Search

We performed polyacrylamide gel electrophoresis of human proteins with sodium dodecyl sulfate, isolated proteins at multiple positions, and then used liquid chromatography and tandem mass spectrometry (LC-MS/MS) to determine the protein identities. Although beta-actin (ACTB) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) are 41.7 and 36 kDa proteins, respectively, LC-MS/MS identified their peptides at all the positions studied. The National Center for Biotechnology Information (USA) database lists only one ACTB mRNA but five GAPDH mRNAs and one noncoding RNA. The five GAPDH mRNAs encode three protein isoforms, while our bioinformatics analysis identified a 17.6 kDa isoform encoded by the noncoding RNA. All LC-MS/MS-identified GAPDH peptides at all positions studied are unique, but some of the identified ACTB peptides are shared by ACTC1, ACTBL2, POTEF, POTEE, POTEI, and POTEJ. ACTC1 and ACTBL2 belong to the ACT family with significant similarities to ACTB in protein sequence, whereas the four POTEs are ACTB-containing chimeric genes with the C-terminus of their proteins highly similar to the ACTB. These data lead us to conclude that GAPDH and ACTB are poor reference genes for determining the protein loading in such techniques as Western blotting, a leading role these two genes have been playing for decades in biomedical research.

The article reviews the web site Geographic Information Systems (GIS) Dictionary, located at http://support.esri.com/en/knowledgebase/Gisdictionary/browse from geographic information system company Environmental Systems Research Institute (Esri).

The article reviews the website Sanborn Maps located at https ://www.loc.gov/collections/sanborn-maps/ from the Library of Congress.

The article reviews the website EJView, US EPA, located at www.epa.gov/environmentaljustice/mapping.html, which was developed by the U.S. Environmental Protection Agency (EPA) to produce informational maps and reports about U.S. regions, including data on topics such as public heath and pollution.

The article reviews the website USGS (United States Geological Survey) National Geologic Map Database, found at http://ngmdb.usgs.gov/ngm-bin/ngm_compsearch.pl, from the Association of American State Geologists and the USGS.

The article reviews the website The National Map, located at http://nationalmap.gov/, from the U.S. Geological Survey.

A review is presented for the website "Drought Risk Atlas," hosted by the National Drought Mitigation Center at http://droughtatlas.unl.edu/

The article reviews the Internet resource "Atlas of Historical County Boundaries" from the Newberry Library website, located at http://publications.newberry.org/ahcbp/.

The article reviews the website USGS (United States Geological Survey) National Geologic Lexicon Database: Geolex, found at http://ngmdb.usgs.gov/Geolex/.

The article reviews the website National Historical Geographic Information System (NHGIS), found online at http://www.nhgis.org, from the University of Minnesota.

The article reviews the web site GIS Bibliography, located at www.training.esri.com/campus/library/index.cfm, from the GIS technology company ESRI, Inc.

The article reviews the website Bodleian Library Map Room, Oxford University, located at http://www.bodley.ox.ac.uk/users/nnj/maproom, from Oxford University.

The article presents a review of the web site Petroleum Abstracts TULSA from EBSCO accessible at http://www.ebscohost.com.

The article reviews the website Paleontology Portal, which can be accessed at www.paleoportal.org.

We determined RNA spectrum of the human RSK4 (hRSK4) gene (also called RPS6KA6) and identified 29 novel mRNA variants derived from alternative splicing, which, plus the NCBI-documented ones and the five we reported previously, totaled 50 hRSK4 RNAs that, by our bioinformatics analyses, encode 35 hRSK4 protein isoforms of 35-762 amino acids. Many of the mRNAs are bicistronic or tricistronic for hRSK4. The NCBI-normalized NM_014496.5 and the protein it encodes are designated herein as the Wt-1 mRNA and protein, respectively, whereas the NM_001330512.1 and the long protein it encodes are designated as the Wt-2 mRNA and protein, respectively. Many of the mRNA variants responded differently to different situations of stress, including serum starvation, a febrile temperature, treatment with ethanol or ethanol-extracted clove buds (an herbal medicine), whereas the same stressed situation often caused quite different alterations among different mRNA variants in different cell lines. Mosifloxacin, an antibiotics and also a functional inhibitor of hRSK4, could inhibit the expression of certain hRSK4 mRNA variants. The hRSK4 gene likely uses alternative splicing as a handy tool to adapt to different stressed situations, and the mRNA and protein multiplicities may partly explain the incongruous literature on its expression and comports., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

