Examination of Various Abutment Designs Behavior Depending on Load Using Finite Element Analysis.

Studies on dental implant abutments' geometric design and material selection offer significant innovations and results. These studies aim to improve the abutments' functionality and aesthetic performance, minimize microcavities' formation, and ensure implant-supported prostheses' longevity. For example, CAD-CAM fabricated custom abutments have been found to produce a better marginal fit and fewer microgaps than standard abutments. In an in vitro study, transepithelial abutments offered lower microgap values than titanium-based abutments and provided a better fit at the implant-abutment interface. It is known that studies to improve mechanical and biological performance with Polyether Ether Ketone (PEEK) material have been addressed. New materials such as PEEK and zirconia have offered significant advantages in biocompatibility and aesthetics. Along with those studies, different abutment designs are also important. Abutment geometry is optimized to improve stress distribution and minimize peri-implant bone loss. In implant and abutment connections with different angles, mechanical life performances may vary depending on static and dynamic load. These studies emphasize the importance of material research on different types of connections to improve dental implants' durability, homogeneous load distribution, and reliability. The abutment parts used in implant treatment are insufficient to distribute the load homogeneously against chewing pressure due to their materials and geometry. Non-uniform load distribution damages the abutment and the prosthetic crown, accelerating the wear process. This study aimed to create different abutment designs to improve dental implants' biomechanical performance and longevity. This study aimed to increase the mechanical durability of the implant-abutment connection by reducing stress concentrations in response to masticatory compression on the abutment in different directions and forces and to guarantee the long-term success of the implant system by providing a more homogeneous stress distribution. It aimed to apply different forces in the axial direction to these models in a simulation environment and to calculate and compare the deformation and stress load distribution. As a method, three-dimensional models of the parts used in implant treatments and forming the implant system were designed. Different abutment designs were created with these models. Taking the current material values used in implant treatments as a reference, finite element analysis (FEA) was performed by applying different axial loads to each implant system model in the ANSYS software (version 24.1). Comparative analysis graphs were prepared and interpreted for the stress values obtained after the applied load. This study evaluated the mechanical performance of different abutment models (A, B, C, D, and E) under a 100 N load using the Kruskal-Wallis test. The Kruskal-Wallis test showed significant differences between the groups (p < 0.001). The greatest difference was observed between models E and A (q' = 6.215), with a significant difference also found between models C and A (q' = 3.219, p < 0.005). Regarding stress values, the highest stress on the abutment was observed in Model B (97.4 MPa), while the lowest stress was observed in Model E (9.6 MPa). The crown exhibited the highest stress in Model B (22.7 MPa) and the lowest in Model E (17.3 MPa). The implant stress was highest in Model C (14.8 MPa) and lowest in Model B (11.3 MPa). The stress values for the cortical bone and cancellous bone were quite similar across the models, showing no significant differences. These findings indicate that the abutment design and material selection significantly impact mechanical performance. Among the implant systems created with five different abutment models, in which the existing abutment geometry was also compared, homogeneous and axial distribution of the load on the abutment was achieved, especially with viscoelastic and surface area increased abutment designs. Clinically, the inadequacy and limited mounting surface or geometry of the abutments used in today's implant treatment applications have led to different design searches. It was concluded that the designs in this study, which are considered alternatives to existing abutment models, contribute positively to the mechanical life of the abutment material, considering the von Mises stresses and directions. This study brings a new perspective to today's practices and offers an alternative to treatment practices.

The Effect of Birth Weight on Fattening Performance, Meat Quality, and Muscle Fibre Characteristics in Lambs of the Karayaka Native Breed.

