Exploring aptamers for targeted enrichment of X sperm in bovine: unraveling selective potential.

Nucleic acid aptamers have been used in the past for the development of diagnostic methods against a number of targets such as bacteria, pesticides, cancer cells etc. In the present study, six rounds of Cell-SELEX were performed on a ssDNA aptamer library against X-enriched sperm cells from Sahiwal breed cattle. Sequencing was used to examine the aptamer sequences that shown affinity for sperm carrying the X chromosome in order to find any possible X-sperm-specific sequences. Out of 35 identified sequences, 14 were selected based on bioinformatics analysis like G-Score and Mfold structures. Further validation of their specificity was done via fluorescence microscopy. The interaction of biotinylated-aptamer with sperm was also determined by visualizing the binding of streptavidin coated magnetic beads on the head region of the sperm under bright field microscopy. Finally, a real-time experiment was designed for the validation of X-sperm enrichment by synthesized aptamer sequences. Among the studied sequences, aptamer 29a exhibited a higher affinity for X sperm compared to Y sperm in a mixed population of sperm cells. By using aptamer sequence 29a, we obtained an enrichment of 70% for X chromosome bearing sperm cells.

Alzheimer's disease: A role of biomarkers in early diagnosis and evidences from African ethnomedicinal knowledge.

Alzheimer's disease (AD) is a neurological ailment that primarily affects the elderly and necessitates an efficient treatment regimen backed up by extensive care. Despite advancement in the in vivo imaging techniques focussing on early diagnosis of reliable biomarkers using novel magnetic resonance imaging (MRI) and positron emission topography (PET) scans, AD remains largely unexplained and effective preventative and treatment strategies are still lacking. Consequently, research groups are constantly attempting to improve its early detection, using both invasive and non-invasive techniques with established core markers like Aß and Tau (t-tau and p-tau) proteins. Unfortunately, African American and other black races are facing an increasing burden of closely associated risk factors, and only a few attempts have been made to find effective complementary and alternative therapies for AD cure and management. A greater epidemiology and natural product research are required to deal with the concurrent rise of dementia among quickly ageing African population, which so far have largely been ignored in addition to a disparity in the AD risk factors. We have tried to bring attention to the issue by reviewing up on this predisposition while generating a perspective on how race may affect AD risk and expression. This article also puts emphasis on finding new research leads from African phytodiversity while presenting several of the important species along with their biological agents found helpful in dementia related symptoms.

Skin Cancer Diagnosis Based on Neutrosophic Features with a Deep Neural Network.

Recent years evidenced an increase in the total number of skin cancer cases, and it is projected to grow exponentially. This paper proposes a computer-aided diagnosis system for the classification of a malignant lesion, where the acquired image is primarily pre-processed using novel methods. Digital artifacts such as hair follicles and blood vessels are removed, and thereafter, the image is enhanced using a novel method of histogram equalization. Henceforth, the pre-processed image undergoes the segmentation phase, where the suspected lesion is segmented using the Neutrosophic technique. The segmentation method employs a thresholding-based method along with a pentagonal neutrosophic structure to form a segmentation mask of the suspected skin lesion. The paper proposes a deep neural network base on Inception and residual blocks with softmax block after each residual block which makes the layer wider and easier to learn the key features more quickly. The proposed classifier was trained, tested, and validated over PH2, ISIC 2017, ISIC 2018, and ISIC 2019 datasets. The proposed segmentation model yields an accuracy mark of 99.50%, 99.33%, 98.56% and 98.04% for these datasets, respectively. These datasets are augmented to form a total of 103,554 images for training, which make the classifier produce enhanced classification results. Our experimental results confirm that the proposed classifier yields an accuracy score of 99.50%, 99.33%, 98.56%, and 98.04% for PH2, ISIC 2017, 2018, and 2019, respectively, which is better than most of the pre-existing classifiers.

Modulation of granulocyte colony stimulating factor conformation and receptor binding by methionine oxidation.

