scholarly journals DNA Satellites Are Transcribed as Part of the Non-Coding Genome in Eukaryotes and Bacteria

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1651
Author(s):  
Juan A. Subirana ◽  
Xavier Messeguer
Keyword(s):  
Tandem Repeats ◽  
Bacillus Coagulans ◽  
C Elegans ◽  
Rna Transcripts ◽  
New Family ◽  
Satellite Rnas ◽  
Bacterium Bacillus ◽  
And Control ◽  
First Time

It has been shown in recent years that many repeated sequences in the genome are expressed as RNA transcripts, although the role of such RNAs is poorly understood. Some isolated and tandem repeats (satellites) have been found to be transcribed, such as mammalian Alu sequences and telomeric/centromeric satellites in different species. However, there is no detailed study on the eventual transcription of the interspersed satellites found in many species. Therefore, we decided to study for the first time the transcription of the abundant DNA satellites in the bacterium Bacillus coagulans and in the nematode Caenorhabditis elegans. We have updated the data for C. elegans satellites using the latest version of the genome. We analyzed the transcription of satellites in both species in available RNA-seq results and found that they are widely transcribed. Our demonstration that satellite RNAs are transcribed adds a new family of non-coding RNAs. This is a field that requires further investigation and will provide a deeper understanding of gene expression and control.

Predictive value of the neutrophil-to-lymphocyte ratio, monocyte-to-lymphocyte ratio, platelet-to-neutrophil ratio, and neutrophil-to-monocyte ratio in lupus nephritis

Lupus ◽  
2020 ◽  
Vol 29 (9) ◽  
pp. 1031-1039
Author(s):  
Peng Liu ◽  
Peiyuan Li ◽  
Zhong Peng ◽  
Yazhou Xiang ◽  
Chenqi Xia ◽  
...  
Keyword(s):  
Lupus Nephritis ◽  
Healthy Subjects ◽  
Area Under The Curve ◽  
Neutrophil To Lymphocyte Ratio ◽  
Control Group ◽  
Receiver Operating Characteristic Curves ◽  
Lymphocyte Ratio ◽  
And Control ◽  
First Time

Objective To evaluate the role of neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), monocyte-to-lymphocyte ratio (MLR), platelet-to-neutrophil ratio (PNR), platelet-to-monocyte ratio (PMR), and neutrophil-to-monocyte ratio (NMR) as predictors for lupus nephritis (LN) patients without infection or as biomarkers for distinguishing between infection or flare with LN patients. Methods LN patients were divided into three groups: LN without infection, LN with infection, and LN with flare. A total of 57 healthy subjects were enrolled as controls. The differentiation was analyzed between LN without infection and control group, and LN with infection and LN with flare. Correlations among variables were assessed in the LN group without infection. Receiver operating characteristic curves were constructed in two comparable groups. Results NLR, PLR, and MLR were increased significantly in the LN group without infection as compared with those in healthy controls. NLR (area under the curve (AUC): 0.75) and MLR (AUC: 0.79) were useful for distinguishing between LN patients without infection and healthy subjects. In differentiating LN patients without infection from the controls, optimal cutoffs of NLR and MLR were 3.43 (sensitivity: 45.6%, specificity: 96.5%, and overall accuracy: 68.8%) and 0.24 (sensitivity: 75.0%, specificity: 73.7%, and overall accuracy: 73.6%), respectively. In addition, NLR ( r = 0.322, p = 0.011) and PLR ( r = 0.283, p = 0.026) were positively correlated with CRP. Importantly, NLR and NMR were increased while PNR was decreased in the LN group with infection in comparison with those in the LN group with flare. NLR (AUC: 0.80), NMR (AUC: 0.78), and PNR (AUC: 0.74) were useful in differentiating LN patients with infection and flare, and their optimal cutoffs were 4.02 (sensitivity: 82.6%, specificity: 69.6%, and overall accuracy: 75.5%), 12.19 (sensitivity: 80.4%, specificity: 73.9%, and overall accuracy: 77.5%), and 28.26 (sensitivity: 65.2%, specificity: 76.8%, and overall accuracy: 71.6%), respectively. Conclusions We demonstrated, for the first time, that MLR or NMR had the best accuracy in differentiating LN patients without infection from healthy subjects, or differentiating infection from flare in LN patients, respectively. Our results implied that NLR, MLR, PNR, and NMR may be useful biomarkers in predicting LN.

