Wind environment evaluation on major town of Malaysia

This study focus on wind flow or wind environment of residential areas in Peninsular Malaysia, Sabah and Sarawak. Natural wind flow is one of the most effective methods to help achieve the energy saving in large cities especially under the tropical climate like Malaysia. The weather in Malaysia is characterized by four monsoon regimes, namely, the southwest monsoon, northeast monsoon and two shorter periods of inter-monsoon seasons. For this study, the data of wind velocity in twentytwo (22) weather station in Malaysia obtained from Meteorological Department and considered in wind environment evaluations. Then that data of wind velocities will convert to 1.5 in height at all measuring points were calculated by using the law. The result compared by Table 2.2 in previous researches (Kubota and Miura et al., 2002). From the study, it was found out, in Malaysia there are only two type of wind. First type is weak wind means that area are discomfort thermal and the second type is comfort range to strong wind means that area are comfort thermal. The minimum value of mean wind speed from 2005 to 2009 is O.mis in mean temperature is over 2C at Sitiawan. For the maximum value of mean wind speed is I .7m/s in average value of mean temperature is 276C at Mersing. Base on results, it can be concluded that when considering wind flow at a residential area, terrace housing is not a suitable option for towns located on the south of the Peninsular. It was prefer for high-rise building because it was considered this location of towns was weak wind condition. On the other hand, the major towns exclude the south of the Peninsular including Sabah and Sarawak, they was under the comfort thermal. So, terrace housing or high-rise building is suitable option

A RT-qPCR system using a degenerate probe for specific identification and differentiation of SARS-CoV-2 Omicron (B.1.1.529) variants of concern

Fast surveillance strategies are needed to control the spread of new emerging SARS-CoV-2 variants and gain time for evaluation of their pathogenic potential. This was essential for the Omicron variant (B.1.1.529) that replaced the Delta variant (B.1.617.2) and is currently the dominant SARS-CoV-2 variant circulating worldwide. RT-qPCR strategies complement whole genome sequencing, especially in resource lean countries, but mutations in the targeting primer and probe sequences of new emerging variants can lead to a failure of the existing RT-qPCRs. Here, we introduced an RT-qPCR platform for detecting the Delta- and the Omicron variant simultaneously using a degenerate probe targeting the key ΔH69/V70 mutation in the spike protein. By inclusion of the L452R mutation into the RT-qPCR platform, we could detect not only the Delta and the Omicron variants, but also the Omicron sub-lineages BA.1, BA.2 and BA.4/BA.5. The RT-qPCR platform was validated in small- and large-scale. It can easily be incorporated for continued monitoring of Omicron sub-lineages, and offers a fast adaption strategy of existing RT-qPCRs to detect new emerging SARS-CoV-2 variants using degenerate probes.</p

Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters

Members of the candidate phylum Hyd24-12 are globally distributed, but no genomic information or knowledge about their morphology, physiology or ecology is available. In this study, members of the Hyd24-12 lineage were shown to be present and abundant in full-scale mesophilic anaerobic digesters at Danish wastewater treatment facilities. In some samples, a member of the Hyd24-12 lineage was one of the most abundant genus-level bacterial taxa, accounting for up to 8% of the bacterial biomass. Three closely related and near-complete genomes were retrieved using metagenome sequencing of full-scale anaerobic digesters. Genome annotation and metabolic reconstruction showed that they are Gram-negative bacteria likely involved in acidogenesis, producing acetate and hydrogen from fermentation of sugars, and may play a role in the cycling of sulphur in the digesters. Fluorescence in situ hybridization revealed single rod-shaped cells dispersed within the flocs. The genomic information forms a foundation for a more detailed understanding of their role in anaerobic digestion and provides the first insight into a hitherto undescribed branch in the tree of life

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2

Rocco: an example metagenome dataset for the mmgenome R package

<p>Rocco: an example metagenome dataset for the mmgenome R package</p

Thousands of primer-free, high-quality, full-length SSU rRNA sequences from all domains of life

AbstractRibosomal RNA (rRNA) genes are the consensus marker for determination of microbial diversity on the planet, invaluable in studies of evolution and, for the past decade, high-throughput sequencing of variable regions of ribosomal RNA genes has become the backbone of most microbial ecology studies. However, the underlying reference databases of full-length rRNA gene sequences are underpopulated, ecosystem skewed1, and subject to primer bias2, which hamper our ability to study the true diversity of ecosystems. Here we present an approach that combines reverse transcription of full-length small subunit (SSU) rRNA genes and synthetic long read sequencing by molecular tagging, to generate primer-free, full-length SSU rRNA gene sequences from all domains of life, with a median raw error rate of 0.17%. We generated thousands of full-length SSU rRNA sequences from five well-studied ecosystems (soil, human gut, fresh water, anaerobic digestion, and activated sludge) and obtained sequences covering all domains of life and the majority of all described phyla. Interestingly, 30% of all bacterial operational taxonomic units were novel, compared to the SILVA database (less than 97% similarity). For the Eukaryotes, the novelty was even larger with 63% of all OTUs representing novel taxa. In addition, 15% of the 18S rRNA OTUs were highly novel sequences with less than 80% similarity to the databases. The generation of primer-free full-length SSU rRNA sequences enabled eco-system specific estimation of primer-bias and, especially for eukaryotes, showed a dramatic discrepancy between the in-silico evaluation and primer-free data generated in this study. The large amount of novel sequences obtained here reaffirms that there is still vast, untapped microbial diversity lacking representatives in the SSU rRNA databases and that there might be more than millions after all1, 3. With our new approach, it is possible to readily expand the rRNA databases by orders of magnitude within a short timeframe. This will, for the first time, enable a broad census of the tree of life.</jats:p

The effect of PCR settings on observed microbial community.

<p>(A) Principal component analysis of all PCR settings tested. (B) Differential abundance analysis of OTUs as an effect of different annealing temperatures. (C) The 10 most significantly differential abundant OTUs as a result of a change in annealing temperature.</p

The effect of bead beating on the observed microbial community composition.

<p>(A) Percentage read abundance of the 11 most abundant phyla as function of bead beating intensity (Proteobacteria are show at class level). The data is visualized as a table with the underlying colors visualizing the changes. (B) Principal component analysis of the samples extracted with different bead beating intensities compared to the samples taken at different dates, but extracted with the same bead beating settings (160 s at 6 m/s).</p