Miracle-dz/UniFAR-FTUs huggingface dataset:
Mrub_2120, Mrub_2121, Mrub_2122, Mrub_2123 and Mrub_2124 are orthologs of E. coli genes b3458, b3457, b3456, b3455 and b3454, respectively, and make up an operon that codes for the branched-chain amino acid ABC transporter in Meiothermus ruber DSM 1279

In this project we investigated the biological function of the genes Mrub_2120, Mrub_2121, Mrub 2122, Mrub_2123 and Mrub_2124 (KEGG map number 02010). We predict these genes encode components of a branched-chain amino acid ATP Binding Cassette (ABC) transporter: 1) Mrub_2120 (DNA coordinates 2169247-2170416 on the reverse strand) encodes the branched-chain amino acid binding protein that is localized to the periplasm; 2) Mrub_2121 (DNA coordinates 2170433.2171353 on the reverse strand) encodes the first TMD; 3) Mrub_2122 (DNA coordinates 2171365.2172279 on the reverse strand) encodes the second TMD; 4) Mrub_2123 (DNA coordinates 2172276.2173028 on the reverse strand) encodes the first NBD; 5) Mrub_2124 (DNA coordinates 2173025.2173735 on the reverse strand) encodes the second NBD. This branched-chain amino acid transport system has been found in E. coli K12 MG1655 which was used as the model organism in this study. The predicted homologs of Mrub_2120, Mrub_2121, Mrub_2122, Mrub_2123 and Mrub_2124, are livK, livH, livM, livG and livF, respectively. Together, these genes form an operon encoding for an ABC transporter that selectively transports branched-chain amino acids across the intracellular plasma membrane of bacteria. This project is part of the Meiothermus ruber genome analysis project, which predicts gene function using the bioinformatics tools collected under the umbrella of the Guiding Education through Novel Investigation–Annotation Collaboration Toolkit (GENI-ACT).
Complete assembly of Escherichia coli ST131 genomes using long reads demonstrates antibiotic resistance gene variation within diverse plasmid and chromosomal contexts

The incidence of infections caused by extraintestinal Escherichia coli (ExPEC) is rising globally, which is a major public health concern. ExPEC strains that are resistant to antimicrobials have been associated with excess mortality, prolonged hospital stays and higher healthcare costs. E. coli ST131 is a major ExPEC clonal group worldwide with variable plasmid composition, and has an array of genes enabling antimicrobial resistance (AMR). ST131 isolates frequently encode the AMR genes blaCTX-M-14/15/27, which are often rearranged, amplified and translocated by mobile genetic elements (MGEs). Short DNA reads do not fully resolve the architecture of repetitive elements on plasmids to allow MGE structures encoding blaCTX-M genes to be fully determined. Here, we performed long read sequencing to decipher the genome structures of six E. coli ST131 isolated from six patients. Most long read assemblies generated entire chromosomes and plasmids as single contigs, contrasting with more fragmented assemblies created with short reads alone. The long read assemblies highlighted diverse accessory genomes with blaCTX-M-15, blaCTX-M-14 and blaCTX-M-27 genes identified in three, one and one isolates, respectively. One sample had no blaCTX-M gene. Two samples had chromosomal blaCTX-M-14 and blaCTX-M-15 genes, and the latter was at three distinct locations, likely transposed by the adjacent MGEs: ISEcp1, IS903B and Tn2. This study showed that AMR genes exist in multiple different chromosomal and plasmid contexts even between closely-related isolates within a clonal group such as E. coli ST131. Importance Drug-resistant bacteria are a major cause of illness worldwide and a specific subtype called Escherichia coli ST131 cause a significant amount of these infections. ST131 become resistant to treatment by modifying their DNA and by transferring genes among one another via large packages of genes called plasmids, like a game of pass-the-parcel. Tackling infections more effectively requires a better understanding of what plasmids are being exchanged and their exact contents. To achieve this, we applied new high-resolution DNA sequencing technology to six ST131 samples from infected patients and compared the output to an existing approach. A combination of methods shows that drug-resistance genes on plasmids are highly mobile because they can jump into ST131’s chromosomes. We found that the plasmids are very elastic and undergo extensive rearrangements even in closely related samples. This application of DNA sequencing technologies illustrates at a new level the highly dynamic nature of ST131 genomes.
Some broad-scale effects of recent and future climate change among migratory birds in Beringia

