Synthetic gene design - The rationale for codon optimization and implications for molecular pharming in plants.

Degeneracy in the genetic code allows multiple codon sequences to encode the same protein. Codon usage bias in genes is the term given to the preferred use of particular synonymous codons. Synonymous codon substitutions had been regarded as "silent" as the primary structure of the protein was not affected; however, it is now accepted that synonymous substitutions can have a significant effect on heterologous protein expression. Codon optimization, the process of altering codons within the gene sequence to improve recombinant protein expression, has become widely practised. Multiple inter-linked factors affecting protein expression need to be taken into consideration when optimizing a gene sequence. Over the years, various computer programmes have been developed to aid in the gene sequence optimization process. However, as the rulebook for altering codon usage to affect protein expression is still not completely understood, it is difficult to predict which strategy, if any, will design the 'optimal' gene sequence. In this review, codon usage bias and factors affecting codon selection will be discussed and the evidence for codon optimization impact will be reviewed for recombinant protein expression using plants as a case study. These developments will be relevant to all recombinant expression systems, however, molecular pharming in plants is an area which has consistently encountered difficulties with low levels of recombinant protein expression, and should benefit from an evidence based rational approach to synthetic gene design

Mesoporous Magnesium Oxide Adsorbent Prepared via Lime (Citrus aurantifolia) Peel Bio-templating for CO2 Capture

The utilization of the lime (Citrus aurantifolia) peel as a template can improve the adsorbent’s structural properties, which consequently affect its CO2 uptake capacity. Herein, a mesoporous magnesium oxide (MgO-lime (Citrus aurantifolia) peel template (LPT)) adsorbent was synthesized using an LPT. MgO-LPT demonstrated improved structural properties and excellent CO2 uptake capacity. Moreover, another MgO adsorbent was prepared via thermal decomposition (MgO-TD) for comparison. The prepared adsorbents were characterized by N2 physisorption, Fourier transform infrared spectroscopy and thermogravimetric analysis. The CO2 uptake of these adsorbents was under 100% CO2 gas and ambient temperature and pressure conditions. MgO-LPT exhibited a higher Brunauer–Emmett–Teller surface area, Barrett–Joyner–Halenda pore volume, and pore diameter of 23 m2.g−1, 0.142 cm3.g−1, and 24.6 nm, respectively, than those of MgO-TD, which indicated the mesoporous structure of MgO-LPT. The CO2 uptake capacity of MgO-LPT is 3.79 mmol CO2.g−1, which is 15 times that of MgO-TD. This study shows that the application of lime peel as a template for the synthesis of MgO adsorbents is a promising approach to achieve MgO adsorbents with enhanced surface area and thus increased CO2 capture performance. Copyright © 2021 by Authors, Published by BCREC Group. This is an open access article under the CC BY-SA License (https://creativecommons.org/licenses/by-sa/4.0).

2′,3,4,4′-Tetra­meth­oxy­chalcone

In the title compound [systematic name: 1-(2,4-dimethoxyphenyl)-3-(3,4-dimethoxyphenyl)prop-2-en-1-one], C19H20O5, the dihedral angle between the benzene rings is 26.88 (5)°. One of the meth­oxy groups is twisted slightly away from the plane [C—O—C—C torsion angle = −12.8 (3)°] while the others are almost co-planer [C—O—C—C torsion angles = −3.2 (3), 2.6 (3) and −3.6 (3)°]. The crystal packing is stabilized by inter­molecular C—H⋯O inter­actions. A weak intra­molecular C—H⋯O inter­action occurs

Patterns of RAPD markers and heavy metal concentrations in Perna viridis (L.), collected from metal-contaminated and uncontaminated coastal waters: Are they correlated with each other?

