scholarly journals Few SINEs of life: Alu elements have little evidence for biological relevance despite elevated translation

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Laura Martinez-Gomez ◽  
Federico Abascal ◽  
Irwin Jungreis ◽  
Fernando Pozo ◽  
Manolis Kellis ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Strong Evidence ◽  
Human Population ◽  
Population Variation ◽  
Alu Elements ◽  
Alternative Transcripts ◽  
Biological Relevance ◽  
Functional Regions ◽  
Variation Data ◽  
Almost All

Abstract Transposable elements colonize genomes and with time may end up being incorporated into functional regions. SINE Alu elements, which appeared in the primate lineage, are ubiquitous in the human genome and more than a thousand overlap annotated coding exons. Although almost all Alu-derived coding exons appear to be in alternative transcripts, they have been incorporated into the main coding transcript in at least 11 genes. The extent to which Alu regions are incorporated into functional proteins is unclear, but we detected reliable peptide evidence to support the translation to protein of 33 Alu-derived exons. All but one of the Alu elements for which we detected peptides were frame-preserving and there was proportionally seven times more peptide evidence for Alu elements as for other primate exons. Despite this strong evidence for translation to protein we found no evidence of selection, either from cross species alignments or human population variation data, among these Alu-derived exons. Overall, our results confirm that SINE Alu elements have contributed to the expansion of the human proteome, and this contribution appears to be stronger than might be expected over such a relatively short evolutionary timeframe. Despite this, the biological relevance of these modifications remains open to question.

scholarly journals Regulation of Activator/Dissociation Transposition by Replication and DNA Methylation

Genetics ◽  
2001 ◽  
Vol 157 (4) ◽  
pp. 1723-1733
Author(s):  
Francesca Ros ◽  
Reinhard Kunze
Keyword(s):  
Dna Methylation ◽  
Transposable Elements ◽  
Strong Evidence ◽  
Complementary Strand ◽  
Regulatory Effect ◽  
Ds Excision ◽  
Dna Strand ◽  
Petunia Protoplasts ◽  
Ac Transposase ◽  
High Binding Affinity

Abstract In maize the transposable elements Activator/Dissociation (Ac/Ds) transpose shortly after replication from one of the two resulting chromatids (“chromatid selectivity”). A model has been suggested that explains this phenomenon as a consequence of different affinity for Ac transposase binding to holo-, hemi-, and unmethylated transposon ends. Here we demonstrate that in petunia cells a holomethylated Ds is unable to excise from a nonreplicating vector and that replication restores excision. A Ds element hemi-methylated on one DNA strand transposes in the absence of replication, whereas hemi-methylation of the complementary strand causes a >6.3-fold inhibition of Ds excision. Consistently in the active hemi-methylated state, the Ds ends have a high binding affinity for the transposase, whereas binding to inactive ends is strongly reduced. These results provide strong evidence for the above-mentioned model. Moreover, in the absence of DNA methylation, replication enhances Ds transposition in petunia protoplasts >8-fold and promotes formation of a predominant excision footprint. Accordingly, replication also has a methylation-independent regulatory effect on transposition.

scholarly journals Delineating urban functional regions by considering interaction cohesiveness and function diversity

2019 ◽  
Vol 1 ◽  
pp. 1-1
Author(s):  
Fei-Ying Kuo ◽  
Tzai-Hung Wen
Keyword(s):  
Public Transportation ◽  
Urban System ◽  
Market Area ◽  
Functional Region ◽  
Trip Purpose ◽  
Functional Regions ◽  
Human Movements ◽  
Local Labour ◽  
Almost All ◽  
And Function

<p><strong>Abstract.</strong> A functional region is usually defined as a region characterized by not only interaction cohesiveness but also function diversity. The former indicates that places within a region should share a cohesive interacting pattern of human movements, such as commute or daily travel; the latter means that the places should possess diverse functions like residence, commerce, etc. Due to these two characteristics, people living and moving in one region can acquire almost all their daily needs, and they do not need to frequently move to other regions. In other words, a functional region resembles a life circle. Based on this definition, many previous studies have developed different methods to analyse human flow data so that they can properly profile different types of functional regions like Local labour market area (LLMA) or daily urban system (DUS), which helps people better understand how functional regions compose an area. Existing methods have considered interaction cohesiveness in a functional region, but function diversity is ignored. This is because these studies only used specific-purpose-trip data, such as journey to work or to shop. These kinds of trips describe people moving from their home to their office or to shopping malls, so each trip has an inherent distinction of functions between its origin and destination; thus, a functional region consisting of these trips indirectly owns function diversity. However, this framework has some problems. First, it cannot profile a functional region shaped by composite functions, for only one trip purpose can be taken into account each time. Second, collecting the data of specific-purpose trips needs either some questionnaires or some surveys, so it is often costly and time consuming. Finally, the purpose-unrecorded-trip data provided by rapidly developed smart card systems in several countries can be collected quickly, yet it cannot properly profile functional regions through the aforementioned framework due to the lack of trip purposes. Therefore, we propose a new spatial partitioning algorithm which can simultaneously consider both interaction cohesiveness and function diversity in profiling functional regions. Compared with previous methods, the proposed algorithm can better profile functional regions from many purpose-unrecorded-trip data based on the inclusion of land-use data. Our results provide deeper insights for understanding how various functions of lands and human movements together shape the boundary of a region. It could be significant reference for developing policies for urban planning or public transportation management.</p>

