Poly (ADP-ribose) polymerase (PARP) inhibitors as anticancer agents: An outlook on clinical progress, synthetic strategies, biological activity, and structure-activity relationship.

Poly (ADP-ribose) polymerase (PARP) is considered an essential component in case of DNA (Deoxyribonucleic acid) damage, response by sensing DNA damage and engaging DNA repair proteins. Those proteins repair the damaged DNA via an aspect of posttranslational modification, known as poly (ADP-Ribosyl)ation (PARylation). Specifically, PARP inhibitors (PARPi) have shown better results when administered alone in a variety of cancer types with BRCA (Breast Cancer gene) mutation. The clinical therapeutic benefits of PARP inhibitors have been diminished by their cytotoxicity, progression of drug resistance, and limitation of indication, regardless of their tremendous clinical effectiveness. A growing number of PARP-1 inhibitors, particularly those associated with BRCA-1/2 mutations, have been identified as potential cancer treatments. Recently, several researchers have identified various promising scaffolds, which have resulted in the resuscitation of the faith in PARP inhibitors as cancer therapies. This review provided a comprehensive update on the anatomy and physiology of the PARP enzyme, the profile of FDA (Food and Drug Administration) and CFDA (China Food and Drug Administration)-approved drugs, and small-molecule inhibitors of PARP, including their synthetic routes, biological evaluation, selectivity, and structure-activity relationship.

Search for chromosomal instability aiding variants reveal naturally occurring kinetochore gene variants that perturb chromosome segregation.

Chromosomal instability (CIN) is a hallmark of cancers, and CIN-promoting mutations are not fully understood. Here, we report 141 chromosomal instability aiding variant (CIVa) candidates by assessing the prevalence of loss-of-function (LoF) variants in 135 chromosome segregation genes from over 150,000 humans. Unexpectedly, we observe both heterozygous and homozygous CIVa in Astrin and SKA3, two evolutionarily conserved kinetochore and microtubule-associated proteins essential for chromosome segregation. To stratify harmful versus harmless variants, we combine live-cell microscopy and controlled protein expression. We find the naturally occurring Astrin p.Q1012∗ variant is harmful as it fails to localize normally and induces chromosome misalignment and missegregation, in a dominant negative manner. In contrast, the Astrin p.L7Qfs∗21 variant generates a shorter isoform that localizes and functions normally, and the SKA3 p.Q70Kfs∗7 variant allows wild-type SKA complex localisation and function, revealing distinct resilience mechanisms that render these variants harmless. Thus, we present a scalable framework to predict and stratify naturally occurring CIVa, and provide insight into resilience mechanisms that compensate for naturally occurring CIVa.

Opportunities and challenges for deep learning in cell dynamics research.

The growth of artificial intelligence (AI) has led to an increase in the adoption of computer vision and deep learning (DL) techniques for the evaluation of microscopy images and movies. This adoption has not only addressed hurdles in quantitative analysis of dynamic cell biological processes but has also started to support advances in drug development, precision medicine, and genome-phenome mapping. We survey existing AI-based techniques and tools, as well as open-source datasets, with a specific focus on the computational tasks of segmentation, classification, and tracking of cellular and subcellular structures and dynamics. We summarise long-standing challenges in microscopy video analysis from a computational perspective and review emerging research frontiers and innovative applications for DL-guided automation in cell dynamics research.

Impact of biofertilisers on iron homeostasis and grain quality in the rice variety Uma under Elevated CO2.

The diminishing nutritional quality of rice with increasing concentrations of atmospheric CO2 is currently a major global concern. The present study was designed with the objective of assessing the impact of biofertilisers on grain quality and iron homeostasis in rice under elevated CO2. A completely randomised design with four treatments ([KAU, POP (control), POP+Azolla, POP+PGPR, and POP+AMF]), each replicated three times under ambient and elevated CO2 conditions, was followed. The analysed data revealed that yield, grain quality, and iron uptake and translocation were modified in an unfavourable manner under elevated CO2, which was reflected in the lower quality and iron content of the grains. The response of iron homeostasis in the experimental plants to the application of biofertilisers, especially plant-growth-promoting rhizobacteria (PGPR), under elevated CO2 strongly suggests the possibility of utilising them for designing iron management strategies for achieving higher quality in rice.

Deep learning techniques and mathematical modeling allow 3D analysis of mitotic spindle dynamics.

