Prediction of tight turns and their types in proteins

A tight turn in protein structure is defined as a site where (i) a polypeptide chain reverses its overall direction, i.e., leads the chain to fold back on itself by nearly 180 degrees, and (ii) the amino acid residues directly involved in forming the turn are no more than six. Tight turns are generally categorized as delta-turn, gamma-turn, beta-turn, alpha-turn, and pi-turn, which are formed by two-, three-, four-, five-, and six-amino-acid residues, respectively. According to the folding mode, each of such tight turns can be further classified into several different types. Tight turns play an important role in globular proteins from both the structural and functional points of view. In view of this, various efforts have been made to predict tight turns and their types. This Review summarizes the development in this area, with an emphasis focused on the most recent work concerned that is featured by the sequence-coupled model. Meanwhile, the future challenge in this area has also been briefly addressed.     

Complementary specificity of restriction endonucleases of Diplococcus pneumoniae with respect to DNA methylation.

An algorithm is presented to identify peptide chain turns from X-ray-elucidated co-ordinate data. Chain turns are those regions in a globular protein where the backbone is folded back upon itself. The concept of a turn is important both because turns constitute recognizable structural units in proteins and because turns are situated at the solvent-accessible surface of the molecule.Current algorithms for turn identification are highly operational in character, often finding false turns and omitting actual ones. The algorithm presented here uses only the C-alpha co-ordinates for every residue in the protein. No other information of any kind is required, and notions about hydrogen bonding at these loci are irrelevant to the geometric nature of the argument. In this sense, the algorithm provides an objective criterion for the recognition of turns as strictly structural components in proteins.The algorithm is used to find the turns in a test set of proteins. Results of this application are in excellent agreement with visual turn identification from physical models.     

The cost of cowardice: punitive sentiments towards free riders in Turkana raids

Models indicate that large-scale cooperation can be sustained by indirect reciprocity or direct punishment, but the relative importance of these mechanisms is unresolved. Unlike direct punishment, indirect sanctions can be meted out without cost to the sanctioner, but direct punishment is advantageous when the scale of cooperation exceeds the network size of individuals. It is of great interest to assess the importance of these mechanisms in small-scale acephalous groups in which people have lived for most of our evolutionary history. Here we evaluate sentiments towards free riders in combat among the Turkana, an acephalous nomadic pastoral society in East Africa who periodically mobilize for cattle-raids against neighboring ethnic groups. Using vignette studies, we probed participants’ motivation to sanction fictitious warriors who were cowards or deserters in a raid and compared it respectively to their reactions to an unskilled warrior or a warrior who turns back due to illness. Our results indicate that the Turkana are motivated to impose both indirect and direct sanctions on cowards consistent with indirect reciprocity and punishment models of cooperation. Our findings imply that both these mechanisms have shaped human cooperative psychology, and sheds light on how prestate societies solve the collective action problem in warfare.     

Differential diagnosis of the genera in the family Trichodinidae (Ciliophora: Peritrichida) with the description of a new genus ectoparasitic on freshwater fish from southern Africa

A trichodinid ectoparasite was collected from mormyrid fish in the Olifants River System, South Africa. A new genus, Hemitrichodina, is described to accomodate these trichodinid ciliophorans of which the blades are reduced and with an adoral spiral of more than 360°, but less than two full turns. A differential diagnosis of the genera within the family Trichodinidae is presented.     

The significance of the oil palm (Elaeis guineensis Jacq.) in the late Holocene environments of west and west central Africa: A further consideration

Abundant archaeological evidence of the occurrence of the endocarp of the oil palm,Elaeis guineensis, in the rain forest and woodland savanna zones of west and central Africa from about 5000 B.P. has shown the tree to be an important element in the subsistence economy of the region; its pollen also has been recorded in most of the regional terrestrial sediments studied so far. The distinct and consistently sudden and more marked increases in this pollen during the late Holocene when compared with the late Tertiary and late Pleistocene frequencies strongly indicate that the late Holocene upsurges were due to both natural and human factors favourable for the expansion of this heliophytic tree. Reasons are given for suggesting that upsurges in oil palm pollen during the late Holocene period in this region can be used as indices of plant cultivation. While the oil palm is known from early Tertiary deposits in west Africa, its earliest palynological record from terrestrial sediments in the west central part dates back only to the early Holocene. More palynological studies of Tertiary and Quaternary terrestrial cores are required to establish with more certainty the antiquity ofE. guineensis in west central Africa.     