This investigation aimed to assess the influence of birth weight on post-weaning fattening performance, meat quality, muscle fibre characteristics, and carcass traits in Karayaka lambs. The study categorized the lambs into three distinct groups based on birth weight: low birth weight (LBW), medium birth weight (MBW), and high birth weight (HBW). Throughout the fattening phase, the lambs were given ad libitum access to food and water, culminating in the slaughter at the end of the study. Following slaughter, warm and cold carcasses were weighted, and specific muscles (longissimus thoracis et lumborum [LTL], semitendinosus [ST], and semimembranosus [SM]) were isolated for the evaluation of muscle weights, muscle fibre types (Type I, Type IIA, and Type IIB), and muscle fibre numbers. Carcass characteristics were also determined, including eye muscle (LTL) fat, loin thickness, and meat quality characteristics, such as pH, colour, texture, cooking loss, and water-holding capacity. The statistical analysis revealed highly significant differences among the experimental groups concerning muscle weights and warm and cold carcass weights (p < 0.01), with the lambs in the HBW group exhibiting a notably higher carcass yield (in females: 45.65 ± 1.34% and in males: 46.18 ± 0.77%) and LTL, ST, and SM (except for female lambs) muscle weights than the lambs in LBW group (p < 0.01). However, apart from the texture of LTL and ST muscles, no significant differences in meat quality parameters were observed among the treatment groups (p > 0.05). Notably, the birth weight of lambs did not impart a discernible effect on the total number and metabolic activity of muscle fibres in LTL, ST, and SM muscles. Nonetheless, a noteworthy distinction in the fibre area of Type I fibres in the LTL muscle of male lambs (LBW: 30.4 ± 8.9, MBW: 29.1 ± 7.3 and HBW; 77.3 ± 15.4) and in the ST muscle of female lambs (LBW: 44.1 ± 8.1, MBW: 38.8 ± 7.7 and HBW: 36.9 ± 7.1) were evident among the birth weight groups (p < 0.05). The study also found that the mean fat thickness values of eye muscles in Karayaka lambs, as obtained by ultrasonic tests, were below the typical range for sheep. In synthesis, the outcomes of this study underscore the considerable impact of birth weight on slaughtered and carcass weights, emphasizing the positive association between higher birth weights and enhanced carcass yield. Remarkably, despite these pronounced effects on carcass traits, the birth weight did not demonstrate a statistically significant influence on meat quality or overall muscle fibre characteristics, except for the area of Type I fibres in the LTL muscle. This nuanced understanding contributes valuable insights into the intricate relationship between birth weight and various physiological and carcass parameters in Karayaka lambs undergoing post-weaning fattening.

Multi-Trait Single-Step Genomic Prediction for Milk Yield and Milk Components for Polish Holstein Population.

The objective of our study was to evaluate the predictive ability of a multi-trait genomic prediction model that accounts for interactions between marker effects to estimate heritability and genetic correlations of traits including 305-day milk yield, milk fat percentage, milk protein percentage, milk lactose percentage, and milk dry matter percentage in the Polish Holstein Friesian cow population. For this aim, 14,742 SNP genotype records for 586 Polish Holstein Friesian dairy cows from Poland were used. Single-Trait-ssGBLUP (ST) and Multi-Trait-ssGBLUP (MT) methods were used for estimation. We examined 305-day milk yield (MY, kg), milk fat percentage (MF, %), milk protein percentage (MP, %), milk lactose percentage (ML, %), and milk dry matter percentage (MDM, %). The results showed that the highest marker effect rank correlation was found between milk fat percentage and milk dry matter. The weakest marker effect rank correlation was found between ML and all other traits. Obtained accuracies of this study were between 0.770 and 0.882, and 0.773 and 0.876 for MT and ST, respectively, which were acceptable values. All estimated bias values were positive, which is proof of underestimation. The highest heritability value was obtained for MP (0.3029) and the lowest heritability value was calculated for ML (0.2171). Estimated heritability values were low for milk yield and milk composition as expected. The strongest genetic correlation was estimated between MDM and MF (0.4990) and the weakest genetic correlation was estimated between MY and ML (0.001). The genetic relations with milk yield were negative and can be ignored as they were not significant. In conclusion, multi-trait genomic prediction can be more beneficial than single-trait genomic prediction.

