Vector redesign and in-droplet cell-growth improves enrichment and recovery in live Escherichia coli.

Directed evolution (DE) is a widely used method for improving the function of biomolecules via multiple rounds of mutation and selection. Microfluidic droplets have emerged as an important means to screen the large libraries needed for DE, but this approach was so far partially limited by the need to lyse cells, recover DNA, and retransform into cells for the next round, necessitating the use of a high-copy number plasmid or oversampling. The recently developed live cell recovery avoids some of these limitations by directly regrowing selected cells after sorting. However, repeated sorting cycles used to further enrich the most active variants ultimately resulted in unfavourable recovery of empty plasmid vector-containing cells over those expressing the protein of interest. In this study, we found that engineering of the original expression vector solved the problem of false positives (i.e. plasmids lacking an insert) cells containing empty vectors. Five approaches to measure activity of cell-displayed enzymes in microdroplets were compared. By comparing various cell treatment methods prior to droplet sorting two things were found. Substrate encapsulation from the start, that is prior to expression of enzyme, showed no disadvantage to post-induction substrate addition by pico-injection with respect to recovery of true positive variants. Furthermore in-droplet cell growth prior to induction of enzyme production improves the total amount of cells retrieved (recovery) and proportion of true positive variants (enrichment) after droplet sorting.

Ancestral sequences of a large promiscuous enzyme family correspond to bridges in sequence space in a network representation.

Evolutionary relationships of protein families can be characterized either by networks or by trees. Whereas trees allow for hierarchical grouping and reconstruction of the most likely ancestral sequences, networks lack a time axis but allow for thresholds of pairwise sequence identity to be chosen and, therefore, the clustering of family members with presumably more similar functions. Here, we use the large family of arylsulfatases and phosphonate monoester hydrolases to investigate similarities, strengths and weaknesses in tree and network representations. For varying thresholds of pairwise sequence identity, values of betweenness centrality and clustering coefficients were derived for nodes of the reconstructed ancestors to measure the propensity to act as a bridge in a network. Based on these properties, ancestral protein sequences emerge as bridges in protein sequence networks. Interestingly, many ancestral protein sequences appear close to extant sequences. Therefore, reconstructed ancestor sequences might also be interpreted as yet-to-be-identified homologues. The concept of ancestor reconstruction is compared to consensus sequences, too. It was found that hub sequences in a network, e.g. reconstructed ancestral sequences that are connected to many neighbouring sequences, share closer similarity with derived consensus sequences. Therefore, some reconstructed ancestor sequences can also be interpreted as consensus sequences.

High-Throughput, Lysis-Free Screening for Sulfatase Activity Using Escherichia coli Autodisplay in Microdroplets.

Directed evolution of enzymes toward improved catalytic performance has become a powerful tool in protein engineering. To be effective, a directed evolution campaign requires the use of high-throughput screening. In this study we describe the development of an ultra high-throughput lysis-free procedure to screen for improved sulfatase activity by combining microdroplet-based single-variant activity sorting with E. coli autodisplay. For the first step in a 4-step screening procedure, we quantitatively screened >105 variants of the homodimeric arylsulfatase from Silicibacter pomeroyi (SpAS1), displayed on the E. coli cell surface, for improved sulfatase activity using fluorescence activated droplet sorting. Compartmentalization of the fluorescent reaction product with living E. coli cells autodisplaying the sulfatase variants ensured the continuous linkage of genotype and phenotype during droplet sorting and allowed for direct recovery by simple regrowth of the sorted cells. The use of autodisplay on living cells simplified and reduced the degree of liquid handling during all steps in the screening procedure to the single event of simply mixing substrate and cells. The percentage of apparent improved variants was enriched >10-fold as a result of droplet sorting. We ultimately identified 25 SpAS1 variants with improved performance toward 4-nitrophenyl sulfate (up to 6.2-fold) and/or fluorescein disulfate (up to 30-fold). In SpAS1 variants with improved performance toward the bulky fluorescein disulfate, many of the beneficial mutations occur in residues that form hydrogen bonds between α-helices in the C-terminal oligomerization region, suggesting a previously unknown role for the dimer interface in shaping the substrate binding site of SpAS1.

Involvement of cholinergic mechanisms in the central control of respiration in the cane toad, Bufo marinus.

