Functional genomic analysis of Arabidopsis thaliana glycoside hydrolase family 1

In plants, Glycoside Hydrolase (GH) Family 1 -glycosidases are believed to play important roles in many diverse processes including chemical defense against herbivory, lignification, hydrolysis of cell wall-derived oligosaccharides during germination, and control of active phytohormone levels. Completion of the Arabidopsis thalianagenome sequencing project has enabled us, for the first time, to determine the total number of Family 1 members in a higher plant. Reiterative database searches revealed a multigene family of 48 members that includes eight probable pseudogenes. Manual reannotation and analysis of the entire family were undertaken to rectify existing misannotations and identify phylogenetic relationships among family members. Forty-seven members (designated BGLU1 through BGLU47) share a common evolutionary origin and were subdivided into approximately 10 subfamilies based on phylogenetic analysis and consideration of intron–exon organizations. The forty-eighth member of this family (At3g06510; sfr2) is a -glucosidase-like gene that belongs to a distinct lineage. Information pertaining to expression patterns and potential functions of Arabidopsis GH Family 1 members is presented. To determine the biological function of all family members, we intend to investigate the substrate specificity of each mature hydrolase after its heterologous expression in the Pichia pastoris expression system. To test the validity of this approach, the BGLU44-encoded hydrolase was expressed in P. pastoris and purified to homogeneity. When tested against a wide range of natural and synthetic substrates, this enzyme showed a preference for -mannosides including 1,4--D-mannooligosaccharides, suggesting that it may be involved in A. thaliana in degradation of mannans, galactomannans, or glucogalactomannans. Supporting this notion, BGLU44 shared high sequence identity and similar gene organization with tomato endosperm -mannosidase and barley seed -glucosidase/-mannosidase BGQ60.     

Cellular redox potential and the biomolecular electrochemical series: a systems hypothesis

The role of cellular redox potential in the regulation of protein activity is becoming increasingly appreciated and characterized. In this paper we put forward a new hypothesis relating to redox regulation of cellular physiology. We have exemplified our hypothesis using apoptosis since its redox phenomenology is well established, but believe that it is equally applicable to several other pathways. Our hypothesis is that since multiple proteins in the apoptosis pathway are thought to be regulated via oxidation/reduction reactions and since cellular redox potentials have been shown to become progressively more oxidative during apoptosis, that the proteins could be arranged in an electrochemical series where the protein's standard potential correlates with its position in the pathway. Since the most stable oxidation state of the protein is determined by its standard potential and the redox potential of its environment (in a way predictable by the Nernst equation), a quantitative model of the redox regulation of the pathway could be developed. We have outlined our hypothesis, illustrating it using a pathway map which assembles a selection of the literature on apoptosis into a readable graphical format. We have also outlined experimental approaches suitable for testing our hypothesis.     

Synonymous codon usage pattern among the S,M, and L segments in Crimean-congo hemorrhagic fever virus

Crimean-Congo hemorrhagic fever (CCHF) virus is one among the major zoonosis viral diseases that use the Hyalomma ticks as their transmission vector to cause viral infection to the human and mammalian community. The fatality of infectious is high across the world especially in Africa, Asia, Middle East, and Europe. This study regarding codon usage bias of S, M, and L segments of the CCHF virus pertaining to the host Homo sapiens, reveals in-depth information about the evolutionary characteristics of CCHFV. Relative Synonymous Codon Usage (RSCU), Effective number of codons (ENC) were calculated, to determine the codon usage pattern in each segment. Correlation analysis between Codon adaptation index (CAI), GRAVY (Hydrophobicity), AROMO (Aromaticity), and nucleotide composition revealed bias in the codon usage pattern. There was no strong codon bias found among any segments of the CCHF virus, indicating both the factors i.e., natural selection and mutational pressure shapes the codon usage bias.     

Behavioural responses of captive hippopotamus(hippopotamus amphibius)in lactation season:Maternal investment and plasticity of infant self-independence

