Search

Abstract Afrotheria is a clade of African-origin species with striking dissimilarities in appearance and habitat. In this study, we compared whole proteome sequences of six Afrotherian species to obtain a broad viewpoint of their underlying molecular make-up, to recognize potentially unique proteomic signatures. We find that 62% of the proteomes studied here, predominantly involved in metabolism, are orthologous, while the number of homologous proteins between individual species is as high as 99.5%. Further, we find that among Afrotheria, L. africana has several orphan proteins with 112 proteins showing

The evolution of homologous and functionally equivalent multiprotein assemblies is intriguing considering sequence divergence of constituent proteins. Here, we studied the implications of protein sequence divergence on the structure, dynamics and function of homologous yeast and human SF3b spliceosomal subcomplexes. Human and yeast SF3b comprise of 7 and 6 proteins respectively, with all yeast proteins homologous to their human counterparts at moderate sequence identity. SF3b6, an additional component in the human SF3b, interacts with the N-terminal extension of SF3b1 while the yeast homologue Hsh155 lacks the equivalent region. Through detailed homology studies, we show that SF3b6 is absent not only in yeast but in multiple lineages of eukaryotes implying that it is critical in specific organisms. We probed for the potential role of SF3b6 in the spliceosome assembled form through structural and flexibility analyses. By analysing normal modes derived from anisotropic network models of SF3b1, we demonstrate that when SF3b1 is bound to SF3b6, similarities in the magnitude of residue motions (0.86) and inter-residue correlated motions (0.94) with Hsh155 are significantly higher than when SF3b1 is considered in isolation (0.21 and 0.89 respectively). We observed that SF3b6 promotes functionally relevant ‘open-to-close’ transition in SF3b1 by enhancing concerted residue motions. Such motions are found to occur in the Hsh155 without SF3b6. The presence of SF3b6 influences motions of 16 residues that interact with U2 snRNA/branchpoint duplex and supports the participation of its interface residues in long-range communication in the SF3b1. These results advocate that SF3b6 potentially acts as an allosteric regulator of SF3b1 for BPS selection and might play a role in alternative splicing. Furthermore, we observe variability in the relative orientation of SF3b4 and in the local structure of three β-propeller domains of SF3b3 with reference to their yeast counterparts. Such differences influence the inter-protein interactions of SF3b between these two organisms. Together, our findings highlight features of SF3b evolution and suggests that the human SF3b may have evolved sophisticated mechanisms to fine tune its molecular function.

Multi-protein assemblies are complex molecular systems that perform highly sophisticated biochemical functions in an orchestrated manner. They are subject to changes that are governed by the evolution of individual components. We performed a comparative analysis of the ancient and functionally conserved spliceosomal SF3b complex, to recognize molecular signatures that contribute to sequence divergence and functional specializations. For this, we recognized homologous sequences of individual SF3b proteins distributed across 10 supergroups of eukaryotes and identified all seven protein components of the complex in 578 eukaryotic species. Using sequence and structural analysis, we establish that proteins occurring on the surface of the SF3b complex harbor more sequence variation than the proteins that lie in the core. Further, we show through protein interface conservation patterns that the extent of conservation varies considerably between interacting partners. When we analyze phylogenetic distributions of individual components of the complex, we find that protein partners that are known to form independent subcomplexes are observed to share similar profiles, reaffirming the link between differential conservation of interface regions and their inter-dependence. When we extend our analysis to individual protein components of the complex, we find taxa-specific variability in molecular signatures of the proteins. These trends are discussed in the context of proline-rich motifs of SF3b4, functional and drug binding sites of SF3b1. Further, we report key protein-protein interactions between SF3b1 and SF3b6 whose presence is observed to be lineage-specific across eukaryotes. Together, our studies show the association of protein location within the complex and subcomplex formation patterns with the sequence conservation of SF3b proteins. In addition, our study underscores evolutionarily flexible elements that appear to confer adaptive features in individual components of the multi-protein SF3b complexes and may contribute to its functional adaptability.

Middle ear disease is a common clinical entity; imaging, especially High resolution Computed Tomography (HRCT), plays a crucial role in diagnosis and assessing the disease extent, helping to decide appropriate management. Temporal bone imaging is challenging and involves thorough understanding of the anatomy, especially in relation to HRCT imaging. Most of the middle ear pathologies appear as "soft tissue" on imaging. Careful analysis of the soft tissue on the HRCT is crucial in achieving the right diagnosis; clinical information is essential and the imaging findings need correlation with clinical presentation and otoscopic findings. The purpose of this pictorial essay is to enlist the pathologies that present as soft tissue in middle ear and to provide a structured and practical imaging approach that will serve as a guide for confident reporting in daily practice.

