Is there a close relationship between synonymous codon bias and codon-anticodon binding strength in human genes?

Synonymous codon bias has been examined in 78 human genes (19967 codons) and measured by relative synonymous codon usage (RSCU). Relative frequencies of all kinds of dinucleotides in 2,3 or 3,4 codon positions have been calculated, and codon-anticodon bin

Maintenance of Multifemale Social Organization in a Group of Nomascus concolor at Wuliang Mountain, Yunnan, China

Many short-term studies have reported groups of black crested gibbons containing >= 2 adult females (Nomascus concolor). We report the stability of multifemale groups in this species over a period of 6 yr. Our focal group and 2 neighboring groups included 2 breeding females between March 2003 and June 2009. We also habituated 1 multifemale group to observers and present detailed information concerning their social relationships over a 9-mo observation period. We investigated interindividual distances and agonistic behavior among the 5 group members. The spatial relationship between the 3 adult members (1 male, 2 females) formed an equilateral triangle. A subadult male was peripheral to the focal group, while a juvenile male maintained a closer spatial relationship with the adult members. We observed little agonistic behavior among the adult members. The close spatial relationship and lack of high rates of agonistic behavior among females suggest that the benefits of living in a multifemale group were equal to or greater than the costs for both females, given their ecological and social circumstances. The focal group occupied a large home range that was likely to provide sufficient food sources for the 2 females and their offspring. Between March 2003 and June 2009, 1 adult female gave 2 births and the other one gave 1 birth. All individuals in the focal group survived to June 2009. A long-term comparative study focused on females living in multifemale groups and females living in pair-living groups would provide insight into understanding the evolutionary mechanisms of the social system in gibbons.

Intergroup interactions in Tibetan macaques at Mt. Emei, China

Data on intergroup-interactions (I-I) were collected in 5 seasonally provisioned groups (A, B, D, D-1, and E) of Tibetan macaques (Macaca Thibetana) at Mt. Emei in three 70-day periods between 1991 April-June (P1), September-November (P2), December-1992 February (P3). The I-I were categorized as forewarning made by high-ranking males (including Branch Shaking and/or Loud Calls), long-distance interactions in space (specified by changes in their foraging movements), and close encounters (with Affinitive Behavior, Male's Herding Female, Sexual Interaction, Severe Conflict, Adult Male-male Conflict, Opportunistic Advance and Retreat, etc. performed by different age-sex classes). From periods Fl to P3, the I-I rate decreased with reduction in population density as a positive correlate of food clumpedness or the number of potential feeders along a pedestrian trail. On the other hand, from the birth season (BS, represented by P1 and P3) to the mating season (MS, represented by P2) the dominance relation between groups, which produced a winner and a loser in the encounters, became obscure; the proportion of close encounters in the I-I increased; the asymmetry (local groups over intruders) of forewarning signals disappeared; the rate of branch shaking decreased; and sometimes intergroup cohesion appeared. Considering that sexual interactions also occurred between the encountering groups, above changes in intergroup behaviors may be explained with a model of the way in which the competition for food (exclusion) and the sexual attractiveness between opposite sexes were in a dynamic equilibrium among the groups, with the former outweighing the latter in the BS, and conversely in the MS. Females made 93% of severe conflicts, which occurred in 18% of close encounters. Groups fissioned in the recent past shared the same home range, and showed the highest hostility to each other by females. In conspicuous contrast with females' great interest in intergroup food/range competition, adult male-male conflicts that were normally without body contact occurred in 66% bf close encounters; high-ranking male herding of females, which is typical in baboons, appeared in 83% of close encounters, and showed no changes with season and sexual weight-dimorphism; peripheral juvenile and subadult males were the main performers of the affinitive behaviors, opportunistic advance and retreat, and guarding at the border. In brief, all males appeared to "sit on the fence" at the border, likely holding out hope of gaining the favor of females both within and outside the group. Thus, females and males attempted to maximize reproductive values in different ways, just as expected by Darwin-Trivers' theory of sexual selection. In addition, group fission was observed in the largest and highest-ranking group for two times (both in the MS) when its size increased to a certain level, and the mother group kept their dominant position in size and rank among the groups that might encounter, suggesting that fission takes a way of discarding the "superfluous part" in order to balance the cost of competition for food and mates within a group, and the benefit of cooperation to access the resources for animals in the mother group. (C) 1997 Wiley-Liss, Inc.