Genetic variation due to heavy metal contamination has always been an interesting topic of study. Because of the numerous contaminants being found in coastal and intertidal waters, there is always much discussion and argument as to which contaminant(s) caused the variations in the genetic structures of biomonitors. This study used a Single Primer Amplification Reaction (SPAR) technique, namely Random Amplified Polymorphic DNA (RAPD), to determine the genetic diversity of the populations of the green-lipped mussel Perna viridis collected from a metal-contaminated site at Kg. Pasir Puteh and those from four relatively uncontaminated sites (reference sites). Heavy metal levels (Cd, Cu, Pb, and Zn) were also measured in the soft tissues and byssus of the mussels from all the sites. Cluster analyses employing UPGMA based on the RAPD markers grouped the populations into two major clusters; the Bagan Tiang, Pantai Lido, Pontian, and Kg. Pasir Puteh populations were in one cluster, while the Sg. Belungkor population clustered by itself. This indicated that the genetic diversity based on bands resulting from the use of all four RAPD primers on P. viridis did not indicate its potential use as a biomarker of heavy metal pollution in coastal waters. However, based on a correlation analysis between a particular metal and a band resulting from a specific RAPD primer revealed some significant (P < 0.01) correlations between the primers and the heavy metal concentrations in the byssus and soft tissues. Thus, the correlation between a particular metal and the bands resulting from the use of a specific RAPD primer on P. viridis could be used as biomonitoring tool of heavy metal pollution

The discovery of Silk Route: Cultural and technology communication between China, Korea and Japan

One of the earliest civilizations took place in Asia, particularly the East Asian region. As a main result of war, historical travel, such as trading and pilgrimage, influenced the daily life of most people in the region. The Han Dynasty was traced back as the most significant period that triggered travelling activities during the discovery of the Silk Road. Since then, travelling facilities were developed, which consequently led to the increased inter-region movement of people and merchants. This study explores the historical development of travels in Eastern Asia, with a particular focus on the expansion of the Silk Road throughout several dynastic periods of China, as well as its influence on peninsular Korea and Japan. This study concludes that the Silk Road is an important channel for the exchange of tangible and intangible elements between China, Japan, and peninsular Korea as a sinicization process, particularly in the exchange of food, papermaking, and printing technology. An increased understanding of Asia’s travel history helps to assess the travelling patterns in the region by revisiting the influence of tourists’ socio-demographic factors to include the cultural background with historical element

The risk of miscarriage following COVID-19 vaccination: a systematic review and meta-analysis

STUDY QUESTION: What is the risk of miscarriage among pregnant women who received any of the COVID-19 vaccines? SUMMARY ANSWER: There is no evidence that COVID-19 vaccines are associated with an increased risk of miscarriage. WHAT IS KNOWN ALREADY: In response to the COVID-19 pandemic, the mass roll-out of vaccines helped to boost herd immunity and reduced hospital admissions, morbidity and mortality. Still, many were concerned about the safety of vaccinesfor pregnancy, which may have limited their uptake among pregnant women and those planning a pregnancy. STUDY DESIGN, SIZE, DURATION: For this systematic review and meta-analysis, we searched MEDLINE, EMBASE and Cochrane CENTRAL from inception until June 2022 using a combination of keywords and MeSH terms. PARTICIPANTS/MATERIALS, SETTING, METHODS: We included observational and interventional studies that enrolled pregnant women and evaluated any of the available COVID-19 vaccines compared to placebo or no vaccination. We primarily reported on miscarriage in addition to ongoing pregnancy and/or live birth. MAIN RESULTS AND THE ROLE OF CHANCE: We included data from 21 studies (5 randomised trials and 16 observational studies) reporting on 149,685 women. The pooled rate of miscarriage among women who received a COVID-19 vaccine was 9% (n = 147,49/123,185, 95%CI 0.05-0.14). Compared to those who received a placebo or no vaccination, women who received a COVID-19 vaccine did not have a higher risk of miscarriage (RR 1.07, 95%CI 0.89-1.28, I2 35.8%) and had comparable rates for ongoing pregnancy or live birth (RR 1.00, 95%CI 0.97-1.03, I2 10.72%). LIMITATIONS, REASONS FOR CAUTION: Our analysis was limited to observational evidence with varied reporting, high heterogeneity and risk of bias across included studies, which may limit the generalisability and confidence in our findings. WIDER IMPLICATIONS OF THE FINDINGS: COVID-19 vaccines are not associated with an increase in the risk of miscarriage or reduced rates of ongoing pregnancy or live birth among women of reproductive age. The current evidence remains limited and larger population studies are needed to further evaluate the effectiveness and safety of COVID-19 in pregnancy. STUDY FUNDING/COMPETING INTEREST: No direct funding was provided to support this work. MPR is funded by the Medical Research Council Centre for Reproductive Heath Grant No: MR/N022556/1. BHA hold a personal development award from the National Institute of Health Research in the UK. All authors declare no conflict of interest. REGISTRATION NUMBER: CRD42021289098

