Using molecular straps to engineer conjugated porous polymer growth, chemical doping, and conductivity.

Controlling network growth and architecture of 3D-conjugated porous polymers (CPPs) is challenging and therefore has limited the ability to systematically tune the network architecture and study its impact on doping efficiency and conductivity. We have proposed that π-face masking straps mask the π-face of the polymer backbone and therefore help to control π-π interchain interactions in higher dimensional π-conjugated materials unlike the conventional linear alkyl pendant solubilizing chains that are incapable of masking the π-face. Herein, we used cycloaraliphane-based π-face masking strapped monomers and show that the strapped repeat units, unlike the conventional monomers, help to overcome the strong interchain π-π interactions, extend network residence time, tune network growth, and increase chemical doping and conductivity in 3D-conjugated porous polymers. The straps doubled the network crosslinking density, which resulted in 18 times higher chemical doping efficiency compared to the control non-strapped-CPP. The straps also provided synthetic tunability and generated CPPs of varying network size, crosslinking density, dispersibility limit, and chemical doping efficiency by changing the knot to strut ratio. For the first time, we have shown that the processability issue of CPPs can be overcome by blending them with insulating commodity polymers. The blending of CPPs with poly(methylmethacrylate) (PMMA) has enabled them to be processed into thin films for conductivity measurements. The conductivity of strapped-CPPs is three orders of magnitude higher than that of the poly(phenyleneethynylene) porous network.

Plasticity of rosette size in response to nitrogen availability is controlled by an RCC1-family protein.

Nitrogen (N) is fundamental to plant growth, development and yield. Genes underlying N utilization and assimilation are well-characterized, but mechanisms underpinning plasticity of different phenotypes in response to N remain elusive. Here, using Arabidopsis thaliana accessions, we dissected the genetic architecture of plasticity in early and late rosette diameter, flowering time and yield, in response to three levels of N in the soil. Furthermore, we found that the plasticity in levels of primary metabolites were related with the plasticities of the studied traits. Genome-wide association analysis identified three significant associations for phenotypic plasticity, one for early rosette diameter and two for flowering time. We confirmed that the gene At1g19880, hereafter named as PLASTICITY OF ROSETTE TO NITROGEN 1 (PROTON1), encoding for a regulator of chromatin condensation 1 (RCC1) family protein, conferred plasticity of rosette diameter in response to N. Treatment of PROTON1 T-DNA line with salt implied that the reduced plasticity of early rosette diameter was not a general growth response to stress. We further showed that plasticities of growth and flowering-related traits differed between environmental cues, indicating decoupled genetic programs regulating these traits. Our findings provide a prospective to identify genes that stabilize performance under fluctuating environments.

Plasticity in metabolism underpins local responses to nitrogen in Arabidopsis thaliana populations.

Nitrogen (N) is central for plant growth, and metabolic plasticity can provide a strategy to respond to changing N availability. We showed that two local A. thaliana populations exhibited differential plasticity in the compounds of photorespiratory and starch degradation pathways in response to three N conditions. Association of metabolite levels with growth-related and fitness traits indicated that controlled plasticity in these pathways could contribute to local adaptation and play a role in plant evolution.

Versatile and multifaceted CRISPR/Cas gene editing tool for plant research.

The ability to create desirable gene variants through targeted changes offers tremendous opportunities for the advancement of basic and applied plant research. Gene editing technologies have opened new avenues to perform such precise gene modifications in diverse biological systems. These technologies use sequence-specific nucleases, such as homing endonucleases, zinc-finger nucleases, transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (CRISPR/Cas) complexes to enable targeted genetic manipulations. Among these, the CRISPR/Cas system has emerged as a broadly applicable and valued gene editing system for its ease of use and versatility. The adaptability of the CRISPR/Cas system has facilitated rapid and continuous innovative developments to the precision and applications of this technology, since its introduction less than a decade ago. Although developed in animal systems, the simple and elegant CRISPR/Cas gene editing technology has quickly been embraced by plant researchers. From early demonstration in model plants, the CRISPR/Cas system has been successfully adapted for various crop species and enabled targeting of agronomically important traits. Although the approach faces several efficiency and delivery related challenges, especially in recalcitrant crop species, continuous advances in the CRISPR/Cas system to address these limitations are being made. In this review, we discuss the CRISPR/Cas technology, its myriad applications and their prospects for crop improvement.

A role for TOR signaling at every stage of plant life.