Social organization and range use in the Yunnan snub-nosed monkey Rhinopithecus bieti

We studied social organization, behavior, and range use of the Yunnan snub-nosed monkey (Rhinopithecus bieti) at Wuyapiya (99 degrees 12'E, 28 degrees 30'N, the People's Republic of China) over 12 months between May 1992 and June 1994. The Wuyapiya band contained greater than or equal to 175 members and had two levels of social organization. At one level, the monkeys formed multifemale, one-male units (OMUs) similar to those of many other colobines. At another level, 15 to 18 OMUs traveled together in a cohesive band. Unlike the bands of other species of Rhinopithecus, the Wuyapiya band of R. bieti did not show seasonal fission-fusion, although some social behavior, such as male-male aggression, was seasonal. With regard to range use, the Wuyapiya band had a large home range and long daily travel distances compared with other colobines. Minimum range size in 1 year at Wuyapiya is 16.25 km(2), although there is no asymptote for range size as a function of observation time. Range size for the Wuyapiya band is 25.25 km(2) over the 2-year study and appeared to cover 100 km(2) between 1985 and 1994. The primary food of R. bieti at Wuyapiya is lichens, which are ubiquitous in fir frees. The multitiered social organization of R. bieti appears to result from the interaction of food resource characters with the forces of mate competition, with band sizes based on female responses to the spatial and temporal characteristics of lichens and subdivisions within bands based on male competition for mates.

Acoustic signals of Chinese alligators (Alligator sinensis): Social communication

This paper reports the first systematic study of acoustic signals during social interactions of the Chinese alligator (Alligator sinensis). Sound pressure level (SPL) measurements revealed that Chinese alligators have an elaborate acoustic communication system with both long-distance signal-bellowing-and short-distance signals that include tooting, bubble blowing, hissing, mooing, head slapping and whining. Bellows have high SPL and appear to play an important role in the alligator's long range intercommunion. Sounds characterized by low SPL are short-distance signals used when alligators are in close spatial proximity to one another. The signal spectrographic analysis showed that the acoustic signals of Chinese alligators have a very low dominant frequency, less than 500 Hz. These frequencies are consistent with adaptation to a habitat with high density vegetation. Low dominant frequency sound attenuates less and could therefore cover a larger spatial range by diffraction in a densely vegetated environment relative to a higher dominant frequency sound. (C) 2007 Acoustical Society of America.

Range-wide Yangtze freshwater dolphin expedition: The last chance to see Baiji?