Chemical substrates, central sites and central mechanisms underlying the regulation of breathing in lower vertebrates have not been well characterized. The present study was undertaken to determine the effect of pH changes and cholinergic agents on the central control of respiration in the cane toad, Bufo marinus. Adult toads were anesthetized, catheterized and unidirectionally ventilated before exposing the brainstem. An airtight buccal cannula was also inserted through the tympanum to record buccal pressure. The animal was decerebrated, anesthetic removed and the responses to pH changes of solutions bathing the ventral surface of the medulla (VSM) were tested by superfusing the VSM with mock cerebrospinal fluid (mCSF) of pH 7.8-normal, 7.2-acidic and 8.4-basic. The acidic solution increased respiratory activity, the basic solution decreased activity and the normal solution had no effect. In addition, cholinergeric agents (acetylcholine-ACh, physostigmine-Phy, nicotine-Nic, and atropine-Atr) dissolved in mCSF were applied bilaterally onto the VSM using filter paper pledgets. ACh, Phy and Nic increased episodic breathing frequency by 14.3+/-9.7, 9.4+/-5.4 and 29.1+/-11.8 %, respectively, whereas, Atr caused a decrease (-26.6+/-16.6%). These agents had no effect on blood pressure. It is therefore, concluded that the VSM is pH sensitive and a cholinergic mechanism is involved in the central modulation of respiration in Bufo.

Alpha2 adrenergic receptors and the central control of breathing in the cane toad, Bufo marinus.

The effect of adrenergic agents on the central control of breathing in the cane toad, Bufo marinus, was tested by applying adrenergic agents to the ventral medullary surface of decerebrate adult toads. Toads were unidirectionally ventilated while recording lung, buccal, and artery blood pressures (BPI), as well as heart rate (HR). Following a control period, filter paper pledgets soaked in the appropriate solution (epinephrine - 0.023, 0.05, 0.10, and 0.23 mM; norepinephrine - 0.002, 0.016, 0.032, and 0.16 mM; clonidine - 0.00375, 0.0375, and 0.375 mM; or yohimbine - 0.43) mM) were placed bilaterally on the ventral medullary surface. Epinephrine significantly increased the number of breaths (26%), lung amplitude (9%), and episode duration (21%), but had no effect on BP or HR. The alpha2-agonist. clonidine, significantly increased respiratory activity at moderate doses (0.0375 mM) and decreased activity at high doses (0.375 mM), however, it failed to elicit significant changes in BP or HR. Pretreatment with the alpha2-adrenoceptor antagonist, yohimbine (0.43 mM), blocked the clonidine induced changes in respiratory activity. Yohimbine had no effect on cardiorespiratory parameters. Norepinephrine had no effect on either cardiovascular or respiratory variables. Thus, it appears that an alpha2 adrenergic mechanism is involved in the central control of respiration in this lower vertebrate.

Ventilatory mechanics and the effects of water depth on breathing pattern in the aquatic caecilian Typhlonectes natans.

The breathing pattern in the aquatic caecilian Typhlonectes natans was investigated by recording airflow via a pneumotachograph under unrestrained normal physiological conditions. Ventilatory mechanics were assessed using airflow and pressure measurements from the buccal cavity and trachea. The breathing pattern consisted of an expiratory phase followed by a series of 10-15 small buccal pumps to inflate the lung, succeeded by a long non-ventilatory period. T. natans separate the expiratory and inspiratory gases in the buccal cavity and take several inspiratory pumps, distinguishing their breathing pattern from that of sarcopterygians. Hydrostatic pressure assisted exhalation. The tracheal pressure was greater than the water pressure at that depth, suggesting that pleuroperitoneal pressure as well as axial or pulmonary smooth muscles may have contributed to the process of exhalation. The frequency of lung ventilation was 6.33+/-0.84 breaths h(-)(1), and ventilation occurred via the nares. Compared with other amphibians, this low ventilatory frequency suggests that T. natans may have acquired very efficient pulmonary respiration as an adaptation for survival in their seasonally fluctuating natural habitat. Their respiratory pathway is quite unique, with the trachea separated into anterior, central and posterior regions. The anterior region serves as an air channel, the central region is attached to the tracheal lung, and the posterior region consists of a bifurcated air channel leading to the left and right posterior lungs. The lungs are narrow, elongated, profusely vascularized and compartmentalized. The posterior lungs extend to approximately two-thirds of the body length. On the basis of their breathing pattern, it appears that caecilians are phylogenetically derived from two-stroke breathers.

Cardiorespiratory responses to glutamate microinjected into the medullary raphé.

The involvement of the medullary raphé in modulating cardiorespiratory activity was examined by microinjecting L-glutamate (L-Glu) into the raphé of rats. Animals were vagotomized, paralyzed, artificially ventilated, maintained at 37 degrees C, and instrumented to record arterial blood pressure (BP) and phrenic nerve activity (PNA). Mock cerebrospinal fluid (mCSF, 10 nl, pH 7.4; control) and L-Glu dissolved in mCSF (10, 100, 1000 mM; 10 nl; pH 7.4; experimental) were microinjected into the raphé. L-Glu affected both BP and PNA in a dose dependent manner. Blood pressure was reduced by 6.30 +/- 0.97 and 12.98 +/- 1.29% by 100 and 1000 mM L-Glu, respectively, without affecting heart rate. PNA increased by 23 and 38% with 100 and 1000 mM L-Glu, respectively. Mock CSF and 10 mM L-Glu had no effect. It is concluded that there are sites in the medullary raphé that affect blood pressure only and other sites which can affect both blood pressure and respiration.

