Prospective Cohort Study to Evaluate Toxicity and Cosmesis between Interstitial APBI and Ultra-Hypo-Fractionated Whole Breast Irradiation in Patients with Early Breast Cancer

PURPOSE/OBJECTIVE(S)

Both interstitial multi-catheter brachytherapy based accelerated partial breast irradiation (APBI) and ultra-hypo-fractionated whole breast irradiation (WBI) with 5 fractions can complete treatment in a short time and result in lower treatment-related costs. Although data are available on their toxicity compared with conventional and hypo-fractionated regimens, there are few data directly comparing these two techniques.

MATERIALS/METHODS

This prospective cohort study enrolled early breast cancer patients with negative ink margin, T1 or T2 stage, and tumor size of 3 cm or less, with 0 to 3 positive lymph nodes after adequate axillary dissection or negative sentinel lymph node biopsy (N0-1), regardless of receptor status (ER, PR, HER2neu). Of the total 31 patients, 15 received APBI with multi-catheter interstitial brachytherapy (35 Gy in10 fractions over 5 days with a minimum interval of 6 hours between fractions) and 16 patients received WBI (27 Gy in 5 fractions over 5 days) with either 3DCRT or VMAT technique. Acute toxicity was assessed using the RTOG toxicity grading and breast cosmesis was assessed using the Harvard breast cosmesis score. Toxicity and cosmesis were assessed immediately after treatment, after one month, and after three months of treatment. Results were compared between groups using the Mann Whitney U test.

RESULTS

All patients completed a 3-month follow-up after completion of treatment. There was no statistically significant difference between the 2 groups in terms of highest grade toxicity (p = 0.97) and acute toxicity immediately after RT (p = 1.0) and after 1 month of RT (p = 0.91). However, at 3 months, more patients in the WBI group had a residual skin reaction than in the APBI group (p = 0.03). There was no statistically significant difference in breast cosmesis scores at any time point. 53.3%, 6.6% had grade 1 and 2 skin toxicities respectively immediately after RT in the APBI group and 62.5% of patients had grade 1 skin toxicity in WBI group. After 1 month 26.6%, 26.6% & 13.3% patients had grade 2, grade 1 and grade 3 toxicities respectively. In the WBI group, at 1 month, 50%, 18.7% and 12.5% patients had grade 1, 3 and 2 skin toxicities respectively. At 3 months, 42.8% and 7.1% of patients in the APBI group had grade 1 and grade 2 toxicities, respectively. In the WBI group, 78.5% and 7.1% of patients had grade 1 and 2 skin toxicities respectively.

CONCLUSION

In this study, no difference in acute toxicity or breast cosmesis was demonstrated between APBI-based interstitial brachytherapy and ultra-hypo-fractionated WBI. Since both regimens can be administered within 5 days, the decision between them is challenging for both physicians and patients. This study can be considered hypothesis-generating and used for further planning of equivalence or noninferiority studies.

Patient-Reported Outcomes Evaluating the Impact of Hypo-Fractionated Palliative Quadshot Radiotherapy and Concurrent CDDP Treatment on Health-Related Quality of Life in Patients with Locally Advanced Squamous Cell Carcinoma of the Head and Neck

PURPOSE/OBJECTIVE(S)

In locally advanced squamous cell carcinoma of the head and neck (LAHNSCC), the main goal of treatment remains survival while improving quality of life (QOL). In recent decades, there has been a paradigm shift in the measurement of clinical outcomes in patients diagnosed with cancer, focusing on the patient perspective by incorporating patient-reported outcomes (PROs). The primary objective of this study was to evaluate the improvement in quality of life with the use of cyclic hypo-fractionated palliative QUAD SHOT radiotherapy (RT) with concurrent cisplatin (CDDP) in previously untreated patients with incurable LAHNSCC.

MATERIALS/METHODS

In this prospective interventional phase- II study, 60 patients with locally advanced squamous cell carcinoma of the head and neck, majority stage IVB, ECOG PS ≤ 3, were treated with QUAD SHOT RT (14 Gy/4 fractions/2 days - BD with 6-hour interval and concurrent CDDP at 6 mg/m2. This treatment was repeated at 4-week intervals for 2 additional cycles if tumor progression did not occur. Serial changes in HR -QoL were assessed using EORTC QLQ C-30 and H&N-35) at 4 different time points. Statistical methods such as the Wilcoxon signed-rank test and Friedman test were used to compare QoL values at different time points with Bonferroni correction for multiple comparisons to control for type I errors.

RESULTS

The median global health score (GHS) at baseline was 41.667, with an initial increase in score at 4 weeks (50.00) and at 8 weeks (54.167) that did not continue at 12 weeks (41.667). Symptoms related to toxicities (speech, social contact, sticky saliva, dry mouth, senses in H&N 35) were lower after 4 weeks. Application of the Friedman test for four time points revealed significant improvement in role function at 4 weeks, which remained constant at 8 weeks but was not sustained at 12 weeks. Comparison of HN-35 symptom scores between the four time points showed improvement in symptoms such as pain, swallowing, and mouth opening at 4 and 8 weeks. The mean QLQ C30 summary score for these patients improved at four weeks but did not remain constant at 8 and 12 weeks.

CONCLUSION

Our study showed significant improvement in quality-of-life parameters and reduction in symptom burden at 4 and 8 weeks due to disease control and symptom palliation by QUADSHOT CTRT, while quality-of-life scores worsened and symptom scores were not maintained at 12 weeks due to disease progression and occurrence of acute toxicities. This phase II study may serve as the basis for designing a phase III randomized control trial to compare quality of life changes with QUADSHOT CTRT and other palliative CTRT regimens.

Role of Stereotactic Body Radiation Therapy in Portal Vein Tumor Thrombosis in Hepatocellular Carcinoma: A Prospective Single Institute Experience

PURPOSE/OBJECTIVE(S)

Patients diagnosed with Hepatocellular carcinoma (HCC) complicated with portal vein tumor thrombosis (PVTT) have a limited number of treatment options available and are associated with an overall poor prognosis. With the recent developments in the field of radiation therapy, the role of radiotherapy particularly Stereotactic Body radiotherapy (SBRT) has increased as a loco-regional therapy for HCC. This study was planned to evaluate the role of SBRT in Locally advanced HCC complicated with PVTT and its role as loco-regional therapy.

MATERIALS/METHODS

We conducted a prospective study that included patients diagnosed with HCC complicated with PVTT Child-Turcotte Pugh (CTP) Class A/B with a maximum score of 7, diagnosed on triple phase Contrast-Enhanced - MRI unsuitable for other ablative procedures. Patients with Bilirubin levels > 4 mg/dl, active Hepatitis, CTP score >7, normal liver volume <700cc or history of prior radiotherapy were excluded from the study. Patients underwent a contrast enhanced 4D-CT simulation with abdominal compression and were planned for SBRT using VMAT technique. Patients were followed-up as per Institute protocol. CECT or MRI for a radiological response was done for response assessment using mRECIST criteria version 1.1. A baseline MRI was done at one-month post-SBRT to understand any RT changes in the liver and to differentiate from tumor progression during the response assessment at three months.

