Striking nucleotide frequency pattern at the borders of highly conserved vertebrate non-coding sequences

Here, we report the draft genome sequence of Pseudorhodobacter sp. strain E13, a Gram-negative, aerobic, nonflagellated, and rod-shaped bacterium which was isolated from the Yellow Sea in South Korea. The assembled genome sequence is 3,878,578 bp long with 3,646 protein-coding sequences in 159 contigs.

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Profile of Organophosphorus Poisoning

KYAMC Journal ◽

10.3329/kyamcj.v9i3.38786 ◽

2018 ◽

Vol 9 (3) ◽

pp. 133-135

Author(s):

Joya Debnath ◽

Arpan Kumar Basak ◽

Md Zubaidur Rahman ◽

Anujit Saha

Keyword(s):

Organophosphorus Compound ◽

Economic Status ◽

Frequency Pattern ◽

Major Health Problem ◽

Major Health ◽

The Public ◽

Medical College ◽

Phosphorus Poisoning ◽

Life Threatening ◽

The Government

Background : Self poisoning with organophosphate pesticides is a major health problem in world wide. Organophosphorus compound poisoning is a very common toxicological emergency encountered at Mirzapur in Tangail. It is particularly common among the rural agricultural worker's which comprise a substantial group of the population of this region.Objective: The objective of this study was to find out the incidence, frequency, pattern of poisoning, outcome and aetiological aspect of Organo phosphorus poisoning patient admitted in Kumudini Women's Medical college Hospital.Methods: A total 366 cases of OPC poisoning were analysed during 1 year from January 2015 to December 2015. The emphasis was given on age, sex, socio-economic status, occupation, motive of poisoning, types of compound consumed its quality, place, distance from referral place and the ultimate outcome.Results: Young population of rural background, particularly agricultural workers were the commonest patients (51.91%). The most common motive of poisoning was with a suicidal intent, both in males (27.59%) and females (66.39%). Financial crisis was one of the most common reasons analysed as the motive behind the poisoning (54.20%). Three hundred forty four Patients recovered and 22 were expired. The major cause of death in these cases was respiratory failure followed by multi-organ failure.Conclusion : Strict of the pesticide act and involving a new policy by the government to educate the public and youth in large about the dangerous, life threatening effects of Organophosphorus compound could help amelerioating the harmful effects of such poisoning.KYAMC Journal Vol. 9, No.-3, October 2018, Page 133-135

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Analysis of HLA-G long-read genomic sequences in mother–offspring pairs with preeclampsia

Scientific Reports ◽

10.1038/s41598-020-77081-3 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Ayako Nishizawa ◽

Kazuki Kumada ◽

Keiko Tateno ◽

Maiko Wagata ◽

Sakae Saito ◽

...

Keyword(s):

Single Molecule ◽

Gene Polymorphisms ◽

Genomic Dna ◽

Genomic Sequences ◽

Genomic Sequencing ◽

Public Database ◽

Coding Sequences ◽

Pacbio Rs Ii ◽

Potential Association ◽

Long Read

AbstractPreeclampsia is a pregnancy-induced disorder that is characterized by hypertension and is a leading cause of perinatal and maternal–fetal morbidity and mortality. HLA-G is thought to play important roles in maternal–fetal immune tolerance, and the associations between HLA-G gene polymorphisms and the onset of pregnancy-related diseases have been explored extensively. Because contiguous genomic sequencing is difficult, the association between the HLA-G genotype and preeclampsia onset is controversial. In this study, genomic sequences of the HLA-G region (5.2 kb) from 31 pairs of mother–offspring genomic DNA samples (18 pairs from normal pregnancies/births and 13 from preeclampsia births) were obtained by single-molecule real-time sequencing using the PacBio RS II platform. The HLA-G alleles identified in our cohort matched seven known HLA-G alleles, but we also identified two new HLA-G alleles at the fourth-field resolution and compared them with nucleotide sequences from a public database that consisted of coding sequences that cover the 3.1-kb HLA-G gene span. Intriguingly, a potential association between preeclampsia onset and the poly T stretch within the downstream region of the HLA-G*01:01:01:01 allele was found. Our study suggests that long-read sequencing of HLA-G will provide clues for characterizing HLA-G variants that are involved in the pathophysiology of preeclampsia.

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Erratum to: “The correlation of protein hydropathy with the base composition of coding sequences” [Gene 238 (1999) 3–14]

Gene ◽

10.1016/s0378-1119(99)00504-1 ◽

2000 ◽

Vol 241 (2) ◽

pp. 341

Author(s):

Giuseppe D'Onofrio ◽

Kamel Jabbari ◽

Hector Musto ◽

Giorgio Bernardi

Keyword(s):

Base Composition ◽

Coding Sequences

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Development of central auditory processes in Polish children and adolescents at the age from 7 to 16 years

Current Psychology ◽

10.1007/s12144-021-01540-x ◽

2021 ◽

Author(s):

Monika Lewandowska ◽

Rafał Milner ◽

Małgorzata Ganc ◽

Elżbieta Włodarczyk ◽

Joanna Dołżycka ◽

...

