Y-chromosome evidence for no independent origin of modern human in China

East Asia is one of the few regions in the world where a large number of human fossils have been unearthed. The continuity of hominid fossils in East Asia, particularly in China has been presented as strong evidence supporting an independent origin of mod

Independent origin of the growth hormone gene family in New World monkeys and Old World monkeys/hominoids

The growth hormone (GH) gene family represents an erratic and complex evolutionary pattern, involving many evolutionary events, such as multiple gene duplications, positive selection, the birth-and-death process and gene conversions. In the present study, we cloned and sequenced GH-like genes from three species of New World monkeys (NWM). Phylogenetic analysis strongly suggest monophyly for NWM GH-like genes with respect to those of Old World monkeys (OWM) and hominoids, indicating that independent gene duplications have occurred in NWM GH-like genes. There are three main clusters of genes in putatively functional NWM GH-like genes, according to our gene tree. Comparison of the ratios of nonsynonymous and synonymous substitutions revealed that these three clusters of genes evolved under different kinds of selective pressures. Detailed analysis of the evolution of pseudogenes showed that the evolutionary pattern of this gene family in platyrrhines is in agreement with the so-called birth-and-death process.

Strikingly different penetrance of LHON in two Chinese families with primary mutation G11778A is independent of mtDNA haplogroup background and secondary mutation G13708A

The penetrance of Leber's hereditary optic neuropathy (LHON) in families with primary mitochondrial DNA (mtDNA) mutations is very complex. Matrilineal and nuclear genetic background, as well as environmental factors, have been reported to be involved in d

Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication

Background: Various evolutionary models have been proposed to interpret the fate of paralogous duplicates, which provides substrates on which evolution selection could act. In particular, domestication, as a special selection, has played important role in crop cultivation with divergence of many genes controlling important agronomic traits. Recent studies have indicated that a pair of duplicate genes was often sub-functionalized from their ancestral functions held by the parental genes. We previously demonstrated that the rice cell-wall invertase (CWI) gene GIF1 that plays an important role in the grain-filling process was most likely subjected to domestication selection in the promoter region. Here, we report that GIF1 and another CWI gene OsCIN1 constitute a pair of duplicate genes with differentiated expression and function through independent selection. Results: Through synteny analysis, we show that GIF1 and another cell-wall invertase gene OsCIN1 were paralogues derived from a segmental duplication originated during genome duplication of grasses. Results based on analyses of population genetics and gene phylogenetic tree of 25 cultivars and 25 wild rice sequences demonstrated that OsCIN1 was also artificially selected during rice domestication with a fixed mutation in the coding region, in contrast to GIF1 that was selected in the promoter region. GIF1 and OsCIN1 have evolved into different expression patterns and probable different kinetics parameters of enzymatic activity with the latter displaying less enzymatic activity. Overexpression of GIF1 and OsCIN1 also resulted in different phenotypes, suggesting that OsCIN1 might regulate other unrecognized biological process. Conclusion: How gene duplication and divergence contribute to genetic novelty and morphological adaptation has been an interesting issue to geneticists and biologists. Our discovery that the duplicated pair of GIF1 and OsCIN1 has experiencedsub-functionalization implies that selection could act independently on each duplicate towards different functional specificity, which provides a vivid example for evolution of genetic novelties in a model crop. Our results also further support the established hypothesis that gene duplication with sub-functionalization could be one solution for genetic adaptive conflict.

Independent Transport and Sorting of Functionally Distinct Protein Families in Tetrahymena thermophila Dense Core Secretory Granules

Dense core granules (DCGs) in Tetrahymena thermophila contain two protein classes. Proteins in the first class, called granule lattice (Grl), coassemble to form a crystalline lattice within the granule lumen. Lattice expansion acts as a propulsive mechanism during DCG release, and Grl proteins are essential for efficient exocytosis. The second protein class, defined by a C-terminal beta/gamma-crystallin domain, is poorly understood. Here, we have analyzed the function and sorting of Grt1p (granule tip), which was previously identified as an abundant protein in this family. Cells lacking all copies of GRT1, together with the closely related GRT2, accumulate wild-type levels of docked DCGs. Unlike cells disrupted in any of the major GRL genes, Delta GRT1 Delta GRT2 cells show no defect in secretion, indicating that neither exocytic fusion nor core expansion depends on GRT1. These results suggest that Grl protein sorting to DCGs is independent of Grt proteins. Consistent with this, the granule core lattice in Delta GRT1 Delta GRT2 cells appears identical to that in wild-type cells by electron microscopy, and the only biochemical component visibly absent is Grt1p itself. Moreover, gel filtration showed that Grl and Grt proteins in cell homogenates exist in nonoverlapping complexes, and affinity-isolated Grt1p complexes do not contain Grl proteins. These data demonstrate that two major classes of proteins in Tetrahymena DCGs are likely to be independently transported during DCG biosynthesis and play distinct roles in granule function. The role of Grt1p may primarily be postexocytic; consistent with this idea, DCG contents from Delta GRT1 Delta GRT2 cells appear less adhesive than those from the wild type.