Evolutionary and biogeographical history of an ancient and global group of arachnids (Arachnida: Opiliones: Cyphophthalmi) with a new taxonomic arrangement

We investigate the phylogeny, biogeography, time of origin and diversification, ancestral area reconstruction and large‐scale distributional patterns of an ancient group of arachnids, the harvestman suborder Cyphophthalmi. Analysis of molecular and morphological data allow us to propose a new classification system for the group; Pettalidae constitutes the infraorder Scopulophthalmi new clade , sister group to all other families, which are divided into the infraorders Sternophthalmi new clade and Boreophthalmi new clade . Sternophthalmi includes the families Troglosironidae, Ogoveidae, and Neogoveidae; Boreophthalmi includes Stylocellidae and Sironidae, the latter family of questionable monophyly. The internal resolution of each family is discussed and traced back to its geological time origin, as well as to its original landmass, using methods for estimating divergence times and ancestral area reconstruction. The origin of Cyphophthalmi can be traced back to the Carboniferous, whereas the diversification time of most families ranges between the Carboniferous and the Jurassic, with the exception of Troglosironidae, whose current diversity originates in the Cretaceous/Tertiary. Ancestral area reconstruction is ambiguous in most cases. Sternophthalmi is traced back to an ancestral land mass that contained New Caledonia and West Africa in the Permian, whereas the ancestral landmass for Neogoveidae included the south‐eastern USA and West Africa, dating back to the Triassic. For Pettalidae, most results include South Africa, or a combination of South Africa with the Australian plate of New Zealand or Sri Lanka, as the most likely ancestral landmass, back in the Jurassic. Stylocellidae is reconstructed to the Thai‐Malay Penisula during the Jurassic. Combination of the molecular and morphological data results in a hypothesis for all the cyphophthalmid genera, although the limited data available for some taxa represented only in the morphological partition negatively affects the phylogenetic reconstruction by decreasing nodal support in most clades. However, it resolves the position of many monotypic genera not available for molecular analysis, such as Iberosiro, Odontosiro, Speleosiro, Managotria or Marwe, although it does not place Shearogovea or Ankaratra within any existing family. The biogeographical data show a strong correlation between relatedness and formerly adjacent landmasses, and oceanic dispersal does not need to be postulated to explain disjunct distributions, especially when considering the time of divergence. The data also allow testing of the hypotheses of the supposed total submersion of New Zealand and New Caledonia, clearly falsifying submersion of the former, although the data cannot reject the latter. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 92–130.     

History of click-speaking populations of Africa inferred from mtDNA and Y chromosome genetic variation

Little is known about the history of click-speaking populations in Africa. Prior genetic studies revealed that the click-speaking Hadza of eastern Africa are as distantly related to click speakers of southern Africa as are most other African populations. The Sandawe, who currently live within 150 km of the Hadza, are the only other population in eastern Africa whose language has been classified as part of the Khoisan language family. Linguists disagree on whether there is any detectable relationship between the Hadza and Sandawe click languages. We characterized both mtDNA and Y chromosome variation of the Sandawe, Hadza, and neighboring Tanzanian populations. New genetic data show that the Sandawe and southern African click speakers share rare mtDNA and Y chromosome haplogroups; however, common ancestry of the 2 populations dates back >35,000 years. These data also indicate that common ancestry of the Hadza and Sandawe populations dates back >15,000 years. These findings suggest that at the time of the spread of agriculture and pastoralism, the click-speaking populations were already isolated from one another and are consistent with relatively deep linguistic divergence among the respective click languages.     

猪笼草叶的形态解剖结构研究

对猪笼草 (N epenthes mirabilis)叶进行形态、解剖学的观察和研究 ,结果表明猪笼草的叶是一种变态的单身复叶。其基部的两个侧生小叶与总叶柄合生 ,总叶柄顶端扩大反卷为瓶状体 ,瓶状体一侧也有 2片附生小叶 ,顶生小叶与总叶柄连接处有关节 ,关节上还有 2～ 5片退化的小叶     

A model for the separation of large DNA molecules by crossed field gel electrophoresis.

