Genome-wide identification and expression analysis of Hsp70 family genes in Cassava (Manihot esculenta Crantz).

Hsp70 proteins function as molecular chaperones, regulating various cellular processes in plants. In this study, a genome-wide analysis led to the identification of 22 Hsp70 (MeHsp70) genes in cassava. Phylogenetic relationship studies with other Malpighiales genomes (Populus trichocarpa, Ricinus communis and Salix purpurea) classified MeHsp70 proteins into eight groups (Ia, Ib, Ic, Id, Ie, If, IIa and IIb). Promoter analysis of MeHsp70 genes revealed the presence of tissue-specific, light, biotic and abiotic stress-responsive cis-regulatory elements showing their functional importance in cassava. Meta-analysis of publically available RNA-seq transcriptome datasets showed constitutive, tissue-specific, biotic and abiotic stress-specific expression patterns among MeHsp70s in cassava. Among 22 Hsp70, six MeHsp70s viz., MecHsp70-3, MecHsp70-6, MeBiP-1, MeBiP-2, MeBiP-3 and MecpHsp70-2 displayed constitutive expression, while three MecHsp70s were induced under both drought and cold stress conditions. Five MeHsp70s, MecHsp70-7, MecHsp70-11, MecHsp70-12, MecHsp70-13, and MecHsp70-14 were induced under drought stress conditions. We predicted that 19 MeHsp70 genes are under the regulation of 24 miRNAs. This comprehensive genome-wide analysis of the Hsp70 gene family in cassava provided valuable insights into their functional roles and identified various potential Hsp70 genes associated with stress tolerance and adaptation to environmental stimuli. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03760-3.

Magnetically Detected Protein Binding Using Spin-Labeled Slow Off-Rate Modified Aptamers.

Recent developments in aptamer chemistry open up opportunities for new tools for protein biosensing. In this work, we present an approach to use immobilized slow off-rate modified aptamers (SOMAmers) site-specifically labeled with a nitroxide radical via azide-alkyne click chemistry as a means for detecting protein binding. Protein binding induces a change in rotational mobility of the spin label, which is detected via solution-state electron paramagnetic resonance (EPR) spectroscopy. We demonstrate the workflow and test the protocol using the SOMAmer SL5 and its protein target, platelet-derived growth factor B (PDGF-BB). In a complete site scan of the nitroxide over the SOMAmer, we determine the rotational mobility of the spin label in the absence and presence of target protein. Several sites with sufficiently tight affinity and large rotational mobility change upon protein binding are identified. We then model a system where the spin-labeled SOMAmer assay is combined with fluorescence detection via diamond nitrogen-vacancy (NV) center relaxometry. The NV center spin-lattice relaxation time is modulated by the rotational mobility of a proximal spin label and thus responsive to SOMAmer-protein binding. The spin label-mediated assay provides a general approach for transducing protein binding events into magnetically detectable signals.

Design, characterization and evaluation of a new 99mTc-labeled folate derivative with affinity towards folate receptor.

Folate receptors (FRs) are known to be over-expressed in several human malignancies and therefore serve as an important target for small radiolabeled folate derivatives for non-invasive imaging of tumor, which is an important tool for future treatment recourse. In the present article, we report the synthesis of a new 99mTc-labeled radiotracer for the aforementioned application following the well-established 99mTc-'4+1' chemistry. Formation of the desired [99mTc]Tc-complex with >95% radiochemical purity was confirmed by radio-HPLC and its structure was ascertained by characterizing a natural rhenium analogue of the said complex. Although the ligand exhibited a weaker affinity towards FRs compared to native folic acid (IC50 8.09 µM vs 29.46 nM), the 99mTc-labeled complex was found to bind folate receptor-positive KB cells with high specificity (∼90%). Similar studies in a folate receptor negative cell line viz. A549 further corroborated the receptor-specificity of the synthesized complex. In vivo studies in KB tumor xenograft showed moderate uptake of ∼2.6% upto 3 h post-injection with high specificity (∼80%). The favorable features observed warrant further screening of the current design towards achieving an improved molecular probe for the said application.

