Cell-type-specific transcriptomics uncovers spatial regulatory networks in bioenergy sorghum stems.

Bioenergy sorghum is a low-input, drought-resilient, deep-rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum's 4-5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about cell-type gene expression and regulation in stems was available to enable engineering. To obtain this information, laser capture microdissection was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell-type-specific and cell-preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell-type-specific gene regulatory networks (GRNs) revealed that unique transcription factor families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell-specific transcriptome data was combined with known secondary cell wall (SCW) networks to identify the GRNs that differentially activate SCW formation in vascular sclerenchyma and epidermal cells. The spatial transcriptomic dataset provides a valuable source of information about the function of different sorghum cell types and GRNs that will enable the engineering of bioenergy sorghum stems, and an interactive web application developed during this project will allow easy access and exploration of the data (https://mc-lab.shinyapps.io/lcm-dataset/).

De Novo Elastin Assembly Alleviates Development of Supravalvular Aortic Stenosis-Brief Report.

BACKGROUND: A series of incurable cardiovascular disorders arise due to improper formation of elastin during development. Supravalvular aortic stenosis (SVAS), resulting from a haploinsufficiency of ELN, is caused by improper stress sensing by medial vascular smooth muscle cells, leading to progressive luminal occlusion and heart failure. SVAS remains incurable, as current therapies do not address the root issue of defective elastin. METHODS: We use SVAS here as a model of vascular proliferative disease using both human induced pluripotent stem cell-derived vascular smooth muscle cells and developmental Eln+/- mouse models to establish de novo elastin assembly as a new therapeutic intervention. RESULTS: We demonstrate mitigation of vascular proliferative abnormalities following de novo extracellular elastin assembly through the addition of the polyphenol epigallocatechin gallate to SVAS human induced pluripotent stem cell-derived vascular smooth muscle cells and in utero to Eln+/- mice. CONCLUSIONS: We demonstrate de novo elastin deposition normalizes SVAS human induced pluripotent stem cell-derived vascular smooth muscle cell hyperproliferation and rescues hypertension and aortic mechanics in Eln+/- mice, providing critical preclinical findings for the future application of epigallocatechin gallate treatment in humans.

Investigating the synergistic effects of biochar, trans-zeatin riboside, and Azospirillum brasilense on soil improvement and enzymatic activity in water-stressed wheat.

BACKGROUND: Water stress is a major danger to crop yield, hence new approaches to strengthen plant resilience must be developed. To lessen the negative effects of water stress on wheat plants, present study was arranged to investigate the role of synergistic effects of biochar, trans-zeatin riboside (t-ZR), and Azospirillum brasilense on soil improvement and enzymatic activity in water-stressed wheat. RESULTS: In a three-replication experiment comprising of four treatments (T0: Control, T1: Drought stress (DS), T2: DS + t-ZR with biochar, T3: DS + A. brasilense with biochar), we observed notable improvements in soil quality and enzymatic activities in water-stressed wheat plants with the application of t-ZR and A. brasilense with biochar. In drought stress, Treatment having the application of A. brasilense with biochar performs best as compared to the other and significant increased the enzymatic activities such as peroxidase (7.36%), catalase (8.53%), superoxide dismutase (6.01%), polyphenol oxidase (14.14%), and amylase (16.36%) in wheat plants. Different enzymatic activities showed different trends of results. Soil organic C, dissolved organic C, dissolved organic N also enhanced 29.46%, 8.59%, 22.70% respectively with the application of A. brasilense with biochar under drought stress condition. CONCLUSIONS: The synergistic action of A. brasilense and biochar creates an effective microbiological environment that supports essential plant physiological processes during drought stress. This enhancement is attributed to improved soil fertility and increased organic matter content, highlighting the potential of these novel strategies in mitigating water stress effects and enhancing crop resilience.

Treatment of Hidradenitis Suppurativa Evaluation Study (THESEUS): a prospective cohort study.