Comparison of the data mining and machine learning algorithms for predicting the final body weight for Romane sheep breed.

The current study aimed to predict final body weight (weight of fourth months of age to select the future reproducers) by using birth weight, birth type, sex, suckling weight, age at suckling weight, weaning weight, age at weaning weight, and age of final body weight for the Romane sheep breed. For this purpose, classification and regression tree (CART), multivariate adaptive regression splines (MARS), and support vector machine regression (SVR) algorithms were used for training (80%) and testing (20%) sets. Different data mining and machine learning algorithms were used to predict final body weight of 393 Romane sheep (238 female and 155 male animals) were used with different artificial intelligence algorithms. The best prediction model was obtained by CART model, both training and testing set. Constructed CART models indicated that sex, suckling weight, weaning weight, age of weaning weight, and age of final weight could be used as an indirect selection measure to get a superior sheep flock on the final body weight of Romane sheep. If genetically established, the Romane sheep whose sex is female, age of final weight is over 142 days, and weaning weight is over 28 kg could be chosen for affording genetic improvement in final body weight. In conclusion, the usage of CART procedure may be worthy of reflection for identifying breed standards and choosing superior sheep for meat yield in France.

Usage of the XGBoost and MARS algorithms for predicting body weight in Kajli sheep breed.

This study aimed to utilize the XGBoost and MARS algorithms to predict present weight from body measurements. The algorithms have the potential to model nonlinear relationships between body measurements and weight, and this study attempted to find a model that provided the most accurate predictions of present weight. The current study was conducted with 152 animals in order to achieve a certain goal. To compare the model performances, goodness-of-fit criteria such as R2, r, RMSE, CV, SDratio, PI, MAPE, AIC were used. According to the results of this study, the XGBoost algorithm was the most reliable model for predicting present weight from body measurement. Even if the XGBoost algorithm was the most accurate model, the MARS algorithm was the reliable model for the same aim. In addition, it is hoped that the results of this study will help researchers and breeders better understand the relationship between body measurements and weight and ultimately be able to help individuals better manage their weight. As a conclusion, in the current study, the XGBoost algorithm is an effective, efficient, and reliable tool for accurately estimating present weight from body measurements. This makes it an invaluable tool in rural areas, where traditional weighing scales may not be available or reliable.

Use of Multivariate Adaptive Regression Splines Algorithm to Predict Body Weight from Body Measurements of Anatolian buffaloes in Türkiye.

Anatolian buffalo is an important breed reared for meat and milk in various regions of Türkiye. The present study was performed to estimate body weight (BW) from several body measurements, such as tail length (TL), shoulder height (SH), withers height (WH), body length (BL), chest circumference (CC), shank diameter (SD) and birth weight (BiW). The data set was taken from Mus Province of Türkiye. In this respect, 171 Anatolian buffaloes were used. To estimate the BW, different proportions of the training and test sets were used with the MARS algorithm. The optimal MARS was determined at a proportion of 70-30%. The MARS model displays the heaviest BW that can be produced by Anatolian buffalo according to tail length, body length, chest circumference and shoulder height. In conclusion, it could be suggested that the MARS algorithm may allow animal breeders to obtain an elite population and to determine the body measurements affecting BW as indirect selection criteria for describing the breed description of Anatolian buffalo and aiding sustainable meat production and rural development in Türkiye.

Macromolecules Influence Cellular Competence and Expression Level of IGFs Genes in Bovine Oocytes In Vitro.

