Human tumor suppressor protein Pdcd4 binds at the mRNA entry channel in the 40S small ribosomal subunit

Translation is regulated mainly in the initiation step, and its dysregulation is implicated in many human diseases. Several proteins have been found to regulate translational initiation, including Pdcd4 (programmed cell death gene 4). Pdcd4 is a tumor suppressor protein that prevents cell growth, invasion, and metastasis. It is downregulated in most tumor cells, while global translation in the cell is upregulated. To understand the mechanisms underlying translational control by Pdcd4, we used single-particle cryo-electron microscopy to determine the structure of human Pdcd4 bound to 40S small ribosomal subunit, including Pdcd4-40S and Pdcd4-40S-eIF4A-eIF3-eIF1 complexes. The structures reveal the binding site of Pdcd4 at the mRNA entry site in the 40S, where the C-terminal domain (CTD) interacts with eIF4A at the mRNA entry site, while the N-terminal domain (NTD) is inserted into the mRNA channel and decoding site. The structures, together with quantitative binding and in vitro translation assays, shed light on the critical role of the NTD for the recruitment of Pdcd4 to the ribosomal complex and suggest a model whereby Pdcd4 blocks the eIF4F-independent role of eIF4A during recruitment and scanning of the 5' UTR of mRNA.

Genetic predisposition of BDNF (rs6265) gene is susceptible to Schizophrenia: A prospective study and updated meta-analysis

INTRODUCTION

Genetic polymorphism in the BDNF gene has been found to cause neuronal alterations and has been identified as a causal factor for many neuropsychiatric disorders. Therefore, various neurological case-control studies and meta-analyses have been conducted to find the possible link between BDNF and susceptibility to schizophrenia.

METHOD

This meta-analysis gathered data from 25 case-control studies including a total of 8384 patients with schizophrenia and 8821 controls in order to identify the relationship between the rs6265 single nucleotide polymorphism and the disease, evaluating the combined odds ratio and 95% confidence intervals under 5 different genetic models. Validation followed the "Leave one out" method, and we used the Egger test and Begg's funnel plot to identify publication bias.

RESULTS

Research into the rs6265 (G/A) polymorphism revealed a non-significant association with schizophrenia in all 5 genetic models; in the subgroup analysis, no association was found between white and Asian populations, with a p value>.05.

CONCLUSIONS

Overall, the updated meta-analysis revealed that rs6265 exonic polymorphisms do not increase susceptibility to this disease. However, to better understand the pathogenesis of the disease, there is a need for further case-control studies into the BDNF polymorphism including larger sample sizes and different ethnic groups.

The structure of a human translation initiation complex reveals two independent roles for the helicase eIF4A

Eukaryotic translation initiation involves recruitment of the 43S pre-initiation complex to the 5' end of mRNA by the cap-binding complex eIF4F, forming the 48S translation initiation complex (48S), which then scans along the mRNA until the start codon is recognized. We have previously shown that eIF4F binds near the mRNA exit channel of the 43S, leaving open the question of how mRNA secondary structure is removed as it enters the mRNA channel on the other side of the 40S subunit. Here we report the structure of a human 48S that shows that, in addition to the eIF4A that is part of eIF4F, there is a second eIF4A helicase bound at the mRNA entry site, which could unwind RNA secondary structures as they enter the 48S. The structure also reveals conserved interactions between eIF4F and the 43S, probaby explaining how eIF4F can promote mRNA recruitment in all eukaryotes.