scholarly journals An Upper Limit on the Functional Fraction of the Human Genome

2017 ◽  
Vol 9 (7) ◽  
pp. 1880-1885 ◽  
Author(s):  
Dan Graur
Keyword(s):  
Human Genome ◽  
Human Population ◽  
Mutational Load ◽  
Deleterious Mutations ◽  
Replacement Level ◽  
Functional Regions ◽  
Upper Limit ◽  
Constant Size ◽  
Mean Fitness ◽  
The Mean

AbstractFor the human population to maintain a constant size from generation to generation, an increase in fertility must compensate for the reduction in the mean fitness of the population caused, among others, by deleterious mutations. The required increase in fertility due to this mutational load depends on the number of sites in the genome that are functional, the mutation rate, and the fraction of deleterious mutations among all mutations in functional regions. These dependencies and the fact that there exists a maximum tolerable replacement level fertility can be used to put an upper limit on the fraction of the human genome that can be functional. Mutational load considerations lead to the conclusion that the functional fraction within the human genome cannot exceed 15%.

scholarly journals What have humans done for evolutionary biology? Contributions from genes to populations

2017 ◽  
Vol 284 (1866) ◽  
pp. 20171164 ◽  
Author(s):  
Michael Briga ◽  
Robert M. Griffin ◽  
Vérane Berger ◽  
Jenni E. Pettay ◽  
Virpi Lummaa
Keyword(s):  
Natural Selection ◽  
Evolutionary Biology ◽  
Human Study ◽  
Human Studies ◽  
Human Populations ◽  
Evolutionary Processes ◽  
Biological Relevance ◽  
Evolutionary Studies ◽  
Almost All ◽  
Study Designs

Many fundamental concepts in evolutionary biology were discovered using non-human study systems. Humans are poorly suited to key study designs used to advance this field, and are subject to cultural, technological, and medical influences often considered to restrict the pertinence of human studies to other species and general contexts. Whether studies using current and recent human populations provide insights that have broader biological relevance in evolutionary biology is, therefore, frequently questioned. We first surveyed researchers in evolutionary biology and related fields on their opinions regarding whether studies on contemporary humans can advance evolutionary biology. Almost all 442 participants agreed that humans still evolve, but fewer agreed that this occurs through natural selection. Most agreed that human studies made valuable contributions to evolutionary biology, although those less exposed to human studies expressed more negative views. With a series of examples, we discuss strengths and limitations of evolutionary studies on contemporary humans. These show that human studies provide fundamental insights into evolutionary processes, improve understanding of the biology of many other species, and will make valuable contributions to evolutionary biology in the future.

scholarly journals Adaptação acústico-prosódica entre falantes

2018 ◽  
pp. 18-33
Author(s):  
Vera Cabarrão ◽  
Helena Moniz ◽  
Fernando Batista ◽  
Isabel Trancoso ◽  
Ana Isabel Mata
Keyword(s):  
Strong Evidence ◽  
Global Analysis ◽  
Gender Effects ◽  
European Portuguese ◽  
And Gender ◽  
Almost All ◽  
Distinct Features

This paper presents a global analysis of entrainment in map-task dialogues in European Portuguese, including 48 dialogues, between 24 speakers. Our main goal is to analyze the acoustic-prosodic similarities between speaker pairs, namely if there are global entrainment cues displayed in the dialogues, if entrainment is manifested in distinct sets of features shared amongst the speakers, if entrainment depends on the gender and role of the speaker (giver or follower), and if speakers tend to entrain more with specific interlocutors regardless of the role. Results show that globally speakers tend to be more similar to their partners than to their own speech in the majority of the analyzed features, a strong evidence for entrainment. Moreover, almost all the pairs of speakers display cues of global entrainment, even though in different degrees (speakers entrain but in distinct features). Additionally, the role and gender effects tend to be less striking than the specific interlocutor effect. Our results support the fact that all prosodic parameters are monitored by the speakers in our corpus, contrarily to studies for other languages, which indicate that the main cues are energy related.