Time-lapse microscopy movies have transformed the study of subcellular dynamics. However, manual analysis of movies can introduce bias and variability, obscuring important insights. While automation can overcome such limitations, spatial and temporal discontinuities in time-lapse movies render methods such as 3D object segmentation and tracking difficult. Here, we present SpinX, a framework for reconstructing gaps between successive image frames by combining deep learning and mathematical object modeling. By incorporating expert feedback through selective annotations, SpinX identifies subcellular structures, despite confounding neighbor-cell information, non-uniform illumination, and variable fluorophore marker intensities. The automation and continuity introduced here allows the precise 3D tracking and analysis of spindle movements with respect to the cell cortex for the first time. We demonstrate the utility of SpinX using distinct spindle markers, cell lines, microscopes, and drug treatments. In summary, SpinX provides an exciting opportunity to study spindle dynamics in a sophisticated way, creating a framework for step changes in studies using time-lapse microscopy.

Improved transformation of Agrobacterium assisted by silver nanoparticles.

In transgenic plant development, the low transformation efficiency of Agrobacterium with exogenous DNA is the major constraint, and hence, methods to improve its transformation efficiency are needed. Recently, nanoparticlemediated gene transfer has evolved as a key transformational tool in genetic transformation. Since silver nanoparticles (AgNPs) can induce pores on the cell membrane, their efficacy in the improvement of conventional calcium chloride freeze-thaw technique of transformation of Agrobacterium was explored in this study. Agrobacterium cells in the exponential growth phase were exposed to different concentrations of AgNPs (0.01, 1, 5, 10, and 20 mg/l), and the half-maximal effective concentration (EC50) was determined via Probit analysis using the SPSS software. Transformation efficiency of AgNPs alone and in combination with calcium chloride was compared with that of the conventional calcium chloride freeze-thaw technique. AgNPs at a concentration of 0.01 mg/l in combination with calcium chloride (20 mM) showed a ten fold increase in the transformation efficiency (3.33 log CFU (colony-forming unit/microgram of DNA) of Agrobacterium tumefaciens strain EHA 105 with plasmid vector pART27 compared with the conventional technique (2.31 log CFU/µg of DNA). This study indicates that AgNPs of size 100 nm can eliminate the freeze-thaw stage in the conventional Agrobacterium transformation technique, with a 44% improvement in efficiency. The use of AgNPs (0.01 mg/l) along with 20 mM calcium chloride was found to be an economically viable method to improve the transformation of Agrobacterium with exogenous plasmid DNA.

Counteraction between Astrin-PP1 and Cyclin-B-CDK1 pathways protects chromosome-microtubule attachments independent of biorientation.

Defects in chromosome-microtubule attachment can cause chromosomal instability (CIN), frequently associated with infertility and aggressive cancers. Chromosome-microtubule attachment is mediated by a large macromolecular structure, the kinetochore. Sister kinetochores of each chromosome are pulled by microtubules from opposing spindle-poles, a state called biorientation which prevents chromosome missegregation. Kinetochore-microtubule attachments that lack the opposing-pull are detached by Aurora-B/Ipl1. It is unclear how mono-oriented attachments that precede biorientation are spared despite the lack of opposing-pull. Using an RNAi-screen, we uncover a unique role for the Astrin-SKAP complex in protecting mono-oriented attachments. We provide evidence of domains in the microtubule-end associated protein that sense changes specific to end-on kinetochore-microtubule attachments and assemble an outer-kinetochore crescent to stabilise attachments. We find that Astrin-PP1 and Cyclin-B-CDK1 pathways counteract each other to preserve mono-oriented attachments. Thus, CIN prevention pathways are not only surveying attachment defects but also actively recognising and stabilising mature attachments independent of biorientation.

Silver nanoparticles for biolistic transformation in Nicotiana tabacum L.

The present study reports the use of silver nanoparticles as a gene carrier, substituting gold microcarrier for biolistic gene delivery in Nicotiana tabacum L. Efficiency of biolistic transformation using silver nanoparticles (100 nm) was compared with that of gold microcarriers (0.6 micron) under varying helium pressure (450 psi, 650 psi, 900 psi and 1100 psi) and target distance (6 cm and 9 cm). Among the different concentrations (0.01-100 mgL-1) of silver nanoparticles tried, 10 mgL-1 produced the highest number of transient GUS expression (30) with statistical significance. Helium pressure of 650 and target distance of 9 cm, and 900 psi pressure and 6 cm distance resulted in the highest GUS expression with gold microcarriers and silver nanoparticles, respectively. Transformation efficiency was significantly higher with silver nanoparticles than gold microparticles as carriers resulting in a reduction up to 37.5-fold on the cost of consumables. Regeneration efficiencies of tissues bombarded with gold microcarriers and silver nanoparticles were 62.5% and 70.83%, respectively.