The molecular basis of translation initiation and its regulation in eukaryotes

The regulation of gene expression is fundamental for life. Whereas the role of transcriptional regulation of gene expression has been studied for several decades, it has been clear over the past two decades that post-transcriptional regulation of gene expression, of which translation regulation is a major part, can be equally important. Translation can be divided into four main stages: initiation, elongation, termination and ribosome recycling. Translation is controlled mainly during its initiation, a process which culminates in a ribosome positioned with an initiator tRNA over the start codon and, thus, ready to begin elongation of the protein chain. mRNA translation has emerged as a powerful tool for the development of innovative therapies, yet the detailed mechanisms underlying the complex process of initiation remain unclear. Recent studies in yeast and mammals have started to shed light on some previously unclear aspects of this process. In this Review, we discuss the current state of knowledge on eukaryotic translation initiation and its regulation in health and disease. Specifically, we focus on recent advances in understanding the processes involved in assembling the 43S pre-initiation complex and its recruitment by the cap-binding complex eukaryotic translation initiation factor 4F (eIF4F) at the 5' end of mRNA. In addition, we discuss recent insights into ribosome scanning along the 5' untranslated region of mRNA and selection of the start codon, which culminates in joining of the 60S large subunit and formation of the 80S initiation complex.

3D Visualization, Skeletonization and Branching Analysis of Blood Vessels in Angiogenesis

Angiogenesis is the process of new blood vessels growing from existing vasculature. Visualizing them as a three-dimensional (3D) model is a challenging, yet relevant, task as it would be of great help to researchers, pathologists, and medical doctors. A branching analysis on the 3D model would further facilitate research and diagnostic purposes. In this paper, a pipeline of vision algorithms is elaborated to visualize and analyze blood vessels in 3D from formalin-fixed paraffin-embedded (FFPE) granulation tissue sections with two different staining methods. First, a U-net neural network is used to segment blood vessels from the tissues. Second, image registration is used to align the consecutive images. Coarse registration using an image-intensity optimization technique, followed by finetuning using a neural network based on Spatial Transformers, results in an excellent alignment of images. Lastly, the corresponding segmented masks depicting the blood vessels are aligned and interpolated using the results of the image registration, resulting in a visualized 3D model. Additionally, a skeletonization algorithm is used to analyze the branching characteristics of the 3D vascular model. In summary, computer vision and deep learning is used to reconstruct, visualize and analyze a 3D vascular model from a set of parallel tissue samples. Our technique opens innovative perspectives in the pathophysiological understanding of vascular morphogenesis under different pathophysiological conditions and its potential diagnostic role.

Microdermabrasion facilitates direct current stimulation by lowering skin resistance

Background

Transcranial direct current stimulation (tDCS) is reported to induce irritating skin sensations and occasional skin injuries, which limits the applied tDCS dose. Additionally, tDCS hardware safety profile prevents high current delivery when skin resistance is high.

Objective

To test if decreasing skin resistance can enable high-dose tDCS delivery without increasing tDCS-related skin sensations or device hardware limits.

Methods

We compared the effect of microdermabrasion and sonication on 2 mA direct current stimulation (DCS) through forearm skin for 2-3 min on 20 subjects. We also surveyed the subjects using a questionnaire throughout the procedure. We used a linear mixed-effects model for repeated-measures and multiple logistic regression, with adjustments for age, race, gender and visit.

Results

Microdermabrasion, with/out sonication, led to significant decrease in skin resistance (1.6 ± 0.1 kΩ or ∼32% decrease, p < 0.0001). The decrease with sonication alone (0.4 ± 0.1 kΩ or ∼7% decrease, p = 0.0016) was comparable to that of sham (0.3 ± 0.1 kΩ or ∼5% decrease, p = 0.0414). There was no increase in the skin-electrode interface temperature. The perceived DCS-related sensations did not differ across skin preparation procedures (p > 0.16), but microdermabrasion (when not combined with sonication) led to increased perceived sensation (p < 0.01).

Conclusions

Microdermabrasion (with/out sonication) resulted in reduced skin resistance without increase in perceived skin sensations with DCS. Higher current can be delivered with microdermabrasion-pre-treated skin without changing the device hardware while reducing, otherwise higher voltage required to deliver the same amount of current.

