Molecular Biology Laboratory Research Articles

Machine learning random forest for predicting oncosomatic variant NGS analysis

Since 2017, we have used IonTorrent NGS platform in our hospital to diagnose and treat cancer. Analyzing variants at each run requires considerable time, and we are still struggling with some variants that appear correct on the metrics at first, but are found to be negative upon further investigation. Can any machine learning algorithm (ML) help us classify NGS variants? This has led us to investigate which ML can fit our NGS data and to develop a tool that can be routinely implemented to help biologists. Currently, one of the greatest challenges in medicine is processing a significant quantity of data. This is particularly true in molecular biology with the advantage of next-generation sequencing (NGS) for profiling and identifying molecular tumors and their treatment. In addition to bioinformatics pipelines, artificial intelligence (AI) can be valuable in helping to analyze mutation variants. Generating sequencing data from patient DNA samples has become easy to perform in clinical trials. However, analyzing the massive quantities of genomic or transcriptomic data and extracting the key biomarkers associated with a clinical response to a specific therapy requires a formidable combination of scientific expertise, biomolecular skills and a panel of bioinformatic and biostatistic tools, in which artificial intelligence is now successful in developing future routine diagnostics. However, cancer genome complexity and technical artifacts make identifying real variants challenging. We present a machine learning method for classifying pathogenic single nucleotide variants (SNVs), single nucleotide polymorphisms (SNPs), multiple nucleotide variants (MNVs), insertions, and deletions detected by NGS from different types of tumor specimens, such as: colorectal, melanoma, lung and glioma cancer. We compared our NGS data to different machine learning algorithms using the k-fold cross-validation method and to neural networks (deep learning) to measure the performance of the different ML algorithms and determine which one is a valid model for confirming NGS variant calls in cancer diagnosis. We trained our machine learning with 70% of our data samples, extracted from our local database (our data structure had 7 parameters: chromosome, position, exon, variant allele frequency, minor allele frequency, coverage and protein description) and validated it with the 30% remaining data. The model offering the best accuracy was chosen and implemented in the NGS analysis routine. Artificial intelligence was developed with the R script language version 3.6.0. We trained our model on 70% of 102,011 variants. Our best error rate (0.22%) was found with random forest machine learning (ntree = 500 and mtry = 4), with an AUC of 0.99. Neural networks achieved some good scores. The final trained model with the neural network achieved an accuracy of 98% and an ROC-AUC of 0.99 with validation data. We tested our RF model to interpret more than 2000 variants from our NGS database: 20 variants were misclassified (error rate < 1%). The errors were nomenclature problems and false positives. After adding false positives to our training database and implementing our RF model routinely, our error rate was always < 0.5%. The RF model shows excellent results for oncosomatic NGS interpretation and can easily be implemented in other molecular biology laboratories. AI is becoming increasingly important in molecular biomedical analysis and can be very helpful in processing medical data. Neural networks show a good capacity in variant classification, and in the future, they may be useful in predicting more complex variants.

Treatment Free Survival (TFS) in Patients (pts) with Chronic Myeloid Leukemia (CML) Carrying Atypical BCR-ABL1 Fusion Transcripts: The French CML Group (Fi-LMC) Experience