scholarly journals Bioactive Building Blocks and Potential Pharmacological Perspectives of Green Coffee: A Review

2021 ◽  
pp. 78-93
Author(s):  
Namrata Kundu ◽  
Gaurav Pant
Keyword(s):  
Chlorogenic Acid ◽  
Functional Food ◽  
Human Population ◽  
Building Blocks ◽  
Biologically Active ◽  
Pharmacological Effects ◽  
Coffee Beans ◽  
Excessive Consumption ◽  
Almost All ◽  
Multiple Health

Coffee is known to be one of the popular beverages today on the globe. Due to its easy availability and preparation, it is consumed by the population of almost all countries. This wonder crop was discovered in the 6th century in Ethiopia. Since then, people have also used various brewing methods to extract hundreds of the bioactive compounds present in these aromatic seeds. No doubt, excessive consumption of the same can be harmful too. As a functional food, coffee is known to have multiple health benefits. Coffee beans contain vitamins, minerals, caffeine, chlorogenic acid, and various other biologically active ingredients. This review briefly describes the major biologically active compounds present in these seeds – caffeine, trigonelline, diterpenes, and chlorogenic acid (CGA). It also aims to describe various bioactive activities such as antioxidant, antiproliferative, antibacterial, antiviral, etc., against variable hallmarks. Thus, explaining different pharmacological effects for the welfare of the human population.

A single mutation in ACTR8 gene results in lineage-specific expression in primates

2020 ◽  
Author(s):  
Se-Hee Choe ◽  
Sang-je Park ◽  
Hyeon-Mu Cho ◽  
Hye-Ri Park ◽  
Ja-Rang Lee ◽  
...  
Keyword(s):  
World Monkey ◽  
Single Gene ◽  
In Silico Analysis ◽  
Acceptor Site ◽  
Single Mutation ◽  
Specific Expression ◽  
Old World ◽  
Alu Elements ◽  
Alternative Transcripts ◽  
Novel Transcript

Abstract Background: Alternative splicing (AS) generate various transcripts from a single gene and thus plays a significant role in transcriptomic diversity and proteomic complexity. Alu elements are primate-specific transposable elements (TEs) and can provide a donor or acceptor site for AS. In a study on TE-mediated AS, we recently identified a novel AluSz6-exonized ACTR8 transcript of a crab-eating monkey (Macaca fascicularis). In the present study, we sought to analyse the molecular mechanism of AluSz6-derived exonization in ACTR8 gene. Results: We performed RT-PCR and genomic PCR using the tissue RNA and DNA samples from the crab-eating monkey and various other primates, including humans, to study AluSz6-derived exonization in ACTR8 gene and transcript variants expression. AluSz6 integration was estimated to have occurred before the divergence of simians and prosimians. The novel transcript was expressed only in Old world monkeys and apes, and humans. Lineage-specific expression of ACTR8 gene was due to a ‘G’ duplication in the AluSz6 sequences of Old world monkey and ape lineages. Six alternative transcripts (TV1-TV6) generated by various AS mechanisms were newly identified. Based on in-silico analysis, the alternative transcripts were transcribed into new isoforms with C-terminus deletion. Conclusion: ‘G’ duplication together with TE exonization and AS via various mechanisms resulted in a different fate of ACTR8 gene expression during primate evolution.

Field Experiments with a Totem Animal

2020 ◽  
pp. 231-268
Author(s):  
Nicolas Langlitz
Keyword(s):  
Human Population ◽  
Field Experiments ◽  
Agricultural Landscape ◽  
Political Conflict ◽  
Primary Forest ◽  
Small Patch ◽  
Anthropogenic Environment ◽  
Female Immigrants ◽  
Cultural Primatology ◽  
Almost All

This chapter follows Tetsuro Matsuzawa and his coworkers to their outdoor laboratory in Bossou, Guinea. Revered as the totem animal of the Manon and deprived of almost all primary rainforest, the Bossou chimpanzees had learned to live on human crops in an agricultural landscape. In contrast to Christophe Boesch's emphasis on so-called wild cultures, Matsuzawa speculated that historically, this chimpanzee community might have learned from the human population how to crack the oil palm nuts that local farmers cultivated. Field experiments allowed the primatologists to study how female immigrants passed on their knowledge of how to crack other kinds of nuts within the group. At this point, Japanese cultural primatology contradicted the Manon's mythological understanding of “their” apes as a bounded community of nonnatural animals. Chimpanzee road crossings provided an opportunity for a natural — or really “naturecultural” — experiment in an anthropogenic environment. Ethnoprimatologists collaborating with Matsuzawa studied the ecological interface between humans and primates and used their insights for conservationist ends. After a political conflict over the protection of a small patch of primary forest on a sacred hill, the Japanese primatologists took over the Manon's position that the livelihood of the Bossou chimpanzees was better served by plantations than by a nature reserve.