Biosimilars offer an avenue for potential cost savings and enhanced patient access to various emerging therapies in a budget neutral way. Biosimilars of the granulocyte colony stimulating factor (GCSF) are an excellent example in this regard with as many as 18 versions of the drug being currently approved across globe for treatment of neutropenia. Here, we identified oxidation of the various methionine residues in GCSF as a key heterogeneity that adversely impact its efficacy. In agreement with earlier studies, it was found that oxidation of Met 122 and Met 127 significantly contributes toward reduction of GCSF efficacy, measured using binding affinity to the GCSF receptor. The combination of molecular dynamics simulation along with structural characterization studies established that oxidation of Met 127 and Met 122 brings about a small local conformational change around the B-C loop in GCSF structure due to slight displacement of Asp113 and Thr117 residues. The simulation studies were validated using fluorescence quenching experiments using acrylamide as quencher and site-directed mutagenesis by replacing Met 122 and Met 127 residues with alanine. The results of this study lead to an enhanced mechanistic understanding of the oxidation in GCSF and should be useful in protein engineering efforts to design stable, safe, and efficacious GCSF product. In addition, the structure-function information can provide targets for protein engineering during early drug development and setting specifications of allowable limits of product variants in biosimilar products.

Understanding Oxidation Propensity in GCSF and Assessment of its Safety and Efficacy.

PURPOSE: To understand the impact of methionine oxidation in GCSF on efficacy (neutrophil production/activation) and safety (biochemical and histopathological changes). METHODS: Nine GCSF biosimilars were analyzed for the levels of residual iron and copper content. Oxidation in GCSF was induced by H2O2 treatment and four samples were prepared: wtGCSF (no oxidation), MetO (1138), MetO (1,138,127) and MetO (1138,127,122). These samples were used to evaluate binding affinity with the GCSF receptor (GCSFR) using biolayer interferometry, thermal stability using circular dichroism and in vitro potency using a relevant cell-based assay. In vivo pharmacodynamics examined changes in neutrophil production upon GCSF methionine oxidation, with the outcome correlated with the differential expression of genes implicated in the GCSF mediated neutrophil activation/ maturation. Pre-clinical safety studies including biochemical and histopathological changes were also performed. RESULTS: Met 122 and Met 127 have the most deleterious effect on the potency. Lower binding affinity with GCSFR was identified as the underlying cause for lower efficacy and potency. Role of Asp 110 in GCSF as the critical residue having adverse impact on efficacy in context of methionine oxidation has been elucidated. Impairment of in vitro binding affinity with GCSF manifests as in vivo pharmacodynamic differences via differential expression of downstream genes required for neutrophil maturation. CONCLUSION: The data from the present study suggests that methionine oxidation in GCSF is a critical quality attribute that needs careful monitoring and control during commercial manufacturing and subsequent supply chain stages.

Late-Onset Hepatic Failure in Children: Risk Factors that Determine the Outcome.

BACKGROUND: Late-onset hepatic failure (LOHF) is a distinct entity of intractable liver diseases with limited pediatric experience. We aimed to identify the etiology and risk factors that determine the poor outcome (PO) of pediatric LOHF. METHODS: LOHF was defined as liver failure occurring 5-24 weeks after onset of jaundice and without any evidence of underlying chronic liver disease. PO (death or liver transplantation within 160 days) was compared with spontaneous recovery (SR; complete normalization of liver functions in the native liver). Pediatric end-stage liver disease (PELD) score and King's College Criteria (KCC) were applied to investigate their prognostic value. RESULTS: We enrolled 47 children (6 [2-16] years) with LOHF. Hepatitis A was the most common etiology (15, 32%) and 64% complicated with infections. Twelve children (25%) had SR over 6 (1-24) months, while 28 (60%) children had PO. Univariate analysis showed indeterminate etiology, hepatic encephalopathy (HE), infection, acute kidney injury, and high PELD score determined PO. On multivariate regression analysis, only PELD score with a cutoff 32 (area under curve 0.833, sensitivity 68%, specificity 92%) predicted PO. KCC showed a sensitivity of 85.7%, specificity of 41.7% to determine PO in our cohort. CONCLUSION: Indeterminate etiology, presence of HE, occurrence of infection at any site, and acute kidney injury lead to the PO. PELD score ≥32 can be utilized to optimize the listing for liver transplantation. A significant proportion survives with the native liver.

