Folding up and Moving on—Nascent Protein Folding on the Ribosome

All cellular proteins are synthesized by the ribosome, an intricate molecular machine that translates the information of protein coding genes into the amino acid alphabet. The linear polypeptides synthesized by the ribosome must generally fold into specific three-dimensional structures to become biologically active. Folding has long been recognized to begin before synthesis is complete. Recently, biochemical and biophysical studies have shed light onto how the ribosome shapes the folding pathways of nascent proteins. Here, we discuss recent progress that is beginning to define the role of the ribosome in the folding of newly synthesized polypeptides.     

Effect of Dephosphorylation on the Self-association and the Precipitation of β-Casein

The pyrolyzate of the nondialyzable melanoidin prepared from glucose-ammonia reaction system (kept in pH 5.3~6.0 during the reaction) was fractionated to volatile fraction and nonvolatile fraction. Among the volatile components, two pyridines and four alkylpyrazines were identified. On the other hand, one imidazole compound and two β-hydroxypyridines isolated from the nonvolatile fraction were identified as 4(5)-methylimidazole, 3-hydroxypyridine and 2-methyl-5-hydroxypyridine, respectively. It is inferred that these compounds are not produced by the fission of the main skeleton in the melanoidin molecule, but formed by pyrolysis of the heterocyclic compounds present as a small moiety in the melanoidin.     

Investigations on the genetics and population genetics of the β2 polymorphism

Summary The results of studies on 49 families with 107 children and various populations of Caucasoid, Negroid and Mongoloid origin concerning the genetics and population genetics of the ₂-glycoprotein I polymorphism are reported. In general the genetical model proposed by Cleve (1968) is confirmed: two autosomal alleles Bg^N and Bg^D controlling the phenotypes Bg N-N, Bg N-D and Bg D-D. However, divergences from this model were found in two families. They indicate the assumption of non-genetic factors influencing the phenotype expression rather than more complicated genetical control mechanisms. Within Caucasoid populations phenotype and gene frequencies show almost a homogeneous distribution. This racial stock is striking due to a significant higher ₂-glycoprotein I concentration in serum as compared to Negroids and Mongoloids. In connection with this, these racial stocks differ obviously in the gene frequencies: Caucasoids Bg^N=0.937, Negroids=0.742, Mongoloids =0.780; resp. Bg^D=0.063, 0.258, 0.220.Supported by the Deutsche Forschungsgemeinschaft.D 77.     

Effect of estradiol-17 β on the cytology of the liver,gonads and pituitary,and on plasma electrolytes in the female freshwater eel

Summary Female freshwater eels injected with estradiol-17 (E2) for 15–78 days appear paler and secrete more mucus than controls. The resulting strongly opalescent blood plasma indicates that vitellogenin synthesis occurs in the liver, which shows a significant hypertrophy, an increased vacuolization (lipid material) and glycogen depletion. Plasma sodium is lowered, but calcium levels are considerably increased. The gonosomatic index increases (0.92±0.1 to a maximum of 2.21). Oocytes are enlarged, but the incorporation of vitellogenin remains discrete. Gonadotrophs (GTH cells), small and scarcely visible in the pituitary of control eels, are hypertrophied and contain numerous glycoprotein granules after E2-administration. E2 may act on the pituitary and/or hypothalamus via a positive feedback to induce gonadotrophin (GTH) synthesis; GTH release seems to be very limited as indicated by the ovarian response. The differentiation of GTH cells in eels treated with fish pituitary extracts is most probably due to secretion of E2 by the ovary, which reacts on the pituitary. Various hypotheses are considered to explain the low GTH release.Thyrotrophs, somatotrophs and prolactin cells of the pituitary are stimulated. In the pars intermedia, MSH and PAS-positive cells appear less active. A possible antidopaminergic effect of E2 is discussed.E2 administration constitutes a simple and economic technique to induce the synthesis of GTH and will facilitate the biochemical and biological study of the latter hormone in eels.     

Genomic insights on the ethno-history of the Maya and the ‘Ladinos’ from Guatemala

Background

Guatemala is a multiethnic and multilingual country located in Central America. The main population groups separate ‘Ladinos’ (mixed Native American-African-Spanish), and Native indigenous people of Maya descent. Among the present-day Guatemalan Maya, there are more than 20 different ethnic groups separated by different languages and cultures. Genetic variation of these communities still remains largely unexplored. The principal aim of this study is to explore the genetic variability of the Maya and ‘Ladinos’ from Guatemala by means of uniparental and ancestry informative markers (AIMs).

