Plant Artificial Chromosomes: Construction and Transformation.

With the decline of cultivated land and increase of the population in recent years, an agricultural revolution is urgently needed to produce more food to improve the living standards of humans. As one of the foundations of synthetic biology, artificial chromosomes hold great potential for advancing crop improvement. They offer opportunities to increase crop yield and quality, while enhancing crop resistance to disease. The progress made in plant artificial chromosome technology enables selective modification of existing chromosomes or the synthesis of new ones to improve crops and study gene function. However, current artificial chromosome technologies still face limitations, particularly in the synthesis of repeat sequences and the transformation of large DNA fragments. In this review, we will introduce the structure of plant centromeres, the construction of plant artificial chromosomes, and possible methods for transforming large fragments into plant cells.

A Rapid Label-Free Disposable Electrochemical Salivary Point-of-Care Sensor for SARS-CoV-2 Detection and Quantification.

The coronavirus disease 2019 (COVID-19) pandemic has created an urgent need for accurate early diagnosis and monitoring. A label-free rapid electrochemical point-of-care (POC) biosensor for SARS-CoV-2 detection in human saliva is reported here to help address the shortcomings of traditional nucleic acid amplification methods and give a quantitative assessment of the viral load to track infection status anywhere, using disposable electrochemical sensor chips. A new chemical construct of gold nanoparticles (GNp) and thionine (Th) are immobilized on carboxylic acid functionalized carbon nanotubes (SWCNT-COOH) for high-performance biosensing. The sensor uses saliva with a one-step pretreatment and simple testing procedure as an analytical medium due to the user-friendly and non-invasive nature of its procurement from patients. The sensor has a response time of 5 min with a limit of detection (LOD) reaching 200 and 500 pM for the freely suspended spike (S) protein in phosphate buffer saline (PBS) and human saliva, respectively. The sensor's performance was also proven for detecting a COVID-19 pseudovirus in an electrolyte solution with a LOD of 106 copies/mL. The results demonstrate that the optimized POC sensor developed in this work is a promising device for the label-free electrochemical biosensing detection of SARS-CoV-2 and different species of viruses.

An On-Chip Disposable Salivary Glucose Sensor for Diabetes Control.

BACKGROUND: Self-management of blood glucose (BG) is considered a norm for diabetes control. However, this invasive process is uncomfortable for patients, especially when intensive measurements with frequent finger pricks are required. Saliva, an alternative body fluid that is easily accessible and contains trace amount of glucose can be potentially used for the noninvasive monitoring of diabetes. METHODS: As a solution for real-time glucose measurements using saliva for diabetic care, we have developed an on-chip disposable glucose nano-biosensor through a layer-by-layer assembly process. In this work, a clinical study of 10 healthy subjects was conducted to determine the potential usefulness of salivary glucose (SG) sensors for glycemic control. RESULTS: Findings revealed (1) the individual BG/SG ratio at fasting was consistent over an entire year when there was no significant change of personal health; (2) the individual SG levels tracked closely with BG levels after meals; (3) a time difference of 15-30 minutes exists between peak levels of BG and SG; (4) 2 hours after a meal, the BG/SG ratio returned to a similar value at fasting. CONCLUSIONS: We propose to measure fasting and pre- and 2-hour postprandial SG levels for self-management of glycemic levels. As a result, this article is not intended to replace the common BG tests. With preliminary results, we believe SG itself could be used as means for reliable diabetes monitoring and a potential fluid for prognosis of future disease.

Sensing of Salivary Glucose Using Nano-Structured Biosensors.