scholarly journals Propensity of undulatory swimmers, such as worms, to go against the flow

2015 ◽  
Vol 112 (12) ◽  
pp. 3606-3611 ◽  
Author(s):  
Jinzhou Yuan ◽  
David M. Raizen ◽  
Haim H. Bau
Keyword(s):  
Control Strategies ◽  
Aquatic Organisms ◽  
Life Cycles ◽  
Environmental Cues ◽  
Mechanical Forces ◽  
C Elegans ◽  
The Subject ◽  
And Function ◽  
First Time

The ability to orient oneself in response to environmental cues is crucial to the survival and function of diverse organisms. One such orientation behavior is the alignment of aquatic organisms with (negative rheotaxis) or against (positive rheotaxis) fluid current. The questions of whether low-Reynolds-number, undulatory swimmers, such as worms, rheotax and whether rheotaxis is a deliberate or an involuntary response to mechanical forces have been the subject of conflicting reports. To address these questions, we use Caenorhabditis elegans as a model undulatory swimmer and examine, in experiment and theory, the orientation of C. elegans in the presence of flow. We find that when close to a stationary surface the animal aligns itself against the direction of the flow. We elucidate for the first time to our knowledge the mechanisms of rheotaxis in worms and show that rheotaxis can be explained solely by mechanical forces and does not require sensory input or deliberate action. The interaction between the flow field induced by the swimmer and a nearby surface causes the swimmer to tilt toward the surface and the velocity gradient associated with the flow rotates the animal to face upstream. Fluid mechanical computer simulations faithfully mimic the behavior observed in experiments, supporting the notion that rheotaxis behavior can be fully explained by hydrodynamics. Our study highlights the important role of hydrodynamics in the behavior of small undulating swimmers and may assist in developing control strategies to affect the animals’ life cycles.

Anucleate Caenorhabditis elegans sperm can crawl, fertilize oocytes and direct anterior-posterior polarization of the 1-cell embryo

Development ◽  
2000 ◽  
Vol 127 (2) ◽  
pp. 355-366 ◽  
Author(s):  
P.L. Sadler ◽  
D.C. Shakes
Keyword(s):  
Cellular Transformation ◽  
Sperm Nucleus ◽  
Sperm Chromatin ◽  
Egg Activation ◽  
C Elegans ◽  
Oocyte Meiosis ◽  
Cell Embryo ◽  
First Time ◽  
Anterior Posterior

It has long been appreciated that spermiogenesis, the cellular transformation of sessile spermatids into motile spermatozoa, occurs in the absence of new DNA transcription. However, few studies have addressed whether the physical presence of a sperm nucleus is required either during spermiogenesis or for subsequent sperm functions during egg activation and early zygotic development. To determine the role of the sperm nucleus in these processes, we analyzed two C. elegans mutants whose spermatids lack DNA. Here we show that these anucleate sperm not only differentiate into mature functional spermatozoa, but they also crawl toward and fertilize oocytes. Furthermore, we show that these anucleate sperm induce both normal egg activation and anterior-posterior polarity in the 1-cell C. elegans embryo. The latter finding demonstrates for the first time that although the anterior-posterior embryonic axis in C. elegans is specified by sperm, the sperm pronucleus itself is not required. Also unaffected is the completion of oocyte meiosis, formation of an impermeable eggshell, migration of the oocyte pronucleus, and the separation and expansion of the sperm-contributed centrosomes. Our investigation of these mutants confirms that, in C. elegans, neither the sperm chromatin mass nor a sperm pronucleus is required for spermiogenesis, proper egg activation, or the induction of anterior-posterior polarity.

Home parenteral nutrition in advanced cancer: where are we?

