Accurate structure prediction of biomolecular interactions with AlphaFold 3.

The introduction of AlphaFold 21 has spurred a revolution in modelling the structure of proteins and their interactions, enabling a huge range of applications in protein modelling and design2-6. Here we describe our AlphaFold 3 model with a substantially updated diffusion-based architecture that is capable of predicting the joint structure of complexes including proteins, nucleic acids, small molecules, ions and modified residues. The new AlphaFold model demonstrates substantially improved accuracy over many previous specialized tools: far greater accuracy for protein-ligand interactions compared with state-of-the-art docking tools, much higher accuracy for protein-nucleic acid interactions compared with nucleic-acid-specific predictors and substantially higher antibody-antigen prediction accuracy compared with AlphaFold-Multimer v.2.37,8. Together, these results show that high-accuracy modelling across biomolecular space is possible within a single unified deep-learning framework.

Lack of evidence for ribosomal frameshifting in ATP7B mRNA decoding.

The research article describing the discovery of ribosomal frameshifting in the bacterial CopA gene also reported the occurrence of frameshifting in the expression of the human ortholog ATP7B based on assays using dual luciferase reporters. An examination of the publicly available ribosome profiling data and the phylogenetic analysis of the proposed frameshifting site cast doubt on the validity of this claim and prompted us to reexamine the evidence. We observed similar apparent frameshifting efficiencies as the original authors using the same type of vector that synthesizes both luciferases as a single polyprotein. However, we noticed anomalously low absolute luciferase activities from the N-terminal reporter that suggests interference of reporter activity or levels by the ATP7B test cassette. When we tested the same proposed ATP7B frameshifting cassette in a more recently developed reporter system in which the reporters are released without being included in a polyprotein, no frameshifting was detected above background levels.

Programmed Ribosomal Frameshifting Generates a Copper Transporter and a Copper Chaperone from the Same Gene.

Metal efflux pumps maintain ion homeostasis in the cell. The functions of the transporters are often supported by chaperone proteins, which scavenge the metal ions from the cytoplasm. Although the copper ion transporter CopA has been known in Escherichia coli, no gene for its chaperone had been identified. We show that the CopA chaperone is expressed in E. coli from the same gene that encodes the transporter. Some ribosomes translating copA undergo programmed frameshifting, terminate translation in the -1 frame, and generate the 70 aa-long polypeptide CopA(Z), which helps cells survive toxic copper concentrations. The high efficiency of frameshifting is achieved by the combined stimulatory action of a "slippery" sequence, an mRNA pseudoknot, and the CopA nascent chain. Similar mRNA elements are not only found in the copA genes of other bacteria but are also present in ATP7B, the human homolog of copA, and direct ribosomal frameshifting in vivo.

The AAA+ superfamily: a review of the structural and mechanistic principles of these molecular machines.

ATPases associated with diverse cellular activities (AAA+ proteins) are a superfamily of proteins found throughout all domains of life. The hallmark of this family is a conserved AAA+ domain responsible for a diverse range of cellular activities. Typically, AAA+ proteins transduce chemical energy from the hydrolysis of ATP into mechanical energy through conformational change, which can drive a variety of biological processes. AAA+ proteins operate in a variety of cellular contexts with diverse functions including disassembly of SNARE proteins, protein quality control, DNA replication, ribosome assembly, and viral replication. This breadth of function illustrates both the importance of AAA+ proteins in health and disease and emphasizes the importance of understanding conserved mechanisms of chemo-mechanical energy transduction. This review is divided into three major portions. First, the core AAA+ fold is presented. Next, the seven different clades of AAA+ proteins and structural details and reclassification pertaining to proteins in each clade are described. Finally, two well-known AAA+ proteins, NSF and its close relative p97, are reviewed in detail.

Plasmonic Refractive Index and Temperature Sensor Based on Graphene and LiNbO3.