The anxiety and pain associated with frequent finger pricking has always been troublesome for diabetics measuring blood glucose (BG) in their daily lives. For this reason, a reliable glucose monitoring system that allows noninvasive measurements is highly desirable. Our main objective is to develop a biosensor that can detect low-level glucose in saliva (physiological range 0.5-20 mg/dL). Salivary glucose (SG) sensors were built using a layer-by-layer self-assembly of single-walled carbon nanotubes, chitosan, gold nanoparticles, and glucose oxidase onto a screen-printed platinum electrode. An electrochemical method was utilized for the quantitative detection of glucose in both buffer solution and saliva samples. A standard spectrophotometric technique was used as a reference method to validate the glucose content of each sample. The disposable glucose sensors have a detection limit of 0.41 mg/dL, a sensitivity of 0.24 µA·s·dL·mg(-1), a linear range of 0.5-20 mg/dL in buffer solution, and a response time of 30 s. A study of 10 healthy subjects was conducted, and SG levels between 1.1 to 10.1 mg/dL were successfully detected. The results revealed that the noninvasive SG monitoring could be an alternative for diabetes self-management at home. This paper is not intended to replace regular BG tests, but to study SG itself as an indicator for the quality of diabetes care. It can potentially help patients control and monitor their health conditions, enabling them to comply with prescribed treatments for diabetes.

Ranking of Molecular Biomarker Interaction with Targeted DNA Nucleobases via Full Atomistic Molecular Dynamics.

DNA-based sensors can detect disease biomarkers, including acetone and ethanol for diabetes and H2S for cardiovascular diseases. Before experimenting on thousands of potential DNA segments, we conduct full atomistic steered molecular dynamics (SMD) simulations to screen the interactions between different DNA sequences with targeted molecules to rank the nucleobase sensing performance. We study and rank the strength of interaction between four single DNA nucleotides (Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)) on single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) with acetone, ethanol, H2S and HCl. By sampling forward and reverse interaction paths, we compute the free-energy profiles of eight systems for the four targeted molecules. We find that dsDNA react differently than ssDNA to the targeted molecules, requiring more energy to move the molecule close to DNA as indicated by the potential of mean force (PMF). Comparing the PMF values of different systems, we obtain a relative ranking of DNA base for the detection of each molecule. Via the same procedure, we could generate a library of DNA sequences for the detection of a wide range of chemicals. A DNA sensor array built with selected sequences differentiating many disease biomarkers can be used in disease diagnosis and monitoring.

Materiomics for Oral Disease Diagnostics and Personal Health Monitoring: Designer Biomaterials for the Next Generation Biomarkers.

We live in exciting times for a new generation of biomarkers being enabled by advances in the design and use of biomaterials for medical and clinical applications, from nano- to macro-materials, and protein to tissue. Key challenges arise, however, due to both scientific complexity and compatibility of the interface of biology and engineered materials. The linking of mechanisms across scales by using a materials science approach to provide structure-process-property relations characterizes the emerging field of 'materiomics,' which offers enormous promise to provide the hitherto missing tools for biomaterial development for clinical diagnostics and the next generation biomarker applications towards personal health monitoring. Put in other words, the emerging field of materiomics represents an essentially systematic approach to the investigation of biological material systems, integrating natural functions and processes with traditional materials science perspectives. Here we outline how materiomics provides a game-changing technology platform for disruptive innovation in biomaterial science to enable the design of tailored and functional biomaterials--particularly, the design and screening of DNA aptamers for targeting biomarkers related to oral diseases and oral health monitoring. Rigorous and complementary computational modeling and experimental techniques will provide an efficient means to develop new clinical technologies in silico, greatly accelerating the translation of materiomics-driven oral health diagnostics from concept to practice in the clinic.

A Mobile Acoustic Subsurface Sensing (MASS) system for rapid roadway assessment.

Surface waves are commonly used for vibration-based nondestructive testing for infrastructure. Spectral Analysis of Surface Waves (SASW) has been used to detect subsurface properties for geologic inspections. Recently, efforts were made to scale down these subsurface detection approaches to see how they perform on small-scale structures such as concrete slabs and pavements. Additional efforts have been made to replace the traditional surface-mounted transducers with non-contact acoustic transducers. Though some success has been achieved, most of these new approaches are inefficient because they require point-to-point measurements or off-line signal analysis. This article introduces a Mobile Acoustic Subsurface Sensing system as MASS, which is an improved surface wave based implementation for measuring the subsurface profile of roadways. The compact MASS system is a 3-wheeled cart outfitted with an electromagnetic impact source, distance register, non-contact acoustic sensors and data acquisition/ processing equipment. The key advantage of the MASS system is the capability to collect measurements continuously at walking speed in an automatic way. The fast scan and real-time analysis advantages are based upon the non-contact acoustic sensing and fast air-coupled surface wave analysis program. This integration of hardware and software makes the MASS system an efficient mobile prototype for the field test.