BACKGROUND: Hidradenitis suppurativa (HS) is a chronic, painful disease affecting flexures and other skin regions, producing nodules, abscesses and skin tunnels. Laser treatment targeting hair follicles and deroofing of skin tunnels are standard HS interventions in some countries but are rarely offered in the UK. OBJECTIVES: To describe current UK HS management pathways and influencing factors to inform the design of future randomized controlled trials (RCTs). METHODS: THESEUS was a nonrandomized 12-month prospective cohort study set in 10 UK hospitals offering five interventions: oral doxycycline 200 mg daily; oral clindamycin and rifampicin both 300 mg twice daily for 10 weeks, extended for longer in some cases; laser treatment targeting hair follicles; deroofing; and conventional surgery. The primary outcome was the combination of clinician-assessed eligibility and participant hypothetical willingness to receive each intervention. The secondary outcomes were the proportion of participants selecting each intervention as their final treatment option; the proportion who switch treatments; treatment fidelity; and attrition rates. THESEUS was prospectively registered on the ISRCTN registry: ISRCTN69985145. RESULTS: The recruitment target of 150 participants was met after 18 months, in July 2021, with two pauses due to the COVID-19 pandemic. Baseline demographics reflected the HS secondary care population: average age 36 years, 81% female, 20% non-White, 64% current or ex-smokers, 86% body mass index ≥ 25, 68% with moderate disease, 19% with severe disease and 13% with mild disease. Laser was the intervention with the highest proportion (69%) of participants eligible and willing to receive treatment, then deroofing (58%), conventional surgery (54%), clindamycin and rifampicin (44%), and doxycycline (37%). Laser was ranked first choice by the greatest proportion of participants (41%). Attrition rates were 11% and 17% after 3 and 6 months, respectively. Concordance with doxycycline was 52% after 3 months due to lack of efficacy, participant choice and adverse effects. Delays with procedural interventions were common, with only 43% and 26% of participants starting laser and deroofing, respectively, after 3 months. Uptake of conventional surgery was too small to characterize the intervention. Switching treatment was uncommon and there were no serious adverse events. CONCLUSIONS: THESEUS has established laser treatment and deroofing for HS in the UK and demonstrated their popularity with patients and clinicians for future RCTs.

Silica-Based Superhydrophobic and Superoleophilic Cotton Fabric with Enhanced Self-Cleaning Properties for Oil-Water Separation and Methylene Blue Degradation.

Superhydrophobic textiles with multifunctional characteristics are highly desired and have attracted tremendous research attention. This research employs a simple dip-coating method to obtain a fluorine-free silica-based superhydrophobic and superoleophilic cotton fabric. Pristine cotton fabric is coated with SiO2 nanoparticles and octadecylamine. SiO2 nanoparticles are anchored on the cotton fabric to increase surface roughness, and octadecyl amine lowers the surface energy, turning the hydrophilic cotton fabric into superhydrophobic. The designed cotton fabric exhibits a water contact angle of 159° and a sliding angle of 7°. The prepared cotton fabric is characterized by attenuated total reflectance-fourier transform infrared spectroscopy, X-ray diffraction, atomic force microscopy, scanning electron microscopy, and energy-dispersive X-ray spectroscopy. In addition, the coated fabric reveals excellent features, including mechanical and chemical stability, superhydrophobicity, superoleophilicity, and the self-cleaning ability. SiO2 nanoparticles and octadecylamine-coated cotton fabric demonstrate exceptional oil-water separation and wastewater remediation performance by degrading the methylene blue solution up to 89% under visible light. The oil-water separation ability is tested against five different oils with more than 90% separation efficiency. This strategy has the advantages of low-cost precursors, a simple and scalable coating method, enhanced superhydrophobicity and superoleophilicity, self-cleaning ability, efficient oil-water separation, and exceptional wastewater remediation performance.

Evaluation of clinical and laboratory characteristics of dengue viral infection and risk factors of dengue hemorrhagic fever: a multi-center retrospective analysis.