RESULTS

A total of 22 patients with HCC were recruited and received SBRT to PVTT, with a dosage between 30-42 Gy over 6 fractions treated on alternate days. Patients were assessed post-treatment with triphasic CE-MRI every 3 months as per institute protocol. Five patients had achieved Complete response in form of Portal vein recanalization. Three patients had Partial response to the treatment. Seven patients maintained stable disease status whereas six patients had disease progression during the entire course of treatment. The response rate (CR+PR) to treatment was 36.3% at the time of analysis. The Overall Response rate (CR+PR+SD) was 69%. No grade 3 or 4 toxicities were observed and treatment was tolerated well by patients. Kaplan-Meier method was applied to calculate the survival probability at various follow-up intervals. The median time for overall survival was 25 months ((95% CI: 15-35). Out of the 22 subjects included in the study, 6 patients died. There was a 78% survival probability at 12 months and a 68% survival probability at 18 months of follow-up.

CONCLUSION

This prospective single-arm study demonstrated the vital role of SBRT in the treatment of Hepatocellular carcinoma with Portal vein tumor thrombosis and its efficacy in terms of achieving excellent local control with relatively lesser toxicities compared with existing treatment modalities. Patients have shown benefit post-treatment in terms of thrombus reduction and restoration of Portal vein flow making them suitable for further treatment like Resection or TACE.

Multiple Sessions vs. Single Session Image-Based Intracavitary Brachytherapy for Locally Advanced Cervical Cancer: A Randomized Control Trial

PURPOSE/OBJECTIVE(S)

The objectives of this study are: 1) To compare the acute toxicity caused in the treatment of locally advanced cervical cancer (LACC) treated with weekly multiple applications vs. a single application for image-guided intracavitary High Dose Rate (HDR) brachytherapy (BT) after External Beam Radiation Therapy (EBRT) 2) To compare the loco-regional control of cancer at six months in the two arms MATERIALS/METHODS: In a prospective study, 40 patients with biopsy-proven LACC with FIGO-2018 stage IIB-IIIC1 disease, underwent EBRT to the pelvis at a dose of 50.4 Gy/ 28 fractions over 5.5 weeks with weekly concurrent cisplatin. After completion of EBRT, they were randomized into two arms with 20 patients each. In the Control arm (Arm-A), BT sessions were given with weekly 3 applications whereas, in the experimental arm (Arm-B), all the sessions were given with a single application at 6-12 hours intervals with aim of the high-risk clinical target volume receiving >80 Gy EQD2 and 2 cm3 of the bladder and rectum/sigmoid receiving <85 Gy and <75 Gy, respectively. The OAR contouring was done on CT RESULTS: All 40 patients were treated as per protocol. The mean duration of treatment including EBRT and BT was 73.15 days [95% CI 68.63-77.66] in Arm A and 55.85 days [95% CI 52.11-59.58] in Arm B which was significant. After 6 months, 37 patients came for follow-up, all 19 patients in Arm A had Grade 1 or Grade 2 rectal toxicity. In Arm B as well all 18 patients had Grade 1 or Grade 2 rectal toxicity. Bladder toxicity was Grade 1 or Grade 2 in 18 patients and Grade 3 severity in 1 patient among Arm A. Among 18 patients of Arm B, bladder toxicity of Grade 1 or Grade 2 was seen in 16 patients, and 2 patients had grade 3 toxicity. 2 patients in Arm A and 3 in Arm B complained of Grade 1 urinary incontinence. Moreover, Abdominal pain at 6 months was of Grade 1 in around 6 patients in Arm A but 14 patients had abdominal pain in Arm B which was of Grade 1 in 8, 4 had grade 2 and 2 patients had grade 3 severity abdominal pain. In the monthly analysis of acute toxicity, none of the patients showed Grade 3 or 4 toxicity at the 1st, 2nd, or 3rd month of completion of treatment. When comparing local control in both arms at 6 months, 2 patients had treatment failure in the Experimental Arm compared to only 1 patient in the Control Arm CONCLUSION: Single Application Multiple Fraction Intracavitary Brachytherapy post concurrent CTRT is a safe option for the treatment of locally advanced cervical cancer. When compared to the weekly application arm, single-application ICRT showed a comparable acute toxicity profile and comparable local control rates as well. Some patients in Single Application Arm showed abdominal pain which needs to be investigated with further trials. The overall treatment time in the single application arm is significantly lower than the standard weekly application arm.

Biological Response Assessment in Hepatocellular Carcinoma Post Stereotactic Body Radiotherapy

PURPOSE/OBJECTIVE(S)

Biological Response in Hepatocellular carcinoma (HCC) is measured in terms of serum alpha-fetoprotein (AFP) which is elevated in nearly 60% HCC patients at baseline and is directly related to the severity of the disease. This biological response is defined as the reduction of more than 50% from the baseline levels and is associated with an increased percentage of tumor necrosis and is directly related to increased loco-regional control. Patients diagnosed with HCC have very limited treatment modalities. With the recent advances in the field of radiation therapy and the development of Stereotactic Body radiotherapy (SBRT), the role of radiotherapy has increased as a loco-regional modality for HCC. In this single-arm prospective study, we evaluated the biological response post-SBRT in patients diagnosed with HCC.

MATERIALS/METHODS

We conducted a prospective study that included patients diagnosed with HCC with baseline elevation of serum AFP, Child-Turcotte Pugh (CTP) Class A/B with a maximum score of 7. Patient's serum AFP levels were recorded at baseline, pre-treatment, and post-treatment. The biological response was measured at 3 months post-treatment and compared with the baseline serum AFP levels using Wilcoxon signed rank test.

RESULTS

A total of 14 patients with HCC were recruited and received SBRT to the target lesion, with a dose between 30-42 Gy over 6 fractions treated on alternate days. Patients were assessed post-treatment at one month with triphasic CEMRI and serum AFP levels. 12 out of 14 patients (85.71%) had a biological response at 3 months follow-up and levels showed further decline unless a progression was found. The median (IQR) serum AFP level was 1131 ng/ml (359-5668 ng/ml) at baseline. Post-treatment serum AFP levels had a median (IQR) value of 156 ng/ml (15-372 ng/ml) showing a near reduction of 86% from baseline, which was significant. 2/14 pts (14.28%) showed no reduction or even increase in serum AFP levels post-treatment.

CONCLUSION

This prospective single-arm study demonstrated the vital role of SBRT in the treatment of HCC and its importance in achieving a better disease control. The response was achieved in 86% of patients with marked reduction of nearly 90% in serum AFP levels as compared to the baseline and increased median OS and PFS as compared to patients not receiving radiotherapy. Further prospective studies are warranted to confirm our findings.