Experimental investigation of anomalous molecular probe diffusion in entangled polymer melts

Investigations on the diffusion of small molecules or particles in polymeric materials are important to numerous technologies and can also be used to gain insight on polymer chain dynamics. Systems where the probe size is comparable to (or smaller than) a characteristic length of the polymer chain, the tube diameter for example, are of particular interest because the diffusion coefficient of the probe can be orders of magnitude larger than the value predicted by the Stokes-Einstein relation. In the present study, we employ the optical technique known as forced Rayleigh scattering to study the diffusion of a molecular probe (dye) in several entangled polymer melts over a wide range of length and time scales. The probe size is much smaller than the tube diameter for the systems studied. We find the diffusion coefficient is larger by four to five orders of magnitude than the Stokes-Einstein prediction. More interestingly, we observe anomalous, non-Fickian, diffusion where the value of the measured diffusion coefficient can abruptly change by as much as 50%. We suggest that this unexpected behavior occurs when the time scale for diffusion is larger than the relaxation time associated with the constraint release mechanism for polymer chain dynamics.

Quantitative Diffusion and Spectroscopic Neuroimaging Combined with a Novel Early-Developmental Assessment Improves Models for 1-Year Developmental Outcomes

BACKGROUND AND PURPOSE

Preterm infants are at risk for overt and silent CNS injury, with developmental consequences that are difficult to predict. The novel Specific Test of Early Infant Motor Performance, administered in preterm infants at term age, is indicative of later developmental gross motor and cognitive scores at 12 months. Here, we assessed whether functional performance on this early assessment correlates with CNS integrity via MR spectroscopy or diffusional kurtosis imaging and whether these quantitative neuroimaging methods improve predictions for future 12-month developmental scores.

MATERIALS AND METHODS

MR spectroscopy and quantitative diffusion MR imaging data were acquired in preterm infants (n = 16) at term. Testing was performed at term and 3 months using the Specific Test of Early Infant Motor Performance and the Bayley Scales of Infant and Toddler Development, Third Edition, at 12 months. We modeled the relationship of MR spectroscopy and diffusion MR imaging data with both test scores via multiple linear regression.

RESULTS

MR spectroscopy NAA ratios at a TE of 270 ms in the frontal WM and basal ganglia and kurtosis metrics in major WM tracts correlated strongly with total Specific Test of Early Infant Motor Performance scores. The addition of MR spectroscopy and diffusion separately improved the functional predictions of 12-month outcomes.

CONCLUSIONS

Microstructural integrity of the major WM tracts and metabolism in the basal ganglia and frontal WM strongly correlate with early developmental performance, suggesting that the Specific Test of Early Infant Motor Performance reflects CNS integrity after preterm birth. This study demonstrates that combining quantitative neuroimaging and early functional movement improves the prediction of 12-month outcomes in premature infants.

Visualizing formation of the active site in the mitochondrial ribosome

Ribosome assembly is an essential and conserved process that is regulated at each step by specific factors. Using cryo-electron microscopy (cryo-EM), we visualize the formation of the conserved peptidyl transferase center (PTC) of the human mitochondrial ribosome. The conserved GTPase GTPBP7 regulates the correct folding of 16S ribosomal RNA (rRNA) helices and ensures 2'-O-methylation of the PTC base U3039. GTPBP7 binds the RNA methyltransferase NSUN4 and MTERF4, which sequester H68-71 of the 16S rRNA and allow biogenesis factors to access the maturing PTC. Mutations that disrupt binding of their Caenorhabditis elegans orthologs to the large subunit potently activate mitochondrial stress and cause viability, development, and sterility defects. Next-generation RNA sequencing reveals widespread gene expression changes in these mutant animals that are indicative of mitochondrial stress response activation. We also answer the long-standing question of why NSUN4, but not its enzymatic activity, is indispensable for mitochondrial protein synthesis.