Evidence for central chemoreception in the midline raphé.

We injected acetazolamide (AZ; 5 x 10(-6) M; 1 nl; n = 14), its inactive analogue 2-acetylamino-1,3,4-thiadiazole-5-sulfon-t-butylamide (5 x 10(-5) M; n = 6), or mock cerebrospinal fluid (n = 5) into the caudal raphé in the midline brain stem of anesthetized paralyzed ventilated rats. These AZ injections have been shown to produce a focal region of tissue acidosis with a radius < 350 microns and are used as a probe for sites of central chemosensitivity. Compared with control injections, AZ injection into the raphé, as demonstrated by anatomic analysis of injection location, significantly increased the amplitude of the integrated phrenic neurogram over 10-40 min. Not all raphé injections produced such a response. AZ injections identified as responders (n = 8 of 14) increased integrated phrenic amplitude 43.3 +/- 10.7% (SE) of baseline 20 min after the injection. We conclude that the midline caudal raphé contains sites of ventilatory chemoreception.

Cholinergic-opioid interactions at brainstem respiratory chemosensitive areas in cats.

Central respiratory chemosensitivity has been ascribed to CO2-sensitive neurons located on the ventral brainstem surface. The effects of cholinergic mechanisms on CO2-sensitive neuronal activity recorded extracellularly at the brainstem respiratory chemosensitive area at the caudal ventral medullary surface (cVMS) were investigated in cats (n = 14) anesthetized with chloralose-urethane. The neurons increased their firing rate from 10.4 +/- 1.6 Hz to 33.9 +/- 5.2 Hz when the mock cerebrospinal fluid (mCSF) superfusing buffer solution was changed from pH 7.4 (control) to pH 7.0 (acidic). Atropine (ATR) applied topically to the cVMS depressed the H(+)-ion-induced increase in neuronal frequency from 32.8 +/- 4.8 Hz to 13.4 +/- 2.2 Hz. ATR also depressed the inspired-CO2-induced increase in neuronal activity from 33.2 +/- 8.3 Hz to 18.9 +/- 4.9 Hz, suggesting the possibility of a muscarinic cholinergic involvement in cVMS neuronal responses to changes in PCO2 and mCSF-pH. Acetylcholine (ACh) increased the activity of cVMS CO2-sensitive neurons by 237.5% +/- 34.9%, and naloxone applied topically to the cVMS augmented the ACh responsiveness to 338.6% +/- 52.7%. Physostigmine (PHY) increased neuronal activity by 254.3% +/- 42.9%, and this increase was augmented to 435.4% +/- 61.2% by naloxone. Although responses of the CO2-sensitive neurons to PHY were biphasic, the depressant phase failed to appear whenever the cVMS was pretreated with naloxone. Naloxone also augmented the responsiveness of cVMS neurons to increased H+ ion superfusion. These findings suggest that the endogenous opiates may be involved in the central regulation of respiration by interaction with CO2-sensitive cholinergic structures at the cVMS.(ABSTRACT TRUNCATED AT 250 WORDS)

Naloxone application to the ventrolateral medulla enhances the respiratory response to inspired carbon dioxide.

Previous studies have shown that systemic administration of the opiate antagonist naloxone potentiates the ventilatory response to inspired carbon dioxide. The present study was designed to localize the site of action of naloxone for increasing the respiratory chemosensitivity to inhaled carbon dioxide (CO2) in cats. Naloxone applied topically to the caudal chemosensitive area on the ventral medullary surface (VMS) during hypercapnic breathing produced a 75% greater increase in minute ventilation than hypercapnic breathing alone. Furthermore, hypercapnic breathing produced a 200% increase in neuronal activity of VMS chemosensitive cells; this was further increased 120% by naloxone. It is concluded that naloxone increases the sensitivity of neurons in the caudal respiratory chemosensitive area of cats to hypercapnia, and that endogenous opiates may act as modulators at VMS chemosensitive sites during hypercapnic breathing.

Age differences in responsiveness of brainstem chemosensitive neurons to extracellular pH changes.

The sensitivity of neurons in the caudal chemosensitive area on the ventrolateral surface of the medulla oblongata (VMS) to extracellular pH changes was examined in newborn and young developing kittens and compared to that of adult cats. The pH was varied by superfusion of the VMS with mock cerebrospinal fluid (CSF) of pH 7.4 (control), 7.0 (acid) and 7.8 (alkaline). A total of 97 neuronal units in the three age groups changed their firing rates inversely in response to extracellular fluid (ECF) pH changes. The greatest sensitivity was found in the adult group where acid superfusion caused an increase in neuronal activity. The least sensitivity was observed in the newborn group (1-6 days old), whereas the young kitten group (4-6 weeks old) exhibited an intermediate sensitivity. Neurons of kittens older than 7 weeks of age demonstrated a response pattern characteristic of the adult group. Neurons of neonates older than seven days, exhibited a response pattern characteristic of the young kitten group.