Electrically tunable lenses - eliminating mechanical axial movements during high-speed 3D live imaging.

The successful investigation of photosensitive and dynamic biological events, such as those in a proliferating tissue or a dividing cell, requires non-intervening high-speed imaging techniques. Electrically tunable lenses (ETLs) are liquid lenses possessing shape-changing capabilities that enable rapid axial shifts of the focal plane, in turn achieving acquisition speeds within the millisecond regime. These human-eye-inspired liquid lenses can enable fast focusing and have been applied in a variety of cell biology studies. Here, we review the history, opportunities and challenges underpinning the use of cost-effective high-speed ETLs. Although other, more expensive solutions for three-dimensional imaging in the millisecond regime are available, ETLs continue to be a powerful, yet inexpensive, contender for live-cell microscopy.

Multinucleation associated DNA damage blocks proliferation in p53-compromised cells.

Nuclear atypia is one of the hallmarks of cancers. Here, we perform single-cell tracking studies to determine the immediate and long-term impact of nuclear atypia. Tracking the fate of newborn cells exhibiting nuclear atypia shows that multinucleation, unlike other forms of nuclear atypia, blocks proliferation in p53-compromised cells. Because ~50% of cancers display compromised p53, we explored how multinucleation blocks proliferation. Multinucleation increases 53BP1-decorated nuclear bodies (DNA damage repair platforms), along with a heterogeneous reduction in transcription and protein accumulation across the multi-nucleated compartments. Multinucleation Associated DNA Damage associated with 53BP1-bodies remains unresolved for days, despite an intact NHEJ machinery that repairs laser-induced DNA damage within minutes. Persistent DNA damage, a DNA replication block, and reduced phospho-Rb, reveal a novel replication stress independent cell cycle arrest caused by mitotic lesions. These findings call for segregating protective and prohibitive nuclear atypia to inform therapeutic approaches aimed at limiting tumour heterogeneity.

High temperature induced changes in quality and yield parameters of tomato (Solanum lycopersicum L.) and similarity coefficients among genotypes using SSR markers.

High temperature induced by climatic fluctuations are an important threat for plant growth, development and quality of agricultural produces. Adaptableness to environmental changes generally derives from a large set of genetic traits affecting physio-morphological, biochemical and agronomic parameters. Therefore, the identification of genotypes with higher yield and good quality parameters at high temperatures is becoming increasingly necessary for future breeding programs. Here, we analyzed the performance of different tomato genotypes grown under elevated temperatures in terms of yield and nutritional quality of the fruit. High temperature stress was induced from flower initiation to maturity stage by keeping the pots in a temperature controlled green house facility for 45 days. The quality and yield parameters were taken at the harvesting stage. Starch and soluble sugar concentration in the leaves of tomato genotypes showed significant reduction in its amount under heat stress. Titrable acidity (TA), total soluble solids (TSS) and ascorbic acid content of tomato fruits were highest under high temperature conditions compared to ambient condition but lycopene content decreased with rise in temperature. The yield attributes viz., number of fruits/plant, fruit set %, average fruit weight (g), yield per plant (g/plant) were significantly lower for Arka Saurabh, Arka Rakshak and Pusa Rohini when compared to other genotypes under study. Molecular characterization of selected 22 tomato genotypes were assessed using 25 simple sequence repeat (SSR) markers. Phylogenetic tree was constructed by the unweighted neighbour-joining method (UPGMA) using NTSYSpc cluster analysis software. The Jaccard's similarity matrix was constructed using the SIMQUAL method using UPGMA algorithm in NTSYSpc. Jaccard's similarity matrix among these tomato genotypes ranged from a minimum of 0.22 to a maximum of 1 with an average genetic similarity of 0.67. Hence this study has importance in identifying genotypes that could maintain good quality and higher yield under high temperature condition.

Water stress mediated root trait dynamics and identification of microsatellite markers associated with root traits in rice (Oryza sativa L.).

To identify microsatellite markers associated with root traits for drought tolerance in rice (Oryza sativa L.) a study was conducted at Department of Plant Physiology, College of Agriculture, Trivandrum, Kerala Agricultural University. A set of thirty-five rice genotypes were exposed to water stress and evaluated for physio-morphological components as indices of water stress tolerance. Observations were made on leaf rolling score and root traits, especially the root length, root dry weight, root volume and root shoot ratio at booting stage. As of the data obtained, ten tolerant and ten susceptible varieties were selected for bulk line analysis to identify the DNA markers linked with target gene conferring drought tolerance. Out of 150 SSR primers screened, RM474 showed polymorphism between the tolerant and susceptible bulks. Individual genotypes of the bulks also showed the same product size of the respective tolerant and susceptible bulks.