Hypo-Fractionated Palliative QUADSHOT Radiotherapy and Concurrent CDDP in Patients with LAHNSCC: Toxicities and Clinical Outcomes

PURPOSE/OBJECTIVE(S)

Shorter palliative hypo-fractionated radiotherapy regimens given concurrently with chemotherapy, preferably cisplatin (radiosensitizer), increase response rates with acceptable toxicity, leading to better compliance of patients with locally advanced squamous cell carcinoma of the head and neck (LAHNSCC) in whom late toxicities due to chemoradiotherapy are less relevant. This single institution prospective interventional phase II study was conducted with the goal of achieving high rates of locoregional control with acceptable treatment-related toxicity.

MATERIALS/METHODS

In this prospective interventional phase- II study, 60 patients with LAHNSCC (treatment naive), the majority in stage IVB and ECOG PS ≤ 3, were treated with QUAD SHOT RT using the conventional 2D technique (14Gy in 4 fractions on 2 consecutive days twice daily with a 6-hour interval between the two fractions) and concurrent cisplatin (CDDP) at a dose of 6 mg/m2. This treatment was repeated at 4-week intervals for 2 additional cycles if tumor progression did not occur. The Kaplan-Meier method was used to determine survival probability for progression-free survival (PFS) and overall survival (OS). Descriptive statistics with number and percentage were used for each toxicity and tumor response at different time points. A P value of less than 0.05 was considered significant.

RESULTS

In our study, all patients received at least one cycle of QUADSHOT chemoradiotherapy (CTRT), while 35 and 18 patients received the 2nd and 3rd QUADSHOT CTRT, respectively. Of the patients who completed the first cycle of QUADSHOT CTRT, 27 (45%) patients had a partial response (PR) and 22 (36.7%) had stable disease (SD). Of the patients who completed the second cycle QUADSHOT CTRT, 77.2% had SD, while 11.4% had PR and 11.4% had PD. After the 3rd QUADSHOT CTRT, 72.2% had SD, while 11.1% had PR and 16.7% had PD. The overall response rate (SD +PR) in our study was 81%, 88.6%, and 83% after the 1st, 2nd, and 3rd QUADSHOT CTRT, respectively. After the 3rd QUADSHOT CTRT, no patient showed grade 4 toxicity. Most patients had grade I/ II toxicities e.g., skin (grade I -83%), mucositis (grade II -50%), salivary gland toxicity (grade II -50%), grade I laryngitis (83.3%). Grade- III oral mucositis and pharyngitis were seen in 27% and 6.7% of patients, respectively. Median OS and PFS were 7.9 months and 6.2 months, respectively.

CONCLUSION

Concurrent chemotherapy acts as a radiosensitizer and provides a synergistic effect when coupled with hypo-fractionated radiation, resulting in more effective control of locoregional disease in locally advanced head and neck tumors with acceptable toxicities. This study is hypothesis-generating and may serve as a basis for developing optimal CTRT regimens for patients with LAHNSCC who are not suitable for curative treatment.

Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome

Aminoglycosides are a class of antibiotics that bind to ribosomal RNA and exert pleiotropic effects on ribosome function. Amikacin, the semisynthetic derivative of kanamycin, is commonly used for treating severe infections with multidrug-resistant, aerobic Gram-negative bacteria. Amikacin carries the 4-amino-2-hydroxy butyrate (AHB) moiety at the N1 amino group of the central 2-deoxystreptamine (2-DOS) ring, which may confer amikacin a unique ribosome inhibition profile. Here we use in vitro fast kinetics combined with X-ray crystallography and cryo-EM to dissect the mechanisms of ribosome inhibition by amikacin and the parent compound, kanamycin. Amikacin interferes with tRNA translocation, release factor-mediated peptidyl-tRNA hydrolysis, and ribosome recycling, traits attributed to the additional interactions amikacin makes with the decoding center. The binding site in the large ribosomal subunit proximal to the 3'-end of tRNA in the peptidyl (P) site lays the groundwork for rational design of amikacin derivatives with improved antibacterial properties.

Insights into translocation mechanism and ribosome evolution from cryo-EM structures of translocation intermediates of Giardia intestinalis

Giardia intestinalis is a protozoan parasite that causes diarrhea in humans. Using single-particle cryo-electron microscopy, we have determined high-resolution structures of six naturally populated translocation intermediates, from ribosomes isolated directly from actively growing Giardia cells. The highly compact and uniquely GC-rich Giardia ribosomes possess eukaryotic rRNAs and ribosomal proteins, but retain some bacterial features. The translocation intermediates, with naturally bound tRNAs and eukaryotic elongation factor 2 (eEF2), display characteristic ribosomal intersubunit rotation and small subunit's head swiveling-universal for translocation. In addition, we observe the eukaryote-specific 'subunit rolling' dynamics, albeit with limited features. Finally, the eEF2·GDP state features a uniquely positioned 'leaving phosphate (Pi)' that proposes hitherto unknown molecular events of Pi and eEF2 release from the ribosome at the final stage of translocation. In summary, our study elucidates the mechanism of translocation in the protists and illustrates evolution of the translation machinery from bacteria to eukaryotes from both the structural and mechanistic perspectives.

Lamotrigine compromises the fidelity of initiator tRNA recruitment to the ribosomal P-site by IF2 and the RbfA release from 30S ribosomes in Escherichia coli

Lamotrigine (Ltg), an anticonvulsant drug, targets initiation factor 2 (IF2), compromises ribosome biogenesis and causes toxicity to Escherichia coli. However, our understanding of Ltg toxicity in E. coli remains unclear. While our in vitro assays reveal no effects of Ltg on the ribosome-dependent GTPase activity of IF2 or its role in initiation as measured by dipeptide formation in a fast kinetics assay, the in vivo experiments show that Ltg causes accumulation of the 17S precursor of 16S rRNA and leads to a decrease in polysome levels in E. coli. IF2 overexpression in E. coli increases Ltg toxicity. However, the overexpression of initiator tRNA (i-tRNA) protects it from the Ltg toxicity. The depletion of i-tRNA or overexpression of its 3GC mutant (lacking the characteristic 3GC base pairs in anticodon stem) enhances Ltg toxicity, and this enhancement in toxicity is synthetic with IF2 overexpression. The Ltg treatment itself causes a detectable increase in IF2 levels in E. coli and allows initiation with an elongator tRNA, suggesting compromise in the fidelity/specificity of IF2 function. Also, Ltg causes increased accumulation of ribosome-binding factor A (RbfA) on 30S ribosomal subunit. Based on our genetic and biochemical investigations, we show that Ltg compromises the function of i-tRNA/IF2 complex in ribosome maturation.