A novel approach for protein identification from complex cell proteome using modified peptide mass fingerprinting algorithm.

A unique peptide based search algorithm for identification of protein mixture using PMF is proposed. The proposed search algorithm utilizes binary search and heapsort programs to generate frequency chart depicting the unique peptides corresponding to all proteins in a proteome. The use of binary search program significantly reduces the time for frequency chart preparation to ∼2 s for a proteome comprising ∼23 000 proteins. The algorithm was applied to a three-protein mixture identification, host cell protein (HCP) analysis, and a simulation-generated data set. It was found that the algorithm could identify at least one unique peptide of a protein even in the presence of fourfold higher concentration of another protein. In addition, two HCPs that are known to be difficult to remove were missed by MS/MS approach and were exclusively identified using the presented algorithm. Thus, the proposed algorithm when used along with standard proteomic approaches present avenues for enhanced protein identification efficiency, particularly for applications such as HCP analysis in biopharmaceutical research, where identification of low-abundance proteins are generally not achieved due to dynamic range limitations between the target product and HCPs.

Need for recognizing atypical manifestations of childhood sporadic acute viral hepatitis warranting differences in management.

Various atypical manifestations have been described in acute viral hepatitis (AVH). We evaluated the prevalence, clinical features, response to treatment and outcome of various atypical manifestations of AVH in children. Consecutive children (≤ 18 years) with AVH due to hepatitis A, B, or E were studied while patients with acute or acute on chronic liver failure were excluded. Diagnosis of atypical manifestations was based on standard criteria. A total of 477 children with AVH (median age 7.0 (5-11) years, 74% boys) were seen; 22% (n = 106) had atypical manifestations. Prolonged cholestasis was the most common (11%), followed by ascites (7%), intravascular hemolysis (3%), relapsing hepatitis (2%), acute pancreatitis (1.3%), and thrombocytopenia (0.7%). Atypical manifestations were more common in HAV as compared to HBV (30% vs. 3%, p = 0.00) and HEV (30% vs. 15%, p = 0.07). Prolonged cholestasis was significantly more common in older children (20% in > 10 years vs. 9% in 6-10 years ; p = 0.009 and 5% in 0-5 years of age [p < 0.000]). Ascites was more common in younger children, although not significant. All patients recovered with supportive treatment.Conclusions: Twenty-two percent of children with AVH have atypical manifestations, more often with HAV infection, and prolonged cholestasis is most common. Recognition of these manifestations ensures correct diagnosis and treatment. What is Known: • Acute viral hepatitis is a major public health problem in developing countries. • There is limited information about atypical manifestations which may lead to unnecessary investigations, delayed diagnosis and morbidity. What is New: • Atypical manifestations are common in children, seen most often with HAV infection, and prolonged cholestasis is most common. • Prompt recognition of these manifestations helps in early diagnosis, appropriate management, and preventing unnecessary investigations. • Ensure follow-up until complete recovery and not to miss underlying chronic liver disease.

Rheological evaluations and molecular marker analysis of cultivated bread wheat varieties of India.

The aim of this study was to screen Indian cultivated wheat varieties and list out the parameters/genes required to be improved for an end-product. Therefore, 30 Indian wheat varieties under cultivation by farmers were screened for 14 physico-chemical and rheological parameters, sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) for high molecular weight glutenin subunits (HMW-GS), DNA based molecular markers for low molecular weight glutenin subunits (LMW-GS) and puroindolines (Pin) genes. Based on grain texture, sedimentation value, farinographic, alveographic, HMW-GS and LMW-GS and biscuit making parameters, HS490 was found to be a highly suited for biscuit and soft wheat products. HI1563 and DBW14 were also found to possess characteristics such as low protein, low to medium SDS-sedimentation value and combination of 2*, 7+8 and 2+12 (HMW-GS). DBW14 also had LMW alleles desirable for biscuit quality. DBW14 needs to be improved for grain softness to make it suitable for biscuit quality while both grain softness and LMW alleles need to be improved for HI1563 to improve its biscuit spread factor and alveographic indices for extensible gluten. Rest varieties showed moderate to very strong gluten but the gluten lacked extensibility. Only four varieties K307, DBW39, NI5439 and DBW17 possessed high flour protein and moderately strong gluten. They had more balanced deformation energy (W) and configuration ratio (P/L) combination suggestive of strong and extensible gluten needed for raised bread making. Marker assisted backcross breeding is suggested as solution to produce end-use specific varieties where appropriate alleles at only a few loci need to be incorporated.