Morphology and Interconnected Microstructure-Driven High-Rate Capability of Li-Rich Layered Oxide Cathodes.

A Li-rich layered oxide (LLO) cathode with morphology-dependent electrochemical performance with the composition Li1.23Mn0.538Ni0.117Co0.114O2 in three different microstructural forms, namely, randomly shaped particles, platelets, and nanofibers, is synthesized through the solid-state reaction (SSR-LLO), hydrothermal method (HT-LLO), and electrospinning process (ES-LLO), respectively. Even though the cathodes possess different morphologies, structurally they are identical. The elemental dispersion studies using energy-dispersive X-ray spectroscopy mapping in scanning transmission electron microscopy show uniform distribution of elements. However, SSR-LLO and ES-LLO nanofibers show slight Co-rich regions. The electrochemical studies of LLO cathodes are evaluated in terms of charging/discharging, C-rate capability, and cyclic stability performances. A high reversible capacity of 275 mA h g-1 is achieved in the fibrous LLO cathode which also demonstrates good high-rate capability (80 mA h g-1 at 10 C-rate). These capacities and rate capabilities are superior to those of SSR-LLO [210.5 mA h g-1 (0.1 C-rate) and 4 mA h g-1 (3 C-rate)] and HT-LLO [242 mA h g-1 (0.1 C-rate) and 22 mA h g-1 (10 C-rate)] cathodes. The ES-LLO cathode exhibits 88% capacity retention after 100 cycles at 1 C-rate. A decrease in voltage on cycling is found to be common in all three cathodes; however, minimal voltage decay and capacity loss are observed in ES-LLO upon cycling. Well-connected small LLO particles constituting fibrous microstructural forms in ES-LLO provide an enhanced electrolyte/cathode interfacial area and reduced diffusion path length for Li+. This, in turn, facilitates superior electrochemical performance of the electrospun Co-low LLO cathode suitable for quick charge battery applications.

Kinetochores attached to microtubule-ends are stabilised by Astrin bound PP1 to ensure proper chromosome segregation.

Microtubules segregate chromosomes by attaching to macromolecular kinetochores. Only microtubule-end attached kinetochores can be pulled apart; how these end-on attachments are selectively recognised and stabilised is not known. Using the kinetochore and microtubule-associated protein, Astrin, as a molecular probe, we show that end-on attachments are rapidly stabilised by spatially-restricted delivery of PP1 near the C-terminus of Ndc80, a core kinetochore-microtubule linker. PP1 is delivered by the evolutionarily conserved tail of Astrin and this promotes Astrin's own enrichment creating a highly-responsive positive feedback, independent of biorientation. Abrogating Astrin:PP1-delivery disrupts attachment stability, which is not rescued by inhibiting Aurora-B, an attachment destabiliser, but is reversed by artificially tethering PP1 near the C-terminus of Ndc80. Constitutive Astrin:PP1-delivery disrupts chromosome congression and segregation, revealing a dynamic mechanism for stabilising attachments. Thus, Astrin-PP1 mediates a dynamic 'lock' that selectively and rapidly stabilises end-on attachments, independent of biorientation, and ensures proper chromosome segregation.

MARK2/Par1b kinase present at centrosomes and retraction fibres corrects spindle off-centring induced by actin disassembly.

Tissue maintenance and development requires a directed plane of cell division. While it is clear that the division plane can be determined by retraction fibres that guide spindle movements, the precise molecular components of retraction fibres that control spindle movements remain unclear. We report MARK2/Par1b kinase as a novel component of actin-rich retraction fibres. A kinase-dead mutant of MARK2 reveals MARK2's ability to monitor subcellular actin status during interphase. During mitosis, MARK2's localization at actin-rich retraction fibres, but not the rest of the cortical membrane or centrosome, is dependent on its activity, highlighting a specialized spatial regulation of MARK2. By subtly perturbing the actin cytoskeleton, we reveal MARK2's role in correcting mitotic spindle off-centring induced by actin disassembly. We propose that MARK2 provides a molecular framework to integrate cortical signals and cytoskeletal changes in mitosis and interphase.

A novel approach for increasing transformation efficiency in E. coli DH5α cells using silver nanoparticles.