Objective: To determine the impact of adverse social and behavioral determinants of health (SBDH) on health care use in a safety-net community hospital (SNCH) heart failure (HF) population., Methods: We performed a retrospective analysis of HF patients at a single SNCH between 2018-2019 (N= 4594)., Results: At least one adverse SBDH was present in 21% of the study population. Patients with at least one adverse SBDH were younger (57 vs. 68 years), more likely to identify as Black (50% vs. 36%), be male (68% vs. 53%), and have Medicaid insurance (48% vs. 22%), p<.001. Presence of at least one adverse SBDH (homelessness, substance use, or incarceration) correlated with increased hospitalizations (2.3 vs 1.4/patient) and ED visits (5.1 vs 2.1/patient), p<.0001. Adverse SBDH were independent predictors of HF readmissions. Prescribing of guideline-directed medical therapy was similar among all patients., Conclusions: In a SNCH HF cohort, adverse SBDH predominantly afflict younger Black men on Medicaid and are associated with increased utilization.

Background: Previous studies revealed the connection between left atrial appendage peak flow velocity (LAA-PEV) and postoperative persistent atrial fibrillation (AF) recurrence. Yet, this association is not necessarily generalizable to persistent AF patients undergoing initial cryoballoon ablation due to current gaps in the literature., Methods: We prospectively studied 74 consecutive individuals with persistent atrial fibrillation undergoing a cryoballoon ablation for the first time between January 2018 and January 2020. Before ablation, LAA-PEV was documented by transesophageal echocardiography (TEE). Subsequently, demographic information and other clinical characteristics of these participants were collected. A 96-h continuous cardiac monitor was reviewed regularly for recurrence of atrial fibrillation. Cox proportional hazards regression was used to investigate LAA-PEV as well as other clinical characteristics as a predictor of AF recurrence., Results: Our study found that AF recurrences had lower LAA-PEV than those without AF recurrence. A nonlinear relationship between the LAA-PEV and AF recurrence was observed in this study, which had an inflection point of 34.9. Subgroup analysis of female participants showed that LAA-PEV had a positive correlation with AF recurrence [β = 0.8, 95% CI (0.7, 0.9), p  < 0.05]., Conclusion: A low LAA-PEV is related to recurrence of atrial fibrillation and may predict AF recurrence after initial cryoballoon ablation for persistent atrial fibrillation. This finding may help improve treatment and care strategies for patients with persistent atrial fibrillation., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Wang, Zhang, Zhou, Chen, Li, Tang, Chen, Zhang, Zellmer, Chen, Chen, Li, Liu and Zhou.)

Background: Patients with a history of cardiac disease are prone to develop cardiovascular adverse events such as hypotension, hypertension, and tachycardia during anesthesia induction. Therefore, hemodynamic stability is one of the most important concerns for induction of anesthesia in patients undergoing cardiac surgery. Remimazolam tosilate is a new, ultra-short-acting benzodiazepine agent, with the advantages of rapid onset, rapid offset, and minimal cardiorespiratory depression. We aim to compare the effect of remimazolam tosilate and etomidate on hemodynamics during anesthesia induction in patients undergoing valve replacement surgery., Methods/design: The trial is a prospective, randomized, double-blinded, controlled, single-center trial to compare the effect of remimazolam tosilate and etomidate on hemodynamics in patients undergoing valve replacement surgery. One hundred seventeen patients undergoing selective valve replacement surgery between January 1, 2022, and December 31, 2023, will be enrolled and randomly allocated into one of three groups: low-dose remimazolam group (Group LR), high-dose remimazolam group (Group HR), or etomidate group (Group E). The primary outcome is hemodynamic fluctuations during anesthesia induction (the difference between mean arterial pressure [MAP] to baseline, ▴MAP; and the difference between maximum or minimum heart rate [HR] and baseline, ▴HR). Secondary outcomes include the incidence of adverse cardiovascular events (hypotension, severe bradycardia, hypertension, tachycardia, and arrhythmia), the cumulative doses of vasoactive drugs used per patient, incidence and degree of injection pain and myoclonus, blood glucose values, and vital signs at different time points., Discussion: This research will determine the effectiveness and safety of remimazolam tosilate induction on hemodynamics in patients undergoing valve replacement surgery., Trial Registration: www.chictr.org .cn identifier ChiCTR2100052535 . Registered on 17th Dec 2021, http://www.chictr.org.cn/ )., (© 2022. The Author(s).)