Mechanistic insights into translation inhibition by aminoglycoside antibiotic arbekacin

How aminoglycoside antibiotics limit bacterial growth and viability is not clearly understood. Here we employ fast kinetics to reveal the molecular mechanism of action of a clinically used, new-generation, semisynthetic aminoglycoside Arbekacin (ABK), which is designed to avoid enzyme-mediated deactivation common to other aminoglycosides. Our results portray complete picture of ABK inhibition of bacterial translation with precise quantitative characterizations. We find that ABK inhibits different steps of translation in nanomolar to micromolar concentrations by imparting pleotropic effects. ABK binding stalls elongating ribosomes to a state, which is unfavorable for EF-G binding. This prolongs individual translocation step from ∼50 ms to at least 2 s; the mean time of translocation increases inversely with EF-G concentration. ABK also inhibits translation termination by obstructing RF1/RF2 binding to the ribosome. Furthermore, ABK decreases accuracy of mRNA decoding (UUC vs. CUC) by ∼80 000 fold, causing aberrant protein production. Importantly, translocation and termination events cannot be completely stopped even with high ABK concentration. Extrapolating our kinetic model of ABK action, we postulate that aminoglycosides impose bacteriostatic effect mainly by inhibiting translocation, while they become bactericidal in combination with decoding errors.

Repurposing tRNAs for nonsense suppression

Three stop codons (UAA, UAG and UGA) terminate protein synthesis and are almost exclusively recognized by release factors. Here, we design de novo transfer RNAs (tRNAs) that efficiently decode UGA stop codons in Escherichia coli. The tRNA designs harness various functionally conserved aspects of sense-codon decoding tRNAs. Optimization within the TΨC-stem to stabilize binding to the elongation factor, displays the most potent effect in enhancing suppression activity. We determine the structure of the ribosome in a complex with the designed tRNA bound to a UGA stop codon in the A site at 2.9 Å resolution. In the context of the suppressor tRNA, the conformation of the UGA codon resembles that of a sense-codon rather than when canonical translation termination release factors are bound, suggesting conformational flexibility of the stop codons dependent on the nature of the A-site ligand. The systematic analysis, combined with structural insights, provides a rationale for targeted repurposing of tRNAs to correct devastating nonsense mutations that introduce a premature stop codon.

842 Safety and Efficacy of Tranexamic Acid to Minimise Perioperative Bleeding in Extrahepatic Abdominal Surgery: A Systematic Review

Introduction

Perioperative bleeding is a major risk during and after surgery, which can result in increased mortality and morbidity. Tranexamic acid (TXA), in the setting of trauma, minimises perioperative bleeding and its associated risks. However, there is a lack of evidence of its use in elective abdominal surgery. This meta-analysis of randomised controlled trials (RCTs) evaluated the effectiveness and safety of TXA in elective extrahepatic abdominal surgery.

Method

A comprehensive search of PubMed, Embase, and Clinicaltrial.gov databases was undertaken to identify RCTs from January 1947 to May 2020. The primary outcomes of intraoperative blood loss, and the secondary outcomes of need for perioperative blood transfusion, thromboembolic events, and mortality were extracted from included studies. Quantitative pooling of data was based on the random effects model.

Results

Nineteen studies reporting on 2205 patients were included. TXA reduced intraoperative blood loss (weighted mean difference (WMD) -188.35mL; 95% CI -254.65 to -121.72) and the need for perioperative blood transfusion (odds ratio (OR) 0.43; 95% CI 0.28 to 0.65). Importantly, TXA had no impact on the incidence of thromboembolic events (OR 0.49; 95% CI 0.18 to 1.35). There were no reported deaths in any of the studies.

Conclusions

TXA reduces intra-operative blood loss without an increase in complications.

Optimization of a fluorescent-mRNA based real-time assay for precise kinetic measurements of ribosomal translocation

Kinetic characterization of ribosomal translocation is important for understanding the mechanism of elongation in protein synthesis. Here we have optimized a popular fluorescent-mRNA based translocation assay conducted in stopped-flow, by calibrating it with the functional tripeptide formation assay in quench-flow. We found that a fluorescently labelled mRNA, ten bases long from position +1 (mRNA+10), is best suited for both assays as it forms tripeptide at a fast rate equivalent to the longer mRNAs, and yet produces a large fluorescence change upon mRNA movement. Next, we compared the commonly used peptidyl tRNA analog, N-acetyl-Phe-tRNA^Phe, with the natural dipeptidyl fMet-Phe-tRNA^Phe in the stopped-flow assay. This analog translocates about two times slower than the natural dipeptidyl tRNA and produces biphasic kinetics. The rates reduce further at lower temperatures and with higher Mg²⁺ concentration, but improve with higher elongation factor G (EF-G) concentration, which increase both rate and amplitude of the fast phase significantly. In summary, we present here an improved real time assay for monitoring mRNA-translocation with the natural- and an N-Ac-analog of dipeptidyl tRNA.

GGQ methylation enhances both speed and accuracy of stop codon recognition by bacterial class-I release factors

Accurate translation termination in bacteria requires correct recognition of the stop codons by the class-I release factors (RFs) RF1 and RF2, which release the nascent peptide from the peptidyl tRNA after undergoing a "compact to open" conformational transition. These RFs possess a conserved Gly-Gly-Gln (GGQ) peptide release motif, of which the Q residue is posttranslationally methylated. GGQ-methylated RFs have been shown to be faster in peptide release than the unmethylated ones, but it was unknown whether this modification had additional roles. Using a fluorescence-based real-time in vitro translation termination assay in a stopped-flow instrument, we demonstrate that methylated RF1 and RF2 are two- to four-fold more accurate in the cognate stop codon recognition than their unmethylated variants. Using pH titration, we show that the lack of GGQ methylation facilitates the "compact to open" transition, which results in compromised accuracy of the unmethylated RFs. Furthermore, thermal melting studies using circular dichroism and SYPRO-orange fluorescence demonstrate that GGQ methylation increases overall stability of the RF proteins. This increased stability, we suspect, is the basis for the more controlled conformational change of the methylated RFs upon codon recognition, which enhances both their speed and accuracy. This GGQ methylation-based modulation of the accuracy of RFs can be a tool for regulating translational termination in vivo.

Kinetic Analysis Suggests Evolution of Ribosome Specificity in Modern Elongation Factor-Tus from "Generalist" Ancestors

It has been hypothesized that early enzymes are more promiscuous than their extant orthologs. Whether or not this hypothesis applies to the translation machinery, the oldest molecular machine of life, is not known. Efficient protein synthesis relies on a cascade of specific interactions between the ribosome and the translation factors. Here, using elongation factor-Tu (EF-Tu) as a model system, we have explored the evolution of ribosome specificity in translation factors. Employing presteady state fast kinetics using quench flow, we have quantitatively characterized the specificity of two sequence-reconstructed 1.3- to 3.3-Gy-old ancestral EF-Tus toward two unrelated bacterial ribosomes, mesophilic Escherichia coli and thermophilic Thermus thermophilus. Although the modern EF-Tus show clear preference for their respective ribosomes, the ancestral EF-Tus show similar specificity for diverse ribosomes. In addition, despite increase in the catalytic activity with temperature, the ribosome specificity of the thermophilic EF-Tus remains virtually unchanged. Our kinetic analysis thus suggests that EF-Tu proteins likely evolved from the catalytically promiscuous, “generalist” ancestors. Furthermore, compatibility of diverse ribosomes with the modern and ancestral EF-Tus suggests that the ribosomal core probably evolved before the diversification of the EF-Tus. This study thus provides important insights regarding the evolution of modern translation machinery.

