Vaccine priming of rare HIV broadly neutralizing antibody precursors in nonhuman primates.

Germline-targeting immunogens hold promise for initiating the induction of broadly neutralizing antibodies (bnAbs) to HIV and other pathogens. However, antibody-antigen recognition is typically dominated by heavy chain complementarity determining region 3 (HCDR3) interactions, and vaccine priming of HCDR3-dominant bnAbs by germline-targeting immunogens has not been demonstrated in humans or outbred animals. In this work, immunization with N332-GT5, an HIV envelope trimer designed to target precursors of the HCDR3-dominant bnAb BG18, primed bnAb-precursor B cells in eight of eight rhesus macaques to substantial frequencies and with diverse lineages in germinal center and memory B cells. We confirmed bnAb-mimicking, HCDR3-dominant, trimer-binding interactions with cryo-electron microscopy. Our results demonstrate proof of principle for HCDR3-dominant bnAb-precursor priming in outbred animals and suggest that N332-GT5 holds promise for the induction of similar responses in humans.

Acute presentation of Wunderlich syndrome in a pregnant woman treated with supra-selective cannulation of renal segmental arteries and nephrectomy: A case report.

Wunderlich syndrome is characterized by the presence of abdominal pain, hematuria, and hypovolemic shock. We report a rare case of a 25-year-old pregnant woman, who came to the emergency department due to the sudden onset of low back pain and diaphoresis. The patient, during medical evaluation, experienced an altered state of consciousness. Diagnosed with hypovolemic shock, she was admitted to the operating room, where examination of the abdominal cavity revealed a left retroperitoneal hematoma. Damage control surgery was performed, but given the postoperative clinical deterioration, computerized tomography angiography of the abdomen was performed, showing a mass-like lesion arising from the upper pole of the left kidney, consistent with Wunderlich syndrome. Left nephrectomy was the definitive treatment for the 10-cm renal angiomyolipoma. Since Wunderlich syndrome is a potentially lethal entity, CT is usually the preferred diagnostic approach, and supra-selective vascular embolization is the first-line treatment.

Engineered mRNA-ribosome fusions for facile biosynthesis of selenoproteins.

Ribosomes are often used in synthetic biology as a tool to produce desired proteins with enhanced properties or entirely new functions. However, repurposing ribosomes for producing designer proteins is challenging due to the limited number of engineering solutions available to alter the natural activity of these enzymes. In this study, we advance ribosome engineering by describing a novel strategy based on functional fusions of ribosomal RNA (rRNA) with messenger RNA (mRNA). Specifically, we create an mRNA-ribosome fusion called RiboU, where the 16S rRNA is covalently attached to selenocysteine insertion sequence (SECIS), a regulatory RNA element found in mRNAs encoding selenoproteins. When SECIS sequences are present in natural mRNAs, they instruct ribosomes to decode UGA codons as selenocysteine (Sec, U) codons instead of interpreting them as stop codons. This enables ribosomes to insert Sec into the growing polypeptide chain at the appropriate site. Our work demonstrates that the SECIS sequence maintains its functionality even when inserted into the ribosome structure. As a result, the engineered ribosomes RiboU interpret UAG codons as Sec codons, allowing easy and site-specific insertion of Sec in a protein of interest with no further modification to the natural machinery of protein synthesis. To validate this approach, we use RiboU ribosomes to produce three functional target selenoproteins in Escherichia coli by site-specifically inserting Sec into the proteins' active sites. Overall, our work demonstrates the feasibility of creating functional mRNA-rRNA fusions as a strategy for ribosome engineering, providing a novel tool for producing Sec-containing proteins in live bacterial cells.

Role of the first WHO mutation catalogue in the diagnosis of antibiotic resistance in Mycobacterium tuberculosis in the Valencia Region, Spain: a retrospective genomic analysis.