Birds from all seven continents come to Beringia to breed in the northern summer. For birds breeding there, Beringia’s position at the head of the Pacific Ocean requires substantial longitudinal (east to west and west to east) movements coming and going. These movements are most apparent to us in continental “crossover” species, Asian taxa breeding in North America and North American birds breeding in Asia. Those individuals reaching range limits in Beringia commonly travel long distances to take advantage of short summers, and many of their range limits are likely caused by time constraints: travel time plus the time required to successfully reproduce and (for most) to molt must fit into the finite constraints of the length of the summer. These constraints become most apparent when a breeding range limit is longitudinally distant from the nearest wintering area, and the most visible examples involve species whose ranges stop before the limit of apparently appropriate habitat. It is these species whose ranges we expect to change most rapidly when even small increases in the time available at high latitudes (i.e., a longer growing season) give them more time to travel farther east or west at these latitudes.
High-resolution cryo-EM structures of outbreak strain human norovirus shells reveal size variations

Significance Despite being a leading cause of foodborne illnesses, accounting for 58% of all outbreaks and over 96% of nonbacterial outbreaks, there are no approved treatments available for norovirus infections. Assembled shells of the viruses without genetic materials enclosed are currently being used as candidates for vaccine trials. Although the virus shells have been thought to exist in a single-sized assembly, our structures in near-atomic detail reveal clear variations in size between different outbreak strains, and in spatial and angular arrangements of the antigenic surface spikes. The structures we present serve as valuable templates for facilitating vaccine formulations. Noroviruses are a leading cause of foodborne illnesses worldwide. Although GII.4 strains have been responsible for most norovirus outbreaks, the assembled virus shell structures have been available in detail for only a single strain (GI.1). We present high-resolution (2.6- to 4.1-Å) cryoelectron microscopy (cryo-EM) structures of GII.4, GII.2, GI.7, and GI.1 human norovirus outbreak strain virus-like particles (VLPs). Although norovirus VLPs have been thought to exist in a single-sized assembly, our structures reveal polymorphism between and within genogroups, with small, medium, and large particle sizes observed. Using asymmetric reconstruction, we were able to resolve a Zn2+ metal ion adjacent to the coreceptor binding site, which affected the structural stability of the shell. Our structures serve as valuable templates for facilitating vaccine formulations.
Platform Design When Sellers Use Pricing Algorithms

We investigate the ability of a platform to design its marketplace to promote competition, improve consumer surplus, and increase its own payoff. We consider demand‐steering rules that reward firms that cut prices with additional exposure to consumers. We examine the impact of these rules both in theory and by using simulations with artificial intelligence pricing algorithms (specifically Q‐learning algorithms, which are commonly used in computer science). Our theoretical results indicate that these policies (which require little information to implement) can have strongly beneficial effects, even when sellers are infinitely patient and seek to collude. Similarly, our simulations suggest that platform design can benefit consumers and the platform, but that achieving these gains may require policies that condition on past behavior and treat sellers in a nonneutral fashion. These more sophisticated policies disrupt the ability of algorithms to rotate demand and split industry profits, leading to low prices.
siRNA containing a unique 5-nucleotide motif acts as a quencher of IFI16-mediated innate immune response

We previously reported that small interfering RNA (siRNA) enhances DNA or DNA virus mediated-interferon (IFN)-λ1 induction through retinoic acid-inducible gene I (RIG-I) and interferon gamma-inducible protein 16 (IFI16) crosstalk-signalling pathway. Here we provide further evidence of a new role for siRNA. siRNA containing a 5-nucleotide (nt) motif sequence suppresses DNA-mediated IFNs and inflammatory cytokines. We determined that motif siRNA inhibits the induction when the motif is located at the 3’ or 5’-terminus of siRNA. Using THP1-Lucia ISG cells with various DNA stimulants, it is demonstrated that motif siRNA inhibits DNA or DNA virus but not RNA virus-mediated signaling. Motif siRNA specifically interrupts IFI16 binding to DNA and has 2.5-fold higher affinity to IFI16 than that of siRNA without the motif. Collectively, these findings may shed lights on a novel function of siRNA with the 5-nt motif as a quencher of innate immunity and facilitate the development of potential therapeutics to treat diseases in which this pathway is dysregulated.
Evaluation of the performance of copy number variant prediction tools for the detection of deletions from whole genome sequencing data