Age-Decline in the Activity of the Plasma Membrane Ca2+ Pump (PMCA) of Normal Human Red Blood Cells (RBCs).

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 1670-1670
Author(s):  
Robert M. Bookchin ◽  
Nuala Daw ◽  
Zipora Etzion ◽  
Teresa Tiffert ◽  
Virgilio L. Lew
Keyword(s):  
Glycosylated Hemoglobin ◽  
Inverse Correlation ◽  
Population Variation ◽  
Channel Activation ◽  
Hb A1c ◽  
Human Red Blood Cells ◽  
Age Related ◽  
Gardos Channel ◽  
High K ◽  
Almost All

Abstract We recently demonstrated that the activity of the PMCA varies greatly among the RBCs in a normal blood sample (Lew et al., Blood102:4206,2003). To test the possibility that these variations might be related to cell age, we designed a new experimental protocol to separate RBCs with different PMCA Vmax, which used glycosylated hemoglobin (Hb) A1c as an age marker for the normal RBCs, and avoided Co2+ (used in our usual PMCA activity assay) which we found to interfere with Hb A1c measurements: The ionophore A21837 was used to generate a high, rapid and uniform [CaT]i in RBCs, which were suspended in a 90mM-K+ buffer to prevent RBC dehydration by Gardos channel activation. These RBCs were then washed in high-K+ buffer (ice-cold to inhibit the Ca2+ pump) with 1% albumin to remove the ionophore. At t=0, the washed and packed ionophore-free cells were delivered into 20 volumes of high-K+ buffer at 37oC to initiate Ca2+ extrusion by the PMCA, and then sampled at 15 sec intervals into 25 vol of an ice-cold, K+-free, isotonic buffer containing 10 mM SCN−; these conditions were designed to trap un-extruded Ca2+ and to elicit rapid dehydration of those cells which had not yet pumped out all their Ca2+ load. After ~ 40 min at 0oC each sample was spun; the packed RBCs were resuspended in 10 vol of the same buffer and spun again through diethylphthalate oil (D=1.117 g/ml) to separate the dehydrated RBCs (pellets) from the non-dehydrated cells. The fraction of cells in pellets and on top of the oil was estimated in each sample from Hb measurements, and their Hb A1c content was measured by HPLC. Initially, almost all RBCs, except those with the most vigorous pumps, were recovered in the pellets, but with time, the fraction of cells which had fully extruded their Ca2+ load and were recovered on top of the oil approached 100%. The progressively smaller pellets contained RBCs with progressively weaker pumps; their Hb A1c fraction increased with decrease in the yield of RBCs in the pellet. This inverse correlation between yield and Hb A1c fraction in the pellets was observed in all six experiments performed with RBCs from four donors. Since the decline in PMCA activity correlated directly with an increase in Hb A1c, the observed population variation in PMCA activity reflects an age-related decline in PMCA activity. Whether this decline is due to progressive glycosylation of of a lysine residue near the catalytic ATP domain on the pump ATPase (Gonzalez Flecha et al., J Membr Biol171:25,1999) or to other mechanisms, remains to be determined. The age-decline in PMCA activity may be responsible for the increasing density of aging RBCs, by allowing intermittent episodes of [Ca2+]i elevations in the circulation, with transient Gardos channel activation and gradual dehydration by net KCl and water loss.

scholarly journals Lipid rafts make for slippery platforms

2003 ◽  
Vol 162 (3) ◽  
pp. 365-370 ◽  
Author(s):  
Eric C. Lai
Keyword(s):  
Lipid Rafts ◽  
Cell Membranes ◽  
Size Composition ◽  
Membrane Dynamics ◽  
Biological Relevance ◽  
Almost All

What's in a raft? Although cell membranes are certainly not homogeneous mixtures of lipids and proteins, almost all aspects of lipid rafts—how to define them, their size, composition, lifetime, and biological relevance—remain controversial. The answers will shape our views of signaling and of membrane dynamics.

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