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BioRxiv : the Preprint Server For... Jun 2024We present CRISPRware, an efficient method for generating guide RNA (gRNA) libraries against transcribed, translated, and noncoding regions. CRISPRware leverages...
We present CRISPRware, an efficient method for generating guide RNA (gRNA) libraries against transcribed, translated, and noncoding regions. CRISPRware leverages next-generation sequencing data to design context-specific gRNAs and accounts for genetic variation, which allows allele-specific guide design on a genome-wide scale. The latter ability holds promise for the development of gene therapy in the context of gene dosing and dominant negative mutations.
PubMed: 38948878
DOI: 10.1101/2024.06.18.599405 -
BioRxiv : the Preprint Server For... Jun 2024Kidney tubular cells are submitted to two distinct mechanical forces generated by the urine flow: shear stress and hydrostatic pressure. In addition, the mechanical...
Kidney tubular cells are submitted to two distinct mechanical forces generated by the urine flow: shear stress and hydrostatic pressure. In addition, the mechanical properties of the surrounding extracellular matrix modulate tubule deformation under constraints. These mechanical factors likely play a role in the pathophysiology of kidney diseases as exemplified by autosomal dominant polycystic kidney disease, in which pressure, flow and matrix stiffness have been proposed to modulate the cystic dilation of tubules with mutations. The lack of systems recapitulating the mechanical environment of kidney tubules impedes our ability to dissect the role of these mechanical factors. Here we describe a perfused kidney-on-chip with tunable extracellular matrix mechanical properties and hydrodynamic constraints, that allows a decoupling of shear stress and flow. We used this system to dissect how these mechanical cues affect tubule dilation. Our results show two distinct mechanisms leading to tubular dilation. For PCT cells (proximal tubule), overproliferation mechanically leads to tubular dilation, regardless of the mechanical context. For mIMCD-3 cells (collecting duct), tube dilation is associated with a squamous cell morphology but not with overproliferation and is highly sensitive to extracellular matrix properties and hydrodynamic constraints. Surprisingly, flow alone suppressed mIMCD-3 tubule dilation observed in static conditions, while the addition of luminal pressure restored it. Our model emulating nephron geometrical and mechanical organization sheds light on the roles of mechanical constraints in ADPKD and demonstrates the importance of controlling intraluminal pressure in kidney tubule models.
PubMed: 38948811
DOI: 10.1101/2024.06.18.599137 -
BioRxiv : the Preprint Server For... Jun 2024Non-alcoholic fatty liver disease (NAFLD), recently renamed metabolic-associated fatty liver disease (MAFLD), is the most common liver disease worldwide. The progression...
Non-alcoholic fatty liver disease (NAFLD), recently renamed metabolic-associated fatty liver disease (MAFLD), is the most common liver disease worldwide. The progression to fibrosis, occurring against a backdrop of hepatic steatosis and inflammation, critically determines liver-related morbidity and mortality. Inflammatory processes contribute to various stages of MAFLD and thought to instigate hepatic fibrosis. For this reason, targeting inflammation has been heavily nominated as a strategy to mitigate liver fibrosis. Lipopolysaccharide binding protein (LBP) is a secreted protein that plays an established role in innate immune responses. Here, using adoptive transfer studies and tissue-specific deletion models we show that hepatocytes are the dominant contributors to circulating LBP. In a murine model of MAFLD, hepatocyte-specific deletion of LBP restrained hepatic inflammation and improved liver function abnormalities, but not measures of fibrosis. Human studies, including genetic evidence, corroborate an important role for LBP in hepatic inflammation with minimal impact on fibrosis. Collectively, our data argues against the idea that targeting hepatic inflammation is a viable approach to reducing fibrosis.
PubMed: 38948798
DOI: 10.1101/2024.06.17.599212 -
BioRxiv : the Preprint Server For... Jun 2024Behavioral states such as sleep and wake are highly correlated with specific patterns of rhythmic activity in the cortex. During low arousal states such as slow wave...