BACKGROUND: In June, 2021, WHO published the most complete catalogue to date of resistance-conferring mutations in Mycobacterium tuberculosis. Here, we aimed to assess the performance of genome-based antimicrobial resistance prediction using the catalogue and its potential for improving diagnostics in a real low-burden setting. METHODS: In this retrospective population-based genomic study M tuberculosis isolates were collected from 25 clinical laboratories in the low-burden setting of the Valencia Region, Spain. Culture-positive tuberculosis cases reported by regional public health authorities between Jan 1, 2014, and Dec 31, 2016, were included. The drug resistance profiles of these isolates were predicted by the genomic identification, via whole-genome sequencing (WGS), of the high-confidence resistance-causing variants included in the catalogue and compared with the phenotype. We determined the minimum inhibitory concentration (MIC) of the isolates with discordant resistance profiles using the resazurin microtitre assay. FINDINGS: WGS was performed on 785 M tuberculosis complex culture-positive isolates, and the WGS resistance prediction sensitivities were: 85·4% (95% CI 70·8-94·4) for isoniazid, 73·3% (44·9-92·2) for rifampicin, 50·0% (21·1-78·9) for ethambutol, and 57·1% (34·0-78·2) for pyrazinamide; all specificities were more than 99·6%. Sensitivity values were lower than previously reported, but the overall pan-susceptibility accuracy was 96·4%. Genotypic analysis revealed that four phenotypically susceptible isolates carried mutations (rpoB Leu430Pro and rpoB Ile491Phe for rifampicin and fabG1 Leu203Leu for isoniazid) known to give borderline resistance in standard phenotypic tests. Additionally, we identified three putative resistance-associated mutations (inhA Ser94Ala, katG Leu48Pro, and katG Gly273Arg for isoniazid) in samples with substantially higher MICs than those of susceptible isolates. Combining both genomic and phenotypic data, in accordance with the WHO diagnostic guidelines, we could detect two new multidrug-resistant cases. Additionally, we detected 11 (1·6%) of 706 isolates to be monoresistant to fluoroquinolone, which had been previously undetected. INTERPRETATION: We showed that the WHO catalogue enables the detection of resistant cases missed in phenotypic testing in a low-burden region, thus allowing for better patient-tailored treatment. We also identified mutations not included in the catalogue, relevant at the local level. Evidence from this study, together with future updates of the catalogue, will probably lead in the future to the partial replacement of culture testing with WGS-based drug susceptibility testing in our setting. FUNDING: European Research Council and the Spanish Ministerio de Ciencia.

Occupational Balance and Emotional Regulation in People With and Without Serious Mental Illness.

Background. Serious mental illness affects daily functioning, including occupational balance. Purpose. This study aims to compare occupational balance and emotional regulation between people with serious mental illness and the healthy population and to examine the relationship between occupational balance and emotional regulation. Method. A cross-sectional study was performed. Occupational balance and emotional regulation were measured using the Occupational Balance Questionnaire and the Emotional Regulation Questionnaire, respectively. A multivariate analysis (analysis of covariance) was conducted. Findings. The sample consisted of 112 individuals, divided into two groups: the serious mental illness group (n = 55); and the healthy group (n = 57). People with serious mental illness reported lower occupational balance and lower cognitive reappraisal than the healthy population. Furthermore, the higher cognitive reappraisal, the higher the occupational balance, and the higher the expressive suppression, the lower the occupational balance. Conclusion. The results provide preliminary evidence of the relationship between occupational balance and emotional regulation.

Second TURB, restaging TURB or repeat TURB in primary T1 non-muscle invasive bladder cancer: impact on prognosis?