Sperm transcripts aside from providing genetic material have an eminent role in post-fertilization events and embryonic development. The current study was carried out to study the gene expression in Osmanabadi buck (Capra hircus) supplemented with organic minerals. Organic minerals alone or in combination with different concentrations were fed to the treatment groups (T2- Zn 20 mg, T3- Zn 40 mg, T4- Zn 60 mg, T5- Cu 12.5 mg, T6- Cu 25 mg, T7- Cu 37.5 mg, T8- Zn 20 mg + Cu 12.5 mg, T9- Zn 40 mg + Cu 25 mg, T10- Zn 60 mg + Cu 37.5 mg) along with the concentration mixture and roughages; whereas control (T1) group was fed concentrate mixture and roughages. The sperm samples were processed for gene expression studies of Ras Homolog Family Member A (RHOA), Mesoderm Specific Transcript (MEST), Nucleoside diphosphate-linked moiety X motif 6 (NUDT6), Protamine 1 (PRM1), Protamine 2 (PRM2) and Heat shock protein 90 alpha family class A member 1 (HSP90AA) using qRT-PCR and the protein-protein interaction analysis was carried out through String database version 11.0. Supplementation of trace minerals has enhanced the gene expression at a significant level (P

Bioactive compounds with varied functional properties found in microalgae such as Chlorella vulgaris can serve as antioxidants supplement against free radicals causing oxidative stress in food animals, but there is a need to quantify these antioxidants in the algae for effective applications. Therefore, this study quantified antioxidants in Chlorella vulgaris and derivatives prepared with the microalgae biomass for enhancing its application in animal nutrition. Eight derivatives prepared using the Chlorella vulgaris biomass were subjected to in vitro antioxidant supplements in animals for attenuation of oxidative stress to improve performances and productivity because of their antioxidant potentials. Antioxidant assessments including ferric antioxidant power, hydrogen peroxide scavenging potential, total antioxidant capacity, and total phenolic content. The results showed that the mean total capacities of the preparations were 621.83±36.41 µmol/g ascorbic acid equivalent, ferric reducing antioxidant power (FRAP) was 1.28±0.09, while the hydrogen peroxide scavenging (HPS) potential was 34.04±3.18%, and the total phenolic content was 30.54 mg/g ellagic acid equivalent. It was concluded from these observations that the microalgae Chlorella vulgaris and its derivatives as prepared in this study could be used as antioxidant supplements in animals for attenuation of oxidative stress to improve performances and productivity because of their antioxidant potentials.

This study aimed to investigate the influence of calcium and magnesium supplementation on the skewing of sex ratio and placental genes expression in New Zealand White Rabbits. A total of 25 rabbits were allocated to 5 groups; each treatment group was supplemented with Ca and Mg; T1 (0.4% and 0.01%), T2 (0.6% and 0.02%), T3 (0.8% and 0.03%), and T4 (1.0% and 0.04%) respectively, while the C group was provided with regular feed and subjected to three breeding. The T3 group produced a female-biased litter and hence, the F1 female kits (n=12) of T3 and C group was provided same supplementation management. At 21 days of gestation, three animals from each group were sacrificed and placental samples were collected, the remaining animals were allowed for full-term delivery. The selected F1 produced female-biased litter with elevated serum Ca and Mg concentrations and reduced sodium and cholesterol levels. A total of 15 genes related to mineral absorption, placental development and immunity were selected to study the influence of diet on sex and placental gene expression. The expression of genes such as PEG10, SOD1, SLC30A, TLR4, AR, and TRPM6 was high in the treatment placenta compared to the control. RTL1, ESR2, CALM2, and TRPM6 upregulated in the treatment female placenta. The study concluded that the intake of 0.8% Ca and 0.03% Mg could lead to the production of more females and upregulation of some placental genes could serve as the molecular mechanism in response to intake of the minerals and fetal sex.

The great expectation of the dairy owners from the frozen semen industry is quality semen with high fertility. Many researchers concentrate in this area to produce frozen semen of high quality and fertility. However, the problem still exists to minimize or reduce the cryoinjury related damages that occur during the process of cryopreservation with the use of all kinds of semen additives. The success rate of the additives added semen is variable at a larger scale. Therefore, any new molecules which can effectively prevent or minimize the cryoinjury are warranted and it could be low cost substances. Our incidental finding and protein identification with molecular weight ≈ 19 kDa (cold-inducible RNA-binding protein CIRBP) in goat spermatozoa seems to be effective in minimizing cryoinjury. The identified CIRBP was confirmed via Western blotting. In future, further studies are needed to confirm the molecular mechanism of the CIRBP on the cryoinjury as semen additives, and application of this protein added semen in the field to improve the level of conception rate in cattle.