Quantification of residual pneumoperitoneum after robotic-assisted laparoscopic surgery

Objective

Laparoscopic surgery improves the postoperative recovery process and relies on CO2 insufflation to establish the operative field. Most residual CO2 is expelled prior to port and incision closure. Computed tomography (CT) is often used to assess an acute abdomen and is highly sensitive in detecting free intra-abdominal air – the hallmark sign of a bowel injury. Yet, the clinical significance of free air in the early postoperative period is confounded by residual CO2 and is not usually due to a visceral injury. The aim of this prospective study was to systematically quantify the residual pneumoperitoneum (RPP) at varying timepoints after robotic-assisted laparoscopic surgery.

Methods

Patients undergoing robot-assisted laparoscopic intervention, both radical prostatectomies and left hemicolectomies, were prospectively enrolled in the study. At the conclusion of each operation, manual abdominal pressure was applied to aid in exsufflation of residual CO2. Very-low-dose CT scans were performed on postoperative days (POD) 3, 5, and 7, with subsequent volumetric quantification of RPP. To investigate potential factors influencing the quantity of RPP, correlation plots were made against BMI, age, operative time, total insufflation volume, intra-abdominal pressure, time to flatus and first bowel movement, pain score, and postoperative analgesic requirement.

Results

Thirty-one patients undergoing robotic assisted laparoscopic prostatectomy were untill now enrolled in the study, of which only one experienced a Clavien-Dindo 2 complication; all others were free of any complications during post-operative assessment period. On POD3, 5, and 7, 97%, 94%, and 68% of patients, respectively, demonstrated RPP. The RPP volumes were noted to be 9.6 mL (IQR = 3.9-31.8; maximum = 247 mL) on POD3, 1.0 mL (0.1-5.1; maximum = 221 mL) on POD5, and 0.08 mL (1-1.2; maximum = 112 mL) on POD7. A significant correlation was only appreciated between RPP volume and BMI; those with higher BMIs had lower initial volumes of RPP on POD3 and exhibited a more rapid decrease in RPP over one week.

Conclusion

One week after robot-assisted laparoscopic operations, a majority of patients will exhibit clinically insignificant RPP, even with volumes as high as 250 mL. Larger patients tend to have smaller residuals of CO2. Our data provide new basic knowledge regarding RPP and may help to interpret postoperative CT-scans.

The Olfactory Cleft Endoscopy Scale: a multi-institutional validation study in chronic rhinosinusitis

BACKGROUND

Olfactory dysfunction (OD) associated with chronic rhinosinusitis (CRS) remains quite challenging. Instruments to precisely assess olfactory cleft anatomy and their association with olfaction are needed.

METHODS

The olfactory cleft endoscopy scale (OCES) was used to assess the olfactory cleft in healthy control subjects and a cohort of patients with CRS. Psychophysical and psychosocial olfactory function were assessed and correlations with OCES scores were measured.

RESULTS

Control subjects and subjects with CRS with nasal polyps (CRSwNP) and CRS without nasal polyps (CRSsNP) were enrol- led. OCES correlated with both psychophysical and psychosocial olfaction, as measured by threshold, discrimination and identi- fication (TDI) scores and Questionnaire on Olfactory Disorders (QOD-NS) scores for all case and control subjects combined. OCES improved in both CRS groups postoperatively with the highest correlation seen in postoperative olfaction in CRSwNP patients. CRS patients who achieve near perfect OCES and sinus endoscopy scores after surgery have olfactory metrics that are indistin- guishable from controls regardless of polyp status.

CONCLUSIONS

The OCES is a valid olfactory-specific measure that demonstrates strong validity and provides complimentary infor- mation to traditional sinus endoscopy to aid in our understanding of OD associated with CRS.

Comparison of PEAK PlasmaBlade™ to conventional diathermy in abdominal-based free-flap breast reconstruction surgery-A single-centre double-blinded randomised controlled trial

BACKGROUND

Electrosurgery makes dissection with simultaneous haemostasis possible. The produced heat can cause injury to the surrounding tissue. The PEAK PlasmaBlade™(PPB) is a new electrosurgery device which may overcome this by having the ability to operate on a lower temperature, therefore reducing collateral thermal damage.

