Miracle-dz/UniFAR-FTUs huggingface dataset:
Physical and Functional Constraints on Viable Belowground Acquisition Strategies

Since their emergence onto land, terrestrial plants have developed diverse strategies to acquire soil resources. However, we lack a framework that adequately captures how these strategies vary among species. Observations from around the world now allow us to quantify the variation observed in commonly-measured fine-root traits but it is unclear how root traits are interrelated and whether they fall along an “economic” spectrum of acquisitive to conservative strategies. We assessed root trait variation and mycorrhizal colonization rates by leveraging the largest global database of fine-root traits (the Fine-Root Ecology Database; FRED). We also developed a heuristic model to explore the role of mycorrhizal fungi in defining belowground exploration efficiency across a gradient of thin- to thick-diameter roots. In support of the expectations of the “root economic spectrum,” we found that root diameter was negatively related to specific root length (Pearson’s r=-0.76). However, we found an unexpected negative relationship between root diameter and root tissue density (Pearson’s r = -0.40), and we further observed that root nitrogen content was largely unrelated to other economic traits. Mycorrhizal colonization was most closely associated with root diameter (Pearson’s r = 0.62) and was unrelated to root tissue density and root nitrogen. The heuristic model demonstrated that while thinner roots have inherently greater capacity to encounter soil resources based on higher surface area per unit mass, the potential for increased associations with mycorrhizal fungi in thicker roots, combined with greater hyphal growth, can result in equally acquisitive strategies for both thin- and thick roots. Taken together, our assessments of root trait variation, trade-offs with mycorrhizal fungi, and broader connections to root longevity allowed us to propose a series of fundamental constraints on belowground resource acquisition strategies. Physical tradeoffs based on root construction (i.e., economic traits) and functional limitations related to the capacity of a root to encounter and acquire soil resources combine to limit the two-dimensional belowground trait space. Within this trait space there remains a diversity of additional variation in root traits that facilitates a wide range of belowground resource acquisition strategies.
The inclusion of Leucaena diversifolia in a Colombian beef cattle production system: An economic perspective

Keynote paper presented at the International Leucaena Conference, 1‒3 November 2018, Brisbane, Queensland, Australia.Despite the great potential of legumes in cattle production, their adoption and use throughout the tropical world remain limited. While this is largely attributed to factors such as limited knowledge or access to credit, lack of information on the viability and profitability of the technology can influence the adoption decision. The objective of this study is to evaluate the profitability of including Leucaena diversifolia, accession ILRI 15551 in a Colombian beef cattle production system. For this purpose, we use data from a grazing experiment comparing a grass-legume association (Brachiaria hybrid cv. Cayman and L. diversifolia) with a grass monoculture (cv. Cayman) in the Valle del Cauca department, both with the purpose of beef production. We use a discounted cash flow model, developed with the simulation software @Risk, which considers inherent risk and uncertainty factors in these types of rural investment projects, under three different pasture degradation scenarios. The results indicate that the inclusion of L. diversifolia is financially profitable and substantially improves the associated risk and performance indicators. Profitability indicators increased in a range of 15‒110%, and the probability of suffering economic losses decreased from 72% to 0%. The results were directly related to the increases in animal productivity (49%) and efficiency resulting from including the legume. This work shows that L. diversifolia has significant potential to increase both animal production and profitability, which is conducive to the sustainable intensification of beef production in grazing systems.
Complete mitochondrial genome and the phylogenetic position of the common cuckoo, Cuculus canorus bakeri (Aves: Cuculiformes)

Abstract The complete mitochondrial genome of Common Cuckoo (Cuculus canorus bakeri) is determined in this study and was deposited in Genbank with accession number MN067867. The length of the mitogenome is 17,457 base pairs (bp) including 13 protein-coding genes (PCGs), 22 transfer (t RNA) RNA genes, two ribosomal RNA (r RNA) genes, one control region (CR) and one short pseudo-control region. The structure is similar to mitochondrial genome of other Cuculiforme species. Phylogenetic tree shows that C. canorus bakeri is closely related to C. poliocephalus. The study has provided useful information for further studies on the evolution, genetic diversity, and phylogenetic relationships in Common Cuckoo.
Causes and consequences of facultative sea crossing in a soaring migrant