Results

Analyses of uniparental genetic markers indicate that Maya have a dominant Native American ancestry (mitochondrial DNA [mtDNA]: 100%; Y-chromosome: 94%). ‘Ladino’, however, show a clear gender-bias as indicated by the large European ancestry observed in the Y-chromosome (75%) compared to the mtDNA (0%). Autosomal polymorphisms (AIMs) also mirror this marked gender-bias: (i) Native American ancestry: 92% for the Maya vs. 55% for the ‘Ladino’, and (ii) European ancestry: 8% for the Maya vs. 41% for the ‘Ladino’. In addition, the impact of the Trans-Atlantic slave trade on the present-day Guatemalan population is very low (and only occurs in the ‘Ladino’; mtDNA: 9%; AIMs: 4%), in part mirroring the fact that Guatemala has a predominant orientation to the Pacific Ocean instead of a Caribbean one. Sequencing of entire Guatemalan mitogenomes has led to improved Native American phylogeny via the addition of new haplogroups that are mainly observed in Mesoamerica and/or the North of South America.

Conclusions

The data reveal the existence of a fluid gene flow in the Mesoamerican area and a predominant unidirectional flow towards South America, most likely occurring during the Pre-Classic (1800 BC-200 AD) and the Classic (200–1000 AD) Eras of the Mesoamerican chronology, coinciding with development of the most distinctive and advanced Mesoamerican civilization, the Maya. Phylogenetic features of mtDNA data also suggest a demographic scenario that is compatible with moderate local endogamy and isolation in the Maya combined with episodes of gene exchange between ethnic groups, suggesting an ethno-genesis in the Guatemalan Maya that is recent and supported on a cultural rather than a biological basis.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1339-1) contains supplementary material, which is available to authorized users.     

Effect of the Support Size on the Properties of β-Galactosidase Immobilized on Chitosan: Advantages and Disadvantages of Macro and Nanoparticles

The effect of the support size on the properties of enzyme immobilization was investigated by using chitosan macroparticles and nanoparticles. They were prepared by precipitation and ionotropic gelation, respectively, and were characterized by Fourier transform infrared (FTIR) spectroscopy, differential scanning calorimetry (DSC), transmission electron microscopy (TEM), light scattering analysis (LSA), and N(2) adsorption-desorption isotherms. β-Galactosidase was used as a model enzyme. It was found that the different sizes and porosities of the particles modify the enzymatic load, activity, and thermal stability of the immobilized biocatalysts. The highest activity was shown by the enzyme immobilized on nanoparticles when 204.2 mg protein·(g dry support)(-1) were attached. On the other hand, the same biocatalysts presented lower thermal stability than macroparticles. β-Galactosidase immobilized on chitosan macro and nanoparticles exhibited excellent operational stability at 37 °C, because it was still able to hydrolyze 83.2 and 75.93% of lactose, respectively, after 50 cycles of reuse.     

Sex differences and the effects of ovariectomy on the β-adrenergic contractile response

The presence of sex differences in myocardial β-adrenergic responsiveness is controversial, and limited studies have addressed the mechanism underlying these differences. Studies were performed using isolated perfused hearts from male, intact female and ovariectomized female mice to investigate sex differences and the effects of ovarian hormone withdrawal on β-adrenergic receptor function. Female hearts exhibited blunted contractile responses to the β-adrenergic receptor agonist isoproterenol (ISO) compared with males but not ovariectomized females. There were no sex differences in β(1)-adrenergic receptor gene or protein expression. To investigate the role of adenylyl cyclase, phosphodiesterase, and the cAMP-signaling cascade in generating sex differences in the β-adrenergic contractile response, dose-response studies were performed in isolated perfused male and female hearts using forskolin, 3-isobutyl-1-methylxanthine (IBMX), and 8-(4-chlorophenylthio)adenosine 3',5'-cyclic monophosphate (CPT-cAMP). Males showed a modestly enhanced contractile response to forskolin at 300 nM and 5 μM compared with females, but there were no sex differences in the response to IBMX or CPT-cAMP. The role of the A(1) adenosine receptor (A(1)AR) in antagonizing the β-adrenergic contractile response was investigated using both the A(1)AR agonist 2-chloro-N(6)-cyclopentyl-adenosine and A(1)AR knockout (KO) mice. Intact females showed an enhanced A(1)AR anti-adrenergic effect compared with males and ovariectomized females. The β-adrenergic contractile response was potentiated in both male and female A(1)ARKO hearts, with sex differences no longer present above 1 nM ISO. The β-adrenergic contractile response is greater in male hearts than females, and minor differences in the action of adenylyl cyclase or the A(1)AR may contribute to these sex differences.     