In vitro maturation (IVM) of mammalian oocytes, which influences subsequent in vitro development of embryos, is affected by the macromolecule content in culture media for the success of oocyte maturation competence, in which the cytoplasmic and nuclear reprogramming events occur. The insulin-like growth factor family (IGFs) promotes the maturation of bovine oocytes and the expansion of cumulus cells and also inhibits apoptosis. This study was, therefore, designed to examine the effects of macromolecules (bovine serum albumin, BSA; fetal calf serum, FCS; and polyvinyl alcohol, PVA) on in vitro nuclear maturation, total cellular protein, glutathione peroxidase (GPx) enzyme activity, and the gene expression level of IGF1, IGF2, and their receptor in bovine oocytes. Oocytes obtained from bovine ovaries were cultured in bicarbonate-buffered medium 199 supplemented with 4 mg/mL BSA, 10% FCS, 1 mg/mL PVA, and without macromolecule supplement (control) during 22 h in the air with a humidified atmosphere and 5% CO2 at 38.5 °C temperature. Supplementation of BSA and FCS increased (χ2 = 9.84; p < 0.05) the percentages of oocytes that reached metaphase II compared to the control and PVA. The amount of protein per ml of cell extracts of oocytes matured in FCS supplemented culture media was higher (p < 0.05) than the oocytes in the PVA and control. The levels of GPx enzyme activity in cell extracts isolated from oocytes in each experimental group did not change over time, but the GPx enzyme activity in oocytes matured in PVA-supplemented culture media was lower (p < 0.05) than in oocytes in the other experimental groups. Transcript for the IGF1 gene was not detected in all experimental groups, but the supplementation of BSA and FCS significantly elevated the transcript level of the IGF2 gene. In addition, the maturation of oocytes with BSA-supplemented media increased the transcript level of the IGF1R gene, whereas the transcript level of the IGF2R gene was similar among macromolecule supplementation groups. The current study concluded that BSA and FCS could improve in vitro bovine oocyte development due to supporting nuclear maturation and increasing the total cellular protein content, GPx enzyme, and transcript activity.

Comparison of Random Regression Models with Different Order Legendre Polynomials for Genetic Parameter Estimation on Race Completion Speed of Arabian Horses.

This work aimed to compare the fitting performance of the random regression models applied to the different order orthogonal Legendre polynomials on the race completion speed (m/s) of Arabian racing horses. Legendre polynomial function for additive genetic, permanent environmental variances and heritability values with the L(2,2), L(2,3), L(3,2) and L(3,3) models (where L(i,j) means L(order of fit for additive genetic effects, order of fit for permanent environmental effects)) was estimated. A total of 233,491 race speed records (m/s) of Arabian horses were taken from the Jockey Club of Turkey between 2005 and 2016. The mean and standard deviation of heritability values were estimated as 0.294 ± 0.0746, 0.285 ± 0.0620, 0.302 ± 0.0767 and 0.290 ± 0.1018 for L(2,2), L(2,3), L(3,2), and L(3,3), respectively. The steady decreasing trend of permanent environmental variances for L(2,2) provided stationery for heritability values. According to Akaike information criterion (AIC) and Bayesian information criterion (BIC) values, the L(2,2) model could be reliably used to estimate heritability values for the racing speed of Arabian horses in the presence of repeated observations.

Farmers' Risk Perception on Climate Change: Transhumance vs. Semi-Intensive Sheep Production Systems in Türkiye.

Sheep farmers' perceptions of climate change and its impacts and the adaptation strategies they consider to address these risks are of great importance in ensuring the resilience of farming practice. This study focused on sheep farmers' perception of climate change and the risks and actions taken to mitigate these impacts. A total of 68 surveys were carried out among sheep farmers (39 transhumance and 29 semi-intensive farmers) by two different representative production systems in Türkiye. Variables regarding the socio-economic profile, climate change impacts, and adaptation strategies were identified and analyzed. Principal component analysis and a Pearson Chi-square test were used to evaluate the data. Both farmers' groups accepted and perceived climate change, showing good awareness and perception. The farmers' attitudes towards adaptation to climate change were associated with production systems. Transhumance farmers had limited adaptation and coping strategies compared to semi-intensive farmers. Transhumance farmers focused mainly on selling livestock (mostly to cope with degraded natural grassland/feed deficiency) as an adaptive strategy. In contrast, semi-intensive farmers focused on modifying their farm management and feed operations, such as changing the feed ratio and supplement use, improving water and feed storage, and considering crop feed production. The knowledge obtained from this study could be helpful for farmers and policymakers who develop long-term small ruminant production strategies that consider the effects of climate change and adapt them to different farming systems in the Türkiye.