▪AimsLife expectancy of CML pts optimally responding to tyrosine kinase inhibitors (TKI) is close to that of the general population and recently, TFR has been acknowledged as a new goal of CML management. TKI discontinuation in the view of TFR requires the achievement of deep and long-lasting molecular responses (MR). The gold standard BCR-ABL mRNA quantification technology and MR definitions rely on internationally standardized (IS) RT-qPCR but atypical transcripts located outside the Major-BCR region, harbored by 1-2% of pts, cannot be expressed on the IS scale. Thus, most trials and clinical practice recommendations prevent such pts from attempting TFR. The Fi-LMC group retrospectively collected real-life observations to assess TFR likelihood in this rare population.MethodsData from CML pts with precise characterization of atypical transcripts in whom any line TKI was stopped for any reason but after at least 2 years of undetectable molecular residual disease (UMRD) by individualized non-standardized RT-qPCR were collected. RT-qPCR sensitivity varied depending on transcript type and local molecular biology laboratory. TFS was estimated by the Kaplan-Meier method. Relapse was analyzed using the cumulative incidence function, relapse being as UMRD loss at any time and any level during follow-up (FU).ResultsOur series comprised 16 adult CP CML pts with atypical BCR-ABL fusions including 12 males (75%). Median age at CML diagnosis was 56 years (range: 21-75) and that at TKI discontinuation was 67 years [range: 29-82]. Sokal score was low, intermediate and high in 7, 8 and 1 pts, respectively. ELTS score was low and intermediate in 10 and 4 pts, respectively and unknown in 2. Most pts expressed e19a2 (n=6) followed by e6a2 (n=4), b3a3 (n=3), b2a3 (n=2) and e8a2 (n=1). Seven pts discontinued imatinib, 4 stopped dasatinib, 4 nilotinib and 1 bosutinib. Number of lines of therapy was 2 in 8 pts, 1 in 5 pts and 3 in 3 pts. Median TKI treatment duration before discontinuation was 64 months (range: 31-218) and median duration of UMRD was 41 months (range: 21-168). The median FU after TKI discontinuation was 68 months (range: 3-149). Five pts experienced relapse leading to TKI resumption. Four relapses occurred within 3-6 months and included 2 loss of hematologic response in CP, 1 loss of hematologic response in accelerated phase CML and 1 molecular recurrence with BCR-ABL transcripts up to 1.5%. One relapse occurred at 49 months and consisted in loss of a complete cytogenetic response. These 5 pts resumed TKI and regained UMRD within 6 months, including 1 pt who died in UMRD from non-CML-related cause at the age of 82 years and 1 pt who rapidly failed a 2 nd TKI discontinuation attempt.In 1 additional pt, BCR-ABL transcripts became detectable intermittently with maximum transcript level of 0.15% and TKI was not resumed. The median FU of pts who remained treatment-free was 68 months (range: 8-149).Overall, the 5-year cumulative incidence of relapse regardless of whether TKI was resumed was 41.6% (95% confidence interval: 21.9%-78.7%) (Figure 1). The 5-year TFS rate was 65.2% (95% confidence interval: 40.3%-90.2%) (Figure 2).ConclusionsOur observational study of TKI discontinuation in CML pts with atypical BCR-ABL transcripts is the largest reported so far. While effort must be made for proper assessment of deep MR, preliminary results suggest that TFS pattern might favorably compare with that obtained in pts with Major-type BCR-ABL transcripts. However, relapses may be more aggressive and caution is required in order to avoid loss of hematologic responses and progression. Whether the type of atypical fusion gene influences TKI discontinuation outcome, as well as other potential prognostic factors, need to be determined in a larger series. [Display omitted] DisclosuresCharbonnier: Novartis: Speakers Bureau; Incyte: Speakers Bureau. Rea: Novartis: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Incyte: Honoraria, Membership on an entity's Board of Directors or advisory committees; Pfizer: Honoraria, Membership on an entity's Board of Directors or advisory committees. Etienne: Novartis: Consultancy, Speakers Bureau; Incyte: Consultancy, Speakers Bureau. Rousselot: Incyte, Pfizer: Consultancy, Research Funding. Nicolini: Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: travel, accommodations, expenses, Research Funding; Kartos Therapeutics: Consultancy, Membership on an entity's Board of Directors or advisory committees; Sun Pharma Ltd.: Consultancy, Membership on an entity's Board of Directors or advisory committees; Incyte Biosciences: Honoraria, Other: travel, accommodations, expenses, Research Funding, Speakers Bureau; BMS: Honoraria.