In order to promote hippopotamus management in the captive and ex-situ environment, especially the control of behavioural and physiological status during breeding and lactation seasons, we conducted a preliminary study on behavioural responses of a pair of hippos including both mother and infant in Hangzhou Wildlife Park, China. The study of the captive hippos for about 1-month in the lactation season was carried out during August and September, 2009. The behavioural patterns were identified by all occurrence sampling and instantaneous scanning sampling methods with 5-10 min intervals. As a result, mother-offspring conflicts and interactions did occur throughout the whole study period. Early maternal investment showed a positive trend in activity rhythms (slope = 0.0014, Z = 0.3027, P ＜0.001) and a negative trend (slope = -0.0066, Z = 0.8807, P＜0.001) in territorial occupation of water, all of which supported our hypotheses that the mother hippo might exert less care for the infant and cut down on her own obligations in nursing. For infant self-independence, during the whole lactation season, the primary trends of activities and territorial occupation dynamics of the infant hippo were slightly different from before, judging from linear models (slope = -0.0017, Z = 0. 3309, P＜0.001). However, the frequencies of activities were not stable, especially at around 12 days of age. The trends of territorial occupation (slope = -0.0071, Z= 0. 904, P＜0.001) also showed negative dynamics in water body occupation by the time the infant hippo grew up. The general trend (slope = -0.005, Z = 0.06, P＜0.001) of suckling dynamics was demonstrably negative, with an upwards fluctuation at period 3 (10-15th day). This also illustrated that as the infant developed, the dependency on the mother was reduced at the end of the lactation season. In addition, a sharp decline between P3 and P4 also supported the mother-offspring conflict theory. In general, time budgets of hippos in active behaviour were (31.8±2.1)% for the mother and (32.1 ±2.6)% for the infant. Spatial distributions in water within temporal limitations were (80.1 ±2.7)% for the mother and (81.8±2.7)% for the infant. Behavioural dynamics showed strong synchronous relations between maternal investment and infant independence. Our current short-term investigation proves to be a key in management and conservation of hippopotami during the lactation season.     

Behavioural responses of <Emphasis Type="Italic">ex-situ</Emphasis> captive hippopotamus (<Emphasis Type="Italic">Hippopotamus amphibius</Emphasis>) in lactation season: Maternal investment and plasticity of infant self-independence

In order to promote hippopotamus management in the captive and ex-situ environment, especially the control of behavioural and physiological status during breeding and lactation seasons, we conducted a preliminary study on behavioural responses of a pair of hippos including both mother and infant in Hangzhou Wildlife Park, China. The study of the captive hippos for about 1-month in the lactation season was carried out during August and September, 2009. The behavioural patterns were identified by all occurrence sampling and instantaneous scanning sampling methods with 5–10 min intervals. As a result, mother-offspring conflicts and interactions did occur throughout the whole study period. Early maternal investment showed a positive trend in activity rhythms (slope = 0.0014, Z = 0.3027, P<0.001) and a negative trend (slope = − 0.0066, Z = 0.8807, P<0.001) in territorial occupation of water, all of which supported our hypotheses that the mother hippo might exert less care for the infant and cut down on her own obligations in nursing. For infant self-independence, during the whole lactation season, the primary trends of activities and territorial occupation dynamics of the infant hippo were slightly different from before, judging from linear models (slope = − 0.0017, Z = 0. 3309, P<0.001). However, the frequencies of activities were not stable, especially at around 12 days of age. The trends of territorial occupation (slope = − 0.0071, Z = 0. 904, P<0.001) also showed negative dynamics in water body occupation by the time the infant hippo grew up. The general trend (slope = − 0.005, Z = 0.06, P<0.001) of suckling dynamics was demonstrably negative, with an upwards fluctuation at period 3 (10–15th day). This also illustrated that as the infant developed, the dependency on the mother was reduced at the end of the lactation season. In addition, a sharp decline between P3 and P4 also supported the mother-offspring conflict theory. In general, time budgets of hippos in active behaviour were (31.8±2.1)% for the mother and (32.1±2.6)% for the infant. Spatial distributions in water within temporal limitations were (80.1±2.7)% for the mother and (81.8±2.7)% for the infant. Behavioural dynamics showed strong synchronous relations between maternal investment and infant independence. Our current short-term investigation proves to be a key in management and conservation of hippopotami during the lactation season.     

VCP Associated Inclusion Body Myopathy and Paget Disease of Bone Knock-In Mouse Model Exhibits Tissue Pathology Typical of Human Disease

Dominant mutations in the valosin containing protein (VCP) gene cause inclusion body myopathy associated with Paget''s disease of bone and frontotemporal dementia (IBMPFD). We have generated a knock-in mouse model with the common R155H mutation. Mice demonstrate progressive muscle weakness starting approximately at the age of 6 months. Histology of mutant muscle showed progressive vacuolization of myofibrils and centrally located nuclei, and immunostaining shows progressive cytoplasmic accumulation of TDP-43 and ubiquitin-positive inclusion bodies in quadriceps myofibrils and brain. Increased LC3-II staining of muscle sections representing increased number of autophagosomes suggested impaired autophagy. Increased apoptosis was demonstrated by elevated caspase-3 activity and increased TUNEL-positive nuclei. X-ray microtomography (uCT) images show radiolucency of distal femurs and proximal tibiae in knock-in mice and uCT morphometrics shows decreased trabecular pattern and increased cortical wall thickness. Bone histology and bone marrow derived macrophage cultures in these mice revealed increased osteoclastogenesis observed by TRAP staining suggestive of Paget bone disease. The VCP^R155H/+ knock-in mice replicate the muscle, bone and brain pathology of inclusion body myopathy, thus representing a useful model for preclinical studies.