From scientific advances in medical research to the plethora of anti-aging products available, our obsession with slowing the aging process and increasing life span is indisputable. A large research effort has been levied towards this perpetual search for the fountain of youth, yet the molecular mechanisms governing an organism's life span and the causes of aging are only beginning to emerge in animals and remain largely unanswered in plants. As one central pathway in eukaryotes controlling cell growth, development, and metabolism, the target of rapamycin (TOR) plays an evolutionarily conserved role in aging and the determination of life span. The modulation of TOR pathway components in a wide range of species, including the model plant Arabidopsis thaliana, has effects on life span. However, the mechanisms enabling some of the longest living species to endure, including trees that can live for millennia, have not been defined. Here, we introduce key TOR research from plant systems and discuss its implications in the plant life cycle and the broader field of life span research. TOR pathway functions in plant life cycle progression and life span determination are discussed, noting key differences from yeast and animal systems and the importance of 'omics' research for the continued progression of TOR signaling research.

Gene expression atlas of embryo development in Arabidopsis.

Embryogenesis represents a critical phase in the life cycle of flowering plants. Here, we characterize transcriptome landscapes associated with key stages of embryogenesis by combining an optimized method for the isolation of developing Arabidopsis embryos with high-throughput RNA-seq. The resulting RNA-seq datasets identify distinct overlapping patterns of gene expression, as well as temporal shifts in gene activity across embryogenesis. Network analysis revealed stage-specific and multi-stage gene expression clusters and biological functions associated with key stages of embryo development. Methylation-related gene expression was associated with early- and middle-stage embryos, initiation of photosynthesis components with the late embryogenesis stage, and storage/energy-related protein activation with late and mature embryos. These results provide a comprehensive understanding of transcriptome programming in Arabidopsis embryogenesis and identify modules of gene expression corresponding to key stages of embryo development. This dataset and analysis are a unique resource to advance functional genetic analysis of embryo development in plants.

Establishing a sample-to cut-off ratio for lab-diagnosis of hepatitis C virus in Indian context.

INTRODUCTION: Lab-diagnosis of hepatitis C virus (HCV) is based on detecting specific antibodies by enzyme immuno-assay (EIA) or chemiluminescence immuno-assay (CIA). Center for Disease Control reported that signal-to-cut-off (s/co) ratios in anti-HCV antibody tests like EIA/CIA can be used to predict the probable result of supplemental test; above a certain s/co value it is most likely to be true-HCV positive result and below that certain s/co it is most likely to be false-positive result. A prospective study was undertaken in patients in tertiary care setting for establishing this "certain" s/co value. MATERIALS AND METHODS: The study was carried out in consecutive patients requiring HCV testing for screening/diagnosis and medical management. These samples were tested for anti-HCV on CIA (VITROS(®) Anti-HCV assay, Ortho-Clinical Diagnostics, New Jersey) for calculating s/co value. The supplemental nucleic acid test used was polymerase chain reaction (PCR) (Abbott). PCR test results were used to define true negatives, false negatives, true positives, and false positives. Performance of different putative s/co ratios versus PCR was measured using sensitivity, specificity, positive predictive value and negative predictive value and most appropriate s/co was considered on basis of highest specificity at sensitivity of at least 95%. RESULTS: An s/co ratio of ≥6 worked out to be over 95% sensitive and almost 92% specific in 438 consecutive patient samples tested. CONCLUSION: The s/co ratio of six can be used for lab-diagnosis of HCV infection; those with s/co higher than six can be diagnosed to have HCV infection without any need for supplemental assays.

A cost effective model for appropriate administration of red cell units and salvaging un-transfused red cell units by using temperature sensitive indicators for blood component transportation in a hospital setting.

BACKGROUND: A rule called "30-min rule" defines that red cell unit cannot be used if it has been out of blood bank refrigerator for over 30 min. This rule is useful to guide initiation of transfusion, but is inadequate for deciding whether to reuse or discard units received-back at blood transfusion services (BTS). A simple cost-effective temperature-sensitive indicator was evaluated to decide upon reuse (cold chain was uninterrupted) or discard (where cold chain was interrupted) in a simulation exercise. MATERIALS AND METHODS: Temperature-sensitive indicators TH-F™ that irreversibly changed color from white to red demonstrated that heat excursion has occurred and the cumulative temperature has exceeded 10°C for over 30 min, were used in outdated red cells for simulating units, which are not used and received-back. These units were also tagged with a standard temperature monitoring device, which was a re-usable credit card sized device, which would log the actual time and temperature. In few units percent hemolysis was also calculated. RESULTS: Statistically insignificant elevation in average temperature was noted in 102 simulated units at the time of return to BTS (Δ 0.04°C), despite the fact that these units were in the transport box for over 4 h. The average supernatant hemoglobin in these units was 0.24%, much below the prescribed threshold. CONCLUSION: Transportation of blood in controlled conditions with temperature-sensitive indicator is a cost-effective model to save blood, a precious human resource.