Safety and efficacy of tranexamic acid in minimizing perioperative bleeding in extrahepatic abdominal surgery: meta-analysis

BACKGROUND

Perioperative bleeding is associated with increased morbidity and mortality in patients undergoing elective abdominal surgery. The antifibrinolytic agent tranexamic acid (TXA) has been shown to reduce perioperative bleeding and mortality risk in patients with traumatic injuries, but there is a lack of evidence for its use in elective abdominal and pelvic surgery. This meta-analysis of RCTs evaluated the effectiveness and safety of TXA in elective extrahepatic abdominopelvic surgery.

METHODS

PubMed, Embase, and ClinicalTrial.gov databases were searched to identify relevant RCTs from January 1947 to May 2020. The primary outcome, intraoperative blood loss, and secondary outcomes, need for perioperative blood transfusion, units of blood transfused, thromboembolic events, and mortality, were extracted from included studies. Quantitative pooling of data was based on a random-effects model.

RESULTS

Some 19 studies reporting on 2205 patients who underwent abdominal, pelvic, gynaecological or urological surgery were included. TXA reduced intraoperative blood loss (mean difference -188.35 (95 per cent c.i. -254.98 to -121.72) ml) and the need for perioperative blood transfusion (odds ratio (OR) 0.43, 95 per cent c.i. 0.28 to 0.65). TXA had no impact on the incidence of thromboembolic events (OR 0.49, 0.18 to 1.35). No adverse drug reactions or in-hospital deaths were reported.

CONCLUSION

TXA reduces intraoperative blood loss during elective extrahepatic abdominal and pelvic surgery without an increase in complications.

Collateral Toxicity Limits the Evolution of Bacterial Release Factor 2 toward Total Omnipotence

When new genes evolve through modification of existing genes, there are often tradeoffs between the new and original functions, making gene duplication and amplification necessary to buffer deleterious effects on the original function. We have used experimental evolution of a bacterial strain lacking peptide release factor 1 (RF1) in order to study how peptide release factor 2 (RF2) evolves to compensate the loss of RF1. As expected, amplification of the RF2-encoding gene prfB to high copy number was a rapid initial response, followed by the appearance of mutations in RF2 and other components of the translation machinery. Characterization of the evolved RF2 variants by their effects on bacterial growth rate, reporter gene expression, and in vitro translation termination reveals a complex picture of reduced discrimination between the cognate and near-cognate stop codons and highlights a functional tradeoff that we term "collateral toxicity." We suggest that this type of tradeoff may be a more serious obstacle in new gene evolution than the more commonly discussed evolutionary tradeoffs between "old" and "new" functions of a gene, as it cannot be overcome by gene copy number changes. Further, we suggest a model for how RF2 autoregulation responds to alterations in the demand not only for RF2 activity but also for RF1 activity.

Ribosomal RNA Modulates Aggregation of the Podospora Prion Protein HET-s

The role of the nucleic acids in prion aggregation/disaggregation is becoming more and more evident. Here, using HET-s prion from fungi Podospora anserina (P. anserina) as a model system, we studied the role of RNA, particularly of different domains of the ribosomal RNA (rRNA), in its aggregation process. Our results using Rayleigh light scattering, Thioflavin T (ThT) binding, transmission electron microscopy (TEM) and cross-seeding assay show that rRNA, in particular the domain V of the major rRNA from the large subunit of the ribosome, substantially prevents insoluble amyloid and amorphous aggregation of the HET-s prion in a concentration-dependent manner. Instead, it facilitates the formation of the soluble oligomeric “seeds”, which are capable of promoting de novo HET-s aggregation. The sites of interactions of the HET-s prion protein on domain V rRNA were identified by primer extension analysis followed by UV-crosslinking, which overlap with the sites previously identified for the protein-folding activity of the ribosome (PFAR). This study clarifies a missing link between the rRNA-based PFAR and the mode of propagation of the fungal prions.

International Nosocomial Infection Control Consortium (INICC) report, data summary of 45 countries for 2012-2017: Device-associated module

BACKGROUND

We report the results of International Nosocomial Infection Control Consortium (INICC) surveillance study from January 2012 to December 2017 in 523 intensive care units (ICUs) in 45 countries from Latin America, Europe, Eastern Mediterranean, Southeast Asia, and Western Pacific.

METHODS

During the 6-year study period, prospective data from 532,483 ICU patients hospitalized in 242 hospitals, for an aggregate of 2,197,304 patient days, were collected through the INICC Surveillance Online System (ISOS). The Centers for Disease Control and Prevention-National Healthcare Safety Network (CDC-NHSN) definitions for device-associated health care-associated infection (DA-HAI) were applied.

RESULTS

Although device use in INICC ICUs was similar to that reported from CDC-NHSN ICUs, DA-HAI rates were higher in the INICC ICUs: in the medical-surgical ICUs, the pooled central line-associated bloodstream infection rate was higher (5.05 vs 0.8 per 1,000 central line-days); the ventilator-associated pneumonia rate was also higher (14.1 vs 0.9 per 1,000 ventilator-days,), as well as the rate of catheter-associated urinary tract infection (5.1 vs 1.7 per 1,000 catheter-days). From blood cultures samples, frequencies of resistance, such as of Pseudomonas aeruginosa to piperacillin-tazobactam (33.0% vs 18.3%), were also higher.

CONCLUSIONS

Despite a significant trend toward the reduction in INICC ICUs, DA-HAI rates are still much higher compared with CDC-NHSN's ICUs representing the developed world. It is INICC's main goal to provide basic and cost-effective resources, through the INICC Surveillance Online System to tackle the burden of DA-HAIs effectively.

Inhibition of translation termination by small molecules targeting ribosomal release factors

The bacterial ribosome is an important drug target for antibiotics that can inhibit different stages of protein synthesis. Among the various classes of compounds that impair translation there are, however, no known small-molecule inhibitors that specifically target ribosomal release factors (RFs). The class I RFs are essential for correct termination of translation and they differ considerably between bacteria and eukaryotes, making them potential targets for inhibiting bacterial protein synthesis. We carried out virtual screening of a large compound library against 3D structures of free and ribosome-bound RFs in order to search for small molecules that could potentially inhibit termination by binding to the RFs. Here, we report identification of two such compounds which are found both to bind free RFs in solution and to inhibit peptide release on the ribosome, without affecting peptide bond formation.