Phylogenomics and rapid diversification of the genus Eutrema on the Qinghai–Tibet Plateau and adjacent regions

Both geographic isolation and polyploidization are assumed to play an important role in driving species diversification. However, this is rarely illustrated through phylogenomic analyses. The genus Eutrema (Brassicaceae), which also includes the salt-resistant species, are distributed mainly in Asia with extensive species diversification in the Qinghai–Tibet Plateau (QTP) and adjacent regions. In this study, we revealed almost fully resolved backbone relationships of the genus with genome re-sequencing data for genomes of 168 individuals from 28 species. Phylogenetic analyses of both plastomes and single-copy nuclear genes from the whole genome recovered six well-supported clades with almost consistent relationships. The first two clades are mainly distributed in central China and central Asia, while the other four in the QTP and adjacent regions. All of them diversified within 12 million years. Within each clade, we recovered numerous conflicts in the interspecific relationships between nuclear and plastome phylogenies, likely suggesting hybridization and incomplete lineage sorting during species diversification. Our estimation of genome size and comparison of the number of the single-copy nuclear genes demonstrated frequent occurrences of polyploids in the genus. Except for an establishment of the backbone phylogeny, our phylogenomic analyses suggest that in addition to strong geographic isolation, polyploidization may have played an important role in species diversification of this genus.     

Effects of β-alanine treatment on the taurine and DNA content of the rat heart and retina

Experimental evidence has suggested that the high endogenous levels of taurine found in the rat heart and retina are maintained to a large extent by transport processes out of the blood, rather than by endogenous biosynthesis. When these high levels are depleted, dysfunction ensues. In vitro studies have shown that -alanine is a good antagonist of these transport processes. The current studies were done to evaluate the feasibility of depleting heart and retinal taurine levels in vivo through treatment of adult rats either orally or with injections of -alanine. None of the treatments had significant effects on retinal taurine content; ventricular taurine was reduced in some situations, but the effects were not maintained, nor as large as with another transport antagonist. No functional changes were observed. Oral treatment with -alanine had fewer obvious side effects than injections, but all treated rats had body weights less than age-matched controls.     

Update on the laboratory diagnosis and monitoring of HIV infection

In China, the estimated number of HIV infected cases is approaching one million. Although public education has been initiated for awareness and behavioral modification for this devastating infection, better diagnostic methods are needed to identify infected persons and manage infection. Simple and more accurate diagnostic tools have become available, particularly for early detection and to monitor treatment in those who receive anti-retroviral treatment. In this short review, we summarize some of the common and new methodologies that can be used in clinical laboratories, in the field, or in private laboratories. These range from simple antibody tests to more sophistical methods that are used to monitor disease progression and identify drug resistance. These tools can assist physicians, medical practitioners, and laboratory personnel to select suitable diagnostic tools for the diagnosis, blood screening, monitoring of disease progression, and for detection of drug resistance to anti-retroviral therapies.     

Preliminary Study on the Pathogenesis and Treatment in Simian AIDS

AIDSis a severe immunodeficiency and autoimmunity disease caused by HIVin human beings.It ruins some areaintheworld.About200macaques were usedtoinvestigatethe pathogenesis of simian AIDS(SAIDS)by means of pathological andim-munological processes.There are some data of SAIDS pathogenesis as bellows:1.Primary SIVinfection in monkeys.When SIVentered into CD4+Tlymphocytes,it replicated and delivered intobloodto be high viremia.Some SIV-CD4+Tlymphocyte went tothe lymphoidtissue.The …     

IsoSVM – Distinguishing isoforms and paralogs on the protein level

Background  

Recent progress in cDNA and EST sequencing is yielding a deluge of sequence data. Like database search results and proteome databases, this data gives rise to inferred protein sequences without ready access to the underlying genomic data. Analysis of this information (e.g. for EST clustering or phylogenetic reconstruction from proteome data) is hampered because it is not known if two protein sequences are isoforms (splice variants) or not (i.e. paralogs/orthologs). However, even without knowing the intron/exon structure, visual analysis of the pattern of similarity across the alignment of the two protein sequences is usually helpful since paralogs and orthologs feature substitutions with respect to each other, as opposed to isoforms, which do not.     