Background Whole genome sequencing (WGS) has increased in popularity and decreased in cost over the past decade, rendering this approach as a viable and sensitive method for variant detection. In addition to its utility for single nucleotide variant detection, WGS data has the potential to detect Copy Number Variants (CNV) to fine resolution. Many CNV detection software packages have been developed exploiting four main types of data: read pair, split read, read depth, and assembly based methods. The aim of this study was to evaluate the efficiency of each of these main approaches in detecting deletions. Methods WGS data and high confidence deletion calls for the individual NA12878 from the Genome in a Bottle consortium were the benchmark dataset. The performance of Breakdancer, CNVnator, Delly, FermiKit, and Pindel was assessed by comparing the accuracy and sensitivity of each software package in detecting deletions exceeding 1kb. Results There was considerable variability in the outputs of the different WGS CNV detection programs. The best performance was seen from Breakdancer and Delly, with 92.6% and 96.7% sensitivity, respectively and 34.5% and 68.5% false discovery rate (FDR), respectively. In comparison, Pindel, CNVnator, and FermiKit were less effective with sensitivities of 69.1%, 66.0%, and 15.8%, respectively and FDR of 91.3%, 69.0%, and 31.7%, respectively. Concordance across software packages was poor, with only 27 of the total 612 benchmark deletions identified by all five methodologies. Conclusions The WGS based CNV detection tools evaluated show disparate performance in identifying deletions ≥1kb, particularly those utilising different input data characteristics. Software that exploits read pair based data had the highest sensitivity, namely Breakdancer and Delly. Breakdancer also had the second lowest false discovery rate. Therefore, in this analysis read pair methods (Breakdancer in particular) were the best performing approaches for the identification of deletions ≥1kb, balancing accuracy and sensitivity. There is potential for improvement in the detection algorithms, particularly for reducing FDR. This analysis has validated the utility of WGS based CNV detection software to reliably identify deletions, and these findings will be of use when choosing appropriate software for deletion detection, in both research and diagnostic medicine.
Influence of drought on the photosynthetic apparatus activity, senescence rate, and productivity in wheat plants

Effects of soil drought at flowering stage on the functional state of photosynthetic apparatus and chloroplast enzymatic antioxidant defense systems in flag leaf during reproductive period, and the productivity of winter wheat plants of high-protein Natalka variety and drought-tolerant Podolyanka variety were studied in pot experiment. Until flowering and for the control plants during the entire vegetation, the soil moisture content was maintained at a level of 60—70 % of field capacity (FC). Drought treatment (soil moisture 30 % FC) was applied for 7 days covering flowering—early kernel watery ripe period (BBCH 61—71). After that, watering of plants was resumed to a control level which was maintained until the end of the growing season. The estimation of the chlorophyll and Rubisco content, the chloroplast antioxidant enzymes activity, and the net CO2 assimilation and transpiration rates was carried out on flag leaves. The measurements were taken on the third day of watering cessation (the first day the soil moisture reached 30 % FC, BBCH 61), at the end of the drought period (seventh day at 30 % FC, BBCH 71), and after watering resumed at the medium milk (BBCH 75) and late milk (BBCH 77) stages. The components of plant grain productivity were determined by weighing air-dry material at grain full ripeness. It was revealed, that drought stress during flowering inhibited CO2 assimilation and accelerated induction of senescence processes in wheat plants associated with degradation of photosynthetic apparatus and manifested in quicker ontogenetic drop in chlorophyll and Rubisco contents and loss of leaf photosynthetic activity. This exacerbated the drought impact on the plant organism so that after optimal watering return, the physiological and biochemical parameters were not restored to the values of control plants that were all time under optimal moisture supply. Stress-induced premature senescence reduced the supply of plants with assimilates and ultimately led to a decrease in their grain productivity. Impact of drought on flag leaf photosynthetic activity and especially on senescence induction were much more pronounced in the high-protein wheat variety Natalka with a genetically programmed earlier start of the nitrogen-containing compounds remobilization from leaves than in Podolyanka variety. The drought-tolerant variety Podolyanka keep ability to maintain much higher CO2 assimilation activity during drought period and to preserve photosynthetic apparatus from early induction of senescence due to likely more efficient chloroplast antioxidant defense systems, thereby gaining a better assimilates supply for yield formation.
Impact of the Słupia River waters on microbial communities in the port of Ustka and adjacent Baltic Sea waters