RNA modulates aggregation of the recombinant mammalian prion protein by direct interaction

Recent studies have proposed that nucleic acids act as potential cofactors for protein aggregation and prionogenesis. By means of sedimentation, transmission electron microscopy, circular dichroism, static and dynamic light scattering, we have studied how RNA can influence the aggregation of the murine recombinant prion protein (rPrP). We find that RNA, independent of its sequence, source and size, modulates rPrP aggregation in a bimodal fashion, affecting both the extent and the rate of rPrP aggregation in a concentration dependent manner. Analogous to RNA-induced liquid-liquid phase transitions observed for other proteins implicated in neurodegenerative diseases, high protein to RNA ratios stimulate rPrP aggregation, while low ratios suppress it. However, the latter scenario also promotes formation of soluble oligomeric aggregates capable of seeding de novo rPrP aggregation. Furthermore, RNA co-aggregates with rPrP and thereby gains partial protection from RNase digestion. Our results also indicate that rPrP interacts with the RNAs with its N-terminus. In summary, this study elucidates the proposed adjuvant role of RNA in prion protein aggregation and propagation, and thus advocates an auxiliary role of the nucleic acids in protein aggregation in general.

Outcomes of surgery for post-cholecystectomy bile duct injuries: An audit from a tertiary referral center

AIM OF THE STUDY

Bile duct injury (BDI) after cholecystectomy is a serious complication. It often requires surgical repair. The aim of this study was to report on the short and long-term outcomes of surgery for post-cholecystectomy BDI.

PATIENTS AND METHODS

All the patients, who underwent surgery for post-cholecystectomy BDI between August 2007 and September 2017, were retrospectively reviewed. McDonald grading system was used to assess the long-term outcome. The risk factors for unsatisfactory long-term outcome were analyzed by univariate and multivatiate logistic regression analysis.

RESULTS

In total, 228 patients had a Roux-en-Y hepaticojejunostomy. Open cholecystectomy was the major cause of BDI (61%). The median time from injury to definitive repair was 6 months. The types of BDI were as follows: E1 in 13 (5.7%), E2 in 68 (29.82%), E3 in 108 (47.36%), E4 in 28 (12.28%), and E5 in 11 (4.82%) patients respectively. Postoperative morbidity and mortality were 25% and 1.31% respectively. After a median follow-up of 58 months, 90% patients had excellent to good outcome. Recurrent stricture developed in 6 (3%) patients. On multivariate analysis, long injury-repair interval and previous attempt at repair were independent predictors for unsatisfactory long-term outcome.

CONCLUSION

Surgical reconstruction affords excellent to good results for majority of the patients with post-cholecystectomy BDI. As longer delay in definitive repair and previous attempt at repair were associated with unsatisfactory long-term outcome, early referral to a specialized hepatobiliary surgery unit is recommended.

Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-TuH84A

The GTPase EF-Tu in ternary complex with GTP and aminoacyl-tRNA (aa-tRNA) promotes rapid and accurate delivery of cognate aa-tRNAs to the ribosomal A site. Here we used cryo-EM to study the molecular origins of the accuracy of ribosome-aided recognition of a cognate ternary complex and the accuracy-amplifying role of the monitoring bases A1492, A1493 and G530 of the 16S rRNA. We used the GTPase-deficient EF-Tu variant H84A with native GTP, rather than non-cleavable GTP analogues, to trap a near-cognate ternary complex in high-resolution ribosomal complexes of varying codon-recognition accuracy. We found that ribosome complexes trapped by GTPase-deficicent ternary complex due to the presence of EF-Tu^H84A or non-cleavable GTP analogues have very similar structures. We further discuss speed and accuracy of initial aa-tRNA selection in terms of conformational changes of aa-tRNA and stepwise activation of the monitoring bases at the decoding center of the ribosome.

The mechanism of error induction by the antibiotic viomycin provides insight into the fidelity mechanism of translation

Applying pre-steady state kinetics to an Escherichia-coli-based reconstituted translation system, we have studied how the antibiotic viomycin affects the accuracy of genetic code reading. We find that viomycin binds to translating ribosomes associated with a ternary complex (TC) consisting of elongation factor Tu (EF-Tu), aminoacyl tRNA and GTP, and locks the otherwise dynamically flipping monitoring bases A1492 and A1493 into their active conformation. This effectively prevents dissociation of near- and non-cognate TCs from the ribosome, thereby enhancing errors in initial selection. Moreover, viomycin shuts down proofreading-based error correction. Our results imply a mechanism in which the accuracy of initial selection is achieved by larger backward rate constants toward TC dissociation rather than by a smaller rate constant for GTP hydrolysis for near- and non-cognate TCs. Additionally, our results demonstrate that translocation inhibition, rather than error induction, is the major cause of cell growth inhibition by viomycin.

QSAR modelling on a series of arylsulfonamide-based hydroxamates as potent MMP-2 inhibitors

Matrix metalloproteinase-2 (MMP-2) is a lucrative therapeutic target as far as anticancer drug discovery is concerned. Overexpression of MMP-2 is found to facilitate tumour propagation through the involvement of vascular endothelial growth factor (VEGF). However, even after different techniques, finding a target-specific MMP-2 inhibitor with respectable pharmacodynamic properties is still a challenging task. Regression-dependent quantitative structure-activity relationship (QSAR) strategies might be among the possible drug design methods to explore the essential structural features that would be valuable to find a suitable MMP-2 inhibitor. In this paper, 72 molecules were explored using the PaDEL descriptors and stepwise multiple linear regression (S-MLR). The partial least squares (PLS) method was also used to create a viable statistical model with an acceptable metric related to these models. The final statistical models were formed with statistical parameters within acceptable range (r² = 0.797, Q² = 0.725 and r²_pred = 0.643 for the MLR model, and r² = 0.780, Q² = 0.685 and r²_pred = 0.666 for the PLS model). The models were analysed and compared with those already published on the same endpoint.

Transpectoral Anterior Approach to the Axilla for Lymph Node Dissection in Association with Mastectomy Preserving Both Pectoral Muscles and Their Neurovascular Bundles

In Patey's mastectomy, which is still the most common operation for breast cancer, axillary node dissection (AND) is performed through the base of the axilla after retracting the pectoralis major muscle and excising the pectoralis minor muscle (some surgeons preserve the latter). This has the disadvantage of inadequate exposure of the axilla and the risk of damage to the neurovascular bundles supplying the pectoral muscles, which in the long run may lead to atrophy of these muscles. A transpectoral anterior approach to the axilla for AND in association with mastectomy was attempted in 115 cases to obviate the above-mentioned disadvantages. The approach included: 1) splitting of the pectoralis major between the clavicular and sternal fibers; 2) mobilization and swinging of the pectoralis minor into different directions by means of a sling to facilitate AND at selected levels. The major advantages of this approach were: 1) total preservation of both pectoral muscles with their neurovascular bundles maintained the normal anatomy and function of the shoulder; 2) the axilla was directly approached through the anterior wall instead of through the base; in this way the axillary contents were exposed almost at surface level; 3) the dissection plane could be limited to anterior to and below the axillary vein and the risk of postoperative lymphedema could thus be minimized; 4) change of position of the ipsilateral arm was not necessary; 5) the duration of surgery was reduced. Monoblock ablation of significant and suspected tissues, maintaining the normal anatomy and function of the shoulder, could be easily accomplished with this approach.