High sensitivity-low cost detection of SARS-CoV-2 by two steps end point RT-PCR with agarose gel electrophoresis visualization

More than one year since Coronavirus disease 2019 (COVID-19) pandemic outbreak, the gold standard technique for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection is still the RT-qPCR. This is a limitation to increase testing capacities, particularly at developing countries, as expensive reagents and equipment are required. We developed a two steps end point RT-PCR reaction with SARS-CoV-2 Nucleocapsid (N) gene and Ribonuclease P (RNase P) specific primers where viral amplicons were verified by agarose gel electrophoresis. We carried out a clinical performance and analytical sensitivity evaluation for this two-steps end point RT-PCR method with 242 nasopharyngeal samples using the CDC RT-qPCR protocol as a gold standard technique. With a specificity of 95.8%, a sensitivity of 95.1%, and a limit of detection of 20 viral RNA copies/uL, this two steps end point RT-PCR assay is an affordable and reliable method for SARS-CoV-2 detection. This protocol would allow to extend COVID-19 diagnosis to basic molecular biology laboratories with a potential positive impact in surveillance programs at developing countries.

Fabrication of graphene nanoplatelets embedded “partition cartridge” for efficient separation of target-bound ssDNA during SELEX

Graphene oxide (GO)-a carbon allotrope is widely used in aptamer generation process called SELEX (systematic evolution of ligands by exponential enrichment) and efficiently adsorbs non-target specific ssDNA onto its surface during the partitioning step of SELEX. The amount of GO required to adsorb ssDNA is high that imposes new challenges. Here, we have demonstrated graphene nanoplatelets (GrNP) that can be exploited with less material for efficient partitioning. Further, we have compared the non-target specific ssDNA adsorption on graphene oxide (GO), and graphene nanoplatelets (GrNP) and fabricated the “partitioning cartridge” for efficient separation of target (Monocrotophos and Endosulfan) bound-ssDNA from unbound ssDNA (non-target specific). To fabricate the partitioning cartridge, the spin column was utilized from common molecular biology lab waste. The fabricated “partition cartridge” alienated the target bound ssDNA efficiently and used further for polymerase chain reaction successfully. The fabricated partitioning cartridge is easy to fabricate, cost effective and recycles the plastic waste thus the environment friendly approach.

Beeporter: Tools for high-throughput analyses of pollinator-virus infections.

Pollinators are in decline thanks to the combined stresses of disease, pesticides, habitat loss, and climate. Honey bees face numerous pests and pathogens but arguably none are as devastating as Deformed wing virus (DWV). Understanding host-pathogen interactions and virulence of DWV in honey bees is slowed by the lack of cost-effective high-throughput screening methods for viral infection. Currently, analysis of virus infection in bees and their colonies is tedious, requiring a well-equipped molecular biology laboratory and the use of hazardous chemicals. Here we describe virus clones tagged with green fluorescent protein (GFP) or nanoluciferase (nLuc) that provide high-throughput detection and quantification of virus infections. GFP fluorescence is measured noninvasively in living bees via commonly available long-wave UV light sources and a smartphone camera, or a standard ultraviolet transilluminator gel imaging system. Nonlethal monitoring with GFP allows continuous screening of virus growth and serves as a direct breeding tool for identifying honey bee parents with increased antiviral resistance. Expression using the nLuc reporter strongly correlates with virus infection levels and is especially sensitive. Using multiple reporters, it is also possible to visualize competition, differential virulence, and host tissue targeting by co-occuring pathogens. Finally, it is possible to directly assess the risk of cross-species "spillover" from honey bees to other pollinators and vice versa.

Polymorphism of p53 Codon 72 Gene on Cervical Cancer Incidence in Malay Population