Behavioral states such as sleep and wake are highly correlated with specific patterns of rhythmic activity in the cortex. During low arousal states such as slow wave sleep, the cortex is synchronized and dominated by low frequency rhythms coordinated across multiple regions. Although recent evidence suggests that GABAergic inhibitory neurons are key players in cortical state modulation, the circuit mechanisms coordinating synchronized activity among local and distant neocortical networks are not well understood. Here, we show that somatostatin and chondrolectin co-expressing cells (Sst-Chodl cells), a sparse and unique class of neocortical inhibitory neurons, are selectively active during low arousal states and are largely silent during periods of high arousal. In contrast to other neocortical inhibitory neurons, we show these neurons have long-range axons that project across neocortical areas. Activation of Sst-Chodl cells is sufficient to promote synchronized cortical states characteristic of low arousal, with increased spike co-firing and low frequency brain rhythms, and to alter behavioral states by promoting sleep. Contrary to the prevailing belief that sleep is exclusively driven by subcortical mechanisms, our findings reveal that these long-range inhibitory neurons not only track changes in behavioral state but are sufficient to induce both sleep-like cortical states and sleep behavior, establishing a crucial circuit component in regulating behavioral states.
PubMed: 38948753
DOI: 10.1101/2024.06.20.599756 -
Journal of Family Medicine and Primary... May 2024Birt-Hogg-Dubé syndrome (BHDS) is a rare hereditary autosomal dominant condition characterized by benign cutaneous lesions, lung cysts, and increased risk of...
Birt-Hogg-Dubé syndrome (BHDS) is a rare hereditary autosomal dominant condition characterized by benign cutaneous lesions, lung cysts, and increased risk of spontaneous pneumothorax and renal cancer. We report a case of a young Indian boy with bilateral pneumothorax as the first symptom of BHDS. Detailed history examination and investigation showed multiple facial lesions; his computerized tomography was suggestive of renal angiomyolipoma, hepatic angiomyolipoma, pulmonary cyst with pneumothorax, and small bilateral subependymal soft tissue density lesion with calcification in the brain, all of which were collectively suggestive of BHDS. Identification of the above commonly presented clinical features as a syndrome is important for even a primary care physician so as to ensure the timely management and if required referral to a higher center.
PubMed: 38948613
DOI: 10.4103/jfmpc.jfmpc_1451_23 -
PeerJ 2024Anurans are among the most vocally active vertebrate animals and emit calls with different functions. In order to attract a mate, during the breeding season male frogs...
Anurans are among the most vocally active vertebrate animals and emit calls with different functions. In order to attract a mate, during the breeding season male frogs produce mating calls which have species-specific structure and parameters, and have been successfully used to resolve issues in taxonomy and phylogenetic relations. This is particularly useful when closely related taxa are concerned, as many species are morphologically almost identical, but still their status is well-supported by molecular and genetic data, suggesting the existence of mechanisms for reproductive isolation. Such is the case for treefrogs from the group, which are now recognized as several distinct species. The present study aims to establish differences in call parameters between the European tree frog, , and the Eastern tree frog, , which both occur on the territory of Bulgaria. Using autonomous audio loggers, calls from six sites (three in the range of and three in the range of ) were recorded between 7 p.m. and 12 a.m. during the breeding season in 2020-2023. The following parameters in a total of 390 mating calls were analyzed: call count, pulse count, call series duration, call period, peak (dominant) frequency, entropy. Results indicated that sites formed two distinct groups, which corresponded to the known distribution ranges of and . The first two components of the PCA explained 71% of the total variance, with variables call count, call series duration, peak frequency and entropy being most important for differentiation between the sites. This study presents the first attempt to differentiate between the calls of these two sister taxa, which both fall within the "short-call treefrogs" group, and results are discussed in terms of known data for mating calls in sp., as well as limitations and future perspectives.
PubMed: 38948235
DOI: 10.7717/peerj.17574 -
PeerJ 2024Combining ability status of the inbred lines is crucial information for hybrid breeding program. Diallel or line × tester mating designs are frequently used to evaluate...
