Ravi Goyal

Background and objectives: The linear relation between human metaphase chromosome length and DNA content has never been rigorously reconciled with modern Hi-C models of mitotic chromatin folding. We tested whether the relation implies a quantitative unit of mitotic chromosome organization. Methods: We pooled metaphase lengths for 24 human chromosomes from five cytogenetic studies of cultured peripheral lymphocytes and regressed length against base-pair content from GRCh38 and T2T-CHM13 v2.0. Pre-specified analyses comprised ordinary least-squares and power-law fits, arm-level decomposition, and reconciliation with the Gibcus 2018 helical loop-array model. Orthogonal validation used Rao 2014 Hi-C boundary counts and Pope 2014 Repli-Seq. Results: Length scales linearly with DNA content as L (μm) = 0.0329 x Mb + 0.043 (R-squared = 0.998, power-law exponent 0.98 + /- 0.01), with a cross-karyotype compaction density of 33.4 + /- 1.0 nm/Mb. T2T-CHM13 reanalysis identifies satellite over-condensation; the arm-level residual correlates with p-arm fraction (r = 0.65, p = 5.6e-4). We propose an operational Metaphase Chromatin Unit (MCU) as a quantitative scaling unit (not a discrete structural quantum, as quantization tests are negative): 1 MCU = 7.6 Mb DNA = 0.25 μm axial length, numerically corresponding to one Gibcus late-metaphase helical turn; the human haploid genome scales to 406 MCUs. The pairwise megabase-shift slope of 32.75 nm/Mb (R-squared = 0.996) and the approximately 6 Mb Abbe optical detection threshold correctly classify 9 of 9 microdeletion syndromes as karyotype-visible versus FISH-required. Conclusions: The MCU provides a unified quantitative unit for human mitotic chromosome organization, integrating cytogenetic, Hi-C, polymer-biophysical, and clinical scales.

Reliable monitoring of uterine contractility underpins the assessment of labor, the diagnosis of preterm labor, and the timing of obstetric intervention, yet routine methods measure only the mechanical consequences of contraction. External tocodynamometry and cardiotocography (CTG) are operator- and position-dependent and perform poorly with maternal obesity, detecting as few as ~54% of the contractions confirmed by an intrauterine pressure catheter, whereas surface electrohysterography (EHG) detects upward of ~94% by recording the myometrial electrical activity that drives contraction. This review examines EHG and uterine electromyography (EMG) as measurement modalities, covering their physiological origin, acquisition hardware, signal characteristics, feature extraction, and machine-learning analysis, and compares them with CTG against the intrauterine pressure catheter reference standard. Electrical approaches additionally yield predictive parameters, notably spectral peak frequency and propagation velocity, that mechanical methods cannot provide. The principal barrier to translation is methodological heterogeneity rather than physiology: differences in electrodes, filtering, feature definitions, and outcome measures preclude cross-study comparison and meta-analysis. As its central contribution, this review consolidates prior calls for standardization into a minimum reporting set for EHG studies and appraises translational readiness, identifying prospective external validation, shared datasets, explainable models, and outcome-linked trials as priorities.

Background and Objectives: The linear relation between human metaphase chromosome length and DNA content has never been rigorously reconciled with modern Hi-C models of mitotic chromatin folding. We tested whether the relation implies a quantitative unit of mitotic chromosome organization. Methods: We pooled metaphase lengths for 24 human chromosomes from five cytogenetic studies of cultured peripheral lymphocytes and regressed length against base-pair content from GRCh38 and T2T-CHM13 v2.0. Pre-specified analyses comprised ordinary least-squares and power-law fits, arm-level decomposition, and reconciliation with the Gibcus 2018 helical loop-array model. Orthogonal validation used Rao 2014 Hi-C boundary counts and Pope 2014 Repli-Seq. Results: Length scales linearly with DNA content as L (μm) = 0.0329 x Mb + 0.043 (R-squared = 0.998, power-law exponent 0.98 +/-0.01), with a cross-karyotype compaction density of 33.4 +/-1.0 nm/Mb. T2T-CHM13 reanalysis identifies satellite over-condensation; the arm-level residual correlates with p-arm fraction (r = 0.65, p = 5.6e-4). We propose an operational Metaphase Chromatin Unit (MCU) as a quantitative scaling unit (not a discrete structural quantum, as quantization tests are negative): 1 MCU = 7.6 Mb DNA = 0.25 μm axial length, numerically corresponding to one Gibcus late-metaphase helical turn; the human haploid genome scales to 406 MCUs. The pairwise megabase-shift slope of 32.75 nm/Mb (R-squared = 0.996) and the approximately 6 Mb Abbe optical detection threshold correctly classify 9 of 9 microdeletion syndromes as karyotype-visible versus FISH-required. Conclusions: The MCU provides a unified quantitative unit for human mitotic chromosome organization, integrating cytogenetic, Hi-C, polymer-biophysical, and clinical scales.