BACKGROUND: Dengue Viral Infection (DVI) has become endemic in Pakistan since the first major outbreak in Karachi in 1996. Despite aggressive measures taken by relevant authorities, Pakistan has been dealing with a worsening dengue crisis for the past two decades. DHF is severe form of dengue infection which is linked with significant morbidity and mortality. Early identification of severe dengue infections can reduce the morbidity and mortality. In this context we planned current study in which we find out the different factors related with DHF as well as clinical laboratory features of DHF and compare them to DF so that patients can be best evaluated for DHF and managed accordingly at admission. METHODS: Retrospective study conducted over a period of 6 years (2013-2018) in two tertiary care hospitals in Pakistan. Data were collected by using a pre-structured data collection form. Data were statistically analyzed to determine the clinical and laboratory characteristics of DVI and risk factors of dengue hemorrhagic fever (DHF). RESULTS: A total 512 dengue cases (34.05 ± 15.08 years; Male 69.53%) were reviewed. Most common clinical manifestations of DVI were fever (99.60%), headache (89.1%), chills (86.5%), rigors (86.5%), myalgia (72.3%). Less common clinical manifestations were vomiting (52.5%), arthralgia (50.2%) and skin rashes (47.5%). Furthermore, nasal bleeding (44.1%), gum bleeding (32.6%), pleural effusion (13.9%) and hematuria (13.1%) were more profound clinical presentations among DHF patients. Mortality rate was 1.5% in this study. Logistic regression analysis indicated that delayed hospitalization (OR: 2.30) and diabetes mellitus (OR:2.71), shortness of breath (OR:2.21), association with risk groups i.e., living near stagnant water, travelling to endemic areas, living in endemic regions (OR:1.95), and presence of warning signs (OR:2.18) were identified as risk factors of DHF. Statistically we found that there is strong association of diabetes mellitus (DM) with DHF while the patient suffering from DM individually had higher odds (2.71) of developing DHF than patients without disease. CONCLUSIONS: The current study demonstrated that the clinical and laboratory profiles of DF and DHF are significantly distinct. Significant predictors of DHF were advanced age, diabetes mellitus, ascites, pleural effusion, thick gallbladder and delayed hospitalization. The identification of these factors at early stage provides opportunities for the clinicians to identify high risk patients and to reduce dengue-related morbidity and mortality.

Impact of medication dosage on Helicobacter pylori eradication rates among pediatric patients.

OBJECTIVES: Helicobacter pylori rates of eradication to common first-line regimens continue to decline globally. Prescription of the appropriate medication dosage is an important consideration, particularly in the pediatric population due to medication weight-based dosing. Limited data is available on the impact of guideline-recommended weight-based dosing on the successful eradication of H. pylori in children. METHODS: Retrospective study of patients with histologic evidence of H. pylori from two pediatric tertiary care centers in New England. We excluded patients who were not treated or those missing eradication data. We compared the eradication rates of patients prescribed recommended weight-based dosages, duration, and frequency of treatment with those who were not. RESULTS: One hundred forty-four patients were included. The overall eradication rate was 73.6% (106/144). All treatment regimens were properly prescribed for 14 days. There was a high rate of improper weight-based dosing: proton pump inhibitor (PPI) 31.2% (45/144), amoxicillin 31.7% (39/123), metronidazole (MET) 19.4% (12/62), clarithromycin (CLA) 23.9% (22/70), tetracycline 50% (6/12), bismuth 26.1% (6/23). When PPIs were properly weight-dosed, there was a 78.8% eradication rate that dropped to 62.2% with suboptimal dosing (p = 0.036, odds ratio [OR]: 2.26, confidence interval [CI]: 1.04-4.87). When amoxicillin was properly weight-dosed, successful eradication was achieved in 81% versus only 53.8% when improperly dosed (p = 0.002; OR: 3.64, CI: 1.58-8.37). There was no statistically significant impact on eradication rates with improper weight-based dosing of MET, CLA, tetracycline, or bismuth. CONCLUSION: Proper weight-based dosing of amoxicillin and PPI is important for the successful eradication of H. pylori among children in the New England area.

Autophagy related genes mediated mitophagy in yeast, mammals and higher plants.

