Exploration of the pearl millet phospholipase gene family to identify potential candidates for grain quality traits.

BACKGROUND: Phospholipases constitute a diverse category of enzymes responsible for the breakdown of phospholipids. Their involvement in signal transduction with a pivotal role in plant development and stress responses is well documented. RESULTS: In the present investigation, a thorough genome-wide analysis revealed that the pearl millet genome contains at least 44 phospholipase genes distributed across its 7 chromosomes, with chromosome one harbouring the highest number of these genes. The synteny analysis suggested a close genetic relationship of pearl millet phospholipases with that of foxtail millet and sorghum. All identified genes were examined to unravel their gene structures, protein attributes, cis-regulatory elements, and expression patterns in two pearl millet genotypes contrasting for rancidity. All the phospholipases have a high alpha-helix content and distorted regions within the predicted secondary structures. Moreover, many of these enzymes possess binding sites for both metal and non-metal ligands. Additionally, the putative promoter regions associated with these genes exhibit multiple copies of cis-elements specifically responsive to biotic and abiotic stress factors and signaling molecules. The transcriptional profiling of 44 phospholipase genes in two genotypes contrasting for rancidity across six key tissues during pearl millet growth revealed a predominant expression in grains, followed by seed coat and endosperm. Specifically, the genes PgPLD-alpha1-1, PgPLD-alpha1-5, PgPLD-delta1-7a, PgPLA1-II-1a, and PgPLD-delta1-2a exhibited notable expression in grains of both the genotypes while showing negligible expression in the other five tissues. The sequence alignment of putative promoters revealed several variations including SNPs and InDels. These variations resulted in modifications to the corresponding cis-acting elements, forming distinct transcription factor binding sites suggesting the transcriptional-level regulation for these five genes in pearl millet. CONCLUSIONS: The current study utilized a genome-wide computational analysis to characterize the phospholipase gene family in pearl millet. A comprehensive expression profile of 44 phospholipases led to the identification of five grain-specific candidates. This underscores a potential role for at least these five genes in grain quality traits including the regulation of rancidity in pearl millet. Therefore, this study marks the first exploration highlighting the possible impact of phospholipases towards enhancing agronomic traits in pearl millet.

Solving the Pervasive Problem of Protocol Non-Compliance in MRI using an Open-Source tool mrQA.

Pooling data across diverse sources acquired by multisite consortia requires compliance with a predefined reference protocol i.e., ensuring different sites and scanners for a given project have used identical or compatible MR physics parameter values. Traditionally, this has been an arduous and manual process due to difficulties in working with the complicated DICOM standard and lack of resources allocated towards protocol compliance. Moreover, issues of protocol compliance is often overlooked for lack of realization that parameter values are routinely improvised/modified locally at various sites. The inconsistencies in acquisition protocols can reduce SNR, statistical power, and in the worst case, may invalidate the results altogether. An open-source tool, mrQA was developed to automatically assess protocol compliance on standard dataset formats such as DICOM and BIDS, and to study the patterns of non-compliance in over 20 open neuroimaging datasets, including the large ABCD study. The results demonstrate that the lack of compliance is rather pervasive. The frequent sources of non-compliance include but are not limited to deviations in Repetition Time, Echo Time, Flip Angle, and Phase Encoding Direction. It was also observed that GE and Philips scanners exhibited higher rates of non-compliance relative to the Siemens scanners in the ABCD dataset. Continuous monitoring for protocol compliance is strongly recommended before any pre/post-processing, ideally right after the acquisition, to avoid the silent propagation of severe/subtle issues. Although, this study focuses on neuroimaging datasets, the proposed tool mrQA can work with any DICOM-based datasets.

Enhancing Transcriptome Mapping with Rapid PRO-seq Profiling of Nascent RNA.