PURPOSE: A re-transurethral resection of the bladder (re-TURB) is a well-established approach in managing non-muscle invasive bladder cancer (NMIBC) for various reasons: repeat-TURB is recommended for a macroscopically incomplete initial resection, restaging-TURB is required if the first resection was macroscopically complete but contained no detrusor muscle (DM) and second-TURB is advised for all completely resected T1-tumors with DM in the resection specimen. This study assessed the long-term outcomes after repeat-, second-, and restaging-TURB in T1-NMIBC patients. METHODS: Individual patient data with tumor characteristics of 1660 primary T1-patients (muscle-invasion at re-TURB omitted) diagnosed from 1990 to 2018 in 17 hospitals were analyzed. Time to recurrence, progression, death due to bladder cancer (BC), and all causes (OS) were visualized with cumulative incidence functions and analyzed by log-rank tests and multivariable Cox-regression models stratified by institution. RESULTS: Median follow-up was 45.3 (IQR 22.7-81.1) months. There were no differences in time to recurrence, progression, or OS between patients undergoing restaging (135 patients), second (644 patients), or repeat-TURB (84 patients), nor between patients who did or who did not undergo second or restaging-TURB. However, patients who underwent repeat-TURB had a shorter time to BC death compared to those who had second- or restaging-TURB (multivariable HR 3.58, P = 0.004). CONCLUSION: Prognosis did not significantly differ between patients who underwent restaging- or second-TURB. However, a worse prognosis in terms of death due to bladder cancer was found in patients who underwent repeat-TURB compared to second-TURB and restaging-TURB, highlighting the importance of separately evaluating different indications for re-TURB.

IgM marks persistent IgG anti-human leukocyte antigen antibodies in highly sensitized heart transplant patients.

BACKGROUND: Sensitization to human leukocyte antigens (HLA) is a persistent problem in heart transplant (HT) candidates. We sought to characterize the anti-HLA antibody and circulating B cell repertoire in a cohort of highly sensitized HT candidates. METHODS: We assessed immunoglobulin G (IgG) and immunoglobulin M (IgM) anti-HLA antibodies using Luminex single antigen bead assays in a cohort of 11 highly sensitized (HS; calculated panel reactive antibody ≥ 90%) and 3 mildly sensitized (MS) candidates. We also performed B cell receptor repertoire sequencing (BCRseq) in HS candidates and 33 non-candidate controls. HLA antibody strength was measured by mean fluorescence intensity (MFI). RESULTS: We found that IgM anti-HLA antibodies were present in all HS candidates, but with a lower breadth and strength as compared to IgG. When anti-HLA IgG specificities intersected with IgM, binding strength was higher. In contrast, there were IgM but no intersecting IgG specificities for the MS group. In four candidates in the HS group, IgG anti-HLA antibodies decreased in both breadth and strength after HT, but the decrease in strength was smaller if the IgG possessed a specificity that intersected with pre-transplant IgM. BCRseq revealed larger B cell clonotypes in HS candidates but similar diversity as compared to controls. CONCLUSIONS: IgM marks IgG anti-HLA antibodies with higher strength before HT and persistence after HT. The presence of IgM intersecting IgG for an anti-HLA specificity may be a useful approach to determine which donor HLA should be avoided for a sensitized candidate.

Impacto de la COVID-19 en los enfermos con diagnóstico de cáncer de pulmón en el Hospital Universitario General Calixto García / Impact of COVID-19 on Ill Patients Diagnosed with Lung Cancer at Hospital Universitario General Calixto García

Introducción: En enero de 2020 la Organización Mundial de la Salud declara el estado de pandemia por COVID-19. Los enfermos con cáncer de pulmón tienen gran vulnerabilidad ante esta enfermedad. Objetivo: Evaluar el impacto de la COVID-19 en los enfermos con diagnóstico de cáncer de pulmón. Método: Se realizó un estudio descriptivo, retrospectivo y longitudinal en 273 enfermos con cáncer de pulmón, discutidos en el Grupo Multidisciplinario de Tórax del Hospital Universitario General Calixto García desde el 2019 hasta el 2021. Se analizaron diferentes variables y se aplicaron análisis estadísticos, tales como porcentaje, desviación estándar y media. Resultados: El mayor número de enfermos operados discutidos en el grupo multidisciplinario fue durante el 2019 (21 para un 19,45 porciento). La etapa clínica II predominó en el año 2019, en 10 pacientes. La lobectomía fue la técnica más empleada y predominó en el 2019 en 16 enfermos (76,2 porciento), mientras que durante el 2020-2021 fueron 7. En estos años se diagnosticaron con COVID-19 un total de 17 individuos no operados y fallecieron 11. Conclusiones: Durante el período 2020-2021 disminuyó el número de casos discutidos por cáncer de pulmón en el Grupo Multidisciplinario de Tórax del Hospital Universitario General Calixto García. La mayoría no tuvo criterio de cirugía. La lobectomía fue la técnica quirúrgica más empleada, aunque se redujo su realización durante el 2020-2021. La mayoría de los enfermos que contrajeron COVID-19 no fueron operados y más de la mitad de ellos fallecieron(AU)