2008 ◽  
Vol 33 (1) ◽  
pp. 1-11 ◽  
Author(s):  
Michelle L. Mackenzie ◽  
Leah Gramlich
Keyword(s):  
Parenteral Nutrition ◽  
Advanced Cancer ◽  
Disease Process ◽  
Home Parenteral Nutrition ◽  
Burden Of Care ◽  
Incurable Cancer ◽  
New Family ◽  
The Individual ◽  
And Control

Patients with advanced and incurable cancer are a compelling group. Questions and comments that these individuals and their families have may include: “My daughter is expecting our first grandchild in 3 months — can I hope to see our new family member?”; “I can’t keep any food down — is there anything I can do?”; “I am worried about losing so much weight, and feeling tired and weak — is there anything that may help?”; “Will I suffer a lot?”. Indeed, the most pressing concerns of the patient relate to predictions about survival and control of symptoms. The clinician taking care of the patient may wonder what is the utility or futility of home parenteral nutrition (HPN) in both the individual with advanced cancer and in this population of patients at large, whether there is potential for harm such as increasing the burden of care or prolonging suffering, and how to optimize care and communication with the patient and their families. The nutrition scientist may want to know what the implications of advanced cancer are on nutrient requirements and utilization, whether there are markers that would differentiate between cachexia and simple starvation, and whether it is possible to use specific nutrients to modify the disease process. This review will provide insights into the understanding of the role of HPN in advanced cancer and opportunities for further investigation.

scholarly journals AB0010 ASSOCIATION OF SAA1 GENE POLYMORPHISM -13T/C (RS12218) WITH ANKYLOSING SPONDYLITIS IN RUSSIAN POPULATION

2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 1040.1-1040
Author(s):  
I. Guseva ◽  
K. Sakharova ◽  
M. Krylov ◽  
E. Samarkina ◽  
S. Erdes
Keyword(s):  
Ankylosing Spondylitis ◽  
Gene Polymorphism ◽  
Protein Concentration ◽  
Control Group ◽  
Amyloid A ◽  
Systemic Inflammatory Disease ◽  
Allele Specific ◽  
And Control ◽  
First Time

Background:Ankylosing spondylitis is a chronic systemic inflammatory disease. Inflammation and high levels of serum amyloid A (SAA) protein are predisposing factors for secondary AA amyloidosis. The role of SAA1 gene polymorphisms in AS is not well understood.Objectives:To investigate the association of SAA1 gene polymorphism -13T/C (rs12218) with ankylosing spondylitis and to evaluate the influence of this polymorphism on SAA protein concentration.Methods:123 AS patients (72 males, 51 females; age - M (SD) 37.51 (12.77) years; disease duration - 14.28 (11.22) years; BASDAI – 5.59 (1.13); B27-positive - 111 (90.2%) pts) and 95 gender, age matched healthy individuals (control group) were included in this study. SAA1 gene polymorphism -13T/C was genotyped using allele-specific RT-PCR assay. SAA protein concentration was measured using nephelometry in AS patients.Results:The distribution of genotypes TT, TC and CC differed statistically between AS and control groups (24.4%, 56.1%, 19.5% and 41.1%, 44.2%, 14.7% respectively, χ 2=6.9, p=0.03).The presence of the C allele was associated with the development of AS (OR=1.55 [CI 1.04-2.33], p=0.03). The SAA1 -13T/C polymorphism tended to be associated with SAA protein value in AS patients: TT+TC genotypes -13.8 mg/l [4.2; 91.0], CC genotype -7.8 mg/l [1.6; 29.6], p=0.07. ESR, CRP and BASDAI values did not correlated with SAA1 - 13T/C polymorphism (p=0.6, p=0.4, p=0.4 respectively).Conclusion:The results of our study demonstrated for the first time that SAA1 gene polymorphism -13T/C (rs12218) is associated with susceptibility to AS. It is also shown that this polymorphism can affect the SAA protein level. Our findings need to be verified in AS patients with high levels of SAA protein in various ethnic and population groups.Disclosure of Interests:None declared

scholarly journals DEGR-factor Xa blocks disseminated intravascular coagulation initiated by Escherichia coli without preventing shock or organ damage