Precision nuclear run-on (PRO) sequencing (PRO-seq) is a powerful technique for mapping polymerase active sites with nucleotide resolution and measuring newly synthesized transcripts at both promoters and enhancer elements. The current PRO-seq protocol is time-intensive, technically challenging, and requires a large amount of starting material. To overcome these limitations, we developed rapid PRO-seq (rPRO-seq) which utilizes pre-adenylated single-stranded DNAs (AppDNA), a dimer blocking oligonucleotide (DBO), on-bead 5' RNA end repair, and column-based purification. These modifications enabled efficient transcriptome mapping within a single day (∼12 hours) increasing ligation efficiency, abolished adapter dimers, and reduced sample loss and RNA degradation. We demonstrate the reproducibility of rPRO-seq in measuring polymerases at promoters, gene bodies, and enhancers as compared to original PRO-seq protocols. Additionally, rPRO-seq is scalable, allowing for transcriptome mapping with as little as 25,000 cells. We apply rPRO-seq to study the role of Integrator in mouse hematopoietic stem and progenitor cell (mHSPC) homeostasis, identifying Ints11 as an essential component of transcriptional regulation and RNA processing in mHSPC homeostasis. Overall, rPRO-seq represents a significant advance in the field of nascent transcript analyses and will be a valuable tool for generating patient-specific genome-wide transcription profiles with minimal sample requirements.

CRISPR/Cas9-mediated mutagenesis of phytoene desaturase in pigeonpea and groundnut.

The CRISPR/Cas9 technology, renowned for its ability to induce precise genetic alterations in various crop species, has encountered challenges in its application to grain legume crops such as pigeonpea and groundnut. Despite attempts at gene editing in groundnut, the low rates of transformation and editing have impeded its widespread adoption in producing genetically modified plants. This study seeks to establish an effective CRISPR/Cas9 system in pigeonpea and groundnut through Agrobacterium-mediated transformation, with a focus on targeting the phytoene desaturase (PDS) gene. The PDS gene is pivotal in carotenoid biosynthesis, and its disruption leads to albino phenotypes and dwarfism. Two constructs (one each for pigeonpea and groundnut) were developed for the PDS gene, and transformation was carried out using different explants (leaf petiolar tissue for pigeonpea and cotyledonary nodes for groundnut). By adjusting the composition of the growth media and refining Agrobacterium infection techniques, transformation efficiencies of 15.2% in pigeonpea and 20% in groundnut were achieved. Mutation in PDS resulted in albino phenotype, with editing efficiencies ranging from 4 to 6%. Sequence analysis uncovered a nucleotide deletion (A) in pigeonpea and an A insertion in groundnut, leading to a premature stop codon and, thereby, an albino phenotype. This research offers a significant foundation for the swift assessment and enhancement of CRISPR/Cas9-based genome editing technologies in legume crops.

Macronutrient composition of term and preterm human milk of different socio economic groups.

Assessment of the nutritional composition of Human Breast Milk (HBM) is important to understand its sufficiency as the sole nutrient source in infants. The present study is aimed to analyze the proximate composition along with total amino acid and fatty acid profile in term and preterm HBM of different socio economic status. This cross sectional study included, 120 lactating mothers with term or preterm gestation from maternity hospitals located in Hyderabad, Telangana. Nutritional proximate, total amino and fatty acid profiles were estimated in pooled human milk collected from each participant within the first week of postpartum. The macronutrient composition in term was similar to that of preterm breast milk. The essential amino acid Leucine was significantly high in preterm (8.91 ± 0.18) when compared to term (8.61 ± 0.23). ω-5 fatty acid Myristoleic acid was significantly high in preterm (0.14 ± 0.02) when compared to term (0.11 ± 0.02), whereas ω-6 fatty acids like Docosadienoic Acid and Eicosadienoic acid were found to be significantly high in term when compared to preterm. Further, it was also found that the mono unsaturated and ω-9 fatty acids were significantly high in lower socio economic group, whereas, poly unsaturated and ω -3 and 6 fatty acids were significantly high in upper socio economic group. The present study concludes that, nutritional composition like essential amino and fatty acids of human milk vary significantly between different gestational age as well as in socio economic groups.

The Integrator complex regulates microRNA abundance through RISC loading.

MicroRNA (miRNA) homeostasis is crucial for the posttranscriptional regulation of their target genes during development and in disease states. miRNAs are derived from primary transcripts and are processed from a hairpin precursor intermediary to a mature 22-nucleotide duplex RNA. Loading of the duplex into the Argonaute (AGO) protein family is pivotal to miRNA abundance and its posttranscriptional function. The Integrator complex plays a key role in protein coding and noncoding RNA maturation, RNA polymerase II pause-release, and premature transcriptional termination. Here, we report that loss of Integrator results in global destabilization of mature miRNAs. Enhanced ultraviolet cross-linking and immunoprecipitation of Integrator uncovered an association with duplex miRNAs before their loading onto AGOs. Tracing miRNA fate from biogenesis to stabilization by incorporating 4-thiouridine in nascent transcripts pinpointed a critical role for Integrator in miRNA assembly into AGOs.