In Indonesia, the cases of cervical cancer are estimated at around 50 per 100.000 people. Itwas estimatedthattherearemore than 1 millionwomenworldwidewho have cervical cancer,and most of them have not been diagnosed yet or do not have access to screening and medicaltreatment. P53 codon 72 polymorphism can affect the risk of cervical cancer through theregulation of proliferationandcellapoptosis.The purpose of this research was to investigate theassociation between p53 codon 72 polymorphism and cases of cervical cancer. This researchwas observational analytic research. The research was done by examining in the laboratory ofMolecular Biology, Faculty of Medicine, Universitas Sriwijaya by using a case-control studyapproach.Thesampleoftheresearchconsistedof 70 subjects,and they were divided into twogroups:35 in case group and 35 in the control group. The determination of genotype andallotype was done by using PCR-RFLP technics. The results of the research showed there wasa significant difference between p53 codon 72 polymorphism between the case group andcontrol group. The results of genotypes of p53 codon 72 polymorphism in the case groupwere seven respondents (20.0%) with Pro/Pro genotype, five respondents (14.3%) withArg/Arg genotype, and 23 respondents (65.7%) with Pro/Arg. While in control group, there were28 respondents (80.0%) with Pro/Pro genotype, 0 respondent (0.0%) with Arg/Arg genotype,and 7 respondents (20%) with Pro/Arg. The frequency of the Prolin allele in case group was 37(52.9%), and the Arginin allele was 33 (47.1%), while the frequency of the Prolin allele in thecontrol group was 63 (90%), and the Arginin allele was 7 (10%). The Chi-Squareofgenotypewasvalued0.000,OR1,304andCI95%1,071-5,891,whiletheallelewas valued 0.000, OR 8.027 andCI 95% 3.228-19.962. There was anassociation between genotype and allele of p53 codon 72polymorphismandcases of cervicalcancer.

Construction of DNA ladder for determination of small size DNA fragments

DNA marker is commonly used to determine the size of DNA fragments by electrophoresis in routine molecular biology laboratories. In this study, we report a new procedure to prepare recombinant plasmids pSY-60 which was partially digested by one restriction enzyme for generating DNA markers of 7 fragments from 60 to 420 bp. The procedure included a synthesis of 60 bp DNA fragment with EcoRI sites at both ends using PCR extension, self-ligation of the 60 bp fragments and subcloning the ligated product into plasmid, generating recombinant pSY-60. Once being cloned, 500 ng of 420 bp fragment purified from 100 µL PCR product was incompletely digested by EcoRI, sufficiently producing to 50 acrylamide gels. Our procedure for production of DNA markers could be simple, time saving and inexpensive in comparison with current ones widely used in most laboratories.

Locating disease spread: cholera to coronavirus and the art of the image.

This article considers the history of medical image-making to shed light on an aspect of the COVID-19 pandemic. Starting from a contemporary art commission in the Science Museum's ‘Medicine: The Wellcome Galleries’, we look at the role of image production and presentation in understanding the spread of disease. From the intertwined histories of art and scientific image-making, we explore five examples of iconic medical images, by John Snow, Florence Nightingale, Arthur Schuster, Donald Caspar and Aaron Klug, ending with a model of the coronavirus by the Cambridge University Laboratory of Molecular Biology. We trace how images have provided the means for discovery, for description and for diagnosis and outline the different ways in which diseases have been located in the history of the medical image: in the community, in the body, in the cell and on the image itself.

Integrating active learning activities and metacognition into STEM writing courses.

Although active learning is highly recognized and recommended in the educational community, instructors are still struggling with how to incorporate active learning tools into writing courses. This study aims to 1) describe specific challenges encountered in the course of Molecular Cell Biology Laboratory-Critical Thinking through Writing (BIOL3810-CTW); 2) introduce the active learning approaches and metacognition integrated into this writing-intensive course; 3) demonstrate the effectiveness of these active learning approaches in engaging students in classes; and 4) share the principles of integrating active learning activities into writing courses in science, technology, engineering, and mathematics (STEM) and beyond.

Development of Transgenic Sugarcane Resistant to Stem Borer by Transforming cry1Ab-cry1Ac Fusion Gene through Agrobacterium tumefaciens Transformation Method