A high-efficiency dual-purpose plasmonic perfect absorber sensor based on LiNbO3 and graphene layers was investigated in this paper for the refractive index and thermal sensing. The sensor design was kept simple for easy fabrication, comprising a LiNbO3 substrate with a quartz layer, thin layer of graphene, four gold nanorods, and a nanocavity in each unit cell. The nanocavity is located in the middle of the cell to facilitate the penetration of EM energy to the subsurface layers. The proposed sensor design achieved an output response of 99.9% reflection, which was easy to detect without having any specialized conditions for operability. The performance of the device was numerically investigated for the biomedical refractive index range of 1.33 to 1.40, yielding a sensitivity value of 981 nm/RIU with a figure-of-merit of 61.31 RIU-1. By including an additional polydimethylsiloxane polymer functional layer on the top, the device was also tested as a thermal sensor, which yielded a sensitivity level of -0.23 nm/°C.

Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon.

BACKGROUND: POLG, located on nuclear chromosome 15, encodes the DNA polymerase γ(Pol γ). Pol γ is responsible for the replication and repair of mitochondrial DNA (mtDNA). Pol γ is the only DNA polymerase found in mitochondria for most animal cells. Mutations in POLG are the most common single-gene cause of diseases of mitochondria and have been mapped over the coding region of the POLG ORF. RESULTS: Using PhyloCSF to survey alternative reading frames, we found a conserved coding signature in an alternative frame in exons 2 and 3 of POLG, herein referred to as ORF-Y that arose de novo in placental mammals. Using the synplot2 program, synonymous site conservation was found among mammals in the region of the POLG ORF that is overlapped by ORF-Y. Ribosome profiling data revealed that ORF-Y is translated and that initiation likely occurs at a CUG codon. Inspection of an alignment of mammalian sequences containing ORF-Y revealed that the CUG codon has a strong initiation context and that a well-conserved predicted RNA stem-loop begins 14 nucleotides downstream. Such features are associated with enhanced initiation at near-cognate non-AUG codons. Reanalysis of the Kim et al. (2014) draft human proteome dataset yielded two unique peptides that map unambiguously to ORF-Y. An additional conserved uORF, herein referred to as ORF-Z, was also found in exon 2 of POLG. Lastly, we surveyed Clinvar variants that are synonymous with respect to the POLG ORF and found that most of these variants cause amino acid changes in ORF-Y or ORF-Z. CONCLUSIONS: We provide evidence for a novel coding sequence, ORF-Y, that overlaps the POLG ORF. Ribosome profiling and mass spectrometry data show that ORF-Y is expressed. PhyloCSF and synplot2 analysis show that ORF-Y is subject to strong purifying selection. An abundance of disease-correlated mutations that map to exons 2 and 3 of POLG but also affect ORF-Y provides potential clinical significance to this finding.

Ablation of Programmed -1 Ribosomal Frameshifting in Venezuelan Equine Encephalitis Virus Results in Attenuated Neuropathogenicity.

The alphaviruses Venezuelan equine encephalitis virus (VEEV), eastern equine encephalitis virus (EEEV), and western equine encephalitis virus (WEEV) are arthropod-borne positive-strand RNA viruses that are capable of causing acute and fatal encephalitis in many mammals, including humans. VEEV was weaponized during the Cold War and is recognized as a select agent. Currently, there are no FDA-approved vaccines or therapeutics for these viruses. The spread of VEEV and other members of this family due to climate change-mediated vector range expansion underscores the need for research aimed at developing medical countermeasures. These viruses utilize programmed -1 ribosomal frameshifting (-1 PRF) to synthesize the viral trans-frame (TF) protein, which has previously been shown to be important for neuropathogenesis in the related Sindbis virus. Here, the alphavirus -1 PRF signals were characterized, revealing novel -1 PRF stimulatory structures. -1 PRF attenuation mildly affected the kinetics of VEEV accumulation in cultured cells but strongly inhibited its pathogenesis in an aerosol infection mouse model. Importantly, the decreased viral titers in the brains of mice infected with the mutant virus suggest that the alphavirus TF protein is important for passage through the blood-brain barrier and/or for neuroinvasiveness. These findings suggest a novel approach to the development of safe and effective live attenuated vaccines directed against VEEV and perhaps other closely related -1 PRF-utilizing viruses. IMPORTANCE: Venezuelan equine encephalitis virus (VEEV) is a select agent that has been weaponized. This arthropod-borne positive-strand RNA virus causes acute and fatal encephalitis in many mammals, including humans. There is no vaccine or other approved therapeutic. VEEV and related alphaviruses utilize programmed -1 ribosomal frameshifting (-1 PRF) to synthesize the viral trans-frame (TF) protein, which is important for neuropathogenesis. -1 PRF attenuation strongly inhibited VEEV pathogenesis in mice, and viral replication analyses suggest that the TF protein is critical for neurological disease. These findings suggest a new approach to the development of safe and effective live attenuated vaccines directed against VEEV and other related viruses.