Growth and Slaughter Characteristics of Weaning Male Kids of Turkish Native Goat Breeds.

There is little knowledge about the carcass potential of Turkish native goat breeds raised under different rearing conditions. It is necessary to compare the carcass characteristics of these breeds to minimize the effect of the rearing conditions. Therefore, this study aims to compare the growth, slaughter, and carcass characteristics of male kids at weaning age to eliminate the impact of rearing conditions. Kids born to Angora (n = 6), Hair (n = 6), Honamli (n = 6), and Kilis (n = 6) Turkish native goat breeds, ranging in age from 2-3 years, were slaughtered at 90 days of weaning age and carcass characteristics were determined immediately. There were differences (p < 0.05) among breeds in terms of birth weight (BW) and daily weight gain (DWG) from birth to weaning age. Honamli kids had higher BW and DWG than those of other breeds (p < 0.05). Similarly, carcass weights (hot-cold) and yields (hot-cold) of Honamli kids were higher compared to kids born to other breeds (p < 0.05). Additionally, Honamli and Hair kids had higher longissimus-dorsi (LD), and semitendinosus (ST) muscle weights compared to Kilis and Angora kids. Interestingly, Kilis kids had lower BW and DWG than those of other breeds (p < 0.05). There were significant differences (p < 0.05) among breeds in terms of non-carcass parts and organ weights. Positive correlations were calculated between cross-sectional area and weight (r = 0.793; p < 0.01), length and weight (r = 0.723; p < 0.01), and depth and weight (r = 0.698; p < 0.01) in LD muscle of all kids. A similar correlation trend was calculated for the ST muscle (cross-sectional area and weight; r = 0.699; p < 0.01, length and weight; r = 0.751; p < 0.01, and depth and weight; r = 0.528; p < 0.05) in all kids. In conclusion, the present study results showed that Honamli kids could be used for fattening material due to their good carcass quality compared to other native breeds.

Impact of delay in cystoscopic surveillance on recurrence and progression rates in patients with non-muscle-invasive bladder cancer during the COVID-19 pandemic.

PURPOSE: To evaluate the impact of delay in cystoscopic surveillance on recurrence and progression rates in non-muscle-invasive bladder cancer (NMIBC). MATERIALS AND METHODS: A total of 407 patients from four high-volume centres with NMIBC that applied for follow-up cystoscopy were included in our study prospectively. Patients' demographics and previous tumour characteristics, the presence of tumour in follow-up cystoscopy, the pathology results of the latest transurethral resection of bladder tumour (if tumour was detected) and the delay in cystoscopy time were recorded. Our primary outcomes were tumour recurrences detected by follow-up cystoscopy and progression. Multivariate logistic regression analysis was performed using the possible factors identified with univariate analyses (P values ≤ .2). RESULTS: A total of 105 patients (25.8%) had tumour recurrence in follow-up cystoscopy, and 20 (5.1%) of these patients had disease progression according to grade or stage. In multivariate analysis, the number of recurrences (OR: 1.307, P < .001) and the cystoscopy delay time (62-147 days, OR: 2.424, P = .002; >147 days, OR: 4.883, P < .001) were significant risk factors for tumour recurrence on follow-up cystoscopy; the number of recurrences (OR: 1.255, P = .024) and cystoscopy delay time (>90 days, OR: 6.704, P = .002) were significant risk factors for tumour progression. CONCLUSIONS: This study showed that a 2-5 months of delay in follow-up cystoscopy increases the risk of recurrence by 2.4-fold, and delay in cystoscopy for more than 3 months increases the probability of progression by 6.7-fold. We suggest that cystoscopic surveillance should be done during the COVID-19 pandemic according to the schedule set by relevant guidelines.