Interactions between proteins are vital in almost all biological processes. The characterization of protein–protein interactions helps us understand the mechanistic basis of biological processes, thereby enabling the manipulation of proteins for biotechnological and clinical purposes. The interface residues of a protein–protein complex are assumed to have the following two properties: (a) they always interact with a residue of a partner protein, which forms the basis for distance‐based interface residue identification methods, and (b) they are solvent‐exposed in the isolated form of the protein and become buried in the complex form, which forms the basis for Accessible Surface Area (ASA)‐based methods. The study interrogates this popular assumption by recognizing interface residues in protein–protein complexes through these two methods. The results show that a few residues are identified uniquely by each method, and the extent of conservation, propensities, and their contribution to the stability of protein–protein interaction varies substantially between these residues. The case study analyses showed that interface residues, unique to distance, participate in crucial interactions that hold the proteins together, whereas the interface residues unique to the ASA method have a potential role in the recognition, dynamics, and specificity of the complex and can also be a hotspot. Overall, the study recommends applying both distance and ASA methods so that some interface residues missed by either method but crucial to the stability, recognition, dynamics, and function of protein–protein complexes are identified in a complementary manner. [ABSTRACT FROM AUTHOR]

Abstract Background Chlorella vulgaris (CV) is a natural source of functional antioxidants capable of protecting against oxidative stress; its dietary supplementation in animals can serve as a way of improving animals’ performance and productive output; on this background, the microalgae was supplemented to growing New Zealand white rabbits and its effects on performances and oxidative stress status were evaluated. Method Thirty-five (35) 6-week-old New Zealand White rabbits (935.48 ± 5.92 g) were divided into five groups (n = 7 per group) in a completely randomized design experiment; rabbits in control groups were fed only commercial rabbits feed, while rabbits in treatment groups were supplemented with 200, 300, 400, and 500 mg Chlorella vulgaris biomass per kilogram of the body weight along with commercial rabbits feed daily. Feed intake and body weight changes were recorded daily and weekly; at the end of the study, blood was collected and subjected to chemical assays for evaluation of serum oxidative stress markers and antioxidant activities. Results Dietary supplementation of the microalgae significantly increased the rabbits’ growth weights (p < 0.01) without significant increase or reduction in feed intakes (p < 0.56), but significantly enhanced feed to gain ratio. The microalgae supplementation significantly protected the rabbits against oxidative stress damages through the reduction of malondialdehyde concentrations (p < 0.001) and increased total antioxidant capacity (p < 0.003). It also led to higher superoxide dismutase activity (p < 0.001), increased catalase activity (p < 0.003), and higher concentration of reduced glutathione (p < 0.001). Conclusion It was concluded from outcomes of both performance and biochemical analysis of the rabbits that daily supplementation of Chlorella vulgaris between 200 and 500 mg per kilogram of the body weight in prepubertal rabbits significantly improved performances in forms of higher weight gains and enhanced feed utilization; it also protected against oxidative stress damages hence it was recommended as dietary antioxidant supplement for growing prepubertal rabbits.

Oxidative stress negatively affects animals during gestation period and this condition is almost inevitable in the Tropics because of temperature elevation; therefore, objective of this study was evaluation of antioxidant effects of Chlorella vulgaris supplementation in pregnant rabbits. New Zealand white rabbits (40) were randomly distributed into five groups (n = 8) on day 0 of their gestation and were supplemented with 0, 200, 300, 400 and 500 mg Chlorella vulgaris biomass per kg body weight respectively throughout the gestation period. Blood was collected from the animals in the last week of gestation for serum oxidative stress and biochemical profile assessments. There was significant difference in serum malondialdehyde concentration, total antioxidant capacity but protein carbonyl content was not significantly different. There was also significant difference in superoxide dismutase activity, catalase activity and glutathione concentration. Furthermore, the results showed that serum biochemical profiles of the rabbits were within the normal ranges for healthy rabbits. The study therefore concluded that supplementation of Chlorella vulgaris significantly protects the rabbits against oxidative stress damage and has no deleterious effects on their organs function; hence, the microalga was recommended as an antioxidant supplement for pregnant rabbits.