The synthesis of astaxanthin esters, independent of the formation of cysts, highly correlates with the synthesis of fatty acids in Haematococcus pluvialis

The compositions and contents of astaxanthin esters and fatty acids in four types of Haematococcus pluvialis cells were studied by HPLC and GC-MS. Results showed that the synthesis and accumulation of astaxanthin was independent of the formation of cysts, but was highly correlated with the synthesis and accumulation of fatty acids, though it is an well known phenomenon that the accumulation of astaxanthin is usually accompanied by the formation of cyst. The red cysts contain more than 30% of fatty acids, with 81% of the unsaturated fatty acids. Taken together, besides a resource of astaxanthin, H. pluvialis would be a good resource of valuable fatty acids.

Growth and production of free-living heterotrophic nanoflagellates in a eutrophic lake - Lake Donghu, Wuhan, China

In situ growth of heterotrophic nanoflagellates (HNF) in Lake Donghu, a eutrophic shallow lake in mainland China, was studied from January 1999 to March 2000 using a modified Weisse protocol. The study results indicated that the growth rates of HNF showed pronounced seasonal variation (-0.37-1.25 d(-1)), reaching the maximum during spring to early summer. When the water temperature was higher than 25.5 degreesC, HNF growth was inversely proportional to water temperature. There was an effect by bacterial abundance and autotrophic picoplankton on HNF growth that depended on location. HNF biomass was the highest in late spring, and the HNF production ranged from -2.25 to 35.45 mg l(-1) d(-1) with mean of 3.17 mg l(-1) d(-1). When considered in the context of biomass and production data for zooplankton in Lake Donghu, it was evident that HNF contributed significantly to the total zooplankton production in Lake Donghu. These in situ studies indicate that temperature and food supply are the major determinants of HNF abundance and productivity.

Inland free-living nematodes in China: A historical review of taxonomic studies with descriptions of Aphanonchus orientalis sp nov (Chromadorida : Leptolaimidae) and Daptonema limnobia sp nov (Monhysterida : Xyalidae)

The study of inland free-living nematodes is relatively imperfect in China, only seventeen papers were previously published. Since the early researches in 20-30s, few works have been accomplished until 80s. Altogether 171 taxa were formerly recorded, among which, over eighty species have been re-combined. A checklist of the former records with notes on their distribution is presented in this paper. Recently, the function of free-living nematodes has received much attention from Chinese zoologists. Hence, the present authors carried out their studies with emphasis on taxonomy of inland nematodes. During the survey of freshwater lakes, two species are found to be nem to science. Aphanonchus orientalis sp. nov. is characterized by having sclerotized vagina, the presence of 10-11 tubular supplements and 42-62 alveoli supplements in males, but no alveoli in females. Daptonema limnobia sp, nov. is distinguished from other species of the genus in the presence of larger and more anteriorly located amphids, shorter bifurcated spicules, smaller apophysis of gubernaculum, shorter terminal setae, and postvulval uterine sac in females.

Independent adaptation to riverine habitats allowed survival of ancient cetacean lineages

The four species of "river dolphins" are associated with six separate great river systems on three subcontinents and have been grouped for more than a century into a single taxon based on their similar appearance. However, several morphologists recently questioned the monophyly of that group. By using phylogenetic analyses of nucleotide sequences from three mitochondrial and two nuclear genes, we demonstrate with statistical significance that extant river dolphins are not monophyletic and suggest that they are relict species whose adaptation to riverine habitats incidentally insured their survival against major environmental changes in the marine ecosystem or the emergence of Delphinidae.

Design and fabrication of polarization-independent micro-ring resonators

Origin of polarization sensitivity of photonic wire waveguides (PWWs) is analysed and the effective refractive indices of two different polarization states are calculated by the three-dimensional full-vector beam propagation method. We find that PWWs are polarization insensitive if the distribution of its refractive index is uniform and the cross section is square. An MRR based on such a polarization-insensitive PWW is fabricated on an 8-inch silicon-on-insulator wafer using 248-nm deep ultraviolet lithography and reactive ion etching. The quasi-TE mode is resonant at 1542.25 nm and 1558.90 nm, and the quasi-TM mode is resonant at 1542.12 nm and 1558.94 nm. The corresponding polarization shift is 0.13 nm at the shorter wavelength and 0.04 nm at the longer wavelength. Thus the fabricated device is polarization independent. The extinction ratio is larger than 10 dB. The 3 dB bandwidth is about 2.5 nm and the Qvalue is about 620 at 1558.90 nm.