Autophagy is classified into macro-autophagy and micro-autophagy. Two major types of autophagy in the complex eukaryotic organism are microautophagy and macroautophagy. During microautophagy, cytoplasmic components that need to be degraded are taken up by lysosomes in animals and by vacuole in yeast and plants via the invagination of tonoplast. While macroautophagy is initiated after the formation of a cup-shaped membrane structure, a phagophore develops at cargo that grows in size and is sealed by double-membrane vesicles to form autophagosome; a generalized mechanism for degradation of the organelle. Autophagic removal of damaged mitochondria is a conserved cellular process to maintain a healthy mitochondrion called Mitophagy. In plants and animals, mitophagy has crucial roles in stress responses, senescence, development, and programmed cell death. Mitophagy appears in mammals, fungi, and plants but many genes that controlled mitophagy are absent from plants. Numerous studies have been conducted by using ATG mutants for the identification of functional roles of Autophagy Related Genes (ATG) required during the autophagy process at various steps like; auto phagosome formation, ATG protein recruitment, etc. The role of more than 25 ATG genes in mitophagy has been discussed in this review paper. The main parameters, reviewed and summarized in this review paper, are the name of species, common name, function, domain, deletion, induction, and localization of these autophagy-related genes in the cell. This review will facilitate the students, researchers, and academics for their further research insights.

Ecological characteristics of sugar beet plant and rhizosphere soil in response to high boron stress: A study of the remediation potential.

High boron (B) stress degrades the soil environment and reduces plant productivity. Sugar beet has a high B demand and potential for remediation of B-toxic soils. However, the mechanism regarding the response of sugar beet plants and rhizosphere soil microbiome to high B stress is not clear. In the potted soil experiment, we set different soil effective B environments (0.5, 5, 10, 30, 50, and 100 mg kg-1) to study the growth status of sugar beets under different B concentrations, as well as the characteristics of soil enzyme activity and microbial community changes. The results showed that sugar beet growth was optimal at 5 mg kg-1 of B. Exceeding this concentration the tolerance index decreased. The injury threshold EC20 was reached at an available B concentration of 35.8 mg kg-1. Under the treatment of 100 mg kg-1, the B accumulation of sugar beet reached 0.22 mg plant-1, and the tolerance index was still higher than 60%, which had not yet reached the lethal concentration of sugar beet. The abundance of Acidobacteriota, Chloroflexi and Patescibacteria increased, which was beneficial to the resistance of sugar beet to high B stress. In summary, under high B stress sugar beet had strong tolerance, enhanced capacity for B uptake and enrichment, and changes in soil microbial community structure. This study provides a theoretical basis for clarifying the mechanism of sugar beet resistance to high B stress and soil remediation.

Research on phytotoxicity assessment and photosynthetic characteristics of nicosulfuron residues on Beta vulgaris L.

Nicosulfuron is a common herbicide used to control weeds in maize fields. In northeast China, sugar beet is often grown as a subsequent crop after maize, and its frequently suffers from soil nicosulfuron residue damage, but the related toxicity evaluation and photosynthetic physiological mechanisms are not clear. Therefore, we experimented to evaluate the impacts of nicosulfuron residues on beet growth, photochemical properties, and antioxidant defense system. The results showed that when the nicosulfuron residue content reached 0.3 µg kg-1, it inhibited the growth of sugar beet. When it reached 36 µg kg-1 (GR50), the growth stagnated. Compared to the control group, a nicosulfuron residue of 36 µg kg-1 significantly decreased beet plant height (70.93 %), leaf area (91.85 %), dry weights of shoot (70.34 %) and root (32.70 %). It also notably reduced the potential photochemical activity (Fv/Fo) by 12.41 %, the light energy absorption performance index (PIabs) by 46.09 %, and light energy absorption (ABS/CSm) by 6.56 %. It decreased the capture (TRo/CSm) by 9.30 % and transferred energy (ETo/CSm) by 16.13 % per unit leaf cross-section while increasing the energy flux of heat dissipation (DIo/CSm) by 22.85 %. This ultimately impaired the photochemical capabilities of PSI and PSII, leading to a reduction in photosynthetic performance. Furthermore, nicosulfuron increased malondialdehyde (MDA) content while decreasing superoxide dismutase (SOD) and catalase (CAT) activities. In conclusion, this research clarified the toxicity risk level, lethal dose, and harm mechanism of the herbicide nicosulfuron residue. It provides a theoretical foundation for the rational use of herbicides in agricultural production and sugar beet planting management.

Alterations in the composition and metabolite profiles of the saline-alkali soil microbial community through biochar application.

