quality figures for scientific publications using PyMOL (Protocol 1); perform homology modeling with MODELLER (Protocol 2); perform protein-ligand docking calculations using HADDOCK (Protocol 3); run a virtual screening protocol of a small compound database of SARS-CoV-2 candidate inhibitors with AutoDock 4 and AutoDock Vina (Protocol 4); and, finally, sample the conformational space at the atomic level between SARS-CoV-2 Mpro and the α-ketoamide inhibitor with Molecular Dynamics simulations using GROMACS (Protocol 5). Guidelines for careful data analysis and interpretation are also provided for each Protocol.

pK a Calculations in Membrane Proteins from Molecular Dynamics Simulations.

The conformational changes of membrane proteins are crucial to their function and usually lead to fluctuations in the electrostatic environment of the protein surface. A very effective way to quantify these changes is by calculating the pK a values of the protein's titratable residues, which can be regarded as electrostatic probes. To achieve this, we need to take advantage of the fast and reliable pK a calculators developed for globular proteins and adapt them to include the explicit effects of membranes. Here, we provide a detailed linear response approximation protocol that uses our own software (PypKa) to calculate reliable pK a values from short MD simulations of membrane proteins.

Improved Protocol to Tackle the pH Effects on Membrane-Inserting Peptides.

Many important biological pathways rely on membrane-interacting peptides or proteins, which can alter the biophysical properties of the cell membrane by simply adsorbing to its surface to undergo a full insertion process. To study these phenomena with atomistic detail, model peptides have been used to refine the current computational methodologies. Improvements have been made with force-field parameters, enhanced sampling techniques to obtain faster sampling, and the addition of chemical-physical properties, such as pH, whose influence dramatically increases at the water/membrane interface. The pH (low) insertion peptide (pHLIP) is a peptide that inserts across a membrane bilayer depending on the pH due to the presence of a key residue (Asp14) whose acidity-induced protonation triggers the whole process. The complex nature of these peptide/membrane interactions resulted in sampling limitations of the protonation and configurational space albeit using state-of-the-art methods such as the constant-pH molecular dynamics. To address this issue and circumvent those limitations, new simulations were performed with our newly developed pH-replica exchange method using wild-type (wt)-pHLIP in different 2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine membrane sizes. This technique provided enhanced sampling and allowed for the calculation of more complete Asp14 pKa profiles. The conformational heterogeneity derived from strong electrostatic interactions between Asp14 and the lipid phosphate groups was identified as the source of most pKa variability. In spite of these persistent and harder-to-equilibrate phosphate interactions, the pKa values at deeper regions (6.0-6.2) still predicted the experimental pK of insertion (6.0) since the electrostatic perturbation decays as the residue inserts further into the membrane. We also observed that reducing the system size leads to membrane deformations where it increasingly loses the ability to accommodate the pHLIP-induced perturbations. This indicates that large membrane patches, such as 256 or even 352 lipids, are needed to obtain stable and more realistic pHLIP/membrane systems. These results strengthen our method pKa predictive and analytical capabilities to study the intricate play of electrostatic effects of the peptide/membrane interface, granting confidence for future applications in similar systems.