Introduction: In January 2020, the World Health Organization declares a pandemic status due to the COVID-19. Lung cancer patients are highly vulnerable to this disease. Objective: To evaluate the impact of COVID-19 in patients diagnosed with lung cancer. Methods: A descriptive, retrospective and longitudinal study was carried out in 273 patients with lung cancer, discussed in the multidisciplinary thorax group at Hospital Universitario General Calixto García from 2019 to 2021. Different variables were analyzed and statistical analyses were applied, such as percentage, standard deviation and mean. Results: The highest number of operated patients discussed in the multidisciplinary group was reported during 2019 (21, accounting for 19.45 percent). The clinical stage II predominated in 2019, with 10 patients. Lobectomy was the most used technique and the predominant in 2019, with 16 patients (76.2 percent), while 7 were reported during 2020-2021. A total of 17 nonoperated individuals were diagnosed with COVID-19 in these years and 11 died. Conclusions: During 2020-2021, there was a decrease in the number of lung cancer cases discussed in the multidisciplinary thorax group at Hospital Universitario General Calixto García decreased. Most of them did not have surgery criteria. Lobectomy was the most used surgical technique, although its realization was reduced during 2020-2021. Most of the patients who contracted COVID-19 were not operated and over half of them died(AU)

Tick infestation in spur-thighed tortoise population: a pilot study for unraveling epidemiological patterns and demographic consequences.

Ectoparasites, such as ticks, modulate host population dynamics by impacting demographic traits. They transmit infectious agents among their hosts, posing a critical threat to animal and public health. This study aimed to characterize and analyze the Hyalomma aegyptium infestation on one of its main hosts, the spur-thighed tortoise, its effects on demographic traits, and to determine the diversity of infectious agents present in both ticks and tortoises in the Maamora forest (northwestern Morocco). Our results show that 100% of the tortoises were parasitized by adult ticks in spring, an infestation intensity of 4 ticks/tortoise (5.1 and 3.6 ticks/tortoise in males and females, respectively; 4.2 and 3.3 ticks/tortoise in gravid and non-gravid females, respectively) and an abundance ranging from 1 to 12. Although without significant differences, male tortoises had higher tick abundances than females. The interaction of tortoise sex and body condition was significantly related to tick abundance, male body condition decreased with higher tick abundance in contrast to females. Nevertheless, the interaction of body condition and reproductive stage of females was not significantly related to tick abundance. Gravid females were significantly associated with tick abundance, showing a slightly higher infestation than non-gravid females. Molecular analysis of pooled tick samples revealed the presence of Ehrlichia ewingii, Candidatus Midichloria mitochondrii, and Rickettsia africae, with a minimum infection rate of 0.61 to 1.84%. However, blood sample analysis of the tortoises was infectious agent-free, pinpointing a lack of significant health problems. Given the possible effect on the transmission of zoonotic diseases by spur-thighed tortoises associated with their frequent collection as pets, it should be surveyed to control possible human health problems. In conservation terms, as a long-lived species, the role of tick infestation in demographic traits might be included in the management and conservation programs of spur-thighed tortoises.

Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR.