A note on sporadic nonperiodic oscillations in the activity of the endocrine system and on the endocrine—Nervous system feedback

By generalizing a previous paper on periodicities in the endocrine system (Bull. Math. Biophysics,30, 735–749, 1968), it is shown that nonperiodic, sporadic oscillations in the system are also possible. A procedure of describing the feedback mechanism between the endocrine system and the central nervous system is suggested. It is shown that the combined system: endocrine—CNS, also may show sporadic fluctuations.     

Sugar Specificity in the Induction and on the Activity of Streptomyces α-d-Galactosidases

The α-d-galactosidases of six Streptomyces strains were examined on their inducer susceptibility, substate specificity, and inhibitor susceptibility. In all strains examined, α-d-galactosidase was induced by d-galactose, but neither by d-fucose nor by l-arabinose. α-d-Fucosidase activity was always induced accompanying with α-d-galactosedase activity. β-l-Arabinosidase activity, however, was never observed. These α-d-galactosidases were purified to electrophoretically pure degree by successive ammonium sulfate and ethanol precipitation, and ion exchange and gel filtration chromatography. The purified preparations from six strains were different from each other in their chromatographic behaviors and in some physical properties, but they all showed strong α-d-fucosidase activity as well. The α-d-galactosidase activities were strongly inhibited by d-galactose and l-arabinose, but scarcely by d-fucose. On the other hand, their α-d-fucosidase activities were inhibited by d-fucose as well as by d-galactose and l-arabinose.     

CTXφ Replication Depends on the Histone-Like HU Protein and the UvrD Helicase

The Vibrio cholerae bacterium is the agent of cholera. The capacity to produce the cholera toxin, which is responsible for the deadly diarrhea associated with cholera epidemics, is encoded in the genome of a filamentous phage, CTXφ. Rolling-circle replication (RCR) is central to the life cycle of CTXφ because amplification of the phage genome permits its efficient integration into the genome and its packaging into new viral particles. A single phage-encoded HUH endonuclease initiates RCR of the proto-typical filamentous phages of enterobacteriaceae by introducing a nick at a specific position of the double stranded DNA form of the phage genome. The rest of the process is driven by host factors that are either essential or crucial for the replication of the host genome, such as the Rep SF1 helicase. In contrast, we show here that the histone-like HU protein of V. cholerae is necessary for the introduction of a nick by the HUH endonuclease of CTXφ. We further show that CTXφ RCR depends on a SF1 helicase normally implicated in DNA repair, UvrD, rather than Rep. In addition to CTXφ, we show that VGJφ, a representative member of a second family of vibrio integrative filamentous phages, requires UvrD and HU for RCR while TLCφ, a satellite phage, depends on Rep and is independent from HU.     

Plant diversity and ecology on the Qinghai–Tibet Plateau

The Qinghai–Tibet Plateau (QTP) comprises a platform (sometimes called the Qinghai–Tibet Plateau sensu stricto), the Himalayas, and Hengduan Mountains (Liang et al.,2018; Mao et al.,2021). The latter two parts and adjacent highlands are also called the Pan-Himalaya. Numerous plants are distributed there with many endemic species, probably because of the high diverse landscapes created by continuous geological and climatic activities (Favre et al.,2015; Mao et al.,2021). As the well known biodiversity hotspot of the alpine plants in the world (Sun et al.,2017), many studies have been conducted on evolutionary origin and ecological adaptation of those species occurring in the QTP (e.g., Wen et al.,2014, 2019; Zhang et al.,2019). In the present special issue, we collected 15 related papers on this topic. Among them, two are invited reviews. Mao et al. (2021) provide a comprehensive review of evolutionary origin of species diversity on the QTP. Especially, they outlined major disputes and likely causes in this research topic, including circumscribing and naming the QTP, the QTP uplifts, dating of molecular phylogenetic trees, non-causal correlations between QTP uplifts and species diversification and the unified ice sheet. The authors also summarized genomic advancements related to high-altitude adaptation of both plants and animals. Tong et al. (2021) reviewed the reproductive strategies of animal-pollinated alpine plants on the QTP, involving pollination system, pollen limitation, self-pollination, and sexual system. In this region, 95.4% of animal-pollinated plants are pollinated by insects (i.e., bees, moths, butterflies, and flies) with only 4% by vertebrates (i.e., bats and birds). Self-pollination through self-compatibility shift from outcrossing has become an effective reproductive strategy to overcome pollen limitation in alpine plants. The other 13 research papers aimed to address origin and adaptation of alpine flora involving three major lines of evidence: genomics, ecology, and paleobotany. We hope that the collection of these papers will increase our understanding of the origin, speciation, and adaptation of alpine species on the QTP.