&lt;p&gt;Bulu Lawang (BL) is a sugarcane variety preferred by farmers in Indonesia due to its high yield, but this cultivar is susceptible to shoot and stem borer insect pests. Genetic engineering using cry1Ab and cry1Ac fusion gene is an effort to generate BL varieties resistant to the insect pests. This study aimed to 1) transform T-DNA containing cry1Ab-cry1Ac fusion gene into sugarcane genome by using Agrobacterium tumefaciens method, 2) obtain selection media composition of callus transformants, and 3) obtain transformation efficiency comparison of A. tumefaciens strains EHA105 and GV3101. The research was conducted at the Laboratory of Cell and Tissue Biology, the Laboratory of Molecular Biology, and the greenhouse of the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Bogor from March to August 2019. Research activities consisted of four parts namely 1) callus induction and Agrobacterium culture preparation containing pCambia5300-cry1Ab-cry1Ac ///// pCambia-5300_OaRbcS-prom-cTP-cry1Ab-cry1Ac plasmid, 2) callus incubation in cocultivation and resting media, 3) selection and differentiation of shoots on regeneration media, and 4) molecular analysis using PCR method. Results showed that the composition of media, both for selection and regeneration processes of putative plant transformants, was the key to the success of this experiment. A. tumefaciens strain EHA105 resulted in higher transformation efficiency (11.1%) compared to that of strain GV3101 (9.0%). Molecular analysis showed that cryIAb-cryIAc fusion gene was successfully inserted into the sugarcane genome suggesting that the transgenic plant containing cry1Ab-cry1Ac fusion gene was obtained. The putative transgenic plants need further assay through bioassay tests to verify its resistance phenotype to the insect pests.&lt;/p&gt;

UJI AKTIVITAS ANTIBAKTERI DAN ANTI-UV DARI EKSTRAK ETIL ASETAT ISOLAT JAMUR AFBK 5c YANG BERSIMBION DENGAN ASCIDIA Sigilina sp. DARI PERAIRAN PULAU BANGKA

Bioactive compounds are toxic compounds produced by organisms for use in self-defense from a wide variety of predators residing in their environment. The aim of the study was to test antibacterial activity and prove the UV-preventing effectiveness of the AFBK 5c mushroom isolate ethyl acetate extract that is in conjunction with ascidia. This research was conducted for 1 month in two locations, namely for antibacterial testing conducted in the Laboratory of Molecular Biology and Marine Pharmaceuticals, FPIK and for anti-UV testing conducted at the Pharmaceutical Laboratory, FMIPA, UNSRAT. The results showed that; This type of fungus that has been extracted and used is a fungus with the isolate code AFBK 5c This mushroom is a fungus that is connected with sigilina sp type ascidia. The rough extract of ascidia symbiont mushrooms is obtained from the process of meseration using ethyl acetate, then antibacterial testing of S. aureus and E. coli test bacteria and showing results such as antibacterial activity with an average value in S. aureus 09.00 and E. coli 11.05 mm which shows that there is antibacterial activity of AFBK 5c fungus isolate against E. coli and S. aureus test bacteria so that it can be said that the symbiont fungus has the potential as an ingredient. manufacture of antibacterial drugs. Furthermore, anti-UV testing, and the results of testing anti-UV compounds using rough extracts of AFBK 5c fungus isolates can produce absorption in UV-B (λ 290-320 nm) and UV-A (λ 320-400 nm) so that it has the potential to be used as an anti-UV material.Keywords: Bioactive Compound, Ascidia, Meceration, Antibacterial, Anti-UV

42P Method optimization for the detection of chimerism by real-time PCR and droplet digital PCR

The objective of the present study was to select combinations of primers for genetic polymorphisms (INDELS) used in the analysis of chimerism associated with post-transplant hematopoietic regeneration as well as to test them under real-time PCR (qPCR) and droplet digital PCR (ddPCR) conditions. We searched for genetic polymorphisms, using the EMBL - European Molecular Biology Laboratory - database taking into account certain criteria for selection. There were 85 polymorphisms left at the end of the selection process. For both techniques, we designed primers with the following characteristics: 65°C annealing temperature, amplicon length below 120 bp, at least 3 different nucleotides at the 3’ end between variants and temperature difference between forward and reverse primer of maximum 1°C. Depending on the distribution of genotypes, assays were designed for one or both alleles. Human blood samples from subjects without hematological diseases were obtained in accordance with the Helsinki declaration and genotyped. A novel genotyping protocol, based on 2 reference genes and one allele per polymorphism, was developed. Samples bearing different genotypes were serially diluted to simulate various chimerism levels. In general, for ddPCR increasing primer concentration determines the increase of the amplitude difference between the negative and the positive droplets without affecting the allele specificity. At the same time, the decrease of the annealing extension temperature determined the same phenomenon. Some of the assays showed no differences between 35 and 45 cycles. The new protocol allows the use of smaller sample volumes as compared to traditional genotyping, by reducing reaction number and template quantity. Simulated and obtained chimerism levels showed good correlation between 50% and 1.5% (R2=0.998), the limit of quantification corresponding to 50 molecules. The differences between positive and negative samples are more clearly determined in the case of ddPCR, which confirms that this method is more accurate than the qPCR method. In this context we believe that the ddPCR is a valuable technique for early detection in hematopoietic malignancies. Ioana M. Lambrescu and Victor S. Ionescu - equal contribution.