Placental Characteristics Classification of Various Native Turkish Sheep Breeds.

The aim of this study was to classify placental characteristics of Akkaraman, Morkaraman, Karayaka, Awassi, Malya, and Bafra sheep breeds using the hierarchical clustering method. In total, 240 individual data records were used as experimental material. Placental characteristics such as total cotyledon surface area, small and large cotyledon length, small cotyledon depth, etc. were used as explanatory variables to classify the breeds' characteristics. Hierarchical clustering was used with the nearest neighbour method with Euclidean distance in order to classify the sheep breeds' variations. As a result, six breeds were separated into three clusters: the first cluster consisted of Bafra, Karayaka, and Awassi breeds; the second consisted of Akkaraman and Malya breeds; and the third cluster included only the Morkaraman breed. Bafra and Karayaka were pointed as the nearest breeds, with a similarity of 98.7% in terms of placental characteristics. The similarity rate of the Akkaraman and Malya breeds was at a level of 97.5%, whereas it was 96.8% for Bafra, Karayaka, and Awassi breeds. The similarity of Akkaraman, Karayaka, Awassi, Malya, and Bafra sheep breeds was estimated as 95.7%. The overall similarity was found to be at a level of 93.2% among sheep breeds. The outcomes of the study might be useful as a selection tool for reproductivity and can be used to select the breed to be reared.

Resilience to drought in semi-desert sheep: Effects of water restriction during pregnancy on placental efficiency in the Awassi breed.

Assessing the resilience of Awassi sheep to water shortages during pregnancy, thereby investigating the effects of water scarcity on gestation efficiency in animals, could provide valuable and pertinent insight into future scenarios posed by climate change risks. In this study, 40 pregnant Awassi ewes randomly allocated to free watering group (C, n = 20) received water ad libitum and the water restricted group (WR) received 50% less water than the amount provided to group C. Water restriction decreased (p < .05) lambs' birth weights, placental weights (PWs), and cotyledon numbers (CNs). Placental efficiency (PE) and cotyledon efficiency (CE) were significantly higher in the WR group (p < .05). A marked difference in cotyledon weight - an increase of 12.1% - was recorded in the C group. The body weights of the pregnant ewes in the WR group decreased significantly (p < .05) by 22% during pregnancy. Significant increases (p < .05) in plasma ADH, cholesterol, Cl- , and Na+ levels were observed in the WR group ewes, indicating intense dehydration. We conclude that the Awassi breed of sheep can endure 50% water restriction during pregnancy and maintain successful parturition, a key outcome for sustainability.

Meat production characteristics of Turkish native breeds: II. meat quality, fatty acid, and cholesterol profile of lambs.

The study conducted a comparison of meat quality, fatty acid profile, and cholesterol amounts of longissimus dorsi (LD) and semitendinosus (ST) muscles of male lambs born to Turkish indigenous sheep breeds raised under intensive conditions. A total of 36 singleton male lambs were used as experimental animals of the Akkaraman (A), Morkaraman (M), Awassi (IW), Karayaka (KR), Kivircik (KV), and Middle Anatolian Merino (MAM) pure breeds. All lambs were fed the same diet until they reached a target weight of 40 kg weight. After the feeding period, all lambs were slaughtered and LD and ST muscle samples were collected to determine meat quality traits, fatty acid profile, and cholesterol amounts. Although there were no significant differences between lambs in terms of the fatty acid profile of LD and ST muscles, KR lambs had a higher cholesterol content in both muscles in comparison with the lambs born to other breeds ( p < 0.05 ). While water-holding capacity, dripping loss, pH, color, dry matter, ash, and intramuscular fat values of ST muscles showed differences among breeds ( p < 0.05 ), dripping loss, pH, cooking loss, color, dry matter, ash, protein, and intramuscular fat values of LD muscles differed between breeds ( p < 0.05 ). The data of the current study indicated that meat quality characteristics and cholesterol contents of Turkish indigenous breeds showed differences, and these differences may be used for alternative lamb meat production for the consumer.