Evaluation of a new serological test for syphilis based on chemiluminescence assay in a tertiary care hospital.

CONTEXT: Syphilis is a transfusion transmissible infections and it is mandatory to do serological test for syphilis (STS) on all donor blood samples. STS is usually based on detection of antibodies against the cardiolipin-lecithin antigen or against the Treponema-specific antigen. STS with good sensitivity and specificity helps enhance blood safety and consolidation of STS along with other transfusion transmittable infections such as human immunodeficiency virus, hepatitis-C virus, and hepatitis-B virus helps in reducing the errors and enhances efficiency. AIMS: This study was designed to evaluate the performance of newly introduced VITROS(®) syphilis Treponema pallidum agglutination (TPA) assay based on enhanced chemiluminescence principle for its analytical performance for use as a STS on donor blood samples at a tertiary care health center in National Capital Region, India. MATERIALS AND METHODS: A total of 108 random blood units collected from the donors (both voluntary and replacement donors) and 28 known syphilis sero-reactive samples stored at -20°C, were used to evaluate the performance of VITROS(®) syphilis TPA assay based on enhanced chemiluminescence assay on VITROS(®) ECiQ immunodiagnostics system along with its analytical performance in terms of its sensitivity, precision, cross-reactivity and interference studies. RESULTS: VITROS(®) syphilis TPA showed 100% sensitivity and specificity with precision (20 days study) of <10% co-efficient of variation. There was no cross-reactivity with other viral and auto-immune antibodies. No interference was observed from endogenous interfering substances like free hemoglobin or fats. CONCLUSIONS: Performance of the VITROS(®) syphilis TPA assay meets the requirements for its use as STS in blood bank, thus allowing consolidation with other transfusion transmittable infections screening assay on chemiluminescence platform, which is highly valuable for optimizing workflow and efficiency.

Technicalities and Glitches of Terminal Restriction Fragment Length Polymorphism (T-RFLP).

Terminal restriction fragment length polymorphism (T-RFLP) is a rapid, robust, inexpensive and simple tool for microbial community profiling. Methods used for DNA extraction, PCR amplification and digestion of amplified products have a considerable impact on the results of T-RFLP. Pitfalls of the method skew the similarity analysis and compromise its high throughput ability. Despite a high throughput method of data generation, data analysis is still in its infancy and needs more attention. Current article highlights the limitations of the methods used for data generation and analysis. It also provides an overview of the recent methodological developments in T-RFLP which will assist the readers in obtaining real and authentic profiles of the microbial communities under consideration while eluding the inherent biases and technical difficulties.

Etiology and survival of aplastic anemia: a study based on clinical investigation.

BACKGROUND: Management of aplastic anemia is etiology driven, whether constitutional or acquired. Age, gender, and severity of disease also play crucial role in the survival of aplastic anemia. Since, inadequate data are available from India, the present study was conducted with the aim to evaluate the etiology and survival of aplastic anemia. METHODS: Three hundred patients were enrolled between May 2007 and April 2010. Severity analysis and chromosomal breakage study was performed and patients were followed up to calculate the survival rate. RESULTS: Only 9.4% of the cases demonstrated the evidence of constitutional disease. Patients with acquired disease showed a significantly higher odd ratio for hepatitis. Overall survival was found to be independent of the gender and inherited etiology. Phenotype resembling to constitutional disease was present in only 22.22% (6/27) of patients. Similar ratio of the constitutional and acquired disease in both the age groups was observed. CONCLUSION: Irrespective of the age and phenotype, chromosomal breakage study should be mandatory for all patients with aplastic anemia. Hepatitis as a preceding event may be associated with the cause of aplastic anemia. Young age and less severe disease were strongly associated with better survival. Lack of tertiary care facility in the country, time lag between diagnosis and treatment, and unaffordability to abide the treatment cost could be the major contributory factors for poorer survival.

Molecular typing of fecal eukaryotic microbiota of human infants and their respective mothers.

The micro-eukaryotic diversity from the human gut was investigated using universal primers directed towards 18S rRNA gene, fecal samples being the source of DNA. The subjects in this study included two breast-fed and two formula-milk-fed infants and their mothers. The study revealed that the infants did not seem to harbour any microeukaryotes in their gut. In contrast, there were distinct eukaryotic microbiota present in the mothers. The investigation is the first of its kind in the comparative study of the human feces to reveal the presence of micro-eukaryotic diversity variance in infants and adults from the Indian subcontinent. The micro-eukaryotes encountered during the investigation include known gut colonizers like Blastocystis and some fungi species. Some of these micro-eukaryotes have been speculated to be involved in clinical manifestations of various diseases. The study is an attempt to highlight the importance of micro-eukaryotes in the human gut.