Dynamic tire pressure sensor for measuring ground vibration.

This work presents a convenient and non-contact acoustic sensing approach for measuring ground vibration. This approach, which uses an instantaneous dynamic tire pressure sensor (DTPS), possesses the capability to replace the accelerometer or directional microphone currently being used for inspecting pavement conditions. By measuring dynamic pressure changes inside the tire, ground vibration can be amplified and isolated from environmental noise. In this work, verifications of the DTPS concept of sensing inside the tire have been carried out. In addition, comparisons between a DTPS, ground-mounted accelerometer, and directional microphone are made. A data analysis algorithm has been developed and optimized to reconstruct ground acceleration from DTPS data. Numerical and experimental studies of this DTPS reveal a strong potential for measuring ground vibration caused by a moving vehicle. A calibration of transfer function between dynamic tire pressure change and ground acceleration may be needed for different tire system or for more accurate application.

Gallstone abscess as a result of dropped gallstones during laparoscopic cholecystectomy.

INTRODUCTION: With the advent of laparoscopic cholecystectomy we have seen a "disease of medical progress" (DOMP). Herein we report a complication that developed 7 years after laparoscopic cholecystectomy. PRESENTATION OF CASE: A 42 year old woman presented with worsening right-sided pain and tenderness. Seven years prior she underwent a laparoscopic cholecystectomy. Computed tomography demonstrated a subhepatic retroperitoneal inflammatory mass. On open exploration a 4cm×6cm retroperitoneal mass was excised. The mass contained purulent material and gallstones. DISCUSSION: Laparoscopic cholecystectomy has become the "gold standard" for the treatment of symptomatic gallstones. Prior to laparoscopic cholecystectomy there was no body of literature about lost gallstones thus making this a DOMP. In contrast, it is reported that as many as 5.4-19% of laparoscopic cholecystectomies have stones spilled with variable rates of retrieval. Our case demonstrates an extreme example of a complication resulting seven years after a laparoscopic cholecystectomy with gallstones left behind. CONCLUSION: Recognizing that gallstones will be lost during some cases of laparoscopic cholecystectomy, we must remain vigilant and make a full attempt to retrieve all stones to prevent such rare but not insignificant potential complications.

Presence of tannins in sorghum grains is conditioned by different natural alleles of Tannin1.

Sorghum, an ancient old-world cereal grass, is the dietary staple of over 500 million people in more than 30 countries in the tropics and semitropics. Its C4 photosynthesis, drought resistance, wide adaptation, and high nutritional value hold the promise to alleviate hunger in Africa. Not present in other major cereals, such as rice, wheat, and maize, condensed tannins (proanthocyanidins) in the pigmented testa of some sorghum cultivars have been implicated in reducing protein digestibility but recently have been shown to promote human health because of their high antioxidant capacity and ability to fight obesity through reduced digestion. Combining quantitative trait locus mapping, meta-quantitative trait locus fine-mapping, and association mapping, we showed that the nucleotide polymorphisms in the Tan1 gene, coding a WD40 protein, control the tannin biosynthesis in sorghum. A 1-bp G deletion in the coding region, causing a frame shift and a premature stop codon, led to a nonfunctional allele, tan1-a. Likewise, a different 10-bp insertion resulted in a second nonfunctional allele, tan1-b. Transforming the sorghum Tan1 ORF into a nontannin Arabidopsis mutant restored the tannin phenotype. In addition, reduction in nucleotide diversity from wild sorghum accessions to landraces and cultivars was found at the region that codes the highly conserved WD40 repeat domains and the C-terminal region of the protein. Genetic research in crops, coupled with nutritional and medical research, could open the possibility of producing different levels and combinations of phenolic compounds to promote human health.

Parallel domestication of the Shattering1 genes in cereals.