Allelic variability in the adaptive immune receptor loci, which harbor the gene segments that encode B cell and T cell receptors (BCR/TCR), has been shown to be of critical importance for immune responses to pathogens and vaccines. In recent years, B cell and T cell receptor repertoire sequencing (Rep-Seq) has become widespread in immunology research making it the most readily available source of information about allelic diversity in immunoglobulin (IG) and T cell receptor (TR) loci in different populations. Here we present a novel algorithm for extra-sensitive and specific variable (V) and joining (J) gene allele inference and genotyping allowing reconstruction of individual high-quality gene segment libraries. The approach can be applied for inferring allelic variants from peripheral blood lymphocyte BCR and TCR repertoire sequencing data, including hypermutated isotype-switched BCR sequences, thus allowing high-throughput genotyping and novel allele discovery from a wide variety of existing datasets. The developed algorithm is a part of the MiXCR software ( https://mixcr.com ) and can be incorporated into any pipeline utilizing upstream processing with MiXCR. We demonstrate the accuracy of this approach using Rep-Seq paired with long-read genomic sequencing data, comparing it to a widely used algorithm, TIgGER. We applied the algorithm to a large set of IG heavy chain (IGH) Rep-Seq data from 450 donors of ancestrally diverse population groups, and to the largest reported full-length TCR alpha and beta chain (TRA; TRB) Rep-Seq dataset, representing 134 individuals. This allowed us to assess the genetic diversity of genes within the IGH, TRA and TRB loci in different populations and demonstrate the connection between antibody repertoire gene usage and the number of allelic variants present in the population. Finally we established a database of allelic variants of V and J genes inferred from Rep-Seq data and their population frequencies with free public access at https://vdj.online .

Case report: Endovascular stent-graft repair of aortic penetrating trauma, literature review, and case report.

Penetrating aortic injuries are infrequent. Its incidence is unknown because most patients die of hemorrhage even before they receive adequate treatment. Aortic wounds generally require conventional thoracotomy/laparotomy repair and are related to high mortality rates. Recently with the advent of endovascular techniques, most authors prefer endovascular management when feasible due to better (still poor) outcomes. The short- and mid-term results of immediate endovascular repair of traumatic aortic injuries are promising, especially when compared with open surgical treatment, indicating that endovascular therapy is preferable in patients with multi-trauma and traumatic ruptures of the thoracic aorta. Here we present the diagnosis and treatment of a 30 years-old male patient with multiple traumatic stab wounds, including anterior aortic laceration with a grade II aortic lesion successfully managed with an endovascular stent graft.

SeQual-Stream: approaching stream processing to quality control of NGS datasets.

BACKGROUND: Quality control of DNA sequences is an important data preprocessing step in many genomic analyses. However, all existing parallel tools for this purpose are based on a batch processing model, needing to have the complete genetic dataset before processing can even begin. This limitation clearly hinders quality control performance in those scenarios where the dataset must be downloaded from a remote repository and/or copied to a distributed file system for its parallel processing. RESULTS: In this paper we present SeQual-Stream, a streaming tool that allows performing multiple quality control operations on genomic datasets in a fast, distributed and scalable way. To do so, our approach relies on the Apache Spark framework and the Hadoop Distributed File System (HDFS) to fully exploit the stream paradigm and accelerate the preprocessing of large datasets as they are being downloaded and/or copied to HDFS. The experimental results have shown significant improvements in the execution times of SeQual-Stream when compared to a batch processing tool with similar quality control features, providing a maximum speedup of 2.7[Formula: see text] when processing a dataset with more than 250 million DNA sequences, while also demonstrating good scalability features. CONCLUSION: Our solution provides a more scalable and higher performance way to carry out quality control of large genomic datasets by taking advantage of stream processing features. The tool is distributed as free open-source software released under the GNU AGPLv3 license and is publicly available to download at https://github.com/UDC-GAC/SeQual-Stream .

Application of Machine Learning Algorithms to Describe the Characteristics of Dairy Sheep Lactation Curves.

In recent years, machine learning (ML) algorithms have emerged as powerful tools for predicting and modeling complex data. Therefore, the aim of this study was to evaluate the prediction ability of different ML algorithms and a traditional empirical model to estimate the parameters of lactation curves. A total of 1186 monthly records from 156 sheep lactations were used. The model development process involved training and testing models using ML algorithms. In addition to these algorithms, lactation curves were also fitted using the Wood model. The goodness of fit was assessed using correlation coefficient (r), mean absolute error (MAE), root mean square error (RMSE), relative absolute error (RAE), and relative root mean square error (RRSE). SMOreg was the algorithm with the best estimates of the characteristics of the sheep lactation curve, with higher values of r compared to the Wood model (0.96 vs. 0.68) for the total milk yield. The results of the current study showed that ML algorithms are able to adequately predict the characteristics of the lactation curve, using a relatively small number of input data. Some ML algorithms provide an interpretable architecture, which is useful for decision-making at the farm level to maximize the use of available information.