Background, Aim and Scope. There are two species of fresh water cetaceans surviving in the Yangtze River system in China: Baiji (Lipotes vexillifer) and Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis). As a result of the expansion of human activities on the river, their distribution ranges appear to be decreasing and in the case of the Baiji, are even being restricted to several sections. The Baiji is the world's most critically endangered cetacean species with a population estimated at only a few tens of individuals. The Yangtze finless porpoise is the world's only freshwater-adapted population of the species, and it has been estimated that only around 1,000 individuals remain in the river system. In order to prevent the extinction of Baiji and a sharp decline in the abundance of the porpoise, in situ conservation (i.e. in the river) and two ex situ conservation (i.e. in semi-natural reserves and in captivity) strategies were proposed and have been implemented since the early 1990s. In view of both the severely endangered status of the animals and the severely degraded conditions of their habitats, the feasibility and actual status of these two strategies are raised for discussion. Main Features. The threats faced by the cetaceans are mainly from the unfettered exploitation of the river's resources. In the past 20 years, five nature reserves have been established along the river. Imposing maximum prohibition of harmful and illegal fishing methods in the reserves might prolong the process of extinction of these cetaceans in the wild, but so far, the administrative measures taken in the reserves have not yet kept the abundance from sharply declining. As human use of the river and its resources is expected to intensify for many decades into the future, the ability of the river to continue to support these species is certainly undecided. Therefore, rescuing animals from the river and establishing viable breeding populations in semi-natural reserves, in which the environment is similar to the main stream of the river, and in captivity, has to be considered urgently as the short-term goal of ex situ strategies. Since the abundance of porpoises is higher than that of the Baiji, we have first established breeding populations of them in the semi-natural reserves and in captivity. But, considering the extremely low density of Baiji in the river, an immediate range-wide Yangtze Baiji survey is an urgent need for locating and capturing sufficient Baiji for successfully establishing a breeding population of them in semi-natural reserves. Results. Two semi-natural reserves (in Shishou, Hubei Province, and Tongling, Anhui Province) have been set up along the river in order to establish breeding populations of the Baiji and the porpoises. So far, several small groups of porpoises that were caught in the main stream of the river have successively been introduced into the semi-natural reserves. Under careful management, these animals in both of the semi-natural reserves not only survive, but can also reproduce naturally and successfully. At least one or three calves were born in each reserve each year. Additionally, a breeding group of porpoises is being established at the Baiji Dolphinarium at the Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan. There are presently four adults and one calf living in the Dolphinarium. The calf, born in July, 2005, is the first captive bred Yangtze Finless Porpoise in the world. In preparation for the range-wide Yangtze cetacean survey, a 9-day pilot expedition on the river near Wuhan was conducted in March, 2006, in order to develop methods for locating the Baiji. No Baiji were expected to be seen in such a short period but about 40 porpoise sightings were observed. Results of the pilot survey indicated that traditional visual and acoustical survey methods for cetaceans should be adapted to find the elusive Baiji in the river. Currently, the range-wide Yangtze cetacean survey is in preparation. The survey will cover over 1,700 km of the Yangtze River from Yichang to Shanghai, and is expected to provide detailed information on Baiji and porpoise numbers and distribution patterns in the river. Discussion. Although the short-term goal of ex situ conservation is to rescue cetaceans from the river and to establish viable breeding populations in semi-natural reserves and in captivity, the long-term goal of releasing the animals back into the river when the threats have decreased and the natural environment has been improved, should not be neglected. Moreover, the in situ conservation efforts in the natural reserves, and even in the entire Yangtze River system, including the lakes, should not be ignored or abandoned at any time. The activities contributing to the conservation of the Baiji and the porpoise in the wild have the incidental effect of benefiting the entire Yangtze ecosystem and other rare threatened species. The dynamics of the groups of porpoises in semi-natural reserves should be monitored continually, in order to guide the establishment of breeding groups of Baiji in these semi-natural reserves in the near future. Conclusions. Under the existing severely degraded conditions of the Yangtze system, the sharply fall populations of Baiji and porpoises will not be suspended in the foreseeable future. Therefore, ex situ conservation should be emphasized, and the severely threatened Baiji in the river should be removed and translocated to semi-natural reserves for establishing viable breeding populations. The successful program of capturing, translocating and maintaining finless porpoises in the Shishou semi-natural reserve has demonstrated its adequacy as an ex situ environment for cetaceans. Following the successful pilot survey in the river, the immediate range-wide Yangtze cetacean survey is proposed and is in preparation. The range-wide survey is expected to ensure that any remaining Baiji can be found reliably and captured successfully after the survey. Recommendations and Perspectives. During the range-wide survey, not only the Baiji but also the porpoise as well as their habitats should be investigated based on visual and acoustical methods that adapted to the river and the animals. Meanwhile, the current risk levels to the Baiji and porpoises should be evaluated at each area where Baiji or porpoises can be reliably sighted. Any capture efforts should be targeted on the most threatened areas, or where there is maximum risk of injury or death. The immediate track of the Baiji should be carried out once a Baiji is sighted during the range-wide survey in order to obtain the movement route of the animals, which is crucial information for the successful capture operation. Additionally, the need to establish new semi-natural reserves for the porpoises should be placed on the agenda of local and central governments in the near future.