A key step during crop domestication is the loss of seed shattering. Here, we show that seed shattering in sorghum is controlled by a single gene, Shattering1 (Sh1), which encodes a YABBY transcription factor. Domesticated sorghums harbor three different mutations at the Sh1 locus. Variants at regulatory sites in the promoter and intronic regions lead to a low level of expression, a 2.2-kb deletion causes a truncated transcript that lacks exons 2 and 3, and a GT-to-GG splice-site variant in the intron 4 results in removal of the exon 4. The distributions of these non-shattering haplotypes among sorghum landraces suggest three independent origins. The function of the rice ortholog (OsSh1) was subsequently validated with a shattering-resistant mutant, and two maize orthologs (ZmSh1-1 and ZmSh1-5.1+ZmSh1-5.2) were verified with a large mapping population. Our results indicate that Sh1 genes for seed shattering were under parallel selection during sorghum, rice and maize domestication.

Genetic diversity and population structure analysis of accessions in the US historic sweet sorghum collection.

Sweet sorghum has the potential to become a versatile feedstock for large-scale bioenergy production given its sugar from stem juice, cellulose/hemicellulose from stalks, and starch from grain. However, for researchers to maximize its feedstock potential a first step includes additional evaluations of the 2,180 accessions with varied origins in the US historic sweet sorghum collection. To assess genetic diversity of this collection for bioenergy breeding and population structure for association mapping, we selected 96 accessions and genotyped them with 95 simple sequence repeat markers. Subsequent genetic diversity and population structure analysis methods identified four subpopulations in this panel, which correlated well with the geographic locations where these accessions originated or were collected. Model comparisons for three quantitative traits revealed different levels of population structure effects on flowering time, plant height, and brix. Our results suggest that diverse germplasm accessions curated from different geographical regions should be considered for plant breeding programs to develop sweet sorghum cultivars or hybrids, and that this sweet sorghum panel can be further explored for association mapping.

Discovering and verifying DNA polymorphisms in a mung bean [V. radiata (L.) R. Wilczek] collection by EcoTILLING and sequencing.

BACKGROUND: Vigna radiata, which is classified in the family Fabaceae, is an important economic crop and a dietary staple in many developing countries. The species radiata can be further subdivided into varieties of which the variety sublobata is currently acknowledged as the putative progenitor of radiata. EcoTILLING was employed to identify single nucleotide polymorphisms (SNPs) and small insertions/deletions (INDELS) in a collection of Vigna radiata accessions. FINDINGS: A total of 157 DNA polymorphisms in the collection were produced from ten primer sets when using V. radiata var. sublobata as the reference. The majority of polymorphisms detected were found in putative introns. The banding patterns varied from simple to complex as the number of DNA polymorphisms between two pooled samples increased. Numerous SNPs and INDELS ranging from 4-24 and 1-6, respectively, were detected in all fragments when pooling V. radiata var. sublobata with V. radiata var. radiata. On the other hand, when accessions of V. radiata var. radiata were mixed together and digested with CEL I relatively few SNPs and no INDELS were detected. CONCLUSION: EcoTILLING was utilized to identify polymorphisms in a collection of mung bean, which previously showed limited molecular genetic diversity and limited morphological diversity in the flowers and pod descriptors. Overall, EcoTILLING proved to be a powerful genetic analysis tool providing the rapid identification of naturally occurring variation.

Genetic diversity of cultivated and wild-type peanuts evaluated with M13-tailed SSR markers and sequencing.

Thirty-one genomic SSR markers with a M13 tail attached were used to assess the genetic diversity of the peanut mini core collection. The M13-tailed method was effective in discriminating almost all the cultivated and wild accessions. A total of 477 alleles were detected with an average of 15.4 alleles per locus. The mean polymorphic information content (PIC) score was 0.687. The cultivated peanut (Arachis hypogaea L.) mini core produced a total of 312 alleles with an average of 10.1 alleles per locus. A neighbour-joining tree was constructed to determine the interspecific and intraspecific relationships in this data set. Almost all the peanut accessions in this data set classified into subspecies and botanical varieties such as subsp. hypogaea var. hypogaea, subsp. fastigiata var. fastigiata, and subsp. fastigiata var. vulgaris clustered with other accessions with the same classification, which lends further support to their current taxonomy. Alleles were sequenced from one of the SSR markers used in this study, which demonstrated that the repeat motif is conserved when transferring the marker across species borders. This study allowed the examination of the diversity and phylogenetic relationships in the peanut mini core which has not been previously reported.