Assay Optimization Can Equalize the Sensitivity of Real-Time PCR with ddPCR for Detection of Helicoverpa armigera (Lepidoptera: Noctuidae) in Bulk Samples.

Simple SummaryInvasive species are a constant threat to agriculture throughout the world against which early detection is one of the primary defenses. The Old World bollworm is one of the most important invasive agricultural pests in the world. While historically absent from the Americas, this species was first found in South America in 2013 and poses an ongoing threat of spreading into North America. Surveys are conducted each year, which result in hundreds or thousands of traps that must be screened for this species. Unfortunately, the most common non-target is the native corn earworm, which is nearly identical morphologically to the Old World bollworm and cannot be easily separated. Molecular methods have been developed to screen these trap samples, but the required equipment is expensive and not commonly available. This study details improvements to current molecular methods that will allow for screening of bulk trap samples using standard laboratory instruments and protocols. The ability to perform these methods in nearly any molecular biology lab will greatly enhance our ability to detect and exclude this important pest.Helicoverpa armigera (Hübner) is one of the most important agricultural pests in the world. This historically Old World species was first reported in Brazil in 2013 and has since spread throughout much of South America and into the Caribbean. Throughout North America, H. armigera surveys are ongoing to detect any incursions. Each trap is capable of capturing hundreds of native Helicoverpa zea (Boddie). The two species cannot be separated without genitalic dissection or molecular methods. A ddPCR assay is currently used to screen large trap samples, but this equipment is relatively uncommon and expensive. Here, we optimized a newly designed assay for accurate and repeatable detection of H. armigera in bulk samples across both ddPCR and less costly, and more common, real-time PCR methods. Improvements over previously designed assays were sought through multiple means. Our results suggest bulk real-time PCR assays can be improved through changes in DNA extraction and purification, so that real-time PCR can be substituted for ddPCR in screening projects. While ddPCR remains a more sensitive method for detection of H. armigera in bulk samples, the improvements in assay design, DNA extraction, and purification presented here also enhance assay performance over previous protocols.

Connecting research and teaching introductory cell and molecular biology using an Arabidopsis mutant screen.

A complex research project was translated into a Course-based Undergraduate Research Experience (CURE), which was implemented in sections of an introductory Cell and Molecular Biology laboratory course. The research laboratory generated an engineered plant line producing a growth-inhibiting, lipid-derived plant hormone and mutagenized this line. Students in the CURE cultured the mutagenized plant population and selected and characterized suppressor mutants. They learned to observe phenotypes related to the biosynthesis and perception of the plant hormone and explored the genetic and biochemical basis of these phenotypes. As the students studied the relevant genetic, molecular and biochemical concepts during this CURE, they were able to translate this knowledge into practice and develop scientific arguments. This CURE was a successful collaboration between the teaching lab and the research lab. It benefited both parties as the students had a real-life, deep learning experience in scientific methodology, while the research lab gathered data and materials for further studies.

