Miracle-dz/UniFAR-FTUs huggingface dataset:
Avances en la Fisiología Digestiva y Nutrición de la Mojarra Tenguayaca Petenia splendida

La mojarra tenguayaca Petenia splendida es uno de los ciclidos nativos mas apreciados en la region sureste de Mexico, por lo que desde hace varios anos, se han realizado varias investigaciones que han permitido cerrar el ciclo de vida de la especie e iniciar su cultivo a escala experimental. Sin embargo, durante el cultivo se ha utilizado ampliamente el alimento desarrollado para las truchas, por lo cual el crecimiento es lento provocando que hasta la fecha el cultivo a escala comercial no sea rentable. En este sentido, los estudios relacionados con la determinacion de los requerimientos nutricionales y la evaluacion de la capacidad digestiva en los periodos de vida de la especie son de vital importancia para lograr el diseno de alimentos especificos que permitan optimizar el cultivo. Es asi que desde hace varios anos, se iniciaron los estudios en relacion al desarrollo de una linea de alimentos especificos que permitan fomentar el cultivo de esta especie en la region sureste de Mexico. El presente trabajo se enfoca en los estudios realizados por la Universidad Juarez Autonoma de Tabasco en colaboracion con varias instituciones donde se ha investigado la fisiolologia digestiva durante la ontogenia inicial aplicando tecnicas histologicas, bioquimicas y moleculares. Nuestros resultados muestran que esta especie tiene un patron de desarrollo similar al de otros ciclidos con un desarrollo precoz del sistema digestivo y la aparicion temprana de las enzimas digestivas. La caracterizacion de las proteasas digestivas permitio determinar que esta especie presenta habitos alimenticios carnivoros; al estudiarse diferentes ingredientes proteinicos por medio de la tecnica de pH-STAT, se logro determinar que los mejores ingredientes para la alimentacion de los juveniles fueron la harina de pescado, harina de jaiba, harina de cerdo, entre otras. Esto se corroboro ya que el requerimiento de proteinas es de 45.1 %, mientras que el requerimiento de lipidos es de 15%. Por su parte, la sustitucion de harina de pescado con gluten de trigo es posible hasta en un 25%, aunque es necesario estudiar otros ingredientes que permitan no depender del uso de harina y aceite de pescado para la alimentacion de P. splendida.
DYNAMICS OF SEED BANK AND WEED FLORA IN RAIN-FED WHEAT AS AFFECTED BY DIFFERENT TILLAGE SYSTEMS

Weed seeds represent the main source of annual weed invasion and establishes a weed seed bank in agricultural production and development system (Montaldo, 1995). The weed seed bank reproduces the history of weeds, weeds control and is an indicator of future competition between weeds and crops. The addition of new seeds into the seed bank is affected by how effective the weed control method is. Variations in the weed seed bank are due to direct effect of tillage practices on the existing weed seeds in soil and the plenty of seed producing weeds. Tillage practices influence the weed seed bank where some weed seeds are encouraged to germinate (Roberts and Feast, 1972), although other weed seeds are buried and remain viable in the deep soil for a long period of time (Roberts and Feast, 1972; Mohler and Galford, 1997). Tillage practices work as a filter that influences weed species and weed seed distribution in the soil seed bank. Research show changes in weed species composition as a significance of tillage practices (Cussans, 1975). Different tillage systems can affect the weed species composition of agricultural plant populations varying from traditional tillage to conservation tillage (Ball and Miller, 1993). Dorado et al. (1999) studied the weed seed bank response to crop rotation and tillage i.e. moldboard plow and NT (no-tillage) and they found largest and most diverse weed seed bank in no-tillage system but, according to Wrzesinska et al. (2013) weed species composition and diversity of soil seed bank after ploughing and direct drilling (DD) was same, although in NT treatment this number was lower by three species. Weed control is becoming harder in conservation tillage because of decrease or complete removal of mechanical operations and for this reason, it is important to gain advanced research information about the soil weed seed bank (Forcella et al., Pak. J. Agri. Sci., Vol. 54(4), 907-917; 2017 ISSN (Print) 0552-9034, ISSN (Online) 2076-0906 DOI: 10.21162/PAKJAS/17.5023 http://www.pakjas. com.pk
Uremic Retention Solutes