METHOD

A single-centre, double-blinded, randomised controlled trial (RCT) was conducted which included 108 abdominal-based free-flap breast reconstruction patients who had their flap raise performed using either the PPB (n = 56) or the conventional diathermy (n = 52). Data were collected during their in-patient stay and out-patient appointments. The primary outcome value was the number of days the abdominal drains were required.

RESULTS

Baseline characteristics were similar between the groups, except a significantly lower flap weight in the PPB group. The median number of days the drains were required did not differ significantly (p = 0.48; 6.0 days for the diathermy and 5.0 days for the PPB). The total drain output (p = 0.68), the inflammatory cytokine in the drain fluid (p>0.054) and complications (p>0.24) did not differ significantly between the two groups. At the 2-week follow-up appointment, there was a trend towards less abdominal seromas on abdominal ultrasound (p = 0.09) in the PPB group which were significantly smaller (p = 0.04).

CONCLUSION

The use of the PPB did not result in a significant reduction of drain requirement, total drain output or inflammatory cytokines but did reduce the size of seroma collections at the 2-week follow-up appointment. Therefore, the use of the PPB device could reduce early seroma formation after drain removal.

Safety of major reconstructive surgery during the peak of the COVID-19 pandemic in the United Kingdom and Ireland - multicentre national cohort study

Background

The safety of surgery during and after the coronavirus disease-2019 (COVID-19) pandemic is paramount. Early reports of excessive perioperative mortality in COVID-positive patients promoted the widespread avoidance of operations. However, cancelling or delaying operations for cancer, trauma, or functional restitution has resulted in increased morbidity and mortality.

Methods

A national multicentre cohort study of all major reconstructive operations carried out over a 12-week period of the ‘COVID-19 surge’ in the United Kingdom and Ireland was performed. Primary outcome was 30-day mortality and secondary outcome measures were major complications (Clavien-Dindo grade ≥3) and COVID-19 status of patients and healthcare professionals before and after surgery.

Results

A total of 418 patients underwent major reconstructive surgery with a mean operating time of 7.5 hours and 12 days’ inpatient stay. Cancer (59.8%) and trauma (29.4%) were the most common indications. COVID-19 infection was present in 4.5% of patients. The 30-day post-operative mortality was 0.2%, reflecting the death of one patient who was COVID-negative. Overall complication rate was 20.8%. COVID status did not correlate with major or minor complications. Eight healthcare professionals developed post-operative COVID-19 infection, seven of which occurred within the first three weeks.

Conclusions

Major reconstructive operations performed during the COVID-19 crisis have been mostly urgent cases involving all surgical specialties. This cohort is a surrogate for all major operations across all surgical specialties. Patient safety and surgical outcomes have been the same as in the pre-COVID era. With adequate precautions, major reconstructive surgery is safe for patients and staff. This study helps counsel patients of COVID-19 risks in the perioperative period.

Structure of a human 48S translational initiation complex

A key step in translational initiation is the recruitment of the 43S preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to form the 48S initiation complex (i.e., the 48S). The 48S then scans along the mRNA to locate a start codon. To understand the mechanisms involved, we used cryo-electron microscopy to determine the structure of a reconstituted human 48S The structure reveals insights into early events of translation initiation complex assembly, as well as how eIF4F interacts with subunits of eIF3 near the mRNA exit channel in the 43S The location of eIF4F is consistent with a slotting model of mRNA recruitment and suggests that downstream mRNA is unwound at least in part by being "pulled" through the 40S subunit during scanning.

Rapidly progressive dementia in the COVID‐19 era

Background

Rapidly progressive dementias(RPD) are conditions that typically cause dementia over weeks or months.¹ Due to the current COVID‐19 pandemic, it has become difficult for dementia caregivers on the one hand, and relevant detailed examination and management in the hospitals worldwide, on the other. Recent studies shows that ApoE e4 genotype is associated with both dementia and delirium². Hence further research into the possible genetic link between dementia and COVID‐19 is the need of the hour.