Yield of Endoscopic Ultrasound in Children and Adolescent With Acute Recurrent Pancreatitis.

OBJECTIVES: Endoscopic ultrasound (EUS) is an established tool for evaluation of adults with acute recurrent pancreatitis (ARP) whereas data in pediatrics is limited. Our study assessed the role of EUS in identifying etiology including changes of chronic pancreatitis (CP) in children and adolescents with ARP. METHODS: Children with ARP (≥2 episodes of acute pancreatitis [AP]) were prospectively evaluated with a detailed clinical proforma and EUS. Subjects with known etiology of ARP or CP on ultrasonography/computed tomography and magnetic resonance cholangiopancreatography (MRCP, Cambridge grade ≥3) were excluded. Parenchymal and ductal changes on EUS as per minimal standards terminology (MST) features were noted. RESULTS: Thirty-two children (22 boys, age 14 [8-18] years) with ARP (median of 3 [2-5] episodes of AP) were enrolled. EUS was safe and technically successful in all. Gall bladder sludge was found in 1 (3%) case and none had other pancreatobiliary structural abnormalities. EUS diagnosis of CP (≥4 features) was made in 10/32 (31%) cases. Subjects with CP on EUS had a longer disease duration than those without CP (45 [10-97] vs 22 [8-78] months; P = ns). MRCP was normal in 28 and showed pancreas divisum in 1 case. Three cases had equivocal (Cambridge II) changes at initial MRCP and 2 of them had repeat MRCP, which showed definite (Cambridge IV) CP. All these 3 cases had CP on EUS. CONCLUSIONS: EUS diagnosed CP (≥4 features) in 31% and biliary abnormality in 3% children with ARP. EUS is safe, sensitive, and useful for early diagnosis of CP in children with ARP.

Should charge variants of monoclonal antibody therapeutics be considered critical quality attributes?

Charge variants, namely acidic and basic variants, are typically found in mAb therapeutics. Charge heterogeneity is typically not regarded to affect safety and efficacy of the product. As a result, the commonly followed approach involves assignment of a specification for the variants based on statistical analysis of variability in levels that is seen during commercial manufacturing. This is followed by monitoring of product quality to demonstrate consistency. This paper aims to demonstrate that this perception of charge variants warrants a more in-depth investigation to evaluate the role charge variants play in safety and efficacy of a mAb therapeutic. In addition, a novel procedure has been suggested for making this assessment and alleviate the problems that are traditionally faced when isolating these variants for characterization. The suggested procedure utilizes the principles of bioseparations, cell biology, and statistics and it is demonstrated that this is significantly more efficient than the approach practiced today.

Impact assessment of integrated-pathy on cancer-related fatigue in cancer patients: an observational study.