Saline-alkali soil poses significant chanllenges to sustainable development of agriculture. Although biochar is commonly used as a soil organic amendment, its microbial remediation mechanism on saline-alkali soil requires further confirmation. To address this, we conducted a pot experiment using cotton seedlings to explore the potential remediation mechanism of rice straw biochar (BC) at three different levels on saline-alkaline soil. The results showed that adding of 2% biochar greatly improved the quality of saline-alkaline soil by reducing pH levels, electrical conductivity (EC), and water-soluble ions. Moreover, biochar increased the soil organic matter (SOM), nutrient availability and extracellular enzyme activity. Interestingly, it also reduced soil salinity and salt content in various cotton plant tissues. Additionally, biochar had a notable impact on the composition of the microbial community, causing changes in soil metabolic pathways. Notably, the addition of biochar promoted the growth and metabolism of dominant salt-tolerant bacteria, such as Proteobacteria, Bacteroidota, Acidobacteriota, and Actinobacteriota. By enhancing the positive correlation between microorganisms and metabolites, biochar alleviated the inhibitory effect of salt ions on microorganisms. In conclusion, the incorporation of biochar significantly improves the soil microenvironment, reduces soil salinity, and shows promise in ameliorating saline-alkaline soil conditions.

Dietary phosphorus requirement of silver CARP (Hypophthalmichthys molitrix) fingerlings.

The aim of this study was to determine the optimal dietary phosphorus (P) requirement and its effects on growth performance, body composition, mineralization and alkaline phosphate (ALP) activity in silver carp (Hypophthalmichthys molitrix). A total of 360 fish with an average initial weight of 7.0 ± 0.15 g were divided into 18 tanks (70 L capacity each) with a stocking density of 20 fish per tank in triplicate. The fish were fed diets containing six levels of P (3.3, 4.4, 5.5, 6.5, 7.5 and 8.6 g/kg) up to satiation for 90 days twice daily at 09:00 and 16:00. The results showed that fish fed diets containing 6.5 and 7.5 g/kg dietary P had significantly higher (p < 0.05) growth performance in terms of final weight gain, average weight gain (AWG), weight gain% (WG%), protein efficiency ratio (PER) and specific growth rate (SGR) than fish fed other diets. The best value of the feed conversion ratio (FCR) was observed in fish fed the 6.5 g/kg P diet, which was not significantly different from the 7.5 g/kg P diet. Increasing P supplementation above 6.5 g/kg significantly reduced (p < 0.05) the feed intake of silver carp. Whole-body composition analysis indicated that increasing P levels resulted in a decrease (p < 0.05) in crude fat (CF) and an increase (p < 0.05) in crude ash (CA) content, while crude protein (CP) and moisture content remained unaffected (p > 0.05). Fish fed diets containing ≥6.5 g/kg P had significantly higher (p < 0.05) Ca content in the whole body, bones and scales compared to those fed diets containing ≤5.5 g/kg P. A similar trend was observed for P and Mg contents in the whole body, bones and scales. The Zn content tended to decrease (p < 0.05) with increasing P supplementation in the whole body and bones, but fish fed diets containing ≥6.5 g/kg P had significantly higher (p < 0.05) Zn content compared to fish fed diets containing ≤5.5 g/kg P. The Ca/P ratio was significantly affected by P supplementation. Fish fed diets containing ≥6.5 g/kg P had significantly higher (p < 0.05) Ca and P contents in the serum than fish fed other diets. ALP activity increased (p < 0.05) with increasing P levels up to 6.5 g/kg P and decreased (p < 0.05) thereafter. In conclusion, supplementing P up to 6.35 g/kg is recommended for the optimal growth of silver carp.

Impact of dichromatic lighted incubation on hatching result and post-hatch performance of broiler chickens.

This study was planned to evaluate the impact of dichromatic lights during incubation on the hatching and post-hatch performance of broiler chickens. A total of 500 eggs of broiler breeder (Ross 308; Age 44 weeks) were evenly divided according to a completely randomized design into 4 treatments having 5 replicates and 25 eggs each. Treatments consisted of dichromatic lights Blue + Red (BR), Green + Red (GR) and Green + Blue (GB) provided at an intensity of 250 lx for 12 h a day along with a Dark (D) environment. After hatching 200 chicks (50 from each respective light group) were divided into 4 treatments with 5 replicates each having 10 chicks. Results indicated a higher embryo index (13.12%) in the GR group on the 12th day of incubation; while an ideal hatch window was observed in GR and GB (98.18% and 96.00% hatched chicks) lighting groups. In hatching traits, higher hatchability (86.15) and hatch of fertile (93.85) percentages were observed in GR lighting followed by GB, BR and Dark treatment groups; while dead-in shell embryos were lowest in the GR group. In growth performance, higher feed intake (513.20 g) and body weight (479.20 g) were observed in the GB group followed by GR, BR and dark group; and feed conversion ratio (FCR) was better in the GR group (1.06). In welfare parameters, improved physical asymmetry (0.90 mm) and tonic immobility (54.40 s) were measured in the GR group followed by GB, BR and the dark group. It was concluded that under experimental conditions when broiler breeder eggs are provided with GR lighting during incubation, it can help to improve hatchability, growth performance and welfare traits in chicks.

