MAVRICS: A Robust and Safe Magnetic Nanoparticle based RNA Extraction Method Compatible with Phenol-chloroform Inactivated Infectious Samples v2

Diagnosis and surveillance of emerging pathogens such as SARS-CoV-2 depend on nucleic acid isolation from clinical and environmental samples. Under normal circumstances, samples would be processed using commercial proprietary reagents in Biosafety 2 (BSL-2) or higher facilities. A pandemic at the scale of COVID-19 has caused a global shortage of proprietary reagents and BSL-2 laboratories to safely perform testing. Therefore, alternative solutions are urgently needed to address these challenges. We developed an open-source method called Magneticnanoparticle-Aided Viral RNA Isolation of Contagious Samples (MAVRICS) that is built upon reagents that are either readily available or can be synthesized in any molecular biology laboratory with basic equipment. Unlike conventional methods, MAVRICS works directly in samples inactivated in acid guanidinium thiocyanate-phenol-chloroform (e.g., TRIzol), thus allowing infectious samples to be handled safely without biocontainment facilities.

Physics for biological breakthroughs

It might not sound like an obvious place for a physicist to work, but the European Molecular Biology Laboratory (EMBL) is highly multidisciplinary, employing people from across all scientific fields. Laura Hiscott speaks to Wolfgang Huber, a physicist at EMBL who uses his mathematical skills to contribute to the life sciences.

TEACHING AND LEARNING OF BIOLOGY PRACTICAL COURSES FOR FOUNDATION SCIENCE STUDENTS DURING COVID-19 PANDEMIC

This article aims to communicate several teaching and learning activities that were redesigned for biology practical courses for Universiti Malaysia Sabah’s Foundation Science students during the restriction control movement (RMO) due to the Covid-19 outbreak. When RMO has been started the closure of the university campus resulted in postponed of biology practical face-to-face sessions in the laboratory. The teaching and learning activities have been guided by the Foundation Science Biology Laboratory Manual, however, during the pandemic, the delivery approach was modified using online platforms, including video-based blog or vlog, pre-recorded video, using real-time video conferencing i.e. Google Meet, Webex, scheduled online discussions via mobile apps i.e Whatsapp, Telegram, and greater utilization of Universiti Malaysia Sabah online learning platform, SmartV3UMS. The purpose of these redesigned methodologies that are presented in this paper was mainly focusing on delivering the established practical courses’ contents to achieve the intended learning outcomes. A total of 353 students registered for these practical courses. They were divided into 16 groups, with 22 or 23 students per group. All these interventions have facilitated students to sustain their access to Foundation in Science study despite the physical engagement limitation and have opened a pathway to a new normal of science education.

KEANEKARAGAMAN MIKROALGA DI BENDUNGAN BARATA DESA E.WONOKWERTO KABUPATEN MUSI RAWAS

<pre><span class="y2iqfc"><em><span lang="IN">This study aims to determine the diversity of microalgae in the Barata Dam area, E. Wonokerto Village, Musi Rawas Regency. This research is included in quantitative descriptive research, this study uses a survey method by taking samples of microalgae in the Barata Dam Area, E. Wonokerto Village, Musi Rawas Regency, then the sample is examined at the Biology Laboratory of STKIP-PGRI Lubuklinggau. Types of microalgae found in the Barata Dam, E. Wonokerto Village, Musi Rawas Regency, 3 Divisions, 5 Classes, 14 Orders, 15 families, 15 genera and 15 species. The data that has been obtained from the research is then analyzed using the formula (Shannon-winer). The results of the diversity index of microalgae species at station I are 2,479, at station II the diversity index is 2,550 and at station III the diversity index is 2,836, the average diversity index from the three stations is 2,622 the index is classified as moderate. The types of microalgae from the Bacillariophytaceae class consist of 6 species including: Synedra ulna, Cylotella sp., Asterionella sp., Surirella sp., Tablelaria sp., and Rhizosolenia sp., Chlorophyceae class consists of 6 species including: Pleurotaenium sp. , Spirogyra sp., Closteridium sp., Selenastrum sp., Pediastrum duplex, and Microspora sp., Trebouxiophyceae class consists of 1 species namely: Chlorella sp., Ulvophyceae class consists of 1 species namely: Ulothrix sp., and Chyanophyta class consists of of only 1 species, namely: Oscillatoria sp., Abiotic factors found in the Barata Dam Area, E. Wonokerto Village, Musi Rawas Regency, namely: temperature (water) with an average (27.6 C), pH (water) with an average (7.7 ) and brightness (water ) with an average (76.1 Cm).</span></em></span><em></em></pre>

Keanekaragaman Jenis dan Kepadatan Zooplankton di Perairan Pulau Makassar Kota Baubau

The purpose of the study was to determine the type and amount of zooplankton in the waters of Makassar Island, Baubau City. From the results of this study, it is expected that significant information regarding the types and zooplankton found in the sea around Makassar Island, Baubau City, whose waters are suitable for aquaculture. Furthermore, it is hoped that the results of this study can help improve and optimize the use of aquatic biological resources in the future. This research was conducted in the waters of Makassar Island, Baubau City, from August to October 2021. Sample identification was carried out at the Biology Laboratory of the Muhammadiyah University of Buton. The tool in this research field is plankton net no. 25 to filter zooplankton, GPS determines the sampling location, thermometer measures temperature, handrefactometer measures salinity, DO (Dissolved Oxygen) meter measures sea air oxygen, plastic bottles store seawater samples, small plastic bottles store zooplankton samples, and cool boxes for storing samples. Materials in the field are label paper and markers to label the sample, 70% alcohol to preserve the sample, and aqua water to sterilize the instrument. 1) From the three highest locations found 18 genera of zooplankton belonging to the Crustacea group. 2) With 33 ind/l, the genus OIthona dominates the waters of Makasar Island, Baubau City. 3) In the three locations, there was no variation in zooplankton density.