Rescue Stenting for Refractory Large Vessel Occlusions in the Thrombectomy Era: Intracranial Use of Coronary Stents in Low-mid Economic Settings.

BACKGROUND:  Failed mechanical thrombectomy due to a refractory emergent large vessel occlusion (RELVO) in patients presenting with an acute stroke poses a major challenge to the outcomes. OBJECTIVE:  We demonstrate the use of coronary stents in the intracranial circulation as rescue stenting for an already expensive mechanical thrombectomy procedure in a mid-low socioeconomic setting. METHODS:  A retrospective, multicenter study was conducted between December 2015 and January 2021. The studied cohort were patients who required the use of a rescue stenting using a coronary stent for emergent large vessel occlusion to avoid failed recanalization. Failed recanalization was defined as failed vessel recanalization after at least two passes. Patient demographic data, procedure specifics, type of stent used, and procedural outcomes were collected. RESULTS:  A total of 26 patients with acute ischemic stroke were included from eight different centers across India. Out of 26 patients, 19 (73.0%) were male and seven were female (26.9%). The mean age was 53.6 years, the youngest patient was 23 years old and the eldest was 68 years old. Seven patients (26.9%) had posterior circulation stroke due to occlusion of the vertebral or basilar artery and 19 patients (73.0%) had anterior circulation stroke median NIHSS at presentation was 16 (range 10 to 28) in anterior circulation stroke and 24 (range 16 to 30) in posterior circulation stroke. Intravenous thrombolysis with tissue plasminogen activator (IV tPA) was given in three patients (11.5%). The hospital course of two patients was complicated by symptomatic intracranial hemorrhage (sICH), which was fatal. Favorable revascularization outcome and favorable functional outcome was achieved in 22 patients (84.6%), three patients passed away (11.5%), and one patient was lost to follow up. CONCLUSIONS:  Overall, our study finds that rescue stenting using coronary stents can potentially improve outcomes in refractory large vessel occlusions while minimizing costs in low-mid economic settings.

Membrane Domain Localization and Interaction of the Prion-Family Proteins, Prion and Shadoo with Calnexin.

The cellular prion protein (PrPC) is renowned for its infectious conformational isoform PrPSc, capable of templating subsequent conversions of healthy PrPCs and thus triggering the group of incurable diseases known as transmissible spongiform encephalopathies. Besides this mechanism not being fully uncovered, the protein's physiological role is also elusive. PrPC and its newest, less understood paralog Shadoo are glycosylphosphatidylinositol-anchored proteins highly expressed in the central nervous system. While they share some attributes and neuroprotective actions, opposing roles have also been reported for the two; however, the amount of data about their exact functions is lacking. Protein-protein interactions and membrane microdomain localizations are key determinants of protein function. Accurate identification of these functions for a membrane protein, however, can become biased due to interactions occurring during sample processing. To avoid such artifacts, we apply a non-detergent-based membrane-fractionation approach to study the prion protein and Shadoo. We show that the two proteins occupy similarly raft and non-raft membrane fractions when expressed in N2a cells and that both proteins pull down the chaperone calnexin in both rafts and non-rafts. These indicate their possible binding to calnexin in both types of membrane domains, which might be a necessary requisite to aid the inherently unstable native conformation during their lifetime.

Integrator enforces the fidelity of transcriptional termination at protein-coding genes.

Integrator regulates the 3'-end processing and termination of multiple classes of noncoding RNAs. Depletion of INTS11, the catalytic subunit of Integrator, or ectopic expression of its catalytic dead enzyme impairs the 3'-end processing and termination of a set of protein-coding transcripts termed Integrator-regulated termination (IRT) genes. This defect is manifested by increased RNA polymerase II (RNAPII) readthrough and occupancy of serine-2 phosphorylated RNAPII, de novo trimethylation of lysine-36 on histone H3, and a compensatory elevation of the cleavage and polyadenylation (CPA) complex beyond the canonical polyadenylation sites. 3' RNA sequencing reveals that proximal polyadenylation site usage relies on the endonuclease activity of INTS11. The DNA sequence encompassing the transcription end sites of IRT genes features downstream polyadenylation motifs and an enrichment of GC content that permits the formation of secondary structures within the 3'UTR. Together, this study identifies a subset of protein-coding transcripts whose 3' end processing requires the Integrator complex.