Background : The currently available methods for sexing human or mouse cells have weaknesses. Therefore, it is necessary to establish new methods. Methods : We used bioinformatics approach to identify genes that have alleles on both the X and Y chromosomes of mouse and human genomes and have a region showing a significant difference between the X and Y alleles. We then used polymerase chain reactions (PCR) followed by visualization of the PCR amplicons in agarose gels to establish these genomic regions as genetic sex markers. Results : Our bioinformatics analyses identified eight mouse sex markers and 56 human sex markers that are new, i.e . are previously unreported. Six of the eight mouse markers and 14 of the 56 human markers were verified using PCR and ensuing visualization of the PCR amplicons in agarose gels. Most of the tested and untested sex markers possess significant differences in the molecular weight between the X- and Y-derived PCR amplicons and are thus much better than most, if not all, previously-reported genetic sex markers. We also established several simple and essentially cost-free methods for extraction of crude genomic DNA from cultured cells, blood samples, and tissues that could be used as template for PCR amplification. Conclusion : We have established new sex genetic markers and methods for extracting genomic DNA and for sexing human and mouse cells. Our work may also lend some methodological strategies to the identification of new genetic sex markers for other organismal species., (© 2022 Bentham Science Publishers.)

Although the concept that cancer is caused by mutations has been widely accepted, there still are ample data deprecating it. For example, embryonic cells displaced in non-embryonic environments may develop to cancer, whereas cancer cells placed in embryonic environments may be reverted to phenotypic normal. Although many intracellular or extracellular aberrations are known to be able to initiate a lengthy tumorigenesis, the molecular or cellular alterations that directly establish a neoplastic state, namely cellular immortality and autonomy, still remain unknown. Hereditary traits are encoded not only by gene sequences but also by karyotype and DNA or chromosomal structures that may be altered via non-mutational mechanisms, such as post-translational modifications of nuclear proteins, to initiate tumorigenesis. However, the immortal and autonomous nature of neoplasms makes them "new" organisms, meaning that neoplasms should have mutations to distinguish themselves from their host patients in the genome. Neoplasms are malignant if they bear epigenetic or genetic alterations in mutator genes, i.e. the genes whose alterations accelerate other genes to mutate, whereas neoplasms are benign if their epigenetic or genetic aberrations occur only in non-mutator genes. Future mechanistic research should be focused on identifying the alterations that directly establish cellular immortality and autonomy. Benign tumors may have many fewer alterations and thus be much better models than cancers for such research. Future translational research should be aimed at identifying the cellular factors that control cancer cells' phenotypes and at establishing approaches of directing cancer cells towards differentiation, which should be a promising therapeutic tactic., Competing Interests: Competing Interests: The authors have declared that no competing interest exists., (© The author(s).)