Abstract The distribution of bacterial and ciliate abundance, ciliate community composition and other parameters were studied during summer along a transect from the mouth of the Słupia River to offshore waters (southern Baltic Sea). Bacteria were examined under an epifluorescence microscope and ciliates were observed under an inverted microscope. Two water masses were identified along the transect. Less saline waters in the river mouth and in the surface layer in the port of Ustka were characterized by high bacterial abundance (5.51–6.16 × 106 ml−1) and low ciliate abundance (0.34–0.90 cells ml−1). More saline waters in the near-bottom zone in the port of Ustka and in the surface layer outside the port contained smaller numbers of bacteria (0.99–2.14 × 106 ml−1) and larger numbers of ciliates (2.65–5.40 cells ml−1). The differences were statistically significant. The separation of the two water masses indicated that the Słupia River exerted a minor impact on the marine waters. The ciliate community composition changed along the transect studied. The main statistically significant difference observed was the low contribution of oligotrichs and choreotrichs to ciliate biomass (3–4%) in less saline waters and their dominance (45–80% of ciliate biomass) in more saline waters.
The effect of ewe prelamb body condition on triplet lamb performance in a commercial flock

Triplet-bearing ewes (n = 999) were identified at pregnancy scanning (PS) and randomly assigned to two pasture feeding treatments through to lamb weaning, FeedPlus (FP) and Control (C). FeedPlus ewes were fed according to theoretical requirements based on live weight and a fetal number of three while C ewes were fed as for twinning ewes. Ewe body condition score (BCS) was similar for FP and C ewes at PS (BCS 3). FP ewes had higher BCS than C ewes at set-stocking one month before the mean lambing date (PL, BCS 2.9 ± 0.1 versus 2.6 ± 0.1, P <0.001). Every unit increase in BCS at PS improved litter survival to weaning by 0.33 ± 0.17 of a lamb. An increase of BCS at set-stocking improved litter survival to weaning by 0.45 ± 0.18 of a lamb (P <0.05). Litter weight increased with increasing BCS PL (β = 1.2 ± 0.5 kg/unit BCS, P <0.05). Low BCS ewes (BCS ≤ 2.5) at PS weaned 3.5 kg less lamb than medium BCS ewes at PS (BCS ≥ 3) (82.4 ± 1.1 kg versus 85.9 ± 1.4 kg, P <0.05) when rearing triplets. Pre-lamb BCS had a positive effect on lamb weaning weight (β = 1.3 ± 0.6 kg/unit BCS, P <0.05) and on lamb growth rates from birth to weaning (β = 13.5 ± 6.0 g/day per unit increase in PL BCS, P <0.05). The study highlighted the importance of ewe body condition score at PS and PL on triplet ewe performance.
Residu Antibiotika pada Hati dan Karkas Ayam Pedaging

This study aims to determine the residue antibiotic on liver and broiler carcass at the market Dukuh Pakis district. Location and time of the research carried out at the Laboratory of Veterinary Public Health Faculty of Veterinary Medicine Wijaya Kusuma University of Surabaya. Sampling by liver and broiler carcass performed in markets around the market Dukuh Pakis district. This study is an observational study, using liver and broiler carcass were taken from a sub market of Dukuh Pakis tested for antibiotic residues were detected comparing the market where the highest levels of antibiotic residues. Samples in the form of livers and broiler carcasses must come from the same broiler taken from the traditional markets and supermarkets around the Dukuh Pakis District. The data obtained were analyzed using descriptive methods.Antibiotic residues on broiler carcasses in Dukuh Pakis market based on the results of the test showed that 27.5% positive and 72.5% negative. While antibiotic residues in broiler liver in Dukuh Pakis Market based testing showed positive results of 32.5% and negative 67.5%.
Ectopic expression of an Arabidopsis glutaredoxin increases thermotolerance in maize during reproductive developmental stages