Imaging and pathological discordance amongst the plethora of breast lesions in breast biopsies.

INTRODUCTION: Imaging-guided breast tissue biopsy has become an acceptable alternative to open surgical biopsy for nonpalpable breast lesions. Discussion of abnormal results of the correlation between imaging and pathological findings can be very challenging as it can assist in decision-making with regard to the further treatment options by arriving at a comprehensive diagnosis. MATERIALS AND METHODS: This was a retrospective study. Radiological data from imaging-guided breast biopsies of 500 patients during a 6-year period was collected and classified by a specialist radiologist as per the BI-RADS format. Histopathology reports were studied and discordance analyzed. RESULTS: A total of 500 cases were reviewed. Approximately 33% (168) cases fell into the BI-RADS 3 category, 24.4% (122) into the BI-RADS 4, and 37% (187) into BI-RADS 5 categories. Approximately 50% (n = 250) cases were benign, 2.6% (13) belonged to the high-risk category, and 47.4% (237) were malignant. The number of discordant cases was 12 (2.4%), mostly due to technical factors. Sensitivity of biopsies to detect malignancy was 85%, specificity was 96%, and accuracy of biopsy in diagnosing cancer was 90%. DISCUSSION: The "triple assessment" is the most sensitive method for detecting early breast cancer. An effective communication pathway must be established between a clinician, radiologist, and pathologist for surgical excision in discordance as it carries a high prevalence of carcinoma in these lesions. CONCLUSION: In discordant cases, either due to abnormal results of imaging or of abnormal pathological findings, the final decision is based on two concordant findings, out of the three parameters. This involves a multidisciplinary breast conference and an active participation by the pathologist.

Hybrid PSO-SVM algorithm for Covid-19 screening and quantification.

Corona Virus Disease (COVID) 19 has shaken the earth at its root and the devastation has increased the diagnostic burden of radiologists by large. At this crucial juncture, Artificial Intelligence (AI) will go a long way in decreasing the workload of physicians working in the outbreak zone, aiding them to accurately diagnose the new disease. In this work, a hybrid Particle Swarm Optimization-Support Vector Machine based AI algorithm is deployed to analyze the Computed Tomography images automatically providing a high probability in determining the presence of pneumonia due to COVID19. This paper presents a model for training the system to segregate and classify the presence of pneumonia which will in turn save around 50% of the time frame for physicians. This will be especially useful in places of outbreaks where a team of people are working together with the aid of artificial intelligence and/or medical background. The AI incorporated system was distributed in all areas of across the globe. It has been observed that challenges such as data security, testing time effectiveness of model, data discrepancy etc. were positively handled using the deployed system. Moreover, since the AI integrated system identifies the infected patients immediately physicians can confirm the infection and segregate the patients at the right period. A total of 200 training cases have been observed of which 150 were identified to be infected. The proposed work shows specificity of 0.85, a sensitivity of 0.956 and an accuracy of 95.78%.

Pre evaluation of cassava (Manihot esculenta Crantz) germplasm for genotypic variation in the identification of K efficient genotypes through different statistical tools.