Background: Social determinants of health play a fundamental role in a patient's health status. In recent years, health systems across the nation have implemented numerous strategies aimed at identifying and addressing the health-related social needs of the patients they serve. Despite the influx of peer-reviewed research highlighting outcomes of specific health-related social needs interventions, the spectrum of practices utilized by primary care clinics has not been established., Objective: To determine the range of ways primary care clinics address health-related social needs after identification and initial contact with a frontline staff person is completed., Design: We conducted 12 semi-structured, in-person interviews with staff from purposively sampled clinics. If the interview included more than one staff person, all participants were interviewed together., Participants: Twenty-one administrative staff and frontline clinic personnel with experience in 24 separate primary care clinics in the Minneapolis-St. Paul, Minnesota metropolitan area., Approach: Interviews focused on the range of health-related social needs processes utilized by clinics, including staff titles, referral procedures, and barriers to addressing needs. Interview recordings were transcribed and coded using thematic analysis., Key Results: Thematic analysis identified variation in four key areas involving how clinics address patients' health-related social needs after identification and initial contact by frontline staff: clinic personnel involved in addressing needs, clinic referral processes, "resource" and "success" definitions, and barriers to accessing community-based supports., Conclusions: This study describes the large variation in primary care clinic practices to address health-related social needs after they are identified. The results suggest challenges to standardization and real-world application of previously published studies. Our findings also highlight the opportunity for improved relationships between health systems and community-based agencies., (© 2021. Society of General Internal Medicine.)

The small nucleolar RNA host gene 16 (SNHG16) has recently been shown to be a putative oncogene in gastric cancer (GC) and other cancer types, but how its four lncRNA variants are expressed in any physiological and pathological situation remains unknown. To investigate the expression and function of the four lncRNA variants of SNHG16, mainly the variant 1, in GC, we performed quantitative PCR to determine the RNA levels of the four variants in 60 GC tissue samples and several cell lines. We also studied how knocking down of SNHG16 with siRNA affected proliferation, apoptosis, cell cycle progression, as well as migration and invasion of GC cells. Our results showed that variants 1 and 4 were overexpressed in GC tissues compared with adjacent uninvolved tissues. Knockdown of the four variants, mainly the variant 1, enhanced apoptosis and inhibited cell cycle progression of a GC cell line by arresting the cells at the G1 phase. These cellular effects were associated not only with decreased protein levels of c-Myc, PCNA, cyclins D1, E1, A2 and B, as well as CDKs 2 and 6, but also with increased protein levels of the p21, p27 and p53. Knockdown of total SNHG16 lncRNAs also inhibited invasion and migration of the GC cells in vitro. These results collectively suggest that SNHG16 may be oncogenic in GC by regulating cell cycle progression and may serve as a GC biomarker.

Bone mass loss (osteoporosis) seen in postmenopausal women is an adverse factor for implant denture. Using an ovariectomized rat model, we studied the mechanism of estrogen-deficiency-caused bone loss and the therapeutic effect of Zoledronic acid. We observed that ovariectomized-caused resorption of bone tissue in the mandible was evident at four weeks and had not fully recovered by 12 weeks post-ovariectomized compared with the sham-operated controls. Further evaluation with a TUNEL assay showed ovariectomized enhanced apoptosis of osteoblasts but inhibited apoptosis of osteoclasts in the mandible. Zoledronic acid given subcutaneously as a single low dose was shown to counteract both of these ovariectomized effects. Immunohistochemical staining showed that ovariectomized induced the protein levels of RANKL and the 65-kD subunit of the NF-κB complex mainly in osteoclasts, as confirmed by staining for TRAP, a marker for osteoclasts, whereas zoledronic acid inhibited these inductions. Western blotting showed that the levels of RANKL, p65, as well as the phosphorylated form of p65, and IκB-α were all higher in the ovariectomized group than in the sham and ovariectomized + zoledronic acid groups at both the 4th- and 12th-week time points in the mandible. These data collectively suggest that ovariectomized causes bone mass loss by enhancing apoptosis of osteoblasts and inhibiting apoptosis of osteoclasts. In osteoclasts, these cellular effects may be achieved by activating RANKL-NF-κB signalling. Moreover, zoledronic acid elicits its therapeutic effects in the mandible by counteracting these cellular and molecular consequences of ovariectomized.