This chapter will address the broad subject of uremic retention solutes (URS), also known as uremic toxins. Some of these solutes had been recognized for decades, and in 1999 when the European Uremic Toxin Work Group was established, a fuller description of URS was presented. The group sought to identify and characterize the solutes in the serum of patients with impaired glomerular filtration, in order to explore their role in the pathogenesis of the uremic syndrome and improve current therapeutic options. This chapter will review the different types of URS, as well as the adverse effects associated with their accumulation. It will also cover current and potential therapeutic approaches to reduce their levels.
Cloning and Functional Analysis of three Cold Regulated CBF Genes in the Overwintering Crucifer Boechera stricta

In this research, we isolated three CBF (C-repeat-Binding Factors) genes from two genotypes of Boechera stricta with contrasting freezing tolerance and characterized their structure and expression patterns in response to cold treatment. An amino acid sequence comparison revealed that the CBF genes in B. stricta showed high conservation in the AP2 domain and PKKP/RAGR motif like other cold adaptable Brassicaceae. The pairwise sequence alignment of the CBF genes isolated from two genotypes of B. stricta showed non-synonymous mutations in CBF 2 and 3. Gene expression analysis demonstrated that CBF genes in B. stricta have expression patterns similar to CBFs in A. thaliana in response to cold treatment, while differential expression at the molecular level in CBF and COR genes was presented between two genotypes of B. stricta. Our results suggest that signal transduction of three CBF genes can be one of the central pathways in the development of freezing tolerance in B. stricta.
Systemic resistance induction by plant growth promoting rhizobacteria (pgpr) in solanum tuberosum

Currently many studies have been made on the use of natural products as substitutes for chemical control, due to possible ecological and economic advantages that many of these compounds offer, especially in crop protection. Many natural products have compounds with the ability to stimulate defense mechanisms in plants; defense reactions to the nearest tissue infection are restricted in some cases, resistance induction is associated to the expression of some defense genes, such as those coding for proteins linked to the pathogenesis. For example phenylalanine ammonia lyase and synthesis phytoalexins are highly toxic compounds to the pathogen. On the other hand the increase of peroxidases, can increase the mechanical strength of the host cells walls, inhibiting or possibly restricting a pathogen invasion. The objective of this study was to compare the effect of the PGPR consortium at 6, 12 and 24 hours after application, against Fusarium oxysporum and Rhizoctonia solani, determined by leaf tissue, quantification of protein and enzyme activities of phenylalanine ammonia lyase and peroxidase. The results presented in this paper clearly demonstrated the potential of the PGPR consortium strains to activate resistance against F. oxysporum or R. solani.
Effect of biochar on soil structure – review

Soil structure is usually defined as the spatial arrangement of soil particles and soil voids (i. e. soil pores), which may also be defined as the spatial distribution of soil properties. Soil structure includes the physical habitat of soil living organisms, and controls many important physical, chemical and biological soil functions and associated ecosystem services (Dexter, 1988). However, soil structure is more than only the physical arrangement of particles and pores and includes structural stability (i. e. the ability to resist endogenous factors or stresses) and structural resilience (i. e. the ability of recover upon stress removal) (Kay and Angers, 2001). Soil aggregation is responsible for soil structure and it is fundamental for soil to function as well as agricultural productivity.
Comparison of two pressurized irrigation systems on lettuce seedlings production

Automatized irrigation systems under nursery conditions have become an essential tool to satisfy rationally the water needs for plants without forgetting the sustainability aspects. The present study aimed to evaluate two sprinkler irrigation systems under nursery conditions: one with fixed laterals (fixed system) and another with self-propelled laterals (mobile system) and study the effect of their use on the behavior of tree lettuce seedlings production. The experiment was conducted on a greenhouse with a polystyrene (PVC) plastic film coverture and laterals closed with 60% plastic screen. The statistical design used was a 2x3 completely randomized factorial with four replicates, and the results analyzed using the Tukey test. To compare the lettuce seedlings behavior under both irrigation systems it was evaluated the leaves number, seedling's height, root length and fresh and dry mass of the aerial and root part of the plant. The Christiansen uniformity coefficient (CUC) and the water distribution coefficient (WDC) for the fixed irrigation system were considered adequate and for the self-propelled laterals system (mobile system) they were considered excellent. The volume of water used with the fixed system was 109.12% higher than with the self-propelled system. The lettuce seedlings irrigated with the self-propelled system had a growth, production and a seedling quality statistically superior than when irrigated with the fixed system. Independent of the irrigation system used, the Elizabeth lettuce cultivar had a greater seedling behavior. According with the results obtained, it is recommended the use of the self-propelled irrigation system (mobile system) on the production of lettuce seedlings.
Habitat fragmentation, not habitat loss, drives the prevalence of blood parasites in a Caribbean passerine