The present study is the first report on the application of silver nanoparticles for efficient bacterial transformation. EC50 value of 100 nm silver nanoparticles against E. coli DH5α cells was recorded as 4.49 mg L-1 in toxicity assay. Competency induction in E. coli DH5α cells by treatment with 100 nm silver nanoparticles at a concentration of 1 mg L-1 for 60 min and transformation using three plasmid vectors of different sizes, viz. pUC18, pBR322 and pCAMBIA resulted in tenfold increase in the bacterial transformation efficiency, i.e. 8.3 × 104, 8.0 × 104 and 7.9 × 104 cfu ng-1 of DNA, respectively, even without heat shock compared to the conventional chemical method using 0.1 M calcium chloride (2.3 × 103 cfu ng-1 of DNA).

Calcium alginate encapsulated synthetic seed production in Plumbago rosea L. for germplasm exchange and distribution.

Plumbago rosea L. (Plumbaginaceae), is a medicinal shrub commercially exploited for its naphthoquinone principle, plumbagin, extracted from the roots especially for treating skin disorders. As the plant is exploited from the wild without being replenished, conservation of the species becomes inevitable. Synthetic seeds would provide for effective conservation, germplasm exchange and distribution of this species. A reliable protocol for synthetic seed production in Plumbago rosea has been developed encapsulating the axillary buds. The axillary buds from P. rosea cultures established and multiplied using the nodal explants in Murashige and Skoog (MS) medium supplemented with Benzyl Adenine (BA) 1.5 mg/L and Indole 3-Acetic acid 1.0 mg/L, were used for synseed production. The plantlet conversion efficiency was the highest in synthetic seeds developed with sodium alginate 2.5% in modified MS with 0.4 M sucrose and CaCl2 100 mM. This combination gave the earliest bud initiation (9.19 ± 0.39 days) and maximum number of shoots per explant (2.31 ± 0.16 shoots). Microshoots from the culture, when inoculated on to MS medium supplemented with Naphthalene Acetic Acid 1.0 mg/L gave the best rooting response with 10.67 ± 0.94 roots per plant and 5.42 ± 0.29 cm root length. This is the first report of synthetic seed production in P. rosea using axillary buds as explant.

Spindle rotation in human cells is reliant on a MARK2-mediated equatorial spindle-centering mechanism.

The plane of cell division is defined by the final position of the mitotic spindle. The spindle is pulled and rotated to the correct position by cortical dynein. However, it is unclear how the spindle's rotational center is maintained and what the consequences of an equatorially off centered spindle are in human cells. We analyzed spindle movements in 100s of cells exposed to protein depletions or drug treatments and uncovered a novel role for MARK2 in maintaining the spindle at the cell's geometric center. Following MARK2 depletion, spindles glide along the cell cortex, leading to a failure in identifying the correct division plane. Surprisingly, spindle off centering in MARK2-depleted cells is not caused by excessive pull by dynein. We show that MARK2 modulates mitotic microtubule growth and length and that codepleting mitotic centromere-associated protein (MCAK), a microtubule destabilizer, rescues spindle off centering in MARK2-depleted cells. Thus, we provide the first insight into a spindle-centering mechanism needed for proper spindle rotation and, in turn, the correct division plane in human cells.

Aurora-B kinase pathway controls the lateral to end-on conversion of kinetochore-microtubule attachments in human cells.

Human chromosomes are captured along microtubule walls (lateral attachment) and then tethered to microtubule-ends (end-on attachment) through a multi-step end-on conversion process. Upstream regulators that orchestrate this remarkable change in the plane of kinetochore-microtubule attachment in human cells are not known. By tracking kinetochore movements and using kinetochore markers specific to attachment status, we reveal a spatially defined role for Aurora-B kinase in retarding the end-on conversion process. To understand how Aurora-B activity is counteracted, we compare the roles of two outer-kinetochore bound phosphatases and find that BubR1-associated PP2A, unlike KNL1-associated PP1, plays a significant role in end-on conversion. Finally, we uncover a novel role for Aurora-B regulated Astrin-SKAP complex in ensuring the correct plane of kinetochore-microtubule attachment. Thus, we identify Aurora-B as a key upstream regulator of end-on conversion in human cells and establish a late role for Astrin-SKAP complex in the end-on conversion process.Human chromosomes are captured along microtubule walls and then tethered to microtubule-ends through a multi-step end-on conversion process. Here the authors show that Aurora-B regulates end-on conversion in human cells and establish a late role for Astrin-SKAP complex in the end-on conversion process.