Endometrial receptivity assessment currently requires an invasive tissue biopsy, yet recent randomized trials have called into question the clinical utility of biopsy-based approaches. Here we present EndoTwin-W, a four-layer mechanistic computational model that simulates human endometrial remodeling from hormone inputs through receptor binding, pathway scoring, and continuous-time Markov chain cell-state transitions across 17 cell states. Transition rates were optimized against scRNA-seq and microarray data, then validated by 5-fold cross-validation on an independent bulk RNA-seq cohort (n=236 biopsies), achieving significant correlations for 16 of 17 cell states (mean Spearman r = 0.505) with benchmark dominance over three null models for 13 of 17 states. The model identifies glycodelin-A (PAEP) and CA-125 (MUC16) as mechanistically grounded candidate circulating biomarkers capturing two principal receptivity failure modes: inadequate decidualization and excessive inflammation. Hill-function prediction of serum glycodelin-A shows strong rank-order calibration (Spearman rho = 0.833, p = 0.010). Cross-condition held-out validation against 9 independent datasets (244 samples) achieves significant concordance in 5 of 9 datasets (median rho = 0.435). A cross-dataset receptivity index analysis across 18 GEO datasets (21 comparisons) demonstrates mean AUC = 0.599 with correct direction in 76% of analyses, including significant RNA-seq validation (AUC = 0.770, p = 0.003). The divergence between predicted and measured biomarker values defines a Progesterone Resistance Score quantifying decidualization deficit and inflammation burden. EndoTwin-W provides a mechanistic framework and candidate blood-based biomarkers for receptivity assessment; prospective paired serum-tissue validation is required before clinical use. An open research version of EndoTwin-W is available at https://endotwin-w.com (mirror: https://endotwinw.com ).

Fetal growth restriction (FGR) is a risk factor for obesity in adult life. Importantly, growth‐restricted females are more prone to obesity than males. The mechanisms involved in this sexually dimorphic programming are not known. Previously, we have demonstrated that ambient hyperthermia (40°C) led to placental insufficiency and significant FGR, and the perirenal adipose tissue undergoes sexually dimorphic gene expression. We demonstrated that males undergo significant changes in gene expression with growth restriction. This was not the case in females. We have also demonstrated that the isolated preadipocytes from male FGR (MFGR) have reduced differentiation potential compared to control males & females and female FGR (FFGR). Thus, we hypothesized that growth restriction differentially programs gene expression and genetic pathways in perirenal preadipocytes, which reduces their differentiation potential in male fetuses in a sexually dimorphic manner. We created FGR by exposing pregnant sheep to ambient hyperthermia. After isolating preadipocytes from perirenal adipose tissue, we differentiated them following published protocols. We examined the gene expression before and after differentiation from control male, control female, MFGR, and FFGR female. We also compared our data with other published studies in mouse and human preadipocytes. Our results demonstrate that a set of 21 genes altered with preadipocyte differentiation to mature adipocytes is common in adipose tissue from both sexes, humans, mice, and sheep, at different organismal ages (embryonic, fetal, and adult) and different sites (subcutaneous inguinal, pancreatic, perirenal). We also demonstrate that female FFGR fetuses demonstrate all these 21 genes altered similar to control males and females; however, MFGR fetuses have six genes (Dgat2, Fabp4, Lipe, Lrrfip1, Spred3, and Thrsp) that are not changed with preadipocyte differentiation to mature adipocyte. These genes may be responsible for reduced differentiation potential and obesity in FGR males compared to FGR females. Another important finding of the present study is that Lrrfip1, known to be associated with obesity, was upregulated with FGR and requires further investigation. Overall, our studies provide several target genes that may play a crucial role in reducing the risk of MFGR for obesity.