Habitat destruction due to human land-use activities is well recognized as a central threat to biodiversity. However, there is still debate about the relative influence of its two components, habitat loss and habitat fragmentation, mostly because few studies have been able to disentangle their respective effects. We studied mechanisms by which habitat destruction might influence the prevalence of vector-transmitted haemosporidian blood parasites of the genera Plasmodium and Haemoproteus infecting the Lesser Antillean bullfinch Loxigilla noctis on the Caribbean islands of Guadeloupe and Martinique. Starting from a large set of environmental descriptors (including metrics reflecting habitat loss, habitat fragmentation and landscape heterogeneity; as well as other variables not linked to habitat destruction, such as climatic conditions), we used PLS regression analyses to determine which variables were driving parasite prevalence on the islands. Our results showed that variables related to forest destruction were much more influential than other factors for all parasites analyzed on both islands. Remarkably, the effects documented were almost exclusively due to forest fragmentation, as opposed to habitat loss. This positive effect of forest fragmentation on blood parasite prevalence is proposed to happen through its effects on insect vectors and/or host biology. Increased understanding of the role of habitat fragmentation as a driver of parasitic diseases can help limiting the risk of emergence and proliferation of wildlife pathogenic outbreaks and zoonosis through informed landscape planning.
Detection of biofilm producing coagulase positive Staphylococcus aureus from bovine mastitis, their pigment production, hemolytic activity and antibiotic sensitivity pattern

A total of 50 milk samples of bovine mastitis origin were examined aiming at detecting and characterizing biofilm producing coagulase positive Streptococcus aureus (CPSA). The bacterium was isolated from all the samples, in which 35 isolates were positive in coagulase test. The microtiter-plate test revealed that among 35 CPSA isolates, 15 were in vitro biofilm producer of which 10 were weakly adherent and 5 were moderately adherent to the inert surface, which is the first report in Bangladesh. Among the CPSA, 9(25.71%), 18(51.43%) and 8(22.86%) produced golden yellow, yellow and white colonies, respectively. A figure of 71.43% CPSA produced beta-hemolysis on blood agar. Antibiotic sensitivity tests of CPSA demonstrated that spiramycin and gentamicin inhibited the growth of 35(100%) and 32(91.43%) isolates, respectively. On the other hand, penicillin-G, amoxycillin, sulphamethoxazole, oxytetracycline, streptomycin and ciprofloxacin showed 17.14, 62.86, 62.86, 57.14, 74.28 and 85.71% inhibition of the CPSA isolates, respectively.
The chromosome complement of the hybrid Bacillus whitei complex (Insecta phasmatodea). I : The paleo- and neo-standard karyotypes

The thelytokous hybrid Bacillus whitei (2n=35, XX female) endemic to Southeastern Sicily, is clearly derived from B. rossius×grandii, but a variety of cytotypes have been found in these parthenogens. The most widespread, standard karyotype perfectly fits the suggested hybrid derivation except for the fourth metacentric element, certainly deriving from B. rossius, in which, however, nowadays invariably shows a corresponding acrocentric chromosome; on the other hand the acrocentric “modern” element has been found in hybridogenetic strains of B. whitei, very recently discovered among clonal ones. Linking together reproductive biology and geographical distribution of the “metacentric” and “acrocentric” standard karyotypes, two hybridization events between B. grandii and either a “paleo” or “neo” B. rossius, respectively, are here suggested.C-positive satellites and corresponding Ag-NOR, are found on a wide array of chromosomes, mostly reflecting those of both parental species, but also on new locations. The high dinamics of rDNA cistrons, mainly evidenced in the B. rossius genome, makes NORs not entirely reliable as long-term cytotaxonomical markers, but rather useful in short-term comparisons.
Greater potentiality of sperm membrane bound fertility associated antigen to withstand oxidative stress ensuing improved sperm function of cryopreserved bull spermatozoa