The idea that large DNA molecules adopt a stretched conformation as they pass through gels suggests a simple mechanism for the separation of DNA by crossed field electrophoresis: at each change in field direction a DNA molecule takes off in the new direction of the field by a movement which is led by what was formerly its back end. The effect of this ratcheting motion is to subtract from the DNA molecule's forward movement, at each step, an amount which is proportional to its length. We find that this model explains most of the features of the separation, and we describe experiments, using a novel electrophoresis apparatus, which support the model. The apparatus turns the gel between two preset orientations in a uniform electric field at preset time intervals. This separation method has the practical advantage over some others that the DNA molecules follow straight tracks. A further advantage is that the parameters which determine the separation are readily predicted from the simple theory describing their motion.     

What Factors Might Have Led to the Emergence of Ebola in West Africa?

An Ebola outbreak of unprecedented scope emerged in West Africa in December 2013 and presently continues unabated in the countries of Guinea, Sierra Leone, and Liberia. Ebola is not new to Africa, and outbreaks have been confirmed as far back as 1976. The current West African Ebola outbreak is the largest ever recorded and differs dramatically from prior outbreaks in its duration, number of people affected, and geographic extent. The emergence of this deadly disease in West Africa invites many questions, foremost among these: why now, and why in West Africa? Here, we review the sociological, ecological, and environmental drivers that might have influenced the emergence of Ebola in this region of Africa and its spread throughout the region. Containment of the West African Ebola outbreak is the most pressing, immediate need. A comprehensive assessment of the drivers of Ebola emergence and sustained human-to-human transmission is also needed in order to prepare other countries for importation or emergence of this disease. Such assessment includes identification of country-level protocols and interagency policies for outbreak detection and rapid response, increased understanding of cultural and traditional risk factors within and between nations, delivery of culturally embedded public health education, and regional coordination and collaboration, particularly with governments and health ministries throughout Africa. Public health education is also urgently needed in countries outside of Africa in order to ensure that risk is properly understood and public concerns do not escalate unnecessarily. To prevent future outbreaks, coordinated, multiscale, early warning systems should be developed that make full use of these integrated assessments, partner with local communities in high-risk areas, and provide clearly defined response recommendations specific to the needs of each community.     

Arrestment responses of the predatory mite, Phytoseiulus persimilis, to steep odour gradients of a kairomone

ABSTRACT. The response of the predatory mite, Phytoseiulus persimilis Athias-Henriot, to steep gradients of a volatile kairomone emitted by its prey, Tetranychus urticue Koch, was studied in a vertical air flow chamber. The orientation to wind direction was eliminated by using an olfactometer that had an air stream approaching the predator from below a gauze screen upon which the predator walked. The steep gradient of odour was obtained by putting a cylinder filled with prey-infested leaves vertically below the screen. Starved predators were arrested in the odour patch by walking more slowly and tortuously than well-fed predators. The latter mites did not show a significant ortho- or klinokinetic response to the presence of odour. Both well-fed and starved predators showed a chemotactic response to steep gradients at the border of the circular odour patch. Predators that happened to walk out of the patch, frequently turned back to it. This response is presumably based on idiothetic information about the predator's immediately previous walking directions, because it occurred in the odour-free zone after passing the steep gradient of prey odour. Right-about turns can help the predator to stay in static odour plumes with steep gradients at the borders. This type of plume is present only close to the odour source. Further away from the source the odour plume tends to move to and fro due to variation in wind direction. For the predator to keep track of these snaking plumes the right-about turns are unlikely to be of any value because the response is of short duration and because the response to a moving plume appeared to be inadequate; by moving the cylinder below the screen (and consequently the odour patch) it was found that the predator turned back even if the odour gradient was made to pass the predator in the same direction as that of the predator's movement.     

Turn scanning by site-directed mutagenesis: application to the protein folding problem using the intestinal fatty acid binding protein