Blood ◽  
1991 ◽  
Vol 78 (2) ◽  
pp. 364-368 ◽  
Author(s):  
FB Jr Taylor ◽  
AC Chang ◽  
GT Peer ◽  
T Mather ◽  
K Blick ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Cell Injury ◽  
Factor Xa ◽  
Organ Damage ◽  
Lethal Outcome ◽  
Chloromethyl Ketone ◽  
E Coli ◽  
And Control ◽  
First Time

One of the aims of research in the area of thrombosis has been to design an effective anticoagulant that would function in a predictable and direct manner. In evaluating the role of coagulation in sepsis we used factor Xa blocked in the active center with [5-(dimethylamino)1- naphthalenesulfonyl]-glutamylglycylarginyl+ ++ chloromethyl ketone (DEGR-Xa). We infused 1 mg/kg of DEGR-Xa together with LD100 concentrations of Escherichia coli (4 x 10(10) organisms/kg) into five baboons. As controls, we infused E coli alone into five baboons. The inflammatory, coagulant, and cell injury responses to E coli of both the treated and control groups were lethal and were similar in every respect except for the complete inhibition of the consumption of fibrinogen in the DEGR-Xa group. The half life of DEGR-Xa was approximately 10 hours and 2 hours, as determined by isotopic and enzyme-linked immunosorbent assays, respectively. These results for the first time demonstrate that, although coagulation occurs in E coli sepsis, fibrin formation per se did not influence the lethal outcome in this model. These results also show the effectiveness of DEGR-Xa as an anticoagulant and raise the possibility that it could serve as an alternative to anticoagulants currently in use.

scholarly journals DEGR-factor Xa blocks disseminated intravascular coagulation initiated by Escherichia coli without preventing shock or organ damage

Blood ◽  
1991 ◽  
Vol 78 (2) ◽  
pp. 364-368 ◽  
Author(s):  
FB Jr Taylor ◽  
AC Chang ◽  
GT Peer ◽  
T Mather ◽  
K Blick ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Cell Injury ◽  
Factor Xa ◽  
Organ Damage ◽  
Lethal Outcome ◽  
Chloromethyl Ketone ◽  
E Coli ◽  
And Control ◽  
First Time

Abstract One of the aims of research in the area of thrombosis has been to design an effective anticoagulant that would function in a predictable and direct manner. In evaluating the role of coagulation in sepsis we used factor Xa blocked in the active center with [5-(dimethylamino)1- naphthalenesulfonyl]-glutamylglycylarginyl+ ++ chloromethyl ketone (DEGR-Xa). We infused 1 mg/kg of DEGR-Xa together with LD100 concentrations of Escherichia coli (4 x 10(10) organisms/kg) into five baboons. As controls, we infused E coli alone into five baboons. The inflammatory, coagulant, and cell injury responses to E coli of both the treated and control groups were lethal and were similar in every respect except for the complete inhibition of the consumption of fibrinogen in the DEGR-Xa group. The half life of DEGR-Xa was approximately 10 hours and 2 hours, as determined by isotopic and enzyme-linked immunosorbent assays, respectively. These results for the first time demonstrate that, although coagulation occurs in E coli sepsis, fibrin formation per se did not influence the lethal outcome in this model. These results also show the effectiveness of DEGR-Xa as an anticoagulant and raise the possibility that it could serve as an alternative to anticoagulants currently in use.

scholarly journals Protein Biomarker Identification in the CSF of Patients With CNS Lymphoma

2008 ◽  
Vol 26 (1) ◽  
pp. 96-105 ◽  
Author(s):  
Sushmita Roy ◽  
S. Andrew Josephson ◽  
Jane Fridlyand ◽  
Jon Karch ◽  
Cigall Kadoch ◽  
...  
Keyword(s):  
Brain Biopsy ◽  
Enzyme Linked Immunosorbent Assay ◽  
Cns Lymphoma ◽  
Protein Biomarkers ◽  
Rna Transcripts ◽  
Csf Proteins ◽  
Validation Set ◽  
Cns Lymphomas ◽  
And Control ◽  
First Time