Fertility associated antigen (FAA) are more abundant in semen of bulls with high fertility. The objective was to investigate relationship of FAA, either membrane bound and/or in seminal plasma, with that of markers of oxidative stress, mitochondrial activity and acrosome integrity of live cells, in cryopreserved spermatozoa. Grouping of bulls was done by electrophoretic profiling of proteins from seminal plasma (SP), and sperm membrane (SM), based on presence/absence of the FAA in SP and/or SM or both. Group I had detectable FAA in both SP and SM; Group II, FAA detected only in SM; Group III, detectable FAA only in SP and Group IV, undetectable FAA in both SP and SM. At post-thaw stage, the lipid peroxide levels were significantly lower (p Lass Than 0.05) and the activity of primary free radical scavengers (superoxide dismutase and catalase) was significantly higher (p Lass Than 0.05) in Groups I and II. Correspondingly, Group I and II showed significantly higher (p Lass Than 0.05) per cent of acrosome intact live spermatozoa and sperm cells with functionally active mitochondria. Collectively, this study showed that the presence of FAA on the sperm membrane is related to greater protection against oxidative stress ensuing improved acrosome intact live-sperm cells with functional mitochondria.
Net cover color influence nutritive quality of African nightshade and spiderplant

ABSTRACT Indigenous leafy vegetables play a major role in strategies to attain food and nutritional security for African households. However, the potential of these vegetables in meeting the nutritional requirements have not been adequately exploited. This study assessed effects of shadenets on nutritive value of African indigenous leafy vegetables. The vegetables African nightshade (Solanum scabrum Mill.) and spiderplant (Cleome gynandra L.) and net covers colored white, gray, blue, and yellow, with unnetted plants as a control were used. From the 7th week after sowing (spiderplant) and transplanting (African nightshade) and at 2-week intervals nutritive quality variables were determined. Compared to open field, white net produced higher leaf β-carotene at 13 weeks after planting by 6% and 17% for African nightshade and spiderplant, respectively. Use of blue net cover reduced leaf vitamin C content by 94.5% and 79% in African nightshade and spiderplant, respectively, compared to open field at 15 weeks after planting. Higher leaf calcium was consistently recorded for plants grown under yellow net cover for African nightshade and white nets for spiderplant; but was reduced under blue net for both species on most sampling dates. Leaf iron content was maximized under yellow net cover for both crops. Use of net covers reduced leaf crude fiber content compared to open field; high leaf phenolic content was obtained in crops grown under white net for both vegetables. The crop responses were attributed to spectral quality, light intensity, and environmental changes to which the crops were subjected. The different colored agronet covers differentially influenced crop leaf nutritive quality.
Recent fire activity in the boreal eastern interior of North America is below that of the past 2000 yr

The North American boreal forest has been developing since the end of the last glaciation approximately 10,000 yr ago. With climate warming and human occupation, it is anticipated that ﬁ re dan-ger, ignition, and activity will be increasing, compromising forests ’ bene ﬁ ts for generations to come. In this study, we show, however, that a century of rapid climate changes and human densi ﬁ cation has had the opposite effect in the boreal eastern interior of the North American continent, reducing biomass burning to values below two millennia of historical levels. A multi-millennial ﬁ re history was reconstructed for eight forested landscapes from the Lake of the Woods Ecoregion (LWE) located at the boreal – prairie ecotone. Fire history was reconstructed using a combination of archival (period 1920 – 2010), tree-ring (stand initiations and ﬁ re scars: period 1690 – 2010), and lake sediment charcoal (2500 BP to present) records. The archival record revealed recent large ﬁ res ( > 200 ha) in 1948, 1980, and 1988. An additional 19 ﬁ res were identi ﬁ ed by the ﬁ re-scar record. Fire events in 1805, 1840, 1863, and the 1890s were identi ﬁ ed in numerous locations around multiple lakes suggesting that they were of large extents. In accordance with the tree-ring record, the charcoal accumulation rate (CHAR) peak record generally identi ﬁ ed the major ﬁ res but tended to lag from the tree-ring records by several decades. Within LWE, the long-term charcoal record revealed that CHAR was higher for each lake in the earlier portion of the record including the warm Medieval Climate Anomaly (AD (cid:1) 900 to AD 1000), followed by a progressive decrease toward the cool Little Ice Age period. This decline was abruptly interrupted in the mid- to late 19th century with large synchronized ﬁ res, also reported over western and central North America, and resumed approximately four decades later. Fire disturbance level is today below the historical range, despite the accentuated climate warming. Aging of the forest landscape may create biodiversity loss notably in ﬁ re-adapted species while at the same time setting the tone for major ﬁ res in upcoming decades if no action is taken for managing fuels.
Genome-Wide Identification of HES1 Target Genes Uncover Novel Roles for HES1 in Pancreatic Development