BACKGROUND: Integrated-pathy aims to integrate modern medicine with traditional systems via applying the holistic approach of Ayurveda, Yoga, and natural medicine. This is important for addressing the challenges surrounding the delivery of long-term palliative care for chronic ailments including cancer. The prime intent of this study was to substantiate the underlying hypothesis behind the differential and integrative approach having a positive impact on Quality of Life of cancer patients. STUDY DESIGN: Cross-sectional Observational study. METHODS: A standardized questionnaire was developed and used, after obtaining written informed consent from patients to assess the impact of Integrated-pathy on patients (n = 103) diagnosed with cancer receiving care at Patanjali Yoggram. The research was carried out over 8 months. All participants received a uniform treatment protocol as prescribed by Patanjali. For the sample size determination and validation, α and 1-ß was calculated and for the significance of the pre- and post-treatment QoL ratings, Shapiro wilk test and other descriptive statistics techniques were explored. RESULTS: A total of 103 patients seeking cancer special-healthcare were interviewed, out of which 39 (37.86%) remained finally based on the inclusion/exclusion criteria with age (25-65 years), types of cancers (Carcinoma and Sarcoma), chemotherapy/radiotherapy received or not, before opting Integrated-pathy. Follow-ups revealed a significant increase in the QoL (17.91%) after receiving the integrated therapy over a course of at least 1 month. Further, a significant reduction in cancer-related pain followed by an increase in QoL index was reported in the patients. Shapiro-wilk test revealed significant pairing (p < 0.001) with validation of the model using test. CONCLUSIONS: To bolster evidence-based backing for Integrated-pathy, there is a need for clearly delineated clinical indicators that are measurable and trackable over time. Clinical investigators are encouraged to incorporate Integrated-pathy into their proposed interventions and conduct analogous studies to yield sustained advantages in the long run.

Physico-Chemical and Rheological Trait-Based Identification of Indian Wheat Varieties Suitable for Different End-Uses.

India has increased its wheat production phenomenally in the last two decades and it now has a buffer stock of 9.7 million tonnes. However, despite the release of several wheat cultivars, the end-use quality traits of Indian wheat varieties have not been explored in-depth to determine the increasing demand of the domestic processing industry as well as export. In this study, 55 wheat genotypes including 47 released varieties, and 8 genetic stocks were grown along with 10 Australian varieties grown during cropping seasons: 2019-2020 and 2020-2021 and diversity in different physiochemical and rheological traits was evaluated. They showed considerable diversity in all the quality traits studied. However, very few genotypes could be found suitable for any one end-use. Five genotypes were found to possess four to five traits for superior bread-making quality. Two varieties and three advanced breeding lines had up to four good chapati quality traits. None of the released varieties investigated had suitable traits for biscuit making; however, two breeding lines possessed requisite quality traits suitable for biscuit making. It is, therefore, concluded that systematic breeding efforts are required to develop genotypes that bring together the most important quality traits in a single genotype to be suitable for domestic industry as well as for export.

Discrimination of pediatric cryptogenic multifocal ulcerous stenosing enteritis from small bowel Crohn's disease and gastrointestinal tuberculosis: A retrospective study (with videos).

INTRODUCTION: Cryptogenic multifocal ulcerous stenosing enteritis (CMUSE) is a rare entity that mimics various inflammatory strictures of the small intestine. Pediatric literature is scarce. We analyzed the clinical, radiological, endoscopic and histopathological features of children with CMUSE that differentiate it from small bowel Crohn's disease (SBCD) and gastrointestinal tuberculosis (GITB). METHODS: CMUSE was diagnosed by the following criteria: (1) unexplained small bowel strictures with superficial ulcers, (2) chronic/relapsing ulcers of small bowel after resection, (3) no signs of systemic inflammation, (4) absence of other known etiologies of small bowel ulcers. SBCD and GITB were diagnosed based on standard criteria. The clinical features, laboratory parameters, radioimaging, endoscopy (including video capsule endoscopy [VCE], intra-operative endoscopy), histopathological features and treatment outcome were noted. RESULTS: Out of 48, CMUSE was diagnosed in 13 (27%) isolated small bowel and ileocecal strictures, while GITB and SBCD accounted for 41% and 21% cases, respectively. Common presentations were sub-acute obstruction (46%), obscure gastrointestinal bleeding (38%) and protein-losing enteropathy (38%). CMUSE patients had significantly longer disease duration compared to SBCD and GITB (p < 0.001). SBCD (90.0%) and GITB (85%) cases had elevated C-reactive protein (CRP), none with CMUSE had elevated CRP (p < 0.001). The disease was localized in jejunum (100%) and proximal ileum (56%) in CMUSE, ileocecal region (85%) in GITB, but evenly distributed in small intestine in SBCD. Endoscopy showed evenly placed, superficial, circumferential ulcers with strictures in CMUSE, deep linear ulcers in SBCD and circumferential ulcers in GITB. Upfront immunosuppression was given in four; three (75%) of them relapsed. Only surgery was done in three with one (25%) having relapse. Upfront surgery followed by immunosuppression was used in six, but all relapsed and two required repeat surgery. CONCLUSION: CMUSE is important but underdiagnosed in children. Lack of constitutional symptoms, normal inflammatory parameters and characteristic ulcers with strictures helped in differentiating CMUSE from GITB and SBCD.