Among the tropical tuber crops, cassava (Manihot esculenta Crantz) deserves special attention as regards to its higher biological efficiency in terms of dry matter production which incidentally implies to the higher amount of nutrient extraction from the soil resulting in better response to the application of manures and fertilizers. Among the major nutrients, Potassium (K) is considered as the key nutrient for cassava owing to its influence both in tuber yield and tuber quality. The above facts as well as the availability of sufficient cassava genotypes in the germplasm collection of ICAR-CTCRI made us to initiate research work to screen cassava germplasm including the pre breeding lines. The objective being to identify K efficient genotypes which can yield well under limited availability of K so that the external application of K can be reduced. This paper describes the wide variation noticed during the pre evaluation of 83 elite genotypes which was done as a prelude in the screening and identification of K efficient genotypes. The characters studied were tuber yield, tuber characters, plant dry matter percentage, plant K content, tuber quality (starch, cyanogenic glucosides) attributes, physiological efficiency and plant biometric characters. The variation among the genotypes for the above traits was assessed by making some yardstick for classification which in turn helped in determining the percent distribution of genotypes in each category. The variation among the genotypes were further affirmed through principal component analysis, wherein the first five components explained more than 77% of variability and the cluster analysis performed grouped these genotypes into five clusters. The biplot showed the traits which are closely linked to the genotypes. The dendrogram constructed indicated similar genotypes to that of the clusters to the extent of more than 50% revealing the association of members with similar traits in clusters and dendrograms. The study helped in establishing the drastic variation among the genotypes along with identification of six genotypes viz., Aniyoor, 7 Sahya (2), 7 III E3-5, W-19, CR 43-8, 6-6 for further detailed experimentation to identify K efficient genotypes.

Cassava breeding and agronomy in Asia: 50 years of history and future directions.

In Asia, cassava (Manihot esculenta) is cultivated by more than 8 million farmers, driving the rural economy of many countries. The International Center for Tropical Agriculture (CIAT), in partnership with national agricultural research institutes (NARIs), instigated breeding and agronomic research in Asia, 1983. The breeding program has successfully released high-yielding cultivars resulting in an average yield increase from 13.0 t ha-1 in 1996 to 21.3 t ha-1 in 2016, with significant economic benefits. Following the success in increasing yields, cassava breeding has turned its focus to higher-value traits, such as waxy cassava, to reach new market niches. More recently, building resistance to invasive pests and diseases has become a top priority due to the emergent threat of cassava mosaic disease (CMD). The agronomic research involves driving profitability with advanced technologies focusing on better agronomic management practices thereby maintaining sustainable production systems. Remote sensing technologies are being tested for trait discovery and large-scale field evaluation of cassava. In summary, cassava breeding in Asia is driven by a combination of food and market demand with technological innovations to increase the productivity. Further, exploration in the potential of data-driven agriculture is needed to empower researchers and producers for sustainable advancement.

Synthesis and evaluation of 99mTc-analogues of [123/131I]mIBG prepared via [99mTc][Tc(CO)3(H2O)3]+ synthon for targeting norepinephrine transporter.

INTRODUCTION: meta-[123/131I]Iodobenzylguanidine (mIBG) is a clinical agent used for imaging neuroendocrine tumors, where uptake in tumor is via active transport mechanism through norepinephrine transporters (NET). Our group in past have evaluated a 99mTc-analogue of the above tracer, based on 99mTc-4 + 1 labeling approach, which exhibited significant affinity for NET but suffered from reduced specific uptake in comparison to reference standard no-carrier-added (n.c.a.) [125I]mIBG. The present work attempts to synthesize two new 99mTc-analogues of the radio-iodinated derivative following [99mTc]Tc(CO)31+ approach with an aim to improve the above specific uptake content. METHODS: Two different precursors, xylylenediamine and 1,3-bis(chloromethyl)benzene, were synthetically modified to yield meta-functionalized benzylguanidine derivatives bearing iminodiacetate (IDA) and aminoethylglycine (AEG) tridentate chelating moieties, respectively. These ligands were labeled with technetium-99m via [99mTc][Tc(CO)3(H2O)3]+ synthon to form desired radioactive complexes 9 and 10. The radiolabeling yields of the complexes obtained were >90% as confirmed by radio-HPLC. The HPLC purified complexes were used for in vitro and in vivo evaluation to understand the true biological efficacy. Structural characterization of the radiolabeled complexes was carried after synthesizing and characterizing their Re-analogues. RESULTS: Cell uptake studies with the radiolabeled complexes in SK-N-SH neuroblastoma cell lines revealed reduced uptake in the cells (<1% of incubated radioactivity/106 cells) in comparison to n.c.a. [125I]mIBG (~12%). However, limited specificity (~60%) was observed for the complexes as ascertained through desmethylimipramine (DMI) inhibition. Biodistribution studies in normal Wistar rats exhibited desired non-target clearance pharmacokinetics for the complexes but in vivo NET efficacy in myocardium for the neutral complex 10 could not be established. CONCLUSIONS: Tridentate [99mTc]Tc(CO)31+ chelation approach severely affects biological behavior of the present small bioactive molecule under study to a significant extent in comparison to monodentate ligation in 99mTc-4 + 1 strategy.