Decay and coherence of two-photon excited yellow ortho-excitons in Cu2O

Photoluminescence excitation spectroscopy has revealed a novel, highly efficient two-photon excitation method to produce a cold, uniformly distributed high density excitonic gas in bulk cuprous oxide. A study of the time evolution of the density, temperature and chemical potential of the exciton gas shows that the so called quantum saturation effect that prevents Bose-Einstein condensation of the ortho-exciton gas originates from an unfavorable ratio between the cooling and recombination rates. Oscillations observed in the temporal decay of the ortho-excitonic luminescence intensity are discussed in terms of polaritonic beating. We present the semiclassical description of polaritonic oscillations in linear and non-linear optical processes.Comment: 14 pages, 12 figure

High-level expression of the HIV entry inhibitor griffithsin from the plastid genome and retention of biological activity in dried tobacco leaves

The global HIV epidemic continues to grow, with 1.8 million new infections occurring per year. In the absence of a cure and an AIDS vaccine, there is a pressing need to prevent new infections in order to curb the disease. Topical microbicides that block viral entry into human cells can potentially prevent HIV infection. The antiviral lectin griffithsin has been identified as a highly potent inhibitor of HIV entry into human cells. Here we have explored the possibility to use transplastomic plants as an inexpensive production platform for griffithsin. We show that griffithsin accumulates in stably transformed tobacco chloroplasts to up to 5% of the total soluble protein of the plant. Griffithsin can be easily purified from leaf material and shows similarly high virus neutralization activity as griffithsin protein recombinantly expressed in bacteria. We also show that dried tobacco provides a storable source material for griffithsin purification, thus enabling quick scale-up of production on demand

Parallel computing of numerical schemes and big data analytic for solving real life applications

This paper proposed the several real life applications for big data analytic using parallel computing software. Some parallel computing software under consideration are Parallel Virtual Machine, MATLAB Distributed Computing Server and Compute Unified Device Architecture to simulate the big data problems. The parallel computing is able to overcome the poor performance at the runtime, speedup and efficiency of programming in sequential computing. The mathematical models for the big data analytic are based on partial differential equations and obtained the large sparse matrices from discretization and development of the linear equation system. Iterative numerical schemes are used to solve the problems. Thus, the process of computational problems are summarized in parallel algorithm. Therefore, the parallel algorithm development is based on domain decomposition of problems and the architecture of difference parallel computing software. The parallel performance evaluations for distributed and shared memory architecture are investigated in terms of speedup, efficiency, effectiveness and temporal performance

Overcoming data scarcity of Twitter: using tweets as bootstrap with application to autism-related topic content analysis

Notwithstanding recent work which has demonstrated the potential of using Twitter messages for content-specific data mining and analysis, the depth of such analysis is inherently limited by the scarcity of data imposed by the 140 character tweet limit. In this paper we describe a novel approach for targeted knowledge exploration which uses tweet content analysis as a preliminary step. This step is used to bootstrap more sophisticated data collection from directly related but much richer content sources. In particular we demonstrate that valuable information can be collected by following URLs included in tweets. We automatically extract content from the corresponding web pages and treating each web page as a document linked to the original tweet show how a temporal topic model based on a hierarchical Dirichlet process can be used to track the evolution of a complex topic structure of a Twitter community. Using autism-related tweets we demonstrate that our method is capable of capturing a much more meaningful picture of information exchange than user-chosen hashtags.Comment: IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, 201