Structural and Functional Characterization of Programmed Ribosomal Frameshift Signals in West Nile Virus Strains Reveals High Structural Plasticity Among cis-Acting RNA Elements.

West Nile virus (WNV) is a prototypical emerging virus for which no effective therapeutics currently exist. WNV uses programmed -1 ribosomal frameshifting (-1 PRF) to synthesize the NS1' protein, a C terminally extended version of its non-structural protein 1, the expression of which enhances neuro-invasiveness and viral RNA abundance. Here, the NS1' frameshift signals derived from four WNV strains were investigated to better understand -1 PRF in this quasispecies. Sequences previously predicted to promote -1 PRF strongly promote this activity, but frameshifting was significantly more efficient upon inclusion of additional 3' sequence information. The observation of different rates of -1 PRF, and by inference differences in the expression of NS1', may account for the greater degrees of pathogenesis associated with specific WNV strains. Chemical modification and mutational analyses of the longer and shorter forms of the -1 PRF signals suggests dynamic structural rearrangements between tandem stem-loop and mRNA pseudoknot structures in two of the strains. A model is suggested in which this is employed as a molecular switch to fine tune the relative expression of structural to non-structural proteins during different phases of the viral replication cycle.

Genetic Mapping and Phenotypic Analysis of GstE14 E.4.1 on Eye and Antennae Development in Drosophila melanogaster.

Genetic screens are valuable for identifying novel genes involved in the regulation of developmental processes. To identify genes associated with cell growth regulation in Drosophila melanogaster , a mutagenesis screen was performed. Undergraduate students participating in Fly-CURE phenotypically characterized the E.4.1 mutant which is associated with rough eyes and antennae overgrowth. Following complementation analysis and subsequent genomic sequencing, E.4.1 was identified as a novel mutant allele of GstE14 , a gene involved in ecdysone biosynthesis important for the timing of developmental events. The abnormal eye and antenna phenotypes observed resulting from the loss of GstE14 suggest its role in tissue growth.

Omphalomesenteric duct cyst in an omphalocele: a rare association.

Omphalomesenteric duct (OMD) remnants and omphalocele are not infrequently seen in paediatric patients. In most of the cases, OMD remnant in an omphalocele is a Meckel's diverticulum; however rarely there may be other lesions. A one-day old male baby underwent surgery for omphalocele. At exploration a 10 x 12 cm cyst containing gut contents was found as the content of the omphalocele, with proximal and distal ileal loops running in continuity with it. Resection of the cyst with end to end primary gut anastomosis was done. Baby also had complex associated cardiac anomalies and died few days after surgery due to sepsis.

DPP-4 inhibitors for treating T2DM - hype or hope? an analysis based on the current literature.

DPP-4 inhibition is an interesting line of therapy for treating Type 2 Diabetes Mellitus (T2DM) and is based on promoting the incretin effect. Here, the authors have presented a brief appraisal of DPP-4 inhibitors, their modes of action, and the clinical efficiency of currently available drugs based on DPP-4 inhibitors. The safety profiles as well as future directions including their potential application in improving COVID-19 patient outcomes have also been discussed in detail. This review also highlights the existing queries and evidence gaps in DPP-4 inhibitor research. Authors have concluded that the excitement surrounding DPP-4 inhibitors is justified because in addition to controlling blood glucose level, they are good at managing risk factors associated with diabetes.

Human tracking robotic camera based on image processing for live streaming of conferences and seminars.

