Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences

Antibody repertoires reveal insights into the biology of the adaptive immune system and empower diagnostics and therapeutics. There are currently multiple tools available for the annotation of antibody sequences. All downstream analyses such as choosing lead drug candidates depend on the correct annotation of these sequences; however, a thorough comparison of the performance of these tools has not been investigated. Here, we benchmark the performance of commonly used immunoinformatic tools, i.e. IMGT/HighV-QUEST, IgBLAST and MiXCR, in terms of reproducibility of annotation output, accuracy and speed using simulated and experimental high-throughput sequencing datasets

The Nutraceutical Genistein-Lycopene Combination Improves Bone Damage Induced by Glucocorticoids by Stimulating the Osteoblast Formation Process

Chronic glucocorticoid (GC) therapy is the most common cause of iatrogenic osteoporosis and represents an important risk factor for osteoporosis and bone fractures. New therapeutic approaches are required in order to treat osteoporosis and reduce the side effects related to the use of anti-osteoporotic drugs. In this context, previous studies reported the efficacy of some isoflavones and carotenoids, such as lycopene and genistein, on the reduction of the risk of fracture related to osteoporosis. The aim of this study was to investigate the effects of a combined oral treatment, consisting of genistein and lycopene, in an experimental model of glucocorticoid-induced osteoporosis (GIO). GIO was induced by subcutaneous injection of methylprednisolone (MP, 30 mg/kg) for 60 days, whereas the control group (Sham) received saline solution only. Following induction, MP animals randomly were assigned to receive alendronate, genistein, lycopene, or the association of genistein and lycopene or saline solution for additional 60 days together with MP. Femurs obtained from the Sham group were used for osteoblasts extraction; they were then incubated with dexamethasone (DEX) for 24 h to be then treated with lycopene or genistein or the association of lycopene and genistein for an additional 24 h. Treatments with lycopene and genistein restored the impaired mineralization of cells observed following DEX treatment and stimulated osteoblast differentiation by increasing the depressed expression of bALP and RUNX2 (p < 0.0001). Wnt5a, β-catenin, and Nrf-2 expression were significantly increased following genistein and lycopene treatment (p < 0.0001), thus confirming their antioxidant activity as well as their ability in stimulating osteoblast function, mostly when genistein and lycopene were used in association. The combined treatment of genistein and lycopene improved the bone damage induced by glucocorticoids and significantly restored the normal architecture of bones as well as adequate interconnectivity of bone trabeculae, thus increasing bone mineral density parameters. The obtained data demonstrated that genistein and lycopene but in particular their association might prevent GC’s adverse effects, thus stimulating bone formation and reducing bone resorption, improving bone structure and microarchitecture, through different molecular pathways, such as the Wnt/β-catenin and the Nrf-2 signaling

Haiti Earthquake (Mw 7.2): Magnetospheric&ndash;Ionospheric&ndash;Lithospheric Coupling during and after the Main Shock on 14 August 2021

In the last few decades, the efforts of the scientific community to search earthquake signatures in the atmospheric, ionospheric and magnetospheric media have grown rapidly. The increasing amount of good quality data from both ground stations and satellites has allowed for the detections of anomalies with high statistical significance such as ionospheric plasma density perturbations and/or atmospheric temperature and pressure changes. However, the identification of a causal link between the observed anomalies and their possible seismic trigger has so far been prevented by difficulties in the identification of confounders (such as solar and atmospheric activity) and the lack of a global analytical lithospheric&ndash;atmospheric&ndash;magnetospheric model able to explain (and possibly forecast) any anomalous signal. In order to overcome these problems, we have performed a multi-instrument analysis of a low-latitude seismic event by using high-quality data from both ground bases and satellites and preserving their statistical significance. An earthquake (Mw = 7.2) occurred in the Caribbean region on 14 August 2021 under both solar quiet and fair weather conditions, thus proving an optimal case study to reconstruct the link between the lithosphere, atmosphere, ionosphere, and magnetosphere. The good match between the observations and novel magnetospheric&ndash;ionospheric&ndash;lithospheric coupling (M.I.L.C.) modeling of the event confirmed that the fault break generated an atmospheric gravity wave that was able to mechanically perturb the ionospheric plasma density, in turn triggering a variation in the magnetospheric field line resonance frequency

A functional biological network centered on XRCC3: A new possible marker of chemoradiotherapy resistance in rectal cancer patients

Preoperative chemoradiotherapy is widely used to improve local control of disease, sphincter preservation and to improve survival in patients with locally advanced rectal cancer. Patients enrolled in the present study underwent preoperative chemoradiotherapy, followed by surgical excision. Response to chemoradiotherapy was evaluated according to Mandard’s Tumor Regression Grade (TRG). TRG 3, 4 and 5 were considered as partial or no response while TRG 1 and 2 as complete response. From pretherapeutic biopsies of 84 locally advanced rectal carcinomas available for the analysis, only 42 of them showed 70% cancer cellularity at least. By determining gene expression profiles, responders and non-responders showed significantly different expression levels for 19 genes (P < 0.001). We fitted a logistic model selected with a stepwise procedure optimizing the Akaike Information Criterion (AIC) and then validated by means of leave one out cross validation (LOOCV, accuracy D 95%). Four genes were retained in the achieved model: ZNF160, XRCC3, HFM1 and ASXL2. Real time PCR confirmed that XRCC3 is overexpressed in responders group and HFM1 and ASXL2 showed a positive trend. In vitro test on colon cancer resistant/susceptible to chemoradioterapy cells, finally prove that XRCC3 deregulation is extensively involved in the chemoresistance mechanisms. Protein-protein interactions (PPI) analysis involving the predictive classifier revealed a network of 45 interacting nodes (proteins) with TRAF6 gene playing a keystone role in the network. The present study confirmed the possibility that gene expression profiling combined with integrative computational biology is useful to predict complete responses to preoperative chemoradiotherapy in patients with advanced rectal cancer

Strategies for Modulating the pH-Dependent Activity of a Family 11 Glycoside Hydrolase

The pH-dependent activity of wild-type <i>Bacillus circulans</i> xylanase (BcX) is set by the p<i>K</i>_a values of its nucleophile Glu78 and general acid/base Glu172. Herein, we examined several strategies to manipulate these p<i>K</i>_a values and thereby shift the pH_opt at which BcX is optimally active. Altering the global charge of BcX through random succinylation had no significant effect. Mutation of residues near or within the active site of BcX, but not directly contacting the catalytic carboxyls, either had little effect or reduced its pH_opt, primarily by lowering the apparent p<i>K</i>_a value of Glu78. However, mutations causing the largest p<i>K</i>_a changes also impaired activity. Although not found as a general acid/base in naturally occurring xylanases, substitution of Glu172 with a His lowered the pH_opt of BcX from 5.6 to 4.7 while retaining 8% activity toward a xylobioside substrate. Mutation of Asn35, which contacts Glu172, to either His or Glu also led to a reduction in pH_opt by ∼1.2 units. Detailed p<i>K</i>_a measurements by NMR spectroscopy revealed that, despite the opposite charges of the introduced residues, both the N35H and N35E forms of BcX utilize a reverse protonation mechanism. In this mechanism, the p<i>K</i>_a value of the general acid is lower than that of the nucleophile, and only a small population of enzyme is in a catalytically competent ionization state. However, overall activity is maintained due to the increased strength of the general acid. This study illustrates several routes for altering the pH-dependent properties of xylanases, while also providing valuable insights into complex protein electrostatics