Studying the causes and consequences of route selection in animal migration is important for understanding the evolution of migratory systems and how they may be affected by environmental factors at various spatial and temporal scales. One key decision during migration is whether to cross “high transport cost” areas, or to circumvent them. Soaring birds may face this choice when encountering waterbodies where convective updrafts are weak or scarce. Thus, crossing waterbodies requires flying using metabolically costly flapping flight, while circumnavigating them over land permits energetically cheap soaring. We tested how several atmospheric factors (e.g., wind, thermal uplift) and geographic, seasonal and state-related factors (sex and age) affected route selection in migrating white storks (Ciconia ciconia). We used 196 GPS tracks of 70 individuals either crossing or circumventing the north-easternmost section of the Mediterranean Sea, over Iskenderun Bay in southern Turkey. We found that westward and southward winds promoted a cross-bay journey in spring and autumn, respectively, acting as tailwinds. Also, overall weaker winds promoted a sea crossing in spring. Sea crossing was associated with flapping flight and higher values of Overall Dynamic Body Acceleration (ODBA) and resulted in higher groundspeed than travel over land. Notably, daily travel distances of spring migrants crossing the bay when returning to their nesting locations were 60 kilometres and 2 hours longer than those of land-detouring birds. No such benefit was found during autumn. Our findings confirm that atmospheric conditions can strongly affect bird route selection. Consequently, migration timing, speed and movement-related energy expenditure differed considerably between the two migratory seasons and the two route choices, highlighting a time-energy trade-off in the migration of white storks.
Morphology and molecules reveal two new species of Porites (Scleractinia, Poritidae) from the Red Sea and the Gulf of Aden

Two new reef coral species, Porites farasani sp. nov. and Porites hadramauti sp. nov. (Scleractinia, Poritidae), are described from the Red Sea and the Gulf of Aden. Porites farasani sp. nov. only occurs in the Farasan Islands in the southern Red Sea, while P. hadramauti sp. nov. has been collected in the Yemen Hadramaut region in the Gulf of Aden. Both species presented striking in situ differences with respect to other Porites species, and were characterized by small encrusting colonies and unusual polyp colouration. In order to test the genetic distinctiveness of P. farasani sp. nov. and P. hadramauti sp. nov. between each other and with respect to other representatives in the genus Porites, we investigated their evolutionary relationships with eight other morphological species of Porites occurring in the Red Sea and in the Gulf of Aden. Two DNA loci, the mitochondrial putative control region and the nuclear ribosomal ITS region, were sequenced, and three species delimitation approaches based on barcoding threshold (Automated Barcoding Gap Discovery) and coalescence theory (Poisson-Tree process, Generalized Mixed Yule Coalescent) were applied. Phylogenetic and species delimitation analyses were overall concordant, resolving P. farasani sp. nov. and P. hadramauti sp. nov. as two divergent but closely related lineages. Of the other morphologically defined Porites species, three were genetically differentiated (P. rus, P. columnaris and P. fontanesii), but five were genetically indistinguishable. The discovery of two regional endemics confirms the importance of the Red Sea and the Gulf of Aden as regions of high biodiversity and suggests the need for an integration of genome-wide molecular data with the re-evaluation of skeletal structures in the systematics of Porites.
Immune genes, IL1β and Casp9, show sexual dimorphic methylation patterns in the zebrafish gonads

There is a crosstalk between the immune and the reproductive systems in which sexual dimorphism is a common pattern in vertebrates. In the last years, epigenetics has emerged as a way to study the molecular mechanisms involved during gonadal development, which are responsible to integrate environmental information that contributes to assign a specific sexual phenotype (either an ovary or a testis). In the fish gonads, it is known of the existence of the reproduction-immune system interactions although the epigenetic mechanisms involved are far to be elucidated. Here, we used the zebrafish (Danio rerio) as a model to study the DNA methylation patterns of two well-known innate immune genes: IL1β and Casp9. DNA methylation levels were studied by a candidate gene approach at single nucleotide resolution and further, gene expression analysis were carried out. Results showed that there was clear sexual dimorphism in the DNA methylation levels of the two immune studied genes, being significantly higher in the testes when compared to the ovaries. In summary, and although much research is needed, here we present two potential candidates as epimarkers with forthcoming applications in the livestock and fish farming production, for example, in immune fish diseases or sexual control programs.
Beneficial effects of probiotic and phytobiotic as growth promoter alternative to antibiotic for safe broiler production