We have systematically mutated residues located in turns between beta-strands of the intestinal fatty acid binding protein (IFABP), and a glycine in a half turn, to valine and have examined the stability, refolding rate constants and ligand dissociation constants for each mutant protein. IFABP is an almost all beta-sheet protein exhibiting a topology comprised of two five-stranded sheets surrounding a large cavity into which the fatty acid ligand binds. A glycine residue is located in seven of the eight turns between the antiparallel beta-strands and another in a half turn of a strand connecting the front and back sheets. Mutations in any of the three turns connecting the last four C-terminal strands slow the folding and decrease stability with the mutation between the last two strands slowing folding dramatically. These data suggest that interactions between the last four C-terminal strands are highly cooperative, perhaps triggered by an initial hydrophobic collapse. We suggest that this trigger is collapse of the highly hydrophobic cluster of amino acids in the D and E strands, a region previously shown to also affect the last stage of the folding process (Kim et al., 1997). Changing the glycine in the strand between the front and back sheets also results in a unstable, slow folding protein perhaps disrupting the D-E strand interactions. For most of the other turn mutations there was no apparent correlation between stability and refolding rate constants. In some turns, the interaction between strands, rather than the turn type, appears to be critical for folding while in others, turn formation itself appears to be a rate limiting step. Although there is no simple correlation between turn formation and folding kinetics, we propose that turn scanning by mutagenesis will be a useful tool for issues related to protein folding.     

γ-转角的研究进展

γ-转角是所有转角中数量位居第二的结构,约占整个蛋白质结构的3.4%。γ-转角有助于球形结构的形成,帮助肽链改变折叠方向,因此就更加有必要研究γ-转角的预测方法,从而提高蛋白质二级结构的预测精度。近几十年来关于γ-转角的预测方法越来越成熟,预测精度越来越高。本文综述了近年来对γ-转角研究进展,包括它的研究方法以及预测的准确度等。     

Re-emergence of Crimean-Congo hemorrhagic fever virus in Central Africa

Background

Crimean-Congo hemorrhagic fever (CCHF) is a severe tick-borne disease well recognized through Europe and Asia where diagnostic tests and medical surveillance are available. However, it is largely neglected in Africa, especially in the tropical rainforest of Central Africa where only sporadic human cases have been reported and date back to more than 30 years. We describe here an isolated human case that occurred in the Democratic Republic of the Congo in 2008 and performed phylogenetic analysis to investigate whether it resulted from a regional re-emergence or from the introduction of a novel virus in the area.

Methods and Findings

Near complete segment S and partial segment M sequences were characterized. Bayesian phylogenetic analysis and datation were performed to investigate the relationship between this new strain and viral strains from Africa, Europe and Asia. The new strain is phylogenetically close to the previously described regional genotype (II) that appears to be specific to Central Africa. Phylogenetic discrepancy between segment S and M suggested genetic exchange among local sublineages, which was dated back to 130–590 years before present.

Conclusions

The phylogenetic analyses presented here suggest ongoing CCHF virus circulation in Central Africa for a long time despite the absence of reported human cases. Many infections have most probably been overlooked, due to the weakness of healthcare structures and the absence of available diagnostic procedure. However, despite the lack of accurate ecological data, the sporadic reporting of human cases could also be partly associated with a specific sylvatic cycle in Central Africa where deforestation may raise the risks of re-emergence. For these reasons, together with the high risk of nosocomial transmission, public health authorities'' attention should be drawn to this etiological agent.     

Risk Factors and Disability Associated with Low Back Pain in Older Adults in Low- and Middle-Income Countries. Results from the WHO Study on Global AGEing and Adult Health (SAGE)

Background

Back pain is a common disabling chronic condition that burdens individuals, families and societies. Epidemiological evidence, mainly from high-income countries, shows positive association between back pain prevalence and older age. There is an urgent need for accurate epidemiological data on back pain in adult populations in low- and middle-income countries (LMICs) where populations are ageing rapidly. The objectives of this study are to: measure the prevalence of back pain; identify risk factors and determinants associated with back pain, and describe association between back pain and disability in adults aged 50 years and older, in six LMICs from different regions of the world. The findings provide insights into country-level differences in self-reported back pain and disability in a group of socially, culturally, economically and geographically diverse LMICs.

Methods

Standardized national survey data collected from adults (50 years and older) participating in the World Health Organization (WHO) Study on global AGEing and adult health (SAGE) were analysed. The weighted sample (n = 30, 146) comprised respondents in China, Ghana, India, Mexico, South Africa and the Russian Federation. Multivariable regressions describe factors associated with back pain prevalence and intensity, and back pain as a determinant of disability.

Results

Prevalence was highest in the Russian Federation (56%) and lowest in China (22%). In the pooled multi-country analyses, female sex, lower education, lower wealth and multiple chronic morbidities were significant in association with past-month back pain (p<0.01). About 8% of respondents reported that they experienced intense back pain in the previous month.