Heat shock proteins (HSP) serve as chaperones to maintain the physiological conformation and function of numerous cellular proteins when the ambient temperature is increased. To determine how accurate the general assumption that HSP gene expression is increased in febrile situations is, the RNA levels of the HSF1 (heat shock transcription factor 1) gene and certain HSP genes were determined in three cell lines cultured at 37˚C or 39˚C for three days. At 39˚C, the expression of HSF1, HSPB1, HSP90AA1 and HSP70A1L genes demonstrated complex changes in the ratios of expression levels between different RNA variants of the same gene. Several older versions of the RNAs of certain HSP genes that have been replaced by a newer version in the National Center for Biotechnology Information database were also detected, indicating that the older versions are actually RNA variants of these genes. The present study cloned four new RNA variants of the HSP27-encoding HSPB1 gene, which together encode three short HSP27 peptides. Reanalysis of the proteomics data from our previous studies also demonstrated that proteins from certain HSP genes could be detected simultaneously at multiple positions using SDS-PAGE, suggesting that these genes may engender multiple protein isoforms. These results collectively suggested that, besides increasing their expression, certain HSP and associated genes also use alternative transcription start sites to produce multiple RNA transcripts and use alternative splicing of a transcript to produce multiple mature RNAs, as important mechanisms for responding to an increased ambient temperature in vitro ., Competing Interests: The authors declare that they have no competing interests., (Copyright: © Gao et al.)

Hennepin County Adult Detention Center (Jail) is Minnesota's largest jail. In August 2019, the Minnesota Department of Health declared a statewide hepatitis A outbreak. Within three days, Hennepin County Jail Health Services made significant changes to vaccination protocols that increased vaccination rates from 0.6% to 7.1% among detainees, who have a greater risk of contracting hepatitis A. We highlight the opportunity for jails to develop sustainable public health interventions in the setting of community outbreaks.

The most recent build of the human reference genome, GRCh38, was released in 2013. However, many laboratories performing next-generation sequencing (NGS) continue to align to GRCh37. Our aim was to assess the number of clinical diagnostic laboratories that have migrated to GRCh38 and discern factors impeding migration for those still using GRCh37. A brief, five-question survey was electronically administered to 71 clinical laboratories offering constitutional NGS-based testing and analyzed categorically. Twenty-eight responses meeting inclusion criteria were collected from 24 academic and four commercial diagnostic laboratories. Most of these (14; 50%) reported volumes of <500 NGS-based tests in 2019. Only two respondents (7%) had already migrated entirely to GRCh38; most laboratories (15; 54%) had no plans to migrate. The two prevailing reasons for not yet migrating were as follows: laboratories did not feel the benefits outweighed the time and monetary costs (14; 50%); and laboratories had insufficient staff to facilitate the migration (12; 43%). These data, although limited, suggest most clinical molecular laboratories are reluctant to migrate to GRCh38, and there appear to be multiple obstacles to overcome before GRCh38 is widely adopted., (Copyright © 2021 Association for Molecular Pathology and American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.)

Molecular biology research often requires extraction of DNA fragments from agarose gels. In the past decades, there have been many methods developed for this purpose. Currently most researchers, especially novices, use commercial kits for this extraction, although these kits cost money and the procedures involved are not necessarily easier than some erstwhile methods. We herein reintroduce and reassess several simple and cost-free older methods. One method involves excising a slice of the gel containing the DNA fragment, followed by a thaw-and-freeze procedure to release the DNA from the gel slice into the gel-making buffer. The second method involves a dialysis tubing and requires electroelution of the DNA from the gel slice in the tubing. The third one is to centrifuge the gel slice to release the DNA. The fourth method requires electro-transfer of the DNA from the gel into a filter paper, while the fifth one includes either allowing the DNA in the slice to be dissolved into a buffer or dissolving the DNA-containing gel slice, followed by DNA precipitation with ethanol or isopropanol. The strengths and weaknesses of these methods are discussed to assist researchers in making their choice. We also point out that some of the end uses of the DNA fragment in the agarose gel may not actually require extraction of the DNA. For instance, a tiny DNA-containing gel block or filter paper can be directly used as the template in a nested or semi-nested polymerase chain reaction to preliminarily determine the identity of the DNA fragment., Competing Interests: Competing interestsAll authors declare no interest conflicts., (© The Author(s) 2021.)