Objectives: Drug residues in poultry products could lead to the development of antibiotic-resistant bacteria as in any living animal and human alike. Extensive use of antibiotics in animals to promote growth rate, increase feed efficiency, and for prevention of intestinal infections has led to the development of resistant bacteria in the gastrointestinal tract. The present study was conducted to evaluate the effects of biological supplementation of probiotic, phytobiotic, and their combination over antibiotic on growth performance, microbial load, and hematological parameters in Broiler. Materials and methods: Sixty-five broiler chicken were divided into five groups (12 birds in each group), namely, group A (basal diet), group B (antibiotic, Renamycin 100®), group C (phytobiotic, Galibiotic®), group D (probiotic, Bio-Top®), and group E (combination, Galibiotic®+Galibiotic®) and five were sacrificed for baseline data on day 0. Results: Average final live weight gain was highest in group D (probiotic) than other groups. The feed conversion ratio was highest in group A and lowest in the probiotic group (group C). Blood samples were collected on 14th and 28th day for hematological studies. The mean hematology values regarding the total erythrocyte count, hemoglobin concentration, packed cell volume, and erythrocyte sedimentation rate differed significantly (p < 0.05) among groups. The pH of all the treatment groups was significantly decreased compared to the control group (p < 0.05) where group C was significantly (p < 0.05) lower than all other groups. Highest total viable cell count was observed in control (group A) and total coliform count in phytobiotic (group C) was significantly lower than in other treatment groups (p < 0.05). Conclusion: It may conclude that biological supplements have a significant positive impact on growth performance, hematological parameters, and gut microbial load in broiler chicken of which the probiotic showing the best effects. Supplementation of probiotic in feed could be one of the best candidates as an alternative to antibiotics as growth promoter for safe broiler production.
The complete chloroplast genome sequence of Melica scabrosa (Poaceae)

Abstract Melica scabrosa Trin. is an important forage grass of Poaceae, wildly distributed in the Northeast Asia to Qinghai-Xizang Plateau. The complete chloroplast genome sequence of M. scabrosa was obtained by de novo assembly using whole genome sequence data. The chloroplast genome is 134,889 bp in length, containing 80,560 bp in a large single copy (LSC), 12,706 bp in a small single copy (SSC) and 20,810 bp in a pair of inverted repeats (IRs). A total of 129 genes including 83 protein-coding genes and 38 structural RNA genes were identified. Phylogenetic analysis represented close relationship among Melica species. This chloroplast genome sequencing offers a useful resource for future genetics and phylogenetic studies.
Reproductive Cold Stress Tolerance in Sorghum F1 Hybrids is a Heterotic Trait

The sensitivity of sorghum to pre-flowering cold stress, resulting in reduced pollen viability and poor seed set, is a major constraint for expanding growing areas into higher altitudes and latitudes. Nevertheless, compared to juvenile cold tolerance, reproductive cold tolerance in sorghum has received much less attention so far, and very little is known about its inheritance in F1-hybrids. We have composed a representative factorial (n = 49 experimental F1-hybrids) for a comprehensive study on heterosis and combining ability for crucial tolerance traits as spikelet fertility (panicle harvest index), seed yield and pollen viability, using field trials in stress- and control environments in Germany and Mexico as well as climate chamber experiments. Our results indicate a heterotic and rather dominant inheritance of reproductive cold tolerance in sorghum, with strong effects of female general combining ability (GCA) on F1-hybrid performance in our material. These findings, together with the comparatively low contribution of specific combining ability (SCA) effects and high heritability estimates, suggest that robust and efficient enhancement of reproductive cold tolerance is feasible via hybrid breeding.
Estudios cromosómicos en especies de Turnera (Turneraceae)