Natural Enemies Associated with Brevipalpus sp. (Acari: Tenuipalpidae), Vector of Citrus Leprosis

Natural Enemies Associated with <i>Brevipalpus</i> sp. (Acari: Tenuipalpidae), Vector of Citrus Leprosis

From Bench to Monitor – Turning Advanced Life Science Courses into Virtual

The European Molecular Biology Laboratory (EMBL) provides advanced training for life science researchers in state-of-the-art technologies and fosters scientific exchange. The heart of the face-to-face advanced course programme is a strong focus on expert led hands-on training combined with theoretical and application lectures, as well as networking opportunities. Due to the pandemic, the face-to-face life science wet-lab and computational courses were converted into virtual formats. The courses are participant centred and focus on real scientific challenges and problems on the given topic. The need for these advanced molecular biology training courses is reflected by the high numbers of applications. Here we describe one solution to the virtual transformation of EMBL´s course programme, including the first reactions of our international audience and the effect for the future of cutting-edge advanced training courses for lifelong learning in the life sciences.

Interview with 2021 Hooke medal winner Stephen Royle

ABSTRACT Stephen Royle studied Biological Sciences at the University of Sheffield. He then pursued a PhD in the lab of Ruth Murrell-Lagnado at the University of Cambridge, UK, where he investigated the molecular mechanisms of P2X receptor trafficking. In 2002, he joined Leon Lagnado's group at the MRC Laboratory of Molecular Biology in Cambridge for his postdoc to work on synaptic vesicle endocytosis in neurons, and here he also discovered a novel mitotic function of clathrin. Steve set up his lab at the University of Liverpool in 2006, and in 2013 moved to the Centre for Mechanochemical Cell Biology, Warwick Medical School as a Senior Cancer Research UK Fellow; there he has been a Professor since 2019. The Royle lab is interested in understanding molecular mechanisms of membrane trafficking and mitosis. Steve is also on the Board of Directors of The Company of Biologists and the Advisory Groups of Journal of Cell Science and preLights. He is the recipient of the 2021 Hooke medal, established to recognize an emerging leader in cell biology.

The First Wave of COVID-19 Pandemic: Sociodemographic Characteristics of Patients in A Tertiary Level Hospital of Bangladesh

Background: The COVID-19 has led to more than 120 million confirmed cases, with over 2.6 million deaths globally, as of March 2021. As the outbreak continues, several research activities regarding the first wave have been conducted to better understand the incidence and prevention methods. This record will play an important role to take more precautions for overcoming the second wave.&#x0D; Materials and methods: In this retrospective cohort study, we collected the age, sex, and the locality of the suspected and SARS-CoV-2 positive patients and tried to make a bridge among them. We conducted rRT-PCR in the Molecular Biology Laboratory of Chittagong Medical College, Chattogram in between May and August 2020. After that, we used a decision tree and time series evaluation to analyze the data.&#x0D; Results: The highest (50.35%) positive cases were detected in the 3rd and 4th week of May. Men were significantly infected (66.2%) more than women. The 31-40 year age group was mainly affected (24.4%), and 88% of the cases belonged to urban areas.&#x0D; Conclusions: The distribution of cases varied with time, and it will guide the physicians to give better support to humanity.&#x0D; JCMCTA 2021 ; 32 (1) : 65-71

The 2021 FASEB Virtual Science Research Conference on Protein Aggregation: Function, Dysfunction, and Disease, June 23-25, 2021.

The 2021 FASEB Virtual Science Research Conference on Protein Aggregation: Function, Dysfunction, and Disease, June 23-25, 2021.

Simultaneous ribosome profiling of hundreds of microbes from the human microbiome.

Ribosome profiling enables sequencing of ribosome-bound fragments of RNA, revealing which transcripts are being translated as well as the position of ribosomes along mRNAs. Although ribosome profiling has been applied to cultured bacterial isolates, its application to uncultured, mixed communities has been challenging. We present MetaRibo-Seq, a protocol that enables the application of ribosome profiling directly to the human fecal microbiome. MetaRibo-Seq is a benchmarked method that includes several modifications to existing ribosome profiling protocols, specifically addressing challenges involving fecal sample storage, purity and input requirements. We also provide a computational workflow to quality control and trim reads, de novo assemble a reference metagenome with metagenomic reads, align MetaRibo-Seq reads to the reference, and assess MetaRibo-Seq library quality ( https://github.com/bhattlab/bhattlab_workflows/tree/master/metariboseq ). This MetaRibo-Seq protocol enables researchers in standard molecular biology laboratories to study translation in the fecal microbiome in ~5 d.