Hereditary fructose intolerance: A comprehensive review.

Hereditary fructose intolerance (HFI) is a rare autosomal recessive inherited disorder that occurs due to the mutation of enzyme aldolase B located on chromosome 9q22.3. A fructose load leads to the rapid accumulation of fructose 1-phosphate and manifests with its downstream effects. Most commonly children are affected with gastrointestinal symptoms, feeding issues, aversion to sweets and hypoglycemia. Liver manifestations include an asymptomatic increase of transaminases, steatohepatitis and rarely liver failure. Renal involvement usually occurs in the form of proximal renal tubular acidosis and may lead to chronic renal insufficiency. For confirmation, a genetic test is favored over the measurement of aldolase B activity in the liver biopsy specimen. The crux of HFI management lies in the absolute avoidance of foods containing fructose, sucrose, and sorbitol (FSS). There are many dilemmas regarding tolerance, dietary restriction and occurrence of steatohepatitis. Patients with HFI who adhere strictly to FSS free diet have an excellent prognosis with a normal lifespan. This review attempts to increase awareness and provide a comprehensive review of this rare but treatable disorder.

Generation of Ince-Gaussian Beams Using Azocarbazole Polymer CGH.

Ince-Gaussian beams, defined as a solution to a wave equation in elliptical coordinates, have shown great advantages in applications such as optical communication, optical trapping and optical computation. However, to ingress these applications, a compact and scalable method for generating these beams is required. Here, we present a simple method that satisfies the above requirement, and is capable of generating arbitrary Ince-Gaussian beams and their superposed states through a computer-generated hologram of size 1 mm2, fabricated on an azocarbazole polymer film. Other structural beams that can be derived from the Ince-Gaussian beam were also successfully generated by changing the elliptical parameters of the Ince-Gaussian beam. The orthogonality relations between different Ince-Gaussian modes were investigated in order to verify applicability in an optical communication regime. The complete python source code for computing the Ince-Gaussian beams and their holograms are also provided.

Genome-wide association study identifies loci and candidate genes for grain micronutrients and quality traits in wheat (Triticum aestivum L.).

Malnutrition due to micronutrients and protein deficiency is recognized among the major global health issues. Genetic biofortification of wheat is a cost-effective and sustainable strategy to mitigate the global micronutrient and protein malnutrition. Genomic regions governing grain zinc concentration (GZnC), grain iron concentration (GFeC), grain protein content (GPC), test weight (TW), and thousand kernel weight (TKW) were investigated in a set of 184 diverse bread wheat genotypes through genome-wide association study (GWAS). The GWAS panel was genotyped using Breeders' 35 K Axiom Array and phenotyped in three different environments during 2019-2020. A total of 55 marker-trait associations (MTAs) were identified representing all three sub-genomes of wheat. The highest number of MTAs were identified for GPC (23), followed by TKW (15), TW (11), GFeC (4), and GZnC (2). Further, a stable SNP was identified for TKW, and also pleiotropic regions were identified for GPC and TKW. In silico analysis revealed important putative candidate genes underlying the identified genomic regions such as F-box-like domain superfamily, Zinc finger CCCH-type proteins, Serine-threonine/tyrosine-protein kinase, Histone deacetylase domain superfamily, and SANT/Myb domain superfamily proteins, etc. The identified novel MTAs will be validated to estimate their effects in different genetic backgrounds for subsequent use in marker-assisted selection.

Assessment of Functional Characterization and Comparability of Biotherapeutics: a Review.