PurposeElucidation of the CSF proteome may yield insights into the pathogenesis of CNS disease. We tested the hypothesis that individual CSF proteins distinguish CNS lymphoma from benign focal brain lesions.MethodsWe used a liquid chromatography/mass spectrometry–based method to differentially quantify and identify several hundred CSF proteins in CNS lymphoma and control patients. We used enzyme-linked immunosorbent assay (ELISA) to confirm one of these markers in an additional validation set of 101 cases.ResultsApproximately 80 CSF proteins were identified and found to be present at significantly different concentrations, both higher and lower, in training and test studies, which were highly concordant. To further validate these observations, we defined in detail the expression of one of these candidate biomarkers, antithrombin III (ATIII). ATIII RNA transcripts were identified within CNS lymphomas, and ATIII protein was localized selectively to tumor neovasculature. Determination of ATIII concentration by ELISA was significantly more accurate (> 75% sensitivity; > 98% specificity) than cytology in the identification of cancer. Measurement of CSF ATIII levels was found to potentially enhance the ability to diagnose and predict outcome.ConclusionOur findings demonstrate for the first time that proteomic analysis of CSF yields individual biomarkers with greater sensitivity in the identification of cancer than does CSF cytology. We propose that the discovery of CSF protein biomarkers will facilitate early and noninvasive diagnosis in patients with lesions not amenable to brain biopsy, as well as provide improved surrogates of prognosis and treatment response in CNS lymphoma and brain metastasis.

scholarly journals The Role Of The Pro47ser Polymorphism Of The Tr53 Gene In Predisposition To Breast Cancer

2020 ◽  
Vol 02 (12) ◽  
pp. 64-73
Author(s):  
Nodirjon Shakhriqulovich Avezov ◽  
◽  
Dilbar Abdullaevna Kodirova ◽  
Khakimov Golib Abdullevich ◽  
Aminjon Karimovich Karimov ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Odds Ratio ◽  
Control Group ◽  
Control Groups ◽  
Healthy Donors ◽  
Homozygous Genotype ◽  
The World ◽  
And Control ◽  
First Time

Numerous scientific studies have been carried out on the predisposition of the Pro47Ser polymorphism of the TR53 gene to breast cancer in women living in most countries of the world. However, no studies have been conducted on the susceptibility of this Pro47Ser gene polymorphism to breast cancer in Uzbek women. In this article, genotyping of the Pro47Ser polymorphism of the TR53 gene was performed for the first time in 207 Uzbek women. According to the results of our study, the functionally dangerous T allele of the Pro47Ser polymorphism of the TR53 gene was statistically significantly higher than that in healthy donors in patients with breast cancer; (ch2 = 8.2; p = 0.004; OR = 11.2; 95% CI: 1.422-88.38; RR = 10.7; 95% CI: 1.382-82.82). The safe C allele, on the other hand, was more common in the control group than in the main group. The natural S / C genotype was found in the control group with a higher frequency than in the control group. However, the limit of the statistical difference reached a significant level: (ch2 = 8.4; p = 0.004; OR = 0.08; 95% CI: 0.01066-0.676; ch2 = 8.2; p = 0.004; RR = 0.1 ; 95% CI: 0.8489- 0.9723). The S / T genotype of this polymorphism significantly differs in the frequency of occurrence in the main and control groups. Relative risk according to statistical analysis: RR = 10.7; (95% CI: 1.395–82.07) and odds ratio: OR = 11.8; (95% CI: 1.479-93.77). It is known that the minor T allele and the S / T genotype of this polymorphism increase the risk of developing breast cancer by 10.7 times. It should be noted that the unique homozygous genotype of Pro47Ser polymorphism was not identified in patients and control groups studied by T / T. Thus, the T allele and the C / T genotype of the Pro47Ser polymorphism of the TR53 gene are important factors that increase the risk of breast cancer (r <0.05). The C allele and S / S genotype of this polymorphism are reliable protective markers against the development of this pathology. Therefore, we believe that the Pro47Ser polymorphism of the TR53 gene can be used as important genetic markers in determining the likelihood of developing breast cancer.

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