Aggregates of quadrupolar dyes for two-photon absorption: the role of intermolecular interactions

We present a theoretical investigation of small aggregates of quadrupolar (A-π-D-π-A or D-π-A-π-D) charge-transfer dyes, with attention focused on the role of intermolecular interactions in determining their optical properties. We tackle the theoretical issue by adopting essential-state models (ESMs), which describe an isolated molecule in terms of a minimal number of electronic states, corresponding to the resonance structures. ESMs quite naturally describe intermolecular interactions relaxing the dipolar approximation and accounting for molecular polarizabilities. The approach is applied to curcuminoid and squaraine dyes, two families of chromophores with weak and strong quadrupolar character, respectively. The method is validated against experiment and for curcuminoids also against time-dependent density functional theory. ESMs rationalize the strong ultra-excitonic effects recurrently observed in the experimental optical spectra of aggregates of highly polarizable quadrupolar dyes, offering a valuable tool to exploit the supramolecular design of material properties.

New melanocortin-like peptide of E. coli can suppress inflammation via the mammalian melanocortin-1 receptor (MC1R): possible endocrine-like function for microbes of the gut

E. coli releases a 33 amino acid peptide melanocortin-like peptide of E. coli (MECO-1) that is identical to the C-terminus of the E. coli elongation factor-G (EF-G) and has interesting similarities to two prominent mammalian melanocortin hormones, alpha-melanocyte-stimulating hormone (alpha-MSH) and adrenocorticotropin (ACTH). Note that MECO-1 lacks HFRW, the common pharmacophore of the known mammalian melanocortin peptides. MECO-1 and the two hormones were equally effective in severely blunting release of cytokines (HMGB1 and TNF) from macrophage-like cells in response to (i) endotoxin (lipopolysaccharide) or (ii) pro-inflammatory cytokine HMGB-1. The in vitro anti-inflammatoty effects of MECO-1 and of alpha-MSH were abrogated by (i) antibody against melanocortin-1 receptor (MC1R) and by (ii) agouti, an endogenous inverse agonist of MC1R. In vivo MECO-1 was even more potent than alpha-MSH in rescuing mice from death due to (i) lethal doses of LPS endotoxin or (ii) cecal ligation and puncture, models of sterile and infectious sepsis, respectively.

A genetically encoded fluorescent tRNA is active in live-cell protein synthesis

Transfer RNAs (tRNAs) perform essential tasks for all living cells. They are major components of the ribosomal machinery for protein synthesis and they also serve in non-ribosomal pathways for regulation and signaling metabolism. We describe the development of a genetically encoded fluorescent tRNA fusion with the potential for imaging in live Escherichia coli cells. This tRNA fusion carries a Spinach aptamer that becomes fluorescent upon binding of a cell-permeable and non-toxic fluorophore. We show that, despite having a structural framework significantly larger than any natural tRNA species, this fusion is a viable probe for monitoring tRNA stability in a cellular quality control mechanism that degrades structurally damaged tRNA. Importantly, this fusion is active in E. coli live-cell protein synthesis allowing peptidyl transfer at a rate sufficient to support cell growth, indicating that it is accommodated by translating ribosomes. Imaging analysis shows that this fusion and ribosomes are both excluded from the nucleoid, indicating that the fusion and ribosomes are in the cytosol together possibly engaged in protein synthesis. This fusion methodology has the potential for developing new tools for live-cell imaging of tRNA with the unique advantage of both stoichiometric labeling and broader application to all cells amenable to genetic engineering.

R213I mutation in release factor 2 (RF2) is one step forward for engineering an omnipotent release factor in bacteria Escherichia coli

The current understanding of the specificity of the bacterial class I release factors (RFs) in decoding stop codons has evolved beyond a simple tripeptide anticodon model. A recent molecular dynamics study for deciphering the principles for specific stop codon recognition by RFs identified Arg-213 as a crucial residue on Escherichia coli RF2 for discriminating guanine in the third position (G3). Interestingly, Arg-213 is highly conserved in RF2 and substituted by Ile-196 in the corresponding position in RF1. Another similar pair is Leu-126 in RF1 and Asp-143 in RF2, which are also conserved within their respective groups. With the hypothesis that replacement of Arg-213 and Asp-143 with the corresponding RF1 residues will reduce G3 discrimination by RF2, we swapped these residues between E. coli RF1 and RF2 by site-directed mutagenesis and characterized their preference for different codons using a competitive peptide release assay. Among these, the R213I mutant of RF2 showed 5-fold improved reading of the RF1-specific UAG codon relative to UAA, the universal stop codon, compared with the wild type (WT). In-depth fast kinetic studies revealed that the gain in UAG reading by RF2 R213I is associated with a reduced efficiency of termination on the cognate UAA codon. Our work highlights the notion that stop codon recognition involves complex interactions with multiple residues beyond the PXT/SPF motifs. We propose that the R213I mutation in RF2 brings us one step forward toward engineering an omnipotent RF in bacteria, capable of reading all three stop codons.

Regulation of PfEMP1-VAR2CSA translation by a Plasmodium translation-enhancing factor

Pregnancy-associated malaria commonly involves the binding of Plasmodium falciparum-infected erythrocytes to placental chondroitin sulfate A (CSA) through the PfEMP1-VAR2CSA protein. VAR2CSA is translationally repressed by an upstream open reading frame. In this study, we report that the P. falciparum translation enhancing factor (PTEF) relieves upstream open reading frame repression and thereby facilitates VAR2CSA translation. VAR2CSA protein levels in var2csa-transcribing parasites are dependent on the expression level of PTEF, and the alleviation of upstream open reading frame repression requires the proteolytic processing of PTEF by PfCalpain. Cleavage generates a C-terminal domain that contains a sterile-alpha-motif-like domain. The C-terminal domain is permissive to cytoplasmic shuttling and interacts with ribosomes to facilitate translational derepression of the var2csa coding sequence. It also enhances translation in a heterologous translation system and thus represents the first non-canonical translation enhancing factor to be found in a protozoan. Our results implicate PTEF in regulating placental CSA binding of infected erythrocytes.