Common variable immunodeficiency associated enteropathy: A diagnostic enigma in developing countries.

Common variable immunodeficiency (CVID) is the most prevalent primary immunodeficiency disorder with different phenotypes and aetiologies. It is characterised by hypogammaglobulinaemia, defects in specific antibody response, erroneous activation and proliferation of T cells, leading to increased risk of recurrent infections. In CVID, "Variable" refers to the heterogeneity of clinical presentations, which include recurrent infections, autoimmunity, enteropathy, and increased risk of malignancies. This wide spectrum of disease manifestations and being a diagnosis of exclusion poses a diagnostic challenge. It is pertinent to mention that CVID along with associated complications is the commonest symptomatic primary antibody deficiency but is scarcely mentioned in local literature. The main aim of presenting this case is to impress upon the importance of systematic immunological workup in cases of suspected immunodeficiency to prevent morbidity and mortality.

Exploring the Interplay of the CRISPR-CAS System with Antibiotic Resistance in Staphylococcus aureus: A Poultry Meat Study from Lahore, Pakistan.

Staphylococcus aureus is one of the major pathogens responsible for causing food poisoning worldwide. The emergence of antibiotic resistance in this bacterium is influenced by various factors. Among them, bacterial acquired defense systems described as clustered regularly interspaced short palindromic repeats (CRISPR)-cas system might be involved in antibiotic resistance development in bacteria. The current study was designed to assess the prevalence of S. aureus and its antibiotic resistance profile and identify the relationship of the CRISPR-cas system with antimicrobial resistance, followed by phylogenetic analysis. Total samples (n = 188) of poultry meat were collected from the poultry bird market of Lahore, Punjab, Pakistan. We used both phenotypic (antibiotic disc diffusion) and genotypic methods (PCR) to identify multi-drug resistant (MDR) strains of S. aureus. Additionally, the role of the CRISPR-Cas system in the isolated MDR S. aureus was also assessed. In addition, real-time quantitative PCR (qRT-PCR) was used to evaluate the association of the CRISPR-cas system with antimicrobial resistance. All of the S. aureus isolates showed 100% resistance against erythromycin, 97.5% were resistant to tetracycline, and 75% were resistant to methicillin. Eleven isolates were MDR in the current study. The CRISPR system was found in all MDR isolates, and fifteen spacers were identified within the CRISPR locus. Furthermore, MDR S. aureus isolates and the standard strain showed higher expression levels of CRISPR-associated genes. The correlation of said system with MDR isolates points to foreign gene acquisition by horizontal transfer. Current knowledge could be utilized to tackle antibiotic-resistant bacteria, mainly S. aureus.

Signaling network model of cardiomyocyte morphological changes in familial cardiomyopathy.