Low incubation temperature successfully supports the in vitro bovine oocyte maturation and subsequent development of embryos.

OBJECTIVE: The aim of this study was to compare the effects of 36.5°C and 38.5°C incubation temperatures on the maturation of bovine oocytes and developmental competence of embryos. METHODS: In experiment 1, oocytes were maturated in bicarbonate-buffered TCM-199 for 22 hours in a humidified atmosphere of 5% CO2 in the air at either 36.5°C or 38.5°C and nuclear maturation status were determined. In experiment 2, in vitro fertilized oocytes were allocated randomly into synthetic oviductal fluid medium with or without a mixture of 1 mM L-glutathione reduced and 1,500 IU superoxide dismutase and cultured in a humidified atmosphere of 5% CO2, 5% O2, and 90% N2 in the air at 38.5°C for 8 days. RESULTS: There were no significant differences between incubation temperatures in terms of oocyte maturation parameters such as cumulus expansion, first polar body extrusion and nuclear maturation. Incubation temperatures during in vitro maturation had no effects on developmental competence of embryos, but supplementation of antioxidants increased (p< 0.05) developmental competence of the embryos. Blastocysts from oocytes matured at 38.5°C had comparatively higher inner cell mass, but low overall and trophectoderm cell numbers (p<0.05). CONCLUSION: The results of present study showed that maturation of bovine oocytes at 36.5°C may provide a suitable thermal environment for nuclear maturation and subsequent embryo development.

Genome-wide identification and expression profiling of EIL gene family in woody plant representative poplar (Populus trichocarpa).

This study aimed to improve current understanding on ethylene-insensitive 3-like (EIL) members, least explored in woody plants such as poplar (Populus trichocarpa Torr. & Grey). Herein, seven putative EIL members were identified in P. trichocarpa genome and were roughly annotated either as EIN3-like sequence associated with ethylene pathway or EIL3-like sequences related with sulfur (S)-pathway. Motif-distribution pattern of proteins also corroborated this annotation. They were distributed on six chromosomes (chr1, 3, 4 and 8-10), and were revealed to encode a protein of 509-662 residues with nuclear localization. The presence of ethylene insensitive 3 (EIN3; PF04873) domain (covering first 80-280 residues from N-terminus) was confirmed by Hidden Markov Model-based search. The first half of EIL proteins (∼80-280 residues including EIN3 domain) was substantially conserved. The second half (∼300-600 residues) was considerably diverged. Additionally, first half of proteins harbored acidic, proline-rich and glutamine-rich sites, and supported the essentiality of these regions in the transcriptional-activation and protein-function. Moreover, identified six segmental and one-tandem duplications demonstrated the negative or purifying selective nature of mutations. Furthermore, expression profile analysis indicated the possibility of a crosstalk between EIN3- and EIL3-like genes, and co-expression networks implicated their interactions with very diverse panels of biological molecules.

Isolation of a transcription factor DREB1A gene from Phaseolus vulgaris and computational insights into its characterization: protein modeling, docking and mutagenesis.

A transcription factor DREB1A (dehydration-responsive element-binding 1A) gene was amplified and sequenced from the common bean (Phaseolus vulgaris). PvDREB1A had a 777 base pairs (bp) open reading frame encoding a protein of 225 residues. The protein sequence contained a conserved DNA-binding AP2 domain of about 60 residues and a nuclear localization signal (NLS) at N-terminus site. PvDREB1A demonstrated high homology with other DREB1 members only in AP2 domain and NLS site. The phylogenetic distribution of different DREB members showed three main groups as DREB1-3 and PvDREB1A was a member of DREB1 group. Homology modeling and secondary structure analyses revealed that PvDREB1A AP2 domain was packed into the three-stranded antiparallel beta sheets (ß1-3) and an alpha helix (α1) almost parallel to these beta sheets. Moreover, DNA-binding AP2 domain of PvDREB1A and GCC-box containing double helix DNA were docked. The docking analysis showed that PvDREB1A AP2 domain could bind to the major groove of the DNA by three-stranded antiparallel beta sheets, with residues Gly86 or Thr87 in ß1-sheet and Arg63 or Arg64 in ß3-sheet. The docked complex also indicated that AP2 domain has a preferential for the binding of GCC stretches in the double helix DNA. A total of 36 reliably estimated hot spots residues were identified with high mutability grade but none of these residues was essential for the protein function since they are located at outside the DNA-binding AP2 domain of PvDREB1A.