Status epilepticus is not rare in critically ill intensive care unit patients, but its diagnosis is often delayed or missed. The mortality for convulsive status epilepticus is dependent on the underlying aetiologies and the age of the patients and thus varies from study to study. In this context, effective molecular diagnosis in a pediatric patient with a genetically heterogeneous phenotype is essential. Homozygous or compound heterozygous variants in KPTN have been recently associated with a syndrome typified by macrocephaly, neurodevelopmental delay, and seizures. We describe a comprehensive investigation of a 9-yr-old male patient who was admitted to the intensive care unit, with focal epilepsy, static encephalopathy, autism spectrum disorder, and macrocephaly of unknown etiology, who died of status epilepticus. Clinical whole-genome sequencing revealed compound heterozygous variants in the KPTN gene. The first variant is a previously characterized 18-bp in-frame duplication (c.714&#95;731dup) in exon 8, resulting in the protein change p.Met241&#95;Gln246dup. The second variant, c.394 + 1G > A, affects the splice junction of exon 3. These results are consistent with a diagnosis of autosomal recessive KPTN -related disease. This is the fourth clinical report for KPTN deficiency, providing further evidence of a wider range of severity., (© 2020 Thiffault et al.; Published by Cold Spring Harbor Laboratory Press.)

Most genes in evolutionarily complex genomes are expressed to multiple protein isoforms, but there is not yet any simple high-throughput approach to identify these isoforms. Using an oversimplified top-down LC-MS/MS strategy, we detected, around the 26-kD position of SDS-PAGE, proteins produced from 782 genes in a Cdk4-/- mouse embryonic fibroblast cell line. Interestingly, only 213 (27.24%, about one-fourth) of these 782 genes have their proteins with a theoretical molecular mass (TMM) 10% smaller or larger than 26 kD, that is, between 23 and 29 kD, the range set as allowed variation in SDS-PAGE. These 213 proteins are considered as the wild type (WT). The remaining three-fourths includes proteins from 66 (9.44%) genes with a TMM smaller than 23 kD and proteins from 503 (64.32%, nearly two-thirds) genes with a TMM larger than 29 kD; these proteins are categorized into a larger-group or a smaller-group, respectively, for their appearance at a higher or lower position of SDS-PAGE. For instance, at this 26-kD position we detected proteins from the Rps27a, Snrpf, Hist1h4a, and Rps25 genes whose proteins' TMM is 8.6, 9.7, 11.4, and 13.7 kD, respectively, and detected proteins from the Plelc1 and Prkdc genes, whose largest isoform is 533.9 and 471.1 kD, respectively. We extrapolate that many of those proteins migrating unexpectedly in SDS-PAGE may be isoforms besides the WT protein. Moreover, we also detected a Cdk4 protein in this Cdk4-/- cell line, thus wondering whether some of other gene-knockout cells or organisms show similar incompleteness of the knockout., (© 2020 The Protein Society.)

Modern research into carcinogenesis has undergone three phases. Surgeons and pathologists started the first phase roughly 250 years ago, establishing morphological traits of tumors for pathologic diagnosis, and setting immortality and autonomy as indispensable criteria for neoplasms. A century ago, medical doctors, biologists and chemists started to enhance "experimental cancer research" by establishing many animal models of chemical-induced carcinogenesis for studies of cellular mechanisms. In this second phase, the two-hit theory and stepwise carcinogenesis of "initiation-promotion" or "initiation-promotion-progression" were established, with an illustrious finding that outgrowths induced in animals depend on the inducers, and thus are not authentically neoplastic, until late stages. The last 40 years are the third incarnation, molecular biologists have gradually dominated the carcinogenesis research fraternity and have established numerous genetically-modified animal models of carcinogenesis. However, evidence has not been provided for immortality and autonomy of the lesions from most of these models. Probably, many lesions had already been collected from animals for analyses of molecular mechanisms of "cancer" before the lesions became autonomous. We herein review the monumental work of many predecessors to reinforce that evidence for immortality and autonomy is essential for confirming a neoplastic nature. We extrapolate that immortality and autonomy are established early during sporadic human carcinogenesis, unlike the late establishment in most animal models. It is imperative to resume many forerunners' work by determining the genetic bases for initiation, promotion and progression, the genetic bases for immortality and autonomy, and which animal models are, in fact, good for identifying such genetic bases., Competing Interests: Competing Interests: The authors have declared that no competing interest exists., (© The author(s).)