En el presente trabajo se informa por primera vez el numero de cromosomas de 5 especies y 1 variedad de Turnera . Se confirman previos reported en 5 taxones . Los cariotipos de 16 taxones de Turnera se describen por primera vez. Los resultados del analisis de los cromosomas son los siguientes: T.weddelliana , 2n = 2x = 14 = 12m 2sm; T.pumilea , 2n = 2x = 14 = 10 m 4sm; T.hassleriana , 2n = 2x = 14 = 12m 2sm; T.chamaedryfolia , 2n = 2x = 26 = 16m + 8 sm + 2 st; T.caerulea , 2n = 2x = 1O = 8m + 2sm; T.concinna, 2n = 2x = 10 = 8 m + 2sm; T.krapovickasii, 2n = 2x = 10 = 8m + 2sm; T.grandiflora, 2n = 8x = 40 = 32m + 8sm; T. subulata, 2n = 2x = 10 = 8m + 2sm; T.grandidentata, 2n = 4x = 20 = 18m + 2sm; T.angustifolia, 2n = 6x = 30 = 26 m + 4sm; T.orientalis, 2n = 6x = 30 = 26 m +s 4 sm; T.ulmifolia, 2n = 6x = 30 = 24 m + 6sm; T.velutina, 2n = 6x = 30 = 28m + 2sm; T.aurelioi , 2n = 8x = 40 = 36 m + 4 sm y T.cuneiformis, 2n = 8x = 40 = 36 m + 4sm. Los cromosomas son de pequeno tamano. Las especies de la serie Salicifoliae y Leiocarpae (x = 7) tienen cromosomas que son mas pequenos que los de la serie Canaligerae (x = 5) y Papilliferae (x = 13). Todas las especies estudiadas tienen cariotipos simetricos. El diagrama de dispersion muestra que las especies con diferentes numeros basicos son perfectamente separadas. T.chamaedryfolia (x = 13) de la serie Papilliferae es el mas asimetrico, mientras que las especies de la serie Canaligerae son los mas simetricos. Las especies con x = 7 ocupan un lugar central en el diagrama.
The influence of larval growth rate on juvenile recruitment in Lake Erie walleye (Sander vitreus)

Growth-selective mortality as larvae can influence recruitment in marine fishes. Its importance in freshwater fishes, however, remains speculative. We quantified growth trajectories within annual cohorts (2011–2013) of Lake Erie walleye (Sander vitreus) and their relationship with recruitment. We hypothesized that selection against slow or fast growth would be associated with high mortality and poor recruitment, whereas weak or nonexistent growth-selective mortality co-occurring with fast growth would be associated with good recruitment. We used otoliths to reconstruct growth rates during the first 15 days of life from larvae collected during spring and juvenile recruits (survivors) collected during late summer. We documented growth-selective mortality during 2011 and 2013, which exhibited poor recruitment as expected. During 2012, growth selection was absent, but growth was slow when compared to historical averages, resulting in poor recruitment. Growth was also considered slow in 2011 and 2013, due to multiple interacting conditions. Our study indicates that the relationship among larval growth, mortality, and future recruitment is complex, highlighting the need for continued research into how larval processes affect recruitment dynamics in freshwater fishes.
Accuracy of serological tests for diagnosis of chronic pulmonary aspergillosis: A systematic review and meta-analysis

Chronic pulmonary aspergillosis (CPA) is a disease that benefits from cavities as after-effects of tuberculosis, presenting a high mortality rate. Serological tests like double agar gel immunodiffusion test (DID) or the counterimmunoelectrophoresis (CIE) test have been routinely used for CPA diagnosis in the absence of positive cultures; however, they have been replaced by enzyme-linked immunoassay (ELISA), with a variety of methods. This systematic review aims to compare the accuracy of the ELISA test with the reference test (DID and/or CIE) in CPA diagnosis. It was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyzes (PRISMA). The study was registered in PROSPERO under the registration number CRD42016046057. We searched the electronic databases MEDLINE (PubMed), EMBASE (Elsevier), LILACS (VHL), Cochrane library, and ISI Web of Science. Gray literature was researched in Google Scholars and conference abstracts. We included articles with patients or serum samples from CPA patients who underwent two serological tests: ELISA (index test) and IDD and/or CIE (reference test), using the accuracy of the tests as a result. Original articles were considered without a restriction of date or language. The pooled sensitivity, specificity, and summary receiver operating characteristic curves were estimated. We included 13 studies in the review, but only four studies were included in the meta-analysis. The pooled sensitivities and specificities were 0.93 and 0.97 for the ELISA test. For the reference test (DID and/or CIE), these values were 0.64 and 0.99. Analyses of summary receiver operating characteristic curves yielded 0.99 for ELISA and 0.99 for the reference test (DID and/or CIE). Our meta-analysis suggests that the diagnostic accuracy of ELISA is greater than that of the reference tests (DID and/or CIE) in early detection of CPA.
Hallmarks of frailty and osteosarcopenia in prematurely aged PolgAD257A/D257A mice: a preclinical model to test anabolic interventions