Genome-wide identification and expression analysis of sulfate transporter (SULTR) genes in potato (Solanum tuberosum L.).

MAIN CONCLUSION: Solanum tuberosum genome analysis revealed 12 StSULTR genes encoding 18 transcripts. Among genes annotated at group level ( StSULTR I-IV), group III members formed the largest SULTRs-cluster and were potentially involved in biotic/abiotic stress responses via various regulatory factors, and stress and signaling proteins. Employing bioinformatics tools, this study performed genome-wide identification and expression analysis of SULTR (StSULTR) genes in potato (Solanum tuberosum L.). Very strict homology search and subsequent domain verification with Hidden Markov Model revealed 12 StSULTR genes encoding 18 transcripts. StSULTR genes were mapped on seven S. tuberosum chromosomes. Annotation of StSULTR genes was also done as StSULTR I-IV at group level based mainly on the phylogenetic distribution with Arabidopsis SULTRs. Several tandem and segmental duplications were identified between StSULTR genes. Among these duplications, Ka/Ks ratios indicated neutral nature of mutations that might not be causing any selection. Two segmental and one-tandem duplications were calculated to occur around 147.69, 180.80 and 191.00 million years ago (MYA), approximately corresponding to the time of monocot/dicot divergence. Two other segmental duplications were found to occur around 61.23 and 67.83 MYA, which is very close to the origination of monocotyledons. Most cis-regulatory elements in StSULTRs were found associated with major hormones (such as abscisic acid and methyl jasmonate), and defense and stress responsiveness. The cis-element distribution in duplicated gene pairs indicated the contribution of duplication events in conferring the neofunctionalization/s in StSULTR genes. Notably, RNAseq data analyses unveiled expression profiles of StSULTR genes under different stress conditions. In particular, expression profiles of StSULTR III members suggested their involvement in plant stress responses. Additionally, gene co-expression networks of these group members included various regulatory factors, stress and signaling proteins, and housekeeping and some other proteins with unknown functions.

Fattening performance, slaughter, carcass and meat quality traits of Karayaka lambs.

In order to verify the fattening performance, slaughter and carcass characteristics and to investigate the changes in some meat quality traits of Karayaka lambs weaned at 3 months of age, 39 lambs (23 males and 16 females) were used as experimental animals. The lambs were fed a concentrate mixture and alfalfa hay (120 and 168 g crude protein and 2,700 and 1,951 ME/kg, respectively) for a period of 60 days of fattening period. Male lambs were superior (p < 0.05) to female lambs in terms of daily weight gain (270.4 vs. 205.4 g; SEM = 9.46), hot and cold carcass weights (16.7 and 16.0 vs. 14.1 and 13.4 kg, respectively; SEM = 0.35), intra-muscular fat ratios (1.9% vs. 2.5%; SEM = 0.12) and dripping loss of semitendinosus muscle 3 days postmortem (8.1% vs. 10.2%; SEM = 0.36). The relative weights of some organs, the meat quality traits (pH, cooking loss, shear force, CIELab colour characteristics) and proximate analyses (dry matter, protein and ash) of longissimus dorsi and semitendinosus muscle samples from lambs were not affected by sex (p > 0.05). Dripping loss, pH and colour characteristics were affected by storage time (p < 0.05). These results provide a basic understanding of performance and meat quality of Karayaka sheep which may have potentials in improving sheep production using an indigenous sheep breed in Turkey.