Pharmacokinetic Properties of DNA Aptamers with Base Modifications.

The addition of novel side chains at the 5-position of uracil is an effective means to increase chemical diversity of aptamers and hence the success rate for discovery of high-affinity ligands to protein targets. Such modifications also increase nuclease resistance, which is useful in a range of applications, especially for therapeutics. In this study, we assess the impact of these side chains on plasma pharmacokinetics of modified aptamers conjugated to a 40 kDa polyethylene glycol. We show that clearance from plasma depends on relative hydrophobicity: side chains with a negative cLogP (more hydrophilic) result in slower plasma clearance compared with side chains with a positive cLogP (more hydrophobic). We show that clearance increases with the number of side chains in sequences of ≥28 synthons, but this effect is dramatically diminished in shorter sequences. These results serve as a guide for the design of new therapeutic aptamers with diversity-enhancing side chains.

Non-helical DNA Triplex Forms a Unique Aptamer Scaffold for High Affinity Recognition of Nerve Growth Factor.

Discerning the structural building blocks of macromolecules is essential for understanding their folding and function. For a new generation of modified nucleic acid ligands (called slow off-rate modified aptamers or SOMAmers), we previously observed essential functions of hydrophobic aromatic side chains in the context of well-known nucleic acid motifs. Here we report a 2.45-Å resolution crystal structure of a SOMAmer complexed with nerve growth factor that lacks any known nucleic acid motifs, instead adopting a configuration akin to a triangular prism. The SOMAmer utilizes extensive hydrophobic stacking interactions, non-canonical base pairing and irregular purine glycosidic bond angles to adopt a completely non-helical, compact S-shaped structure. Aromatic side chains contribute to folding by creating an unprecedented intercalating zipper-like motif and a prominent hydrophobic core. The structure provides compelling rationale for potent inhibitory activity of the SOMAmer and adds entirely novel motifs to the repertoire of structural elements uniquely available to SOMAmers.

Chemically modified DNA aptamers bind interleukin-6 with high affinity and inhibit signaling by blocking its interaction with interleukin-6 receptor.

Interleukin-6 (IL-6) is a pleiotropic cytokine that regulates immune and inflammatory responses, and its overproduction is a hallmark of inflammatory diseases. Inhibition of IL-6 signaling with the anti-IL-6 receptor antibody tocilizumab has provided some clinical benefit to patients; however, direct cytokine inhibition may be a more effective option. We used the systematic evolution of ligands by exponential enrichment (SELEX) process to discover slow off-rate modified aptamers (SOMAmers) with hydrophobic base modifications that inhibit IL-6 signaling in vitro. Two classes of IL-6 SOMAmers were isolated from modified DNA libraries containing 40 random positions and either 5-(N-benzylcarboxamide)-2'-deoxyuridine (Bn-dU) or 5-[N-(1-naphthylmethyl)carboxamide]-2'-deoxyuridine (Nap-dU) replacing dT. These modifications facilitate the high affinity binding interaction with IL-6 and provide resistance against degradation by serum endonucleases. Post-SELEX optimization of one Bn-dU and one Nap-dU SOMAmer led to improvements in IL-6 binding (10-fold) and inhibition activity (greater than 20-fold), resulting in lead SOMAmers with sub-nanomolar affinity (Kd = 0.2 nm) and potency (IC50 = 0.2 nm). Although similar in inhibition properties, the two SOMAmers have unique sequences and different ortholog specificities. Furthermore, these SOMAmers were stable in human serum in vitro for more than 48 h. Both SOMAmers prevented IL-6 signaling by blocking the interaction of IL-6 with its receptor and inhibited the proliferation of tumor cells in vitro as effectively as tocilizumab. This new class of IL-6 inhibitor may be an effective therapeutic alternative for patients suffering from inflammatory diseases.

Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets.

Selection of aptamers from nucleic acid libraries by in vitro evolution represents a powerful method of identifying high-affinity ligands for a broad range of molecular targets. Nevertheless, a sizeable fraction of proteins remain difficult targets due to inherently limited chemical diversity of nucleic acids. We have exploited synthetic nucleotide modifications that confer protein-like diversity on a nucleic acid scaffold, resulting in a new generation of binding reagents called SOMAmers (Slow Off-rate Modified Aptamers). Here we report a unique crystal structure of a SOMAmer bound to its target, platelet-derived growth factor B (PDGF-BB). The SOMAmer folds into a compact structure and exhibits a hydrophobic binding surface that mimics the interface between PDGF-BB and its receptor, contrasting sharply with mainly polar interactions seen in traditional protein-binding aptamers. The modified nucleotides circumvent the intrinsic diversity constraints of natural nucleic acids, thereby greatly expanding the structural vocabulary of nucleic acid ligands and considerably broadening the range of accessible protein targets.

Pharmacognostic evaluation of leaves of certain Phyllanthus species used as a botanical source of Bhumyamalaki in Ayurveda.

Today, World over, there is a great deal of interest in Ayurvedic system of medicine and thus the demand for various medicinal plants in the production of Ayurvedic medicines is ever increasing. Due to varied geographical locations where these plants grow, a great deal of adulteration or substitution is encountered in the commercial markets. Histological studies of the plant drugs are not only to study the adulterants but also are indispensable in accurate identification. Microscopic observations of the Phyllanthus species revealed the occurrence of anisocytic and paracytic type of stomata in Phyllanthus amarus , while only anisocytic type of stomata is present in P. fraternus and P. maderaspatensis. Epidermal cell walls of P. amarus and P. fraternus are wavy and straight walled epidermal walls are observed in P. maderaspatensis. In India all the above-mentioned species of Phyllanthus are called "Bhumyamalaki" and they are being used in the treatment of various liver disorders. However, all the species of Phyllanthus doesn't have the active constituents responsible for the treatment of liver disorders. In the present investigation by using simple micro techniques accurate identification of different species of Phyllanthus has been established.

Butyrate-induced phosphatase regulates VEGF and angiogenesis via Sp1.

Sp1 is a ubiquitous transcription factor and master regulator of various eukaryotic gene expression. Better understanding of the role of increased Sp1 levels on angiogenic regulation and the regulatory regions of that transcription factor may act as a useful target in 'transcriptional therapy'. At the molecular level, butyrate inhibits Sp1-DNA binding activity by promoting Sp1 protein dephosphorylation in EAT cells. It also inhibits Sp1 binding activity and reduces expression of VEGF gene, thereby inhibiting angiogenesis. It was confirmed that butyrate induces expression of a tyrosine phosphatase by RT-PCR, cDNA sequence analysis, protein ESI-MS analysis and protein sequence homology comparison. Thus our result strongly suggests that inhibition of angiogenesis by butyrate involves Sp1 dephosphorylation and down-regulation of VEGF gene expression. Further, butyrate inhibits neoangiogenesis induced by tumor cells and VEGF in peritoneum of EAT bearing mice and rat cornea.

Octacosanol isolated from Tinospora cordifolia downregulates VEGF gene expression by inhibiting nuclear translocation of NF-B and its DNA binding activity.