Conclusions

Evidence on back pain and its impact on disability is needed in developing countries so that governments can invest in cost-effective education and rehabilitation to reduce the growing social and economic burden imposed by this disabling condition.     

A phylogeny of Anisophylleaceae based on six nuclear and plastid loci: ancient disjunctions and recent dispersal between South America, Africa, and Asia

The Anisophylleaceae comprise 29-34 species of shrubs and trees occurring in lowland forests and swamps in tropical Africa, Asia, and South America. These species are placed in four genera with disjunct geographic distributions; Anisophyllea has 25-30 species in South America, Africa, and Malesia; Combretocarpus has one species in Sumatra and Borneo; Poga one species in equatorial Africa; and Polygonanthus two in the Amazon Basin. Here we use a phylogeny based on six nuclear and plastid loci sequenced for 15 species representing the four genera to infer their relationships and the relative and absolute ages of the range disjunctions. Combretocarpus is sister to the other three genera, and Polygonanthus then sister to Poga and Anisophyllea. Ansiophyllea, represented by 12 species from all three continents, is monophyletic. A relaxed Bayesian clock calibrated with the oldest fossils from a relevant outgroup, Tetramelaceae, suggests that the disjunctions between Combretocarpus, Poga, and Polygonanthus date back to the Cretaceous, Mid-, and Upper Eocene, whereas the intercontinental disjunctions within Anisophyllea appear to date back only some 22-23 million years and thus probably result from long-distance dispersal.     

Gondwanan evolution of the grass alliance of families (Poales)

Phylogenetic interrelationships among all 18 families of Poales were assessed by cladistic analysis of chloroplast DNA rbcL and atpB sequences from 65 species. There are two well-supported main clades; the graminoid clade with Poaceae (grasses), Anarthriaceae, Centrolepidaceae, Ecdeiocoleaceae, Flagellariaceae, Joinvilleaceae, and Restionaceae; and the cyperoid clade with Cyperaceae, Juncaceae, and Thurniaceae. A sister group relationship between Poaceae and Ecdeiocoleaceae is identified with strong support. The sister group of this pair is Joinvilleaceae. These relationships help in elucidating the evolution of grasses and the grass spikelet. Dating of the tree was done by nonparametric rate smoothing of rbcL molecular evolution. Most Poales families date back to the Cretaceous >65 million years ago (mya). Dispersal-vicariance analysis indicates that the Poales originated in South America, the cyperoid clade in West Gondwana (South America or Africa), and the graminoid clade in East Gondwana (Australia). The Trans-Antarctic connection between South America and Australia, and its breakup about 35 mya, probably influenced the evolution of the Poales and the graminoid clade in particular, leading to vicariance between the continents, but the separation of Africa from the other Gondwanan areas, completed about 105 mya, is too old for such a relation.     

Crystal structure of human ERp44 shows a dynamic functional modulation by its carboxy-terminal tail

ERp44 mediates thiol-dependent retention in the early secretory pathway, forming mixed disulphides with substrate proteins through its conserved CRFS motif. Here, we present its crystal structure at a resolution of 2.6 A. Three thioredoxin domains-a, b and b'-are arranged in a clover-like structure. A flexible carboxy-terminal tail turns back to the b' and a domains, shielding a hydrophobic pocket in domain b' and a hydrophobic patch around the CRFS motif in domain a. Mutational and functional studies indicate that the C-terminal tail gates the CRFS area and the adjacent hydrophobic pocket, dynamically regulating protein quality control.     

The African diaspora: mitochondrial DNA and the Atlantic slave trade

Between the 15th and 19th centuries ad, the Atlantic slave trade resulted in the forced movement of approximately 13 million people from Africa, mainly to the Americas. Only approximately 11 million survived the passage, and many more died in the early years of captivity. We have studied 481 mitochondrial DNAs (mtDNAs) of recent African ancestry in the Americas and in Eurasia, in an attempt to trace them back to particular regions of Africa. Our results show that mtDNAs in America and Eurasia can, in many cases, be traced to broad geographical regions within Africa, largely in accordance with historical evidence, and raise the possibility that a greater resolution may be possible in the future. However, they also indicate that, at least for the moment, considerable caution is warranted when assessing claims to be able to trace the ancestry of particular lineages to a particular locality within modern-day Africa.