The role of long intergenic noncoding RNAs (lincRNAs) in fetal development has emerged as a significant area of study, challenging the traditional protein-centric view of gene expression. While messenger RNAs (mRNAs) have long been recognized for their role in encoding proteins, recent advances have illuminated the critical functions of lincRNAs in various biological processes. Initially identified through high-throughput sequencing technologies, lincRNAs are transcribed from intergenic regions between protein-coding genes and exhibit unique regulatory functions. Unlike mRNAs, lincRNAs are involved in complex interactions with chromatin and chromatin-modifying complexes, influencing gene expression and chromatin structure. LincRNAs are pivotal in regulating tissue-specific development and embryogenesis. For example, they are crucial for proper cardiac, neural, and reproductive system development, with specific lincRNAs being associated with organogenesis and differentiation processes. Their roles in embryonic development include regulating transcription factors and modulating chromatin states, which are essential for maintaining developmental programs and cellular identity. Studies using RNA sequencing and genetic knockout models have highlighted the importance of lincRNAs in processes such as cell differentiation, tissue patterning, and organ development. Despite their functional significance, the comprehensive annotation and understanding of lincRNAs remain limited. Ongoing research aims to elucidate their mechanisms of action and potential applications in disease diagnostics and therapeutics. This review summarizes current knowledge on the functional roles of lincRNAs in fetal development, emphasizing their contributions to tissue-specific gene regulation and developmental processes.

Prevailing hypoxemia and hypoglycemia in near-term fetuses with placental insufficiency-induced intrauterine growth restriction (IUGR) chronically increases norepinephrine concentrations, which lower adrenergic sensitivity and lipid mobilization postnatally, indicating a predisposition for adiposity. To determine adrenergic-induced responses, we examined the perirenal adipose tissue transcriptome from IUGR fetuses with or without hypercatecholaminemia. IUGR was induced in sheep with maternal hyperthermia, and hypercatecholaminemia in IUGR was prevented with bilateral adrenal demedullation. Adipose tissue was collected from sham-operated control (CON) and IUGR fetuses and adrenal-demedullated control (CAD) and IUGR (IAD) fetuses. Norepinephrine concentrations were lower in IAD fetuses than in IUGR fetuses despite both being hypoxemic and hypoglycemic. In IUGR fetuses, perirenal adipose tissue mass relative to body mass was greater compared with the CON, adrenal-demedullated control, and IAD groups. Transcriptomic analysis identified 581 differentially expressed genes (DEGs) in CON vs IUGR adipose tissue and 193 DEGs in IUGR vs IAD adipose tissue. Integrated functional analysis of these 2 comparisons showed enrichment for proliferator-activated receptor signaling and metabolic pathways and identified adrenergic responsive genes. Within the adrenergic-regulated DEGs, we identified transcripts that regulate adipocyte proliferation and differentiation: adipogenesis regulatory factor, C/CCAAT/enhancer binding protein α, and sterol carrier protein 2. DEGs associated with the metabolic pathway included pyruvate dehydrogenase kinase 4, 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4, IGF-binding proteins (IGFBP-5 and IGFBP-7). Sex-specific expression differences were also found for adipogenesis regulatory factor, pyruvate dehydrogenase kinase 4, IGFBP5, and IGFBP7. These findings indicate that sustained adrenergic stimulation during IUGR leads to adipocyte hyperplasia with alterations in metabolism, proliferation, and preadipocyte differentiation pathways.

Environmental heat stress triggers a series of compensatory mechanisms in sheep that are dependent on their genetic regulation of thermotolerance. Our objective was to identify genes and regulatory pathways associated with thermotolerance in ewes exposed to heat stress. We performed next-generation RNA sequencing on blood collected from 16 pregnant ewes, which were grouped as tolerant and non-tolerant to heat stress according to a physiological indicator. Additional samples were collected to measure complete blood count. A total of 358 differentially expressed genes were identified after applying selection criteria. Gene expression analysis detected 46 GO terms and 52 KEGG functional pathways. The top-three signaling pathways were p53, RIG-I-like receptor and FoxO, which suggested gene participation in biological processes such as apoptosis, cell signaling and immune response to external stressors. Network analysis revealed ATM, ISG15, IRF7, MDM4, DHX58 and TGFβR1 as over-expressed genes with high regulatory potential. A co-expression network involving the immune-related genes ISG15, IRF7 and DXH58 was detected in lymphocytes and monocytes, which was consistent with hematological findings. In conclusion, transcriptomic analysis revealed a non-viral immune mechanism involving apoptosis, which is induced by external stressors and appears to play an important role in the molecular regulation of heat stress tolerance in ewes.