Factors associated with a nonresponse to prone positioning in patients with severe acute respiratory distress syndrome due to SARS-CoV-2.

OBJECTIVE: To identify risk factors for nonresponse to prone positioning in mechanically ventilated patients with COVID-19-associated severe acute respiratory distress syndrome and refractory hypoxemia in a tertiary care hospital in Colombia. METHODS: Observational study based on a retrospective cohort of mechanically ventilated patients with severe acute respiratory distress syndrome due to SARS-CoV-2 who underwent prone positioning due to refractory hypoxemia. The study considered an improvement ≥ 20% in the PaO2/FiO2 ratio after the first cycle of 16 hours in the prone position to be a 'response'. Nonresponding patients were considered cases, and responding patients were controls. We controlled for clinical, laboratory, and radiological variables. RESULTS: A total of 724 patients were included (58.67 ± 12.37 years, 67.7% males). Of those, 21.9% were nonresponders. Mortality was 54.1% for nonresponders and 31.3% for responders (p < 0.001). Variables associated with nonresponse were time from the start of mechanical ventilation to pronation (OR 1.23; 95%CI 1.10 - 1.41); preintubation PaO2/FiO2 ratio (OR 0.62; 95%CI 0.40 - 0.96); preprone PaO2/FiO2 ratio (OR 1.88. 95%CI 1.22 - 2.94); and radiologic multilobe consolidation (OR 2.12; 95%CI 1.33 - 3.33) or mixed pattern (OR 1.72; 95%CI 1.07 - 2.85) compared with a ground-glass pattern. CONCLUSION: This study identified factors associated with nonresponse to prone positioning in patients with refractory hypoxemia and acute respiratory distress syndrome due to SARS-CoV-2 receiving mechanical ventilation. Recognizing such factors helps identify candidates for other rescue strategies, including more extensive prone positioning or extracorporeal membrane oxygenation. Further studies are needed to assess the consistency of these findings in populations with acute respiratory distress syndrome of other etiologies.

Infectious endocarditis without intracardiac devices or underlying structural heart disease.

OBJECTIVE: To describe clinical, microbiological and echocardiographic aspects of endocarditis in a specific group of patients without intracardiac devices or underlying structural heart disease. METHOD: Retrospective study, clinical records and echocardiographic reports were reviewed during the period 1997 to 2020. Duke's modified criteria were applied. Statistical analysis: univariate expressed in frequencies, using measures of dispersion and central tendency. RESULTS: 30,000 echocardiographic reports were reviewed, only 1350 had infectious endocarditis as a reason for sending, of which 248 cases were selected. The mean age was 48.1 ± 16.7 years. 140 men (56%) and 108 women (44%). The most frequent echocardiographic sign was vegetation, in 278 (93.60%), and most common location was mitral (35.55%), with a higher number of cases in the right ventricle than expected. The most common systemic disease was kidney disease, in 135 (41.08%). A case of Streptococcus thoraltensis not previously reported in Mexico was identified. CONCLUSIONS: The presence of infectious endocarditis has increased due to invasive in-hospital and drug procedures. Due to their complexity, multidisciplinary teams are indispensable.