Combining ability status of the inbred lines is crucial information for hybrid breeding program. Diallel or line × tester mating designs are frequently used to evaluate the combining ability. In the current study a modified diallel model was used, wherein the Griffing's combining ability effects were further partitioned to understand the effects due to maternal and reciprocal. To do this, eight parental lines of maize were crossed in full diallel method and the generated hybrids along with parents were phenotyped. The field data on the quantitative traits was analyzed using both Griffing's and the modified model to determine how well the parents' and the F hybrids combined. For each of the traits, a sizable reciprocal and maternal variance was observed. The number of kernel rows per cob variable had a ratio of additive variance to dominance variance greater than one. All other traits including grain yield had a ratio close to zero, suggesting that non-additive gene action was primarily responsible for the genetic control of most of the traits. The narrow sense heritability was low to moderate for majority of the variables, except for number of kernel rows per cob. With the help of the improved model, it was possible to choose superior parents and cross-parent pairings with accuracy. Based on the modified general combining ability effects and maternal effects, the parental line P5 was recognized as a potential female parent and P7 as a good male parent for grain yield and yield-attributing characteristics. The cross combination of P8×P1 had the highest specific combining ability effect on grain yield. P5×P6 cross had the highest reciprocal effect. The correlation analysis implies that the Griffing's general combining ability effects and specific combining ability effects were found to be less efficient in predicting F performance as compared to the modified model.
PubMed: 38948201
DOI: 10.7717/peerj.17600 -
Frontiers in Neurology 2024Stroke is a cerebrovascular disease with high prevalence and mortality, and upper limb hemiparesis is a major factor limiting functional recovery in stroke patients....
BACKGROUND
Stroke is a cerebrovascular disease with high prevalence and mortality, and upper limb hemiparesis is a major factor limiting functional recovery in stroke patients. Improvement of motor function in stroke patients through various forms of constraint-induced movement therapy (CITM) has been recognized as safe and effective in recent years. This research field lacks a comprehensive systematic and clear vein combing analysis, analyzing the literature research of CIMT in the field of rehabilitation in the past three decades, summarizing the research hotspots and cutting-edge trends in this field, in an effort to offer ideas and references for subsequent researchers.
METHODS
Relevant literature on CIMT in rehabilitation was collected from 1996 to 2024 within the Web of Science database's core dataset by using CiteSpace6.1, VOSviewer1.6.18, R-bibliometrix4.6.1, Pajek5.16, Scimago Graphica 1.0.26 software for visualization and analysis.
RESULTS
There were 970 papers in all United States was ranked first with 401 papers. Alabama Univ was ranked first for institutions with 53 papers. Neurorehabilitation and Neural Repair was ranked first for journals with 78 papers, and Taub E was ranked first for author publications with 64 papers. Research keywords were CIMT, stroke rehabilitation, upper extremity function, lower extremity gait balance, randomized controlled trials, physical therapy techniques (transcranial magnetic stimulation and sensory amplitude electrical stimulation), primary motor cortex plasticity, lateral dominance (spatial behaviors), cerebral vascular accidents, activities of daily living, hand function, disability, functional restoration, bimanual training, aphasia, acquired invalidity, type A Botulinum toxin and joystick riding toys.
CONCLUSION
The current state of research shows that CIMT still has a vast potential for development in the field of rehabilitation research. The research hotspots are the clinical efficacy of CIMT combined with other therapies (botulinum toxin type A, transcranial direct current stimulation, virtual reality, mirror therapy, robotic-assisted) to enhance the functionality of upper limb hemiparesis in stroke patients, the mechanism of CIMT to improve the plasticity of the motor cortex through electrophysiological and imaging methods, and improvement of lower limb gait balance function in stroke patients and aphasia applications, the optimal intervention time and dose, and exploration of CIMT in new settings such as robot-assisted, telemedicine, and home rehabilitation.
PubMed: 38948135
DOI: 10.3389/fneur.2024.1375855 -
Theranostics 2024Synergic reprogramming of metabolic dominates neuroblastoma (NB) progression. It is of great clinical implications to develop an individualized risk prognostication...