Impact of COVID-19 on gastroenterology fellowship training: a multicenter analysis of endoscopy volumes.

Background and study aims The COVID-19 pandemic has had a profound impact on gastroenterology training programs. We aimed to objectively evaluate procedural training volume and impact of COVID-19 on gastroenterology fellowship programs in the United States. Methods This was a retrospective, multicenter study. Procedure volume data on upper and lower endoscopies performed by gastroenterology fellows was abstracted directly from the electronic medical record. The study period was stratified into 2 time periods: Study Period 1, SP1 (03/15/2020 to 06/30/2020) and Study Period 2, SP2 (07/01/2020 to 12/15/2020). Procedure volumes during SP1 and SP2 were compared to Historic Period 1 (HP1) (03/15/2019 to 06/30/2019) and Historic Period 2 (HP2) (07/01/2019 to 12/15/2019) as historical reference. Results Data from 23 gastroenterology fellowship programs (total procedures = 127,958) with a median of 284 fellows (range 273-289; representing 17.8 % of all trainees in the United States) were collected. Compared to HP1, fellows performed 53.6 % less procedures in SP1 (total volume: 28,808 vs 13,378; mean 105.52 ±â€Š71.94 vs 47.61 ±â€Š41.43 per fellow; P  < 0.0001). This reduction was significant across all three training years and for both lower and upper endoscopies ( P  < 0.0001). However, the reduction in volume was more pronounced for lower endoscopy compared to upper endoscopy [59.03 % (95 % CI: 58.2-59.86) vs 48.75 % (95 % CI: 47.96-49.54); P  < 0.0001]. The procedure volume in SP2 returned to near baseline of HP2 (total volume: 42,497 vs 43,275; mean 147.05 ±â€Š96.36 vs 150.78 ±â€Š99.67; P  = 0.65). Conclusions Although there was a significant reduction in fellows' endoscopy volume in the initial stages of the pandemic, adaptive mechanisms have resulted in a return of procedure volume to near baseline without ongoing impact on endoscopy training.

RAC1 plays an essential role in estrogen receptor alpha function in breast cancer cells.

The activity of Rho family GTPase protein, RAC1, which plays important normal physiological functions, is dysregulated in multiple cancers. RAC1 is expressed in both estrogen receptor alpha (ER)-positive and ER-negative breast cancer (BC) cells. However, ER-positive BC is more sensitive to RAC1 inhibition. We have determined that reducing RAC1 activity, using siRNA or EHT 1864 (a small molecule Rac inhibitor), leads to rapid ER protein degradation. RAC1 interacts with ER within the ER complex and RAC1 localizes to chromatin binding sites for ER upon estrogen treatment. RAC1 activity is important for RNA Pol II function at both promoters and enhancers of ER target genes and ER-regulated gene transcription is blocked by EHT 1864, in a dose-dependent manner. Having identified that RAC1 is an essential ER cofactor for ER protein stability and ER transcriptional activity, we report that RAC1 inhibition could be an effective therapeutic approach for ER-positive BC.

Live implant dosimetry may be an effective replacement for postimplant computed tomography in localized prostate cancer patients receiving low dose rate brachytherapy.

PURPOSE: To determine if Live Implant Dosimetry (LIDO) utilizing intraoperative transrectal ultrasound (TRUS) is equivalent to postimplant CT dosimetry (either day 0 or day 30) in patients with localized prostate cancer (PC) treated with low dose rate (LDR) prostate seed brachytherapy. METHODS AND MATERIALS: The treated population consisted of 628 men with localized (T1-T2) PC. All d'Amico risk categories (low, intermediate, and high) were included, and 437 patients were treated with monotherapy (160 Gy) [low and low tier intermediate], and the remainder (191) [high tier intermediate and high risk] with an implant boost (106 Gy) post external beam radiation, to a volume including the prostate and seminal vesicles (46 Gy). LIDO with intraoperative TRUS, postimplant CT (day 0 and day 30) were performed in all cases. Prostate volumes (V), V100 (prostate) and dose (D) D90 (prostate), D30 (urethra), and Rectum D2cc, were recorded. No urinary catheter was used on Day 30 CT. RESULTS: More than 91.33% of monotherapy patients reached the target D90 according to LIDO while only 82.99% of Day 0 CT and 92.82% of Day 30 CT achieved target D90. When considering V100, monotherapy patients recorded target dosimetry in 90.93%, 82.31%, and 92.02% of cases assessed by LIDO, Day 0 CT and Day 30 CT, respectively. Strong correlations are observed in D90, Rectum D2cc and Urethra D30 across imaging modalities but V100 and V150 were poorly correlated due to the relative quantification of this parameter and high degree of error in measurement. Of all monotherapy patients with satisfactory dosimetry on LIDO, 94.82% reached target D90 at day 30 CT and 94.19% reached target V100. CONCLUSIONS: LIDO and CT are both effective tools for assessing postimplant dosimetry. Patients with satisfactory LIDO dosimetry are highly likely to have equivalent dosimetry on CT at follow-up, indicating that postimplant CT may be eliminated in PC a patients implanted with this technique.