OBJETIVO: Describir aspectos clínicos, microbiológicos y ecocardiográficos de endocarditis en un grupo específico de pacientes sin dispositivos intracardiacos ni cardiopatía estructural subyacente. MÉTODO: Estudio retrospectivo en el que se revisaron expedientes clínicos y reportes ecocardiográficos durante el periodo de 1997 a 2020. Se aplicaron los criterios modificados de Duke. Se describió la muestra por edad, sexo, enfermedad sistémica, vegetaciones y agente microbiológico. Se excluyeron pacientes con cardiopatía estructural o Libman-Sacks. Análisis estadístico: univariado expresado en frecuencias, utilizando medidas de dispersión y tendencia central. RESULTADOS: Se revisaron 30,000 reportes ecocardiográficos, de los cuales solo 1350 tenían como motivo de envío endocarditis infecciosa, y de estos se seleccionaron 248 casos. La edad promedio fue de 48.1 ± 16.7 años. Hubo 140 hombres (56%) y 108 mujeres (44%). El signo ecocardiográfico más frecuente fue la vegetación, en 278 (93.60%), y la ubicación más común fue mitral (35.55%), con un número mayor de casos en el ventrículo derecho de lo esperado. La enfermedad sistémica más común fue la enfermedad renal, en 135 (41.08%). Se identificó un caso de Streptococcus thoraltensis no reportado previamente en México. CONCLUSIONES: La presencia de endocarditis infecciosa ha aumentado debido a procedimientos invasivos intrahospitalarios y fármacos. Por su complejidad, los equipos multidisciplinarios son indispensables.

IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data.

In adaptive immune receptor repertoire analysis, determining the germline variable (V) allele associated with each T- and B-cell receptor sequence is a crucial step. This process is highly impacted by allele annotations. Aligning sequences, assigning them to specific germline alleles, and inferring individual genotypes are challenging when the repertoire is highly mutated, or sequence reads do not cover the whole V region. Here, we propose an alternative naming scheme for the V alleles, as well as a novel method to infer individual genotypes. We demonstrate the strengths of the two by comparing their outcomes to other genotype inference methods. We validate the genotype approach with independent genomic long-read data. The naming scheme is compatible with current annotation tools and pipelines. Analysis results can be converted from the proposed naming scheme to the nomenclature determined by the International Union of Immunological Societies (IUIS). Both the naming scheme and the genotype procedure are implemented in a freely available R package (PIgLET https://bitbucket.org/yaarilab/piglet). To allow researchers to further explore the approach on real data and to adapt it for their uses, we also created an interactive website (https://yaarilab.github.io/IGHV_reference_book).

Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire.

Variation in the antibody response has been linked to differential outcomes in disease, and suboptimal vaccine and therapeutic responsiveness, the determinants of which have not been fully elucidated. Countering models that presume antibodies are generated largely by stochastic processes, we demonstrate that polymorphisms within the immunoglobulin heavy chain locus (IGH) impact the naive and antigen-experienced antibody repertoire, indicating that genetics predisposes individuals to mount qualitatively and quantitatively different antibody responses. We pair recently developed long-read genomic sequencing methods with antibody repertoire profiling to comprehensively resolve IGH genetic variation, including novel structural variants, single nucleotide variants, and genes and alleles. We show that IGH germline variants determine the presence and frequency of antibody genes in the expressed repertoire, including those enriched in functional elements linked to V(D)J recombination, and overlapping disease-associated variants. These results illuminate the power of leveraging IGH genetics to better understand the regulation, function, and dynamics of the antibody response in disease.

Anti-Inflammatory Effect of Izalpinin Derived from Chromolaena leivensis: λ-Carrageenan-Induced Paw Edema and In Silico Model.

The flavonoid izalpinin was isolated from the aerial parts of Chromolaena leivensis. Its structural determination was carried out using MS and NMR spectroscopic techniques (1H, 13C). This compound was evaluated for its anti-inflammatory effect in a rat model on λ-carrageenan-induced plantar edema. Paw inflammation was measured at one-hour intervals for seven hours following the administration of λ-carrageenan. Serum creatine kinase (CK) levels were evaluated, obtaining statistically significant results with the treatments at doses of 10 mg/kg (* p < 0.01) and 20 mg/kg (** p < 0.005). The anti-inflammatory effect of the compound was evaluated by using plethysmography, and the results showed significant differences at the three concentrations (10 mg/kg, 20 mg/kg, 40 mg/kg) in the first and third hours after treatment. * p < 0.05; ** p < 0.001; **** p < 0.0001 vs. the negative control group treated with vehicle (DMSO). Lastly, molecular docking analyses reveal that izalpinin has a strong binding affinity with five target proteins involved in the inflammatory process. The analysis using molecular dynamics allowed demonstrating that the ligand-protein complexes present acceptable stability, with RMSD values within the allowed range.