Synergic reprogramming of metabolic dominates neuroblastoma (NB) progression. It is of great clinical implications to develop an individualized risk prognostication approach with stratification-guided therapeutic options for NB based on elucidating molecular mechanisms of metabolic reprogramming. With a machine learning-based multi-step program, the synergic mechanisms of metabolic reprogramming-driven malignant progression of NB were elucidated at single-cell and metabolite flux dimensions. Subsequently, a promising metabolic reprogramming-associated prognostic signature (MPS) and individualized therapeutic approaches based on MPS-stratification were developed and further validated independently using pre-clinical models. MPS-identified MPS-I NB showed significantly higher activity of metabolic reprogramming than MPS-II counterparts. MPS demonstrated improved accuracy compared to current clinical characteristics [AUC: 0.915 vs. 0.657 (), 0.713 (INSS-stage), and 0.808 (INRG-stratification)] in predicting prognosis. AZD7762 and etoposide were identified as potent therapeutics against MPS-I and II NB, respectively. Subsequent biological tests revealed AZD7762 substantially inhibited growth, migration, and invasion of MPS-I NB cells, more effectively than that of MPS-II cells. Conversely, etoposide had better therapeutic effects on MPS-II NB cells. More encouragingly, AZD7762 and etoposide significantly inhibited in-vivo subcutaneous tumorigenesis, proliferation, and pulmonary metastasis in MPS-I and MPS-II samples, respectively; thereby prolonging survival of tumor-bearing mice. Mechanistically, AZD7762 and etoposide-induced apoptosis of the MPS-I and MPS-II cells, respectively, through mitochondria-dependent pathways; and MPS-I NB resisted etoposide-induced apoptosis by addiction of glutamate metabolism and acetyl coenzyme A. MPS-I NB progression was fueled by multiple metabolic reprogramming-driven factors including multidrug resistance, immunosuppressive and tumor-promoting inflammatory microenvironments. Immunologically, MPS-I NB suppressed immune cells via and signaling pathways. Metabolically, the malignant proliferation of MPS-I NB cells was remarkably supported by reprogrammed glutamate metabolism, tricarboxylic acid cycle, urea cycle, etc. Furthermore, MPS-I NB cells manifested a distinct tumor-promoting developmental lineage and self-communication patterns, as evidenced by enhanced oncogenic signaling pathways activated with development and self-communications. This study provides deep insights into the molecular mechanisms underlying metabolic reprogramming-mediated malignant progression of NB. It also sheds light on developing targeted medications guided by the novel precise risk prognostication approaches, which could contribute to a significantly improved therapeutic strategy for NB.
PubMed: 38948053
DOI: 10.7150/thno.93962 -
Heliyon Jun 2024The unique floral fingerprint embedded within honey holds valuable clues to its geographical and botanical origin, playing a crucial role in ensuring authenticity and...
The unique floral fingerprint embedded within honey holds valuable clues to its geographical and botanical origin, playing a crucial role in ensuring authenticity and detecting adulteration. Honey from native and bees in Karangasem, Indonesia, was examined utilizing pollen DNA metabarcoding for honey source identification. In this study, we used ITS2 amplicon sequencing to identify floral DNA in honey samples. The finding reveals distinct pollen signatures for each bee species. Results analysis showed honey generated 179,267 sequence reads, assembled into Amplicon Sequence Variants (ASVs) with a total size of 485,932 bp and an average GC content of 59 %. honey generated 177,864 sequence reads, assembled into ASVs with a total size of 350,604 bp and an average GC content of 57 %. honey exhibited a rich tapestry of pollen from eleven diverse genera, with genus dominating at an impressive relative read abundance of 72.8 %. In contrast, honey displayed a remarkable mono-dominance of the genus, accounting for a staggering 99.95 % of its pollen composition or relative read abundance, highlighting their distinct foraging preferences and floral resource utilization. Notably, all identified pollen taxa were indigenous to Karangasem, solidifying the geographical link between honey and its origin. This study demonstrates pollen DNA metabarcoding may identify honey floral sources. By using pollen profiles from different bee species and their foraging patterns, we may protect consumers against honey adulteration and promote sustainable beekeeping in Karangasem district. Future research could explore expanding the database of reference pollen sequences and investigating the influence of environmental factors on pollen composition in honey. Investigating this technology's economic and social effects on beekeepers and consumers may help promote fair trade and sustainable beekeeping worldwide.
PubMed: 38948039
DOI: 10.1016/j.heliyon.2024.e33094