Octacosanol is a long-chain aliphatic alcohol, which is the main component of policosanol used as a normolipidemic agent. It is known that angiogenesis is involved in tumor growth and metastasis. The present study identified octacosanol isolated from the plant Tinospora cordifolia as a new antiangiogenic compound with inhibitory effects on in vivo angiogenesis assays. Our results showed that octacosanol (i) inhibits proliferation of endothelial cells and Ehrlich ascites tumor cells, (ii) inhibits neovascularization induced by angiogenic factors in chick chorioallantoic membrane and rat cornea in vivo angiogenesis assays, (iii) inhibits secretion of ascites fluid in the growing tumor cells in vivo. Concerning the mechanism of action, octacosanol inhibited secretion of vascular endothelial growth factor into ascites fluid by the tumor cells. At the molecular level octacosanol markedly inhibits activity of matrix metalloproteinases (MMPs) and translocation of transcription factor nuclear factor-B to nucleus. The mechanism of inhibition of angiogenesis by octacosanol reflects on its effect on tumor angiogenesis and metastasis.

Vulvodynia.

Vulvodynia or vulvar pain syndrome is a chronic, heterogeneous, and multifactorial disease with a high prevalence. This condition affects Caucasians, African Americans, Africans and Hispanic women, particularly those sexually active at child-bearing age. The etiology of this condition is complex and remains elusive. An accurate diagnosis requires a comprehensive history, physical examination and targeted diagnostic tests. Although many treatment options have been utilized, a rational therapeutic strategy is still under research. Psychological counseling and group support should be considered in all cases.

Correlation between lipid peroxidation and non-enzymatic antioxidants in pregnancy induced hypertension.

The present study was designed to evaluate the lipid peroxidation and non-enzymatic antioxidants in pregnancyinduced hypertension (PIH) compared with healthy normal pregnant and non-pregnant as controls. 75 cases were studied of which 25 were normal healthy controls (Group A), 25 healthy pregnant women (Group B) of third trimester and 25 were PIH (Group C) of the same trimester. In PIH, malondialdehyde a lipid peroxidation product was significantly increased as compared to normal pregnant and non-pregnant controls. The nonenzymatic antioxidants like reduced glutathione, Vitamin-E, Vitamin-C and Vitamin-A were significantly decreased in normal pregnants as compared to controls. A further significant decrease was noticed in PIH compared to normal pregnants. A significant negative correlation was detected between lipid peroxidation and non-enzymatic antioxidant levels. Our study clearly indicates a relationship between elevated lipid peroxidation, decreased non-enzymatic antioxidant in PIH. The measurement of non-enzymatic antioxidants in plasma may be useful predictor of the likely development of PIH.

Study of oxidative stress and enzymatic antioxidants in normal pregnancy.

Pregnancy is a physiological state accompanied by a high-energy demand and an increased oxygen requirement. Augmented levels of oxidative stress would be expected because of the increased intake and utilization of oxygen. Evidence of increased oxidative stress in normal pregnancy in comparison with nonpregnant controls was estimated by measuring Thiobarbituric acid reactive substance (TBARS), enzymatic antioxidants like Superoxide dismutase, Glutathione peroxidase, Glutathione reductase and catalase. It was observed that pregnant women were more susceptible to oxidative damage than non-pregnants as indicated by increased TBARS and decreased antioxidants.

Angiogenic and proliferative effects of the cytokine VEGF in Ehrlich ascites tumor cells is inhibited by Glycyrrhiza glabra.

Blood vessel plays a crucial role in solid tumor development. It has been suggested that blocking of angiogenesis and the action of the cytokine VEGF could be possible in cancer therapy. In a screen for naturally occurring angiogenic inhibitors, we have identified an extract from the roots of Glycyrrhiza glabra, which has potent antiangiogenic and antitumor activity. The aqueous extract inhibits the in vivo and in vitro proliferation of Ehrlich ascites tumor cells. The angioinhibitory activity of G. glabra was confirmed by its inhibition of angiogenesis in in vivo assays, peritoneal and chorioallantoic membrane assay. Reduction in the levels of the cytokine VEGF and microvessel density count in the peritoneum of mice treated with G. glabra indicated that the plant extract decreased VEGF production and the cytokine induced neovascularization. Our results suggest that the extract from the roots of G. glabra may be a potential supplemental source for cancer therapy.