Cortical Thickness Estimation in Individuals With Cerebral Small Vessel Disease, Focal Atrophy, and Chronic Stroke Lesions.

BACKGROUND: Regional changes to cortical thickness in individuals with neurodegenerative and cerebrovascular diseases (CVD) can be estimated using specialized neuroimaging software. However, the presence of cerebral small vessel disease, focal atrophy, and cortico-subcortical stroke lesions, pose significant challenges that increase the likelihood of misclassification errors and segmentation failures. PURPOSE: The main goal of this study was to examine a correction procedure developed for enhancing FreeSurfer's (FS's) cortical thickness estimation tool, particularly when applied to the most challenging MRI obtained from participants with chronic stroke and CVD, with varying degrees of neurovascular lesions and brain atrophy. METHODS: In 155 CVD participants enrolled in the Ontario Neurodegenerative Disease Research Initiative (ONDRI), FS outputs were compared between a fully automated, unmodified procedure and a corrected procedure that accounted for potential sources of error due to atrophy and neurovascular lesions. Quality control (QC) measures were obtained from both procedures. Association between cortical thickness and global cognitive status as assessed by the Montreal Cognitive Assessment (MoCA) score was also investigated from both procedures. RESULTS: Corrected procedures increased "Acceptable" QC ratings from 18 to 76% for the cortical ribbon and from 38 to 92% for tissue segmentation. Corrected procedures reduced "Fail" ratings from 11 to 0% for the cortical ribbon and 62 to 8% for tissue segmentation. FS-based segmentation of T1-weighted white matter hypointensities were significantly greater in the corrected procedure (5.8 mL vs. 15.9 mL, p < 0.001). The unmodified procedure yielded no significant associations with global cognitive status, whereas the corrected procedure yielded positive associations between MoCA total score and clusters of cortical thickness in the left superior parietal (p = 0.018) and left insula (p = 0.04) regions. Further analyses with the corrected cortical thickness results and MoCA subscores showed a positive association between left superior parietal cortical thickness and Attention (p < 0.001). CONCLUSION: These findings suggest that correction procedures which account for brain atrophy and neurovascular lesions can significantly improve FS's segmentation results and reduce failure rates, thus maximizing power by preventing the loss of our important study participants. Future work will examine relationships between cortical thickness, cerebral small vessel disease, and cognitive dysfunction due to neurodegenerative disease in the ONDRI study.

Does size matter? The relationship between predictive power of single-subject morphometric networks to spatial scale and edge weight.

Network-level analysis based on anatomical, pairwise similarities (e.g., cortical thickness) has been gaining increasing attention recently. However, there has not been a systematic study of the impact of spatial scale and edge definitions on predictive performance, which is necessary to obtain a clear understanding of their relative performance. In this study, we present a histogram-based approach to construct subject-wise weighted networks that enable a principled comparison across different methods of network analysis. We design several weighted networks based on three large publicly available datasets and perform a robust evaluation of their predictive power under four levels of separability. An interesting insight generated is that changes in nodal size (spatial scale) have no significant impact on predictive power among the three classification experiments and two disease cohorts studied, i.e., mild cognitive impairment and Alzheimer's disease from ADNI, and Autism from the ABIDE dataset. We also release an open source python package called graynet to enable others to leverage the novel network feature extraction algorithms presented here. These techniques and toolbox can also be applied to other modalities due to their domain- and feature-agnostic nature) in diverse applications of connectivity research. In addition, the findings from the ADNI dataset are replicated in the AIBL dataset using an open source machine learning tool called neuropredict.