Drought and heat stress are two of the biggest constraints to global food production. Abiotic stress response pathways are complex and consist of osmotic adjustors, macromolecule stabilizers, and antioxidants to counteract the damaging nature of abiotic stress induced reactive oxygen species (ROS) accumulation. In this work, we studied the effect of overexpression of an Arabidopsis glutaredoxin, AtGRXS17, on heat tolerance in maize (Zea mays L.) and drought tolerance in rice (Orzya sativa L.). Glutaredoxins (GRXs) are proteins cable of reducing disulfide bonds, therefore regulating the cellular redox status, and require glutathione for regeneration. Ectopic expression of AtGRXS17 in maize resulted in increased heat stress tolerance during flowering. AtGRXS17 enhanced heat tolerance by increasing kernel set and total grain yield during heat treatments, compared to wild type controls. Our results indicated that AtGRXS17-expressing maize plants produce heat tolerant pollen with higher germination rates than wild type when challenged during heat treatments. Furthermore, AtGRXS17-expressing plants were less susceptible to post pollination heat induced kernel abortion. Rice plants expressing AtGRXS17 were also tolerant to abiotic stress. AtGRXS17-expressing rice was more tolerant to drought stress challenges and consistently survived drought treatments. A nontargeted metabolomics study revealed distinct changes in profiles of key metabolite groups in response to drought stress. Soluble sugars and amino acids accumulate as osmotic adjustors while antioxidants, such as glutathione, accumulate to mediate ROS accumulation and regulate redox activity. All genotypes accumulated amino acids, soluble sugars, and raffinose family oligosaccharides in response to drought stress. Our results indicated AtGRXS17-expression affected several pathways known to increase drought tolerance. Altered sugar metabolites suggested a redox modulation of sucrose synthase activity and significant increases in the secondary sulfur assimilation pathway metabolites suggested altered sulfur metabolism. This research provides new insights into ability of GRXs to improve heat tolerance and crop yield in maize and functions of GRXs in affecting metabolite profiles contributing to increased drought tolerance in rice. Ectopic expression of an Arabidopsis glutaredoxin increases thermotolerance in maize during reproductive developmental stages
Temporal variations in phytoplankton composition in the northeastern Sea of Marmara: potentially toxic species and mucilage event

Temporal variations in phytoplankton composition in the northeastern Sea of Marmara was investigated associated with physico-chemical variables from January 2004 to December 2007. The occurrence of potentially toxic species and a mucilage event was also evaluated during this study period. The confined upper layer of the Sea of Marmara is mesotrophic to eutrophic and has higher productivity when compared to the neighbouring Black Sea and Aegean Sea. 132 taxa in the micro-phytoplankton community were identified, 11 of which are known to be potentially toxic. The most abundant species were Pseudo-nitzschia species from diatoms and Prorocentrum micans from dinoflagellates. Potentially toxic species were more common at the coastal stations. The onset of a mucilage formation was observed in October 2007, and well-known mucilage producers such as Gonyaulax hyalina (reported as G. fragilis) and Thalassiosira gravida (reported as T. rotula) dominated the phytoplankton community during this event. A marked decrease in the number of species and diversity index following June 2007 and reported shifts in the zooplankton community during the same period points to probable cascading effects in the pelagic ecosystem of the Sea of Marmara.
Risk stratification of mantle cell lymphoma (MCL)

Despite of a better understanding of the biology of mantle cell lymphoma (MCL), it remains an incurable disease with very variable disease courses. The biological heterogeneity of MCL requires the identification of prognostic markers for risk stratification and tailored treatment of MCL. The combined MCL International Prognostic Index (MIPI-c) represents a well-established clinical risk stratification model. Based on four clinical parameters: age, performance status, lactate dehydrogenase and leucocyte count combined with the percentage of Ki-67 positive MCL cells the model distinguishes four MCL subgroups with very different outcomes. Further prognostic markers, in particular molecular lesions might help to further improve clinical scoring. We discuss the value of clinical and molecular markers to predict outcome of MCL and how these markers could influence treatment decisions.