Familial cardiomyopathy is a precursor of heart failure and sudden cardiac death. Over the past several decades, researchers have discovered numerous gene mutations primarily in sarcomeric and cytoskeletal proteins causing two different disease phenotypes: hypertrophic (HCM) and dilated (DCM) cardiomyopathies. However, molecular mechanisms linking genotype to phenotype remain unclear. Here, we employ a systems approach by integrating experimental findings from preclinical studies (e.g., murine data) into a cohesive signaling network to scrutinize genotype to phenotype mechanisms. We developed an HCM/DCM signaling network model utilizing a logic-based differential equations approach and evaluated model performance in predicting experimental data from four contexts (HCM, DCM, pressure overload, and volume overload). The model has an overall prediction accuracy of 83.8%, with higher accuracy in the HCM context (90%) than DCM (75%). Global sensitivity analysis identifies key signaling reactions, with calcium-mediated myofilament force development and calcium-calmodulin kinase signaling ranking the highest. A structural revision analysis indicates potential missing interactions that primarily control calcium regulatory proteins, increasing model prediction accuracy. Combination pharmacotherapy analysis suggests that downregulation of signaling components such as calcium, titin and its associated proteins, growth factor receptors, ERK1/2, and PI3K-AKT could inhibit myocyte growth in HCM. In experiments with patient-specific iPSC-derived cardiomyocytes (MLP-W4R;MYH7-R723C iPSC-CMs), combined inhibition of ERK1/2 and PI3K-AKT rescued the HCM phenotype, as predicted by the model. In DCM, PI3K-AKT-NFAT downregulation combined with upregulation of Ras/ERK1/2 or titin or Gq protein could ameliorate cardiomyocyte morphology. The model results suggest that HCM mutations that increase active force through elevated calcium sensitivity could increase ERK activity and decrease eccentricity through parallel growth factors, Gq-mediated, and titin pathways. Moreover, the model simulated the influence of existing medications on cardiac growth in HCM and DCM contexts. This HCM/DCM signaling model demonstrates utility in investigating genotype to phenotype mechanisms in familial cardiomyopathy.

Muscle LIM Protein Force-Sensing Mediates Sarcomeric Biomechanical Signaling in Human Familial Hypertrophic Cardiomyopathy.

BACKGROUND: Familial hypertrophic cardiomyopathy (HCM) is the most common inherited cardiac disease and is typically caused by mutations in genes encoding sarcomeric proteins that regulate cardiac contractility. HCM manifestations include left ventricular hypertrophy and heart failure, arrythmias, and sudden cardiac death. How dysregulated sarcomeric force production is sensed and leads to pathological remodeling remains poorly understood in HCM, thereby inhibiting the efficient development of new therapeutics. METHODS: Our discovery was based on insights from a severe phenotype of an individual with HCM and a second genetic alteration in a sarcomeric mechanosensing protein. We derived cardiomyocytes from patient-specific induced pluripotent stem cells and developed robust engineered heart tissues by seeding induced pluripotent stem cell-derived cardiomyocytes into a laser-cut scaffold possessing native cardiac fiber alignment to study human cardiac mechanobiology at both the cellular and tissue levels. Coupled with computational modeling for muscle contraction and rescue of disease phenotype by gene editing and pharmacological interventions, we have identified a new mechanotransduction pathway in HCM, shown to be essential in modulating the phenotypic expression of HCM in 5 families bearing distinct sarcomeric mutations. RESULTS: Enhanced actomyosin crossbridge formation caused by sarcomeric mutations in cardiac myosin heavy chain (MYH7) led to increased force generation, which, when coupled with slower twitch relaxation, destabilized the MLP (muscle LIM protein) stretch-sensing complex at the Z-disc. Subsequent reduction in the sarcomeric muscle LIM protein level caused disinhibition of calcineurin-nuclear factor of activated T-cells signaling, which promoted cardiac hypertrophy. We demonstrate that the common muscle LIM protein-W4R variant is an important modifier, exacerbating the phenotypic expression of HCM, but alone may not be a disease-causing mutation. By mitigating enhanced actomyosin crossbridge formation through either genetic or pharmacological means, we alleviated stress at the Z-disc, preventing the development of hypertrophy associated with sarcomeric mutations. CONCLUSIONS: Our studies have uncovered a novel biomechanical mechanism through which dysregulated sarcomeric force production is sensed and leads to pathological signaling, remodeling, and hypertrophic responses. Together, these establish the foundation for developing innovative mechanism-based treatments for HCM that stabilize the Z-disc MLP-mechanosensory complex.

The relationship between elastin cross linking and alveolar wall rupture in human pulmonary emphysema.