Notch signalling and the downstream effector HES1 is required for multiple pancreatic cell fate choices during development, but the direct target genes remain poorly characterised. Here we identify direct HES1 target genes on a genome-wide scale using ChIP-seq and RNA-seq analyses combined with human embryonic stem cell (hESC) directed differentiation of CRISPR/Cas9-generated HES1-/- mutant hESC lines. We found that HES1 binds to a distinct set of endocrine-specific genes, a set of genes encoding basic Helix-Loop-Helix (bHLH) proteins not normally expressed in the pancreas, genes in the Notch pathway, and the known HES1 target NEUROG3. RNA-seq analysis of wild type, HES1-/-, NEUROG3-/-, and HES1-/-NEUROG3-/- mutant hESC lines allowed us to uncover NEUROG3-independent, direct HES1 target genes. Among the HES1 bound genes that were derepressed in HES1-/-NEUROG3-/- cells compared to NEUROG3-/- cells, we found members of the endocrine-specific gene set, the Notch pathway genes DLL1, DLL4, and HEY1, as well as the non-pancreatic bHLH genes ASCL1 and ATOH1. We also found a large number of transcripts specific to the intestinal secretory lineage to be increased in HES1-/-NEUROG3-/- cells. Together, our data reveal that HES1 employs a multi-layered control of endocrine differentiation, controls Notch ligand expression independent of NEUROG3, and prevents initiation of ectopic intestinal transcriptional programmes in pancreas progenitors.
Gene expression profiles of rectal cancers with mutant or wild-type Kras.

414 Background: The Kras oncogene is one of the most common mutations in colorectal cancer. Kras mutations are associated with increased tumor aggressiveness, poor response to selected targeted therapies, and reduced patient survival. We have previously shown that rectal cancers carrying a Kras mutation were less likely to achieve a pathologic complete response to radiation compared to tumors with wild type Kras. Our objective was to compare the gene expression profiles of rectal cancers with mutant and wild type Kras to identify genes that could be related to the Kras–dependent aggressive phenotype. Methods: Pretreatment biopsy tissue was collected from 120 patients with stages I, II and III rectal cancer treated in two prospective trials (NCT00335816 and NCT00114231). DNA and total RNA were extracted from microdissected cancer cells. Mutations in codons 12, 13, and 61 of the Kras gene were detected by pCR. 50ng of total RNAs were amplified to generate cDNA libraries using Ovation FFPE WTA System (NuGEN .
Engineering of secondary metabolite production in streptomycetes

Bacteria of the order Actinomycetales are one of the most important sources of bioactive natural products, which are the source of many drugs. However, many of them still lack efficient genome editing methods, some strains even cannot be manipulated at all. This restricts systematic metabolic engineering approaches for boosting known and discovering novel natural products. In order to facilitate the genome editing for actinomycetes, we developed a CRISPR-Cas9 toolkit with high efficiency for actinomyces genome editing. This basic toolkit includes a software for spacer (sgRNA) identification, a system for in-frame gene/gene cluster knockout, a system for gene loss-of-function study, a system for generating a random size deletion library, and a system for gene knockdown. For the latter, a uracil-specific excision reagent (USER) cloning technology was adapted to simplify the CRISPR vector construction process. The application of this toolkit was successfully demonstrated by perturbation of genomes of Streptomyces coelicolor A3(2) and Streptomyces collinus T€ u 365. The CRISPR-Cas9 toolkit and related protocol described here can be widely used for metabolic engineering of actinomycetes.