Hazard analysis critical control points (HACCP) based system is mainly a risk based preventive approach developed to increase food safety assurance level from farm. This program deals with control factors affecting the process and product. A semi-structured questionnaire was administered to 101 farmers in the adopted villages, covering 134 crossbred dairy cows. The baseline data indicated that based on California Mastitis Test (CMT) the incidence of clinical and subclinical mastitis in crossbred cow was 8.21 and 44.78% respectively. The risk factors associated with the incidence of mastitis were parity, level of milk yield, udder hygiene, udder shape, teat length, teat-tip-to-ground distance, animal housing conditions, milking management, post-milking time taken by the animal for lying down, a long gap in tail hair clipping. CCPs identified and developed plan may be suitable for customized and implementation on small-holder dairy farms. This is a logical, effective and systemic approach for control of incidence of mastitis, improve the udder health status and milk quality.

Sperm biomolecules impact the reproductive success of a bull in many ways from fertilization to the health of the offspring. The energy produced within the sperm enables them to remain motile and allows them to participate in fertilization events. In this study, we deciphered the genes associated with energy production and their influence on the fertility rate. Post-thaw buffalo semen samples (n=21) were analysed for sperm kinematics and field fertility for selecting high (n=5) and low (n=5) fertile samples. Sperm total RNAs were extracted using a double lysis method followed by column-based extraction and sequenced using the Illumina platform. The expression levels of the genes involved in energy-regulating pathways were analyzed. Among these genes, 14.6% were significantly (p<0.05) differentially expressed between high and low fertile sperm. The expression levels of up-regulated genes such as JAK3, DDX5, PRKCZ, CHD4, CHD5, and ADCY3 had a strong positive correlation (r>0.5) with progressive motility and velocities. The up-regulated genes were involved in chemokine signaling (ADCY2 and JAK2, p=0.0001), calcium signaling (AGTR1 and SLC25A4,p=0.0002) and oocyte meiosis (ADCY2 and ADCY3, p=0.049). The increase in the expression of ATP-producing genes substantiate the improved progressive motility (64.51±5.79 vs 33.07±3.34 %), curvilinear velocity (70.58±4.32 vs 50.15±4.92 μm/sec), straight-line velocity (39.84±3.16 vs 26.02±2.52 μm/sec) and average path velocity (49.46±3.59 vs 32.99±3.45 μm/sec) in high fertile bulls compared to low fertile bulls. The study suggests that the expression level of differentially expressed genes associated with energy-regulating pathways influences the fertilizing ability of sperm. [ABSTRACT FROM AUTHOR]

Oxidative stress is an exclusive biochemical complication affecting reproduction; hence, dietary antioxidant supplementation for its attenuation is a required nutrition – reproduction improvement strategy. On this background, Chlorella vulgaris (a natural antioxidant) was supplemented to grower female rabbits to maturity. The rabbits were thirty-five in number randomly distributed into five experimental groups in a completely randomized design. Control group was fed only basal feed while treatment groups were fed diets containing 40 %, 60 %, 80 % and 100 % Chlorella vulgaris biomass as T1, T2, T3 and T4 respectively at 500 mg per animal body weight (kg) along with the basal feed daily. Performance records were obtained, blood was collected, and at the end uterus, ovaries and liver were removed from sacrificed animals for analysis. Serum, uterus and liver oxidative stress status were determined while RNA isolated from liver and ovaries samples were used for antioxidant genes expression analysis. Oxidative stress status and antioxidant enzymes activities were determined using chemical assays while antioxidant gene expression levels were determined using real-time quantitative PCR system. There was significant difference in feed intake (p < 0.014), final body weights (p < 0.008), empty carcass weights (p < 0.001) and commercial carcass weights (p < 0.001) of the rabbits as results of the microalgae supplementation. There was also significant difference in malondialdehyde (MDA) concentrations (p < 0.050), total antioxidant capacity (TAC) (p < 0.050) and protein carbonyl (PCO) concentrations (p < 0.050) due to the supplementation of the microalgae; in addition, supplementation of the microalgae significantly improved activities of superoxide dismutase (SOD) (p < 0.050), catalase (CAT) (p < 0.050) and reduced glutathione (GSH) concentration (p < 0.050). Furthermore, there was significant difference in relative expression of primary antioxidant genes sod1 (p < 0.050) and gpx1 (p < 0.050); however, there was no significant difference in relative expression of bre (p > 0.050) and ucp1 (p > 0.050). The study concluded from the outcomes stated above that supplementation of microalgae Chlorella vulgaris improved performances of rabbits through attenuation of oxidative stress, enhancement of antioxidant enzymes activities as well as up-regulation of primary antioxidant genes. Hence, it was recommended as dietary supplement for protection against oxidative stress and improved productivity in rabbits and other food producing mammalian species. In addition, further studies into assessment of its effects on expression of transcripts and immune modulation genes in rabbits and other animals is warranted as future studies in order to established its potential as beneficial nutraceutical for animals and human.