To better define the role of mechanical forces in pulmonary emphysema, we employed methods recently developed in our laboratory to identify microscopic level relationships between airspace size and elastin-specific desmosine and isodesmosine (DID) cross links in normal and emphysematous human lungs. Free DID in wet tissue (a biomarker for elastin degradation) and total DID in formalin-fixed, paraffin-embedded (FFPE) tissue sections were measured using liquid chromatography-tandem mass spectrometry and correlated with alveolar diameter, as determined by the mean linear intercept (MLI) method. There was a positive correlation between free lung DID and MLI (P < 0.0001) in formalin-fixed lungs, and elastin breakdown was greatly accelerated when airspace diameter exceeded 400 µm. In FFPE tissue, DID density was markedly increased beyond 300 µm (P < 0.0001) and leveled off around 400 µm. Elastic fiber surface area similarly peaked at around 400 µm, but to a much lesser extent than DID density, indicating that elastin cross linking is markedly increased in response to early changes in airspace size. These findings support the hypothesis that airspace enlargement is an emergent phenomenon in which initial proliferation of DID cross links to counteract alveolar wall distention is followed by a phase transition involving rapid acceleration of elastin breakdown, alveolar wall rupture, and progression to an active disease state that is less amenable to therapeutic intervention.NEW & NOTEWORTHY The current findings support the hypothesis that airspace enlargement is an emergent phenomenon in which initial proliferation of DID cross links to counteract alveolar wall distention is followed by a phase transition involving rapid acceleration of elastin breakdown, alveolar wall rupture, and progression to an active disease state that is less amenable to therapeutic intervention.

Flavonoids: a review on biosynthesis and transportation mechanism in plants.

In recent years, significant progress has been made in understanding the biosynthetic pathway and regulation of flavonoids through forward genetic approaches. However, there remains a notable gap in knowledge regarding the functional characterization and underlying processes of the transport framework responsible for flavonoid transport. This aspect requires further investigation and clarification to achieve a comprehensive understanding. Presently, there are a total of four proposed transport models associated with flavonoids, namely glutathione S-transferase (GST), multidrug and toxic compound extrusion (MATE), multidrug resistance-associated protein (MRPs), and bilitranslocase-homolog (BTL). Extensive research has been conducted on the proteins and genes related to these transport models. However, despite these efforts, numerous challenges still exist, leaving much to be explored in the future. Gaining a deeper understanding of the mechanisms underlying these transport models holds immense potential for various fields such as metabolic engineering, biotechnological approaches, plant protection, and human health. Therefore, this review aims to provide a comprehensive overview of recent advancements in the understanding of flavonoid transport mechanisms. By doing so, we aim to paint a clear and coherent picture of the dynamic trafficking of flavonoids.

Recurrence mutation in RBBP8 gene causing non-syndromic autosomal recessive primary microcephaly; geometric simulation approach for insight into predicted computational models.

Primary microcephaly is a rare, congenital, and genetically heterogeneous disorder in which occipitofrontal head circumference is reduced by a minimum of three standard deviations (SDs) from average because of the defect in fetal brain development. OBJECTIVE: Mapping of RBBP8 gene mutation that produce autosomal recessive primary microcephaly. Insilco RBBP8 protein models prediction and analysis. METHODS: Consanguineous Pakistani family affected with non-syndromic primary microcephaly was mapped a biallelic sequence variant (c.1807_1808delAT) in the RBBP8 gene via whole-exome sequencing. The deleted variant in the RBBP8 gene in affected siblings (V:4, V:6) of primary microcephaly was confirmed by sanger sequencing. RESULTS: Identified variant c.1807_1808delAT that truncated the protein translation p. Ile603Lysfs*7 and impaired the functioning of RBBP8 protein. This sequence variant was only reported previously in Atypical Seckel syndrome and Jawad syndrome, while we mapped it in the non-syndromic primary microcephaly family. We predicted 3D protein models by using Insilco tools like I TASSER, Swiss model, and phyre2 of wild RBBP8 protein of 897 amino acids and 608 amino acids of the mutant protein. These models were validated through the online SAVES server and Ramachandran plot and refined by using the Galaxy WEB server. A predicted and refined wild protein 3D model was deposited with accession number PM0083523 in Protein Model Database. A normal mode-based geometric simulation approach was used through the NMSim program, to find out the structural diversity of wild and mutant proteins which were evaluated by RMSD and RMSF. Higher RMSD and RMSF in mutant protein reduced the stability of the protein. CONCLUSION: The high possibility of this variant results in nonsense-mediated decay of mRNA, leading to the loss of protein functioning which causes primary microcephaly.