Keyword(s):

Children And Adolescents ◽

School Students ◽

Frequency Pattern ◽

Speech In Noise ◽

Age Related ◽

Right Ear Advantage ◽

The Right ◽

Almost All ◽

Test Retest Reliability ◽

Auditory Processes

AbstractThere are discrepancies in the literature regarding the course of central auditory processes (CAP) maturation in typically developing children and adolescents. The purpose of the study was to provide an overview of age – related improvement in CAP in Polish primary and secondary school students aged 7–16 years. 180 children/adolescents, subdivided into 9 age categories, and 20 adults (aged 18–24 years) performed the Dichotic Digit Test (DDT), Duration Pattern Test (DPT), Frequency Pattern Test (FPT), Gap Detection Test (GDT) and adaptive Speech-in-Noise (aSpN). The 12-year-olds was retested after w week. We found the age effects only for the DDT, DPT and FPT. In the right ear DDT the 7-year-olds performed more poorly than all groups ≥12. In the left ear DDT both 7- and 8-year-olds achieved less correct responses compared with the 13-, 14-, 15-year-olds and with the adults. The right ear advantage was greater in the 7-year-olds than in the 15-year-olds and adult group. At the age of 7 there was lower DPT and FPT scores than in all participants ≥13 whereas the 8-year-olds obtained less correct responses in the FPT than all age categories ≥12. Almost all groups (except for the 7-year-olds) performed better in the DPT than FPT. The test-retest reliability for all tests was satisfactory. The study demonstrated that different CAP have their own patterns of improvement with age and some of them are specific for the Polish population. The psychoacoustic battery may be useful in screening for CAP disorders in Poland.

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Auditory Processing Disorders in Elderly Persons vs. Linguistic and Emotional Prosody

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph18126427 ◽

2021 ◽

Vol 18 (12) ◽

pp. 6427

Author(s):

Anna Rasmus ◽

Aleksandra Błachnio

Keyword(s):

Interpersonal Relationships ◽

Auditory Processing ◽

Temporal Pattern ◽

Right Hemisphere ◽

Elderly Persons ◽

Central Auditory Processing ◽

Auditory Processing Disorders ◽

Emotional Prosody ◽

Frequency Pattern ◽

Central Processing

Background: Language communication, which is one of the basic forms of building and maintaining interpersonal relationships, deteriorates in elder age. One of the probable causes is a decline in auditory functioning, including auditory central processing. The aim of the present study is to evaluate the profile of central auditory processing disorders in the elderly as well as the relationship between these disorders and the perception of emotional and linguistic prosody. Methods: The Right Hemisphere Language Battery (RHLB-PL), and the Brain-Boy Universal Professional (BUP) were used. Results: There are statistically significant relationships between emotional prosody and: spatial hearing (r(18) = 0.46, p = 0.04); the time of the reaction (r(18) = 0.49, p = 0.03); recognizing the frequency pattern (r(18) = 0.49, p = 0.03 (4); and recognizing the duration pattern (r(18) = 0.45, p = 0.05. There are statistically significant correlations between linguistic prosody and: pitch discrimination (r(18) = 0.5, p = 0.02); recognition of the frequency pattern (r(18) = 0.55, p = 0.01); recognition of the temporal pattern; and emotional prosody (r(18) = 0.58, p = 0.01). Conclusions: The analysis of the disturbed components of auditory central processing among the tested samples showed a reduction in the functions related to frequency differentiation, the recognition of the temporal pattern, the process of discriminating between important sounds, and the speed of reaction. De-automation of the basic functions of auditory central processing, which we observe in older age, lowers the perception of both emotional and linguistic prosody, thus reducing the quality of communication in older people.

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SARS-CoV-2 and other human coronavirus show genome patterns previously associated to reduced viral recognition and altered immune response

Scientific Reports ◽

10.1038/s41598-021-90278-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Giovanni Franzo

Keyword(s):

Immune Response ◽

Codon Bias ◽

Synonymous Codon ◽

Rna Degradation ◽

Codon Usage Pattern ◽

Interferon Production ◽

Genome Composition ◽

Coding Sequences ◽

Spike Coding ◽

Viral Recognition

AbstractA new pandemic caused by the betacoronavirus SARS-CoV-2 originated in China in late 2019. Although often asymptomatic, a relevant percentage of affected people can develop severe pneumonia. Initial evidence suggests that dysregulation of the immune response could contribute to the pathogenesis, as previously demonstrated for SARS-CoV. The presence of genome composition features involved in delaying viral recognition is herein investigated for human coronaviruses (HCoVs), with a special emphasis on SARS-CoV-2. A broad collection of HCoVs polyprotein, envelope, matrix, nucleocapsid and spike coding sequences was downloaded and several statistics representative of genome composition and codon bias were investigated. A model able to evaluate and test the presence of a significant under- or over-representation of dinucleotide pairs while accounting for the underlying codon bias and protein sequence was also implemented. The study revealed the significant under-representation of CpG dinucleotide pair in all HcoV, but especially in SARS-CoV and even more in SARS-CoV-2. The presence of forces acting to minimize CpG content was confirmed by relative synonymous codon usage pattern. Codons containing the CpG pair were severely under-represented, primarily in the polyprotein and spike coding sequences of SARS-CoV-2. Additionally, a significant under-representation of the TpA pair was observed in the N and S region of SARS-CoV and SARS-CoV-2. Increasing experimental evidence has proven that CpG and TpA are targeted by innate antiviral host defences, contributing both to RNA degradation and RIG-1 mediated interferon production. The low content of these dinucleotides could contribute to a delayed interferon production, dysregulated immune response, higher viral replication and poor outcome. Significantly, the RIG-1 signalling pathway was proven to be defective in elderlies, suggesting a likely interaction between limited viral recognition and lower responsiveness in interferon production that could justify the higher disease severity and mortality in older patients.

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