Method

We studied two elderly male patients, aged 66 and 68 years, presenting with memory decline of recent events, untimely and non‐sequential Activities of Daily Living and apathetic alongwith way finding difficulty and errors in money transactions. One patient also had forgetfulness of handwashing and face hygiene measures, and of using preventive face masks in public places as advised for public health during COVID‐19 outbreak. On examination, vitals were stable and normal fundus examination with no fever, dry cough or tiredness, and no evidence of Increased Intracranial Pressure(ICP). MMSE score was 16/30 and 17/30 respectively, recent memory and visuospatial skills were impaired and slowness of activities were present. Motor examination was normal, with no focal or non‐focal neurological deficit or sensory impairment. All routine tests were normal. Neuroimaging with contrast in one patient showed well defined hyperdense mass lesion of size 4.0*3.5*3.0 cms. showing heterogenous contrast enhancement in left parieto‐occipital lobes with moderate perilesional edema suggestive of astrocytoma (intermediate type).

Result

High index of suspicion of Space occupying lesions should be made in the background of RPD even in the absence of focal or non focal neurological deficit or without signs of raised ICP.

Conclusion

Most of the etiologies causing RPD especially surgical causes, if diagnosed early and promptly are reversible and treatable. The double hit of dementia and COVID‐19 pandemic necessitates further research globally. References: 1) Paterson RW, Takada LT, Geschwind MD. Diagnosis and treatment of rapidly progressive dementias. Neurol Clin Pract. 2012;2(3):187–200. 2) Kuo C‐L, Pilling LC, Atkins JL, Kuchel GA, Melzer D. ApoE e2 and aging‐related outcomes in 379,000 UK Biobank participants. medRxiv [Internet]. 2020: 2020.02.12.20022459.

Elongational stalling activates mitoribosome-associated quality control

The human mitochondrial ribosome (mitoribosome) and associated proteins regulate the synthesis of 13 essential subunits of the oxidative phosphorylation complexes. We report the discovery of a mitoribosome-associated quality control pathway that responds to interruptions during elongation, and we present structures at 3.1- to 3.3-angstrom resolution of mitoribosomal large subunits trapped during ribosome rescue. Release factor homolog C12orf65 (mtRF-R) and RNA binding protein C6orf203 (MTRES1) eject the nascent chain and peptidyl transfer RNA (tRNA), respectively, from stalled ribosomes. Recruitment of mitoribosome biogenesis factors to these quality control intermediates suggests additional roles for these factors during mitoribosome rescue. We also report related cryo-electron microscopy structures (3.7 to 4.4 angstrom resolution) of elongating mitoribosomes bound to tRNAs, nascent polypeptides, the guanosine triphosphatase elongation factors mtEF-Tu and mtEF-G1, and the Oxa1L translocase.

Regulatory Cross Talk Between SARS-CoV-2 Receptor Binding and Replication Machinery in the Human Host

We dissect the mechanism of SARS-CoV-2 in human lung host from the initial phase of receptor binding to viral replication machinery. Two independent lung protein interactome were constructed to reveal the signaling process on receptor activation and host protein hijacking machinery in the pathogenesis of virus. Further, we test the functional role of the hubs derived from the interactome. Most hubs proteins were differentially regulated on SARS-CoV-2 infection. Also, the proteins in viral replication hubs were related with cardiovascular disease, diabetes and hypertension confirming the vulnerability and severity of infection in the risk individual. Additionally, the hub proteins were closely linked with other viral infection, including MERS and HCoVs which suggest similar infection pattern in SARS-CoV-2. We identified five hubs that interconnect both networks that show the preparation of optimal environment in the host for viral replication process upon receptor attachment. Interestingly, we propose that seven potential miRNAs, targeting the intermediate phase that connects receptor and viral replication process a better choice as a drug for SARS-CoV-2.