Temperature-independent fiber Bragg grating strain sensor using bimetal cantilever

A new packaged fiber Bragg grating using bimetal cantilever beam as the strain agent is presented. The grating is two-point attached on one specific surface of the bimetal beam which consists of two metallic material with different thermal-expansion coefficient. Thereby the grating can be compressed or stretched along with the cantilever beam while temperature varies and temperature compensation can be realized. At the same time, grating chirping can be avoided for the particular attaching method. Experiment results demonstrated that the device is able to automatically compensate temperature induced wavelength shift. The temperature dependence of Bragg wavelength reduced to -0.4 pm/degrees C over the temperature range from -20 to 60 degrees C. This fiber grating package technique is cost effective and can be used in strain sensing. (c) 2005 Elsevier Inc. All rights reserved.

Temperature-independent FBG pressure sensor with high sensitivity

This study develops a fiber Bragg grating (FBG) pressure sensor partly shielded with a metal tube. The thermal-strain cross effect is avoided and its pressure sensitivity is increased to -2.44 x 10(-3) MPa, about 1200 times as that of a bare fiber grating. Due to its good sensing linearity, this sensor can be applied in the measurement of hydraulic pressure and vibration. (c) 2006 Elsevier Inc. All rights reserved.

Information geometry theory of high-dimension space and application for speaker independent continuous digit speech recognition

In the light of descriptive geometry and notions in set theory, this paper re-defines the basic elements in space such as curve and surface and so on, presents some fundamental notions with respect to the point cover based on the High-dimension space (HDS) point covering theory, finally takes points from mapping part of speech signals to HDS, so as to analyze distribution information of these speech points in HDS, and various geometric covering objects for speech points and their relationship. Besides, this paper also proposes a new algorithm for speaker independent continuous digit speech recognition based on the HDS point dynamic searching theory without end-points detection and segmentation. First from the different digit syllables in real continuous digit speech, we establish the covering area in feature space for continuous speech. During recognition, we make use of the point covering dynamic searching theory in HDS to do recognition, and then get the satisfying recognized results. At last, compared to HMM (Hidden Markov models)-based method, from the development trend of the comparing results, as sample amount increasing, the difference of recognition rate between two methods will decrease slowly, while sample amount approaching to be very large, two recognition rates all close to 100% little by little. As seen from the results, the recognition rate of HDS point covering method is higher than that of in HMM (Hidden Markov models) based method, because, the point covering describes the morphological distribution for speech in HDS, whereas HMM-based method is only a probability distribution, whose accuracy is certainly inferior to point covering.

A speaker-independent continuous speech recognition system using biomimetic pattern recognition

In speaker-independent speech recognition, the disadvantage of the most diffused technology (HMMs, or Hidden Markov models) is not only the need of many more training samples, but also long train time requirement. This paper describes the use of Biomimetic pattern recognition (BPR) in recognizing some mandarin continuous speech in a speaker-independent manner. A speech database was developed for the course of study. The vocabulary of the database consists of 15 Chinese dish's names, the length of each name is 4 Chinese words. Neural networks (NNs) based on Multi-weight neuron (MWN) model are used to train and recognize the speech sounds. The number of MWN was investigated to achieve the optimal performance of the NNs-based BPR. This system, which is based on BPR and can carry out real time recognition reaches a recognition rate of 98.14% for the first option and 99.81% for the first two options to the persons from different provinces of China speaking common Chinese speech. Experiments were also carried on to evaluate Continuous density hidden Markov models (CDHMM), Dynamic time warping (DTW) and BPR for speech recognition. The Experiment results show that BPR outperforms CDHMM and DTW especially in the cases of samples of a finite size.

Polarization-Independent Micro-Ring Resonator on Silicon-on-Insulator

Polarization-independent laterally-coupled micro-ring resonator has been designed and demonstrated. The origin of the polarization-sensitivity of the photonic wire waveguide (PWW) was analyzed. A polarization-insensitive PWW structure was designed and a polarization-insensitive MRR based on this PWW structure was designed by finite difference time-domain method and was fabricated on an 8-inch silicon-on-insulator wafer. The offset between the resonant wavelengths of the quasi-TE mode and the quasi-TM mode is smaller than 0.15 nm. The FSR is about 17 nm, extinction ratio about 10 dB and Q about 620.