There are numerous scenarios where the photographer is in difficulty and unable to capture or shoot video as required. This could be due to several factors such as limited space, decreased visibility, and an obstacle in the way. Therefore, this project implements the idea to capture and shoot video of the desired subject through an automatically controlled robotic camera with no need for a photographic bloke. The system comprises functions such as detection, tracking, live streaming, and video/audio recording along with the features of Radio-Frequency-Identification (RFID). Therefore, this robotic camera will detect the desired subject, track and focus it with the help of its position driven through movable motors sensing the RFID tag in case the object is non-stationary. The video/audio will be recorded on a computer along with the live streaming available on an Android-based device. The Viola-Jones algorithm of the image processing technique is used to detect the particular subject features and C for accessing the movable camera protocols. The RFID transmitter and receiver are used to sense the RFID card and serve the purpose to track the subject using the algorithms of image processing, with the advantage of ignoring other obstacles between the camera and the detected subject. Thus, adding a novel functionality to the existing systems, that lacks the feature of focusing the camera on the subject, when an obstacle is detected in between. The live streaming is achieved wirelessly through an open-source platform X-operating system, Apache, MySQL, Php, Perl (XAMPP). The idea is verified through concluded arrangements in self-made scenarios in response to the speed, distance, light, and background noise of the detected subject, which delivered encouraging results. Therefore, the designed system can be used for live conferences, seminars, and other multimedia-required arrangements.

Three-Dimensional Modeling of the Optical Switch Based on Guided-Mode Resonances in Photonic Crystals.

Optical switching is an essential part of photonic integrated circuits and the focus of research at the moment. In this research, an optical switch design working on the phenomenon of guided-mode resonances in a 3D photonic-crystal-based structure is reported. The optical-switching mechanism is studied in a dielectric slab-waveguide-based structure operating in the near-infrared range in a telecom window of 1.55 µm. The mechanism is investigated via the interference of two signals, i.e., the data signal and the control signal. The data signal is coupled into the optical structure and filtered utilizing guided-mode resonance, whereas the control signal is index-guided in the optical structure. The amplification or de-amplification of the data signal is controlled by tuning the spectral properties of the optical sources and structural parameters of the device. The parameters are optimized first using a single-cell model with periodic boundary conditions and later in a finite 3D-FDTD model of the device. The numerical design is computed in an open-source Finite Difference Time Domain simulation platform. Optical amplification in the range of 13.75% is achieved in the data signal with a decrease in the linewidth up to 0.0079 µm, achieving a quality factor of 114.58. The proposed device presents great potential in the field of photonic integrated circuits, biomedical technology, and programmable photonics.

Plasmonic Perfect Absorber Utilizing Polyhexamethylene Biguanide Polymer for Carbon Dioxide Gas Sensing Application.

In this paper a perfect absorber with a photonic crystal cavity (PhC-cavity) is numerically investigated for carbon dioxide (CO2) gas sensing application. Metallic structures in the form of silver are introduced for harnessing plasmonic effects to achieve perfect absorption. The sensor comprises a PhC-cavity, silver (Ag) stripes, and a host functional material-Polyhexamethylene biguanide polymer-deposited on the surface of the sensor. The PhC-cavity is implemented within the middle of the cell, helping to penetrate the EM waves into the sublayers of the structure. Therefore, corresponding to the concentration of the CO2 gas, as it increases, the refractive index of the host material decreases, causing a blue shift in the resonant wavelength and vice versa of the device. The sensor is used for the detection of 0-524 parts per million (ppm) concentration of the CO2 gas, with a maximum sensitivity of 17.32 pm (pico meter)/ppm achieved for a concentration of 366 ppm with a figure of merit (FOM) of 2.9 RIU-1. The four-layer device presents a straightforward and compact design that can be adopted in various sensing applications by using suitable host functional materials.

Sensory deficit screen identifies nsf mutation that differentially affects SNARE recycling and quality control.

The AAA+ NSF complex is responsible for SNARE complex disassembly both before and after membrane fusion. Loss of NSF function results in pronounced developmental and degenerative defects. In a genetic screen for sensory deficits in zebrafish, we identified a mutation in nsf, I209N, that impairs hearing and balance in a dosage-dependent manner without accompanying defects in motility, myelination, and innervation. In vitro experiments demonstrate that while the I209N NSF protein recognizes SNARE complexes, the effects on disassembly are dependent upon the type of SNARE complex and I209N concentration. Higher levels of I209N protein produce a modest decrease in binary (syntaxin-SNAP-25) SNARE complex disassembly and residual ternary (syntaxin-1A-SNAP-25-synaptobrevin-2) disassembly, whereas at lower concentrations binary disassembly activity is strongly reduced and ternary disassembly activity is absent. Our study suggests that the differential effect on disassembly of SNARE complexes leads to selective effects on NSF-mediated membrane trafficking and auditory/vestibular function.