Investigation of blaKPC and blaNDM genes in enterobacteriaceae received in a public health laboratory

Introduction: KPC and NDM carbapenemases production is an important enzymatic mechanism of resistance to carbapenens in bacteria belonging to the Enterobacteriaceae family. These enzymes degrade virtually all beta-lactam antibiotics and are encoded by the blaKPC and blaNDM genes, which can be in mobile genetic elements such as plasmids and transposons. Objectives: This study evaluated the positivity rate of the presence of blaKPC and blaNDM genes in carbapenem-resistant enterobacteria received at the Instituto Adolfo Lutz (IAL) of São José do Rio Preto, Brazil and determined the epidemiological data related to the patients whose isolates were recovered. Methods: From June 2015 to April 2019, bacterial isolates were obtained from different hospitals located in five municipalities in São José do Rio Preto region. In the bacteriology and molecular biology laboratory, DNA extraction and real-time PCR were performed to investigate the blaKPC and blaNDM genes. Afterwards, epidemiological data were surveyed such as the municipality of origin, age, and gender of the patients whose bacterial isolates were recovered. Results: A total of 934 enterobacteria isolates were recovered from the different hospitals. Of these; 93.4% were positive for blaKPC, with 96.3%, 1.85%, and 1.85% of the isolates belonged to the Klebsiella genus, Enterobacter genus, and Escherichia coli species, respectively. Also, 52.5% and 84.4% of the isolates were obtained from women and elderly patients, respectively. The blaNDM gene was detected only in three isolates, two of which originated from surveillance cultures. Conclusion: Therefore, KPC-producing enterobacteria are widespread in all health units of the five municipalities that were studied, suggesting that the blaKPC-carrying Klebsiella sp. isolates may be endemic in these institutions. Additionally, there is a significant role of surveillance cultures in preventing the spread of resistance genes, as observed for blaNDM in this study.

Mesowestern Blot: Simultaneous Analysis of Hundreds of Sub-Microliter Lysates

Western blotting is a widely-used technique for molecular-weight-resolved analysis of proteins and their post-translational modifications, but has been refractory to affordable scale-up. Here, we report the Mesowestern blot, which uses a 3D-printable gel-casting mold to enable affordable, high-throughput Western blotting with standard sample preparation and small (<1 uL) sample sizes. The casted polyacrylamide gel contains 336, 0.5 uL micropipette-loadable sample wells arranged within a standard microplate footprint. Polyacrylamide % can be altered to change molecular weight resolution range. Proof-of-concept experiments using both infrared-fluorescent molecular weight protein ladder as well as cell lysate (RIPA buffer) demonstrate protein loaded in Mesowestern gels is amenable to the standard Western blotting steps. The main difference between Mesowestern and traditional Western is that semi-dry horizontal instead of immersed vertical gel electrophoresis is used. The linear range of detection is approximately 2 orders of magnitude, with a limit of detection (for beta-actin) of around 30 ng of total protein from mammalian cell lysates (~30-3000 cells). Because the gel mold is 3D-printable, users have significant design freedom for custom layouts, and there are few barriers to adoption by the typical cell and molecular biology laboratory already performing Western blots.

Nitrogen-fixation and phosphate-solubilization bacteria isolated from alluvial and latosol soil paddy field

Ikhwani, Saribanon N, Setia TM, Yuniarti E, Jumakir. 2021. Nitrogen-fixation and phosphate-solubilization bacteria isolated from alluvial and latosol soil paddy field. Biodiversitas 22: 4722-4730. This study aims to isolate, select and identify molecular characterization of bacteria from alluvial and latosol soil paddy field. This study has been conducted from February-June 2020 in the Soil Biology Laboratory, ICALRRD, Bogor. Alluvial and latosol soil samples were selected from Pusakanagara and Muara experimental gardens, Muara district. The result showed that bacteria growth in N-free media was higher from latosol soil as compared to alluvial soil. The higher nitrogenase activity isolates, could form ethylene gas concentration 1.1.E + 09 µmol/mL/hours, 1.7.E + 09 µmol/mL/hours and 1.3.E + 09 µmol/mL/hours from alluvial 6, latosol 4, and latosol 9. Three isolates have great PSB performances, i.e. isolates No. 4.2, 2.1 and 2 could dissolve 14.398 mg l-1, 12.648 mg l-1 and 12.145 mg l-1 of phosphate, from latosol soil. The highest N-fixing and solubilization capacity identified by molecular characterization i.e latosol 4, 4.2 and alluvial 7.1, alluvial-1.11. The phylogeny analyzed the presence of bacterial isolates in two distinct groups. Latosol 3.1 and latosol 4.2 isolates clustered in the same as the genus Lysinibacillus bacteria. The Alluvial 7.1 bacterial isolate showed similarities by Fictibacillus sp. and alluvial 1.2 isolate showed similarities by the genus Bacillus sp.

Integrating active learning activities and metacognition into STEM writing courses

While 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. In this article, we have 1) described specific challenges that we have encountered in the course of Molecular Cell Biology Laboratory-Critical Thinking through Writing (BIOL3810-CTW); 2) introduced the active learning approaches and metacognition integrated into this writing-intensive course; 3) demonstrated the effectiveness of these active learning approaches, and 4) shared the principles of integrating active learning activities into writing courses in science, technology, engineering, and mathematics (STEM) and beyond.