Lysis of Aphanizomenon flos-aquae (Cyanobacterium) by a bacterium Bacillus cereus

A phytoplankton-lytic (PL) bacterium, Bacillus cereus, capable of lysing the bloom-forming cyanobacterium. Aphanizomenon flos-aquae was isolated from Lake Dianchi of Yunnan province, China. This bacterium showed lytic activities against a wide range of cyanobacteria/algae, including A. flos-aquae, Microcystis viridis, Microcystis wesenbergi, Microcystis aeruginosa, Chlorella ellipsoidea, Oscillatoria tenuis, Nostoc punctiforme, Anabaena flos-aquae, Spirulina maxima, and Selenastrum capricornutum. Chlorophyll a contents, phycocyanin contents, and photosynthetic activities of the A. flos-aquae decreased evidently in an infected culture for a period. Bacterium B. cereus attacked rapidly A. flos-aquae cells by cell-to-cell contact mechanism. It was shown that the lysis of A. flos-aquae began with the breach of the cyanobacterial cell wall, and the cyanobacterial cell appeared abnormal in the presence of the PL bacterium. Moreover, transmission electron microscope examinations revealed that a close contact between the bacterium and the cyanobacterium was necessary for lysis. Some slime extrusions produced from B. cereus assisted the bacterial cells to be in close association with and lyse the cyanobacterial cells. These findings suggested that this bacterium could play an important role in controlling the Aphanizomenon blooms in freshwaters. (c) 2006 Elsevier Inc. All rights reserved.

Analysis of steric mass-action model for protein adsorption equilibrium onto porous anion-exchange adsorbent

The ion-exchange equilibrium of bovine serum albumin (BSA) to an anion exchanger, DEAE Spherodex M, has been studied by batch adsorption experiments at pH values ranging from 5.26 to 7.6 and ionic strengths from 10 to 117.1 mmol/l. Using the unadjustable adsorption equilibrium parameters obtained from batch experiments, the applicability of the steric mass-action (SMA) model was analyzed for describing protein ion-exchange equilibrium in different buffer systems. The parametric sensitivity analysis was performed by perturbing each of the model parameters, while holding the rest constant. The simulation results showed that, at high salt concentrations or low pHs close to the isoelectric point of the protein, the precision of the model prediction decreased. Parametric sensitivity analysis showed that the characteristic charge and protein steric factor had the largest effects on ion-exchange equilibrium, while the effect of equilibrium constant was about 70%-95% smaller than those of characteristic charge and steric factor under all conditions investigated. The SMA model with the relationship between the adjusted characteristic charge and the salt concentration can well predict the protein adsorption isotherms in a wide pH range from 5.84 to 7.6. It is considered that the SMA model could be further improved by taking into account the effect of salt concentration on the intermolecular interactions of proteins. (c) 2006 Elsevier Ltd. All rights reserved.

Broad host range plasmid-based gene transfer system in the cyanobacterium Gloeobacter violaceus which lacks thylakoids

Gloeobacter violaceus, a cyanobacterium lack of thylakoids, is refractory to genetic manipulations because its cells are enveloped by a thick gelatinous sheath and in colonial form. In this study, a large number of single cells were obtained by repeated pumping with a syringe with the gelatinous sheath removed. And an exogenous broad host range plasmid pKT210 was conjugatively transferred into G. violaceus. Analyses with dot-blot hybridization and restriction mapping showed that the exogenous plasmid pKT210 had been introduced into G. violaceus and stably maintained with no alteration in its structure. pKT210 extracted from G. violaceus exconjugants could be transformed into the mcr - mrr - E. coli strain DH10B but not the mcr(+) mrr(+) strain DH5alpha, which suggests that a methylase system may be present in G. violaceus.

Echolocation range of captive and free-ranging baiji (Lipotes vexillifer), finless porpoise (Neophocaena phocaenoides), and bottlenose dolphin (Tursiops truncatus)

The interclick intervals of captive dolphins are known to be longer than the two-way transit time between the dolphin and a target. In the present study, the interclick intervals of free-ranging baiji, finless porpoises, and bottlenose dolphins in the wild and in captivity were compared. The click intervals in open waters ranged up to 100-200 ms, whereas the click intervals in captivity were in the order of 4-28 ms. Echolocation of free-ranging dolphins appears to adapt to various distance in navigation or ranging, sometimes up to 140 m. Additionally, the difference of waveform characteristics of clicks between species was recognized in the frequency of maximum energy and the click duration. (C) 1998 Acoustical Society of America. [S0001-4966(98)06609-0].