Frailty is a geriatric syndrome characterized by increased susceptibility to adverse health outcomes. One major determinant thereof is the gradual weakening of the musculoskeletal system and the associated osteosarcopenia. To improve our understanding of the underlying pathophysiology and, more importantly, to test potential interventions aimed at counteracting frailty suitable animal models are needed. Here, we report the relevance of a mouse model of accelerated aging (PolgA(D257A/D257A)) as a model for frailty and osteosarcopenia. The longitudinal assessment of the clinical mouse frailty index showed that PolgA(D257A/D257A) mice accumulated health deficits at a higher rate compared to wild type littermates (PolgA(+/+), WT). Concomitantly, PolgA(D257A/D257A) mice displayed progressive musculoskeletal deterioration such as reduced bone and muscle mass as well as impaired functionality thereof. Specifically, PolgA(D257A/D257A) had lower grip-strength and concentric muscle forces as well as reduced bone turnover as assessed by longitudinal micro-CT. In addition, PolgA(D257A/D257A) mutation altered the sensitivity to anabolic stimuli in skeletal muscle, muscle progenitors and bone. While, compared to WT, PolgA(D257A/D257A) caudal vertebrae were not responsive to a cyclic loading regime, PolgA(D257A/D257A) muscles were hypersensitive to eccentric contractions as well as leucine administration, shown by larger downstream signaling response of the mechanistic target of rapamycin complex 1 (mTORC1). However, myogenic progenitors cultured in vitro showed severe anabolic resistance to leucine and robust impairments in cell proliferation. Overall, PolgA(D257A/D257A) mutation leads to hallmarks of age-related frailty and osteosarcopenia as observed in humans and thus, provides a powerful model to better understand the relationship between frailty and the aging musculoskeletal system.
Effect of slow breathing on the blood pressure and the Valsalva ration in prehypertensive Indian students

The purpose of this study was to evaluate the effect of slow breathing and prehypertension (PHT) on cardiovascular and HRV variables and on the Valsalva ratio (VR). ECG was recorded in 39 normotensives and 35 prehypertensives at 5 min resting and slow breathing (6 breaths/min) stages to obtain HR, LF and HF power; SBP and DBP were recorded at the end of each stage. The Valsalva manoeuvre was performed after resting and slow breathing stages. Two-way repeated MANOVA was used to test for the effects of PHT and slow breathing. Stepwise multiple linear regression analysis was used to reveal predictors of HR, SBP and DBP. The normotensives and the prehypertensives demonstrated reduction of SBP during slow breathing (117.95 ± 0.73 vs. 115.18 ± 0.91 mm Hg, P = 0.001 and 130.09 ± 0.08 vs. 125.91 ± 0.96 mm Hg, P < 0.001, respectively). At rest, the VR was lower in prehypertensives (1.69 ± 0.05 vs. 1.87 ± 0.05, P = 0.009). After slow breathing, the VR increased significantly only in prehypertensives (P = 0.008), it was no longer different from that of normotensives (1.82 ± 0.06 vs. 1.90 ± 0.06, P = 0.346). The LnLF power, interpreted according to our hypothesis described previously as sympathoinhibition, increased in both groups. Slow breathing reduced SBP in normotensives and prehypertensives as a result of an increase in sympathoinhibition in both groups and VR, considered as a surrogate marker of the baroreflex activity, in prehypertensives.