The development of monoclonal antibody (mAb) biosimilars is a complex process. The key to their successful development and commercialization is an in-depth understanding of the key product attributes that impact safety and efficacy and the strategies to control them. Functional assessment of mAb is a crucial part of the comparability of biopharmaceutical drugs. The development of a relevant and robust functional assay requires an interdisciplinary approach and sufficient flexibility to balance regulatory concerns as well as dynamics and variability during the manufacturing process. Although many advanced tools are available to study and compare the potency and bioactivity of the protein, most of these techniques suffer from major shortcomings that limit their routine use. These include the complexity of the task, establishment of the relevance of the chosen method with the mechanism of action (MOA) of the biosimilar, cost and extended time of analysis, and often the ambiguity in interpretation of the resulting data. To overcome or to address these challenges, the use of multiple orthogonal state-of-the-art techniques is a necessary prerequisite.

LC-MS based case-by-case analysis of the impact of acidic and basic charge variants of bevacizumab on stability and biological activity.

The present study investigates the impact of charge variants on bevacizumab's structure, stability, and biological activity. Five basic and one acidic charge variants were separated using semi-preparative cation exchange chromatography using linear pH gradient elution with purity > 85%. Based on the commercial biosimilar product's composition, two basic variants, one acidic and the main bevacizumab product, were chosen for further investigation. Intact mass analysis and tryptic peptide mapping established the basic variants' identity as those originating from an incomplete clipping of either one or both C-terminal lysine residues in the heavy chain of bevacizumab. Based on peptide mapping data, the acidic variant formation was attributed to deamidation of asparagine residue (N84), oxidation of M258, and preservation of C-terminal lysine residue, located on the heavy chain of bevacizumab. None of the observed charge heterogeneities in bevacizumab were due to differences in glycosylation among the variants. The basic (lysine) variants exhibited similar structural, functional, and stability profiles as the bevacizumab main product. But it was also noted that both the variants did not improve bevacizumab's therapeutic utility when pooled in different proportions with the main product. The acidic variant was found to have an equivalent secondary structure with subtle differences in the tertiary structure. The conformational difference also translated into a ~ 62% decrease in biological activity. Based on these data, it can be concluded that different charge variants behave differently with respect to their structure and bioactivity. Hence, biopharmaceutical manufacturers need to incorporate this understanding into their process and product development guidelines to maintain consistency in product quality.

Peptide profiling in cow urine reveals molecular signature of physiology-driven pathways and in-silico predicted bioactive properties.

Peptidomics allows the identification of peptides that are derived from proteins. Urinary peptidomics has revolutionized the field of diagnostics as the samples represent complete systemic changes happening in the body. Moreover, it can be collected in a non-invasive manner. We profiled the peptides in urine collected from different physiological states (heifer, pregnancy, and lactation) of Sahiwal cows. Endogenous peptides were extracted from 30 individual cows belonging to three groups, each group comprising of ten animals (biological replicates n = 10). Nano Liquid chromatography Mass spectrometry (nLC-MS/MS) experiments revealed 5239, 4774, and 5466 peptides in the heifer, pregnant and lactating animals respectively. Urinary peptides of <10 kDa size were considered for the study. Peptides were extracted by 10 kDa MWCO filter. Sequences were identified by scanning the MS spectra ranging from 200 to 2200 m/z. The peptides exhibited diversity in sequences across different physiological states and in-silico experiments were conducted to classify the bioactive peptides into anti-microbial, anti-inflammatory, anti-hypertensive, and anti-cancerous groups. We have validated the antimicrobial effect of urinary peptides on Staphylococcus aureus and Escherichia coli under an in-vitro experimental set up. The origin of these peptides was traced back to certain proteases viz. MMPs, KLKs, CASPs, ADAMs etc. which were found responsible for the physiology-specific peptide signature of urine. Proteins involved in extracellular matrix structural constituent (GO:0005201) were found significant during pregnancy and lactation in which tissue remodeling is extensive. Collagen trimers were prominent molecules under cellular component category during lactation. Homophilic cell adhesion was found to be an important biological process involved in embryo attachment during pregnancy. The in-silico study also highlighted the enrichment of progenitor proteins on specific chromosomes and their relative expression in context to specific physiology. The urinary peptides, precursor proteins, and proteases identified in the study offers a base line information in healthy cows which can be utilized in biomarker discovery research for several pathophysiological studies.