Numerical Study of Fabrication-Related Effects of the Structural-Profile on the Performance of a Dielectric Photonic Crystal-Based Fluid Sensor.

In this work, fabrication of a dielectric photonic crystal device and numerical study of its spectral characteristics as a refractive index sensor are presented for near infrared range. The proposed nanosensor device is composed of low-cost dielectric materials, i.e., silicon dioxide and niobium pentoxide, and is fabricated using focused ion-beam milling lithography. In the first part, the fabrication process of the device is discussed, along with the process parameters and their effects on the structural properties of the resulting photonic crystal elements. In the second part, the device is numerically tested as a sensor for the biological refractive index range of 1.33 to 1.4. The performance considerations of the biosensor device are studied for 12 different structural profiles based on the fabrication results. It is shown that the angular-wall-profile of the fabricated structures downgrades the performance of the sensor, and the optimum value of hole depth should be in the range of 930-1500 nm to get the best performance. A sensitivity of 185.117 nm/RIU and a figure of merit of 9.7 were recorded for the optimum design of the device; however, a maximum sensitivity of 296.183 nm/RIU and a figure-of-merit of 13.184 RIU-1 were achieved. The device is recommended for a variety of biosensing applications due to its inert material properties, stable design and easy integration with fiber-optic setups.

Outcome Of The Choice Of Wound Closure Technique In Emergency Laparotomy.

BACKGROUND: Abdominal surgeries are the most common surgeries performed around the world. Closure of abdominal wound is important and a number wound closing techniques are in practice. This study was conducted to determine the outcome of the choice of wound closure technique in emergency laparotomy. METHODS: It was a retrospective study from March-September 2019, conducted at the Surgical A unit, Ayub Teaching Hospital, Abbottabad. Ninety-five patients aged 22-60 years, who underwent emergency laparotomies via midline and para-median incisions were included in the study. RESULTS: There were 74 (77.89%) males and 21 (22.11%) females. Anatomical closure technique was used in 67 (70.53%) of study participants while mass closure technique was used in 28 (29.47%) of study participants. 50 (52.63%) patients had anaemia, 27 (28.42%) had hypo-proteinemia, and 14 (14.74%) developed peritonitis. Post-operative wound infection was noticed in 15 (15.79%) patients. Out of 95 patients, 19 (20%) developed burst abdomen. Overall, 5 (5.26%) patients died in the hospital. All cases of burst abdomen occurred within first two weeks of hospital stay (p= 0.004), had an association with peritonitis (p=0.0001) and post-operative wound infection (p= 0.005). Wound closure technique was not associated with development of post-operative complications including burst abdomen (p >0.05). CONCLUSIONS: Postoperative complications occur independently of wound-closure technique and surgeons should have a low threshold for prevention of post-operative complications where possible.

Prediction of Surface Roughness as a Function of Temperature for SiO2 Thin-Film in PECVD Process.

An analytical model to predict the surface roughness for the plasma-enhanced chemical vapor deposition (PECVD) process over a large range of temperature values is still nonexistent. By using an existing prediction model, the surface roughness can directly be calculated instead of repeating the experimental processes, which can largely save time and resources. This research work focuses on the investigation and analytical modeling of surface roughness of SiO2 deposition using the PECVD process for almost the whole range of operating temperatures, i.e., 80 to 450 °C. The proposed model is based on experimental data of surface roughness against different temperature conditions in the PECVD process measured using atomic force microscopy (AFM). The quality of these SiO2 layers was studied against an isolation layer in a microelectromechanical system (MEMS) for light steering applications. The analytical model employs different mathematical approaches such as linear and cubic regressions over the measured values to develop a prediction model for the whole operating temperature range of the PECVD process. The proposed prediction model is validated by calculating the percent match of the analytical model with experimental data for different temperature ranges, counting the correlations and error bars.