Distinct modulatory role of RNA in the aggregation of the tumor suppressor protein p53 core domain

Inactivation of the tumor suppressor protein p53 by mutagenesis, chemical modification, protein-protein interaction, or aggregation has been associated with different human cancers. Although DNA is the typical substrate of p53, numerous studies have reported p53 interactions with RNA. Here, we have examined the effects of RNA of varied sequence, length, and origin on the mechanism of aggregation of the core domain of p53 (p53C) using light scattering, intrinsic fluorescence, transmission electron microscopy, thioflavin-T binding, seeding, and immunoblot assays. Our results are the first to demonstrate that RNA can modulate the aggregation of p53C and full-length p53. We found bimodal behavior of RNA in p53C aggregation. A low RNA:protein ratio (∼1:50) facilitates the accumulation of large amorphous aggregates of p53C. By contrast, at a high RNA:protein ratio (≥1:8), the amorphous aggregation of p53C is clearly suppressed. Instead, amyloid p53C oligomers are formed that can act as seeds nucleating de novo aggregation of p53C. We propose that structured RNAs prevent p53C aggregation through surface interaction and play a significant role in the regulation of the tumor suppressor protein.

Experimental Evolution of Escherichia coli Harboring an Ancient Translation Protein

The ability to design synthetic genes and engineer biological systems at the genome scale opens new means by which to characterize phenotypic states and the responses of biological systems to perturbations. One emerging method involves inserting artificial genes into bacterial genomes and examining how the genome and its new genes adapt to each other. Here we report the development and implementation of a modified approach to this method, in which phylogenetically inferred genes are inserted into a microbial genome, and laboratory evolution is then used to examine the adaptive potential of the resulting hybrid genome. Specifically, we engineered an approximately 700-million-year-old inferred ancestral variant of tufB, an essential gene encoding elongation factor Tu, and inserted it in a modern Escherichia coli genome in place of the native tufB gene. While the ancient homolog was not lethal to the cell, it did cause a twofold decrease in organismal fitness, mainly due to reduced protein dosage. We subsequently evolved replicate hybrid bacterial populations for 2000 generations in the laboratory and examined the adaptive response via fitness assays, whole genome sequencing, proteomics, and biochemical assays. Hybrid lineages exhibit a general adaptive strategy in which the fitness cost of the ancient gene was ameliorated in part by upregulation of protein production. Our results suggest that an ancient-modern recombinant method may pave the way for the synthesis of organisms that exhibit ancient phenotypes, and that laboratory evolution of these organisms may prove useful in elucidating insights into historical adaptive processes.

AxGxE: Using Flies to Interrogate the Complex Etiology of Neurodegenerative Disease

Progressive and late-onset neurological disorders such as Parkinson's disease and Alzheimer's disease affect up to 50 million people globally-a number postulated to double every 20 years in a continually aging population. While predisposing allelic variants in several genes clearly confer risk, individual age and specific environmental influences are equally important discriminators of disease onset age and progression. However, none of these factors can independently predict disease with significant precision. Therefore, we must actively develop models that accommodate contributions from all factors, potentially resulting in an A × G × E (age-gene-environment) metric that reflects individual cumulative risk and reliably forecasts disease outcomes. This effort can only be enabled by a deep quantitative understanding of the contribution of these factors to neurodegenerative disease, both individually and in combination. This is also an important consideration because neuronal loss typically precedes clinical presentation and disease-modifying therapies are contingent on early diagnosis that is likely to be informed by an accurate estimation of individual risk. Although epidemiological studies continue to make strong advances in these areas with the advent of powerful "omics"-based approaches, systematic phenotypic modeling of AxGxE interactions is currently more feasible in model organisms such as Drosophila melanogaster where all three parameters can be manipulated with manageable experimental burden. Here, we outline the advantages of using fruit flies for investigating these complex interactions and highlight potential approaches that might help synthesize existing information from diverse fields into a cogent description of age-dependent, environmental, and genetic risk factors in the pathophysiology of neurological disorders.

Micrococcin P1 - A bactericidal thiopeptide active against Mycobacterium tuberculosis

The lack of proper treatment for serious infectious diseases due to the emergence of multidrug resistance reinforces the need for the discovery of novel antibiotics. This is particularly true for tuberculosis (TB) for which 3.7% of new cases and 20% of previously treated cases are estimated to be caused by multi-drug resistant strains. In addition, in the case of TB, which claimed 1.5 million lives in 2014, the treatment of the least complicated, drug sensitive cases is lengthy and disagreeable. Therefore, new drugs with novel targets are urgently needed to control resistant Mycobacterium tuberculosis strains. In this manuscript we report the characterization of the thiopeptide micrococcin P1 as an anti-tubercular agent. Our biochemical experiments show that this antibiotic inhibits the elongation step of protein synthesis in mycobacteria. We have further identified micrococcin resistant mutations in the ribosomal protein L11 (RplK); the mutations were located in the proline loop at the N-terminus. Reintroduction of the mutations into a clean genetic background, confirmed that they conferred resistance, while introduction of the wild type RplK allele into resistant strains re-established sensitivity. We also identified a mutation in the 23S rRNA gene. These data, in good agreement with previous structural studies suggest that also in M. tuberculosis micrococcin P1 functions by binding to the cleft between the 23S rRNA and the L11 protein loop, thus interfering with the binding of elongation factors Tu and G (EF-Tu and EF-G) and inhibiting protein translocation.

HflX is a ribosome-splitting factor rescuing stalled ribosomes under stress conditions

Adverse cellular conditions often lead to nonproductive translational stalling and arrest of ribosomes on mRNAs. Here, we used fast kinetics and cryo-EM to characterize Escherichia coli HflX, a GTPase with unknown function. Our data reveal that HflX is a heat shock-induced ribosome-splitting factor capable of dissociating vacant as well as mRNA-associated ribosomes with deacylated tRNA in the peptidyl site. Structural data demonstrate that the N-terminal effector domain of HflX binds to the peptidyl transferase center in a strikingly similar manner as that of the class I release factors and induces dramatic conformational changes in central intersubunit bridges, thus promoting subunit dissociation. Accordingly, loss of HflX results in an increase in stalled ribosomes upon heat shock. These results suggest a primary role of HflX in rescuing translationally arrested ribosomes under stress conditions.

A conserved histidine in switch-II of EF-G moderates release of inorganic phosphate

Elongation factor G (EF-G), a translational GTPase responsible for tRNA-mRNA translocation possesses a conserved histidine (H91 in Escherichia coli) at the apex of switch-II, which has been implicated in GTPase activation and GTP hydrolysis. While H91A, H91R and H91E mutants showed different degrees of defect in ribosome associated GTP hydrolysis, H91Q behaved like the WT. However, all these mutants, including H91Q, are much more defective in inorganic phosphate (Pi) release, thereby suggesting that H91 facilitates Pi release. In crystal structures of the ribosome bound EF-G•GTP a tight coupling between H91 and the γ-phosphate of GTP can be seen. Following GTP hydrolysis, H91 flips ~140° in the opposite direction, probably with Pi still coupled to it. This, we suggest, promotes Pi to detach from GDP and reach the inter-domain space of EF-G, which constitutes an exit path for the Pi. Molecular dynamics simulations are consistent with this hypothesis and demonstrate a vital role of an Mg²⁺ ion in the process.